@article {pmid36750197,
year = {2023},
author = {Tiwari, J and Sur, S and Yadav, A and Kumar, R and Rai, N and Rani, S and Malik, S},
title = {Photoperiod-driven concurrent changes in hypothalamic and brainstem transcription of sleep and immune genes in migratory redheaded bunting.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {1992},
pages = {20222374},
doi = {10.1098/rspb.2022.2374},
pmid = {36750197},
issn = {1471-2954},
abstract = {The molecular regulation of sleep in avian migrants is still obscure. We thus investigated this in migratory redheaded buntings, where four life-history states (LHS; i.e. non-migratory, pre-migratory, migratory and refractory states) were induced. There was increased night-time activity (i.e. Zugunruhe) during the migratory state with reduced daytime activity. The recordings of the sleep-wake cycle in buntings showed increased night-time active wakefulness coupled with drastically reduced front and back sleep during migratory phase. Interestingly, we found the buntings to feed and drink even after lights-off during migration. Gene expression studies revealed increased hypothalamic expression of glucocorticoid receptor (nr3c1), and pro-inflammatory cytokines (il1b and il6) in pre-migratory and migratory states, respectively, whereas in brainstem Ca[2+]/calmodulin-dependent protein kinase 2 (camk2) was upregulated during the migratory state. This suggested a heightened pro-inflammatory state during migration which is a feature of chronic sleep loss, and a possible role of Ca[2+] signalling in promoting wakefulness. In both the hypothalamus and brainstem, the expression of melatonin receptors (mel1a and mel1b) was increased in the pre-migratory state, and growth hormone-releasing hormone (ghrh, known to induce sleep) was reduced during the migratory state. The current results demonstrate key molecules involved in the regulation of sleep-wake cycle across LHS in migratory songbirds.},
}

@article {pmid36748324,
year = {2023},
author = {Wagner, S and Seguin-Orlando, A and Leplé, JC and Leroy, T and Lalanne, C and Labadie, K and Aury, JM and Poirier, S and Wincker, P and Plomion, C and Kremer, A and Orlando, L},
title = {Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16859},
pmid = {36748324},
issn = {1365-294X},
abstract = {Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.},
}

@article {pmid36747166,
year = {2023},
author = {Sarhan, MS and Wurst, C and Tzankov, A and Bircher, AJ and Wittig, H and Briellmann, T and Augsburger, M and Hotz, G and Zink, A and Maixner, F},
title = {A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {9},
pmid = {36747166},
issn = {1741-7007},
abstract = {BACKGROUND: In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.

RESULTS: Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations.

CONCLUSIONS: The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.},
}

@article {pmid36721228,
year = {2023},
author = {Wang, J and Yang, L and Duan, S and Sun, Q and Li, Y and Wu, J and Wu, W and Wang, Z and Liu, Y and Tang, R and Yang, J and Liu, C and Yuan, B and Wang, D and Xu, J and Wang, M and He, G},
title = {Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China.},
journal = {Human genomics},
volume = {17},
number = {1},
pages = {3},
doi = {10.1186/s40246-023-00452-0},
pmid = {36721228},
issn = {1479-7364},
abstract = {BACKGROUND: Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized.

OBJECTIVES: To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling.

RESULTS: The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways.

CONCLUSIONS: Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.},
}

@article {pmid36714834,
year = {2022},
author = {Velsko, IM and Semerau, L and Inskip, SA and García-Collado, MI and Ziesemer, K and Ruber, MS and Benítez de Lugo Enrich, L and Molero García, JM and Valle, DG and Peña Ruiz, AC and Salazar-García, DC and Hoogland, MLP and Warinner, C},
title = {Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology.},
journal = {PNAS nexus},
volume = {1},
number = {4},
pages = {pgac148},
pmid = {36714834},
issn = {2752-6542},
abstract = {Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.},
}

@article {pmid36712342,
year = {2022},
author = {Brown, T and Rijal, DP and Heintzman, PD and Clarke, CL and Blankholm, HP and Høeg, HI and Lammers, Y and Bråthen, KA and Edwards, M and Alsos, IG},
title = {Paleoeconomy more than demography determined prehistoric human impact in Arctic Norway.},
journal = {PNAS nexus},
volume = {1},
number = {5},
pages = {pgac209},
pmid = {36712342},
issn = {2752-6542},
abstract = {Population size has increasingly been taken as the driver of past human environmental impact worldwide, and particularly in the Arctic. However, sedimentary ancient DNA (sedaDNA), pollen and archaeological data show that over the last 12,000 years, paleoeconomy and culture determined human impacts on the terrestrial ecology of Arctic Norway. The large Mortensnes site complex (Ceavccageađgi, 70°N) has yielded the most comprehensive multiproxy record in the Arctic to date. The site saw occupation from the Pioneer period (c. 10,000 cal. years BP) with more intensive use from c. 4,200 to 2,000 cal. years BP and after 1,600 cal. years BP. Here, we combine on-site environmental archaeology with a near-site lake record of plant and animal sedaDNA. The rich animal sedaDNA data (42 taxa) and on-site faunal analyses reveal switches in human dietary composition from early-Holocene fish + marine mammals, to mixed marine + reindeer, then finally to marine + reindeer + domesticates (sheep, cattle, pigs), with highest reindeer concentrations in the last millennium. Archaeological evidence suggests these changes are not directly driven by climate or variation in population densities at the site or in the region, but rather are the result of changing socio-economic activities and culture, probably reflecting settlers' origins. This large settlement only had discernable effects on its hinterland in the last 3,600 years (grazing) and more markedly in the last 1,000 years through reindeer keeping/herding and, possibly domestic stock. Near-site sedaDNA can be linked to and validate the faunal record from archaeological excavations, demonstrating that environmental impacts can be assessed at a landscape scale.},
}

@article {pmid36691623,
year = {2023},
author = {de March, CA and Matsunami, H and Abe, M and Cobb, M and Hoover, KC},
title = {Genetic and functional odorant receptor variation in the Homo lineage.},
journal = {iScience},
volume = {26},
number = {1},
pages = {105908},
pmid = {36691623},
issn = {2589-0042},
abstract = {Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.},
}

@article {pmid36672975,
year = {2023},
author = {Danielewski, M and Żuraszek, J and Zielińska, A and Herzig, KH and Słomski, R and Walkowiak, J and Wielgus, K},
title = {Methodological Changes in the Field of Paleogenetics.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010234},
pmid = {36672975},
issn = {2073-4425},
abstract = {Paleogenetics has significantly changed since its inception almost forty years ago. Initially, molecular techniques available to the researchers offered minimal possibilities for ancient DNA analysis. The subsequent expansion of the scientific tool cabinet allowed for more remarkable achievements, combined has with the newfound popularity of this budding field of science. Finally, a breakthrough was made with the development of next-generation sequencing (NGS) technologies and the update of DNA isolation protocols, through which even very fragmented aDNA samples could be used to sequence whole genomes. In this paper, we review the achievements made thus far and compare the methodologies utilized in this field of science, discussing their benefits and challenges.},
}

@article {pmid36672874,
year = {2023},
author = {Borbély, N and Székely, O and Szeifert, B and Gerber, D and Máthé, I and Benkő, E and Mende, BG and Egyed, B and Pamjav, H and Szécsényi-Nagy, A},
title = {High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010133},
pmid = {36672874},
issn = {2073-4425},
abstract = {Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.},
}

@article {pmid36672816,
year = {2022},
author = {Salado, I and Preick, M and Lupiáñez-Corpas, N and Fernández-Gil, A and Vilà, C and Hofreiter, M and Leonard, JA},
title = {Loss of Mitochondrial Genetic Diversity despite Population Growth: The Legacy of Past Wolf Population Declines.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/genes14010075},
pmid = {36672816},
issn = {2073-4425},
abstract = {Gray wolves (Canis lupus) in the Iberian Peninsula declined substantially in both range and population size in the last few centuries due to human persecution and habitat fragmentation. However, unlike many other western European populations, gray wolves never went extinct in Iberia. Since the minimum number was recorded around 1970, their numbers have significantly increased and then stabilized in recent decades. We analyzed mitochondrial genomes from 54 historical specimens of Iberian wolves from across their historical range using ancient DNA methods. We compared historical and current mitochondrial diversity in Iberian wolves at the 5' end of the control region (n = 17 and 27) and the whole mitochondrial genome excluding the control region (n = 19 and 29). Despite an increase in population size since the 1970s, genetic diversity declined. We identified 10 whole mitochondrial DNA haplotypes in 19 historical specimens, whereas only six of them were observed in 29 modern Iberian wolves. Moreover, a haplotype that was restricted to the southern part of the distribution has gone extinct. Our results illustrate a lag between demographic and genetic diversity changes, and show that after severe population declines, genetic diversity can continue to be lost in stable or even expanding populations. This suggests that such populations may be of conservation concern even after their demographic trajectory has been reversed.},
}

@article {pmid36669262,
year = {2023},
author = {Dzehverovic, M and Jusic, B and Pilav, A and Lukic, T and Cakar, J},
title = {Kinship analysis of skeletal remains from the Middle Ages.},
journal = {Forensic science international. Genetics},
volume = {63},
number = {},
pages = {102829},
doi = {10.1016/j.fsigen.2023.102829},
pmid = {36669262},
issn = {1878-0326},
abstract = {Medieval cemeteries Klisa-Guca Gora, Alihodze and Glavica-Han Bila located in the Travnik area (Travnik, Bosnia and Herzegovina) were archaeologically examined in the period 2011-2014, revealing human skeletal remains of 11 individuals in total. Archaeological skeletal samples, previously deposited in Travnik Homeland Museum (Travnik, Bosnia and Herzegovina) were subjected to genetic analysis. The aim of this research was to test familiar relationship of 11 individuals excavated from three medieval cemeteries and to predict Y-haplogroup for male individuals. In order to perform molecular-genetic characterisation of collected human skeletal remains, two systems of genetic markers were analysed: autosomal and Y-STR loci. Complete or partial data obtained by autosomal STR typing of 11 individuals were subjected to kinship analysis. Male sex was determined in eight samples out of 11. Direct relatives of the "brother-brother" type were detected in one case with high kinship probability (KP) value of 99.99996 %. Complete or nearly complete and usable Y-STR profiles were obtained for six out of eight male individuals. The presence of identical haplotypes at Y-STR loci and results of Y-haplogroup prediction suggest that all male individuals share the same paternal lineage and belong to J2a haplogroup. Overall, this study emphasises the usefulness, efficiency and sensitivity of STR markers in the molecular-genetic characterisation of old skeletal remains as well as the importance of employing additional markers like Y-STRs in archaeogenetic studies, besides traditionally used autosomal STR markers, in order to get a comprehensive information about close and distant relatives, and ancestry.},
}

@article {pmid36661852,
year = {2023},
author = {He, Z and Dai, X and Lyu, W and Beaumont, M and Yu, F},
title = {Estimating temporally variable selection intensity from ancient DNA Data.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad008},
pmid = {36661852},
issn = {1537-1719},
abstract = {Novel technologies for recovering DNA information from archaeological and historical specimens have made available an ever-increasing amount of temporally spaced genetic samples from natural populations. These genetic time series permit the direct assessment of patterns of temporal changes in allele frequencies, and hold the promise of improving power for the inference of selection. Increased time resolution can further facilitate testing hypotheses regarding the drivers of past selection events such as the incidence of plant and animal domestication. However, studying past selection processes through ancient DNA (aDNA) still involves considerable obstacles such as postmortem damage, high fragmentation, low coverage and small samples. To circumvent these challenges, we introduce a novel Bayesian framework for the inference of temporally variable selection based on genotype likelihoods instead of allele frequencies, thereby enabling us to model sample uncertainties resulting from the damage and fragmentation of aDNA molecules. Also, our approach permits the reconstruction of the underlying allele frequency trajectories of the population through time, which allows for a better understanding of the drivers of selection. We evaluate its performance through extensive simulations and demonstrate its utility with an application to the ancient horse samples genotyped at the loci for coat colouration. Our results reveal that incorporating sample uncertainties can further improve the inference of selection.},
}

@article {pmid36661298,
year = {2023},
author = {Henriksen, RA and Zhao, L and Korneliussen, TS},
title = {NGSNGS: Next generation simulator for next generation sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad041},
pmid = {36661298},
issn = {1367-4811},
abstract = {SUMMARY: With the rapid expansion of the capabilities of the DNA sequencers throughout the different sequencing generations, the quantity of generated data has likewise increased. This evolution has also led to new bioinformatical methods, for which in silico data has become crucial when verifying the accuracy of a model or the robustness of a genomic analysis pipeline. Here we present a multithreaded next-generation simulation tool for next-generation sequencing data (NGSNGS), which simulates reads faster than currently available methods and programs. NGSNGS can simulate reads with platform specific characteristics based on nucleotide quality score profiles, as well as including a post-mortem damage model which is relevant for simulating ancient DNA (aDNA). The simulated sequences are sampled (with replacement) from a reference DNA genome, which can represent a haploid genome, polyploid assemblies, or even population haplotypes and allows the user to simulate known variable sites directly. The program is implemented in a multithreading framework and is factors faster than currently available tools while extending their feature set and possible output formats.

