Identification of source‐sink dynamics in mountain lions of the Great Basin

Natural and anthropogenic boundaries have been shown to affect population dynamics and population structure for many species with movement patterns at the landscape level. Understanding population boundaries and movement rates in the field for species that are cryptic and occur at low densities is often extremely difficult and logistically prohibitive; however genetic techniques may offer insights that have previously been unattainable. We analysed thirteen microsatellite loci for 739 mountain lions (Puma concolor) using muscle tissue samples from individuals in the Great Basin throughout Nevada and the Sierra Nevada mountain range to test the hypothesis that heterogeneous hunting pressure results in source‐sink dynamics at the landscape scale. We used a combination of non‐spatial and spatial model‐based Bayesian clustering methods to identify genetic populations. We then used a recently developed Bayesian multilocus genotyping method to estimate asymmetrical rates of contemporary movement between those subpopulations and to identify source and sink populations. We identified two populations at the highest level of genetic structuring with a total of five subpopulations in the Great Basin of Nevada and the Sierra Nevada range. Our results suggest that source‐sink dynamics occur at landscape scales for wide‐ranging species, such as mountain lions, and that source populations may be those that are under relatively less hunting pressure and that occupy refugia.     

Using Mountain Lion Habitat Selection in Management

Wildlife agencies are generally tasked with managing and conserving species at state and local levels simultaneously. Thus, it is necessary for wildlife agencies to understand basic ecological processes of a given species at multiple scales to aid decision making at commensurately varied spatial and behavioral scales. Mountain lions (Puma concolor) occur throughout California, USA, and are at the center of a variety of management and conservation issues. For example, they are genetically and demographically at risk in 1 region yet apparently stable and negatively affecting endangered species in another. Currently, no formal plan exists for mountain lions in California to deal with these diverse scenarios involving issues of local mountain lion population viability and problems related to predation of endangered species. To facilitate development of a state-wide management and conservation plan, we quantified habitat selection by mountain lions at 2 spatial scales across the range of environmental conditions in which the species is found in California. Our analyses used location data from individuals (n = 263) collared across the state from 2001–2019. At the home range scale, mountain lions selected habitat to prioritize meeting energetic demands. At the within home range scale, mountain lions avoided areas of human activity. Further, our analyses revealed 165,350–170,085 km², depending on season, of suitable mountain lion habitat in California. Fifty percent of the suitable habitat was on unprotected lands and thus vulnerable to development. These habitat selection models will help in the development of a state-wide conservation and management plan for mountain lions in California by guiding mountain lion population monitoring through time, prioritization of habitat to be conserved for maintaining demographic connectivity and gene flow, and efforts to mediate mountain lion-prey interactions. Our work and application area will help with wildlife policy and management decisions related to depredation problems at the local scale and issues of habitat connectivity at the statewide scale. © 2019 The Wildlife Society.     

Where do you come from,where do you go? Directional migration rates in landscape genetics

Identifying landscape elements that influence gene flow and migration in wild species is the current main topic of landscape genetics. Most landscape genetic studies infer gene flow and migration from genetic distances among populations or individuals and statistically relate these measurements to landscape composition and configuration. This approach assumes symmetrical gene flow between pairs of populations. Such an assumption, however, will often be violated, especially in source–sink systems. Source populations provide more emigrants than they receive immigrants, and sink populations get many immigrants, but release few emigrants. Source–sink dynamics cannot be explored using common landscape genetic approaches relying on genetic distances. In this issue of Molecular Ecology, Andreasen et al. ( 2012 ) apply an alternative approach allowing them to infer asymmetrical migration. They use a Bayesian assignment test among objectively defined populations of mountain lions (Puma concolor) in western USA to estimate recent and directional migration rates. The study shows that an area with a high amount of wildlife refuges and low hunting pressure harbours a source population for mountain lion dispersal, while areas with high hunting pressures form sink populations; a result helpful in making informed decisions in conservation management.     

