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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

Vai, Stefania et al. ; In the period between 400 to 800 AD, also known as the period of the Barbarian invasions, intense migration is documented in the historical record of Europe. However, little is known about the demographic impact of these historical movements, potentially ranging from negligible to substantial. As a pilot study in a broader project on Medieval Europe, we sampled 102 specimens from 5 burial sites in Northwestern Italy, archaeologically classified as belonging to Lombards or Longobards, a Germanic people ruling over a vast section of the Italian peninsula from 568 to 774. We successfully amplified and typed the mitochondrial hypervariable region I (HVR-I) of 28 individuals. Comparisons of genetic diversity with other ancient populations and haplotype networks did not suggest that these samples are heterogeneous, and hence allowed us to jointly compare them with three isolated contemporary populations, and with a modern sample of a large city, representing a control for the effects of recent immigration. We then generated by serial coalescent simulations 16 millions of genealogies, contrasting a model of genealogical continuity with one in which the contemporary samples are genealogically independent from the medieval sample. Analyses by Approximate Bayesian Computation showed that the latter model fits the data in most cases, with one exception, Trino Vercellese, in which the evidence was compatible with persistence up to the present time of genetic features observed among this early medieval population. We conclude that it is possible, in general, to detect evidence of genealogical ties between medieval and specific modern populations. However, only seldom did mitochondrial DNA data allow us to reject with confidence either model tested, which indicates that broader analyses, based on larger assemblages of samples and genetic markers, are needed to understand in detail the effects of medieval migration. ; This work was supported by the Italian Ministry for Universities and Research (MIUR), PRIN 2012 funds to DC, AA, AT and GB, FIRB funds "Futuro in Ricerca" 2008 (RBFR08U07M) and 2012 (RBFR126B8I) to AA, AO and ER; Compagnia di San Paolo, Turin to DC; the Anneliese Maier Research Award of the Alexander von Humboldt Foundation and the German Federal Ministry for Education and Research to PG; FEDER and Spanish Government grant BFU2012-34157 to CLF; European Research Council (ERC Advanced Grant No. 295733 "LanGeLin") to GB. ; 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

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-IFERFMSH). I.O. was funded by a predoctoral fellowship from the Basque Government (DEUI), and M.S. and J.D. by postdoctoral grants from Fundaçao para a Ciência e a Tecnologia (FCT) and Juan de la Cierva Subprogram (JCI-2011-09543), respectively. Alignment data are available through the Sequence Read Archive (SRA) at the accession code SRP057056.

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

A recent discovery of Iron Age burials (Pazyryk culture) in the Altai Mountains of Mongolia may shed light on the mode and tempo of the generation of the current genetic east-west population admixture in Central Asia. Studies on ancient mitochondrial DNA of this region suggest that the Altai Mountains played the role of a geographical barrier between West and East Eurasian lineages until the beginning of the Iron Age. After the 7th century BC, coinciding with Scythian expansion across the Eurasian steppes, a gradual influx of East Eurasian sequences in Western steppes is detected. However, the underlying events behind the genetic admixture in Altai during the Iron Age are still unresolved: 1) whether it was a result of migratory events (eastward firstly, westward secondly), or 2) whether it was a result of a local demographic expansion in a 'contact zone' between European and East Asian people. In the present work, we analyzed the mitochondrial DNA lineages in human remains from Bronze and Iron Age burials of Mongolian Altai. Here we present support to the hypothesis that the gene pool of Iron Age inhabitants of Mongolian Altai was similar to that of western Iron Age Altaians (Russia and Kazakhstan). Thus, this people not only shared the same culture (Pazyryk), but also shared the same genetic east-west population admixture. In turn, Pazyryks appear to have a similar gene pool that current Altaians. Our results further show that Iron Age Altaians displayed mitochondrial lineages already present around Altai region before the Iron Age. This would provide support for a demographic expansion of local people of Altai instead of westward or eastward migratory events, as the demographic event behind the high population genetic admixture and diversity in Central Asia. © 2012 González-Ruiz et al. ; The authors acknowledge the following grants: Generalitat de Catalunya: SRG 2009- 566; European Union, INTERREG III: I3A-10-319-E; Ministerio de Economía y Competitividad, Gobierno de España, Programa Juan de la Cierva: JCI-2010-08157. ; Peer Reviewed

