A rapid population expansion retains genetic diversity within European rabbits in Australia

The well documented historical translocations of the European rabbit (Oryctolagus cuniculus) offer an excellent framework to test the genetic effects of reductions in effective population size. It has been proposed that rabbits went through an initial bottleneck at the time of their establishment in Australia, as well as multiple founder events during the rabbit's colonization process. To test these hypotheses, genetic variation at seven microsatellite loci was measured in 252 wild rabbits from five populations across Australia. These populations were compared to each other and to data from Europe. No evidence of a genetic bottleneck was observed with the movement of 13 rabbits from Europe to Australia when compared to French data. Within Australia the distribution of genetic diversity did not reflect the suggested pattern of sequential founder effects. In fact, the current pattern of genetic variation in Australia is most likely a result of multiple factors including mutation, genetic drift and geographical differentiation. The absence of reduced genetic diversity is almost certainly a result of the rabbit's rapid population expansion at the time of establishment in Australia. These results highlight the importance of population growth following a demographic bottleneck, which largely determines the severity of genetic loss.     

Home-loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing

Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove because the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mitochondrial DNA (mtDNA) across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X- and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation results from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecology-driven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home-loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones.     

Loss of genetic diversity in sea otters (Enhydra lutris) associated with the fur trade of the 18th and 19th centuries

Sea otter (Enhydra lutris) populations experienced widespread reduction and extirpation due to the fur trade of the 18th and 19th centuries. We examined genetic variation within four microsatellite markers and the mitochondrial DNA (mtDNA) d-loop in one prefur trade population and compared it to five modern populations to determine potential losses in genetic variation. While mtDNA sequence variability was low within both modern and extinct populations, analysis of microsatellite allelic data revealed that the prefur trade population had significantly more variation than all the extant sea otter populations. Reduced genetic variation may lead to inbreeding depression and we believe sea otter populations should be closely monitored for potential associated negative effects.     

How a haemosporidian parasite of bats gets around: the genetic structure of a parasite,vector and host compared

Parasite population structure is often thought to be largely shaped by that of its host. In the case of a parasite with a complex life cycle, two host species, each with their own patterns of demography and migration, spread the parasite. However, the population structure of the parasite is predicted to resemble only that of the most vagile host species. In this study, we tested this prediction in the context of a vector‐transmitted parasite. We sampled the haemosporidian parasite Polychromophilus melanipherus across its European range, together with its bat fly vector Nycteribia schmidlii and its host, the bent‐winged bat Miniopterus schreibersii. Based on microsatellite analyses, the wingless vector, and not the bat host, was identified as the least structured population and should therefore be considered the most vagile host. Genetic distance matrices were compared for all three species based on a mitochondrial DNA fragment. Both host and vector populations followed an isolation‐by‐distance pattern across the Mediterranean, but not the parasite. Mantel tests found no correlation between the parasite and either the host or vector populations. We therefore found no support for our hypothesis; the parasite population structure matched neither vector nor host. Instead, we propose a model where the parasite's gene flow is represented by the added effects of host and vector dispersal patterns.     

Host–parasite coevolution favours parasite genetic diversity and horizontal gene transfer

Host–parasite coevolution is predicted to favour genetic diversity and the underlying mechanisms (e.g. sexual reproduction and, more generally, genetic exchange), because diversity enhances the antagonists' potential for rapid adaptation. To date, this prediction has mainly been tested and confirmed for the host. It should similarly apply to the parasite. Indeed, our previous work demonstrated that experimental coevolution between the nematode Caenorhabditis elegans and its microparasite Bacillus thuringiensis selects for genetic diversity in both antagonists. For the parasite, the previous analysis was based on plasmid‐encoded toxin gene markers. Thus, it was restricted to a very small part of the bacterial genome and did not cover the main chromosome, which harbours a large variety of virulence factors. Here, we present new data for chromosomal gene markers of B. thuringiensis and combine this information with the previous results on plasmid‐encoded toxins. Our new results demonstrate that, in comparison with the control treatment, coevolution with a host similarly leads to higher levels of genetic diversity in the bacterial chromosome, thus indicating the relevance of chromosomal genes for coevolution. Furthermore, the frequency of toxin gene gain is significantly elevated during coevolution, highlighting the importance of horizontal gene transfer as a diversity‐generating mechanism. In conclusion, our study emphasizes the strong influence of antagonistic coevolution on parasite genetic diversity and gene exchange.     

Impact of a population bottleneck on symmetry and genetic diversity in the northern elephant seal

Abstract The northern elephant seal (NES) suffered a severe population bottleneck towards the end of the nineteenth century. Theoretical expectations for the impact of population bottlenecks include the loss of genetic diversity and a loss of fitness (e.g. through a disruption of developmental stability); however, there are few direct demonstrations in natural populations. Here, we report on the comparison of archive samples collected prior to and following the NES population bottleneck. Measures of genetic diversity show a loss of variation consistent with expectations and suggest a strong disruption in the pattern of allele frequencies following the bottleneck. Measures of bilateral characters show an increase in fluctuating asymmetry.     