Effects of slope and riparian habitat connectivity on gene flow in an endangered Panamanian frog, Atelopus varius

Aim Understanding how heterogeneous landscapes shape genetic structure not only sheds light on processes involved in population divergence and speciation, but can also guide management strategies to promote and maintain genetic connectivity of populations of endangered species. This study aimed to (1) identify barriers and corridors for gene flow among populations of the endangered frog, Atelopus varius and (2) assess the relative contributions of alternative landscape factors to patterns of genetic variation among these populations in a hypothesis testing framework. Location This study took place in western Panama and included all nine of the remaining known populations of A. varius at the time of study. Methods The influence of landscape variables on gene flow among populations was examined by testing for correlations between alternative landscape‐resistance scenarios and genetic distance. Fifteen alternative hypotheses about the influence of (1) riparian habitat corridors, (2) steep slopes, and (3) climatic suitability on patterns of genetic structure were tested in a causal modelling framework, using Mantel and partial‐Mantel tests, along with an analysis of molecular variation. Results Only the hypothesis attributing resistance to dispersal across steep slopes (genetic isolation by slope distance) was fully supported by the causal modelling approach. However, the analysis of molecular variance and the paths of least‐slope among populations suggest that riparian habitat connectivity may influence genetic structure as well. Main conclusions These results suggest that patterns of genetic variation among A. varius populations are affected by the slope of the landscape such that areas with steep slopes act as barriers to gene flow. In contrast, areas of low slope, such as streams and mountain ridges, appear to be important corridors for gene flow, especially among high elevation populations. These results engender important considerations for the management of this critically endangered species.     

Desert bighorn sheep habitat selection,group size,and mountain lion predation risk

Bighorn sheep (Ovis canadensis) evolved for thousands of years in the presence of numerous predators, including mountain lions (Puma concolor). Bighorn sheep have presumably developed predator avoidance strategies; however, the effectiveness of these strategies in reducing risk of mountain lion predation is not well understood. These strategies are of increasing interest because mountain lion predation on bighorn sheep has been identified as a leading cause of mortality in some sheep populations. Therefore, we investigated how mountain lions affect both bighorn sheep habitat selection and risk of mortality in Arizona, USA. We used 2 approaches to investigate the predator-prey relationship between mountain lions and bighorn sheep. We fit 103 bighorn sheep (81 females and 22 males) with global positioning system radio-collars in 2 Arizona populations from 2013 to 2017, and used a negative binomial resource selection probability function to evaluate whether bighorn sheep selected for habitat features in accordance with presumed predator avoidance strategies, including terrain ruggedness, slope, topographic position, and horizontal obstruction, in 2 seasons (winter and summer). We then estimated how habitat features such as terrain ruggedness, slope, horizontal obstruction, and group size, influence the risk of mortality due to mountain lion predation using an Andersen-Gill proportional hazards model. Generally, both sexes selected areas with lower horizontal obstruction and intermediate ruggedness and slope, but selection patterns differed between seasons and sexes. The use of more rugged areas and steeper slopes decreased the risk of mortality due to mountain lion predation, consistent with presumed predator avoidance strategies. Increased group size decreased risk of bighorn sheep mortality due to mountain lion predation but this effect became marginal at approximately 10 individuals/group. We did not identify a relationship between horizontal obstruction and bighorn sheep mortality risk. Our findings can be used in habitat and population management decisions such as the prioritization of habitat restoration sites or selection of translocation sites. In addition, we suggest that augmentation of low-density bighorn sheep populations may reduce mountain lion predation risk by increasing group size, and that releasing large groups of bighorn sheep in population augmentation and reintroduction efforts may help to reduce mountain lion predation.     

