Severe Population Bottleneck Research Articles

Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan

Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe. Subspecies littorale shows intermediate selfing rates, while subsp. australe is an obligate outcrosser. We aimed to evaluate the process of mating system evolution and divergence for the two subspecies using restriction site associated DNA sequencing (RAD-seq). The results showed that subsp. littorale had lower genetic diversity and stronger genetic drift than subsp. australe. Fluctuations in the effective population size over time were evaluated by extended Bayesian skyline plot and Stairway plot analyses, both of which revealed a severe population bottleneck about 20,000 years ago in subsp. littorale. This bottleneck and the subsequent range expansion after the LGM appear to have played an important role in the divergence of the two subspecies and the evolution of selfing in subsp. littorale. These results shed new light on the relationship between mating system evolution and past demographic change in fern species.

Phenological tracking of a seasonal climate window in a recovering tropical island bird species

Constraints on evolutionary adaptation and range shifts mean that phenotypic plasticity, which includes physiological, developmental or behavioural responses to environmental conditions, could be an important mode of adaptation to a changing climate for many species with small insular populations. While there is evidence to suggest adaptive plasticity to climate in some island populations, little is known about this capacity in species that have experienced a severe population bottleneck. In a changing climate, plasticity in the timing of life-history events, such as in breeding phenology, is adaptive if timing is optimised in seasonal environments, although these processes are poorly understood for tropical species. Here, we quantify the effects of climate on the breeding phenology and success of the Mauritius kestrel (Falco punctatus), a tropical raptor whose extinction has been averted by conservation management. We show that the timing of egg-laying is advancing in response to warming, at rates similar to temperate bird populations. Individual females show plasticity to temperature, although there is limited variation among individual responses. We show that advances in breeding phenology are likely to be adaptive, as they track changes in a seasonal climate window of favourable conditions, defined by late winter-early spring temperatures and the onset of the summer rainy season. Our results provide a rare example of a small and bottlenecked insular population that has adjusted to recent climate change through phenotypic plasticity. Furthermore, seasonal climate windows and their dynamics may be widespread mechanisms through which tropical species are impacted by and respond to climate change.

Population genomics reveal rapid genetic differentiation in a recently invasive population of Rattus norvegicus

BackgroundInvasive species bring a serious effect on local biodiversity, ecosystems, and even human health and safety. Although the genetic signatures of historical range expansions have been explored in an array of species, the genetic consequences of contemporary range expansions have received little attention, especially in mammal species. In this study, we used whole-genome sequencing to explore the rapid genetic change and introduction history of a newly invasive brown rat (Rattus norvegicus) population which invaded Xinjiang Province, China in the late 1970s.ResultsBayesian clustering analysis, principal components analysis, and phylogenetic analysis all showed clear genetic differentiation between newly introduced and native rat populations. Reduced genetic diversity and high linkage disequilibrium suggested a severe population bottleneck in this colonization event. Results of TreeMix analyses revealed that the introduced rats were derived from an adjacent population in geographic region (Northwest China). Demographic analysis indicated that a severe bottleneck occurred in XJ population after the split off from the source population, and the divergence of XJ population might have started before the invasion of XJ. Moreover, we detected 42 protein-coding genes with allele frequency shifts throughout the genome for XJ rats and they were mainly associated with lipid metabolism and immunity, which could be seen as a prelude to future selection analyses in the novel environment of XJ.ConclusionsThis study presents the first genomic evidence on genetic differentiation which developed rapidly, and deepens the understanding of invasion history and evolutionary processes of this newly introduced rat population. This would add to our understanding of how invasive species become established and aid strategies aimed at the management of this notorious pest that have spread around the world with humans.

