Graphical Abstract Highlights d Nuclear genome and exome analyses of extinct scimitar-toothed cat... more Graphical Abstract Highlights d Nuclear genome and exome analyses of extinct scimitar-toothed cat, Homotherium latidens d Homotherium was a highly divergent lineage from all living cat species (22.5 Ma) d Genetic adaptations to cursorial and diurnal hunting behaviors d Relatively high levels of genetic diversity in this individual Correspondence [email protected] (M.V.W.), [email protected] (M.T.P.G.) In Brief Here, Barnett et al. sequence the nuclear genome of Homotherium latidens through a combination of shotgun and target-capture approaches. Analyses confirm Homotherium to be a highly divergent lineage from all living cat species (22.5 Ma) and reveal genes under selection putatively related to a cursorial and diurnal hunting behavior.
The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late pl... more The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late pleistocene. its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14 c and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52-2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species. The cave lion (Panthera spelaea) was an apex predator across the Holarctic 1,2 until their extinction at the end of the Pleistocene 3 (last occurrence in the fossil record 14,219 ± 112 cal BP 4). Cave lions were larger than extant lions 5 , and Pleistocene cave art suggests that they did not have manes. However they may have shared several behavioural traits with their modern counterparts, such as group living and courtship rituals 6. Cave lion taxonomy has been contentious, being variously considered a subspecies of Panthera leo 7,8 , a sister species to extant lions (Panthera spelaea) 5,9 , or even being more closely related to the tiger (Panthera tigris spe-laea) 10. In particular, the molecular estimate of the timing of the split between cave lions and extant lions has varied considerably between studies (~ 600 kya 8 ; 1.23-2.93 mya 11). Ersmark et al. 12 identified two major cave lion mitochondrial DNA haplogroups (based on ~ 348 bp of ATP8 and control region sequences) and showed that open
Cite this article: Allen R et al. 2020 A mitochondrial genetic divergence proxy predicts the repr... more Cite this article: Allen R et al. 2020 A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids. Proc. R. Soc. B 287: 20200690. http://dx.
Cite this article: Allen R et al. 2020 A mitochondrial genetic divergence proxy predicts the repr... more Cite this article: Allen R et al. 2020 A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids. Proc. R. Soc. B 287: 20200690. http://dx.
Lions are one of the world's most iconic megafauna, yet little is known about their temporal and ... more Lions are one of the world's most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species. lion | genomics | evolution U ntil recently, the lion (Panthera leo), was one of the most widely distributed terrestrial mammals. As an apex predator , lions have important ecological impacts and have featured prominently in human iconography (1). During the Pleistocene, lions ranged over an enormous geographic expanse. This included modern lions (Panthera leo leo) in Eurasia, the cave lion (Panthera leo spelaea) in Eurasia, Alaska, and Yukon, as well as the American lion (Panthera leo atrox)
Evolution; international journal of organic evolution, 2014
Island evolution may be expected to involve fast initial morphological divergence followed by sta... more Island evolution may be expected to involve fast initial morphological divergence followed by stasis. We tested this model using the dental phenotype of modern and ancient common voles (Microtus arvalis), introduced onto the Orkney archipelago (Scotland) from continental Europe some 5000 years ago. First, we investigated phenotypic divergence of Orkney and continental European populations and assessed climatic influences. Second, phenotypic differentiation among Orkney populations was tested against geography, time, and neutral genetic patterns. Finally, we examined evolutionary change along a time series for the Orkney Mainland. Molar gigantism and anterior-lobe hypertrophy evolved rapidly in Orkney voles following introduction, without any transitional forms detected. Founder events and adaptation appear to explain this initial rapid evolution. Idiosyncrasy in dental features among different island populations of Orkney voles is also likely the result of local founder events follo...