Mountain lions on the prairie: habitat selection by recolonizing mountain lions at the edge of their range

Mountain lions (Puma concolor) have historically experienced large‐scale range contractions, but are beginning to recolonize portions of their former range. To reach potential suitable habitats in eastern North America, mountain lions need to move across the grassland and agriculture‐dominated habitats of the Great Plains, which are different from the forested areas associated with mountain lions in western North America. To inform restoration planning in this area, it is important to understand differences in mountain lion habitat selection in this “nontraditional” grassland habitat. We tracked GPS‐collared mountain lions in the Northern Great Plains of Montana and identified movement states (localized or exploratory) using behavioral change point analysis and net‐squared displacement. We compared habitat selection between the different states using step‐selection functions that included several environmental covariates. Similar to elsewhere throughout their range, across both movement states, mountain lions tended to select forested environments that were farther from human development. In contrast to more traditionally occupied mountainous regions, mountain lions in the Great Plains selected areas of lower elevations. They selected areas both near and far from water, but avoided riparian areas and selected more rugged environments when in exploratory movement states. This suggests that mountain lions in the Northern Great Plains are utilizing river corridors, particularly those with rough or broken topography during exploratory phases. To enhance future recolonization and connectivity of mountain lions to the east of our study area, we encourage managers to maintain and restore forest fragments along river corridors in the Great Plains.     

The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics

The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV(Ple)), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA Phi(ST) = 0.92; nDNA F(ST) = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIV(Ple) subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa ( approximately 324,000-169,000 years ago), which expanded during the Late Pleistocene ( approximately 100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition ( approximately 14,000-7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV(Ple) variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.     

Geological barriers and restricted gene flow in the holarctic skipper Hesperia comma (Hesperiidae)

Patterns of genetic variation within a species may be a consequence of historical factors, such as past fragmentation, as well as current barriers to gene flow. Using sequence data from the mitochondrial cytochrome oxidase subunit II region (COII) and the nuclear gene wingless, we conducted a phylogeographical study of the holarctic skipper Hesperia comma to elucidate patterns of genetic diversity and to infer historical and contemporary processes maintaining genetic variation. One hundred and fifty-one individuals were sampled from throughout North America and Eurasia, focusing on California and adjacent regions in the western United States where morphological diversity is highest compared to the rest of the range. Analyses of sequence data obtained from both genes revealed a well-supported division between the Old and New World. Within western North America, wingless shows little geographical structure, while a hierarchical analysis of genetic diversity of COII sequences indicates three major clades: a western clade in Oregon and Northern California, an eastern clade including the Great Basin, Rocky Mountains and British Columbia, and a third clade in southern California. The Sierra Nevada and the Transverse Ranges appear to be the major barriers to gene flow for H. comma in the western United States. Relatively reduced haplotype diversity in Eurasia compared to North America suggests that populations on the two continents have been affected by different historical processes.     

Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity

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.     

Long-distance dispersal vs vicariance: the origin and genetic diversity of alpine plants in the Spanish Sierra Nevada

Here, we investigated the origin and genetic diversity of four alpine plant species co-occurring in the Spanish Sierra Nevada and other high mountains in south-western Europe by analysis of amplified fragment length polymorphisms (AFLPs). In Kernera saxatilis, Silene rupestris and Gentiana alpina we found intraspecific phylogroups corresponding to mountain regions as predicted by the vicariance hypothesis. Moreover, genetic distances between Sierra Nevada and Pyrenees populations were always higher than those between populations from the Pyrenees and the south-western Alps/Massif Central. This suggests successive disruption of gene exchange between mountain ranges as postglacial climatic warming proceeded from south to north. In Papaver alpinum, our data indicate that a central Pyrenean population arose via long-distance dispersal from the Sierra Nevada, and that vicariant separation events between the Sierra Nevada and the Pyrenees and between the Pyrenees and the south-western Alps occurred simultaneously. Overall, Sierra Nevada populations of all species investigated here preserve unexpectedly high (or not exceptionally reduced) genetic diversity. This testifies to the important influence of long-term isolation, i.e. vicariance, on genetic diversity through fostering the accumulation of new mutations and/or the fixation of ancestral ones.     