Historic and recent status of the Kosrae flying fox (Pteropus ualanus) (Chiroptera: Pteropidae) on Kosrae, Micronesia

Seven species of flying foxes of the genus Pteropus have been described from the Caroline Islands and Mariana Islands of Micronesia. Among the five extant species, P. ualanus of Kosrae is the least studied. We review the history of research on P. ualanus and summarize data from recent surveys. Early historical accounts suggest that P. ualanus was abundant until a severe population bottleneck, attributed to an infectious disease, allegedly reduced the population to two individuals during 1926–1927. During 1982 and 1983, we found three colonies and a minimum of 600–700 bats in the mountains. Subsequently two new colonies became established in coastal localities by 1994 and 2002 and currently represent the largest colonies. During 2013 and 2014, Hayes visited four confirmed and two possible colonies (three in the mountains, three along the coast) ranging in size from two to 1038 individuals and counted a minimum of 1765 individuals. Long-term changes occurred in the size of colonies. Because not all individuals were counted and at least one other colony likely exists, the population probably exceeds 2000 and may exceed 3000 individuals. The population may not have reached its carrying capacity and may still be increasing. Potential existential threats include infectious disease, typhoons, overhunting, and habitat loss.

Heterogeneity in migration strategies of Whooping Cranes

AbstractMigratory birds use numerous strategies to successfully complete twice-annual movements between breeding and wintering sites. Context for conservation and management can be provided by characterizing these strategies. Variations in strategy among and within individuals support population persistence in response to changes in land use and climate. We used location data from 58 marked Whooping Cranes (Grus americana) from 2010 to 2016 to characterize migration strategies in the U.S. Great Plains and Canadian Prairies and southern boreal region, and to explore sources of heterogeneity in their migration strategy, including space use, timing, and performance. Whooping Cranes completed ~3,900-km migrations that averaged 29 days during spring and 45 days during autumn, while making 11–12 nighttime stops. At the scale of our analysis, individual Whooping Cranes showed little consistency in stopover sites used among migration seasons (i.e. low site fidelity). In contrast, individuals expressed a measure of consistency in timing, especially migration initiation dates. Whooping Cranes migrated at different times based on age and reproductive status, where adults with young initiated autumn migration after other birds, and adults with and without young initiated spring migration before subadult birds. Time spent at stopover sites was positively associated with migration bout length and negatively associated with time spent at previous stopover sites, indicating Whooping Cranes acquired energy resources at some stopover sites that they used to fuel migration. Whooping Cranes were faithful to a defined migration corridor but showed less fidelity in their selection of nighttime stopover sites; hence, spatial targeting of conservation actions may be better informed by associations with landscape and habitat features rather than documented past use at specific locations. The preservation of variation in migration strategies existing within this species that experienced a severe population bottleneck suggests that Whooping Cranes have maintained a capacity to adjust strategies when confronted with future changes in land use and climate.

The conflict within: origin, proliferation and persistence of a spontaneously arising selfish mitochondrial genome.

Mitochondrial genomes can sustain mutations that are simultaneously detrimental to individual fitness and yet, can proliferate within individuals owing to a replicative advantage. We analysed the fitness effects and population dynamics of a mitochondrial genome containing a novel 499 bp deletion in the cytochrome b(1) (ctb-1) gene (Δctb-1) encoding the cytochrome b of complex III in Caenorhabditis elegans. Δctb-1 reached a high heteroplasmic frequency of 96% in one experimental line during a mutation accumulation experiment and was linked to additional spontaneous mutations in nd5 and tRNA-Asn. The Δctb-1 mutant mitotype imposed a significant fitness cost including a 65% and 52% reduction in productivity and competitive fitness, respectively, relative to individuals bearing wild-type (WT) mitochondria. Deletion-bearing worms were rapidly purged within a few generations when competed against WT mitochondrial DNA (mtDNA) bearing worms in experimental populations. By contrast, the Δctb-1 mitotype was able to persist in large populations comprising heteroplasmic individuals only, although the average intracellular frequency of Δctb-1 exhibited a slow decline owing to competition among individuals bearing different frequencies of the heteroplasmy. Within experimental lines subjected to severe population bottlenecks (n = 1), the relative intracellular frequency of Δctb-1 increased, which is a hallmark of selfish drive. A positive correlation between Δctb-1 and WT mtDNA copy-number suggests a mechanism that increases total mtDNA per se, and does not discern the Δctb-1 mitotype from the WT mtDNA. This study demonstrates the selfish nature of the Δctb-1 mitotype, given its transmission advantage and substantial fitness load for the host, and highlights the importance of population size for the population dynamics of selfish mtDNA. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