AVAILABILITY: The method and associated programs are released as open-source software, code and user manual are available at https://github.com/RAHenriksen/NGSNGS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid36658311,
year = {2023},
author = {Eaton, K and Featherstone, L and Duchene, S and Carmichael, AG and Varlık, N and Golding, GB and Holmes, EC and Poinar, HN},
title = {Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {23},
pmid = {36658311},
issn = {2399-3642},
abstract = {Plague has an enigmatic history as a zoonotic pathogen. This infectious disease will unexpectedly appear in human populations and disappear just as suddenly. As a result, a long-standing line of inquiry has been to estimate when and where plague appeared in the past. However, there have been significant disparities between phylogenetic studies of the causative bacterium, Yersinia pestis, regarding the timing and geographic origins of its reemergence. Here, we curate and contextualize an updated phylogeny of Y. pestis using 601 genome sequences sampled globally. Through a detailed Bayesian evaluation of temporal signal in subsets of these data we demonstrate that a Y. pestis-wide molecular clock is unstable. To resolve this, we developed a new approach in which each Y. pestis population was assessed independently, enabling us to recover substantial temporal signal in five populations, including the ancient pandemic lineages which we now estimate may have emerged decades, or even centuries, before a pandemic was historically documented from European sources. Despite this methodological advancement, we only obtain robust divergence dates from populations sampled over a period of at least 90 years, indicating that genetic evidence alone is insufficient for accurately reconstructing the timing and spread of short-term plague epidemics.},
}

@article {pmid36656838,
year = {2023},
author = {Wu, MY and Forcina, G and Low, GW and Sadanandan, KR and Gwee, CY and van Grouw, H and Wu, S and Edwards, SV and Baldwin, MW and Rheindt, FE},
title = {Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene.},
journal = {PLoS genetics},
volume = {19},
number = {1},
pages = {e1010551},
doi = {10.1371/journal.pgen.1010551},
pmid = {36656838},
issn = {1553-7404},
abstract = {Human activities have precipitated a rise in the levels of introgressive gene flow among animals. The investigation of conspecific populations at different time points may shed light on the magnitude of human-mediated introgression. We used the red junglefowl Gallus gallus, the wild ancestral form of the chicken, as our study system. As wild junglefowl and domestic chickens readily admix, conservationists fear that domestic introgression into junglefowl may compromise their wild genotype. By contrasting the whole genomes of 51 chickens with 63 junglefowl from across their natural range, we found evidence of a loss of the wild genotype across the Anthropocene. When comparing against the genomes of junglefowl from approximately a century ago using rigorous ancient-DNA protocols, we discovered that levels of domestic introgression are not equal among and within modern wild populations, with the percentage of domestic ancestry around 20-50%. We identified a number of domestication markers in which chickens are deeply differentiated from historic junglefowl regardless of breed and/or geographic provenance, with eight genes under selection. The latter are involved in pathways dealing with development, reproduction and vision. The wild genotype is an allelic reservoir that holds most of the genetic diversity of G. gallus, a species which is immensely important to human society. Our study provides fundamental genomic infrastructure to assist in efforts to prevent a further loss of the wild genotype through introgression of domestic alleles.},
}

@article {pmid36653523,
year = {2023},
author = {Nwosu, EC and Brauer, A and Monchamp, ME and Pinkerneil, S and Bartholomäus, A and Theuerkauf, M and Schmidt, JP and Stoof-Leichsenring, KR and Wietelmann, T and Kaiser, J and Wagner, D and Liebner, S},
title = {Early human impact on lake cyanobacteria revealed by a Holocene record of sedimentary ancient DNA.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {72},
pmid = {36653523},
issn = {2399-3642},
abstract = {Sedimentary DNA-based studies revealed the effects of human activity on lake cyanobacteria communities over the last centuries, yet we continue to lack information over longer timescales. Here, we apply high-resolution molecular analyses on sedimentary ancient DNA to reconstruct the history of cyanobacteria throughout the Holocene in a lake in north-eastern Germany. We find a substantial increase in cyanobacteria abundance coinciding with deforestation during the early Bronze Age around 4000 years ago, suggesting increased nutrient supply to the lake by local communities settling on the lakeshore. The next substantial human-driven increase in cyanobacteria abundance occurred only about a century ago due to intensified agricultural fertilisation which caused the dominance of potentially toxic taxa (e.g., Aphanizomenon). Our study provides evidence that humans began to locally impact lake ecology much earlier than previously assumed. Consequently, managing aquatic systems today requires awareness of the legacy of human influence dating back potentially several millennia.},
}

@article {pmid36654346,
year = {2021},
author = {Liu, J and Zeng, W and Sun, B and Mao, X and Zhao, Y and Wang, F and Li, Z and Luan, F and Guo, J and Zhu, C and Wang, Z and Wei, C and Zhang, M and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Hou, W and Ping, W and Wu, X and Andrew Bennett, E and Liu, Y and Fu, Q},
title = {Maternal genetic structure in ancient Shandong between 9500 and 1800 years ago.},
journal = {Science bulletin},
volume = {66},
number = {11},
pages = {1129-1135},
doi = {10.1016/j.scib.2021.01.029},
pmid = {36654346},
issn = {2095-9281},
abstract = {Archaeological and ancient DNA studies revealed that Shandong, a multi-culture center in northern coastal China, was home to ancient populations having ancestry related to both northern and southern East Asian populations. However, the limited temporal and geographical range of previous studies have been insufficient to describe the population history of this region in greater detail. Here, we report the analysis of 86 complete mitochondrial genomes from the remains of 9500 to 1800-year-old humans from 12 archaeological sites across Shandong. For samples older than 4600 years before present (BP), we found haplogroups D4, D5, B4c1, and B5b2, which are observed in present-day northern and southern East Asians. For samples younger than 4600 BP, haplogroups C (C7a1 and C7b), M9 (M9a1), and F (F1a1, F2a, and F4a1) begin to appear, indicating changes in the Shandong maternal genetic structure starting from the beginning of the Longshan cultural period. Within Shandong, the genetic exchange is possible between the coastal and inland regions after 3100 BP. We also discovered the B5b2 lineage in Shandong populations, with the oldest Bianbian individual likely related to the ancestors of some East Asians and North Asians. By reconstructing a maternal genetic structure of Shandong populations, we provide greater resolution of the population dynamics of the northern coastal East Asia over the past nine thousand years.},
}

@article {pmid36650598,
year = {2023},
author = {Popli, D and Peyrégne, S and Peter, BM},
title = {KIN: a method to infer relatedness from low-coverage ancient DNA.},
journal = {Genome biology},
volume = {24},
number = {1},
pages = {10},
pmid = {36650598},
issn = {1474-760X},
abstract = {Genetic kinship of ancient individuals can provide insights into their culture and social hierarchy, and is relevant for downstream genetic analyses. However, estimating relatedness from ancient DNA is difficult due to low-coverage, ascertainment bias, or contamination from various sources. Here, we present KIN, a method to estimate the relatedness of a pair of individuals from the identical-by-descent segments they share. KIN accurately classifies up to 3rd-degree relatives using at least 0.05x sequence coverage and differentiates siblings from parent-child pairs. It incorporates additional models to adjust for contamination and detect inbreeding, which improves classification accuracy.},
}

@article {pmid36649412,
year = {2023},
author = {Wang, X and Skourtanioti, E and Benz, M and Gresky, J and Ilgner, J and Lucas, M and Morsch, M and Peters, J and Pöllath, N and Ringbauer, H and le Roux, P and Schultz, M and Krause, J and Roberts, P and Stockhammer, PW},
title = {Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {4},
pages = {e2210611120},
doi = {10.1073/pnas.2210611120},
pmid = {36649412},
issn = {1091-6490},
abstract = {Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a "revolutionary" social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevalı Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevalı Çori together with newly generated radiocarbon dates. Our results are based on strontium ([87]Sr/[86]Sr), carbon, and oxygen (δ[18]O and δ[13]Ccarb) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevalı Çori. [87]Sr/[86]Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevalı Çori and Ba'ja demonstrate a diverse gene pool at Nevalı Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevalı Çori.},
}

@article {pmid36649410,
year = {2023},
author = {Lewis, CM and Akinyi, MY and DeWitte, SN and Stone, AC},
title = {Ancient pathogens provide a window into health and well-being.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {4},
pages = {e2209476119},
doi = {10.1073/pnas.2209476119},
pmid = {36649410},
issn = {1091-6490},
abstract = {This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.},
}

@article {pmid36646948,
year = {2023},
author = {Skourtanioti, E and Ringbauer, H and Gnecchi Ruscone, GA and Bianco, RA and Burri, M and Freund, C and Furtwängler, A and Gomes Martins, NF and Knolle, F and Neumann, GU and Tiliakou, A and Agelarakis, A and Andreadaki-Vlazaki, M and Betancourt, P and Hallager, BP and Jones, OA and Kakavogianni, O and Kanta, A and Karkanas, P and Kataki, E and Kissas, K and Koehl, R and Kvapil, L and Maran, J and McGeorge, PJP and Papadimitriou, A and Papathanasiou, A and Papazoglou-Manioudaki, L and Paschalidis, K and Polychronakou-Sgouritsa, N and Preve, S and Prevedorou, EA and Price, G and Protopapadaki, E and Schmidt-Schultz, T and Schultz, M and Shelton, K and Wiener, MH and Krause, J and Jeong, C and Stockhammer, PW},
title = {Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {36646948},
issn = {2397-334X},
abstract = {The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean-a region fundamental to Europe's prehistory-the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by 'eastern' gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries BC, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices.},
}

@article {pmid36641836,
year = {2023},
author = {Barrenechea Angeles, I and Romero-Martínez, ML and Cavaliere, M and Varrella, S and Francescangeli, F and Piredda, R and Mazzocchi, MG and Montresor, M and Schirone, A and Delbono, I and Margiotta, F and Corinaldesi, C and Chiavarini, S and Montereali, MR and Rimauro, J and Parrella, L and Musco, L and Dell'Anno, A and Tangherlini, M and Pawlowski, J and Frontalini, F},
title = {Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites.},
journal = {Environment international},
volume = {172},
number = {},
pages = {107738},
doi = {10.1016/j.envint.2023.107738},
pmid = {36641836},
issn = {1873-6750},
abstract = {The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.},
}

@article {pmid36638796,
year = {2022},
author = {Wang, K and Yu, H and Radzevičiūtė, R and Kiryushin, YF and Tishkin, AA and Frolov, YV and Stepanova, NF and Kiryushin, KY and Kungurov, AL and Shnaider, SV and Tur, SS and Tiunov, MP and Zubova, AV and Pevzner, M and Karimov, T and Buzhilova, A and Slon, V and Jeong, C and Krause, J and Posth, C},
title = {Middle Holocene Siberian genomes reveal highly connected gene pools throughout North Asia.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.062},
pmid = {36638796},
issn = {1879-0445},
abstract = {The peopling history of North Asia remains largely unexplored due to the limited number of ancient genomes analyzed from this region. Here, we report genome-wide data of ten individuals dated to as early as 7,500 years before present from three regions in North Asia, namely Altai-Sayan, Russian Far East, and the Kamchatka Peninsula. Our analysis reveals a previously undescribed Middle Holocene Siberian gene pool in Neolithic Altai-Sayan hunter-gatherers as a genetic mixture between paleo-Siberian and ancient North Eurasian (ANE) ancestries. This distinctive gene pool represents an optimal source for the inferred ANE-related population that contributed to Bronze Age groups from North and Inner Asia, such as Lake Baikal hunter-gatherers, Okunevo-associated pastoralists, and possibly Tarim Basin populations. We find the presence of ancient Northeast Asian (ANA) ancestry-initially described in Neolithic groups from the Russian Far East-in another Neolithic Altai-Sayan individual associated with different cultural features, revealing the spread of ANA ancestry ∼1,500 km further to the west than previously observed. In the Russian Far East, we identify 7,000-year-old individuals that carry Jomon-associated ancestry indicating genetic links with hunter-gatherers in the Japanese archipelago. We also report multiple phases of Native American-related gene flow into northeastern Asia over the past 5,000 years, reaching the Kamchatka Peninsula and central Siberia. Our findings highlight largely interconnected population dynamics throughout North Asia from the Early Holocene onward.},
}

@article {pmid36637197,
year = {2023},
author = {Neuenschwander, S and Cruz Dávalos, DI and Anchieri, L and Sousa da Mota, B and Bozzi, D and Rubinacci, S and Delaneau, O and Rasmussen, S and Malaspinas, AS},
title = {Mapache: a flexible pipeline to map ancient DNA.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btad028},
pmid = {36637197},
issn = {1367-4811},
abstract = {SUMMARY: We introduce mapache, a flexible, robust, and scalable pipeline to map, quantify and impute ancient and present-day DNA in a reproducible way. Mapache is implemented in the workflow manager Snakemake and is optimized for low-space consumption, allowing to efficiently (re)map large data sets-such as reference panels and multiple extracts and libraries per sample-to one or several genomes. Mapache can easily be customized or combined with other Snakemake tools.

AVAILABILITY: Mapache is freely available on GitHub (https://github.com/sneuensc/mapache).

SUPPLEMENTARY INFORMATION: The list of software (and their references) used in the pipeline and the benchmark results can be found in the Supplementary files. An extensive manual is provided at https://github.com/sneuensc/mapache/wiki.},
}

@article {pmid36630487,
year = {2023},
author = {Kehlmaier, C and Graciá, E and Ali, JR and Campbell, PD and Chapman, SD and Deepak, V and Ihlow, F and Jalil, NE and Pierre-Huyet, L and Samonds, KE and Vences, M and Fritz, U},
title = {Ancient DNA elucidates the lost world of western Indian Ocean giant tortoises and reveals a new extinct species from Madagascar.},
journal = {Science advances},
volume = {9},
number = {2},
pages = {eabq2574},
doi = {10.1126/sciadv.abq2574},
pmid = {36630487},
issn = {2375-2548},
abstract = {Before humans arrived, giant tortoises occurred on many western Indian Ocean islands. We combined ancient DNA, phylogenetic, ancestral range, and molecular clock analyses with radiocarbon and paleogeographic evidence to decipher their diversity and biogeography. Using a mitogenomic time tree, we propose that the ancestor of the extinct Mascarene tortoises spread from Africa in the Eocene to now-sunken islands northeast of Madagascar. From these islands, the Mascarenes were repeatedly colonized. Another out-of-Africa dispersal (latest Eocene/Oligocene) produced on Madagascar giant, large, and small tortoise species. Two giant and one large species disappeared c. 1000 to 600 years ago, the latter described here as new to science using nuclear and mitochondrial DNA. From Madagascar, the Granitic Seychelles were colonized (Early Pliocene) and from there, repeatedly Aldabra (Late Pleistocene). The Granitic Seychelles populations were eradicated and later reintroduced from Aldabra. Our results underline that integrating ancient DNA data into a multi-evidence framework substantially enhances the knowledge of the past diversity of island faunas.},
}

