Comparison of historical bottleneck effects and genetic consequences of re‐introduction in a critically endangered island passerine

Re‐introduction is an important tool for recovering endangered species; however, the magnitude of genetic consequences for re‐introduced populations remains largely unknown, in particular the relative impacts of historical population bottlenecks compared to those induced by conservation management. We characterize 14 microsatellite loci developed for the Seychelles paradise flycatcher and use them to quantify temporal and spatial measures of genetic variation across a 134‐year time frame encompassing a historical bottleneck that reduced the species to ~28 individuals in the 1960s, through the initial stages of recovery and across a second contemporary conservation‐introduction‐induced bottleneck. We then evaluate the relative impacts of the two bottlenecks, and finally apply our findings to inform broader re‐introduction strategy. We find a temporal trend of significant decrease in standard measures of genetic diversity across the historical bottleneck, but only a nonsignificant downward trend in number of alleles across the contemporary bottleneck. However, accounting for the different timescales of the two bottlenecks (~40 historical generations versus <1 contemporary generation), the loss of genetic diversity per generation is greater across the contemporary bottleneck. Historically, the flycatcher population was genetically structured; however, extinction on four of five islands has resulted in a homogeneous contemporary population. We conclude that severe historical bottlenecks can leave a large footprint in terms of sheer quantity of genetic diversity lost. However, severely depleted genetic diversity does not render a species immune to further genetic erosion upon re‐introduction. In some cases, the loss of genetic diversity per generation can, initially at least, be greater across re‐introduction‐induced bottlenecks.     

Genetic diversity and structure of <Emphasis Type="BoldItalic">Crotalus triseriatus</Emphasis>, a rattlesnake of central Mexico

The isolated and fragmented populations are highly susceptible to stochastic events, increasing the extinction risk because of the decline in putative adaptive potential and individual fitness. The population has high heterozygosity values and a moderate allelic diversity, the heterozygosity values are higher than in most other Crotalus species and snake studies. Possibly these high levels of genetic diversity can be related to a large founder size, high effective population size, multiple paternity and overlapping generations. We did not find the genetic structuring but the effective number of alleles \((N_{\mathrm{e}})\) was 138.1. We found evidence of bottlenecks and the majority of rattlesnakes were unrelated, despite the small sample size, endemic status, the isolated and fragmented habitat. The genetic information provided in this study can be useful as a first approach to try to make informed conservation efforts for this species and also, important to preserve the habitat of this species; the endangered Abies–Pinus forest of the Nevado the Toluca Volcano.     

AlleleRetain: a program to assess management options for conserving allelic diversity in small,isolated populations

Preserving genetic health is an important aspect of species conservation. Allelic diversity is particularly important to conserve, as it provides capacity for adaptation and thus enables long‐term population viability. Allele retention is difficult to predict beyond one generation for real populations with complex demography and life‐history traits, so we developed a computer model to simulate allele retention in small populations. AlleleRetain is an individual‐based model implemented in r and can be applied to assess management options for conserving allelic diversity in small populations of animals with overlapping generations. AlleleRetain remedies the limitations of similar existing software, and its source code is freely available for further modification. AlleleRetain and its supporting materials can be downloaded from https://sites.google.com/site/alleleretain/ or CRAN ( http://cran.r-project.org ).     

Conservation genetics of population bottlenecks: the role of chance,selection, and history

Conservation genetics studies of populations bottlenecks are commonly framed under the detrimental paradigm of inbreeding depression. This conceptual paradigm presupposes a direct and unambiguous relationship between population size, genetic diversity, fitness, and extinction. Here, I review a series of studies that emphasize the role of chance, selection, and history in determining the genetic consequences of population bottlenecks. The variable responses of bottlenecks to fitness, phenotypic variation, and heritable variation emphasize the necessity to explore the relationship between molecular genetic diversity, fitness, adaptive genetic diversity, and extinction beyond the detrimental paradigm of inbreeding depression. Implications for conservation and management are presented as guidelines and testable predictions regarding the potential effects of bottlenecks on population viability and extinction.     

