Genetic diversity of Mediterranean swordfish (Xiphias gladius Linneus) has not been explored exte... more Genetic diversity of Mediterranean swordfish (Xiphias gladius Linneus) has not been explored extensively at its easternmost range so far. In this study, modern X. gladius samples from the eastern part of the Mediterranean basin; north of the Aegean Sea (Aegean-2013, n=26) and the Mediterranean coast of Turkey (N.Levantine-2013, n=42) were studied genetically, along with ancient samples from Yenikapı excavation (n=6). Partial mitochondrial DNA control region sequences (entire sequences, Clade I, and Clade II) were evaluated spatially and temporally together with previously published sequences (Alvarado Bremer et al., 2005b; Viñas et al., 2010; Righi et al., 2020) from the rest of the Mediterranean Sea. By pairwise FST and pairwise AMOVA tests we showed that, in general, groups of eastern populations and western Mediterranean populations have not genetically differed from each other significantly nearly in the last 20 years. On the other hand, our results confirmed the existence of genetic diversity differences between western and eastern Mediterranean, with eastern being low. One-tailed permutation tests revealed that the θ, which is directly proportional to long-term female effective population size (Ne) decreased significantly (p<0.05) in both regions over the last two decades. On the Turkish coasts, the θ is not significantly different from that of the nearly contemporary eastern Mediterranean population. However, θ of the ancient sample was consistently and significantly (p<0.001) higher than those of the eastern and western Mediterranean populations in Clade I and Clade II. Furthermore, it contains two mitochondrial haplotypes that are not observed in modern samples suggesting that, the Ne of X. gladius in the eastern was high in Byzantium times. Eight microsatellite loci were also genotyped in modern samples. The microsatellite based present Ne estimate of the pooled Aegean-2013 and N.Levantine-2013 populations was lower than 1000 according to the upper limit of 95% confidence interval and possibly even lower than 100 according to the mean of MSVAR posterior distribution. These alarming genetic signals for the sustainability of X. gladius on the coasts of Turkey are in agreement with the nearly collapsing X. gladius fisheries as depicted also in the fisheries statistics. Overall, congruent with the previous studies, the data presented here shows that sustainability of the X. gladius population in Mediterranean is under major threat. Therefore, X. gladius around the Turkish coasts need a stringent action and management plan, urgently. This article is protected by copyright. All rights reserved.
SummaryThe history of human inbreeding is controversial. The development of sedentary agricultura... more SummaryThe history of human inbreeding is controversial. The development of sedentary agricultural societies may have had opposite influences on inbreeding levels. On the one hand, agriculture and food surplus may have diminished inbreeding by increasing population sizes and lowering endogamy, i.e. inbreeding due to population isolation. On the other hand, increased sedentism, as well as the advent of private property may have promoted inbreeding through the emergence of consanguineous marriage customs or via ethnic and caste endogamy. The net impact is unknown, and to date, no systematic study on the temporal frequency of inbreeding in human societies has been conducted. Here we present a new approach for reliable estimation of runs of homozygosity (ROH) in genomes with ≥3x mean coverage across >1 million SNPs, and apply this to 440 ancient Eurasian genomes from the last 15,000 years. We show that the frequency of inbreeding, as measured by ROH, has decreased over time. The stro...
We present paleogenomes of three morphologically-unidentified Anatolian equids dating to the 1stm... more We present paleogenomes of three morphologically-unidentified Anatolian equids dating to the 1stmillennium BCE, sequenced to coverages of 0.6-6.4X. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those ofEquus hydruntinus(orEquus hemionus hydruntinus), the extinct European wild ass. The Anatolian wild ass whole genome profiles fall outside the genomic diversity of other extant and past Asiatic wild ass (E.hemionus) lineages. These observations strongly suggest that the three Anatolian wild asses representE.hydruntinus, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Comparative genomic analyses suggest thatE.hydruntinuswas a sister clade to all ancient and present-dayE.hemionuslineages, representing an early split. We also find indication of gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosi...
A major challenge in zooarchaeology is to morphologically distinguish closely related species’ re... more A major challenge in zooarchaeology is to morphologically distinguish closely related species’ remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species’ reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.5x mitochondria...
Whale sharks are a declining species for which little biological data is available. While these a... more Whale sharks are a declining species for which little biological data is available. While these animals are protected in many parts of their range, they are fished legally and illegally in some countries. Baseline biological and ecological data are needed to allow the formulation of an effective conservation plan for whale sharks. It is not known, for example, whether the whale shark is represented by a single worldwide panmictic population or by numerous, reproductively isolated populations. Genetic analysis of population structure is one essential component of the baseline data required for whale shark conservation.
Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked ... more Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product...