BackgroundThe lager brewing yeast, S. pastorianus, is a hybrid between S. cerevisiae and S. eubayanus with extensive chromosome aneuploidy. S. pastorianus is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for S. cerevisiae chromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies of S. pastorianus strains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history.ResultsTo fill this gap, we generated a chromosome-level genome assembly of the S. pastorianus strain CBS 1483 from Oxford Nanopore MinION DNA sequencing data and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history of S. pastorianus strains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between the S. cerevisiae subgenomes of Group 1 and 2 strains, and marked differences from sequenced S. cerevisiae strains.ConclusionsOur findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygous S. cerevisiae strain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.

A 50K SNP array reveals genetic structure for bald eagles (Haliaeetus leucocephalus)

Bald eagles (Haliaeetus leucocephalus) underwent a severe population bottleneck in the mid-1900s due to Dichlorodiphenyltrichloroethane (DDT) use as an insecticide. After its ban in 1972, the population began to recover with the increase being attributed to banning DDT and reintroduction/translocation programs. Although bald eagles have increased and may be in a phase of exponential growth, many populations continue to experience anthropogenic stressors. Assessing levels of standing genetic variation and the partitioning of genetic variation within and among populations is critical for the development of informed conservation management plans. To begin addressing these concerns, we developed a custom 50K Affymetrix Axiom myDesign single nucleotide polymorphism (SNP) array and performed preliminary population genomic analyses on geographically disparate populations of bald eagles to test the utility of this SNP array for assessing levels of standing genetic variation in the gene pool and determining the partitioning of genetic variation within and among populations. To develop the array, a combination of RAD-tag sequencing and genome sequencing was used with the final chip consisting of 50,789 SNPs in both genic and intergenic regions of the genome. After genotyping 169 hatchlings, 45,952 SNPs from the array were found to be of quality and were used in Structure, Admixture, and a discriminant analysis of principal components (DAPC) analyses. Results from all of these analyses indicate that despite the significant population bottleneck, sufficient genetic variation is detectable within the bald eagle gene pool. Moreover, based on our disparate geographic sampling of bald eagles, our preliminary analyses indicate statistically significant partitioning of the genetic variation among broad sampling areas.

Severe population bottleneck and cranial morphology change in the Mednyi Island subspecies of Arctic fox Vulpes lagopus (Carnivora: Canidae)

Abstract Arctic foxes, Vulpes lagopus living on Mednyi Island suffered a drastic decline in population size in the late 1970s due to an outbreak of mange epizootic. This dramatic fall in numbers rendered the subspecies endangered, and the concomitant loss of variability resulted in a population bottleneck. Here, we investigate whether differences in cranial morphology between Mednyi Island Arctic foxes and Bering Island Arctic foxes could be attributed to the severe population bottleneck suffered by the Mednyi population in the 1970s. We used morphometric traits as proxies for genetic data to provide estimates of FST. Results show higher FST estimates for the Mednyi population than for the Bering population, which we interpret as a bottleneck signature. FST results also indicate a pattern of divergence between the two populations consistent with random genetic drift. Bottleneck detection is critical for the interpretation of the demographic history of the endangered Mednyi Island Arctic fox, with consequences for conservation management.

