Genetic diversity and differentiation of Kermode bear populations

Molecular tracking and prevalence of the red colour morph restricted to a harvested leopard population in South Africa

The red leopard (Panthera pardus) colour morph is a colour variant that occurs only in South Africa, where it is confined to the Central Bushveld bioregion. Red leopards have been spreading over the past 40 years, which raises the speculation that the prevalence of this phenotype is related to low dispersal of young individuals owing to high off‐take in the region. Intensive selective hunting tends to remove large resident male leopards from the breeding population, which gives young male leopards the chance to mate with resident female leopards that are more likely to be their relatives, eventually increasing the frequency of rare genetic variants. To investigate the genetic mechanisms underlying the red coat colour morph in leopards, and whether its prevalence in South Africa relates to an increase in genetic relatedness in the population, we sequenced exons of six coat colour‐associated genes and 20 microsatellite loci in twenty Wild‐type and four red leopards. The results were combined with demographic data available from our study sites. We found that red leopards own a haplotype in homozygosity identified by two SNPs and a 1 bp deletion that causes a frameshift in the tyrosinase‐related protein 1 (TYRP1), a gene known to be involved in the biosynthesis of melanin. Microsatellite analyses indicate clear signs of a population bottleneck and a relatedness of 0.11 among all pairwise relationships, eventually supporting our hypothesis that a rare colour morph in the wild has increased its local frequency due to low natal dispersal, while subject to high human‐induced mortality rate.

The relevance of genetic structure in ecotype designation and conservation management

The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome‐enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.

Black bear colour polymorphism through a fragmented Snell’s window

The white colour morph of the black bear (Ursus americanus kermodei) occurring on islands on the coast of British Columbia, western Canada, captures more salmon (Oncorhynchus spp.) than does the black morph and is hypothesized to have reduced contrast against the sky from the visual perspective of the salmon. We tested this hypothesis in a natural salmon stream by recording the number and proximity of chum salmon (Oncorhynchus keta) approaches (N = 1617 fish, 91 trials) towards life-size bear models differing in body and leg coloration under a mixed forest-sky canopy. Although salmon approached the white models at a much higher rate than black models, consistent with camouflage, we found greater abrupt evasions to the black models, largely independent of their contrast against the above-surface or below-surface backgrounds. Upward-facing sub-surface video-imaging through the rippled water-air interface indicated major visual fragmentation of the model’s integrity. We suggest that increased evasiveness to black models reflects an evolutionary response due to 3+ million years of trophic interaction between salmon and bears, and that the major differences between calm vs. rippled conditions through the optical cone (Snell’s window) at the water-air interface remains a largely unexplored theme in assessing foraging preferences and adaptive coloration within and among species using the water-air interface.

Intrapopulation foraging niche variation between phenotypes and genotypes of Spirit bear populations

Foraging niche variation within a species can contribute to the maintenance of phenotypic diversity. The multiniche model posits that phenotypes occupying different niches can contribute to the maintenance of balanced polymorphisms. Using coastal populations of black bears (Ursus americanus kermodei) from British Columbia, Canada, we examined potential foraging niche divergence between phenotypes (black and white "Spirit" coat color) and between genotypes (black-coated homozygote and heterozygous). We applied the Bayesian multivariate models, with biotracers of diet (δ13C and δ15N) together comprising the response variable, to draw inference about foraging niche variation. Variance-covariance matrices from multivariate linear mixed-effect models were visualized as the Bayesian standard ellipses in δ13C and δ15N isotopic space to assess potential seasonal and annual niche variation between phenotypes and genotypes. We did not detect a difference in annual isotopic foraging niche area in comparisons between genotypes or phenotypes. Consistent with previous field experimental and isotopic analyses, however, we found that white phenotype Spirit bears were modestly more enriched in δ15N during the fall foraging season, though with our modest sample sizes these results were not significant. Although also not statistically significant, variation in isotopic niches between genotypes revealed that heterozygotes were moderately more enriched in δ13C along hair segments grown during fall foraging compared with black-coated homozygotes. To the extent to which the pattern of elevated δ15N and δ13C may signal the consumption of salmon (Oncorhynchus spp.), as well as the influence of salmon consumption on reproductive fitness, these results suggest that black-coated heterozygotes could have a minor selective advantage in the fall compared with black-coated homozygotes. More broadly, our multivariate approach, coupled with knowledge of genetic variation underlying a polymorphic trait, provides new insight into the potential role of a multiniche mechanism in maintaining this rare morph of conservation priority in Canada's Great Bear Rainforest and could offer new understanding into polymorphisms in other systems.

