Population structure and its implications for conservation of the great silver beetle Hydrophilus piceus in Britain

1. The great silver water beetle Hydrophilus piceus is one of the largest aquatic insects in Europe. In Britain it is rare and endangered, and confined to a small number of low-lying marshes. Very little is known about the beetle populations in any of these areas, or the connectivity between them.
2. To investigate the population structure of H. piceus in Britain, four polymorphic microsatellite loci were identified and characterized. The genome of this beetle seems to have few microsatellites but contains a high proportion of a larger repeated sequence.
3. All six of the main British populations (Somerset, Lewes, Pevensey, Romney, North Kent and Norfolk) showed substantial genetic diversity at the microsatellite loci. However, estimates of effective population size at one site (Pevensey) were remarkably low, at <10 adults for the period 2004–05.
4. Most of the genetic diversity was partitioned within rather than among the populations, although there was, nevertheless, significant genetic sub-structuring. Almost all population pairwise F _st estimates were significantly different from zero, and there was a clear isolation-by-distance effect. Assignment tests and cluster analyses demonstrated interpopulation relationships largely consistent with their geographical separations.
5. Hydrophilus disperses by flight, and records from moth traps indicated that there was no month in which the beetles never flew, but that flight activity was highest in the spring.
6. The genetic data highlight the need to maintain or regenerate habitat connectivity within flying distance for H. piceus , and to sustain large areas of suitable breeding marshes.     

Mitochondrial DNA reveals formation of nonhybrid frogs by natural matings between hemiclonal hybrids.

The European water frog Rana esculenta (RL), a natural hybrid between R. ridibunda (RR) and R. lessonae (LL), reproduces by hybridogenesis: haploid gametes usually contain an intact chromosome set of R. ridibunda (R); the lessonae nuclear genome (L) is lost from the germ line. Hybridity is restored in the next generation, via fertilization by syntopic R. lessonae. Matings between two hybrids (RL x RL) usually give inviable R. ridibunda (RR) progeny. The adult R. ridibunda subpopulation of Trubeschloo, a gravel pit in northern Switzerland, consists only of females. Fragment patterns for mitochondrial DNA (mtDNA) of these R. ridibunda were identical with those of syntopic R. esculenta and of local populations of R. lessonae; they differed from the patterns in eastern European populations of R. lessonae and of R. ridibunda mtDNAs (3.7% and 9.3% estimated sequence divergence, respectively). In contrast, mtDNAs of two R. ridibunda from an introduced Swiss population with both sexes, although different (2.7% divergence) from each other, were typical R. ridibunda rather than R. lessonae mtDNAs. These data, together with unisexuality, demonstrate conclusively that the all-female R. ridibunda population at Trubeschloo originated from matings between two R. esculenta. The formation of independently reproducing R. ridibunda populations via such hybrid x hybrid matings is precluded because progeny of these matings are unisexual. Recombination in the regenerated fertile R. ridibunda females, followed by matings with R. lessonae, nevertheless provides a mechanism for meiotic reshuffling of genetic material in ridibunda haplotypes that is not typically available in hemiclonal lineages.     

Small founding number and low genetic diversity in an introduced species exhibiting limited invasion success (speckled dace, Rhinichthys osculus)

Molecular evaluations of successful invaders are common, however studies of introduced species that have had limited invasion success, or have died out completely, are rare. We studied an introduced population of speckled dace (Rhinichthys osculus) from northern California, USA that has rapidly increased in abundance but remained restricted to a 25-km stretch of river since its introduction in the mid-1980s. Field and laboratory analyses indicate that invasion success of speckled dace is constrained by the combined effects of multiple predators. The role of bottleneck effects associated with the introduction has not been studied. We assayed variation in seven microsatellite loci and one mitochondrial DNA gene in the introduced population and nine putative source populations to identify the source population and evaluate bottleneck effects. The Trinity River system was supported as the source owing to its genetic similarity and geographic proximity to the introduced population. Consistent with a bottleneck, the introduced population exhibited reduced allelic and haplotype richness in comparison to source populations. Estimates of the genetically effective number of individuals founding the introduced population using nuclear coalescent analyses and a mitochondrial simulation procedure were highly concordant in suggesting that the initial colonizing group was comprised of about 10 individuals. A bottleneck effect in an exotic species exhibiting limited invasion success has rarely been documented and thus introduction of speckled dace represents an important model system for future investigation. Establishing a relationship between genetic diversity and factors limiting invasion success in this system (e.g., predator avoidance) will help determine the extent to which genetic diversity loss has constrained invasion success in speckled dace.     