Evidence for African origins of founders of the asiatic lion species survival plan

The Asiatic lion (Panthera leo persica) exists in the wild as a single relict population of approximately 250 individuals in the protected Gir Forest Sanctuary in western India. In 1981, a species survival plan (SSP) for the Asiatic lion was established by the American Association of Zoological Parks and Aquariums to manage the 200 + descendants of Asiatic lions in captivity in western zoological facilities. This captive population was derived from seven founders. In order to compare the genetic structure of the Gir Forest population with that of the captive SSP population, a genetic survey of 46 electrophoretic allozyme systems resolved from extracts of lion blood was undertaken by using 29 SSP Asiatic lions and 28 wild-caught or captive-bred lions maintained at the Sakkarbaug Zoo in India but originally derived from the Gir Forest. The Gir lion population was found to be genetically monomorphic at each of 46 allozyme loci. This was in contrast to several African lion (Panthera leo leo) populations, which show moderate levels of allozyme variation at the same loci. The SSP lion population was polymorphic at three allozyme loci (IDHI, TF, and PTI) for alleles that were previously found only in African lion populations. Pedigree analysis of the genetic transmission of these three biochemical loci demonstrated that two of the five primary founder animals of the SSP Asiatic lion population (a breeding pair originally imported from the Trivandrum Zoo in southern India) were descendants of the African subspecies. Three other founder animals were pure Asian. A retrospective SSP pedigree analysis of two morphologic characters (prominent abdominal fold and pairing of infraorbital foramen) that are partially diagnostic for persica vs leo was consistent with this conclusion as well. The implications for the management of small captive populations of threatened species and of the Asiatic lion SSP population are discussed.     

A genetically distinct lion (Panthera leo) population from Ethiopia

Lion (Panthera leo) numbers are in serious decline and two of only a handful of evolutionary significant units have already become extinct in the wild. However, there is continued debate about the genetic distinctiveness of different lion populations, a discussion delaying the initiation of conservation actions for endangered populations. Some lions from Ethiopia are phenotypically distinct from other extant lions in that the males possess an extensive dark mane. In this study, we investigated the microsatellite variation over ten loci in 15 lions from Addis Ababa Zoo in Ethiopia. A comparison with six wild lion populations identifies the Addis Ababa lions as being not only phenotypically but also genetically distinct from other lions. In addition, a comparison of the mitochondrial cytochrome b (CytB) gene sequence of these lions to sequences of wild lions of different origins supports the notion of their genetic uniqueness. Our examination of the genetic diversity of this captive lion population shows little effect of inbreeding. Immediate conservation actions, including a captive breeding programme designed to conserve genetic diversity and maintain the lineage, are urgently needed to preserve this unique lion population.     

Individual Identification and Genetic Variation of Lions (Panthera leo) from Two Protected Areas in Nigeria

This survey was conducted in two protected areas in Nigeria to genetically identify individual lions and to determine the genetic variation within and between the populations. We used faecal sample DNA, a non-invasive alternative to the risky and laborious task of taking samples directly from the animals, often preceded by catching and immobilization. Data collection in Yankari Game Reserve (YGR) spanned through a period of five years (2008 –2012), whereas data in Kainji Lake National Park (KLNP) was gathered for a period of three years (2009, 2010 and 2012). We identified a minimum of eight individuals (2 males, 3 females, 3 unknown) from YGR and a minimum of ten individuals (7 males, 3 females) from KLNP. The two populations were found to be genetically distinct as shown by the relatively high fixation index (F_ST  = 0.17) with each population exhibiting signs of inbreeding (YGR F_IS  = 0.49, KLNP F_IS  = 0.38). The genetic differentiation between the Yankari and Kainji lions is assumed to result from large spatial geographic distance and physical barriers reducing gene flow between these two remaining wild lion populations in Nigeria. To mitigate the probable inbreeding depression in the lion populations within Nigeria it might be important to transfer lions between parks or reserves or to reintroduce lions from the zoos back to the wild.     