Archaeogenomic analysis of ancient Anatolians : first genetic indication for Neolithic cultural d... more Archaeogenomic analysis of ancient Anatolians : first genetic indication for Neolithic cultural diffusion in the Near East
Sheep was among the first domesticated animals, but its demographic history is little understood.... more Sheep was among the first domesticated animals, but its demographic history is little understood. Here we present combined analyses of mitochondrial and nuclear polymorphism data from ancient central and west Anatolian sheep dating to the Late Glacial and early Holocene. We observe loss of mitochondrial haplotype diversity around 7500 BCE during the early Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, mitochondrial haplogroup diversity increases, compatible with admixture from other domestication centres and/or from wild populations. Analysing archaeogenomic data, we further find that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds, and especially those from central and north Europe. Our results indicate that Asian contribution to south European breeds in the post-Neolithic era, possibly during the Bronze Age, may explain this pattern.
Over multiple millennia, from the earliest traces of long-term occupation of camp sites (ca 20,00... more Over multiple millennia, from the earliest traces of long-term occupation of camp sites (ca 20,000 BC) to the development of full-scale farming (ca 8000–6000 BC), the Neolithic transition in southwest Asia gradually shaped human societies in dramatic ways (Nadel 2002; Maher et al. 2012; Asouti, Fuller 2013). Here we present recent insights from ancient genomics studies into these societies while focusing on two questions: the population processes driving cultural change in Neolithic central Anatolia and genetic kinship among Çatalhöyük co-burials
Population and conservation genetics of two freshwater fish species, Notropis heterodon and Notro... more Population and conservation genetics of two freshwater fish species, Notropis heterodon and Notropis heterolepis, were evaluated in north-eastern Illinois, U.S.A., where both species have severely declined. Fishes were sampled from two remnant populations occurring in small glacial lakes (source samples) and from two man-made ponds that had been stocked with fishes from those same lakes (sanctuary samples). The goal was to obtain information that would help inform conservation programme planning to reintroduce sanctuary fishes to areas where both species are extirpated. Microsatellite data showed that the two species were genetically quite distinct and there was no evidence of hybridization in either source or sanctuary samples. Within each species, source and sanctuary samples had moderate levels of heterozygosity and were not significantly different from each other. Many alleles observed in the source samples, however, were not detected in the sanctuary samples, indicating that translocation had resulted in reduced allelic diversity of the sanctuary samples. Sibship analysis indicated that full and half sibs occurred within source-lake samples, thus reducing the effective population size of the reintroduced stock. Taken together, these results suggest that source-lake stocks rather than sanctuary stocks are more appropriate for future reintroductions of both species in their native range, unless sanctuary populations can be established with hundreds of fishes. Also, fishes should be harvested from multiple locations in source lakes to avoid over-representation of family groups.
Genetic diversity of Mediterranean swordfish (Xiphias gladius Linneus) has not been explored exte... more Genetic diversity of Mediterranean swordfish (Xiphias gladius Linneus) has not been explored extensively at its easternmost range so far. In this study, modern X. gladius samples from the eastern part of the Mediterranean basin; north of the Aegean Sea (Aegean-2013, n=26) and the Mediterranean coast of Turkey (N.Levantine-2013, n=42) were studied genetically, along with ancient samples from Yenikapı excavation (n=6). Partial mitochondrial DNA control region sequences (entire sequences, Clade I, and Clade II) were evaluated spatially and temporally together with previously published sequences (Alvarado Bremer et al., 2005b; Viñas et al., 2010; Righi et al., 2020) from the rest of the Mediterranean Sea. By pairwise FST and pairwise AMOVA tests we showed that, in general, groups of eastern populations and western Mediterranean populations have not genetically differed from each other significantly nearly in the last 20 years. On the other hand, our results confirmed the existence of genetic diversity differences between western and eastern Mediterranean, with eastern being low. One-tailed permutation tests revealed that the θ, which is directly proportional to long-term female effective population size (Ne) decreased significantly (p<0.05) in both regions over the last two decades. On the Turkish coasts, the θ is not significantly different from that of the nearly contemporary eastern Mediterranean population. However, θ of the ancient sample was consistently and significantly (p<0.001) higher than those of the eastern and western Mediterranean populations in Clade I and Clade II. Furthermore, it contains two mitochondrial haplotypes that are not observed in modern samples suggesting that, the Ne of X. gladius in the eastern was high in Byzantium times. Eight microsatellite loci were also genotyped in modern samples. The microsatellite based present Ne estimate of the pooled Aegean-2013 and N.Levantine-2013 populations was lower than 1000 according to the upper limit of 95% confidence interval and possibly even lower than 100 according to the mean of MSVAR posterior distribution. These alarming genetic signals for the sustainability of X. gladius on the coasts of Turkey are in agreement with the nearly collapsing X. gladius fisheries as depicted also in the fisheries statistics. Overall, congruent with the previous studies, the data presented here shows that sustainability of the X. gladius population in Mediterranean is under major threat. Therefore, X. gladius around the Turkish coasts need a stringent action and management plan, urgently. This article is protected by copyright. All rights reserved.