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, ... more The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
Prior to human arrival in the 13th century, two large birds of prey were the top predators in New... more Prior to human arrival in the 13th century, two large birds of prey were the top predators in New Zealand. In the absence of non-volant mammals, the extinct Haast's eagle (Hieraaetus moorei), the largest eagle in the world, and the extinct Eyles' harrier (Circus teauteensis) the largest harrier in the world, had filled ecological niches that are on other landmasses occupied by animals such as large cats or canines. The evolutionary and biogeographic history of these island giants has long been a mystery. Here we reconstruct the origin and evolution of New Zealand's giant raptors using complete mitochondrial genome data. We show that both Eyles' harrier and Haast's eagle diverged from much smaller, open land adapted Australasian relatives in the late Pliocene to early Pleistocene. These events coincided with the development of open habitat in the previously densely forested islands of New Zealand. Our study provides evidence of rapid evolution of island gigantism in New Zealand's extinct birds of prey. Early Pleistocene climate and environmental changes were likely to have triggered the establishment of Australian raptors into New Zealand. Our results shed light on the evolution of two of the most impressive cases of island gigantism in the world.
Human-induced environmental change and habitat fragmentation pose major threats to biodiversity a... more Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of en- dangered species [1–4]. However, factors such as outbreeding depression [5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management pro- grams. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [7, 8]. We extend this approach to its natural conclusion, by characterizing the com- plete genomic sequences of modern and historic population samples of the crested ibis (Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinc-tion. Though its once tiny population has today recovered to >2,000 individuals [9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymor- phisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.
The Encyclopaedia of Archaeological Sciences, 2018
In the seminal 1984 paper by that first showed the post-mortem survival of ancient DNA and initia... more In the seminal 1984 paper by that first showed the post-mortem survival of ancient DNA and initiated the entire field of ancient DNA studies, the authors used small scraps of muscle tissue found while remounting a specimen of the extinct quagga. Using primitive bacterial cloning methods they showed that recognizably equine DNA sequences were still to be found within. From there, the field split into two main branches: those concerned with getting ancient DNA from human remains and those concerned with getting DNA from other sources. While the study of ancient DNA from human remains requires incredibly stringent laboratory protocols to prevent contamination, working on zooarchaeological material happily circumvents many of these issues due to lower risks associated with working on extinct species, rare specimens, and domesticates.
Toads are likely to have been introduced to Qatar, but little information is available on toad po... more Toads are likely to have been introduced to Qatar, but little information is available on toad populations in the country, including the species present and their probable origin. Therefore, we collected tissue samples for analysis from 32 toads found in six different locations in northern and central Qatar. Phylogenetic analysis based on16S rRNA mitochondrial DNA identified two haplotypes in Qatar, which are identical to those of Sclerophrys regularis from Ismalia and from Rasheed (Rosetta) in Egypt. One haplotype is very common in central Qatar, while the other is more common in the north. It is possible that toads have been introduced from Egypt to Qatar on multiple occasions, although we cannot reject the possibility of a single introduction event containing toads of both haplotypes with subsequent dispersal across the country.
Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread... more Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread population declines in what has hitherto been seen as a common species, robust to anthropogenic disturbance. Here we use non-invasive methods to recover complete mitochondrial genomes from single hair samples collected in the field in order to explore the identity of the Gabonese Plateaux Batéké lion. Comparison of the mitogenomes against a comprehensive dataset of African lion sequences that includes relevant geographically proximate lion populations from both contemporary and ancient sources, enabled us to identify the Plateaux Batéké lion as a close maternal relative to now extirpated populations found in Gabon and nearby Congo during the twentieth century, and to extant populations of Southern Africa. Our study demonstrates the relevance of ancient DNA methods to field conservation work, and the ability of trace field samples to provide copious genetic information about free-ranging animals. Keywords Ancient DNA · Mitochondrial genomes · Panthera leo · Lion · Gabon · Congo · Plateaux Batéké National Park
The genome of the extinct thylacine, also known as the Tasmanian tiger, has been sequenced from a... more The genome of the extinct thylacine, also known as the Tasmanian tiger, has been sequenced from a 109-year-old museum specimen. The sequence resolves the phylogenetic placement of the species and reveals details of convergent evolution between the thylacine and eutherian canines.
Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele f... more Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both argued to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of pre-industrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection.
