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This paper examines how ancient DNA data can enhance radiocarbon dating. Because there is a limit to the number of years that can separate the dates of death of related individuals, the ability to identify first-, second-, and third-degree relatives through aDNA analysis can serve as a constraint on radiocarbon date range estimates. To determine the number of years that can separate related individuals, we modeled maximums derived from biological extremes of human reproduction and death ages and compiled data from historic and genealogical death records. We used these estimates to evaluate the date ranges of a global dataset of individuals that have been radiocarbon dated and for which ancient DNA analysis identified at least one relative. We found that many of these individuals could have their date ranges reduced by building in date of death separation constraints. We examined possible reasons for date discrepancies of related individuals, such as dating of different skeletal elements or wiggles in the radiocarbon curve. Our research demonstrates that when combined, radiocarbon dating and ancient DNA analysis can provide a refined and richer view of the past.

Olalde, Iñigo et al. ; The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the Danube River into Central Europe. Although genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400-year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter–gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible. ; The Centre for GeoGenetics is funded by the Danish National Research Foundation (DNRF94). Cova Bonica work is supported by Servei d'Arqueologia i Paleontologia (2014/100639), Generalitat de Catalunya (2014SGR-108), and Ministerio de Ciencia e Innovación (HAR2011-26193) projects. H.S. was supported by an ERC Synergy Grant (FP7/2007-2013/319209); C.L.-F. by a FEDER and Spanish Government Grant BFU2012-34157; and S.C. by a grant 2014 SGR 464 from Departament d'Economia i Coneixement (Generalitat de Catalunya). D.C.S-G. acknowledges support from the Generalitat Valenciana (VALi + d APOSTD/2014/123), the BBVA Foundation (I Ayudas a Investigadores, Innovadores y Creadores Culturales), and the European Union (FP7/2007-2013—MSCA-COFUND, no. 245743 via a Braudel-IFER-FMSH). I.O. was funded by a predoctoral fellowship from the Basque Government (DEUI), and M.S. and J.D. by postdoctoral grants from Fundação para a Ciência e a Tecnologia (FCT) and Juan de la Cierva Subprogram (JCI-2011-09543), respectively. ; Peer reviewed

Peer reviewed ; Ramírez, Óscar et al.-- Data archiving: Ancient, Iberian, Spanish wild boar and Guatemalan reads have been submitted to SRA (accession SRP044261), aligned mitochondrial fasta file, plink files with genotypic data have been deposited in Dryad (doi:10.5061/dryad.sd784). Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds. This study was funded by 2010ACOM00030 (AGAUR) to MS, FEDER and BFU2012-34157 grant (Spain) to CLF, Consolider CSD2007-00036 'Centre for Research in Agrigenomics' and AGL2010-14822 grants (Spain) to MPE. OR is a postdoctoral Researcher from the JAEDOC program cofounded by ESF, EB is recipient of a FPI grant from ministry of Research (Spain), IO of a predoctoral fellowship from the Basque Government (DEUI, Spain), WBP is funded by COLCIENCIAS (Francisco Jose´ de Caldas fellowship 497/2009, Colombia).

[Background] Although a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. Further, very limited knowledge exists on structural variation in the gray wolf, the ancestor of the dog, or other closely related wild canids. Documenting CNVs variation in wild canids is essential to identify ancestral states and variation that may have appeared after domestication. ; [Results] In this work, we genotyped 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication. We have found an increase in GC-rich regions close to the breakpoints and around 1 kb away from them suggesting that some common motifs might be associated with the formation of CNVs. Among the CNV regions that showed the largest differentiation between dogs and wild canids we found 12 genes, nine of which are related to two known functions associated with dog domestication; growth (PDE4D, CRTC3 and NEB) and neurological function (PDE4D, EML5, ZNF500, SLC6A11, ELAVL2, RGS7 and CTSB). ; [Conclusions] Our results provide insight into the evolution of structural variation in canines, where recombination is not regulated by PRDM9 due to the inactivation of this gene. We also identified genes within the most differentiated CNV regions between dogs and wolves, which could reflect selection during the domestication process. ; R is a postdoctoral Researcher from the JAEdoc program cofounded by European Science Foundation. IO has a predoctoral fellowship from the Basque Government (DEUI). This work has been founded by Spanish Government Grants BFU2011-28549 (to TM-B) and BFU2012-34157 (to CL-F), Andalusian Government Grant "Programa de Captación del Conocimiento para Andalucía C2A" (to CV) and EU ERC Starting Grant 260372 (to TM-B). ; Peer Reviewed