Past population history versus recent population decline – founder effects in island species and their genetic signatures

Island populations are mostly characterized by low genetic diversity if compared with their mainland conspecifics. This is often explained as a consequence of founder effects in the wake of island colonization and concomitant bottlenecks. In a recent contribution, Stuessy et al. (Journal of Biogeography, 2012, 39, 1565–1566) point out that the genetic imprint of past founder effects is no longer visible today, as most island colonizations occurred millions of generations ago. The authors argue that low genetic diversity detectable today is mainly caused by recent environmental factors such as anthropogenic habitat destruction. This scenario should be complemented by the influence of long‐term isolation and small habitat size, which often lead to strong population fluctuations and repeated bottlenecks. In consequence, inbreeding and genetic drift, coupled with the potential effects of purging in small populations, may also result in genetic diversity remaining low for a long time after colonization.     

metapop2: Re‐implementation of software for the analysis and management of subdivided populations using gene and allelic diversity

Management programmes often have to make decisions based on the analysis of the genetic properties and diversity of populations. Expected heterozygosity (or gene diversity) and population structure parameters are often used to make recommendations for conservation, such as avoidance of inbreeding or migration across subpopulations. Allelic diversity, however, can also provide complementary and useful information for conservation programmes, as it is highly sensitive to population bottlenecks, and is more related to long‐term selection response than heterozygosity. Here we present a completely revised and updated re‐implementation of the software metapop for the analysis of diversity in subdivided populations, as well as a tool for the management and dynamic estimation of optimal contributions in conservation programmes. This new update includes computation of allelic diversity for population analysis and management, as well as a simulation mode to forecast the consequences of taking different management strategies over time. Furthermore, the new implementation in C++ includes code optimization and improved memory usage, allowing for fast analysis of large data sets including single nucleotide polymorphism markers, as well as enhanced cross‐software and cross‐platform compatibility.     

Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks

Evolutionary and conservation biologists often use molecular markers to evaluate whether populations have experienced demographic bottlenecks that resulted in a loss of genetic variation. We evaluated the utility of microsatellites for detection of recent, severe bottlenecks and compared the amounts of genetic diversity lost in bottlenecks of different sizes. In experimental mesocosms, we established replicate populations by releasing 1, 2, 4 or 8 pairs of the western mosquitofish, Gambusia affinis (Poeciliidae). Using eight polymorphic microsatellite loci, we quantified seven indices of genetic diversity or change that have been used to assess the effects of demographic bottlenecks on populations. We compared indices for the experimentally bottlenecked populations to those for the source population and examined differences between populations established with different numbers of founders. Direct count heterozygosity and the proportion of polymorphic loci were not very sensitive to genetic changes that resulted from the experimental bottlenecks. Heterozygosity excess and expected heterozygosity were useful to varying degrees in the detection of bottlenecks. Allelic diversity and temporal variance in allele frequencies were most sensitive to genetic changes that resulted from the bottlenecks, and the temporal variance method was slightly more correlated with bottleneck size than was allelic diversity. Based on comparisons to a previous study with allozymes, heterozygosity, temporal variance in allele frequencies and allelic diversity, but not proportion of polymorphic loci, appear to be more sensitive to demographic bottlenecks when quantified using microsatellites. We found that analysis of eight highly polymorphic loci was sufficient to detect a recent demographic bottleneck and to obtain an estimate of the magnitude of bottleneck severity.     

Genetic load,inbreeding depression and heterosis in an age‐structured metapopulation