Genetic variability and history of a native Finnish horse breed

BackgroundThe Finnhorse was established as a breed more than 110 years ago by combining local Finnish landraces. Since its foundation, the breed has experienced both strong directional selection, especially for size and colour, and severe population bottlenecks that are connected with its initial foundation and subsequent changes in agricultural and forestry practices. Here, we used sequences of the mitochondrial control region and genomic single nucleotide polymorphisms (SNPs) to estimate the genetic diversity and differentiation of the four Finnhorse breeding sections: trotters, pony-sized horses, draught horses and riding horses. Furthermore, we estimated inbreeding and effective population sizes over time to infer the history of this breed.ResultsWe found a high level of mitochondrial genetic variation and identified 16 of the 18 haplogroups described in present-day horses. Interestingly, one of these detected haplogroups was previously reported only in the Przewalski’s horse. Female effective population sizes were in the thousands, but declines were evident at the times when the breed and its breeding sections were founded. By contrast, nuclear variation and effective population sizes were small (approximately 50). Nevertheless, inbreeding in Finnhorses was lower than in many other horse breeds. Based on nuclear SNP data, genetic differentiation among the four breeding sections was strongest between the draught horses and the three other sections (FST = 0.007–0.018), whereas based on mitochondrial DNA data, it was strongest between the trotters and the pony-sized and riding horses (ΦST = 0.054–0.068).ConclusionsThe existence of a Przewalski’s horse haplogroup in the Finnhorse provides new insights into the domestication of the horse, and this finding supports previous suggestions of a close relationship between the Finnhorse and eastern primitive breeds. The high level of mitochondrial DNA variation in the Finnhorse supports its domestication from a large number of mares but also reflects that its founding depended on many local landraces. Although inbreeding in Finnhorses was lower than in many other horse breeds, the small nuclear effective population sizes of each of its breeding sections can be considered as a warning sign, which warrants changes in breeding practices.

Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps

The human pathogen Helicobacter pylori displays extensive genetic diversity. While H. pylori is known to evolve during infection, population dynamics inside the gastric environment have not been extensively investigated. Here we obtained gastric biopsies from multiple stomach regions of 16 H. pylori-infected adults, and analyze the genomes of 10 H. pylori isolates from each biopsy. Phylogenetic analyses suggest location-specific evolution and bacterial migration between gastric regions. Migration is significantly more frequent between the corpus and the fundus than with the antrum, suggesting that physiological differences between antral and oxyntic mucosa contribute to spatial partitioning of H. pylori populations. Associations between H. pylori gene polymorphisms and stomach niches suggest that chemotaxis, regulatory functions and outer membrane proteins contribute to specific adaptation to the antral and oxyntic mucosa. Moreover, we show that antibiotics can induce severe population bottlenecks and likely play a role in shaping the population structure of H. pylori.

Understanding the Hidden Complexity of Latin American Population Isolates

Most population isolates examined to date were founded from a single ancestral population. Consequently, there is limited knowledge about the demographic history of admixed population isolates. Here we investigate genomic diversity of recently admixed population isolates from Costa Rica and Colombia and compare their diversity to a benchmark population isolate, the Finnish. These Latin American isolates originated during the 16th century from admixture between a few hundred European males and Amerindian females, with a limited contribution from African founders. We examine whole-genome sequence data from 449 individuals, ascertained as families to build mutigenerational pedigrees, with a mean sequencing depth of coverage of approximately 36×. We find that Latin American isolates have increased genetic diversity relative to the Finnish. However, there is an increase in the amount of identity by descent (IBD) segments in the Latin American isolates relative to the Finnish. The increase in IBD segments is likely a consequence of a very recent and severe population bottleneck during the founding of the admixed population isolates. Furthermore, the proportion of the genome that falls within a long run of homozygosity (ROH) in Costa Rican and Colombian individuals is significantly greater than that in the Finnish, suggesting more recent consanguinity in the Latin American isolates relative to that seen in the Finnish. Lastly, we find that recent consanguinity increased the number of deleterious variants found in the homozygous state, which is relevant if deleterious variants are recessive. Our study suggests that there is no single genetic signature of a population isolate.

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations

BackgroundResolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?ResultsIn this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these.ConclusionsThe phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.

Reduced representation sequencing detects only subtle regional structure in a heavily exploited and rapidly recolonizing marine mammal species.