Pigs (Sus scrofa) have played an important cultural role in Hawaii since Polynesians first introd... more Pigs (Sus scrofa) have played an important cultural role in Hawaii since Polynesians first introduced them in approximately AD 1200. Additional varieties of pigs were introduced following Captain Cook's arrival in Hawaii in 1778 and it has been suggested that the current pig population may descend primarily, or even exclusively, from European pigs. Although populations of feral pigs today are an important source of recreational hunting on all of the major islands, they also negatively impact native plants and animals. As a result, understanding the origins of these feral pig populations has significant ramifications for discussions concerning conservation management, identity and cultural continuity on the islands. Here, we analysed a neutral mitochondrial marker and a functional nuclear coat colour marker in 57 feral Hawaiian pigs. Through the identification of a new mutation in the MC1R gene that results in black coloration, we demonstrate that Hawaiian feral pigs are mostly the descendants of those originally introduced during Polynesian settlement, though there is evidence for some admixture. As such, extant Hawaiian pigs represent a unique historical lineage that is not exclusively descended from feral pigs of European origin.
Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa t... more Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions.
Background: Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly... more Background: Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change.
The extinct cave lion (Panthera spelaea) was an apex predator of the Pleistocene, and one of the ... more The extinct cave lion (Panthera spelaea) was an apex predator of the Pleistocene, and one of the largest felid species ever to exist. We report the first mitochondrial genome sequences for this species, derived from two Beringian specimens, one of which has been radiocarbon dated to 29,860 ± 210 14C a BP. Phylogenetic analysis confirms the placement of the cave lion as the sister taxon to populations of the modern lion (P. leo). Using newly recovered stem pantherine fossils to calibrate a molecular clock, we estimate that P. spelaea and P. leo diverged about 1.89 million years ago (95% credibility interval: 1.23–2.93 million years), highlighting the likely position of this extinct carnivore as a distinct species.
Graphical Abstract Highlights d Nuclear genome and exome analyses of extinct scimitar-toothed cat... more Graphical Abstract Highlights d Nuclear genome and exome analyses of extinct scimitar-toothed cat, Homotherium latidens d Homotherium was a highly divergent lineage from all living cat species (22.5 Ma) d Genetic adaptations to cursorial and diurnal hunting behaviors d Relatively high levels of genetic diversity in this individual Correspondence [email protected] (M.V.W.), [email protected] (M.T.P.G.) In Brief Here, Barnett et al. sequence the nuclear genome of Homotherium latidens through a combination of shotgun and target-capture approaches. Analyses confirm Homotherium to be a highly divergent lineage from all living cat species (22.5 Ma) and reveal genes under selection putatively related to a cursorial and diurnal hunting behavior.
The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late pl... more The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late pleistocene. its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14 c and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52-2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species. The cave lion (Panthera spelaea) was an apex predator across the Holarctic 1,2 until their extinction at the end of the Pleistocene 3 (last occurrence in the fossil record 14,219 ± 112 cal BP 4). Cave lions were larger than extant lions 5 , and Pleistocene cave art suggests that they did not have manes. However they may have shared several behavioural traits with their modern counterparts, such as group living and courtship rituals 6. Cave lion taxonomy has been contentious, being variously considered a subspecies of Panthera leo 7,8 , a sister species to extant lions (Panthera spelaea) 5,9 , or even being more closely related to the tiger (Panthera tigris spe-laea) 10. In particular, the molecular estimate of the timing of the split between cave lions and extant lions has varied considerably between studies (~ 600 kya 8 ; 1.23-2.93 mya 11). Ersmark et al. 12 identified two major cave lion mitochondrial DNA haplogroups (based on ~ 348 bp of ATP8 and control region sequences) and showed that open
Cite this article: Allen R et al. 2020 A mitochondrial genetic divergence proxy predicts the repr... more Cite this article: Allen R et al. 2020 A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids. Proc. R. Soc. B 287: 20200690. http://dx.
Cite this article: Allen R et al. 2020 A mitochondrial genetic divergence proxy predicts the repr... more Cite this article: Allen R et al. 2020 A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids. Proc. R. Soc. B 287: 20200690. http://dx.