Success of classical biocontrol agent Torymus sinensis within its expanding range in Europe

Torymus sinensis Kamijo (Hymenoptera, Torymidae), a classical biocontrol agent of chestnut gall wasp Dryocosmus kuriphilus (Hymenoptera, Cynipidae), was released in Croatia, Slovenia and Hungary in 2015. Following the introduction, the research of parasitism rates and population genetic indices on 40 different sites was performed to monitor and evaluate the success of establishment. The observed parasitism rates were unexpectedly high and negatively correlated with the distance from westernmost locality, while population genetic indices showed that populations of T. sinensis did not suffer from bottleneck‐induced founder effect phenomenon. Moreover, lack of genetic differentiation demonstrates that all populations share similar genetic structure, which could be shaped only by high levels of gene flow. We conclude that T. sinensis established viable and genetically diverse populations and successfully spread naturally from Italy across Slovenia to Croatia and Hungary.     

Genetic diversity and fitness in black-footed ferrets before and during a bottleneck

The black-footed ferret (Mustela nigripes) is an endangered North American carnivore that underwent a well-documented population bottleneck in the mid-1980s. To better understand the effects of a bottleneck on a free-ranging carnivore population, we used 24 microsatellite loci to compare genetic diversity before versus during the bottleneck, and compare the last wild population to two historical populations. We also compared genetic diversity in black-footed ferrets to that of two sibling species, the steppe polecat (Mustela eversmanni) and the European polecat (Mustela putorius). Black-footed ferrets during the bottleneck had less genetic diversity than steppe polecats. The three black-footed ferret populations were well differentiated (F(ST) = 0.57 +/- 0.15; mean +/- SE). We attributed the decrease in genetic diversity in black-footed ferrets to localized extinction of these genetically distinct subpopulations and to the bottleneck in the surviving subpopulation. Although genetic diversity decreased, female fecundity and juvenile survival were not affected by the population bottleneck.     

Genetic structure and diversity of a newly invasive species, the codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae) in China

Cydia pomonella (L.) was firstly reported in China in the 1950s and considered as one of the most serious invasive pest in fruit orchards of China. It spread rapidly from the original site in Xinjiang to other northwestern regions. The pest has further penetrated northeastern China since 2006. With its rapid invasion rate, most pome fruit production areas of China are being threatened. As yet there has been no research into the genetic diversity and structure of the codling moth population in China. We investigated the genetic variations of 12 C. pomonella populations collected from the main distribution regions (Xinjiang, Gansu and Heilongjiang Provinces) in China and compared them with one German and one Swiss population using eight microsatellites loci to infer the characteristics of genetic diversity and genetic structure. We observed sequential loss of genetic diversity and significant structuring associated with distribution but no significant correlation between genetic distance and geographic distance among northwestern populations. There was no genetic evidence for bottleneck effects in any of the populations. The results suggest that the loss of genetic diversity in C. pomonella populations resulted from the successive colonization of founder populations. Recent invasion history led to the lack of any bottleneck effect. The high level of population genetic structuring is related to the weak flight capacity of the codling moth and the human-aided dispersal rather than to geographic distance. These genetic data not only provide us with an understanding of the micro-evolutionary processes related to successful biological invasions, but also provide guidance for pest management strategies.     

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.     