Unraveling the mystery of the glacier bear: Genetic population structure of black bears (Ursus americanus) within the range of a rare pelage type

Glacier bears are a rare grey color morph of American black bear (Ursus americanus) found only in northern Southeast Alaska and a small portion of western Canada. We examine contemporary genetic population structure of black bears within the geographic extent of glacier bears and explore how this structure relates to pelage color and landscape features of a recently glaciated and highly fragmented landscape. We used existing radiocollar data to quantify black bear home-range size within the geographic range of glacier bears. The mean home-range size of female black bears in the study area was 13 km2 (n = 11), whereas the home range of a single male was 86.9 km2. We genotyped 284 bears using 21 microsatellites extracted from noninvasively collected hair as well as tissue samples from harvested bears. We found ten populations of black bears in the study area, including several new populations not previously identified, divided largely by geographic features such as glaciers and marine fjords. Glacier bears were assigned to four populations found on the north and east side of Lynn Canal and the north and west side of Glacier Bay with a curious absence in the nonglaciated peninsula between. Lack of genetic relatedness and geographic continuity between black bear populations containing glacier bears suggest a possible unsampled population or an association with ice fields. Further investigation is needed to determine the genetic basis and the adaptive and evolutionary significance of the glacier bear color morph to help focus black bear conservation management to maximize and preserve genetic diversity.

MinION-Based DNA Barcoding of Preserved and Non-Invasively Collected Wildlife Samples

The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only currently available field-friendly DNA sequencer, the MinION by Oxford Nanopore Technologies, has a high error rate compared to standard laboratory-based sequencing platforms and has not been systematically validated for DNA barcoding accuracy for preserved and non-invasively collected tissue samples. We tested whether various wildlife sample types, field-friendly methods, and our clustering-based bioinformatics pipeline, SAIGA, can be used to generate consistent and accurate consensus sequences for species identification. Here, we systematically evaluate variation in cytochrome b sequences amplified from scat, hair, feather, fresh frozen liver, and formalin-fixed paraffin-embedded (FFPE) liver. Each sample was processed by three DNA extraction protocols. For all sample types tested, the MinION consensus sequences matched the Sanger references with 99.29%-100% sequence similarity, even for samples that were difficult to amplify, such as scat and FFPE tissue extracted with Chelex resin. Sequencing errors occurred primarily in homopolymer regions, as identified in previous MinION studies. We demonstrate that it is possible to generate accurate DNA barcode sequences from preserved and non-invasively collected wildlife samples using portable MinION sequencing, creating more opportunities to apply portable sequencing technology for species identification.

Heritability of plumage colour morph variation in a wild population of promiscuous, long-lived Australian magpies

Colour polymorphisms have evolutionary significance for the generation and maintenance of species diversity. Demonstrating heritability of polymorphic traits can be challenging for wild populations of long-lived species because accurate information is required on trait expression and familial relationships. The Australian magpie Cracticus tibicen has a continent-wide distribution featuring several distinct plumage morphs, differing primarily in colour of back feathers. Black or white-backed morphs occur in eastern Australia, with intermediate morphs common in a narrow hybrid zone where the two morphs meet. This study investigated heritability of back colour phenotypes in a hybrid zone population (Seymour, Victoria) based on long-term observational data and DNA samples collected over an 18 year period (1993-2010). High extra-pair paternity (~ 36% offspring), necessitated verification of parent-offspring relationships by parentage analysis. A total of 538 birds (221 parents and 317 offspring) from 36 territories were analysed. Back colour was a continuous trait scored on a five-morph scale in the field (0-4). High and consistent estimates of back colour heritability (h²) were obtained via weighted mid-parent regression (h² = 0.94) and by animal models (h² = 0.92, C.I. 0.80-0.99). Single-parent heritability estimates indicated neither maternal nor paternal non-genetic effects (e.g., parent body condition) played a large role in determining offspring back colour, and environmental effects of territory group and cohort contributed little to trait heritability. Distinctive back colouration of the Australian magpie behaves as a quantitative trait that is likely polygenic, although mechanisms responsible for maintaining these geographically structured morphs and the hybrid zone where they meet are unknown.

