Fine-scale genetic structure of a long-lived reptile reflects recent habitat modification

Anthropogenic habitat fragmentation — ubiquitous in modern ecosystems — has strong impacts on gene flow and genetic population structure. Reptiles may be particularly susceptible to the effects of fragmentation because of their extreme sensitivity to environmental conditions and limited dispersal. We investigate fine-scale spatial genetic structure, individual relatedness, and sex-biased dispersal in a large population of a long-lived reptile (tuatara, Sphenodon punctatus) on a recently fragmented island. We genotyped individuals from remnant forest, regenerating forest, and grassland pasture sites at seven microsatellite loci and found significant genetic structuring (R_ST = 0.012) across small distances (< 500 m). Isolation by distance was not evident, but rather, genetic distance was weakly correlated with habitat similarity. Only individuals in forest fragments were correctly assignable to their site of origin, and individual pairwise relatedness in one fragment was significantly higher than expected. We did not detect sex-biased dispersal, but natural dispersal patterns may be confounded by fragmentation. Assignment tests showed that reforestation appears to have provided refuges for tuatara from disturbed areas. Our results suggest that fine-scale genetic structuring is driven by recent habitat modification and compounded by the sedentary lifestyle of these long-lived reptiles. Extreme longevity, large population size, simple social structure and random dispersal are not strong enough to counteract the genetic structure caused by a sedentary lifestyle. We suspect that fine-scale spatial genetic structuring could occur in any sedentary species with limited dispersal, making them more susceptible to the effects of fragmentation.     

Increase of genetic variation over time in a recently founded population of great reed warblers (Acrocephalus arundinaceus) revealed by microsatellites and DNA fingerprinting

Genetic similarity within pairs of individuals was examined using both 10 polymorphic microsatellite loci and multi-locus DNA fingerprinting profiles in a semi-isolated population of great reed warblers at Lake Kvismaren, south Central Sweden, in 1987-1993. The population was founded by a few individuals in 1978, followed by a gradual increase in numbers until 1988, since when the population has remained relatively stable with about 60 breeding birds. We have previously found that high genetic similarity between pair-mates in the population during the early part of the study period reduced egg hatching success, and hence reproductive success. The measures of pairwise genetic similarity, microsatellite allele sharing and DNA fingerprinting band sharing, were highly correlated with pedigree-based relatedness. Both microsatellite and DNA fingerprinting similarities between pair-mates declined significantly over the study period, and the pattern was most pronounced in the DNA fingerprinting data. Analyses restricted to the microsatellite data showed that the average annual microsatellite similarity between pairwise combinations of individuals, as well as individual homozygosity in males, declined significantly over the study period, and that several immigrants carrying novel alleles entered the population during the study. Hence, the temporal decline in genetic similarity of mates in the population is probably a consequence of increased immigration, facilitated by the recent expansion of the species in the region. These results suggest that the population has now recovered genetically, or is in the process of recovering, from a recent founder event.     

Pollinating fig wasps: genetic consequences of island recolonization

The levels of genetic diversity and gene flow may influence the long-term persistence of populations. Using microsatellite markers, we investigated genetic diversity and genetic differentiation in island (Krakatau archipelago, Indonesia) and mainland (Java and Sumatra, Indonesia) populations of Liporrhopalum tentacularis and Ceratosolen bisulcatus, the fig wasp pollinators of two dioecious Ficus (fig tree) species. Genetic diversity in Krakatau archipelago populations was similar to that found on the mainland. Population differentiation between mainland coastal sites and the Krakatau islands was weak in both wasp species, indicating that the intervening 40 km across open sea may not be a barrier for wasp gene flow (dispersal) and colonization of the islands. Surprisingly, mainland populations of the fig waSPS may be more genetically isolated than the islands, as gene flow between populations on the Javan mainland differed between the two wasp species. Contrasting growth forms and relative 'immunity' to the effects of deforestation in their host fig trees may account for these differences.     