A strong genetic footprint of the re‐introduction history of Alpine ibex (Capra ibex ibex)

A population’s neutral genetic variation is a composite of its size, degree of isolation and demographic history. Bottlenecks and founder events increase genetic drift, leading to the loss of genetic variation and increased genetic differentiation among populations. Gene flow has the opposite effects. Thus, gene flow can override the genetic patterns caused by founder events. Using 37 microsatellite loci, we investigated the effects of serial bottlenecks on genetic variation and differentiation among 42 Alpine ibex populations in Switzerland with known re‐introduction histories. We detected a strong footprint of re‐introduction events on contemporary genetic structure, with re‐introduction history explaining a substantial part of the genetic differentiation among populations. As a result of the translocation of a considerable number of individuals from the sole formerly surviving population in northern Italy, most of the genetic variation of the ancestral population is now present in the combined re‐introduced Swiss populations. However, re‐introductions split up the genetic variation among populations, such that each contemporary Swiss population showed lower genetic variation than the ancestral population. As expected, serial bottlenecks had different effects on the expected heterozygosity (He) and standardized number of alleles (sNa). While loss of sNa was higher in the first bottlenecks than in subsequent ones, He declined to a similar degree with each bottleneck. Thus, genetic drift was detected with each bottleneck, even when no loss of sNa was observed. Overall, more than a hundred years after the beginning of this successful re‐introduction programme, re‐introduction history was the main determinant of today’s genetic structure.     

Genetics of the Shimokita macaque population suggest an ancient bottleneck

The macaque population of the Shimokita Peninsula represents the northernmost distribution of this species and is isolated from other populations in the Tohoku region of Japan. A previous protein-based study revealed a high level of genetic variability in this population and considerable differentiation from other populations. In order to reassess the genetic features of the Shimokita macaques, we examined 11 autosomal microsatellite loci and three Y chromosomal microsatellite loci. We observed considerable differentiation from other Japanese populations of macaques, but in contrast to the previous results, we observed significantly lower genetic variability in this population. There was a weak indication of a population bottleneck, suggesting a decay over time from an excess of heterozygotes that might be expected in the initial stages of a bottleneck. This may indicate that an ancient bottleneck occurred during the warm period after the last glacial period rather than a recent bottleneck due to hunting in modern times. The frequencies of private alleles were exceptionally high in the Shimokita population, suggesting that the difference in variability as determined in various studies was due to accidental sampling of marker loci with low power to resolve genetic variations in the protein-based studies. The assessments of interpopulation differentiation as determined using autosomal and Y chromosomal markers were highly correlated, and using both types of markers the Shimokita population was found to be the most differentiated of the study populations, probably due to infrequent gene flow with surrounding populations.     

Mitochondrial DNA of ancient Cumanians: culturally Asian steppe nomadic immigrants with substantially more western Eurasian mitochondrial DNA lineages

The Cumanians were originally Asian pastoral nomads who in the 13th century migrated to Hungary. We have examined mitochondrial DNA from members of the earliest Cumanian population in Hungary from two archeologically well-documented excavations and from 74 modern Hungarians from different rural locations in Hungary. Haplogroups were defined based on HVS I sequences and examinations of haplogroup-associated polymorphic sites of the protein coding region and of HVS II. To exclude contamination, some ancient DNA samples were cloned. A database was created from previously published mtDNA HVS I sequences (representing 2,615 individuals from different Asian and European populations) and 74 modem Hungarian sequences from the present study. This database was used to determine the relationships between the ancient Cumanians, modern Hungarians, and Eurasian populations and to estimate the genetic distances between these populations. We attempted to deduce the genetic trace of the migration of Cumanians. This study is the first ancient DNA characterization of an eastern pastoral nomad population that migrated into Europe. The results indicate that, while still possessing a Central Asian steppe culture, the Cumanians received a large admixture of maternal genes from more westerly populations before arriving in Hungary. A similar dilution of genetic, but not cultural, factors may have accompanied the settlement of other Asian nomads in Europe.     

