I investigate the effect of changes in the environment on natural populations. These changes can be across different environments or environmental gradients, or through time. In the extreme, these changes can provoke speciation or extinction. This type of research can be applied to fundamental questions in evolution, and the more specialized areas of conservation biology and domestication. I am particularly interested in how and why so much of the megafauna went extinct (especially in the Americas) at the end of the Pleistocene, about 10,000 years ago. I am also very interested in the opposite process, the evolution and maintenance of the extremely high biodiversity in the tropics.
GENETIC DIVERSITY IN EXTIRPATED US grey WOLVESLegacy lost: genetic variability and population siz... more GENETIC DIVERSITY IN EXTIRPATED US grey WOLVESLegacy lost: genetic variability and population size of extirpated US grey wolves (
An extensive debate concerning the origin and taxonomic status of wolf-like canids in the North A... more An extensive debate concerning the origin and taxonomic status of wolf-like canids in the North American Great Lakes region and the consequences for conservation politics regarding these enigmatic predators is ongoing. Using maternally, paternally and biparentally inherited molecular markers, we demonstrate that the Great Lakes wolves are a unique population or ecotype of gray wolves. Furthermore, we show that the Great Lakes wolves experienced high degrees of ancient and recent introgression of coyote and western gray wolf mtDNA and Y-chromosome haplotypes, and that the recent demographic bottleneck caused by persecution and habitat depletion in the early 1900s is not reflected in the genetic data.
Jennifer A. Leonard,^'^'^ Carles Vilà,^ Kena Fox-Dobbs,* Paul L. Koch," Robert K. Wa... more Jennifer A. Leonard,^'^'^ Carles Vilà,^ Kena Fox-Dobbs,* Paul L. Koch," Robert K. Wayne,^ and Blaire Van Valkenburgh^'* ^ Department of Ecology and Evolutionary Biology University of California Los Angeles, California 90095 ^Genetics Program and Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington, D.C. 20008-0551 ^Department of Evolutionary Biology Uppsala University 75236 Uppsala Sweden '' Department of Earth and Planetary Sciences University of California Santa Cruz, California 95064
clicking here. colleagues, clients, or customers by , you can order high-quality copies for your ... more clicking here. colleagues, clients, or customers by , you can order high-quality copies for your If you wish to distribute this article to others here. following the guidelines can be obtained by Permission to republish or repurpose articles or portions of articles ): January 3, 2012 www.sciencemag.org (this infomation is current as of The following resources related to this article are available online at http://www.sciencemag.org/content/291/5503/474.full.html version of this article at: including high-resolution figures, can be found in the online Updated information and services,
Allee effects reduce the viability of small populations in many different ways, which act synergi... more Allee effects reduce the viability of small populations in many different ways, which act synergistically to lead populations towards extinction vortexes. The Sierra Morena wolf population, isolated in the south of the Iberian Peninsula and composed of just one or few packs for decades, represents a good example of how diverse threats act additively in very small populations. We sequenced the genome of one of the last wolves identified (and road-killed) in Sierra Morena and that of another wolf in the Iberian Wolf Captive Breeding Program and compared them with other wolf and dog genomes from around the world (including two previously published genome sequences from northern Iberian wolves). The results showed relatively low overall genetic diversity in Iberian wolves, but diverse population histories including past introgression of dog genes. The Sierra Morena wolf had an extraordinarily high level of inbreeding and long runs of homozygosity, resulting from the long isolation. In a...
Ancient DNA analyses of historical, archaeological and paleontological remains can contribute imp... more Ancient DNA analyses of historical, archaeological and paleontological remains can contribute important information for the conservation of populations and species that cannot be obtained any other way. In addition to ancient DNA analyses involving a single or few individuals, population level studies are now possible. Biases inherent in estimating population parameters and history from modern genetic diversity are exaggerated when populations are small or have been heavily impacted by recent events, as is common for many endangered species. Going directly back in time to study past populations removes many of the assumptions that undermine conclusions based only on recent populations. Accurate characterization of historic population size, levels of gene flow and relationships with other populations are fundamental to developing appropriate conservation and management plans. The incorporation of ancient DNA into conservation genetics holds a lot of potential, if it is employed respo...