Maintenance of genetic diversity in a small,isolated population of ancient tree Erythrophleum fordii

Ancient trees remaining in natural areas from once widespread forest due to overexploitation and habitat modification would naturally regenerate to form small isolated populations after the halting of disturbance. The genetic processes and consequence of this regeneration are generally unknown, which prevents the effective conservation and management of these populations. One such population, an Erythrophleum fordii population, is located in Dinghushan National Nature Reserve (China). Owing to the remarkably huge trunk of the sole ancient tree (KG) relative to the other individuals in the population, the local people and local tourism administration presume that this population has developed solely from KG. We found, using genetic diversity analyses, that contrary to this presumption, the population might have regenerated from several founders with diverse genetic backgrounds. Severe degradation of genetic diversity within the population did not take place, rather, it possessed the potential ability to maintain and recover gradually with population development. According to the results of simulations, we found that the longevity of tree species with iteroparity offers the potential to maintain genetic diversity in small isolated populations. The results from this study will benefit the restoration and conservation of the endangered species E. fordii, and of other congener species and tree species with similar life history traits.     

Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial

The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000–4000 years in association with a dramatic population decline. In addition, we obtained near‐complete 11‐loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of ‘new’ microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current‐day conservation strategies.     

Helminth parasite diversity discloses age and sex differences in the foraging behaviour of southern lapwings (Vanellus chilensis)

Parasites with heteroxen cycles are important sources of information on the trophic relations of hosts. This is particularly instructive for species whose age‐based or sex‐based differences are hardly detected by behavioural observations. Here, we describe the helminth community of the omnivorous southern lapwing (Vanellus chilensis) and evaluate whether it is affected by the host's sex, age and body size. The species is sexually monomorphic in body length, but males are slightly heavier than females. We analysed 112 individuals collected in Curitiba, Brazil, in March 2010. All hosts were parasitized. The helminth community was composed of 10 species (the digeneans Leucochloridium parcum and Athesmia sp., the cestode Infula macrophallus, the acantocephalans Plagiorhynchus sp., Centrorhynchus sp., Mediorhynchus sp., and an unidentified Gigantorhynchida, and the nematodes Heterakis psophiae, Dispharynx nasuta and an unidentified Capillariidae), seven of which were novel reports for this host species. Prevalence ranged from <1% to 99%. Whereas I. macrophallus was the most prevalent species, D. nasuta showed the highest mean intensity and abundance of infection. The former was found in most hosts as single male–female pairs, suggesting the occurrence of intrasexual competition. The infracommunities of juvenile birds showed a higher parasite species richness than those of adult males and females, suggesting the exploitation of a wider array of prey. However, the three classes harboured seven parasite species. Differences in parasite diversity (lower in juveniles, intermediate in adult males and higher in adult females) reflect the evenness in the distribution of parasite specimens among taxa in each age–sex class and are compatible with differences in their foraging strategy. Finally, we conclude based on the cycles of the heteroxen species that southern lapwings preyed upon molluscs, coleopterans, woodlice and earthworms.     

The genetic signature of rapid range expansions: How dispersal,growth and invasion speed impact heterozygosity and allele surfing

As researchers collect spatiotemporal population and genetic data in tandem, models that connect demography and dispersal to genetics are increasingly relevant. The dominant spatiotemporal model of invasion genetics is the stepping-stone model which represents a gradual range expansion in which individuals jump to uncolonized locations one step at a time. However, many range expansions occur quickly as individuals disperse far from currently colonized regions. For these types of expansion, stepping-stone models are inappropriate. To more accurately reflect wider dispersal in many organisms, we created kernel-based models of invasion genetics based on integrodifference equations. Classic theory relating to integrodifference equations suggests that the speed of range expansions is a function of population growth and dispersal. In our simulations, populations that expanded at the same speed but with spread rates driven by dispersal retained more heterozygosity along axes of expansion than range expansions with rates of spread that were driven primarily by population growth. To investigate surfing we introduced mutant alleles in wave fronts of simulated range expansions. In our models based on random mating, surfing alleles remained at relatively low frequencies and surfed less often compared to previous results based on stepping-stone simulations with asexual reproduction.     

