Biologists focus on thermoregulation of desert mammals in terms of how they minimise heat gain du... more Biologists focus on thermoregulation of desert mammals in terms of how they minimise heat gain during hotter months, and put less effort on how they maximise heat gain during cooler months. Heat gain may contribute to energy savings of desert mammals during cooler period when the ambient temperature in desert is substantially lower than their body temperatures. We investigated the thermoregulation in free-ranging Ethiopian hedgehogs, Paraechinus aethiopicus, during winter using radio-telemetry in Qatar. Temperatures detected by the tag attached to hedgehogs were significantly higher than ambient temperatures throughout the day, and the difference was more extreme during the mid-day. We also observed several hedgehogs basking with their radio-tags exposed to direct sunlight. It is possible that basking is beneficial for the hedgehog's winter thermoregulation in the desert where plenty of solar radiation is available.
The family of Erinaceidae comprises 26 extant species in the subfamily Erinaceinae of spiny hedge... more The family of Erinaceidae comprises 26 extant species in the subfamily Erinaceinae of spiny hedgehogs and the subfamily Galericinae of silky-furred gymnures and moonrats. These animals inhabit various habitats from tropical forests to deserts in Eurasia and Africa. Previous studies hinted that species diversity was likely underestimated. Moreover, erinaceids are among the oldest known living placental mammals originating more than 60 million years ago. The rich fossil records represent both living subfamilies and an extinct subfamily Brachyericinae. Comprehensive understanding of evolutionary history and taxonomic diversity is hampered by the unavailability of samples and the incorporation of molecular and morphological data. Here, we sequenced mitochondrial genomes from museum specimens and morphological data to reconstruct the genealogical relationships of Erinaceidae. Our results finely resolved interspecific relationships of living species and unveiled underestimated species div...
The contrast between the tiger’s (Panthera tigris) 2-3 My age and extant tigers’ coalescence appr... more The contrast between the tiger’s (Panthera tigris) 2-3 My age and extant tigers’ coalescence approximately 110,000 years ago suggests an ancient demographic bottleneck. Here we collected over 60 extinct specimens across mainland Asia and generated whole genome sequences from a 10,600-year-old Russian Far East (RFE) specimen (RUSA21, 8ξ coverage), 14 South China tigers (0.1-12ξ), three Caspian tigers (4-8ξ), plus 17 new mitogenomes. RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some 8,000-10,000-year-old RFE mitogenomes are basal to all tigers, one 2,000-year-old specimen resembles present Amur tigers. The Caspian tiger likely dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic co...
The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely ... more The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely rare species with a distribution limited to a small part of the island of Cuba. Despite its rarity, in 2012 seven individuals of S. cubanus were captured and sampled successfully for DNA analysis, providing new insights into the evolutionary origin of this species and into the origins of the Caribbean fauna, which remain controversial. We conducted molecular phylogenetic analyses of five nuclear genes (Apob, Atp7a, Bdnf, Brca1 and Rag1; total, 4,602 bp) from 35 species of the mammalian order Eulipotyphla. Based on Bayesian relaxed molecular clock analyses, the family Solenodontidae diverged from other eulipotyphlan in the Paleocene, after the bolide impact on the Yucatan Peninsula, and S. cubanus diverged from the Hispaniolan solenodon (S. paradoxus) in the Early Pliocene. The strikingly recent divergence time estimates suggest that S. cubanus and its ancestral lineage originated via ove...
In natural history collections throughout Europe, there are many old lion specimens of unknown or... more In natural history collections throughout Europe, there are many old lion specimens of unknown origin. If these specimens can be shown to have originated from now-extinct populations their value would significantly increase, as would the value of the collections. Recently, a 200-year old mounted skeleton in the Zoological Museum Amsterdam has been identified as the extinct Cape lion Panthera leo melanochaita (Smith, 1842), based primarily on morphological information inferred from a painting of this specimen while it was still alive. To test this hypothesis, we used ancient DNA (aDNA) techniques to extract and sequence mitochondrial DNA (mtDNA) from this specimen, and compared the genetic results with previously published lion mtDNA sequences. Our results show that the specimen is not a Cape lion, but that it instead possesses the mtDNA haplotype of the Asiatic lions P. l. persica (Meyer, 1826) from India. This Indian origin hypothesis is further supported by an investigation of its...
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundate... more The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far north-east Asia) and Eastern Beringia (north-west North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation, and vegetation, impacting faunal community structure and demography. While these paleoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyze mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal c...
Proceedings of the National Academy of Sciences, 2020
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...
A divided infraorbital foramen is an important morphological feature in lion taxonomy and has pre... more A divided infraorbital foramen is an important morphological feature in lion taxonomy and has previously been considered to occur only in the Asian lion, Panthera leo persica. Based on an examination of 498 lion skulls from museum collections in Europe and southern Africa, we report for the first time on the prevalence of the divided infraorbital foramen in African lions, as well as its occurrence in the tiger, P. tigris and the extinct Pleistocene European cave lion, P. leo spelaea. The higher frequency of this characteristic in Asian lions may have occurred after the lion colonised Asia, and can be considered an important morphological feature characterising this population. It is not clear whether recent anthropogenic population bottlenecks have influenced changes in its prevalence over the last 200 years.
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populat... more Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern...
The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct ti... more The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating litter o...