Granulocytic ehrlichiosis and tick infestation in mountain lions in California

Forty-seven mountain lions (Puma concolor) collected year-round in 1996 to 1998 from the Sierra Nevada foothills, the northern coast ranges, and in Monterey County (California, USA) were examined for infestation with Ixodes pacificus and Dermacentor variabilis ticks. Ticks were found predominantly in winter and spring. The seroprevalence of granulocytic ehrlichiae (GE) antibodies (Ehrlichia equi or the agent of human granulocytic ehrlichiosis) was 17% and the PCR-prevalence of DNA characteristic of GE in blood was 16%. There were eight polymerase chain reaction (PCR)-positive but seronegative mountain lions, one that was PCR-positive and seropositive, and eight that were PCR-negative and seropositive. Nineteen percent of engorged tick pools from mountain lions were PCR-positive. Because mountain lions inhabit tick-infested habitat and are frequently bitten by I. pacificus, surveillance for GE antibodies and DNA in mountain lions and other vertebrate hosts may be useful as indicators for geographical regions in which humans are at risk of GE infection.     

Genetic consequences of habitat fragmentation and loss: the case of the Florida black bear (<Emphasis Type="Italic">Ursus americanus floridanus</Emphasis>)

Habitat loss and fragmentation can influence the genetic structure of biological populations. We studied the genetic consequences of habitat fragmentation in Florida black bear (Ursus americanus floridanus) populations. Genetic samples were collected from 339 bears, representing nine populations. Bears were genotyped for 12 microsatellite loci to estimate genetic variation and to characterize genetic structure. None of the nine study populations deviated from Hardy–Weinberg equilibrium. Genetic variation, quantified by mean expected heterozygosity (H _E), ranged from 0.27 to 0.71 and was substantially lower in smaller and less connected populations. High levels of genetic differentiation among populations (global F _ST = 0.224; global R _ST = 0.245) suggest that fragmentation of once contiguous habitat has resulted in genetically distinct populations. There was no isolation-by-distance relationship among Florida black bear populations, likely because of barriers to gene flow created by habitat fragmentation and other anthropogenic disturbances. These factors resulted in genetic differentiation among populations, even those that were geographically close. Population assignment tests indicated that most individuals were genetically assigned to the population where they were sampled. Habitat fragmentation and anthropogenic barriers to movement appear to have limited the dispersal capabilities of the Florida black bear, thereby reducing gene flow among populations. Regional corridors or translocation of bears may be needed to restore historical levels of genetic variation. Our results suggest that management actions to mitigate genetic consequences of habitat fragmentation are needed to ensure long-term persistence of the Florida black bear.     

Population structure of an endangered frog (<Emphasis Type="Italic">Babina subaspera</Emphasis>) endemic to the Amami Islands: possible impacts of invasive predators on gene flow

The otton frog (Babina subaspera) is an endangered species endemic to the Amami Islands, Japan. High predation pressure from an introduced carnivore, the mongoose, has caused declines in the frog populations and created a large habitat gap around an urban area. To promote effective conservation, we investigated the genetic status of the species and examined the effect of the habitat gap on gene flow among populations. Using five polymorphic microsatellite loci and mitochondrial DNA sequences, we investigated genetic diversity, genetic structure and gene flow in B. subaspera populations on the islands of Amami-Oshima and Kakeroma-jima. The expected heterozygosity (H _E) within each locality was generally high (range: 0.67–0.85), indicating that B. subaspera maintains high genetic diversity. However, genetic differentiation was observed, and the two populations, TAG and KAR, showed little gene flow with other populations. The clustering and F _ST analyses also predicted that these two populations were clearly distinct. According to the mitochondrial DNA analysis, the observed genetic differentiation occurred relatively recently. Possible barriers such as mountain ridges, rivers or roads did not result in genetic separation of the populations. These data support the hypothesis that the habitat gap created by an introduced predator prevented the gene flow among B. subaspera populations. When developing conservation strategies for B. subaspera, focus should be directed to these two isolated populations; careful monitoring of population size and genetic diversity should be conducted along with the mongoose elimination project ensues.     