@article {pmid36625884,
year = {2023},
author = {Xu, Y and Wang, N and Gao, S and Li, C and Ma, P and Yang, S and Jiang, H and Shi, S and Wu, Y and Zhang, Q and Cui, Y},
title = {Solving the two-decades-old murder case through joint application of ZooMS and ancient DNA approaches.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {36625884},
issn = {1437-1596},
abstract = {Bones are one of the most common biological types of evidence in forensic cases. Discriminating human bones from irrelevant species is important for the identification of victims; however, the highly degraded bones could be undiagnostic morphologically and difficult to analyze with standard DNA profiling approaches. The same challenge also exists in archaeological studies. Here, we present an initial study of an analytical strategy that involves zooarchaeology by mass spectrometry (ZooMS) and ancient DNA methods. Through the combined strategy, we managed to identify the only biological evidence of a two-decades-old murder case - a small piece of human bone out of 19 bone fragments - and confirmed the kinship between the victim and the putative parents through joint application of next-generation sequencing (NGS) and Sanger sequencing methods. ZooMS effectively screened out the target human bone while ancient DNA methods improve the DNA yields. The combined strategy in this case outperforms the standard DNA profiling approach with shorter time, less cost, as well as higher reliability for the genetic identification results. HIGHLIGHTS: • The first application of zooarchaeology by mass spectrometry technique in the forensic case for screening out human bones from bone fragment mixtures. • Application of ancient DNA technique to recover the highly degraded DNA sequence from the challenging sample that failed standard DNA profiling approaches. • A fast, sensitive, and low-cost strategy that combines the strengths of protein analysis and DNA analysis for kinship identification in forensic research.},
}

@article {pmid36625391,
year = {2023},
author = {Straiton, J},
title = {Ancient DNA sequencing: telling the tale of human history and evolution.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2022-0121},
pmid = {36625391},
issn = {1940-9818},
abstract = {Standfirst: In the last decade, ancient DNA research has provided invaluable insights into the lives of ancient populations, adding detail and enriching the story of human evolution and development. [Formula: see text].},
}

@article {pmid36623185,
year = {2023},
author = {Fleskes, RE and Cabana, GS and Gilmore, JK and Juarez, C and Karcher, E and Oubré, L and Mishoe, G and Ofunniyin, AA and Schurr, TG},
title = {Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {3},
pages = {e2201620120},
doi = {10.1073/pnas.2201620120},
pmid = {36623185},
issn = {1091-6490},
abstract = {In this study, we present the results of community-engaged ancient DNA research initiated after the remains of 36 African-descended individuals dating to the late 18th century were unearthed in the port city of Charleston, South Carolina. The Gullah Society of Charleston, along with other Charleston community members, initiated a collaborative genomic study of these ancestors of presumed enslaved status, in an effort to visibilize their histories. We generated 18 low-coverage genomes and 31 uniparental haplotypes to assess their genetic origins and interrelatedness. Our results indicate that they have predominantly West and West-Central African genomic ancestry, with one individual exhibiting some genomic affiliation with populations in the Americas. Most were assessed as genetic males, and no autosomal kin were identified among them. Overall, this study expands our understanding of the colonial histories of African descendant populations in the US South.},
}

@article {pmid36620416,
year = {2023},
author = {Alfieri, JM and Johnson, T and Linderholm, A and Blackmon, H and Athrey, GN},
title = {Genomic investigation refutes record of most diverged avian hybrid.},
journal = {Ecology and evolution},
volume = {13},
number = {1},
pages = {e9689},
pmid = {36620416},
issn = {2045-7758},
abstract = {The most diverged avian hybrid that has been documented (Numida meleagris × Penelope superciliaris) was reported in 1957. This identification has yet to be confirmed, and like most contemporary studies of hybridization, the identification was based on phenotype, which can be misleading. In this study, we sequenced the specimen in question and performed analyses to validate the specimen's parentage. We extracted DNA from the specimen in a dedicated ancient DNA facility and performed whole-genome short-read sequencing. We used BLAST to find Galliformes sequences similar to the hybrid specimen reads. We found that the proportion of BLAST hits mapped overwhelmingly to two species, N. meleagris and Gallus gallus. Additionally, we constructed phylogenies using avian orthologs and parsed the species placed as sister to the hybrid. Again, the hybrid specimen was placed as a sister to N. meleagris and G. gallus. Despite not being a hybrid between N. meleagris and P. superciliaris, the hybrid still represents the most diverged avian hybrid confirmed with genetic data. In addition to correcting the "record" of the most diverged avian hybrid, these findings support recent assertions that morphological and behavioral-based identifications of avian hybrids can be error-prone. Consequently, this study serves as a cautionary tale to researchers of hybridization.},
}

@article {pmid36618122,
year = {2021},
author = {Margaryan, A and Sinding, MS and Carøe, C and Yamshchikov, V and Burtsev, I and Gilbert, MTP},
title = {The genomic origin of Zana of Abkhazia.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {2},
number = {2},
pages = {e10051},
pmid = {36618122},
issn = {2641-6573},
abstract = {Enigmatic phenomena have sparked the imagination of people around the globe into creating folkloric creatures. One prime example is Zana of Abkhazia (South Caucasus), a well-documented 19th century female who was captured living wild in the forest. Zana's appearance was sufficiently unusual, that she was referred to by locals as an Almasty-the analog of Bigfoot in the Caucasus. Although the exact location of Zana's burial site was unknown, the grave of her son, Khwit, was identified in 1971. The genomes of Khwit and the alleged Zana skeleton were sequenced to an average depth of ca. 3× using ancient DNA techniques. The identical mtDNA and parent-offspring relationship between the two indicated that the unknown woman was indeed Zana. Population genomic analyses demonstrated that Zana's immediate genetic ancestry can likely be traced to present-day East-African populations. We speculate that Zana might have had a genetic disorder such as congenital generalized hypertrichosis which could partially explain her strange behavior, lack of speech, and long body hair. Our findings elucidate Zana's unfortunate story and provide a clear example of how prejudices of the time led to notions of cryptic hominids that are still held and transmitted by some today.},
}

@article {pmid36610858,
year = {2022},
author = {Miao, B and Liu, Y and Yang, R and Feng, X and Liu, F and Cao, P and Dai, Q and Ping, W and Liu, Y and Fu, Q},
title = {Assessment of contaminants associated with gold-standard ancient DNA protocols.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2022.12.027},
pmid = {36610858},
issn = {2095-9281},
}

@article {pmid36593352,
year = {2023},
author = {Montag, A},
title = {[The history of skin color is the history of mankind!].},
journal = {Dermatologie (Heidelberg, Germany)},
volume = {},
number = {},
pages = {},
pmid = {36593352},
issn = {2731-7013},
abstract = {In the early days of mankind, at a time when various other human species populated the earth coexisting with Homo sapiens, the genetic mixing of mankind had already begun. Today, paleogenetics-as a branch of human genetic research-can prove that individuals from the most diverse human species already produced offspring together long before our era. This intermixing was supported from the beginning by massive migratory movements that started in East Africa and led first Homo neanderthalensis and much later also Homo sapiens to as far as Europe-two human species of which we know today that they were lighter-skinned than their ancestors. The adaptation to life in different climatic zones led to development of specific characteristics, which, in addition to physique and physiognomy, also affect specific features of the skin and the integumentary system. The most striking feature among these is the skin color and all associated skin-specific characteristics. These characteristics ensure special protection, but can also be the origin for specific diseases. Any division of Homo sapiens into races has been scientifically refuted. Due to ongoing genetic mixing of mankind, skin color, hair color and all associated characteristics should always be considered individually.},
}

@article {pmid36582485,
year = {2022},
author = {Zhu, K and Du, P and Li, J and Zhang, J and Hu, X and Meng, H and Chen, L and Zhou, B and Yang, X and Xiong, J and Allen, E and Ren, X and Ding, Y and Xu, Y and Chang, X and Yu, Y and Han, S and Dong, G and Wang, CC and Wen, S},
title = {Cultural and demic co-diffusion of Tubo Empire on Tibetan Plateau.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105636},
pmid = {36582485},
issn = {2589-0042},
abstract = {A high point of Tibetan Plateau (TP) civilization, the expansive Tubo Empire (618-842 AD) wielded great influence across ancient western China. However, whether the Tubo expansion was cultural or demic remains unclear due to sparse ancient DNA sampling. Here, we reported ten ancient genomes at 0.017- to 0.867-fold coverages from the Dulan site with typical Tubo archaeological culture dating to 1308-1130 BP. Nine individuals from three different grave types have close relationship with previously reported ancient highlanders from the southwestern Himalayas and modern core-Tibetan populations. A Dulan-related Tubo ancestry contributed overwhelmingly (95%-100%) to the formation of modern Tibetans. A genetic outlier with dominant Eurasian steppe-related ancestry suggesting a potential population movement into the Tubo-controlled regions from Central Asia. Together with archeological evidence from burial styles and customs, our study suggested the impact of the Tubo empire on the northeast edge of the TP involved both cultural and demic diffusion.},
}

@article {pmid36581666,
year = {2022},
author = {Changmai, P and Pinhasi, R and Pietrusewsky, M and Stark, MT and Ikehara-Quebral, RM and Reich, D and Flegontov, P},
title = {Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st-3rd centuries CE.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {22507},
pmid = {36581666},
issn = {2045-2322},
abstract = {Indian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40-50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78-234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations.},
}

@article {pmid36576953,
year = {2022},
author = {Nägele, K and Rivollat, M and Yu, H and Wang, K},
title = {Ancient genomic research - From broad strokes to nuanced reconstructions of the past.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10017},
pmid = {36576953},
issn = {2037-0644},
abstract = {Ancient DNA (aDNA) studies have deployed genetic material from archaeological contexts to investigate human dispersals and interactions, corroborating some longstanding hypotheses and revealing new aspects of human history. After drawing the broad genomic strokes of human history, geneticists have discovered the exciting possibilities of applying this method to answer questions on a smaller scale. This review provides an overview of the commonly used methods, both in the laboratory and the analyses, and summarizes the current state of genomic research. It reviews human dispersals across the continents and additionally highlights some studies that integrated genomics to answer questions beyond biology to understand the cultural and societal traits of past societies. By shining a light from multiple angles, we gain a much better understanding of the real shape of the human past.},
}

@article {pmid36565457,
year = {2022},
author = {Vallini, L and Pagani, L},
title = {The future of the Eurasian past: highlighting plotholes and pillars of human population movements in the Late Pleistocene.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {100},
number = {},
pages = {},
doi = {10.4436/JASS.10013},
pmid = {36565457},
issn = {2037-0644},
abstract = {The major genetic divergences among non-Africans took place within a relatively short period of time, between 50 and 40 thousand years ago. These events shaped human diversity worldwide and set the basis for our current understanding of demographic history, patterns of adaptation and genetic burden across human populations. While the global picture appears already set, with the main human expansion Out of Africa inferred to have occurred between 60 and 70 thousand years ago and the main separation between contemporary East and West Eurasian to have taken place at around 40 thousand years ago, several finer details remain unresolved, including the whereabouts of such expansions and the dynamics of their interactions with archaic hominins and the interplay between environmental, cultural and demographic effectors. Here we review the major events that characterize human movements across and beyond Eurasia until the last glacial maximum and, at the end of each paragraph, spell out in italics the major questions that remain unsolved and that may provide major breakthroughs in the field in the upcoming years.},
}

@article {pmid36555510,
year = {2022},
author = {Abondio, P and Bruno, F and Bruni, AC and Luiselli, D},
title = {Rare Amyloid Precursor Protein Point Mutations Recapitulate Worldwide Migration and Admixture in Healthy Individuals: Implications for the Study of Neurodegeneration.},
journal = {International journal of molecular sciences},
volume = {23},
number = {24},
pages = {},
pmid = {36555510},
issn = {1422-0067},
abstract = {Genetic discoveries related to Alzheimer's disease and other dementias have been performed using either large cohorts of affected subjects or multiple individuals from the same pedigree, therefore disregarding mutations in the context of healthy groups. Moreover, a large portion of studies so far have been performed on individuals of European ancestry, with a remarkable lack of epidemiological and genomic data from underrepresented populations. In the present study, 70 single-point mutations on the APP gene in a publicly available genetic dataset that included 2504 healthy individuals from 26 populations were scanned, and their distribution was analyzed. Furthermore, after gametic phase reconstruction, a pairwise comparison of the segments surrounding the mutations was performed to reveal patterns of haplotype sharing that could point to specific cross-population and cross-ancestry admixture events. Eight mutations were detected in the worldwide dataset, with several of them being specific for a single individual, population, or macroarea. Patterns of segment sharing reflected recent historical events of migration and admixture possibly linked to colonization campaigns. These observations reveal the population dynamics of the considered APP mutations in worldwide human groups and support the development of ancestry-informed screening practices for the improvement of precision and personalized approaches to neurodegeneration and dementia.},
}

@article {pmid36553640,
year = {2022},
author = {Taufik, L and Teixeira, JC and Llamas, B and Sudoyo, H and Tobler, R and Purnomo, GA},
title = {Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects.},
journal = {Genes},
volume = {13},
number = {12},
pages = {},
doi = {10.3390/genes13122373},
pmid = {36553640},
issn = {2073-4425},
abstract = {Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.},
}

@article {pmid36546258,
year = {2022},
author = {Wang, Y},
title = {Ancient environmental DNA reveals Arctic ecosystem dynamics in last 50,000 years.},
journal = {Science bulletin},
volume = {67},
number = {13},
pages = {1304-1306},
doi = {10.1016/j.scib.2022.04.018},
pmid = {36546258},
issn = {2095-9281},
mesh = {*Ecosystem ; DNA, Ancient ; *DNA, Environmental ; Arctic Regions ; },
}

*Ecosystem
DNA, Ancient
*DNA, Environmental
Arctic Regions

@article {pmid36547255,
year = {2022},
author = {van der Kuyl, AC},
title = {Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens.},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {3},
number = {4},
pages = {443-464},
doi = {10.3390/epidemiologia3040034},
pmid = {36547255},
issn = {2673-3986},
abstract = {Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.},
}