Biologists focus on thermoregulation of desert mammals in terms of how they minimise heat gain du... more Biologists focus on thermoregulation of desert mammals in terms of how they minimise heat gain during hotter months, and put less effort on how they maximise heat gain during cooler months. Heat gain may contribute to energy savings of desert mammals during cooler period when the ambient temperature in desert is substantially lower than their body temperatures. We investigated the thermoregulation in free-ranging Ethiopian hedgehogs, Paraechinus aethiopicus, during winter using radio-telemetry in Qatar. Temperatures detected by the tag attached to hedgehogs were significantly higher than ambient temperatures throughout the day, and the difference was more extreme during the mid-day. We also observed several hedgehogs basking with their radio-tags exposed to direct sunlight. It is possible that basking is beneficial for the hedgehog's winter thermoregulation in the desert where plenty of solar radiation is available.
The family of Erinaceidae comprises 26 extant species in the subfamily Erinaceinae of spiny hedge... more The family of Erinaceidae comprises 26 extant species in the subfamily Erinaceinae of spiny hedgehogs and the subfamily Galericinae of silky-furred gymnures and moonrats. These animals inhabit various habitats from tropical forests to deserts in Eurasia and Africa. Previous studies hinted that species diversity was likely underestimated. Moreover, erinaceids are among the oldest known living placental mammals originating more than 60 million years ago. The rich fossil records represent both living subfamilies and an extinct subfamily Brachyericinae. Comprehensive understanding of evolutionary history and taxonomic diversity is hampered by the unavailability of samples and the incorporation of molecular and morphological data. Here, we sequenced mitochondrial genomes from museum specimens and morphological data to reconstruct the genealogical relationships of Erinaceidae. Our results finely resolved interspecific relationships of living species and unveiled underestimated species div...
The contrast between the tiger’s (Panthera tigris) 2-3 My age and extant tigers’ coalescence appr... more The contrast between the tiger’s (Panthera tigris) 2-3 My age and extant tigers’ coalescence approximately 110,000 years ago suggests an ancient demographic bottleneck. Here we collected over 60 extinct specimens across mainland Asia and generated whole genome sequences from a 10,600-year-old Russian Far East (RFE) specimen (RUSA21, 8ξ coverage), 14 South China tigers (0.1-12ξ), three Caspian tigers (4-8ξ), plus 17 new mitogenomes. RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some 8,000-10,000-year-old RFE mitogenomes are basal to all tigers, one 2,000-year-old specimen resembles present Amur tigers. The Caspian tiger likely dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic co...
The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely ... more The Cuban solenodon (Solenodon cubanus) is one of the most enigmatic mammals and is an extremely rare species with a distribution limited to a small part of the island of Cuba. Despite its rarity, in 2012 seven individuals of S. cubanus were captured and sampled successfully for DNA analysis, providing new insights into the evolutionary origin of this species and into the origins of the Caribbean fauna, which remain controversial. We conducted molecular phylogenetic analyses of five nuclear genes (Apob, Atp7a, Bdnf, Brca1 and Rag1; total, 4,602 bp) from 35 species of the mammalian order Eulipotyphla. Based on Bayesian relaxed molecular clock analyses, the family Solenodontidae diverged from other eulipotyphlan in the Paleocene, after the bolide impact on the Yucatan Peninsula, and S. cubanus diverged from the Hispaniolan solenodon (S. paradoxus) in the Early Pliocene. The strikingly recent divergence time estimates suggest that S. cubanus and its ancestral lineage originated via ove...
In natural history collections throughout Europe, there are many old lion specimens of unknown or... more In natural history collections throughout Europe, there are many old lion specimens of unknown origin. If these specimens can be shown to have originated from now-extinct populations their value would significantly increase, as would the value of the collections. Recently, a 200-year old mounted skeleton in the Zoological Museum Amsterdam has been identified as the extinct Cape lion Panthera leo melanochaita (Smith, 1842), based primarily on morphological information inferred from a painting of this specimen while it was still alive. To test this hypothesis, we used ancient DNA (aDNA) techniques to extract and sequence mitochondrial DNA (mtDNA) from this specimen, and compared the genetic results with previously published lion mtDNA sequences. Our results show that the specimen is not a Cape lion, but that it instead possesses the mtDNA haplotype of the Asiatic lions P. l. persica (Meyer, 1826) from India. This Indian origin hypothesis is further supported by an investigation of its...
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundate... more The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far north-east Asia) and Eastern Beringia (north-west North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation, and vegetation, impacting faunal community structure and demography. While these paleoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyze mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal c...
Proceedings of the National Academy of Sciences, 2020
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...
A divided infraorbital foramen is an important morphological feature in lion taxonomy and has pre... more A divided infraorbital foramen is an important morphological feature in lion taxonomy and has previously been considered to occur only in the Asian lion, Panthera leo persica. Based on an examination of 498 lion skulls from museum collections in Europe and southern Africa, we report for the first time on the prevalence of the divided infraorbital foramen in African lions, as well as its occurrence in the tiger, P. tigris and the extinct Pleistocene European cave lion, P. leo spelaea. The higher frequency of this characteristic in Asian lions may have occurred after the lion colonised Asia, and can be considered an important morphological feature characterising this population. It is not clear whether recent anthropogenic population bottlenecks have influenced changes in its prevalence over the last 200 years.
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populat... more Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern...
The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct ti... more The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating litter o...
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