Neandertals disappeared from the fossil record around 40,000 bp, after a demographic history of small and isolated groups with high but variable levels of inbreeding, and episodes of interbreeding with other Paleolithic hominins. It is reasonable to expect that high levels of endogamy could be expressed in the skeleton of at least some Neandertal groups. Genetic studies indicate that the 13 individuals from the site of El Sidrón, Spain, dated around 49,000 bp, constituted a closely related kin group, making these Neandertals an appropriate case study for the observation of skeletal signs of inbreeding. We present the complete study of the 1674 identified skeletal specimens from El Sidrón. Altogether, 17 congenital anomalies were observed (narrowing of the internal nasal fossa, retained deciduous canine, clefts of the first cervical vertebra, unilateral hypoplasia of the second cervical vertebra, clefting of the twelfth thoracic vertebra, diminutive thoracic or lumbar rib, os centrale carpi and bipartite scaphoid, tripartite patella, left foot anomaly and cuboid-navicular coalition), with at least four individuals presenting congenital conditions (clefts of the first cervical vertebra). At 49,000 years ago, the Neandertals from El Sidrón, with genetic and skeletal evidence of inbreeding, could be representative of the beginning of the demographic collapse of this hominin phenotype. ; This research was supported by a grant from the Ministerio de Economía y Competitividad of Spain (CGL2016-75-109-P and Convenio Principado de Asturias–Universidad de Oviedo CN-09–084). L.R. was founded by the Juan de la Cierva program (Spanish Government) and thanks Asier Gómez-Olivencia for providing Neandertal and modern human metric data for the second cervical vertebra and for the discussion of several aspects of the hominin cervical spine. A.E. is founded by the Juan de la Cierva program (Spanish Government). Y.Q. received support from Ministerio de Educación y Ciencia Project N° CGL2015-65387-C3-2-P, MINECO-FEDER and a Predoctoral Grant, University of Burgos. T.L.K is funded by the HP7 European Research Council Starting Grant #336301.

Two Neandertal specimens from El Sidrón, northern Spain, show evidence of retained left mandibular deciduous canines. These individuals share the same mitochondrial (mtDNA) haplotype, indicating they are maternally related and suggesting a potential heritable basis for these dental anomalies. Radiographs and medical CT scans provide evidence of further, more extensive dental pathology in one of these specimens. An anomalous deciduous canine crown morphology that developed before birth subsequently suffered a fracture of the crown exposing the pulp sometime after eruption into functional occlusion. This led to death of the tooth, periapical granuloma formation and arrested deciduous canine root growth at an estimated age of 2.5 years. At some point the underlying permanent canine tooth became horizontally displaced and came to lie low in the trabecular bone of the mandibular corpus. A dentigerous cyst then developed around the crown. Anterior growth displacement of the mandible continued around the stationary permanent canine, leaving it posteriorly positioned in the mandibular corpus by the end of the growth period beneath the third permanent molar roots, which, in turn, suggests a largely horizontal growth vector. Subsequent longstanding repeated infections of the expanding cyst cavity are evidenced by bouts of bone deposition and resorption of the boundary walls of the cyst cavity. This resulted in the establishment of two permanent bony drainage sinuses, one through the buccal plate of the alveolar bone anteriorly, immediately beneath the infected deciduous canine root, and the other through the buccal plate anterior to the mesial root of the first permanent molar. It is probable that this complicated temporal sequence of dental pathologies had an initial heritable trigger that progressed in an unusually complex way in one of these individuals. During life, this individual may have been largely unaware of this ongoing pathology. © 2013 Elsevier Ltd. ; El Sidrón site is being excavated with the support of the Consejería de Cultura of the Asturias Autonomous government. This research is founded by the Spanish Ministry of Economy and Competitiveness (Project CGL2012-36682). ; Peer Reviewed

Neandertals disappeared from the fossil record around 40,000 bp, after a demographic history of small and isolated groups with high but variable levels of inbreeding, and episodes of interbreeding with other Paleolithic hominins. It is reasonable to expect that high levels of endogamy could be expressed in the skeleton of at least some Neandertal groups. Genetic studies indicate that the 13 individuals from the site of El Sidrón, Spain, dated around 49,000 bp, constituted a closely related kin group, making these Neandertals an appropriate case study for the observation of skeletal signs of inbreeding. We present the complete study of the 1674 identified skeletal specimens from El Sidrón. Altogether, 17 congenital anomalies were observed (narrowing of the internal nasal fossa, retained deciduous canine, clefts of the first cervical vertebra, unilateral hypoplasia of the second cervical vertebra, clefting of the twelfth thoracic vertebra, diminutive thoracic or lumbar rib, os centrale carpi and bipartite scaphoid, tripartite patella, left foot anomaly and cuboid-navicular coalition), with at least four individuals presenting congenital conditions (clefts of the first cervical vertebra). At 49,000 years ago, the Neandertals from El Sidrón, with genetic and skeletal evidence of inbreeding, could be representative of the beginning of the demographic collapse of this hominin phenotype. ; This research was supported by a grant from the Ministerio de Economía y Competitividad of Spain (CGL2016-75-109-P and Convenio Principado de Asturias–Universidad de Oviedo CN-09–084). L.R. was founded by the Juan de la Cierva program (Spanish Government) and thanks Asier Gómez-Olivencia for providing Neandertal and modern human metric data for the second cervical vertebra and for the discussion of several aspects of the hominin cervical spine. A.E. is founded by the Juan de la Cierva program (Spanish Government). Y.Q. received support from Ministerio de Educación y Ciencia Project N° CGL2015-65387-C3-2-P, MINECO-FEDER and a Predoctoral Grant, University of Burgos. T.L.K is funded by the HP7 European Research Council Starting Grant #336301. ; 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