Role of propagule pressure in colonization success: disentangling the relative importance of demographic,genetic and habitat effects

High propagule pressure is arguably the only consistent predictor of colonization success. More individuals enhance colonization success because they aid in overcoming demographic consequences of small population size (e.g. stochasticity and Allee effects). The number of founders can also have direct genetic effects: with fewer individuals, more inbreeding and thus inbreeding depression will occur, whereas more individuals typically harbour greater genetic variation. Thus, the demographic and genetic components of propagule pressure are interrelated, making it difficult to understand which mechanisms are most important in determining colonization success. We experimentally disentangled the demographic and genetic components of propagule pressure by manipulating the number of founders (fewer or more), and genetic background (inbred or outbred) of individuals released in a series of three complementary experiments. We used Bemisia whiteflies and released them onto either their natal host (benign) or a novel host (challenging). Our experiments revealed that having more founding individuals and those individuals being outbred both increased the number of adults produced, but that only genetic background consistently shaped net reproductive rate of experimental populations. Environment was also important and interacted with propagule size to determine the number of adults produced. Quality of the environment interacted also with genetic background to determine establishment success, with a more pronounced effect of inbreeding depression in harsh environments. This interaction did not hold for the net reproductive rate. These data show that the positive effect of propagule pressure on founding success can be driven as much by underlying genetic processes as by demographics. Genetic effects can be immediate and have sizable effects on fitness.     

Influence of genetic drift on patterns of genetic variation: The footprint of aquaculture practices in Sparus aurata (Teleostei: Sparidae)

Aquaculture finfish production based on floating cage technology has raised increasing concerns regarding the genetic integrity of natural populations. Accidental mass escapes can induce the loss of genetic diversity in wild populations by increasing genetic drift and inbreeding. Farm escapes probably represent an important issue in the gilthead sea bream (Sparus aurata), which accounted for 76.4% of total escapees recorded in Europe during a 3‐year survey. Here, we investigated patterns of genetic variation in farmed and wild populations of gilthead sea bream from the Western Mediterranean, a region of long gilthead sea bream farming. We focused on the role that genetic drift may play in shaping these patterns. Results based on microsatellite markers matched those observed in previous studies. Farmed populations showed lower levels of genetic diversity than wild populations and were genetically divergent from their wild counterparts. Overall, farmed populations showed the smallest effective population size and increased levels of relatedness compared to wild populations. The small broodstock size coupled with breeding practices that may favour the variance in individual reproductive success probably boosted genetic drift. This factor appeared to be a major driver of the genetic patterns observed in the gilthead sea bream populations analysed in the present study. These results further stress the importance of recommendations aimed at maintaining broodstock sizes as large as possible and equal sex‐ratios among breeders, as well as avoiding unequal contributions among parents.     

生境片断化对植物种群遗传结构的影响及植物遗传多样性保护

生境片断化是指大而连续的生境变成空间隔离的小种群的现象。生境片断化对植物种群遗传效应包括生境片断化过程中的取样效应及其后的小种群效应（遗传漂变、近交等）。理论研究表明,生境片断化后,植物种群的遗传变异程度将降低,而残留的小种群间的遗传分化程度将升高。然而对一些植物的研究表明,生境片断化对植物种群的遗传效应要受其他一些因素的影响,如世代长度、片断化时间、片断种群的大小、基因流的改变等。最后,针对生境     

Microsatellite analysis of population structure and genetic differentiation within and between populations of the root vole, Microtus oeconomus in the Netherlands

Eight microsatellite markers for the root vole (Microtus oeconomus) were developed to assess the amount of genetic variation for nine Dutch root vole populations from four different regions, and to evaluate the degree of differentiation and isolation. All eight microsatellite loci were found to be highly variable with observed heterozygosity values ranging from 0.61 to 0.82. These values are similar to those observed for more distant populations from Norway, Finland and Germany. Therefore, the populations seem not particularly depauperate of genetic variation at the microsatellite level. Genetically, the Dutch populations were found to have diverged considerably. Pairwise comparisons of all populations studied revealed FST values significantly greater than zero for most comparisons. However, the magnitude of these values considerably depends on the compared population pair. The level of differentiation between local populations within Dutch regions is generally significantly lower than the differentiation between Dutch regions. The level of differentiation between Dutch regions, however, is not significantly different from that between populations of larger geographical distance. This implies that the regional Dutch populations are both isolated from each other and from other European populations. The observation that even local populations show low but significant genetic differentiation may be indicative for progressive isolation of these populations.     