#<p>Note that coyotes and gray wolves might not have been the ones that hybridized directly... more #<p>Note that coyotes and gray wolves might not have been the ones that hybridized directly (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003333#s4" target="_blank">discussion</a>).</p
Aim Pleistocene environmental fluctuations had well-characterized impacts on the patterns of with... more Aim Pleistocene environmental fluctuations had well-characterized impacts on the patterns of within-species divergences and diversity in temperate habitats. Here we examine the impact the Pleistocene had on widely distributed forest vertebrates in a tropical system where the distribution of the habitat was affected by those fluctuations. Location Sundaland, tropical Southeast Asia. Methods We conducted a comparative phylogeographical analysis of 28 non-migratory, forest-dependent vertebrates, for which we constructed rooted, in-traspecifc phylogenies based on mitochondrial DNA sequences of individuals from at least the three major landmasses in the area (Borneo, Sumatra and the Malay Peninsula) and compared them to hypothetical phylogenies based on independent geological data and climate models regarding connections and relationships between the major landmasses of Sundaland. Java was included where possible. We dated the phylogenies to determine whether patterns of dif-
subject to many problems caused primarily by low quality and by low quantity of DNA. For these re... more subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characteriza-tion of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplifi-cation of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occur-red. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were uti-lized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another
A lot of effort has been spent in the last few decades demonstrating that the climate is changing... more A lot of effort has been spent in the last few decades demonstrating that the climate is changing more rapidly now than it did through history and prehistory, and that the reason for this rapid change is anthropogenic action. In addition to climate changes, habitats are being directly modified, and organisms are being directly acted upon. Some species are shifting ranges on a global scale resulting in invasions, causing habitat modifications, impacting interspecific interactions, and generating diseases. Other species are being directly persecuted or overharvested to the point that they are no longer able to function in their communities the way they did historically (Jackson, 2008). This has caused many species to become endangered or even go extinct. The future prospects for many species and habitats are in question. Will species be able to survive such rapid environmental changes? Are they flexible enough to adapt to changes of such magnitude? Can we predict which species are at ...
Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, ... more Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus...
Towards high–throughput analyses of fecal samples from wildlife. High–throughput sequencing offer... more Towards high–throughput analyses of fecal samples from wildlife. High–throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor–intensive steps. We evaluate alternative protocols which could allow higher throughput for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods are tested here on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extracti...
We reconstruct the phylogeny of all recognized species of the tropical forest associated Asian ba... more We reconstruct the phylogeny of all recognized species of the tropical forest associated Asian barbets based on mitochon drial and nuclear sequence data and test for the monophyly of species and genera. Tropical regions are well known for their extr aordinarily high levels of biodiversity, but we still have a poor understanding of how this richness was generated and maintained through evolutionary time. Multiple theoretical frameworks have been developed to explain this diversity, including the Pleistocene pump hypothesis and the museum hypothesis. We use our phylogeny of the Asian barbets to test these hypotheses. Our data do not find an increase in speciation in the Pleistocene as predicted by the Pleistocene pump hypothesis. We do find evidence of extinctions, which apparently contradicts the museum hypothesis. However, the extinctions are only in a part of the phylogeny that is distributed mainly across Sundaland (the Malay peninsula and the islands off southeast Asia). The theo...
Background: Grey wolves (Canis lupus) are a widespread, Holarctic species distributed across a wi... more Background: Grey wolves (Canis lupus) are a widespread, Holarctic species distributed across a wide variety of habitats, including deserts, dry plains, boreal forests, and the high arctic. They are generalist carnivores, feeding on a wide variety of species throughout their range. Wolves also disperse readily, with multiple records of over 1000 km. Despite this, surprising examples of differentiation between contiguous wolf populations have been described. Questions: How can population differentiation arise and be maintained in a continuously distributed, generalist species? How might this structure impact evolution and conservation? Data: Previously published genetic, morphological, and ecological data from ancient, historic, and modern populations of grey wolves from across their distribution. Results: Genetic differentiation of wolf populations is tightly associated with habitat characteristics. This requires that dispersing wolves primarily disperse within their natal habitat. A...