Lions are one of the world's most iconic megafauna, yet little is known about their temporal and ... more Lions are one of the world's most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species. lion | genomics | evolution U ntil recently, the lion (Panthera leo), was one of the most widely distributed terrestrial mammals. As an apex predator , lions have important ecological impacts and have featured prominently in human iconography (1). During the Pleistocene, lions ranged over an enormous geographic expanse. This included modern lions (Panthera leo leo) in Eurasia, the cave lion (Panthera leo spelaea) in Eurasia, Alaska, and Yukon, as well as the American lion (Panthera leo atrox)
Evolution; international journal of organic evolution, 2014
Island evolution may be expected to involve fast initial morphological divergence followed by sta... more Island evolution may be expected to involve fast initial morphological divergence followed by stasis. We tested this model using the dental phenotype of modern and ancient common voles (Microtus arvalis), introduced onto the Orkney archipelago (Scotland) from continental Europe some 5000 years ago. First, we investigated phenotypic divergence of Orkney and continental European populations and assessed climatic influences. Second, phenotypic differentiation among Orkney populations was tested against geography, time, and neutral genetic patterns. Finally, we examined evolutionary change along a time series for the Orkney Mainland. Molar gigantism and anterior-lobe hypertrophy evolved rapidly in Orkney voles following introduction, without any transitional forms detected. Founder events and adaptation appear to explain this initial rapid evolution. Idiosyncrasy in dental features among different island populations of Orkney voles is also likely the result of local founder events follo...
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, ... more The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
Prior to human arrival in the 13th century, two large birds of prey were the top predators in New... more Prior to human arrival in the 13th century, two large birds of prey were the top predators in New Zealand. In the absence of non-volant mammals, the extinct Haast's eagle (Hieraaetus moorei), the largest eagle in the world, and the extinct Eyles' harrier (Circus teauteensis) the largest harrier in the world, had filled ecological niches that are on other landmasses occupied by animals such as large cats or canines. The evolutionary and biogeographic history of these island giants has long been a mystery. Here we reconstruct the origin and evolution of New Zealand's giant raptors using complete mitochondrial genome data. We show that both Eyles' harrier and Haast's eagle diverged from much smaller, open land adapted Australasian relatives in the late Pliocene to early Pleistocene. These events coincided with the development of open habitat in the previously densely forested islands of New Zealand. Our study provides evidence of rapid evolution of island gigantism in New Zealand's extinct birds of prey. Early Pleistocene climate and environmental changes were likely to have triggered the establishment of Australian raptors into New Zealand. Our results shed light on the evolution of two of the most impressive cases of island gigantism in the world.
Human-induced environmental change and habitat fragmentation pose major threats to biodiversity a... more Human-induced environmental change and habitat fragmentation pose major threats to biodiversity and require active conservation efforts to mitigate their consequences. Genetic rescue through translocation and the introduction of variation into imperiled populations has been argued as a powerful means to preserve, or even increase, the genetic diversity and evolutionary potential of en- dangered species [1–4]. However, factors such as outbreeding depression [5, 6] and a reduction in available genetic diversity render the success of such approaches uncertain. An improved evaluation of the consequence of genetic restoration requires knowledge of temporal changes to genetic diversity before and after the advent of management pro- grams. To provide such information, a growing number of studies have included small numbers of genomic loci extracted from historic and even ancient specimens [7, 8]. We extend this approach to its natural conclusion, by characterizing the com- plete genomic sequences of modern and historic population samples of the crested ibis (Nipponia nippon), an endangered bird that is perhaps the most successful example of how conservation effort has brought a species back from the brink of extinc-tion. Though its once tiny population has today recovered to >2,000 individuals [9], this process was accompanied by almost half of ancestral loss of genetic variation and high deleterious mutation load. We furthermore show how genetic drift coupled to inbreeding following the population bottleneck has largely purged the ancient polymor- phisms from the current population. In conclusion, we demonstrate the unique promise of exploiting genomic information held within museum samples for conservation and ecological research.
The Encyclopaedia of Archaeological Sciences, 2018
In the seminal 1984 paper by that first showed the post-mortem survival of ancient DNA and initia... more In the seminal 1984 paper by that first showed the post-mortem survival of ancient DNA and initiated the entire field of ancient DNA studies, the authors used small scraps of muscle tissue found while remounting a specimen of the extinct quagga. Using primitive bacterial cloning methods they showed that recognizably equine DNA sequences were still to be found within. From there, the field split into two main branches: those concerned with getting ancient DNA from human remains and those concerned with getting DNA from other sources. While the study of ancient DNA from human remains requires incredibly stringent laboratory protocols to prevent contamination, working on zooarchaeological material happily circumvents many of these issues due to lower risks associated with working on extinct species, rare specimens, and domesticates.