SummaryThe history of human inbreeding is controversial. The development of sedentary agricultura... more SummaryThe history of human inbreeding is controversial. The development of sedentary agricultural societies may have had opposite influences on inbreeding levels. On the one hand, agriculture and food surplus may have diminished inbreeding by increasing population sizes and lowering endogamy, i.e. inbreeding due to population isolation. On the other hand, increased sedentism, as well as the advent of private property may have promoted inbreeding through the emergence of consanguineous marriage customs or via ethnic and caste endogamy. The net impact is unknown, and to date, no systematic study on the temporal frequency of inbreeding in human societies has been conducted. Here we present a new approach for reliable estimation of runs of homozygosity (ROH) in genomes with ≥3x mean coverage across >1 million SNPs, and apply this to 440 ancient Eurasian genomes from the last 15,000 years. We show that the frequency of inbreeding, as measured by ROH, has decreased over time. The stro...
We present paleogenomes of three morphologically-unidentified Anatolian equids dating to the 1stm... more We present paleogenomes of three morphologically-unidentified Anatolian equids dating to the 1stmillennium BCE, sequenced to coverages of 0.6-6.4X. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those ofEquus hydruntinus(orEquus hemionus hydruntinus), the extinct European wild ass. The Anatolian wild ass whole genome profiles fall outside the genomic diversity of other extant and past Asiatic wild ass (E.hemionus) lineages. These observations strongly suggest that the three Anatolian wild asses representE.hydruntinus, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Comparative genomic analyses suggest thatE.hydruntinuswas a sister clade to all ancient and present-dayE.hemionuslineages, representing an early split. We also find indication of gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosi...
A major challenge in zooarchaeology is to morphologically distinguish closely related species’ re... more A major challenge in zooarchaeology is to morphologically distinguish closely related species’ remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species’ reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.5x mitochondria...
Whale sharks are a declining species for which little biological data is available. While these a... more Whale sharks are a declining species for which little biological data is available. While these animals are protected in many parts of their range, they are fished legally and illegally in some countries. Baseline biological and ecological data are needed to allow the formulation of an effective conservation plan for whale sharks. It is not known, for example, whether the whale shark is represented by a single worldwide panmictic population or by numerous, reproductively isolated populations. Genetic analysis of population structure is one essential component of the baseline data required for whale shark conservation.
Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked ... more Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and foodways. We present thirteen ancient genomes (c.8500-7500 calBCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying a mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organised along biological family lines. We document bodily interventions such as head-shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Finally, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesise that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product...
Archaeogenomic analysis of ancient Anatolians : first genetic indication for Neolithic cultural d... more Archaeogenomic analysis of ancient Anatolians : first genetic indication for Neolithic cultural diffusion in the Near East
Sheep was among the first domesticated animals, but its demographic history is little understood.... more Sheep was among the first domesticated animals, but its demographic history is little understood. Here we present combined analyses of mitochondrial and nuclear polymorphism data from ancient central and west Anatolian sheep dating to the Late Glacial and early Holocene. We observe loss of mitochondrial haplotype diversity around 7500 BCE during the early Neolithic, consistent with a domestication-related bottleneck. Post-7000 BCE, mitochondrial haplogroup diversity increases, compatible with admixture from other domestication centres and/or from wild populations. Analysing archaeogenomic data, we further find that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds, and especially those from central and north Europe. Our results indicate that Asian contribution to south European breeds in the post-Neolithic era, possibly during the Bronze Age, may explain this pattern.
Over multiple millennia, from the earliest traces of long-term occupation of camp sites (ca 20,00... more Over multiple millennia, from the earliest traces of long-term occupation of camp sites (ca 20,000 BC) to the development of full-scale farming (ca 8000–6000 BC), the Neolithic transition in southwest Asia gradually shaped human societies in dramatic ways (Nadel 2002; Maher et al. 2012; Asouti, Fuller 2013). Here we present recent insights from ancient genomics studies into these societies while focusing on two questions: the population processes driving cultural change in Neolithic central Anatolia and genetic kinship among Çatalhöyük co-burials
Population and conservation genetics of two freshwater fish species, Notropis heterodon and Notro... more Population and conservation genetics of two freshwater fish species, Notropis heterodon and Notropis heterolepis, were evaluated in north-eastern Illinois, U.S.A., where both species have severely declined. Fishes were sampled from two remnant populations occurring in small glacial lakes (source samples) and from two man-made ponds that had been stocked with fishes from those same lakes (sanctuary samples). The goal was to obtain information that would help inform conservation programme planning to reintroduce sanctuary fishes to areas where both species are extirpated. Microsatellite data showed that the two species were genetically quite distinct and there was no evidence of hybridization in either source or sanctuary samples. Within each species, source and sanctuary samples had moderate levels of heterozygosity and were not significantly different from each other. Many alleles observed in the source samples, however, were not detected in the sanctuary samples, indicating that translocation had resulted in reduced allelic diversity of the sanctuary samples. Sibship analysis indicated that full and half sibs occurred within source-lake samples, thus reducing the effective population size of the reintroduced stock. Taken together, these results suggest that source-lake stocks rather than sanctuary stocks are more appropriate for future reintroductions of both species in their native range, unless sanctuary populations can be established with hundreds of fishes. Also, fishes should be harvested from multiple locations in source lakes to avoid over-representation of family groups.
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