Ecological and conservation genetic studies often use noninvasive sampling, especially with elusi... more Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat...
GENETIC DIVERSITY IN EXTIRPATED US grey WOLVESLegacy lost: genetic variability and population siz... more GENETIC DIVERSITY IN EXTIRPATED US grey WOLVESLegacy lost: genetic variability and population size of extirpated US grey wolves (
An extensive debate concerning the origin and taxonomic status of wolf-like canids in the North A... more An extensive debate concerning the origin and taxonomic status of wolf-like canids in the North American Great Lakes region and the consequences for conservation politics regarding these enigmatic predators is ongoing. Using maternally, paternally and biparentally inherited molecular markers, we demonstrate that the Great Lakes wolves are a unique population or ecotype of gray wolves. Furthermore, we show that the Great Lakes wolves experienced high degrees of ancient and recent introgression of coyote and western gray wolf mtDNA and Y-chromosome haplotypes, and that the recent demographic bottleneck caused by persecution and habitat depletion in the early 1900s is not reflected in the genetic data.
Jennifer A. Leonard,^'^'^ Carles Vilà,^ Kena Fox-Dobbs,* Paul L. Koch," Robert K. Wa... more Jennifer A. Leonard,^'^'^ Carles Vilà,^ Kena Fox-Dobbs,* Paul L. Koch," Robert K. Wayne,^ and Blaire Van Valkenburgh^'* ^ Department of Ecology and Evolutionary Biology University of California Los Angeles, California 90095 ^Genetics Program and Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington, D.C. 20008-0551 ^Department of Evolutionary Biology Uppsala University 75236 Uppsala Sweden '' Department of Earth and Planetary Sciences University of California Santa Cruz, California 95064
clicking here. colleagues, clients, or customers by , you can order high-quality copies for your ... more clicking here. colleagues, clients, or customers by , you can order high-quality copies for your If you wish to distribute this article to others here. following the guidelines can be obtained by Permission to republish or repurpose articles or portions of articles ): January 3, 2012 www.sciencemag.org (this infomation is current as of The following resources related to this article are available online at http://www.sciencemag.org/content/291/5503/474.full.html version of this article at: including high-resolution figures, can be found in the online Updated information and services,
Allee effects reduce the viability of small populations in many different ways, which act synergi... more Allee effects reduce the viability of small populations in many different ways, which act synergistically to lead populations towards extinction vortexes. The Sierra Morena wolf population, isolated in the south of the Iberian Peninsula and composed of just one or few packs for decades, represents a good example of how diverse threats act additively in very small populations. We sequenced the genome of one of the last wolves identified (and road-killed) in Sierra Morena and that of another wolf in the Iberian Wolf Captive Breeding Program and compared them with other wolf and dog genomes from around the world (including two previously published genome sequences from northern Iberian wolves). The results showed relatively low overall genetic diversity in Iberian wolves, but diverse population histories including past introgression of dog genes. The Sierra Morena wolf had an extraordinarily high level of inbreeding and long runs of homozygosity, resulting from the long isolation. In a...
Ancient DNA analyses of historical, archaeological and paleontological remains can contribute imp... more Ancient DNA analyses of historical, archaeological and paleontological remains can contribute important information for the conservation of populations and species that cannot be obtained any other way. In addition to ancient DNA analyses involving a single or few individuals, population level studies are now possible. Biases inherent in estimating population parameters and history from modern genetic diversity are exaggerated when populations are small or have been heavily impacted by recent events, as is common for many endangered species. Going directly back in time to study past populations removes many of the assumptions that undermine conclusions based only on recent populations. Accurate characterization of historic population size, levels of gene flow and relationships with other populations are fundamental to developing appropriate conservation and management plans. The incorporation of ancient DNA into conservation genetics holds a lot of potential, if it is employed respo...