In a metapopulation, the process of recurrent local extinction and recolonization gives rise to an age structure among demes. Recently established demes will tend to differ from older demes in terms of the levels of genetic diversity found within them and the way this diversity is distributed among demes in the same and different ages. The effects of population turnover on average levels of genetic diversity among demes in a metapopulation have been the focus of much attention, both for neutral and nonneutral loci, but much less is known about the distribution of nonneutral genetic diversity among demes of different ages. In this paper, we used computer simulations to study the distribution of genetic load, inbreeding depression and heterosis in an age‐structured metapopulation. We found that, for mildly deleterious mutations, within‐deme inbreeding depression increased, whereas heterosis and genetic load decreased with deme age following severe colonization bottlenecks. In contrast, recessive lethal alleles tended to be purged during colonization, with older populations showing higher genetic load and higher within‐deme inbreeding depression. Heterosis caused by recessive lethal alleles and resulting from gene flow among different demes tended to be greatest for young demes, because the mutations responsible tended to be purged in the first few generations after colonization, but its effects increased again as populations grow older as a result of immigration. Our results point to a need for estimates of genetic diversity, genetic load, within‐deme inbreeding depression and heterosis in demes of different age classes separately.     

Bottlenecked but long-lived: high genetic diversity retained in white-tailed eagles upon recovery from population decline

Most of the white-tailed eagle (Haliaeetus albicilla) populations in Europe experienced dramatic declines during the twentieth century. However, owing to intense conservation actions and the ban of DDT and other persistent pollutants, populations are currently recovering. We show that despite passing through demographic bottlenecks, white-tailed eagle populations have retained significant levels of genetic diversity. Both genetic and ringing data indicate that migration between populations has not been a major factor for the maintenance of genetic variability. We argue that the long generation time of eagles has acted as an intrinsic buffer against loss of genetic diversity, leading to a shorter effective time of the experienced bottleneck. Notably, conservation actions taken in several small sub-populations have ensured the preservation of a larger proportion of the total genetic diversity than if conservation had focused on the population stronghold in Norway. For conservation programmes targeting other endangered, long-lived species, our results highlight the possibility for local retention of high genetic diversity in isolated remnant populations.     

Clonality disguises the vulnerability of a threatened arid zone Acacia

Long‐lived, widespread plant species are expected to be genetically diverse, reflecting the interaction between large population sizes, overlapping generations, and gene flow. Such species are thought to be resilient to disturbance, but may carry an extinction debt due to reproductive failure. Genetic studies of Australian arid zone plant species suggest an unusually high frequency of asexuality, polyploidy, or both. A preliminary AFLP genetic study implied that the naturally fragmented arid zone tree, Acacia carneorum, is almost entirely dependent on asexual reproduction through suckering, and stands may have lacked genetic diversity and interconnection even prior to the onset of European pastoralism. Here we surveyed microsatellite genetic variation in 20 stands to test for variation in life histories and further assessed the conservation status of the species by comparing genetic diversity within protected stands in National Parks and disturbed range lands. Using herbarium records, we estimate that 219 stands are extant, all of which occur in the arid zone, west of the Darling River in southeastern Australia. With two exceptions, all surveyed stands comprised only one multilocus genet and at least eight were putatively polyploid. Although some stands comprise thousands of stems, our findings imply that the species as a whole may represent ~240 distinct genetic individuals, many of which are polyploid, and most are separated by >10 km of unsuitable habitat. With only 34% of stands (and therefore genets) occurring within conservation reserves, A. carneorum may be at much greater risk of extinction than inferred from on‐ground census data. Land managers should prioritize on‐ground preservation of the genotypes within existing reserves, protecting both vegetative suckers and seedlings from herbivory. Importantly, three stands are known to set viable seed and should be used to generate genetically diverse germ‐plasm for ex situ conservation, population augmentation, or translocation.     

Combining genetic and demographic data for prioritizing conservation actions: insights from a threatened fish species

Prioritizing and making efficient conservation plans for threatened populations requires information at both evolutionary and ecological timescales. Nevertheless, few studies integrate multidisciplinary approaches, mainly because of the difficulty for conservationists to assess simultaneously the evolutionary and ecological status of populations. Here, we sought to demonstrate how combining genetic and demographic analyses allows prioritizing and initiating conservation plans. To do so, we combined snapshot microsatellite data and a 30‐year‐long demographic survey on a threatened freshwater fish species (Parachondrostoma toxostoma) at the river basin scale. Our results revealed low levels of genetic diversity and weak effective population sizes (<63 individuals) in all populations. We further detected severe bottlenecks dating back to the last centuries (200–800 years ago), which may explain the differentiation of certain populations. The demographic survey revealed a general decrease in the spatial distribution and abundance of P. toxostoma over the last three decades. We conclude that demo‐genetic approaches are essential for (1) identifying populations for which both evolutionary and ecological extinction risks are high; and (2) proposing conservation plans targeted toward these at risk populations, and accounting for the evolutionary history of populations. We suggest that demo‐genetic approaches should be the norm in conservation practices.     