Next‐generation reduced representation sequencing (RRS) approaches show great potential for resolving the structure of wild populations. However, the population structure of species that have shown rapid demographic recovery following severe population bottlenecks may still prove difficult to resolve due to high gene flow between subpopulations. Here, we tested the effectiveness of the RRS method Genotyping‐By‐Sequencing (GBS) for describing the population structure of the New Zealand fur seal (NZFS, Arctocephalus forsteri), a species that was heavily exploited by the 19th century commercial sealing industry and has since rapidly recolonized most of its former range from a few isolated colonies. Using 26,026 neutral single nucleotide polymorphisms (SNPs), we assessed genetic variation within and between NZFS colonies. We identified low levels of population differentiation across the species range (<1% of variation explained by regional differences) suggesting a state of near panmixia. Nonetheless, we observed subtle population substructure between West Coast and Southern East Coast colonies and a weak, but significant (p = 0.01), isolation‐by‐distance pattern among the eight colonies studied. Furthermore, our demographic reconstructions supported severe bottlenecks with potential 10‐fold and 250‐fold declines in response to Polynesian and European hunting, respectively. Finally, we were able to assign individuals treated as unknowns to their regions of origin with high confidence (96%) using our SNP data. Our results indicate that while it may be difficult to detect population structure in species that have experienced rapid recovery, next‐generation markers and methods are powerful tools for resolving fine‐scale structure and informing conservation and management efforts.

Conservation genetics of an endemic and threatened amphibian (Capensibufo rosei): a leap towards establishing a genetic monitoring framework

Given the ever-increasing anthropogenic changes to natural ecosystems, it is imperative that temporal changes in genetic diversity be monitored to help safeguard the future viability of species. Capensibufo rosei is a small, range-restricted bufonid from South Africa, believed to have experienced an enigmatic decline likely due to the suppression of natural fires and the loss of grazing animals from some areas. Without these disturbances, their habitat becomes overgrown, which might affect the characteristics of their breeding pools. Since the 1980s, four breeding sites have been lost, presumably due to loss of breeding habitat through encroachment of vegetation. Currently, there are only two known populations [Cape of Good Hope (CGH) and Silvermine nature reserves] both within Table Mountain National Park. Consequently, this species may be vulnerable to stochastic events and genetic erosion through the loss of metapopulation connectivity. To assess the genetic status of this species, genetic diversity within both populations was quantified for two time periods using 11 microsatellite markers. Despite evidence of severe population bottlenecks, both populations possess levels of diversity similar to other anurans, and Silvermine has greater diversity than CGH. A close examination of the data revealed both populations to be genetically dynamic through time, with the loss and gain of rare alleles. Both populations also experienced a slight increase in overall diversity between sampling periods. While the latter was not statistically significant, the monitoring period was perhaps too short to understand changes in diversity over time. These results will form the baseline for future monitoring to better understand this threatened and declining species and to track genetic erosion or recovery.

Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus

BackgroundDemographic bottlenecks erode genetic diversity and may increase endangered species’ extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described as the most important genetic component of the mammalian immune system, with broad implications in ecology and evolution. The genus Lynx includes four species differing immensely in demographic history and population size, which provides a suitable model to study the genetic consequences of demographic declines: the Iberian lynx being an extremely bottlenecked species and the three remaining ones representing common and widely distributed species. We compared variation in the most variable exon of the MHCI and MHCII-DRB loci among the four species of the Lynx genus.ResultsThe Iberian lynx was characterised by lower number of MHC alleles than its sister species (the Eurasian lynx). However, it maintained most of the functional genetic variation at MHC loci present in the remaining and genetically healthier lynx species at all nucleotide, amino acid, and supertype levels.ConclusionsSpecies-wide functional genetic diversity can be maintained even in the face of severe population bottlenecks, which caused devastating whole genome genetic erosion. This could be the consequence of divergent alleles being retained across paralogous loci, an outcome that, in the face of frequent gene conversion, may have been favoured by balancing selection.