Gómez-Sánchez, Daniel et al. ; Previous mitochondrial DNA analyses on ancient European remains have suggested that the current distribution of haplogroup H was modeled by the expansion of the Bell Beaker culture (ca 4,500-4,050 years BP) out of Iberia during the Chalcolithic period. However, little is known on the genetic composition of contemporaneous Iberian populations that do not carry the archaeological tool kit defining this culture. Here we have retrieved mitochondrial DNA (mtDNA) sequences from 19 individuals from a Chalcolithic sample from El Mirador cave in Spain, dated to 4,760-4,200 years BP and we have analyzed the haplogroup composition in the context of modern and ancient populations. Regarding extant African, Asian and European populations, El Mirador shows affinities with Near Eastern groups. In different analyses with other ancient samples, El Mirador clusters with Middle and Late Neolithic populations from Germany, belonging to the Rössen, the Salzmünde and the Baalberge archaeological cultures but not with contemporaneous Bell Beakers. Our analyses support the existence of a common genetic signal between Western and Central Europe during the Middle and Late Neolithic and points to a heterogeneous genetic landscape among Chalcolithic groups. © 2014 Gómez-Sánchez et al. ; This work is supported by FEDER and Spanish Government Grant BFU2012-34157. ; Peer Reviewed

Ramírez, Óscar et al.-- Data archiving: Ancient, Iberian, Spanish wild boar and Guatemalan reads have been submitted to SRA (accession SRP044261), aligned mitochondrial fasta file, plink files with genotypic data have been deposited in Dryad (doi:10.5061/dryad.sd784). ; Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds. ; This study was funded by 2010ACOM00030 (AGAUR) to MS, FEDER and BFU2012-34157 grant (Spain) to CLF, Consolider CSD2007-00036 'Centre for Research in Agrigenomics' and AGL2010-14822 grants (Spain) to MPE. OR is a postdoctoral Researcher from the JAEDOC program cofounded by ESF, EB is recipient of a FPI grant from ministry of Research (Spain), IO of a predoctoral fellowship from the Basque Government (DEUI, Spain), WBP is funded by COLCIENCIAS (Francisco Jose´ de Caldas fellowship 497/2009, Colombia). ; Peer reviewed

[Background] Canarian Black (CB) pigs belong to an autochthonous and endangered breed, which is spread throughout the Canarian archipelago. It is commonly accepted that they represent a relic of the pig populations that were bred by the Berbers in North Africa over millennia. It is important to note that the geographic isolation of the Canary Islands has preserved this genetic legacy intact from foreign introgressions until the Spanish conquest of the archipelago in the 15th century. Ten years ago, it was demonstrated that, in CB pigs, the frequency of the Asian A2 cytochrome-b haplogroup reached 73%. The current work aimed at investigating whether this observation is explained by either a recent or an ancient introgression of CB pigs with Far Eastern pigs. ; [Results] Genetic analyses of 23 ancient samples from pre-hispanic Canarian pigs (420 to 2500 years before present) showed that Near Eastern and Far Eastern genetic signatures were totally absent in the primitive Canarian pre-hispanic pigs. Indeed, the haplotypes detected in these pigs were closely related to those of North African and European wild boars. ; [Conclusions] Our results demonstrate that the high frequency of the Far Eastern mitochondrial cytochrome B A2 haplotype in modern Canarian Black pigs probably corresponds to a relatively recent introgression with British breeds. ; IO has a pre-doctoral fellowship from the Basque Government (DEUI). OR is a post-doctoral researcher from the JAEDOC program co-funded by The European Social Fund (ESF). This work has been founded by the grant BFU2012-34157 to C.L-F from the MINECO, Spain. ; Peer reviewed