海南岛海菖蒲种群克隆多样性和遗传结构

海草是生长在潮间带和潮下带的单子叶植物,由海草植物组成的海草床是生态系统服务价值最高的生态系统之一.然而,近几十年人类活动干扰、全球气候变化等因素导致海草床衰退严重.海菖蒲是分布于热带、体型最大的雌雄异株海草,我国位于该物种的分布北缘,本文对其克隆多样性和遗传结构进行研究,以期为该海草的保护提供参考.采用4对多态微卫星标记对采自海南岛4个地点的现存海菖蒲种群的样品进行基因型分型.结果表明:海菖蒲种群克隆多样性和遗传多样性较低,这与所研究种群处于分布区北缘有关;种群间遗传分化值范围较大(0.073~0.309),这可能是由于分布于不同港湾的种群间距离范围较大以及局域绝灭/再拓殖的遗传漂变效应所致;各种群未发现近期经历种群瓶颈的信号,很可能是由于种群内遗传多样性已经很低,种群减小未能导致遗传多样性明显降低.根据种群遗传特征,提出了重点保护种群的建议,鉴于目前我国海菖蒲等海草快速衰退的局面,应强化海草保护并实施海草床生态恢复.     

Demographic fluctuations lead to rapid and cyclic shifts in genetic structure among populations of an alpine butterfly,Parnassius smintheus

Many populations, especially in insects, fluctuate in size, and periods of particularly low population size can have strong effects on genetic variation. Effects of demographic bottlenecks on genetic diversity of single populations are widely documented. Effects of bottlenecks on genetic structure among multiple interconnected populations are less studied, as are genetic changes across multiple cycles of demographic collapse and recovery. We take advantage of a long‐term data set comprising demographic, genetic and movement data from a network of populations of the butterfly, Parnassius smintheus, to examine the effects of fluctuating population size on spatial genetic structure. We build on a previous study that documented increased genetic differentiation and loss of spatial genetic patterns (isolation by distance and by intervening forest cover) after a network‐wide bottleneck event. Here, we show that genetic differentiation was reduced again and spatial patterns returned to the system extremely rapidly, within three years (i.e. generations). We also show that a second bottleneck had similar effects to the first, increasing differentiation and erasing spatial patterns. Thus, bottlenecks consistently drive random divergence of allele frequencies among populations in this system, but these effects are rapidly countered by gene flow during demographic recovery. Our results reveal a system in which the relative influence of genetic drift and gene flow continually shift as populations fluctuate in size, leading to cyclic changes in genetic structure. Our results also suggest caution in the interpretation of patterns of spatial genetic structure, and its association with landscape variables, when measured at only a single point in time.     

Genetic Effects of a Persistent Bottleneck on a Natural Population of Ornate Box Turtles (Terrapene ornata)

Human activities in the past few hundred years have caused enormous impacts on many ecosystems, greatly accelerating the rate of population decline and extinction. In addition to habitat alteration and destruction, the loss of genetic diversity due to reduced population size has become a major conservation issue for many imperiled species. However, the genetic effects of persistent population bottlenecks can be very different for long-lived and short-lived species when considering the time scale of centuries. To investigate the genetic effects of persistent population bottlenecks on long-lived species, we use microsatellite markers to assess the level of genetic diversity of a small ornate box turtle population that has experienced a persistent bottleneck in the past century, and compare it to a large relatively undisturbed population. The genetic signature of a recent bottleneck is detected by examining the deviation from mutation-drift equilibrium in the small population, but the bottleneck had little effect on its level of genetic diversity. Computer simulations combined with information on population structure suggest that an effective population size of 300, which results in a census population size of 700, would be required for the small population to maintain 90% of the average number of alleles per locus in the next 200 years. The life history of long-lived species could mask the accelerated rate of genetic drift, making population recovery a relatively slow process. Statistical analysis of genetic data and empirical-based computer simulations can be important tools to facilitate conservation planning.     