Successful worldwide invasion of the veined rapa whelk, <Emphasis Type="Italic">Rapana venosa</Emphasis>, despite a dramatic genetic bottleneck

Biological invasions represent an important component of global change, with potentially huge detrimental effects on native biological biodiversity and ecosystems. Knowledge about invasion history provides information about the invasion process and the origin and genetic composition of invading populations. To clarify the source and invasive routes of a successful world-wide invader, the veined rapa whelk, Rapana venosa, genetic variability of samples from five representative native populations from coasts of Japan and China and 13 worldwide invasive populations was analyzed using 11 nuclear microsatellite loci. A dramatic decrease of genetic variation was detected in the invasive populations compared with the native populations. The results demonstrated that R. venosa was capable of establishing itself in many areas despite a dramatic genetic bottleneck, suggesting that a remarkable reduction of genetic diversity is not a limiting factor for short-term success of this invasive species. Considering the lack of mitochondrial variation previously observed in the invasive populations, the dramatic genetic bottleneck and the allele distribution detected using microsatellites suggested that the original introduced Black Sea population could have been founded by very few individuals, perhaps only a single female and a single male. The initial invasive Black Sea population was likely an accidental introduction from Japan, and then invaded the Adriatic Sea by range expansion, which served as a source for subsequent invasive populations in Europe and America by various transport vectors. In addition, microsatellite alleles in the invasive populations showed a tendency to mutate with the addition or deletion of a single repeat, which is consistent with the stepwise mutation model. Our findings provide a good example of how an aquatic invader with a drastic genetic bottleneck and very low genetic diversity rapidly expands its geographical range.     

Assessing losses of genetic diversity due to translocation: long-term case histories in Merriam's turkey (<Emphasis Type="Italic">Meleagris gallopavo merriami</Emphasis>)

Translocation is a widely used tool in wildlife management, but populations established as a result of translocations may be subject to a range of genetic problems, including loss of genetic diversity and founder effects. The genetic impact of single translocation events can be difficult to assess because of complex management histories in translocated or source populations. Here we use molecular markers to assess the genetic impact of three well-documented translocation events, each occurring between 42 and 53 years ago and each originating from a native, extant source population that we also included in our study. Comparing translocated populations to their sources, we found genetic evidence of a recent bottleneck in all three translocated populations, including one which is now a very large, productive population. Based on our results, we recommend caution in (1) using short term census data to assess the long term success of a translocation and (2) conducting serial translocations (i.e., using translocated populations as the source for other translocations), which could exacerbate a genetic bottleneck. We also used the data on translocated populations to investigate the relative utility of three bottleneck detection methods. With this dataset, only assessment of the modal allele frequency distribution, described by Luikart etal. [Journal of Heredity, 89, 238–247 (1998)], provided evidence of a bottleneck in the absence of source population data.     

Wherefore and whither the naturalist?

Most, if not all, of the "classic," often-cited examples illustrating the genetic effects of a population bottleneck are open to alternative explanations due to the lack of adequate control populations, that is, low levels of genetic variability are often assumed to be the result of a past population bottleneck without having any prebottleneck measures. Here we provide the first clear case history where both prebottleneck and postbottleneck measures of genetic variability have been collected from a natural system. Analysis of DNA from museum specimens of the greater prairie chicken Tympanuchus cupido from central Illinois revealed the loss of specific alleles (known to have been present earlier in this century) following a demographic contraction. Lost alleles included common ones present in all other populations sampled and others unique to the Illinois population.     

Genetic diversity and population structure of the invasive alien red swamp crayfish

High genetic diversity is thought to characterize successful invasive species, as the potential to adapt to new environments is enhanced and inbreeding is reduced. The red swamp crayfish, Procambarus clarkii, native to northeastern Mexico and south-central USA was introduced to Nanjing, China from Japan in 1929. Little is known about the genetic diversity and population structure of this species in China. We examined the genetic diversity and population structure of six P. clarkii populations using nine polymorphic microsatellites. Among the six populations, Nanjing population showed the highest allele number, allele richness and gene diversity, which is consistent with records indicating Nanjing may be the first site of introduction. In all six populations, significant heterozygote deficit was observed, suggesting founder effects and non-random mating. Analysis of bottleneck under infinite allele model, stepwise mutation model and two-phased model of mutation revealed evidence of a recent bottleneck in all these populations. Pairwise genetic distance analysis, AMOVA and assignment tests demonstrated high genetic differentiation between populations. Pairwise genetic distance did not fit the pairwise geographic distance, suggesting that human mediated dispersal have played a role in the population expansion and genetic differentiation.     