Olalde, Iñigo et al.-- This work is licensed under a Creative Commons Attribution 3.0 Unported License. ; A pyrographically decorated gourd, dated to the French Revolution period, has been alleged to contain a handkerchief dipped into the blood of the French king Louis XVI (1754-1793) after his beheading but recent analyses of living males from two Bourbon branches cast doubts on its authenticity. We sequenced the complete genome of the DNA contained in the gourd at low coverage (∼2.5×) with coding sequences enriched at a higher ∼7.3× coverage. We found that the ancestry of the gourd's genome does not seem compatible with Louis XVI's known ancestry. From a functional perspective, we did not find an excess of alleles contributing to height despite being described as the tallest person in Court. In addition, the eye colour prediction supported brown eyes, while Louis XVI had blue eyes. This is the first draft genome generated from a person who lived in a recent historical period; however, our results suggest that this sample may not correspond to the alleged king. ; This work is supported by FEDER and Spanish Government grants BFU2012-38236 and the Spanish Multiple Sclerosis Netowrk (REEM) of the Instituto de Salud Carlos III (RD12/0032/0011) to A.N., BFU2011-28549 and ERC Starting Grant (260372) to T.M.-B. and BFU2012-34157 to C.L.-F. and S.C., and a predoctoral fellowship from the Basque Government (DEUI) to I.O. ; Peer Reviewed

We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0–14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups.

We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0–14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups. ; FB, RH, KR-B, VH: Fritz-Thyssen-Stiftung project RR8322. KK, K-G S: Swedish Riksbanken grant M16-0455:1. VHeyd: ERC Advanced grant 788616.

We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0-14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups.

We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0–14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups. ; Peer reviewed

The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome. ; C.L.-F. is supported by a PGC2018-0955931-B-100 grant (MCIU/AEI/FEDER, UE) of Spain; T.M.-B. is supported by funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 864203), BFU2017-86471-P (MINECO/FEDER, UE), "Unidad de Excelencia María de Maeztu", funded by the AEI (CEX2018-000792-M), Howard Hughes International Early Career, Secretaria d'Universitats i Recerca and CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). L.v.D. is supportd by a UCL Excellence Fellowship. The Ministry of the Education and Science of the Republic of Kazakhstan permitted and granted the research and the study (Grant number AP09261134). Additional financial contribution was provided by the ISMEO of Rome.

Inversions are one type of structural variants linked to phenotypic differences and adaptation in multiple organisms. However, there is still very little information about polymorphic inversions in the human genome due to the difficulty of their detection. Here, we develop a new high-throughput genotyping method based on probe hybridization and amplification, and we perform a complete study of 45 common human inversions of 0.1-415 kb. Most inversions promoted by homologous recombination occur recurrently in humans and great apes and they are not tagged by SNPs. Furthermore, there is an enrichment of inversions showing signatures of positive or balancing selection, diverse functional effects, such as gene disruption and gene-expression changes, or association with phenotypic traits. Therefore, our results indicate that the genome is more dynamic than previously thought and that human inversions have important functional and evolutionary consequences, making possible to determine for the first time their contribution to complex traits. ; This work was supported by research grants ERC Starting Grant 243212 (INVFEST) from the European Research Council under the European Union Seventh Research Framework Programme (FP7), BFU2013-42649-P and BFU2016-77244-R funded by the Agencia Estatal de Investigación (AEI, Spain) and the European Regional Development Fund (FEDER, EU), and 2014-SGR-1346 and 2017-SGR-1379 from the Generalitat de Catalunya (Spain) to M.C., a PIF PhD fellowship from the Universitat Autònoma de Barcelona (Spain) to C.G.D., a La Caixa Doctoral fellowship to J.L.J., and a FPI PhD fellowship from the Ministerio de Economía y Competitividad (Spain) to M.O. and I.N. M.G.V. was supported in part by POCI-01-0145-FEDER-006821 funded through the Operational Programme for Competitiveness Factors (COMPETE, EU) and UID/BIA/50027/2013 from the Foundation for Science and Technology (FCT, Portugal).