@article {pmid36536113,
year = {2022},
author = {D'Agostino, A and Di Marco, G and Marvelli, S and Marchesini, M and Rizzoli, E and Rolfo, MF and Canini, A and Gismondi, A},
title = {Neolithic dental calculi provide evidence for environmental proxies and consumption of wild edible fruits and herbs in central Apennines.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1384},
pmid = {36536113},
issn = {2399-3642},
mesh = {Humans ; Animals ; *Fruit ; Plants, Edible ; Pollen ; Poaceae ; Forests ; DNA, Ancient ; *Calculi ; },
abstract = {Looking for a biological fingerprint relative to new aspects of the relationship between humans and natural environment during prehistoric times is challenging. Although many issues still need to be addressed in terms of authentication and identification, microparticles hidden in ancient dental calculus can provide interesting information for bridging this gap of knowledge. Here, we show evidence about the role of edible plants for the early Neolithic individuals in the central Apennines of the Italian peninsula and relative cultural landscape. Dental calculi from human and animal specimens exhumed at Grotta Mora Cavorso (Lazio), one of the largest prehistoric burial deposits, have returned an archaeobotanical record made up of several types of palaeoecological proxies. The organic fraction of this matrix was investigated by a multidisciplinary approach, whose novelty consisted in the application of next generation sequencing to ancient plant DNA fragments, specifically codifying for maturase K barcode gene. Panicoideae and Triticeae starches, together with genetic indicators of Rosaceae fruits, figs, and Lamiaceae herbs, suggested subsistence practices most likely still based on wild plant resources. On the other hand, pollen, and non-pollen palynomorphs allowed us to outline a general vegetational framework dominated by woodland patches alternated with meadows, where semi-permanent settlements could have been established.},
}

Humans
Animals
*Fruit
Plants, Edible
Pollen
Poaceae
Forests
DNA, Ancient
*Calculi

@article {pmid36539480,
year = {2022},
author = {Young, JM and Liddicoat, C and van Dijk, KJ and Tabernero, P and Caillet, C and White, NJ and Linacre, A and Austin, JJ and Newton, PN},
title = {Environmental DNA as an innovative technique to identify the origins of falsified antimalarial tablets-a pilot study of the pharmabiome.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {21997},
pmid = {36539480},
issn = {2045-2322},
support = {202935/Z/16/Z//Wellcome Trust/United Kingdom ; 202935/Z/16/Z//Wellcome Trust/United Kingdom ; 202935/Z/16/Z//Wellcome Trust/United Kingdom ; 202935/Z/16/Z//Wellcome Trust/United Kingdom ; },
abstract = {Falsified medicines are a major threat to global health. Antimalarial drugs have been particularly targeted by criminals. As DNA analysis has revolutionized forensic criminology, we hypothesized that these techniques could also be used to investigate the origins of falsified medicines. Medicines may contain diverse adventitious biological contamination, and the sealed nature of blister-packages may capture and preserve genetic signals from the manufacturing processes allowing identification of production source(s). We conducted a blinded pilot study to determine if such environmental DNA (eDNA) could be detected in eleven samples of falsified and genuine artesunate antimalarial tablets, collected in SE Asia, which could be indicative of origin. Massively Parallel Sequencing (MPS) was used to characterize microbial and eukaryote diversity. Two mitochondrial DNA analysis approaches were explored to detect the presence of human DNA. Trace eDNA from these low biomass samples demonstrated sample specific signals using two target markers. Significant differences in bacterial and eukaryote DNA community structures were observed between genuine and falsified tablets and between different packaging types of falsified artesunate. Human DNA, which was indicative of likely east Asian ancestry, was found in falsified tablets. This pilot study of the 'pharmabiome' shows the potential of environmental DNA as a powerful forensic tool to assist with the identification of the environments, and hence location and timing, of the source and manufacture of falsified medicines, establish links between seizures and complement existing tools to build a more complete picture of criminal trade routes. The finding of human DNA in tablets raises important ethical issues that need to be addressed.},
}

@article {pmid36537881,
year = {2022},
author = {Muktupavela, RA and Petr, M and Ségurel, L and Korneliussen, T and Novembre, J and Racimo, F},
title = {Modeling the spatiotemporal spread of beneficial alleles using ancient genomes.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
doi = {10.7554/eLife.73767},
pmid = {36537881},
issn = {2050-084X},
support = {R01 GM132383/NH/NIH HHS/United States ; 951385/ERC_/European Research Council/International ; },
abstract = {Ancient genome sequencing technologies now provide the opportunity to study natural selection in unprecedented detail. Rather than making inferences from indirect footprints left by selection in present-day genomes, we can directly observe whether a given allele was present or absent in a particular region of the world at almost any period of human history within the last 10,000 years. Methods for studying selection using ancient genomes often rely on partitioning individuals into discrete time periods or regions of the world. However, a complete understanding of natural selection requires more nuanced statistical methods which can explicitly model allele frequency changes in a continuum across space and time. Here we introduce a method for inferring the spread of a beneficial allele across a landscape using two-dimensional partial differential equations. Unlike previous approaches, our framework can handle time-stamped ancient samples, as well as genotype likelihoods and pseudohaploid sequences from low-coverage genomes. We apply the method to a panel of published ancient West Eurasian genomes to produce dynamic maps showcasing the inferred spread of candidate beneficial alleles over time and space. We also provide estimates for the strength of selection and diffusion rate for each of these alleles. Finally, we highlight possible avenues of improvement for accurately tracing the spread of beneficial alleles in more complex scenarios.},
}

@article {pmid36531224,
year = {2022},
author = {Xiang, H and Wang, Z and Yang, L and Zhang, X and Zhao, X},
title = {Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {1000123},
pmid = {36531224},
issn = {1664-8021},
abstract = {Ancient DNA is vitally important in evolutionary research, and obtaining authentic ancient DNA sequences is critical for a proper analysis. However, it is difficult to acquire amplicons accurately and efficiently from ancient DNA templates using current techniques. Here, we established a loop-primer-mediated amplification method (L-PCR) to obtain target ancient DNA sequences with high accuracy and efficiency. The method was tested using 66 ancient samples (including 27 pig bones or teeth and 39 chicken bones) and serially diluted modern animal DNA templates. Compared to nested PCR, L-PCR was proven to be more efficient and accurate and could obtain more amplicons from both ancient pig samples and chicken bones and detect as low as 10[-3] ng/μl modern pig template DNA. The efficiency was at least 100-fold that of the nested PCR. The results suggest that L-PCR is advantageous for obtaining authentic DNA sequences from poorly preserved or recalcitrant ancient specimens.},
}

@article {pmid36525814,
year = {2022},
author = {Bardan, F and Higgins, D and Austin, JJ},
title = {A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage.},
journal = {Forensic science international. Genetics},
volume = {63},
number = {},
pages = {102822},
doi = {10.1016/j.fsigen.2022.102822},
pmid = {36525814},
issn = {1878-0326},
abstract = {Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.},
}

@article {pmid36525576,
year = {2022},
author = {de Flamingh, A and Rivera-Colón, AG and Gnoske, TP and Kerbis Peterhans, JC and Catchen, J and Malhi, RS and Roca, AL},
title = {Numt Parser: automated identification and removal of nuclear mitochondrial pseudogenes (numts) for accurate mitochondrial genome reconstruction in Panthera.},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esac065},
pmid = {36525576},
issn = {1465-7333},
abstract = {Nuclear mitochondrial pseudogenes (numts) may hinder the reconstruction of mtDNA genomes and affect the reliability of mtDNA datasets for phylogenetic and population genetic comparisons. Here, we present the program Numt Parser, which allows for the identification of DNA sequences that likely originate from numt pseudogene DNA. Sequencing reads are classified as originating from either numt or true cytoplasmic mitochondrial (cymt) DNA by direct comparison against cymt and numt reference sequences. Classified reads can then be parsed into cymt or numt datasets. We tested this program using whole genome shotgun-sequenced data from two ancient Cape lions (Panthera leo), because mtDNA is often the marker of choice for ancient DNA studies and the genus Panthera is known to have numt pseudogenes. Numt Parser decreased sequence disagreements that were likely due to numt pseudogene contamination and equalized read coverage across the mitogenome by removing reads that likely originated from numts. We compared the efficacy of Numt Parser to two other bioinformatic approaches that can be used to account for numt contamination. We found that Numt Parser outperformed approaches that rely only on read alignment or Basic Local Alignment Search Tool (BLAST) properties, and was effective at identifying sequences that likely originated from numts while having minimal impacts on the recovery of cymt reads. Numt Parser therefore improves the reconstruction of true mitogenomes, allowing for more accurate and robust biological inferences.},
}

@article {pmid36476770,
year = {2022},
author = {Callaway, E},
title = {Oldest-ever DNA shows mastodons roamed Greenland 2 million years ago.},
journal = {Nature},
volume = {612},
number = {7940},
pages = {384},
pmid = {36476770},
issn = {1476-4687},
mesh = {Animals ; Fossils ; Greenland ; *Mastodons/genetics ; *DNA, Ancient/analysis ; History, Ancient ; },
}

Animals
Fossils
Greenland
*Mastodons/genetics
*DNA, Ancient/analysis
History, Ancient

@article {pmid36520391,
year = {2023},
author = {Gorgé, O and Bennett, EA and Massilani, D and Daligault, J and Geigl, EM and Grange, T},
title = {Analysis of Ancient Microbial DNA.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2605},
number = {},
pages = {103-131},
pmid = {36520391},
issn = {1940-6029},
abstract = {The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of ancient human skeletal remains have revolutionized our understanding of human evolution. This research led to the discovery of a new hominin lineage, and demonstrated multiple admixture events with more distantly related archaic human populations such as Neandertals and Denisovans over the last 100,000 years. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes enables the study of their recent evolution, presently covering the last several millennia. These spectacular results have been obtained despite the degradation of DNA that takes place after the death of the host and increases with time. This cumulative degradation results in very short ancient DNA molecules, low in quantity, and highly prone to contamination by modern DNA molecules, especially from human and animal DNA present in reagents used in downstream biomolecular analyses. Finally, the minute amounts of ancient molecules are further diluted in environmental DNA from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples, and the identification of ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.},
}

@article {pmid36518622,
year = {2022},
author = {Anderson, LA},
title = {Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation.},
journal = {Ecology and evolution},
volume = {12},
number = {12},
pages = {e9518},
doi = {10.1002/ece3.9518},
pmid = {36518622},
issn = {2045-7758},
abstract = {Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.},
}

@article {pmid36517229,
year = {2022},
author = {Rohland, N and Mallick, S and Mah, M and Maier, R and Patterson, N and Reich, D},
title = {Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.276728.122},
pmid = {36517229},
issn = {1549-5469},
abstract = {The strategy of in-solution enrichment for hundreds of thousands of single-nucleotide polymorphisms (SNPs) has been used to analyze >70% of individuals with genome-scale ancient DNA published to date. This approach makes it economical to study ancient samples with low proportions of human DNA and increases the rate of conversion of sampled remains into interpretable data. So far, nearly all such data have been generated using a set of bait sequences targeting about 1.24 million SNPs (the "1240k reagent"), but synthesis of the reagent has been cost-effective for only a few laboratories. In 2021, two companies, Daicel Arbor Biosciences and Twist Bioscience, made available assays that target the same core set of SNPs along with supplementary content. We test all three assays on a common set of 27 ancient DNA libraries and show that all three are effective at enriching many hundreds of thousands of SNPs. For all assays, one round of enrichment produces data that are as useful as two. In our testing, the "Twist Ancient DNA" assay produces the highest coverages, greatest uniformity on targeted positions, and almost no bias toward enriching one allele more than another relative to shotgun sequencing. We also identify hundreds of thousands of targeted SNPs for which there is minimal allelic bias when comparing 1240k data to either shotgun or Twist data. This facilitates coanalysis of the large data sets that have been generated using 1240k and Twist capture, as well as shotgun sequencing approaches.},
}

@article {pmid36516232,
year = {2022},
author = {Söylev, A and Çokoglu, SS and Koptekin, D and Alkan, C and Somel, M},
title = {CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.},
journal = {PLoS computational biology},
volume = {18},
number = {12},
pages = {e1010788},
doi = {10.1371/journal.pcbi.1010788},
pmid = {36516232},
issn = {1553-7358},
abstract = {To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.},
}

@article {pmid36514938,
year = {2022},
author = {Rannamäe, E and Saarma, U and Kantanen, J and Bläuer, A},
title = {Maternal genetic diversity of ancient goats in Finland and Estonia and comparison with extant northern European goat breeds.},
journal = {Animal genetics},
volume = {},
number = {},
pages = {},
doi = {10.1111/age.13281},
pmid = {36514938},
issn = {1365-2052},
abstract = {Countries in the northern Baltic Sea region have been historically linked for thousands of years, and animal husbandry is one of the many information sources that enables the study of historical connections. Although goat husbandry in this part of Europe has been evidenced by scant archaeological materials, zooarchaeological and historical evidence has revealed its continuity, at least since the Late Iron Age. To explore the historical relationship between goat lineages and investigate affinities between the past and present-day populations in the Baltic Sea region, we analysed a 476-bp fragment of the mitochondrial DNA control region in 14 ancient goats from Finland and Estonia and 10 extant goats from Finland. The results revealed high mitochondrial diversity among the ancient goats. Two maternal lineages were shared between the Late Iron Age and medieval individuals from Finland and Estonia. Moreover, ancient Finnish and Estonian goats showed maternal affinity to extant Finngoat and Swedish Landrace breeds. Overall, the analysis of maternal goat lineages confirmed tight historical connections in the region.},
}

@article {pmid36513080,
year = {2022},
author = {Peltola, S and Majander, K and Makarov, N and Dobrovolskaya, M and Nordqvist, K and Salmela, E and Onkamo, P},
title = {Genetic admixture and language shift in the medieval Volga-Oka interfluve.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.036},
pmid = {36513080},
issn = {1879-0445},
abstract = {The Volga-Oka interfluve in northwestern Russia has an intriguing history of population influx and language shift during the Common Era. Today, most inhabitants of the region speak Russian, but until medieval times, northwestern Russia was inhabited by Uralic-speaking peoples.[1][,][2][,][3] A gradual shift to Slavic languages started in the second half of the first millennium with the expansion of Slavic tribes, which led to the foundation of the Kievan Rus' state in the late 9[th] century CE. The medieval Rus' was multicultural and multilingual-historical records suggest that its northern regions comprised Slavic and Uralic peoples ruled by Scandinavian settlers.[4][,][5][,][6] In the 10[th]-11[th] centuries, the introduction of Christianity and Cyrillic literature raised the prestige status of Slavic, driving a language shift from Uralic to Slavic.[3] This eventually led to the disappearance of the Uralic languages from northwestern Russia. Here, we study a 1,500-year time transect of 30 ancient genomes and stable isotope values from the Suzdal region in the Volga-Oka interfluve. We describe a previously unsampled local Iron Age population and a gradual genetic turnover in the following centuries. Our time transect captures the population shift associated with the spread of Slavic languages and illustrates the ethnically mixed state of medieval Suzdal principality, eventually leading to the formation of the admixed but fully Slavic-speaking population that inhabits the area today. We also observe genetic outliers that highlight the importance of the Suzdal region in medieval times as a hub of long-reaching contacts via trade and warfare.},
}

@article {pmid36510283,
year = {2022},
author = {Bonczarowska, JH and Susat, J and Mühlemann, B and Jasch-Boley, I and Brather, S and Höke, B and Brather-Walter, S and Schoenenberg, V and Scheschkewitz, J and Graenert, G and Krausse, D and Francken, M and Jones, TC and Wahl, J and Nebel, A and Krause-Kyora, B},
title = {Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {250},
pmid = {36510283},
issn = {1474-760X},
support = {HHSN272201400008C/AI/NIAID NIH HHS/United States ; },
abstract = {BACKGROUND: The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim "Mittelhofen," in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically.