Genetic management of the red squirrel,Sciurus vulgaris: a practical approach to regional conservation

The progressive decline in red squirrel (Sciurus vulgaris) numbers in Wales has led to conservation and reintroduction projects being established on the island of Anglesey. The recovery of the island’s remnant wild population was initially successful, however concern remained over potential loss of genetic diversity resulting from an observed demographic bottleneck. We used mitochondrial DNA (mtDNA) control region sequences and six microsatellite loci to assess current levels of genetic variation in the population. Samples were monomorphic for control region sequences and a historic specimen from the same area carrying a different haplotype demonstrated a loss of mtDNA diversity during the last 20 years. Inclusion of other Welsh haplotypes indicated phylogeographic structure in the region, in contrast to previous UK studies. Genotyping results showed allelic diversity and heterozygosity to be less than 50% of that recorded in other UK populations, with strong evidence for a recent genetic bottleneck. A parallel reintroduction programme on Anglesey included genetic analysis of individuals during the selection of captive breeding pairs. We present analysis of sequence and microsatellite data, and subsequent management decisions taken to maximise diversity in the founder and F1 generations. Population and Habitat Viability Analysis applied to both populations modelled future levels of heterozygosity and allelic diversity. Supplementation of the remnant and reintroduced populations with translocated squirrels was simulated as a potential management tool; results support use of this strategy to reduce loss of diversity and increase survival. The limitations of applying conservation genetic theory within small-scale management projects are discussed.     

Low genetic diversity in the bottlenecked population of endangered non-native banteng in northern Australia

Undomesticated (wild) banteng are endangered in their native habitats in Southeast Asia. A potential conservation resource for the species is a large, wild population in Garig Gunak Barlu National Park in northern Australia, descended from 20 individuals that were released from a failed British outpost in 1849. Because of the founding bottleneck, we determined the level of genetic diversity in four subpopulations in the national park using 12 microsatellite loci, and compared this to the genetic diversity of domesticated Asian Bali cattle, wild banteng and other cattle species. We also compared the loss of genetic diversity using plausible genetic data coupled to a stochastic Leslie matrix model constructed from existing demographic data. The 53 Australian banteng sampled had average microsatellite heterozygosity (HE) of 28% compared to 67% for outbred Bos taurus and domesticated Bos javanicus populations. The Australian banteng inbreeding coefficient (F) of 0.58 is high compared to other endangered artiodactyl populations. The 95% confidence bounds for measured heterozygosity overlapped with those predicted from our stochastic Leslie matrix population model. Collectively, these results show that Australian banteng have suffered a loss of genetic diversity and are highly inbred because of the initial population bottleneck and subsequent small population sizes. We conclude that the Australian population is an important hedge against the complete loss of wild banteng, and it can augment threatened populations of banteng in their native range. This study indicates the genetic value of small populations of endangered artiodactyls established ex situ.     

Signatures of demographic bottlenecks in European wolf populations

Monitoring the loss of genetic diversity in wild populations after a bottleneck event is a priority in conservation and management plans. Here, we used diverse molecular markers to search for signatures of demographic bottlenecks in two wolf populations; an isolated population from the Iberian Peninsula and a non-isolated population from European Russia. Autosomal, mtDNA and Y-chromosomal diversity and the effective population size (N_e) were significantly lower in the Iberian population. Neutrality tests using mtDNA sequences, such as R_2, Fu and Li’s F*, Tajima’s D and Fu’s F_s, were positively significant in the Iberian population, suggesting a population decline, but were not significant for the Russian population, likely due to its larger effective population size. However, three tests using autosomal data confirmed the occurrence of the genetic bottleneck in both populations. The M-ratio test was the only one providing significant results for both populations. Given the lack of consistency among the different tests, we recommend using multiple approaches to investigate possible past bottlenecks. The small effective population size (about 50) in the Iberian Peninsula compared to the presumed extant population size could indicate that the bottleneck was more powerful than initially suspected or an overestimation of the current population. The risks associated with small effective population sizes suggest that the genetic change in this population should be closely monitored in the future. On the other hand, the relatively small effective population size for Russian wolves (a few hundred individuals) could indicate some fragmentation, contrary to what is commonly assumed.     