Genetic composition of the Jadro softmouth trout following translocation into a new habitat

Genetic founder effects of a historical translocation (1965; app. 12 generations ago) of endangered softmouth trout from the only remaining indigenous population to an adjacent uninhabited river were investigated. A comparison of 15 microsatellites from contemporary samples in both the source and re-established populations indicated a very low level of genetic diversity within the two populations. Furthermore, considerable differences in estimates of variability and effective population sizes were detected between populations, but no recent bottlenecks were evident. Our data suggest that the re-established population has lost variation due to genetic drift associated with founder effects following the translocation. Accordingly, in relation to management, we suggest that the re-established population could serve as a secondary source of individuals to buffer possible extinction due to demographic events. Finally, conservation initiatives to enhance the census population size and increase levels of variability in the re-established population are proposed. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Genetic diagnosis of a rare myrmecochorous species,Plagiorhegma dubium (Berberidaceae): Historical genetic bottlenecks and strong spatial structures among populations

Distribution of genetic variation over time and space is relevant to demographic histories and tightly linked to ecological disturbances as well as evolutionary potential of an organism. Therefore, understanding the pattern of genetic diversity is a primary step in conservation and management projects for rare and threatened plant species. We used eight microsatellite markers to examine the level of genetic diversity, spatial structure, and demographic history of Plagiorhegma dubium, a rare myrmecochorous herb, populations sampled across northeast Asia and Siberia. We found low within‐population genetic variation associated with historical bottlenecks. Although pairwise F_ST values were not much higher than the ones found in similar life form species, STRUCTURE and PCoA revealed a clear broadscale spatial pattern of genetic structure. Bayesian clustering (best K = 6) and PCoA identified three populations that are distinctive from neighboring populations in the Korean peninsula, which suggests potential units for conservation and management plans in Korea. MIGRATE‐N and BAYESASS showed that both contemporary (0.003–0.045) and historical migration rates (2 × e^?5?4.6 × e^?4) were low. Our findings provide a good example, where genetic considerations should be integrated for conservation and management plans of rare and threatened species.     

Phylogeography and genetic structure of the threatened Canarian Juniperus cedrus (Cupressaceae)

We used plastid sequences (trnL, trnL‐trnF, petN‐psbM and trnT‐trnL) to infer the phylogenetic relationships and inter‐island connections of the Canarian Juniperus cedrus, and AFLP fingerprints to assess its genetic diversity patterns. Maximum Likelihood, Maximum Parsimony and Bayesian methods suggest independent colonization events for the three Macaronesian junipers and support the monophyly of J. cedrus. Plastid sequences reveal a low genetic diversity (three haplotypes) and do not provide sufficient information to resolve its temporal and geographical origin. AFLPs indicate a greater isolation in J. cedrus than in other Macaronesian trees with similar distributions and dispersal syndromes. Gran Canaria harbours the least genetically diverse population, which justifies immediate conservation actions. This island and Tenerife also show independent genetic structure, meaning that genetic exchange from other islands should be avoided in eventual reinforcements. Populations from La Palma and La Gomera show the highest genetic diversity levels and number of polymorphic AFLPs, probably because a lower incidence of felling has allowed a less dramatic influence of genetic bottlenecks. We suggest that management efforts should prioritize populations from these islands to preserve the evolutionary potential of the species, but we also stress the importance of knowledge of the evolutionary history, genetic structure and ecological interactions in conservation strategies. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 376–394.     