RESULTS: Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK.

CONCLUSIONS: The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later.},
}

@article {pmid36494546,
year = {2022},
author = {Forshaw, R},
title = {Dental calculus - oral health, forensic studies and archaeology: a review.},
journal = {British dental journal},
volume = {233},
number = {11},
pages = {961-967},
doi = {10.1038/s41415-022-5266-7},
pmid = {36494546},
issn = {1476-5373},
abstract = {Dental calculus is recognised as a secondary aetiological factor in periodontal disease, and being a prominent plaque retentive factor, it is routinely removed by the dental team to maintain oral health. Conversely, dental calculus can potentially be useful in forensic studies by supplying data that may be helpful in the identification of human remains and assist in determining the cause of death. During the last few decades, dental calculus has been increasingly recognised as an informative tool to understand ancient diet and health. As an archaeological deposit, it may contain non-dietary debris which permits the exploration of human behaviour and activities. While optical and scanning electron microscopy were the original analytical methods utilised to study microparticles entrapped within the calcified matrix, more recently, molecular approaches, including ancient DNA (aDNA) and protein analyses, have been applied. Oral bacteria, a major component of calculus, is the primary target of these aDNA studies. Such analyses can detect changes in the oral microbiota, including those that have reflected the shift from agriculture to industrialisation, as well as identifying markers for various systemic diseases.},
}

@article {pmid36493775,
year = {2022},
author = {Koptekin, D and Yüncü, E and Rodríguez-Varela, R and Altınışık, NE and Psonis, N and Kashuba, N and Yorulmaz, S and George, R and Kazancı, DD and Kaptan, D and Gürün, K and Vural, KB and Gemici, HC and Vassou, D and Daskalaki, E and Karamurat, C and Lagerholm, VK and Erdal, ÖD and Kırdök, E and Marangoni, A and Schachner, A and Üstündağ, H and Shengelia, R and Bitadze, L and Elashvili, M and Stravopodi, E and Özbaşaran, M and Duru, G and Nafplioti, A and Rose, CB and Gencer, T and Darbyshire, G and Gavashelishvili, A and Pitskhelauri, K and Çevik, Ö and Vuruşkan, O and Kyparissi-Apostolika, N and Büyükkarakaya, AM and Oğuzhanoğlu, U and Günel, S and Tabakaki, E and Aliev, A and Ibrahimov, A and Shadlinski, V and Sampson, A and Kılınç, GM and Atakuman, Ç and Stamatakis, A and Poulakakis, N and Erdal, YS and Pavlidis, P and Storå, J and Özer, F and Götherström, A and Somel, M},
title = {Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.034},
pmid = {36493775},
issn = {1879-0445},
abstract = {We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.},
}

@article {pmid36493597,
year = {2022},
author = {Keeling, BA and Quam, R and Martínez, I and Arsuaga, JL and Maroto, J},
title = {Reassessment of the human mandible from Banyoles (Girona, Spain).},
journal = {Journal of human evolution},
volume = {174},
number = {},
pages = {103291},
doi = {10.1016/j.jhevol.2022.103291},
pmid = {36493597},
issn = {1095-8606},
abstract = {Since the discovery of a human mandible in 1887 near the present-day city of Banyoles, northeastern Spain, researchers have generally emphasized its archaic features, including the lack of chin structures, and suggested affinities with the Neandertals or European Middle Pleistocene (Chibanian) specimens. Uranium-series and electron spin resonance dating suggest the mandible dates to the Late Pleistocene (Tarantian), approximately ca. 45-66 ka. In this study, we reassessed the taxonomic affinities of the Banyoles mandible by comparing it to samples of Middle Pleistocene fossils from Africa and Europe, Neandertals, Early and Upper Paleolithic modern humans, and recent modern humans. We evaluated the frequencies and expressions of morphological features and performed a three-dimensional geometric morphometric analysis on a virtual reconstruction of Banyoles to capture overall mandibular shape. Our results revealed no derived Neandertal morphological features in Banyoles. While a principal component analysis based on Euclidean distances from the first two principal components clearly grouped Banyoles with both fossil and recent Homo sapiens individuals, an analysis of the Procrustes residuals demonstrated that Banyoles did not fit into any of the comparative groups. The lack of Neandertal features in Banyoles is surprising considering its Late Pleistocene age. A consideration of the Middle Pleistocene fossil record in Europe and southwest Asia suggests that Banyoles is unlikely to represent a late-surviving Middle Pleistocene population. The lack of chin structures also complicates an assignment to H. sapiens, although early fossil H. sapiens do show somewhat variable development of the chin structures. Thus, Banyoles represents a non-Neandertal Late Pleistocene European individual and highlights the continuing signal of diversity in the hominin fossil record. The present situation makes Banyoles a prime candidate for ancient DNA or proteomic analyses, which may shed additional light on its taxonomic affinities.},
}

@article {pmid36481947,
year = {2022},
author = {Bundell, S},
title = {Record-breaking ancient DNA found in frozen soil.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-04398-6},
pmid = {36481947},
issn = {1476-4687},
}

@article {pmid36481704,
year = {2022},
author = {Zhang, J and Shi, K and Paerl, HW and Rühland, KM and Yuan, Y and Wang, R and Chen, J and Ge, M and Zheng, L and Zhang, Z and Qin, B and Liu, J and Smol, JP},
title = {Ancient DNA reveals potentially toxic cyanobacteria increasing with climate change.},
journal = {Water research},
volume = {229},
number = {},
pages = {119435},
doi = {10.1016/j.watres.2022.119435},
pmid = {36481704},
issn = {1879-2448},
abstract = {Cyanobacterial blooms in freshwater systems are a global threat to human and aquatic ecosystem health, exhibiting particularly harmful effects when toxin-producing taxa are present. While climatic change and nutrient over-enrichment control the global expansion of total cyanobacterial blooms, it remains unknown to what extent this expansion reflected cyanobacterial assemblage due to the scarcity of long-term monitoring data. Here we use high-throughput sequencing of sedimentary DNA to track ∼100 years of changes in cyanobacterial community in hyper-eutrophic Lake Taihu, China's third largest freshwater lake and the key water source for ∼30 million people. A steady increase in the abundance of Microcystis (as potential toxin producers) during the past thirty years was correlated with increasing temperatures and declining wind speeds, but not with temporal trends in lakewater nutrient concentrations, highlighting recent climate effects on potentially increasing toxin-producing taxa. The socio-environmental repercussions of these findings are worrisome as continued anthropogenic climate change may counteract nutrient amelioration efforts in this critical freshwater resource.},
}

@article {pmid36472532,
year = {2022},
author = {Moraitou, M and Forsythe, A and Fellows Yates, JA and Brealey, JC and Warinner, C and Guschanski, K},
title = {Ecology, not host phylogeny, shapes the oral microbiome in closely related species.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac263},
pmid = {36472532},
issn = {1537-1719},
abstract = {Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through dietary differences. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.},
}

@article {pmid36465121,
year = {2022},
author = {Ma, X and Xu, S},
title = {Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.},
journal = {iScience},
volume = {25},
number = {12},
pages = {105614},
pmid = {36465121},
issn = {2589-0042},
abstract = {Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such as SLC19A2, SLC35F3, and SLC35F4, were assumed to be underlying positive selection in East Asians, but the detailed mechanism remains unknown. Here, we analyzed genome data of 3,823 individuals representing 223 global populations and identified the adaptive haplotypes at thiamine genes. Interestingly, the putative adaptive haplotype at SLC35F4 was of Neanderthal ancestry, while that at SLC35F3 was also likely of archaic origins. Leveraging new methods and available ancient DNA data, we further demonstrated that the beneficial haplotypes reached a high frequency at least 10,000 years ago and are maintained persistently in present-day East Asians. We argue that pathogens, rather than agriculture developed ∼10,000 years ago in East Asia, were likely the initial driving force of the putative positive selection. Notably, the first American people did not carry the putative adaptive haplotype at SLC35F4.},
}

@article {pmid36463384,
year = {2022},
author = {Wang, K and Bleasdale, M and Le Moyne, C and Freund, C and Krause, J and Boivin, N and Schiffels, S},
title = {4000-year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early eastern Africa pastoralists.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {20939},
pmid = {36463384},
issn = {2045-2322},
mesh = {Humans ; *DNA, Ancient ; Africa, Eastern ; *Hair ; Sudan ; Body Remains ; },
abstract = {Petrous bones and teeth are the skeletal elements most often targeted by researchers for ancient DNA (aDNA) extraction, and the sources of the majority of previously published ancient African genomes. However, the high temperature environments that characterise much of Africa often lead to poor preservation of skeletal remains. Here, we successfully reconstruct and analyse genome-wide data from the naturally mummified hair of a 4000-year-old individual from Sudan in northeastern Africa, after failed attempts at DNA extraction from teeth, petrous, and cranium of this and other individuals from the Kadruka cemeteries. We find that hair DNA extracted with an established single-stranded library protocol is unusually enriched in ultra-short DNA molecules and exhibits substantial interior molecular damage. The aDNA was nonetheless amenable to genetic analyses, which revealed that the genome is genetically indistinguishable from that of early Neolithic eastern African pastoralists located 2500 kms away. Our findings are consistent with established models for the southward dispersal of Middle Nile Valley pastoral populations to the Rift Valley of eastern Africa, and provide a possible genetic source population for this dispersal. Our study highlights the value of mummified hair as an alternate source of aDNA from regions with poor bone preservation.},
}

Humans
*DNA, Ancient
Africa, Eastern
*Hair
Sudan
Body Remains

@article {pmid36455558,
year = {2022},
author = {Waldman, S and Backenroth, D and Harney, É and Flohr, S and Neff, NC and Buckley, GM and Fridman, H and Akbari, A and Rohland, N and Mallick, S and Olalde, I and Cooper, L and Lomes, A and Lipson, J and Cano Nistal, J and Yu, J and Barzilai, N and Peter, I and Atzmon, G and Ostrer, H and Lencz, T and Maruvka, YE and Lämmerhirt, M and Beider, A and Rutgers, LV and Renson, V and Prufer, KM and Schiffels, S and Ringbauer, H and Sczech, K and Carmi, S and Reich, D},
title = {Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14[th] century.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2022.11.002},
pmid = {36455558},
issn = {1097-4172},
support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG012287/HG/NHGRI NIH HHS/United States ; },
abstract = {We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14[th] century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14[th] century and highlight late medieval genetic heterogeneity no longer present in modern AJ.},
}

@article {pmid36454815,
year = {2022},
author = {Curry, A},
title = {Meeting the ancestors.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6623},
pages = {940-943},
doi = {10.1126/science.adg0308},
pmid = {36454815},
issn = {1095-9203},
mesh = {*Jews/genetics ; Population/genetics ; Germany ; Cemeteries/history ; DNA, Ancient ; Humans ; },
abstract = {DNA from a medieval German cemetery opens a window on the history of today's largest Jewish population.},
}

*Jews/genetics
Population/genetics
Germany
Cemeteries/history
DNA, Ancient
Humans

@article {pmid36450657,
year = {2022},
author = {Oh, CS and Kim, MJ and Kim, YS and Min, S and Oh, KT and Lee, SD and Shin, DH},
title = {Revealing Joseon period People's single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea.},
journal = {Anatomy & cell biology},
volume = {},
number = {},
pages = {},
doi = {10.5115/acb.22.178},
pmid = {36450657},
issn = {2093-3665},
abstract = {Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.},
}

@article {pmid36437963,
year = {2022},
author = {Charlier, P and Bourdin, V and Augias, A and Brun, L and Kenmogne, JB and Josue, E},
title = {Are museums the future of evolutionary medicine?.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {1043702},
pmid = {36437963},
issn = {1664-8021},
}

@article {pmid36437603,
year = {2022},
author = {Jeunen, GJ and Dowle, E and Edgecombe, J and von Ammon, U and Gemmell, NJ and Cross, H},
title = {CRABS - A software program to generate curated reference databases for metabarcoding sequencing data.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13741},
pmid = {36437603},
issn = {1755-0998},
abstract = {The measurement of biodiversity is an integral aspect of life science research. With the establishment of second- and third-generation sequencing technologies, an increasing amount of metabarcoding data is being generated as we seek to describe the extent and patterns of biodiversity in multiple contexts. The reliability and accuracy of taxonomically assigning metabarcoding sequencing data has been shown to be critically influenced by the quality and completeness of reference databases. Custom, curated, eukaryotic reference databases, however, are scarce, as are the software programs for generating them. Here, we present CRABS (Creating Reference databases for Amplicon-Based Sequencing), a software package to create custom reference databases for metabarcoding studies. CRABS includes tools to download sequences from multiple online repositories (i.e., NCBI, BOLD, EMBL, MitoFish), retrieve amplicon regions through in silico PCR analysis and pairwise global alignments, curate the database through multiple filtering parameters (e.g., dereplication, sequence length, sequence quality, unresolved taxonomy, inclusion/exclusion filter), export the reference database in multiple formats for the immediate use in taxonomy assignment software, and investigate the reference database through implemented visualizations for diversity, primer efficiency, reference sequence length, database completeness, and taxonomic resolution. CRABS is a versatile tool for generating curated reference databases of user-specified genetic markers to aid taxonomy assignment from metabarcoding sequencing data. CRABS can be installed via Docker and is available for download as a conda package and via GitHub (https://github.com/gjeunen/reference_database_creator).},
}