Initial genetic diversity enhances population establishment and alters genetic structuring of a newly established Daphnia metapopulation

When newly created habitats are initially colonized by genotypes with rapid population growth rates, later arriving colonists may be prevented from establishing. Although these priority effects have been documented in multiple systems, their duration may be influenced by the diversity of the founding population. We conducted a large‐scale field manipulation to investigate how initial clonal diversity influences temporal and landscape patterns of genetic structure in a developing metapopulation. Six genotypes of obligately asexual Daphnia pulex were stocked alone (no clonal diversity) or in combination (‘high’ clonal diversity) into newly created experimental woodland ponds. We also measured the population growth rate of all clones in the laboratory when raised on higher‐quality and lower‐quality resources. Our predictions were that in the 3 years following stocking, clonally diverse populations would be more likely to persist than nonclonally diverse populations and exhibit evidence for persistent founder effects. We expected that faster growing clones would be found in more pools and comprise a greater proportion of individuals genotyped from the landscape. Genetic composition, both locally and regionally, changed significantly following stocking. Six of 27 populations exhibited evidence for persistent founder effects, and populations stocked with ‘high’ clonal diversity were more likely to exhibit these effects than nonclonally diverse populations. Performance in the laboratory was not predictive of clonal persistence or overall dominance in the field. Hence, we conclude that although laboratory estimates of fitness did not fully explain metapopulation genetic structure, initial clonal diversity did enhance D. pulex population establishment and persistence in this system.     

Population genetic structure and the effect of founder events on the genetic variability of moose, Alces alces, in Canada

Moose, Alces alces, occur naturally throughout most of Canada but successful introductions of known numbers of animals have been made to the islands of Newfoundland and Cape Breton. Five microsatellite loci were used to investigate the population genetic structure and any change in genetic variability due to founder events of moose in Canada. Comparisons of allele frequencies for moose from 11 regions of the country suggested that there are at least seven genetically distinct populations (P < 0.05) in North America, namely Alberta, eastern Ontario, New Brunswick, Cape Breton, Labrador, western Newfoundland, and the Avalon Peninsula of Newfoundland. The average population heterozygosity was approximately 33% (range from 22 to 41%). UPGMA analysis of Nei's genetic distances produced phenograms similar to what would be expected when geographical location and population history are considered. The loss of heterozygosity due to a single founder event (n = 3; two introductions and a natural colonization) ranged from 14 to 30%, and the cumulative loss of heterozygosity due to two successive founder events (an introduction followed by a natural colonization) was 46%. In these examples loss of genetic variability has not been associated with any known phenotypic deviances, suggesting that populations may be established from a small number of founders. However, the viability of these founded populations over evolutionary timescales cannot be determined and is highly dependent upon chance.     

城市公园生境类型对鸟类群落的影响

2011年12月—2012年11月,在上海世纪公园和滨江森林公园对鸟类群落和植物群落进行调查,通过对12个植被变量进行主成分分析,将两个公园分为8种不同的生境类型。结果表明:2个公园生境构成存在显著差异,滨江森林公园灌木层植物发达的生境(Habitat with developed shrub layer,S型)以及灌木层和地被层植物都发达的生境(Habitat with developed tree layer and shrub layer,T+S型)数量显著多于世纪公园,世纪公园地被层发达的生境(Habitat with developed ground cover layer,G型)以及乔木层和地被层植物都发达的生境(Habitat with developed tree layer and ground cover layer,T+G型)数量显著多于滨江森林公园。世纪公园不同生境中鸟种数差异显著,而滨江森林公园中差异不显著。2个公园有24种共有鸟种,对共有鸟种生境利用率的配对t检验结果表明,滨江森林公园鸟类生境利用率显著高于世纪公园。对2个公园共有生境类型中鸟种数进行分析,发现滨江森林公园鹟科(Muscicapidae)鸟类种数显著大于世纪公园。根据以上结果,上海城市公园不同生境类型对鸟类群落结构存在显著影响。因此,建议在规划和建设大型城市公园时,应构建植被分层结构复杂的生境,多样化种植各类乔木,林下多样化搭配灌木。在保留供游客休憩草坪区域的同时种植各类草本植物,以此提高鸟类生境利用率,增加城市公园的鸟类多样性。     

Urban colonization through multiple genetic lenses: The city‐fox phenomenon revisited