#<p>Note that coyotes and gray wolves might not have been the ones that hybridized directly... more #<p>Note that coyotes and gray wolves might not have been the ones that hybridized directly (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003333#s4" target="_blank">discussion</a>).</p
Aim Pleistocene environmental fluctuations had well-characterized impacts on the patterns of with... more Aim Pleistocene environmental fluctuations had well-characterized impacts on the patterns of within-species divergences and diversity in temperate habitats. Here we examine the impact the Pleistocene had on widely distributed forest vertebrates in a tropical system where the distribution of the habitat was affected by those fluctuations. Location Sundaland, tropical Southeast Asia. Methods We conducted a comparative phylogeographical analysis of 28 non-migratory, forest-dependent vertebrates, for which we constructed rooted, in-traspecifc phylogenies based on mitochondrial DNA sequences of individuals from at least the three major landmasses in the area (Borneo, Sumatra and the Malay Peninsula) and compared them to hypothetical phylogenies based on independent geological data and climate models regarding connections and relationships between the major landmasses of Sundaland. Java was included where possible. We dated the phylogenies to determine whether patterns of dif-
subject to many problems caused primarily by low quality and by low quantity of DNA. For these re... more subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characteriza-tion of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplifi-cation of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occur-red. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were uti-lized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another
A lot of effort has been spent in the last few decades demonstrating that the climate is changing... more A lot of effort has been spent in the last few decades demonstrating that the climate is changing more rapidly now than it did through history and prehistory, and that the reason for this rapid change is anthropogenic action. In addition to climate changes, habitats are being directly modified, and organisms are being directly acted upon. Some species are shifting ranges on a global scale resulting in invasions, causing habitat modifications, impacting interspecific interactions, and generating diseases. Other species are being directly persecuted or overharvested to the point that they are no longer able to function in their communities the way they did historically (Jackson, 2008). This has caused many species to become endangered or even go extinct. The future prospects for many species and habitats are in question. Will species be able to survive such rapid environmental changes? Are they flexible enough to adapt to changes of such magnitude? Can we predict which species are at ...
Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, ... more Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus...
Towards high–throughput analyses of fecal samples from wildlife. High–throughput sequencing offer... more Towards high–throughput analyses of fecal samples from wildlife. High–throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor–intensive steps. We evaluate alternative protocols which could allow higher throughput for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods are tested here on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extracti...
We reconstruct the phylogeny of all recognized species of the tropical forest associated Asian ba... more We reconstruct the phylogeny of all recognized species of the tropical forest associated Asian barbets based on mitochon drial and nuclear sequence data and test for the monophyly of species and genera. Tropical regions are well known for their extr aordinarily high levels of biodiversity, but we still have a poor understanding of how this richness was generated and maintained through evolutionary time. Multiple theoretical frameworks have been developed to explain this diversity, including the Pleistocene pump hypothesis and the museum hypothesis. We use our phylogeny of the Asian barbets to test these hypotheses. Our data do not find an increase in speciation in the Pleistocene as predicted by the Pleistocene pump hypothesis. We do find evidence of extinctions, which apparently contradicts the museum hypothesis. However, the extinctions are only in a part of the phylogeny that is distributed mainly across Sundaland (the Malay peninsula and the islands off southeast Asia). The theo...
Background: Grey wolves (Canis lupus) are a widespread, Holarctic species distributed across a wi... more Background: Grey wolves (Canis lupus) are a widespread, Holarctic species distributed across a wide variety of habitats, including deserts, dry plains, boreal forests, and the high arctic. They are generalist carnivores, feeding on a wide variety of species throughout their range. Wolves also disperse readily, with multiple records of over 1000 km. Despite this, surprising examples of differentiation between contiguous wolf populations have been described. Questions: How can population differentiation arise and be maintained in a continuously distributed, generalist species? How might this structure impact evolution and conservation? Data: Previously published genetic, morphological, and ecological data from ancient, historic, and modern populations of grey wolves from across their distribution. Results: Genetic differentiation of wolf populations is tightly associated with habitat characteristics. This requires that dispersing wolves primarily disperse within their natal habitat. A...
Ecological and conservation genetic studies often use noninvasive sampling, especially with elusi... more Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat...
Uploads
Papers by Jennifer A Leonard