@article {pmid36426357,
year = {2022},
author = {Thuesen, NH and Klausen, MS and Gopalakrishnan, S and Trolle, T and Renaud, G},
title = {Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {987655},
pmid = {36426357},
issn = {1664-3224},
mesh = {Humans ; Sequence Analysis, DNA/methods ; Histocompatibility Testing/methods ; *High-Throughput Nucleotide Sequencing/methods ; *HLA-A Antigens/genetics ; Algorithms ; },
abstract = {Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype's typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools' robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA's typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype's typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high.},
}

Humans
Sequence Analysis, DNA/methods
Histocompatibility Testing/methods
*High-Throughput Nucleotide Sequencing/methods
*HLA-A Antigens/genetics
Algorithms

@article {pmid36414613,
year = {2022},
author = {Quagliariello, A and Modi, A and Innocenti, G and Zaro, V and Conati Barbaro, C and Ronchitelli, A and Boschin, F and Cavazzuti, C and Dellù, E and Radina, F and Sperduti, A and Bondioli, L and Ricci, S and Lognoli, M and Belcastro, MG and Mariotti, V and Caramelli, D and Mariotti Lippi, M and Cristiani, E and Martino, ME and Muntoni, IM and Lari, M},
title = {Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6927},
pmid = {36414613},
issn = {2041-1723},
mesh = {Humans ; *Agriculture ; *Microbiota ; Diet ; Farmers ; Italy ; },
abstract = {The human microbiome has recently become a valuable source of information about host life and health. To date little is known about how it may have evolved during key phases along our history, such as the Neolithic transition towards agriculture. Here, we shed light on the evolution experienced by the oral microbiome during this transition, comparing Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers that populated a same restricted area in Italy. We integrate the analysis of 76 dental calculus oral microbiomes with the dietary information derived from the identification of embedded plant remains. We detect a stronger deviation from the hunter-gatherer microbiome composition in the last part of the Neolithic, while to a lesser extent in the early phases of the transition. Our findings demonstrate that the introduction of agriculture affected host microbiome, supporting the hypothesis of a gradual transition within the investigated populations.},
}

Humans
*Agriculture
*Microbiota
Diet
Farmers
Italy

@article {pmid36410480,
year = {2022},
author = {Paquis, P and Hengst, MB and Florez, JZ and Tapia, J and Molina, V and Pérez, V and Pardo-Esté, C},
title = {Short-term characterisation of climatic-environmental variables and microbial community diversity in a high-altitude Andean wetland (Salar de Huasco, Chile).},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {160291},
doi = {10.1016/j.scitotenv.2022.160291},
pmid = {36410480},
issn = {1879-1026},
abstract = {Microbial community structures are shaped by geochemical factors and their interactions with the lithosphere, hydrosphere, and atmosphere through the processes of chemical mobilisation and mineralisation. High-altitude wetlands and salt flats in the central Andes are characterised by pronounced physicochemical gradients and extreme climatic conditions, representing hotspots of microbial diversity. We here hypothesise about the existence of direct relationships between the local microbiology and the climate cyclicity variables based on meteorological and biogeochemical patterns that develop over a short time scale (five years). We have here analysed the interactions between hydrometeorological and biogeochemical variables and the microbial communities of the Salar de Huasco. These results were obtained by correlating 16S cDNA and DNA gene Illumina sequences with meteorological/satellite data collected both at monitoring stations and by remote sensing between the years 2015 and 2020. The precipitation levels and flooded areas (i.e., areas covered and/or saturated with permanent water) detected in the Salar de Huasco revealed a marked hydric cyclicity that correlated seasonally with intra-annual wet and dry seasons. Overall, at this site, wet periods occurred from December to April, and dry periods from May to November. Meteorological variables such as solar radiation, air temperature, relative humidity, wind speed, atmospheric pressure, and wind direction were well-defined, showing a potential association with the hydrogeology of the area, which is directly related to the wetlands' flooded areas. Finally, the microbial presence and potentially active microbial communities were determined through the sequencing of the 16S gene (DNA and cDNA, respectively), this were associated with climatic seasonality and spatially distributed physical and chemical heterogeneity. Other non-local inter-annual scale processes, such as El Niño-Southern Oscillation (ENSO) events, modify the physical and chemical context of the wetland, thus forming unique ecological niches in the Andean Mountains.},
}

@article {pmid36405775,
year = {2022},
author = {Arzelier, A and Rivollat, M and De Belvalet, H and Pemonge, MH and Binder, D and Convertini, F and Duday, H and Gandelin, M and Guilaine, J and Haak, W and Deguilloux, MF and Pruvost, M},
title = {Neolithic genomic data from southern France showcase intensified interactions with hunter-gatherer communities.},
journal = {iScience},
volume = {25},
number = {11},
pages = {105387},
pmid = {36405775},
issn = {2589-0042},
abstract = {Archaeological research shows that the dispersal of the Neolithic took a more complex turn when reaching western Europe, painting a contrasted picture of interactions between autochthonous hunter-gatherers (HGs) and incoming farmers. In order to clarify the mode, the intensity, and the regional variability of biological exchanges implied in these processes, we report new palaeogenomic data from Occitanie, a key region in Southern France. Genomic data from 28 individuals originating from six sites spanning from c. 5,500 to c. 2,500 BCE allow us to characterize regional patterns of ancestries throughout the Neolithic period. Results highlight major differences between the Mediterranean and Continental Neolithic expansion routes regarding both migration and interaction processes. High proportions of HG ancestry in both Early and Late Neolithic groups in Southern France support multiple pulses of inter-group gene flow throughout time and space and confirm the need for regional studies to address the complexity of the processes involved.},
}

@article {pmid36400919,
year = {2022},
author = {Scorrano, G and Nielsen, SH and Vetro, DL and Sawafuji, R and Mackie, M and Margaryan, A and Fotakis, AK and Martínez-Labarga, C and Fabbri, PF and Allentoft, ME and Carra, M and Martini, F and Rickards, O and Olsen, JV and Pedersen, MW and Cappellini, E and Sikora, M},
title = {Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1262},
pmid = {36400919},
issn = {2399-3642},
mesh = {Humans ; Animals ; *Proteomics ; Dental Calculus ; Diet ; Genomics ; *Microbiota/genetics ; },
abstract = {Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.},
}

Humans
Animals
*Proteomics
Dental Calculus
Diet
Genomics
*Microbiota/genetics

@article {pmid36399972,
year = {2022},
author = {Pilli, E and Morelli, S and Poggiali, B and Alladio, E},
title = {Biogeographical ancestry, variable selection, and PLS-DA method: a new panel to assess ancestry in forensic samples via MPS technology.},
journal = {Forensic science international. Genetics},
volume = {62},
number = {},
pages = {102806},
doi = {10.1016/j.fsigen.2022.102806},
pmid = {36399972},
issn = {1878-0326},
abstract = {As evidenced by the large number of articles recently published in the literature, forensic scientists are making great efforts to infer externally visible features and biogeographical ancestry (BGA) from DNA analysis. Just as phenotypic, ancestry information obtained from DNA can provide investigative leads to identify the victims (missing/unidentified persons, crime/armed conflict/mass disaster victims) or trace their perpetrators when no matches were found with the reference profile or in the database. Recently, the advent of Massively Parallel Sequencing technologies associated with the possibility of harnessing high-throughput genetic data allowed us to investigate the associations between phenotypic and genomic variations in worldwide human populations and develop new BGA forensic tools capable of simultaneously analyzing up to millions of markers if for example the ancient DNA approach of hybridization capture was adopted to target SNPs of interest. In the present study, a selection of more than 3000 SNPs was performed to create a new BGA panel and the accuracy of the new panel to infer ancestry from unknown samples was evaluated by the PLS-DA method. Subsequently, the panel created was assessed using three variable selection techniques (Backward variable elimination, Genetic Algorithm and Regularized elimination procedure), and the best SNPs in terms of inferring bio-geographical ancestry at inter- and intra-continental level were selected to obtain panels to predict BGA with a reduced number of selected markers to be applied in routine forensic cases where PCR amplification is the best choice to target SNPs.},
}

@article {pmid36399550,
year = {2022},
author = {Sugiyama, N and Sugiyama, S and Cagnato, C and France, CAM and Iriki, A and Hughes, KS and Singleton, RR and Thornton, E and Hofman, CA},
title = {Earliest evidence of primate captivity and translocation supports gift diplomacy between Teotihuacan and the Maya.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {47},
pages = {e2212431119},
pmid = {36399550},
issn = {1091-6490},
mesh = {Humans ; Animals ; *Diplomacy ; Ceremonial Behavior ; DNA, Ancient ; *Atelinae ; Mexico ; },
abstract = {A multimethod archaeometry study (zooarchaeological, isotopic, ancient DNA, paleobotanical, and radiocarbon dating) of a spider monkey sacrificed in the ceremonial center of Teotihuacan, Mexico (1 to 550 CE) is interpreted as a diplomatic gift exchange with neighboring Maya. Not only does this spider monkey provide the earliest known instance of primate translocation and captivity in Mesoamerica, it helps date incipient modes of interregional diplomacy between two major powers during Early Classic Mesoamerica: Teotihuacan and the Maya. Details of human-primate interaction include age at capture and transport (before ∼3 y of age), captive duration (over 2 y), anthropogenic diet (staple was maize, though secondary resources unique to anthropogenic diet including arrowroot and chili pepper were also found), context of sacrifice (tethered and associated with complete golden eagle and an array of other statecrafts), and general site context (including presence of Maya vessels and Maya-style murals). The timing of the spider monkey's sacrifice (250 to 300 CE) and its life history suggest a reconsideration of epigraphically attested militaristic involvement of Teotihuacan at certain Maya sites. We propose that a period of more multilateral and fluid ritual exchange with Maya dignitaries preceded the Teotihuacan state's eventual ascent to prominence.},
}

Humans
Animals
*Diplomacy
Ceremonial Behavior
DNA, Ancient
*Atelinae
Mexico

@article {pmid36377787,
year = {2022},
author = {Ausmees, K and Nettelblad, C},
title = {Achieving improved accuracy for imputation of ancient DNA.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btac738},
pmid = {36377787},
issn = {1367-4811},
abstract = {MOTIVATION: Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.

RESULTS: We present an implementation called prophaser, and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU.

AVAILABILITY: The C ++ code for prophaser is available in the GitHub repository https://github.com/scicompuu/prophaser.

SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.},
}

@article {pmid36375244,
year = {2022},
author = {Harvati, K and Reyes-Centeno, H},
title = {Evolution of Homo in the Middle and Late Pleistocene.},
journal = {Journal of human evolution},
volume = {173},
number = {},
pages = {103279},
doi = {10.1016/j.jhevol.2022.103279},
pmid = {36375244},
issn = {1095-8606},
mesh = {Animals ; Humans ; *Hominidae ; Phylogeny ; Biological Evolution ; Fossils ; *Neanderthals ; },
abstract = {The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.},
}

Animals
Humans
*Hominidae
Phylogeny
Biological Evolution
Fossils
*Neanderthals

@article {pmid36373266,
year = {2022},
author = {Gaughran, SJ and vonHoldt, B},
title = {Pleistocene parades of carnivores into North America.},
journal = {Molecular ecology},
volume = {31},
number = {24},
pages = {6387-6389},
doi = {10.1111/mec.16783},
pmid = {36373266},
issn = {1365-294X},
mesh = {Animals ; Humans ; *Carnivora/genetics ; Phylogeography ; *Ursidae/genetics ; Biological Evolution ; *Lions ; North America ; Phylogeny ; },
abstract = {The distribution and movement of species, broadly known as biogeography, is one of the fundamental subfields of ecology and evolutionary biology. However, significant mysteries remain about the processes that gave rise to the modern distribution of biodiversity across the globe. Over the last several decades, the genetic study of ancient and subfossil specimens has started to shed light on past migrations of some species, with a particular focus on humans and megafauna. In this issue of Molecular Ecology, Salis et al. (2021) use ancient mitogenomes and a new phylogeographic method to add an important new piece of evidence to the mystery of megafaunal migrations into North America during the Pleistocene. They found a striking synchronicity of brown bear (Ursus arctos) and lion (Panthera spp.) migrations across the Bering Land Bridge at several time points during the late Pleistocene, which highlights the lasting impact of sea level change on the prehistoric and modern dispersal of terrestrial carnivores across continents.},
}

Animals
Humans
*Carnivora/genetics
Phylogeography
*Ursidae/genetics
Biological Evolution
*Lions
North America
Phylogeny

@article {pmid36371979,
year = {2022},
author = {Howarth, A and Drummond, B and Wasef, S and Matheson, CD},
title = {An assessment of DNA extraction methods from blood-stained soil in forensic science.},
journal = {Forensic science international},
volume = {341},
number = {},
pages = {111502},
doi = {10.1016/j.forsciint.2022.111502},
pmid = {36371979},
issn = {1872-6283},
mesh = {Humans ; *Soil ; Polymerase Chain Reaction/methods ; DNA/analysis ; Chloroform/analysis ; Povidone ; Endopeptidase K ; *Blood Stains ; Silicon Dioxide ; },
abstract = {In forensic crime scene investigations, biological fluids such as blood are commonly found in soil. However, the analysis of blood-stained soil can be challenging due to the presence of inhibitors which limit the effective extraction and amplification of the deoxyribonucleic acid (DNA) required to produce a reportable DNA profile. There are some extraction methods that have been applied to blood-stained soil in forensic science, but these have produced sporadic results. This research has taken a number of different extraction methods from the fields of ancient DNA and environmental DNA and broken them down into the individual steps of pre-treatment, incubation, separation and purification. These steps were assessed independently then combined into various extraction methods to determine the best technique that can effectively and reliably profile human DNA from blood-stained soil. Testing involved assessment of three extraction buffers, (cetyltrimethylammonium bromide, guanidine thiocyanate, and proteinase K), four pre-treatment methods, (polyvinylpyrrolidone, ethylenediaminetetraacetic acid, hydrochloric acid, and sodium hydroxide), three separation steps, (centrifugation, phenol chloroform, and chloroform) and four purification steps, (size exclusion chromatography, bind elute columns, isopropanol precipitation and silica magnetic beads). The most effective procedure was found to be a polyvinylpyrrolidone pre-treatment with a proteinase K extraction buffer followed by magnetic silica bead purification with or without centrifugation. However, centrifugation separation was found to be equally effective after the pre-treatment step as after the incubation step. Our results shows that most of the current forensic procedures would benefit from the addition of a pre-treatment step prior to processing through the automated DNA profiling pipeline.},
}