Bison Conservation in Northern Great Plains National Parks: No Need to Panic

Bison (Bison bison) are a keystone species in the North American Great Plains. They are also a species of conservation concern in part because they suffered a severe population bottleneck at the end of the 19th century and now exist in mostly small and isolated populations. Wind Cave National Park introduced 20 bison in 1913–16; Theodore Roosevelt National Park introduced 29 animals to a South Unit in 1956 and subsequently transferred 20 bison from that herd to the park's North Unit in 1962; and Badlands National Park introduced 53 animals in 1963–64 and another 20 in 1984. The four herds are confined within fences, and no known introduction of new bison into the gene pools has occurred. The four herds are routinely culled down to approximately 425, 350, 200, and 700 animals, respectively. I found no evidence of inbreeding depression as measured by annual population growth and reproductive rates. A population viability analysis also failed to find persuasive evidence of inbreeding depression. Under current management scenarios, gene diversity in 100 years should remain above levels currently known to cause inbreeding depression in bison. I found no compelling reason to introduce new bison into the herds or transfer bison between herds in the foreseeable future.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

BackgroundGenomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction.ResultsWe generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species.ConclusionsThe genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1090-1) contains supplementary material, which is available to authorized users.

Genetic diversity and population differentiation within and between island populations of two sympatric Petroica robins, the Chatham Island black robin and tomtit

Small island populations are particularly prone to extinction due to the effects of genetic drift and inbreeding reducing genetic variation and fitness of such populations. Furthermore, isolated island populations may experience population divergence due to drift or divergent selection. Reciprocal translocations of individuals between populations may be used to stimulate gene flow between such isolated populations. To determine whether populations of the endangered Chatham Island black robin Petroica traversi may benefit from such translocations, we compared levels of genetic diversity and differentiation within and among populations of the black robin and its sympatric sister-species, the Chatham Island tomtit Petroica macrocephala chathamensis. Although the black robin has recovered following a severe population bottleneck, the bottleneck and subsequent intense inbreeding experienced by the black robin have likely had long-term consequences affecting the viability of this endangered species. We analysed the genetic diversity and population structure of the black robin at 15 polymorphic microsatellite loci, and compared this to the level and pattern of genetic diversity from 17 polymorphic loci for the tomtit, which comprises three larger island populations. The black robin displayed a lower number of alleles and expected heterozygosity than the Chatham Island tomtit. We also found that island populations of both species have differentiated from one another, likely due to strong genetic drift acting independently on these populations over a period of isolation. Reciprocal translocations of black robins between islands are recommended to prevent further loss of diversity through drift, and so to improve the probability of species persistence.

Diversity in the Toll-Like Receptor Genes of the African Penguin (Spheniscus demersus).

The African penguin, Spheniscus demersus, is listed as Endangered by the IUCN Red List of Threatened Species due to the drastic reduction in population numbers over the last 20 years. To date, the only studies on immunogenetic variation in penguins have been conducted on the major histocompatibility complex (MHC) genes. It was shown in humans that up to half of the genetic variability in immune responses to pathogens are located in non-MHC genes. Toll-like receptors (TLRs) are now increasingly being studied in a variety of taxa as a broader approach to determine functional genetic diversity. In this study, we confirm low genetic diversity in the innate immune region of African penguins similar to that observed in New Zealand robin that has undergone several severe population bottlenecks. Single nucleotide polymorphism (SNP) diversity across TLRs varied between ex situ and in situ penguins with the number of non-synonymous alterations in ex situ populations (n = 14) being reduced in comparison to in situ populations (n = 16). Maintaining adaptive diversity is of vital importance in the assurance populations as these animals may potentially be used in the future for re-introductions. Therefore, this study provides essential data on immune gene diversity in penguins and will assist in providing an additional monitoring tool for African penguin in the wild, as well as to monitor diversity in ex situ populations and to ensure that diversity found in the in situ populations are captured in the assurance populations.