Intraspecific evolutionary relationships among peregrine falcons in western North American high latitudes

Subspecies relationships within the peregrine falcon (Falco peregrinus) have been long debated because of the polytypic nature of melanin-based plumage characteristics used in subspecies designations and potential differentiation of local subpopulations due to philopatry. In North America, understanding the evolutionary relationships among subspecies may have been further complicated by the introduction of captive bred peregrines originating from non-native stock, as part of recovery efforts associated with mid 20^th century population declines resulting from organochloride pollution. Alaska hosts all three nominal subspecies of North American peregrine falcons–F. p. tundrius, anatum, and pealei–for which distributions in Alaska are broadly associated with nesting locales within Arctic, boreal, and south coastal maritime habitats, respectively. Unlike elsewhere, populations of peregrine falcon in Alaska were not augmented by captive-bred birds during the late 20^th century recovery efforts. Population genetic differentiation analyses of peregrine populations in Alaska, based on sequence data from the mitochondrial DNA control region and fragment data from microsatellite loci, failed to uncover genetic distinction between populations of peregrines occupying Arctic and boreal Alaskan locales. However, the maritime subspecies, pealei, was genetically differentiated from Arctic and boreal populations, and substructured into eastern and western populations. Levels of interpopulational gene flow between anatum and tundrius were generally higher than between pealei and either anatum or tundrius. Estimates based on both marker types revealed gene flow between augmented Canadian populations and unaugmented Alaskan populations. While we make no attempt at formal taxonomic revision, our data suggest that peregrine falcons occupying habitats in Alaska and the North Pacific coast of North America belong to two distinct regional groupings–a coastal grouping (pealei) and a boreal/Arctic grouping (currently anatum and tundrius)–each comprised of discrete populations that are variously intra-regionally connected.

Population genetics of the white-phased "Spirit" black bear of British Columbia

The Spirit (or Kermode) bear is a white-phased black bear found on the northwest coast of British Columbia, and is one of the most striking color polymorphisms found in mammals. A single nucleotide polymorphism at the melanocortin 1 receptor gene (mc1r) locus is the cause of this recessive w variant. Recently, evidence suggests that the white color provides a selective advantage during salmon hunting. Here we examine the effects of favorable selection, gene flow, genetic drift, and positive-assortative mating in an effort to understand the establishment and maintenance of this polymorphism and the observed heterozygote deficiency for mc1r but not for microsatellite loci. It appears that genetic drift was important in the establishment of the w allele and that the selective advantage was important to counteract immigration from populations without the w allele. Positive-assortative mating can result in a deficiency of heterozygotes but needs to be quite high to result in the large deficiency of heterozygotes observed, suggesting that other factors must also be contributing. Examination of population genetic factors, singly and jointly, provides insight into the establishment and maintenance of this unusual polymorphism.

Unbiased relatedness estimation in structured populations

Knowledge of the genetic relatedness between individuals is important in many research areas in quantitative genetics, conservation genetics, forensics, evolution, and ecology. In the absence of pedigree records, relatedness can be estimated from genetic marker data using a number of estimators. These estimators, however, make the critical assumption of a large random mating population without genetic structures. The assumption is frequently violated in the real world where geographic/social structures or nonrandom mating usually lead to genetic structures. In this study, I investigated two approaches to the estimation of relatedness between a pair of individuals from a subpopulation due to recent common ancestors (i.e., relatedness is defined and measured with the current focal subpopulation as reference). The indirect approach uses the allele frequencies of the entire population with and without accounting for the population structure, and the direct approach uses the allele frequencies of the current focal subpopulation. I found by simulations that currently widely applied relatedness estimators are upwardly biased under the indirect approach, but can be modified to become unbiased and more accurate by using Wright's F(st) to account for population structures. However, the modified unbiased estimators under the indirect approach are clearly inferior to the unmodified original estimators under the direct approach, even when small samples are used in estimating both allele frequencies and relatedness.