Genetic analysis of a documented population bottleneck: introduced Bennett's wallabies (Macropus rufogriseus rufogriseus) in New Zealand

Few bottlenecks of wild populations are sufficiently well-documented to constitute models for testing theories about the impact of bottlenecks on genetic variation, and subsequent population persistence. Relevant details of the Bennett's wallaby (Macropus rufogriseus rufogriseus) introduction into New Zealand were recorded (founder number, source and approximate bottleneck duration) and suggest this may provide a rare opportunity to examine the efficacy of tests designed to detect recent bottlenecks in wild populations. We first assessed the accuracy of historic accounts of the introduction using genetic diversity detected in mitochondrial DNA (mtDNA) and at five microsatellite loci. Phylogenetic analyses of mtDNA D-loop sequence haplotypes were consistent with the reported origin of the founders as Tasmania, rather than one of the Bass Strait islands in which Bennett's wallabies are also found. Microsatellite allele frequencies from the Tasmanian source population were then used to seed bottleneck simulations encompassing varying sizes and numbers of generations, in order to assess the severity of bottleneck consistent with diversity observed in the New Zealand population. The results suggested that the founder number was unlikely to have been as small as the three animals suggested by the account of the introduction. Nonetheless, the bottleneck was probably severe; in the range of three to five pairs of wallabies for one to three generations. It resulted in significantly reduced levels of allelic diversity and heterozygosity relative to the source population. This bottleneck is only detectable under the infinite allele model (IAM) and not under the stepwise mutation model (SMM) or the two-phase model (TPM), and possible explanations for this are discussed.     

Genetic depletion at adaptive but not neutral loci in an endangered bird species

Many endangered species suffer from the loss of genetic diversity, but some populations may be able to thrive even if genetically depleted. To investigate the underlying genetic processes of population bottlenecks, we apply an innovative approach for assessing genetic diversity in the last known population of the endangered Pale‐headed Brushfinch (Atlapetes pallidiceps) in Ecuador. First, we measure genetic diversity at eleven neutral microsatellite loci and adaptive SNP variation in five Toll‐like receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift as the main force shaping genetic diversity in this species and indicate a 99 % reduction in population size dating back several hundred years. Second, we compare contemporary microsatellite diversity with historic museum samples of A. pallidiceps, finding no change in genetic diversity. Third, we compare genetic diversity in the Pale‐headed Brushfinch with two co‐occurring‐related brushfinch species (Atlapetes latinuchus, Buarremon torquatus), finding a reduction of up to 91% diversity in the immune system genes but not in microsatellites. High TLR diversity is linked to decreased survival probabilities in A. pallidiceps. Low TLR diversity is thus probably an adaptation to the specific selection regime within its currently very restricted distribution (approximately 200 ha), but could severely restrict the adaptive potential of the species in the long run. Our study illustrates the importance of investigating both neutral and adaptive markers to assess the effect of population bottlenecks and for recommending specific management plans in endangered species.     

Genetic diversity and differentiation of fragmented reedbeds (<Emphasis Type="Italic">Phragmites australis</Emphasis>) in the United Kingdom

Reedbeds, which are dominated by the common reed Phragmites australis, provide one of the most important aquatic habitats in the United Kingdom, and have been identified as a priority habitat under the UK Biodiversity Action Plan. Ongoing conservation and management of reedbeds is necessary because past eradication and fragmentation have been extensive. However, there has been little consideration of the potential long-term effects that may arise if processes such as founder effects during restoration projects, or genetic bottlenecks following harvesting, are leading to reductions in genetic diversity. In this study, we used microsatellite data to compare the genetic diversity of 19 P. australis stands in the UK, and found that neither size, management, nor habitat disturbance were affecting genetic diversity. Mixed reproduction (clonal and sexual), possibly combined with gene flow across relatively small spatial scales, appears to be maintaining genetic diversity within most stands. However, most stands were highly genetically differentiated from one another, which implies low gene flow. Long-term genetic diversity in managed stands may therefore require periodic bolstering from other populations, combined with the simultaneous cultivation of multiple generations. In addition, low gene flow suggests that managers should actively introduce plants into all areas in which reedbeds are desired. In conclusion, our study shows that reedbed restoration and maintenance do not seem to be adversely affecting the population genetics of P. australis, but the importance of genetic diversity should be factored into long-term projects.