Humans
*Soil
Polymerase Chain Reaction/methods
DNA/analysis
Chloroform/analysis
Povidone
Endopeptidase K
*Blood Stains
Silicon Dioxide

@article {pmid36360198,
year = {2022},
author = {Boulygina, E and Sharko, F and Cheprasov, M and Gladysheva-Azgari, M and Slobodova, N and Tsygankova, S and Rastorguev, S and Grigorieva, L and Kopp, M and Fernandes, JMO and Novgorodov, G and Boeskorov, G and Protopopov, A and Hwang, WS and Tikhonov, A and Nedoluzhko, A},
title = {Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear (Ursus arctos) Population during the Holocene.},
journal = {Genes},
volume = {13},
number = {11},
pages = {},
pmid = {36360198},
issn = {2073-4425},
mesh = {Animals ; *Ursidae/genetics ; DNA, Ancient ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.},
}

Animals
*Ursidae/genetics
DNA, Ancient
Phylogeny
DNA, Mitochondrial/genetics
Mitochondria/genetics

@article {pmid36359074,
year = {2022},
author = {Armstrong, AJ and Walker, FM and Sobek, CJ and Sanville, CJ and Martin, SL and Szewczak, JM},
title = {Bat Use of Hollows in California's Old-Growth Redwood Forests: From DNA to Ecology.},
journal = {Animals : an open access journal from MDPI},
volume = {12},
number = {21},
pages = {},
pmid = {36359074},
issn = {2076-2615},
abstract = {The loss of roosting resources, either through disturbance or removal, negatively affects bats. Identifying sensitive species and determining roost requirements are critical components in conserving their habitat. Cavity-roosting bats on the North Coast of California are known to use hollows in large redwood trees. In this study, we examined the factors determining the use of basal tree hollows by different bat species at eight redwood forest sites in Del Norte, Humboldt, and Mendocino Counties, California. Bat guano was collected from 179 basal hollow roosts from 2017 to 2018, and guano mass was used as an index of roosting activity. Nine bat species and one species group were identified by analysis of DNA in guano. We made a total of 253 identifications from 83 hollows into the 10 species categories. The most prevalent species were Myotis californicus (California myotis; 28.5% of all identifications), the Myotis evotis-Myotis thysanodes group (17.4%), Corynorhinus townsendii (17.0%), and Myotis volans (15.0%). We evaluated the extent to which habitat variables at the scales of the hollow, vicinity, and site influenced the level of roost use. The correlations between guano mass and habitat variables were examined using generalized additive mixed models. At the hollow scale, guano mass increased with ceiling height above the opening. At the vicinity scale, guano mass increased with less cover of small trees. At the site scale, there was no association between guano mass and distance to foraging areas, elevation, or the number of nearby hollows. These tree hollow roost preferences can inform land managers when planning the management and conservation of redwood forests.},
}

@article {pmid36348137,
year = {2022},
author = {Kimsis, J and Petersone-Gordina, E and Poksane, A and Vilcāne, A and Moore, J and Gerhards, G and Ranka, R},
title = {Application of natural sciences methodology in archaeological study of Iron Age burials in Latvia: pilot study.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
pmid = {36348137},
issn = {1556-2891},
abstract = {Natural sciences provide several modern methodologies that could be successfully applied in archaeological studies. In this pilot study, archaeological human remains from two Iron Age cemeteries (7th-twelfth centuries AD), Lejasbitēni and Čunkāni-Dreņģeri, which are located in different regions of Latvia, were studied. We applied ancient DNA (aDNA) and tooth enamel peptide analysis to determine the biological sex of the individuals. In addition, aDNA analysis was used to perform mtDNA haplogroup analysis. In most cases, the results of aDNA analysis regarding the biological sex of individuals coincided with the gender assigned based on grave orientation and grave goods. The results of sex determination using peptide analysis in all four individuals for whom data were available matched the possible gender. Of the 17 samples that had sufficient DNA for sequencing, seven samples had enough reads to perform mtDNA haplogroup analysis. The H2a2a, I4a1, H2a2a1, and H16c mtDNA haplogroups were identified in the individuals from the Lejasbitēni cemetery, while the T2b and K1a + 150 mtDNA haplogroups were identified in the individuals from the Čunkāni-Dreņģeri cemetery. Overall, the obtained results demonstrated the feasibility of applying aDNA and tooth enamel peptide analysis for biological sex determination within archaeological studies. The availability of human aDNA data will be highly useful for investigating the demographic history and social structures in Iron Age Latvia.},
}

@article {pmid36344562,
year = {2022},
author = {Miszkiewicz, JJ and Buckley, HR and Feldman, M and Kiko, L and Carlhoff, S and Naegele, K and Bertolini, E and Guimarães, NRD and Walker, MM and Powell, A and Posth, C and Kinaston, RL},
title = {Female bone physiology resilience in a past Polynesian Outlier community.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {18857},
pmid = {36344562},
issn = {2045-2322},
mesh = {Male ; Humans ; Female ; *Haversian System ; *Femur ; Bone and Bones ; Bone Remodeling ; Melanesia ; },
abstract = {Remodelling is a fundamental biological process involved in the maintenance of bone physiology and function. We know that a range of health and lifestyle factors can impact this process in living and past societies, but there is a notable gap in bone remodelling data for populations from the Pacific Islands. We conducted the first examination of femoral cortical histology in 69 individuals from ca. 440-150 BP Taumako in Solomon Islands, a remote 'Polynesian Outlier' island in Melanesia. We tested whether bone remodelling indicators differed between age groups, and biological sex validated using ancient DNA. Bone vascular canal and osteon size, vascular porosity, and localised osteon densities, corrected by femoral robusticity indices were examined. Females had statistically significantly higher vascular porosities when compared to males, but osteon densities and ratios of canal-osteon (~ 8%) did not differ between the sexes. Our results indicate that, compared to males, localised femoral bone tissue of the Taumako females did not drastically decline with age, contrary to what is often observed in modern populations. However, our results match findings in other archaeological samples-a testament to past female bone physiology resilience, also now observed in the Pacific region.},
}

Male
Humans
Female
*Haversian System
*Femur
Bone and Bones
Bone Remodeling
Melanesia

@article {pmid36333301,
year = {2022},
author = {Garcés-Pastor, S and Coissac, E and Lavergne, S and Schwörer, C and Theurillat, JP and Heintzman, PD and Wangensteen, OS and Tinner, W and Rey, F and Heer, M and Rutzer, A and Walsh, K and Lammers, Y and Brown, AG and Goslar, T and Rijal, DP and Karger, DN and Pellissier, L and , and Heiri, O and Alsos, IG},
title = {High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {6559},
pmid = {36333301},
issn = {2041-1723},
mesh = {Humans ; *Climate Change ; *DNA, Ancient ; Plants/genetics ; Lakes ; Pollen ; },
abstract = {The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps.},
}

Humans
*Climate Change
*DNA, Ancient
Plants/genetics
Lakes
Pollen

@article {pmid36329382,
year = {2022},
author = {Lord, E and Marangoni, A and Baca, M and Popović, D and Goropashnaya, AV and Stewart, JR and Knul, MV and Noiret, P and Germonpré, M and Jimenez, EL and Abramson, NI and Vartanyan, S and Prost, S and Smirnov, NG and Kuzmina, EA and Olsen, RA and Fedorov, VB and Dalén, L},
title = {Population dynamics and demographic history of Eurasian collared lemmings.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {126},
pmid = {36329382},
issn = {2730-7182},
support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; P20 GM130443/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Ecosystem ; *Arvicolinae ; Population Dynamics ; Arctic Regions ; DNA, Ancient ; },
abstract = {BACKGROUND: Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species.

RESULTS: Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene.

CONCLUSIONS: This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.},
}

Animals
*Ecosystem
*Arvicolinae
Population Dynamics
Arctic Regions
DNA, Ancient

@article {pmid36322514,
year = {2022},
author = {Campelo Dos Santos, AL and Owings, A and Sullasi, HSL and Gokcumen, O and DeGiorgio, M and Lindo, J},
title = {Genomic evidence for ancient human migration routes along South America's Atlantic coast.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1986},
pages = {20221078},
pmid = {36322514},
issn = {1471-2954},
support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; History, Ancient ; Animals ; *Human Migration ; Genomics ; Genome, Human ; *Neanderthals ; Brazil ; },
abstract = {An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.},
}

Humans
History, Ancient
Animals
*Human Migration
Genomics
Genome, Human
*Neanderthals
Brazil

@article {pmid36322483,
year = {2022},
author = {Hempel, E and Bibi, F and Faith, JT and Koepfli, KP and Klittich, AM and Duchêne, DA and Brink, JS and Kalthoff, DC and Dalén, L and Hofreiter, M and Westbury, MV},
title = {Blue turns to grey - Palaeogenomic insights into the evolutionary history and extinction of the blue antelope (Hippotragus leucophaeus).},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac241},
pmid = {36322483},
issn = {1537-1719},
abstract = {The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (H. equinus) or sable (H. niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavourable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4x mean coverage from a historical specimen (∼200 years old) and one at 2.1x mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest palaeogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelopes, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely a decisive factor in the blue antelope's extinction.},
}

@article {pmid36316412,
year = {2022},
author = {Souilmi, Y and Tobler, R and Johar, A and Williams, M and Grey, ST and Schmidt, J and Teixeira, JC and Rohrlach, A and Tuke, J and Johnson, O and Gower, G and Turney, C and Cox, M and Cooper, A and Huber, CD},
title = {Admixture has obscured signals of historical hard sweeps in humans.},
journal = {Nature ecology & evolution},
volume = {6},
number = {12},
pages = {2003-2015},
pmid = {36316412},
issn = {2397-334X},
mesh = {Animals ; Humans ; *Selection, Genetic ; *Hominidae ; Biological Evolution ; Genome, Human ; Genomics ; },
abstract = {The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.},
}

Animals
Humans
*Selection, Genetic
*Hominidae
Biological Evolution
Genome, Human
Genomics

@article {pmid36316157,
year = {2022},
author = {Mathieson, I and Terhorst, J},
title = {Direct detection of natural selection in Bronze Age Britain.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.276862.122},
pmid = {36316157},
issn = {1549-5469},
abstract = {We developed a novel method for efficiently estimating time-varying selection coefficients from genome-wide ancient DNA data. In simulations, our method accurately recovers selective trajectories, and is robust to mis-specification of population size. We applied it to a large dataset of ancient and present-day human genomes from Britain, and identified seven loci with genome-wide significant evidence of selection in the past 4500 years. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength of selection on individual loci varied substantially over time, suggesting that cultural or environmental factors moderated the genetic response. Of 28 complex anthropometric and metabolic traits, skin pigmentation was the only one with significant evidence of polygenic selection, further underscoring the importance of phenotypes related to vitamin D. Our approach illustrates the power of ancient DNA to characterize selection in human populations and illuminates the recent evolutionary history of Britain.},
}

@article {pmid36300941,
year = {2022},
author = {Nino Barreat, JG and Katzourakis, A},
title = {Evolutionary Analysis of Placental Orthologues Reveals Two Ancient DNA Virus Integrations.},
journal = {Journal of virology},
volume = {96},
number = {22},
pages = {e0093322},
pmid = {36300941},
issn = {1098-5514},
mesh = {Animals ; Female ; Humans ; Pregnancy ; *DNA, Ancient ; Eutheria ; *Evolution, Molecular ; Genome, Human ; *Mammals/genetics/virology ; Marsupialia ; Phylogeny ; Virus Integration ; *DNA Viruses/genetics ; },
abstract = {The genomes of eukaryotes preserve a vast diversity of ancient viruses in the form of endogenous viral elements (EVEs). Study of this genomic fossil record provides insights into the diversity, origin, and evolution of viruses across geological timescales. In particular, Mavericks have emerged as one of the oldest groups of endogenous viruses infecting vertebrates (≥419 million years [My]). They have been found in the genomes of fish, amphibians, birds, and nonavian reptiles but had been overlooked in mammals. Thus, their evolutionary history and the causes of their demise in mammals remain puzzling questions. Here, we conducted a detailed evolutionary study of two Maverick integrations found on human chromosomes 7 and 8. We performed a comparative analysis of the integrations and determined their orthology across placental mammals (Eutheria) via the syntenic arrangement of neighboring genes. The integrations were absent at the orthologous sites in the genomes of marsupials and monotremes. These observations allowed us to reconstruct a time-calibrated phylogeny and infer the age of their most recent common ancestor at 127 to 262 My. In addition, we estimate the age of the individual integrations at ~102 My, which represents the oldest nonretroviral EVEs found in the human genome. Our findings suggest that active Mavericks still existed in the ancestors of modern mammals ~172 My ago (Jurassic Period) and potentially to the end of the Early Cretaceous. We hypothesize that Mavericks could have gone extinct in mammals from the evolution of an antiviral defense system or from reduced opportunities for transmission in terrestrial hosts. IMPORTANCE The genomes of vertebrates preserve a large diversity of endogenous viral elements (remnants of ancient viruses that accumulate in host genomes over evolutionary time). Although retroviruses account for the vast majority of these elements, diverse DNA viruses have also been found and novel lineages are being described. Here, we analyzed two elements found in the human genome belonging to an ancient group of DNA viruses called Mavericks. We studied their evolutionary history, finding that the elements are shared between humans and many different species of placental mammals. These observations suggest that the elements inserted at least ~102 million years ago (Mya) in the most recent common ancestor of placentals. We further estimated the age of the viral ancestor at around 127 to 262 My. Our results provide evidence for some of the oldest viral integrations in the human genome and insights into the ancient interactions of viruses with the ancestors of modern-day mammals.},
}