The genetic and evolutionary basis of colour variation in vertebrates

Variation in pigmentation is one of the most conspicuous phenotypic traits in vertebrates. Although mammals show less variation in body pigmentation than other vertebrate groups, the genetics of colour determination and variation is best understood for them. More than 150 genes have been identified that influence pigmentation, and in many cases, the cause for variation in pigmentation has been identified down to the underlying nucleotide changes. These studies show that while some genes are often responsible for deviating pigmentation, similar or almost identical phenotypes even in the same species may be due to mutations in different genes. In this review we will first discuss the current knowledge about the genes and their functions underlying the biochemical pathways that determine pigmentation and then give examples where the mutations responsible for colour variation have been determined. Finally, we will discuss potential evolutionary causes for and consequences of differences in pigmentation between individuals.

Genetic diversity of the Japanese Marten (Martes melampus) and its implications for the conservation unit

Molecular phylogenetic analyses of combined mitochondrial DNA sequences (2814 bp; cytochrome b gene, displacement loop region, and NADH dehydrogenase subunit 2 gene) identified nine groups among 49 individual Japanese martens, Martes melampus, collected from several areas in Japan. The grouping was not correlated with winter coat color, but was consistent with geography. In particular, the monophyly of 29 Tsushima martens, M. m. tsuensis, was supported by strong clade support and topological tests. Haplotype and nucleotide diversities were much lower for the Tsushima population than for any population on the Japanese main islands. In addition, analyses of heterozygosity in nuclear growth hormone receptor gene sequences (654 bp) showed genetic homogeneity for the Tsushima population. This evidence supports the view that the Tsushima marten's long history of isolation on small islands is responsible for its genetic distinctiveness and uniformity, validating the Tsushima population as an evolutionarily significant unit.

A DNA-based approach for the forensic identification of Asiatic black bear (Ursus thibetanus) in a traditional Asian medicine

Attempts to prevent illegal trade in bile and gallbladders from Asiatic black bears, Ursus thibetanus, are hampered by difficulties associated with identifying such items. We extracted DNA from bile crystals of unknown species origin and generated partial cytochrome b (cyt b) sequences using either universal primers (positioned in conserved regions of cyt b), or primers designed on existing U. thibetanus sequences (UT). Species origin was determined by aligning resolved sequences to reference sequence data. The universal primers were unsuitable for U. thibetanus identification when multiple species templates were present in the samples. The UT primers amplified U. thibetanus DNA from all sample extracts, including those containing mixed species templates. The amplified fragment can distinguish U. thibetanus from the most closely related species, U. americanus, a distinct advantage of DNA sequencing over the methods currently used to analyze suspected U. thibetanus bile.

Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times

The genetic diversity of present-day brown bears (Ursus arctos) has been extensively studied over the years and appears to be geographically structured into five main clades. The question of the past diversity of the species has been recently addressed by ancient DNA studies that concluded to a relative genetic stability over the last 35,000 years. However, the post-last glacial maximum genetic diversity of the species still remains poorly documented, notably in the Old World. Here, we analyse Atlas brown bears, which became extinct during the Holocene period. A divergent brown bear mitochondrial DNA lineage not present in any of the previously studied modern or ancient bear samples was uncovered, suggesting that the diversity of U. arctos was larger in the past than it is now. Specifically, a significant portion (with respect to sequence divergence) of the intraspecific diversity of the brown bear was lost with the extinction of the Atlas brown bear after the Pleistocene/Holocene transition.

Genetic viability and population history of the giant panda, putting an end to the "evolutionary dead end"?