Urbanization is driving environmental change on a global scale, creating novel environments for wildlife to colonize. Through a combination of stochastic and selective processes, urbanization is also driving evolutionary change. For instance, difficulty in traversing human‐modified landscapes may isolate newly established populations from rural sources, while novel selective pressures, such as altered disease risk, toxicant exposure, and light pollution, may further diverge populations through local adaptation. Assessing the evolutionary consequences of urban colonization and the processes underlying them is a principle aim of urban evolutionary ecology. In the present study, we revisited the genetic effects of urbanization on red foxes (Vulpes vulpes) that colonized Zurich, Switzerland. Through use of genome‐wide single nucleotide polymorphisms and microsatellite markers linked to the major histocompatibility complex (MHC), we expanded upon a previous neutral microsatellite study to assess population structure, characterize patterns of genetic diversity, and detect outliers associated with urbanization. Our results indicated the presence of one large evolutionary cluster, with substructure evident between geographic sampling areas. In urban foxes, we observed patterns of neutral and functional diversity consistent with founder events and reported increased differentiation between populations separated by natural and anthropogenic barriers. We additionally reported evidence of selection acting on MHC‐linked markers and identified outlier loci with putative gene functions related to energy metabolism, behavior, and immunity. We concluded that demographic processes primarily drove patterns of diversity, with outlier tests providing preliminary evidence of possible urban adaptation. This study contributes to our overall understanding of urban colonization ecology and emphasizes the value of combining datasets when examining evolutionary change in an increasingly urban world.     

Spatial and demographic population genetic structure in Catasetum viridiflavum across a human-disturbed habitat

Spatial and temporal genetic structures were examined across sites on islands and mainland (continuous forest) populations of an epiphytic orchid, Catasetum viridiflavum, using 17 polymorphic allozyme loci. I tested whether patches on islands or at mainland sites comprised small local populations or a large population. Low among population differentiation was observed across the landscape suggesting that the species-specific pollinator and tiny wind-dispersed seeds maintain interconnections among distant patches. Temporal genetic structure among stage classes, and among breeding individuals are important components of the maintenance of genetic variation in this orchid. The natural history of this species including small breeding populations, probable high frequency of mating among relatives, and the high rates of seed movement among sites contribute to the high FIS. These data show that physically isolated patches in this epiphytic orchid comprise a single larger genetic population, which is independent of the physical distances among sites. Although quite different in ecological and life history characteristics, the genetic structure of this orchid demonstrates a pattern similar to temperate and tropical trees in fragmented landscapes.     

The population genetic structure of a large temperate pollinator species, Bombus pascuorum (Scopoli) (Hymenoptera: Apidae)

The genetic population structure of the bumble bee Bombus pascuorum was studied using six microsatellite loci and a partial sequence of the mitochondrial gene cytochrome b . Eighteen populations from central and northern Europe were included in the analysis. Observed levels of genetic variability and heterozygosity were high. Estimates of population differentiation based on F - and Φ-statistics revealed significant genetic differentiation among B. pascuorum populations and suggest that two partially isolated gene pools, separated by the Alps, do exist. The distribution of mtDNA haplotypes supports this view and presents direct evidence for gene flow across the Alps. Estimates of the number of migrants exchanged among populations north of the Alps suggest that historical events may have left a strong imprint on population structure.     

Independent colonization of multiple urban centres by a formerly forest specialist bird species

Urban areas are expanding rapidly, but a few native species have successfully colonized them. The processes underlying such colonization events are poorly understood. Using the blackbird Turdus merula, a former forest specialist that is now one of the most common urban birds in its range, we provide the first assessment of two contrasting urban colonization models. First, that urbanization occurred independently. Second, that following initial urbanization, urban-adapted individuals colonized other urban areas in a leapfrog manner. Previous analyses of spatial patterns in the timing of blackbird urbanization, and experimental introductions of urban and rural blackbirds to uncolonized cities, suggest that the leapfrog model is likely to apply. We found that, across the western Palaearctic, urban blackbird populations contain less genetic diversity than rural ones, urban populations are more strongly differentiated from each other than from rural populations and assignment tests support a rural source population for most urban individuals. In combination, these results provide much stronger support for the independent urbanization model than the leapfrog one. If the former model predominates, colonization of multiple urban centres will be particularly difficult when urbanization requires genetic adaptations, having implications for urban species diversity.     

Genetic effects of habitat restoration in the Laurentian Great Lakes: an assessment of lake sturgeon origin and genetic diversity

Lake sturgeon (Acipenser fulvescens) have experienced significant habitat loss, resulting in reduced population sizes. Three artificial reefs were built in the Huron‐Erie corridor in the Great Lakes to replace lost spawning habitat. Genetic data were collected to determine the source and numbers of adult lake sturgeon spawning on the reefs and to determine if the founder effect resulted in reduced genetic diversity. DNA was extracted from larval tail clips and 12 microsatellite loci were amplified. Larval genotypes were then compared to 22 previously studied spawning lake sturgeon populations in the Great Lakes to determine the source of the parental population. The effective number of breeders (N_b) was calculated for each reef cohort. The larval genotypes were then compared to the source population to determine if there were any losses in genetic diversity that are indicative of the founder effect. The St. Clair and Detroit River adult populations were found to be the source parental population for the larvae collected on all three artificial reefs. There were large numbers of contributing adults relative to the number of sampled larvae. There was no significant difference between levels of genetic diversity in the source population and larval samples from the artificial reefs; however, there is some evidence for a genetic bottleneck in the reef populations likely due to the founder effect. Habitat restoration in the Huron‐Erie corridor is likely resulting in increased habitat for the large lake sturgeon population in the system and in maintenance of the population's genetic diversity.     