Animals
Female
Humans
Pregnancy
*DNA, Ancient
Eutheria
*Evolution, Molecular
Genome, Human
*Mammals/genetics/virology
Marsupialia
Phylogeny
Virus Integration
*DNA Viruses/genetics

@article {pmid36292573,
year = {2022},
author = {Melchionda, F and Silvestrini, B and Robino, C and Bini, C and Fattorini, P and Martinez-Labarga, C and De Angelis, F and Tagliabracci, A and Turchi, C},
title = {Development and Validation of MPS-Based System for Human Appearance Prediction in Challenging Forensic Samples.},
journal = {Genes},
volume = {13},
number = {10},
pages = {},
pmid = {36292573},
issn = {2073-4425},
mesh = {Humans ; *Eye Color/genetics ; Genetic Markers ; *Polymorphism, Single Nucleotide ; Hair Color/genetics ; DNA/genetics ; },
abstract = {Forensic DNA phenotyping (FDP) provides the ability to predict the human external traits from unknown sample donors, directly from minute amounts of DNA found at the crime scene. We developed a MPS multiplex assay, with the aim of genotyping all 41 DNA markers included in the HIrisPlex-S system for simultaneous prediction of eye, hair and skin colours. Forensic samples such as blood, skeletal remains, touch DNA, saliva swab, artificially degraded samples together with individuals with known phenotypes and a set of 2800 M control DNA were sequenced on the Ion Torrent platform in order to evaluate the concordance testing results and the forensic suitability of the 41-plex MPS assay. The panel was evaluated by testing a different number of PCR cycles and the volume of reagents for library preparation. The study demonstrated that full and reliable profiles were obtained with 0.1-5 ng, even with high degraded DNA. The increment of the number of PCR cycles results in an improvement of correctly genotyping and phenotyping for samples with low amounts of degraded DNA but higher frequencies of artefacts were found. The high DNA degradation level did not influence the correct genotyping and phenotyping and the critical parameter affecting the result is the quantity of input DNA. Eye and hair colour was predicted in 92.60% of individuals and skin colour in 85.15% of individuals. The results suggest that this MPS assay is robust, highly sensitive and useful for human pigmentation prediction in the forensic genetic field.},
}

Humans
*Eye Color/genetics
Genetic Markers
*Polymorphism, Single Nucleotide
Hair Color/genetics
DNA/genetics

@article {pmid36292570,
year = {2022},
author = {Hou, X and Zhao, J and Zhang, H and Preick, M and Hu, J and Xiao, B and Wang, L and Deng, M and Liu, S and Chang, F and Sheng, G and Lai, X and Hofreiter, M and Yuan, J},
title = {Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China.},
journal = {Genes},
volume = {13},
number = {10},
pages = {},
pmid = {36292570},
issn = {2073-4425},
mesh = {Animals ; *Bison/genetics ; Bayes Theorem ; *Genome, Mitochondrial/genetics ; Fossils ; Biological Evolution ; },
abstract = {Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.},
}

Animals
*Bison/genetics
Bayes Theorem
*Genome, Mitochondrial/genetics
Fossils
Biological Evolution

@article {pmid36289417,
year = {2022},
author = {Thompson, B and Bundell, S},
title = {Ancient DNA reveals family of Neanderthals living in Siberian cave.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-022-03460-7},
pmid = {36289417},
issn = {1476-4687},
}

@article {pmid36282902,
year = {2022},
author = {Atmore, LM and Martínez-García, L and Makowiecki, D and André, C and Lõugas, L and Barrett, JH and Star, B},
title = {Population dynamics of Baltic herring since the Viking Age revealed by ancient DNA and genomics.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {45},
pages = {e2208703119},
pmid = {36282902},
issn = {1091-6490},
mesh = {Animals ; Humans ; *Fisheries ; *DNA, Ancient ; Conservation of Natural Resources ; Population Dynamics ; Fishes/genetics ; Genomics ; Baltic States ; },
abstract = {The world's oceans are currently facing major stressors in the form of overexploitation and anthropogenic climate change. The Baltic Sea was home to the first "industrial" fishery ∼800 y ago targeting the Baltic herring, a species that is still economically and culturally important today. Yet, the early origins of marine industries and the long-term ecological consequences of historical and contemporary fisheries remain debated. Here, we study long-term population dynamics of Baltic herring to evaluate the past impacts of humans on the marine environment. We combine modern whole-genome data with ancient DNA (aDNA) to identify the earliest-known long-distance herring trade in the region, illustrating that extensive fish trade began during the Viking Age. We further resolve population structure within the Baltic and observe demographic independence for four local herring stocks over at least 200 generations. It has been suggested that overfishing at Øresund in the 16th century resulted in a demographic shift from autumn-spawning to spring-spawning herring dominance in the Baltic. We show that while the Øresund fishery had a negative impact on the western Baltic herring stock, the demographic shift to spring-spawning dominance did not occur until the 20th century. Instead, demographic reconstructions reveal population trajectories consistent with expected impacts of environmental change and historical reports on shifting fishing targets over time. This study illustrates the joint impact of climate change and human exploitation on marine species as well as the role historical ecology can play in conservation and management policies.},
}

Animals
Humans
*Fisheries
*DNA, Ancient
Conservation of Natural Resources
Population Dynamics
Fishes/genetics
Genomics
Baltic States

@article {pmid36282813,
year = {2022},
author = {Ibrahim, J and Brumfeld, V and Addadi, Y and Rubin, S and Weiner, S and Boaretto, E},
title = {The petrous bone contains high concentrations of osteocytes: One possible reason why ancient DNA is better preserved in this bone.},
journal = {PloS one},
volume = {17},
number = {10},
pages = {e0269348},
pmid = {36282813},
issn = {1932-6203},
mesh = {Humans ; Swine ; Animals ; *Osteocytes/pathology ; *DNA, Ancient ; Petrous Bone/diagnostic imaging ; Bone and Bones ; DNA/genetics ; },
abstract = {The characterization of ancient DNA in fossil bones is providing invaluable information on the genetics of past human and other animal populations. These studies have been aided enormously by the discovery that ancient DNA is relatively well preserved in the petrous bone compared to most other bones. The reasons for this better preservation are however not well understood. Here we examine the hypothesis that one reason for better DNA preservation in the petrous bone is that fresh petrous bone contains more DNA than other bones. We therefore determined the concentrations of osteocyte cells occluded inside lacunae within the petrous bone and compared these concentrations to other bones from the domestic pig using high resolution microCT. We show that the concentrations of osteocyte lacunae in the inner layer of the pig petrous bone adjacent to the otic chamber are about three times higher (around 95,000 lacunae per mm3) than in the mastoid of the temporal bone (around 28,000 lacunae per mm3), as well as the cortical bone of the femur (around 27,000 lacunae per mm3). The sizes and shapes of the lacuna in the inner layer of the petrous bone are similar to those in the femur. We also show that the pig petrous bone lacunae do contain osteocytes using a histological stain for DNA. We therefore confirm and significantly expand upon previous observations of osteocytic lacuna concentrations in the petrous bone, supporting the notion that one possible reason for better preservation of ancient DNA in the petrous bone is that this bone initially contains at least three times more DNA than other bones. Thus during diagenesis more DNA is likely to be preserved in the petrous bone compared to other bones.},
}

Humans
Swine
Animals
*Osteocytes/pathology
*DNA, Ancient
Petrous Bone/diagnostic imaging
Bone and Bones
DNA/genetics

@article {pmid36277234,
year = {2022},
author = {Cessford, C and Neil, B},
title = {The people of the Cambridge Austin friars.},
journal = {Archaeological journal},
volume = {179},
number = {2},
pages = {383-444},
pmid = {36277234},
issn = {2373-2288},
abstract = {The Austin friars in Cambridge was an important religious institution between the late thirteenth and mid-sixteenth centuries. Excavations have revealed well-dated and contextualised burials associated with the friary, as well as a range of material culture. The burials have been subject to a wide range of analyses including osteology, palaeopathology, stable isotopes, ancient DNA and geometric morphometrics. Significantly the distinction between clothed and shrouded burials allows members of the Augustinian order and the laity to be identified. This represents the best-understood published group of burials from an Austin friars in the British Isles and emphasises the importance of nuanced interpretation, as burial at friaries was a structured and multi-local phenomenon. These burials and other material can be interpreted in terms of both mendicant ideals and anti-fraternal criticisms.},
}

@article {pmid36276948,
year = {2022},
author = {Xu, B and Yang, G and Jiao, B and Zhu, H},
title = {Analysis of ancient and modern horse genomes reveals the critical impact of lncRNA-mediated epigenetic regulation on horse domestication.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {944933},
pmid = {36276948},
issn = {1664-8021},
abstract = {Background: The domestication of horses has played critical roles in human civilizations. The excavation of ancient horse DNA provides crucial data for studying horse domestication. Studies of horse domestication can shed light on the general mechanisms of animal domestication. Objective: We wish to explore the gene transcription regulation by long noncoding RNAs (lncRNAs) that influence horse domestication. Methods: First, we assembled the ancient DNA sequences of multiple horses at different times and the genomes of horses, donkeys, and Przewalski horses. Second, we extracted sequences of lncRNA genes shared in ancient horses and sequences of lncRNA genes and the promoter regions of domestication-critical genes shared in modern horses, modern donkeys, and Przewalski horses to form two sample groups. Third, we used the LongTarget program to predict potential regulatory interactions between these lncRNAs and these domestication-critical genes and analyzed the differences between the regulation in ancient/modern horses and between horses/donkeys/Przewalski horses. Fourth, we performed functional enrichment analyses of genes that exhibit differences in epigenetic regulation. Results: First, genes associated with neural crest development and domestication syndrome are important targets of lncRNAs. Second, compared with undomesticated Przewalski horses, more lncRNAs participate in the epigenetic regulation in modern horses and donkeys, suggesting that domestication is linked to more epigenetic regulatory changes. Third, lncRNAs' potential target genes in modern horses are mainly involved in two functional areas: 1) the nervous system, behavior, and cognition, and 2) muscle, body size, cardiac function, and metabolism. Conclusion: Domestication is linked to substantial epigenetic regulatory changes. Genes associated with neural crest development and domestication syndrome underwent noticeable lncRNA-mediated epigenetic regulation changes during horse domestication.},
}

@article {pmid36264804,
year = {2022},
author = {Gibbons, A},
title = {How the Black Death left its mark on immune system genes.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6617},
pages = {237-238},
doi = {10.1126/science.adf3947},
pmid = {36264804},
issn = {1095-9203},
mesh = {Humans ; Immune System ; *Plague/genetics/history/immunology ; *Immunity/genetics ; *Selection, Genetic ; *Pandemics/history ; DNA, Ancient ; },
abstract = {Study of DNA from medieval victims and survivors finds gene that helped protect people from deadly pathogen.},
}

Humans
Immune System
*Plague/genetics/history/immunology
*Immunity/genetics
*Selection, Genetic
*Pandemics/history
DNA, Ancient

@article {pmid36261712,
year = {2022},
author = {Enard, D},
title = {Ancient DNA reveals rapid natural selection during the Black Death.},
journal = {Nature},
volume = {611},
number = {7935},
pages = {237-238},
pmid = {36261712},
issn = {1476-4687},
mesh = {Humans ; *DNA, Ancient ; *Plague ; Selection, Genetic ; Evolution, Molecular ; },
}

Humans
*DNA, Ancient
*Plague
Selection, Genetic
Evolution, Molecular

@article {pmid36261521,
year = {2022},
author = {Klunk, J and Vilgalys, TP and Demeure, CE and Cheng, X and Shiratori, M and Madej, J and Beau, R and Elli, D and Patino, MI and Redfern, R and DeWitte, SN and Gamble, JA and Boldsen, JL and Carmichael, A and Varlik, N and Eaton, K and Grenier, JC and Golding, GB and Devault, A and Rouillard, JM and Yotova, V and Sindeaux, R and Ye, CJ and Bikaran, M and Dumaine, A and Brinkworth, JF and Missiakas, D and Rouleau, GA and Steinrücken, M and Pizarro-Cerdá, J and Poinar, HN and Barreiro, LB},
title = {Evolution of immune genes is associated with the Black Death.},
journal = {Nature},
volume = {611},
number = {7935},
pages = {312-319},
pmid = {36261521},
issn = {1476-4687},
support = {F32 GM140568/GM/NIGMS NIH HHS/United States ; R01 GM146051/GM/NIGMS NIH HHS/United States ; R56 AI146556/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Aminopeptidases/genetics/immunology ; *DNA, Ancient ; *Plague/genetics/immunology/microbiology/mortality ; *Yersinia pestis/immunology/pathogenicity ; *Selection, Genetic/immunology ; Europe/epidemiology/ethnology ; *Immunity/genetics ; Datasets as Topic ; *Genetic Predisposition to Disease ; London/epidemiology ; Denmark/epidemiology ; },
abstract = {Infectious diseases are among the strongest selective pressures driving human evolution[1,2]. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis[3]. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population[4]. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.},
}

Humans
Aminopeptidases/genetics/immunology
*DNA, Ancient
*Plague/genetics/immunology/microbiology/mortality
*Yersinia pestis/immunology/pathogenicity
*Selection, Genetic/immunology
Europe/epidemiology/ethnology
*Immunity/genetics
Datasets as Topic
*Genetic Predisposition to Disease
London/epidemiology
Denmark/epidemiology

@article {pmid36259206,
year = {2022},
author = {Martínez-García, L and Ferrari, G and Cuevas, A and Atmore, LM and López-Arias, B and Culling, M and Llorente-Rodríguez, L and Morales-Muñiz, A and Roselló-Izquierdo, E and Quirós, JA and Marlasca-Martín, R and Hänfling, B and Hutchinson, WF and Jakobsen, KS and Jentoft, S and Orton, D and Star, B and Barrett, JH},
title = {Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1985},
pages = {20221107},
pmid = {36259206},
issn = {1471-2954},
mesh = {Animals ; *DNA, Ancient ; Europe ; Fisheries ; *Gadus morhua/genetics ; Hunting ; Internationality ; },
abstract = {Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050-1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.},
}

Animals
*DNA, Ancient
Europe
Fisheries
*Gadus morhua/genetics
Hunting
Internationality