The giant panda (Ailuropoda melanoleuca) is currently threatened by habitat loss, fragmentation, and human persecution. Its dietary specialization, habitat isolation, and reproductive constraints have led to a perception that this is a species at an "evolutionary dead end," destined for deterministic extinction in the modern world. Here we examine this perception by a comprehensive investigation of its genetic diversity, population structure, and demographic history across its geographic range. We present analysis of 655 base pairs of mitochondrial (mt) control region (CR) DNA and 10 microsatellite loci for samples from its 5 extant mountain populations (Qinling, Minshan, Qionglai, Liangshan, and Lesser Xiangling). Surprisingly, extant populations display average to high levels of CR and microsatellite diversity compared with other bear species. Genetic differentiation among populations was significant in most cases but was markedly higher between Qinling and the other mountain ranges, suggesting, minimally, that the Qinling population should comprise a separate management unit for conservation purposes. Recent demographic inference using microsatellite markers demonstrated a clear genetic signature for population decline starting several thousands years ago or even further back in the past, and being accelerated and enhanced by the expansion of human populations. Importantly, these data suggest that the panda is not a species at an evolutionary "dead end," but in common with other large carnivores, has suffered demographically at the hands of human pressure. Conservation strategies should therefore focus on the restoration and protection of wild habitat and the maintenance of the currently substantial regional genetic diversity, through active management of disconnected populations.

Evolution of Population Structure in a Highly Social Top Predator, the Killer Whale

Intraspecific resource partitioning and social affiliations both have the potential to structure populations, though it is rarely possible to directly assess the impact of these mechanisms on genetic diversity and population divergence. Here, we address this for killer whales (Orcinus orca), which specialize on prey species and hunting strategy and have long-term social affiliations involving both males and females. We used genetic markers to assess the structure and demographic history of regional populations and test the hypothesis that known foraging specializations and matrifocal sociality contributed significantly to the evolution of population structure. We find genetic structure in sympatry between populations of foraging specialists (ecotypes) and evidence for isolation by distance within an ecotype. Fitting of an isolation with migration model suggested ongoing, low-level migration between regional populations (within and between ecotypes) and small effective sizes for extant local populations. The founding of local populations by matrifocal social groups was indicated by the pattern of fixed mtDNA haplotypes in regional populations. Simulations indicate that this occurred within the last 20,000 years (after the last glacial maximum). Our data indicate a key role for social and foraging behavior in the evolution of genetic structure among conspecific populations of the killer whale.

A maximum-likelihood method for the estimation of pairwise relatedness in structured populations

A maximum-likelihood estimator for pairwise relatedness is presented for the situation in which the individuals under consideration come from a large outbred subpopulation of the population for which allele frequencies are known. We demonstrate via simulations that a variety of commonly used estimators that do not take this kind of misspecification of allele frequencies into account will systematically overestimate the degree of relatedness between two individuals from a subpopulation. A maximum-likelihood estimator that includes F(ST) as a parameter is introduced with the goal of producing the relatedness estimates that would have been obtained if the subpopulation allele frequencies had been known. This estimator is shown to work quite well, even when the value of F(ST) is misspecified. Bootstrap confidence intervals are also examined and shown to exhibit close to nominal coverage when F(ST) is correctly specified.

Estimating F-statistics

A moment estimator of, the coancestry coefficient for alleles within a population, was described by Weir & Cockerham in 1984 (100) and is still widely cited. The estimate is used by population geneticists to characterize population structure, by ecologists to estimate migration rates, by animal breeders to describe genetic variation, and by forensic scientists to quantify the strength of matching DNA profiles. This review extends the work of Weir & Cockerham by allowing different levels of coancestry for different populations, and by allowing non-zero coancestries between pairs of populations. All estimates are relative to the average value of theta between pairs of populations. Moment estimates for within- and between-population theta values are likely to have large sampling variances, although these may be reduced by combining information over loci. Variances also decrease with the numbers of alleles at a locus, and with the numbers of populations sampled. This review also extends the work of Weir & Cockerham by employing maximum likelihood methods under the assumption that allele frequencies follow the normal distribution over populations. For the case of equal theta values within populations and zero theta values between populations, the maximum likelihood estimate is the same as that given by Robertson & Hill in 1984 (70). The review concludes by relating functions of theta values to times of population divergence under a pure drift model.