Population genetic consequences of geographic disjunction: a prairie plant isolated on Great Lakes alvars

Species may often exhibit geographic variation in population genetic structure due to contemporary and historical variation in population size and gene flow. Here, we test the predictions that populations on the margins of a species' distribution contain less genetic variation and are more differentiated than populations towards the core of the range by comparing patterns of genetic variation at five microsatellite loci between disjunct and core populations of the perennial, allohexaploid herb Geum triflorum. We sampled nine populations isolated on alvar habitat within the eastern Great Lakes region in North America, habitats that include disjunct populations of several plant species, and compared these to 16 populations sampled from prairie habitat throughout the core of the species' distribution in midwestern Canada and the USA. Alvar populations exhibited much lower within-population diversity and contained only a subset of alleles found in prairie populations. We detected isolation by distance across the species' range and within alvar and prairie regions separately. As predicted, genetic differentiation was higher among alvar populations than among prairie populations, even after controlling for the geographic distance between sampled populations. Low diversity and high differentiation can be accounted for by the greater contemporary spatial isolation of alvar populations. However, the genetic structure of alvar populations may also have been influenced by postglacial range expansion and contraction. Our results are consistent with alvar populations being founded during an expansion of prairie habitat during the warmer, hypsithermal period approximately 5000 bp and subsequently becoming stranded on isolated alvar habitat as the climate grew cooler and wetter.     

Identifying the early genetic consequences of habitat degradation in a highly threatened tropical conifer, Araucaria nemorosa Laubenfels

The early genetic effects of habitat degradation were investigated in the critically endangered conifer Araucaria nemorosa. This species occurs in New Caledonia, a global biodiversity hotspot where the world's greatest concentration of endemic conifer species coincides with an extremely high level of habitat destruction due to fire and mining. Using seven microsatellite loci, estimates were made of genetic marker variation, inbreeding coefficients and population differentiation of adult and seedling cohorts of A. nemorosa. These were contrasted with equivalent estimates, made over similar spatial scales and with the same marker loci, in the locally common and more widespread sister species Araucaria columnaris. There were no significant differences in population genetic parameters between adult populations of the two species, despite their different abundances. However, in A. nemorosa, the juvenile cohort showed a loss of rare alleles and elevated levels of inbreeding when compared to the adult cohort. These genetic differences between the cohorts were not observed in the locally common A. columnaris. This suggests that recent environmental degradation is influencing the genetic structure of A. nemorosa populations. Although this is not detectable among predisturbance adult populations, an early warning of these impacts is evident in more recently established seedling cohorts. The conservation implications of these results are discussed.     

The effects of riverine impoundment on genetic structure and gene flow in two stream fishes in the Mobile River basin

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The sampling scheme matters: Pan troglodytes troglodytes and P. t. schweinfurthii are characterized by clinal genetic variation rather than a strong subspecies break

Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian‐cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between‐subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions. Am J Phys Anthropol 156:181–191, 2015. © 2014 Wiley Periodicals, Inc.     

Maintenance of two genetic entities by habitat selection

Summary In the laboratory, the two species of copepodsLepeophtheirus thompsoni andLepeophtheirus europaensis, ectoparasites of flatfishes, can meet and mate on at least one host species. In the wild however, these two species are found isolated on their sympatric hosts. Habitat selection theoretically represents a powerful enough mechanism to explain the maintenance of genetic heterogeneity in the wide sense. In this paper, the host colonization process is studied for both parasite species. It is shown that each parasite can develop and reach adult age on each host species. However,L. thompsoni is highly selective; it almost totally refuses to colonize hosts other than its natural one.Lepeophtheirus europaensis, on the contrary, readily infests turbot and brill in single-host experiments, but strongly prefers the brill when it has a choice. It appears that these two genetic entities are sympatrically maintained due to strong habitat selection. Such a pattern could theoretically only occur in a soft-selection context (density dependence). This point is discussed with respect to the different patterns in host use found in the geographical distribution of these parasites.