Genomic scanning using AFLP to detect loci under selection in the moss Funaria hygrometrica along a climate gradient in the Sierra Nevada Mountains,Spain

The common cord moss Funaria hygrometrica has a worldwide distribution and thrives in a wide variety of environments. Here, we studied the genetic diversity in F. hygrometrica along an abiotic gradient in the Mediterranean high mountain of Sierra Nevada (Spain) using a genome scan method. Eighty‐four samples from 17 locations from 24 to 2700 m were fingerprinted based on their amplified fragment length polymorphism (AFLP) banding pattern. Using PCA and Bayesian inference we found that the genetic diversity was structured in three or four clusters, respectively. Using a genome scan method we identified 13 outlier loci, which showed a signature of positive selection. Partial Mantel tests were performed between the Euclidean distance matrices of geographic and climatic variables, versus the pair‐wise genetic distance of the AFLP dataset and AFLP‐positive outliers dataset. AFLP‐positive outlier data were significantly correlated with the gradient of the climatic variables, suggesting adaptive variation among populations of F. hygrometrica along the Sierra Nevada Mountains. We highlight the additional analyses necessary to identify the nature of these loci, and their biological role in the adaptation process.     

Dual phylogenetic origins of Nigerian lions (Panthera leo)

Lion fecal DNA extracts from four individuals each from Yankari Game Reserve and Kainji‐Lake National Park (central northeast and west Nigeria, respectively) were Sanger‐sequenced for the mitochondrial cytochrome b gene. The sequences were aligned against 61 lion reference sequences from other parts of Africa and India. The sequence data were analyzed further for the construction of phylogenetic trees using the maximum‐likelihood approach to depict phylogenetic patterns of distribution among sequences. Our results show that Nigerian lions grouped together with lions from West and Central Africa. At the smaller geographical scale, lions from Kainji‐Lake National Park in western Nigeria grouped with lions from Benin (located west of Nigeria), whereas lions from Yankari Game Reserve in central northeastern Nigeria grouped with the lion populations in Cameroon (located east of Nigeria). The finding that the two remaining lion populations in Nigeria have different phylogenetic origins is an important aspect to consider in future decisions regarding management and conservation of rapidly shrinking lion populations in West Africa.     

Genetic evidence for the persistence of the critically endangered Sierra Nevada red fox in California

California is home to both the native state-threatened Sierra Nevada red fox (Vulpes vulpes necator), which historically inhabited high elevations of the Sierra Nevada and Cascade mountains, and to multiple low-elevation red fox populations thought to be of exotic origin. During the past few decades the lowland populations have dramatically expanded their distribution, and possibly moved into the historic range of the native high-elevation fox. To determine whether the native red fox persists in its historic range in California, we compared mitochondrial cytochrome-b haplotypes of the only currently-known high-elevation population (n = 9 individuals) to samples from 3 modern lowland populations (n = 35) and historic (1911–1941) high-elevation (n = 22) and lowland (n = 7) populations. We found no significant population differentiation among the modern and historic high-elevation populations (average pairwise F _ST = 0.06), but these populations differed substantially from all modern and historic lowland populations (average pairwise F _ST = 0.52). Among lowland populations, the historic and modern Sacramento Valley populations were not significantly differentiated from one another (F _ST = −0.06), but differed significantly from recently founded populations in the San Francisco Bay region and in southern California (average pairwise F _ST = 0.42). Analysis of molecular variance indicated that 3 population groupings (mountain, Sacramento Valley, and other lowland regions) explained 45% of molecular variance (F _CT = 0.45) whereas only 4.5% of the variance was partitioned among populations within these groupings (F _SC = 0.08). These findings provide strong evidence that the native Sierra Nevada red fox has persisted in northern California. However, all nine samples from this population had the same haplotype, suggesting that several historic haplotypes may have become lost. Unidentified barriers have apparently prevented gene flow from the Sacramento Valley population to other eastern or southern populations in California. Future studies involving nuclear markers are needed to assess the origin of the Sierra Nevada red fox and to quantify levels of nuclear gene flow.     

Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa

Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (H_E = 0.833) to the modern (H_E = 0.796) populations, whereas mitochondrial genetic diversity was maintained (H_d = 0.98 for both). Although the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified four clusters: Southern, Mixed, Eastern, and Western and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, whereas mitochondrial structure and diversity were maintained over time.