Genetic differentiation of starling (Sturnus vulgaris: Aves) populations in New Zealand and Great Britain

Several hundred starlings (Sturnus vulgaris) were introduced to New Zealand from Great Britain during1860–1880. Allozymic variation at 24 loci was analysed in winter populations sampled at six localities in each country. New Zealand samples had fewer alleles per locus but the same mean heterozygosity (3% per locus) and proportion of polymorphic loci as did British samples. Winter populations in Britain contain European migrants and were genetically homogeneous. Paradoxically, genetic distances among derived New Zealand populations, and between New Zealand and Great Britain were much greater, similar in magnitude to those observed among allopatric populations in other avian species. The geographical pattern of genetic variation in New Zealand suggests that reproductive isolation of populations and random drift have contributed to the development of population differentiation.     

Genetic differentiation of a European caddisfly: past and present gene flow among fragmented larval habitats

We describe the genetic structure of a freshwater insect species and interpret it in terms of present-day population dynamics and possible postglacial colonization history. The sampling regime represented a large area of the species range in northwest Europe, particularly focusing on Britain, a region relatively neglected in molecular population genetic studies. Plectrocnemia conspersa generally showed low levels of genetic variation across the sampled populations (Nei's D = 0.0138) and subdivision was unrelated to the pattern of the drainage network. However, the results do suggest that populations across the region are not at equilibrium and that British populations still show effects of the recolonization of the species following the last glacial maximum. Levels of genetic diversity were lower in Britain than in mainland Europe. Two-dimensional scaling showed genetic differentiation between major regions and the pattern of genetic diversity indicates a more recent origin of populations in the north and west of the area compared with the south and east. We argue that, despite the highly fragmented larval habitat, dispersal over tens of kilometres is frequent. Over longer distances, however, P. conspersa does still show evidence of founder effects and postglacial range expansion into Britain.     

森林砍伐对苦槠种群遗传结构的影响

人类活动严重干扰着自然生态系统,其中砍伐是对森林生态系统最常见的干扰之一,它导致森林退化,植物种群变小,甚至灭绝,遗传多样性也随之下降。当被破坏的森林未被转换性利用时,则会逐渐恢复,但由于瓶颈效应,恢复起来的生态系统中植物种群的遗传结构可能会改变。恢复种群遗传组成的改变一方面与干扰的强度、频度和持续时间有关,另一方面,也受植物生活史特点的深刻影响。然而,我国对于砍伐后恢复起来的森林生态系统中生物多样性的改变,尤其是遗传多样性的改变的研究并不多见。研究在浙江省宁波市天童国家森林公园及周边地区选择了5个苦槠种群,采用SSR微卫星标记来分析砍伐对苦槠种群遗传结构的影响。5对多态SSR引物共得到了29个等位基因。种群内维持了较高的遗传多样性,种群间遗传分化程度较低,基因流达8．68。恢复林和成熟林种群的遗传多样性相差不大,以阿育王寺地区恢复种群的最高;表明砍伐对于苦槠种群遗传多样性的影响不大,这与苦槠较强的萌条能力有关。尽管如此,在恢复种群中观察到近期的种群瓶颈,显示出砍伐对种群遗传组成的影响;而在一个成熟林中也观察到种群瓶颈,这是因片断化导致种群变小之故。植被保存最好的天童国家森林公园内苦槠种群的遗传多样性却较低,这可能与成熟林中苦槠优势度较低有关。