Genetic diversity and origin of a fish population recently colonizing a reservoir: The case of Basilichthys microlepidotus,central Chile

Freshwater ecosystems are among those most affected by human activity. Constructing artificial reservoirs can change freshwater biodiversity, thereby impacting genetic diversity (GD), which is crucial to population-level adaptation. The Maipo River basin, inhabited by the endemic silverside Basilichthys microlepidotus, is one of Chile's most impacted freshwater systems. In this basin, the species is divided into five populations. Recently, a new population was discovered in the reservoir Laguna Esmeralda (LE). We hypothesized that LE silversides possess less GD than other populations and originated from a single basin population. Our evidence shows that the LE is a genetically isolated population with evidence of low genetic variation, but not showing signals of bottleneck or significant reduction in GD. Results consistently identified two sites as unlikely to be the origin of the LE silverside population, suggesting that it was established by the immigration of many individuals from the other three populations.     

Habitat fragmentation and the structure of genetic diversity within disjunct isolates of Anthericum ramosum L. (Anthericaceae) in Scandinavia

The lilioid herb, Anthericum ramosum , occurs in four geographically-isolated regions (Sjælland, Skåne, Öland and Gotland) in Denmark and southern Sweden. We investigated allozyme variation at nine polymorphic loci in A. ramosum from 16 sites (33 populations) in the four regions. There was no clear overall geographic pattern of differentiation between the regions, but the southernmost Gotland and the Öland populations had similar allele frequencies, suggesting that they have had a common history. The total genetic diversity (H_10t) was 0.458 and the between-region, site- and population components of diversity accounted, respectively, for 13%, 10% and 2% of the total diversity. The species is restricted to grassland habitats. Such habitats have become increasingly rare in the Sjælland and Skåne regions, where A. ramosum now has a highly fragmented distribution. Within three of the regions (Sjælland, Skane and Öland) there was a negative relationship between the extent of grassland habitat and the between-site components of genetic diversity. Öland, with its extensive grassland habitats and low levels of population disjunction, showed litde allelic differentiation between sites and the lowest between-site component of diversity (3%), suggesting that there is (or has been) extensive gene flow between sites. The between-site components of diversity were higher within Skåne (7%) and Sjaelland (12%). The high within-region G_ST (25%) for the fourth region, Gotland, cannot be explained in terms of recent habitat disjunction but is, instead, interpreted in terms of the restricted distribution of limestone bedrock on Gotland and the fact that die southern and northern Godand populations appear to have had different origins.     

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise FST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise FST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.     

Association between host's genetic diversity and parasite burden in damselflies

Recent research indicates that low genetic variation in individuals can increase susceptibility to parasite infection, yet evidence from natural invertebrate populations remains scarce. Here, we studied the relationship between genetic heterozygosity, measured as AFLP‐based inbreeding coefficient f_AFLP, and gregarine parasite burden from eleven damselfly, Calopteryx splendens, populations. We found that in the studied populations, 5–92% of males were parasitized by endoparasitic gregarines (Apicomplexa: Actinocephalidae). Number of parasites ranged from none to 47 parasites per male, and parasites were highly aggregated in a few hosts. Mean individual f_AFLP did not differ between populations. Moreover, we found a positive association between individual's inbreeding coefficient and parasite burden. In other words, the more homozygous the individual, the more parasites it harbours. Thus, parasites are likely to pose strong selection pressure against inbreeding and homozygosity. Our results support the heterozygosity‐fitness correlation hypothesis, which suggests the importance of heterozygosity for an individual's pathogen resistance.     

Effects of a recent founding event and intrinsic population dynamics on genetic diversity in an ungulate population

Maintenance of genetic diversity has recently become a management goal for a number of species, due to its importance for present and future population viability. Genetic drift, primarily through differential reproductive success and inbreeding, can accelerate the loss of genetic diversity in recently recovered populations. We attempt to quantify the consequences of these factors on the genetic diversity contained in a small, recently founded wood bison (Bison bison athabascae) population by examining the genetic variation in this conservation herd, the calves born therein, and its large source population. The Hook Lake Wood Bison Recovery Project was initiated to found a disease-free herd of wood bison containing a representative amount of the genetic diversity present in the Wood Buffalo National Park metapopulation. Levels of diversity in the Hook Lake Wood Bison Recovery Project founders are higher than in previous salvage attempts. To examine the effects of differential reproductive success on this population, we monitored parentage of the calves born in the Hook Lake Wood Bison Recovery Project for 3 years since the founders reached sexual maturity. Two of the male founders sired over 90% of the offspring born in this population, which has led to a reduction in diversity in their calves. Monitoring of reproductive success, and incorporation of selective breeding strategies will be required to reduce the rate at which genetic diversity is lost from this small, isolated population. These steps should occur in other recovery projects, particularly when a small number of individuals are capable of dominating reproduction.     

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θ_sil=∼0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima''s D=0.316 vs D=−0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (π_tot=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4N_e generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role.     

Genome-wide genetic diversity,population structure and admixture analysis in African and Asian cattle breeds

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.