Toads are likely to have been introduced to Qatar, but little information is available on toad po... more Toads are likely to have been introduced to Qatar, but little information is available on toad populations in the country, including the species present and their probable origin. Therefore, we collected tissue samples for analysis from 32 toads found in six different locations in northern and central Qatar. Phylogenetic analysis based on16S rRNA mitochondrial DNA identified two haplotypes in Qatar, which are identical to those of Sclerophrys regularis from Ismalia and from Rasheed (Rosetta) in Egypt. One haplotype is very common in central Qatar, while the other is more common in the north. It is possible that toads have been introduced from Egypt to Qatar on multiple occasions, although we cannot reject the possibility of a single introduction event containing toads of both haplotypes with subsequent dispersal across the country.
Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread... more Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread population declines in what has hitherto been seen as a common species, robust to anthropogenic disturbance. Here we use non-invasive methods to recover complete mitochondrial genomes from single hair samples collected in the field in order to explore the identity of the Gabonese Plateaux Batéké lion. Comparison of the mitogenomes against a comprehensive dataset of African lion sequences that includes relevant geographically proximate lion populations from both contemporary and ancient sources, enabled us to identify the Plateaux Batéké lion as a close maternal relative to now extirpated populations found in Gabon and nearby Congo during the twentieth century, and to extant populations of Southern Africa. Our study demonstrates the relevance of ancient DNA methods to field conservation work, and the ability of trace field samples to provide copious genetic information about free-ranging animals. Keywords Ancient DNA · Mitochondrial genomes · Panthera leo · Lion · Gabon · Congo · Plateaux Batéké National Park
The genome of the extinct thylacine, also known as the Tasmanian tiger, has been sequenced from a... more The genome of the extinct thylacine, also known as the Tasmanian tiger, has been sequenced from a 109-year-old museum specimen. The sequence resolves the phylogenetic placement of the species and reveals details of convergent evolution between the thylacine and eutherian canines.
Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele f... more Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both argued to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of pre-industrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection.
Pigs (Sus scrofa) have played an important cultural role in Hawaii since Polynesians first introd... more Pigs (Sus scrofa) have played an important cultural role in Hawaii since Polynesians first introduced them in approximately AD 1200. Additional varieties of pigs were introduced following Captain Cook's arrival in Hawaii in 1778 and it has been suggested that the current pig population may descend primarily, or even exclusively, from European pigs. Although populations of feral pigs today are an important source of recreational hunting on all of the major islands, they also negatively impact native plants and animals. As a result, understanding the origins of these feral pig populations has significant ramifications for discussions concerning conservation management, identity and cultural continuity on the islands. Here, we analysed a neutral mitochondrial marker and a functional nuclear coat colour marker in 57 feral Hawaiian pigs. Through the identification of a new mutation in the MC1R gene that results in black coloration, we demonstrate that Hawaiian feral pigs are mostly the descendants of those originally introduced during Polynesian settlement, though there is evidence for some admixture. As such, extant Hawaiian pigs represent a unique historical lineage that is not exclusively descended from feral pigs of European origin.
Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa t... more Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions.
Background: Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly... more Background: Polar bears (Ursus maritimus) are among those species most susceptible to the rapidly changing arctic climate, and their survival is of global concern. Despite this, little is known about polar bear species history. Future conservation strategies would significantly benefit from an understanding of basic evolutionary information, such as the timing and conditions of their initial divergence from brown bears (U. arctos) or their response to previous environmental change.
The extinct cave lion (Panthera spelaea) was an apex predator of the Pleistocene, and one of the ... more The extinct cave lion (Panthera spelaea) was an apex predator of the Pleistocene, and one of the largest felid species ever to exist. We report the first mitochondrial genome sequences for this species, derived from two Beringian specimens, one of which has been radiocarbon dated to 29,860 ± 210 14C a BP. Phylogenetic analysis confirms the placement of the cave lion as the sister taxon to populations of the modern lion (P. leo). Using newly recovered stem pantherine fossils to calibrate a molecular clock, we estimate that P. spelaea and P. leo diverged about 1.89 million years ago (95% credibility interval: 1.23–2.93 million years), highlighting the likely position of this extinct carnivore as a distinct species.
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Papers by Ross Barnett