A River Metapopulation Structure of a Japanese Freshwater Goby, Odontobutis Obscura, Deduced from Allozyme Genetic Indices

Gene products of 18 allozyme loci from 1268 individuals of a Japanese freshwater goby called donko, Odontobutis obscura (Odontobutidae; Gobioidei), from 33 localities in the Koya River, Yamaguchi Prefecture, Japan, were investigated to determine the extent of genetic divergence and gene flow within a river metapopulation. Genetic indices including GST(mean FST 0.182), FIT(mean 0.192) and D(mean 0.015) indicated a considerable divergence of local populations in the river. The genetic distance (D) and channel distance between pairs of populations did not show a good correlation, and geographical neighbors were not always genetic neighbors. Therefore, the genetic divergence of populations is attributable to independent genetic drift with restricted gene flow among populations. The agricultural dams and weirs constructed across the river must be responsible for the restricted gene flow. The metapopulation structure of O. obscura in the Koya River may be barely sustained by one-way gene flow only from the upper to the lower populations. An occasional artificial transplantation of some individuals from the lower to the upper populations may be one alternative to maintain a river metapopulation structure safely.     

Genetic and phenotypic variation in central and northern European populations of Aedes (Aedimorphus) vexans (Meigen, 1830) (Diptera,Culicidae)

The floodwater mosquito Aedes vexans can be a massive nuisance in the flood plain areas of mainland Europe, and is the vector of Tahyna virus and a potential vector of Dirofilaria immitis. This epidemiologically important species forms three subspecies worldwide, of which Aedes vexans arabiensis has a wide distribution in Europe and Africa. We quantified the genetic and phenotypic variation in Ae. vexans arabiensis in populations from Sweden (northern Europe), Hungary, and Serbia (central Europe). A landscape genetics approach (F_ST, STRUCTURE, BAPS, GENELAND) revealed significant differentiation between northern and southern populations. Similar to genetic data, wing geometric morphometrics revealed two different clusters, one made by Swedish populations, while another included Hungarian and Serbian populations. Moreover, integrated genetic and morphometric data from the spatial analysis suggested groupings of populations into three clusters, one of which was from Swedish and Hungarian populations. Data on spatial analysis regarding an intermediate status of the Hungarian population was supported by observed Isolation‐by‐Distance patterns. Furthermore, a low proportion of interpopulation vs intrapopulation variance revealed by AMOVA and low‐to‐moderate F_ST values on a broader geographical scale indicate a continuous between‐population exchange of individuals, including considerable gene flow on the regional scale, are likely to be responsible for the maintenance of the observed population similarity in Aе. vexans. We discussed data considering population structure in the light of vector control strategies of the mosquito from public health importance.     

The fragmented population structure of the Sardinian chalk hill blue butterfly (Lepidoptera, Lycaenidae)

The endemic Sardinian chalk hill blue butterfly, Polyommatus coridon gennargenti, is considered vulnerable to extinction because of its low genetic variation and restricted distribution. The species also has a fragmented distribution, which follows the patchy distribution pattern of its larval host-plant. A preliminary investigation of the population structure of P. coridon gennargenti was carried out on a small network of four local populations by means of capture–recapture methods. Estimated population sizes and movement rates among the four adjacent local populations suggest that this taxon has a metapopulation structure composed of loosely connected small local populations. Natural fragmentation, isolation, and traditional land use contribute to the vulnerability of P. coridon gennargenti to extinction. Low effective population sizes and restricted movement between habitat patches lead to inbreeding and an increased vulnerability to extinction of this island population.     

Demographic and genetic collapses in spatially structured populations: insights from a long‐term survey in wild fish metapopulations

Unraveling the relationship between demographic declines and genetic changes over time is of critical importance to predict the persistence of at‐risk populations and to propose efficient conservation plans. This is particularly relevant in spatially structured populations (i.e. metapopulations) in which the spatial arrangement of local populations can modulate both demographic and genetic changes. We used ten‐year demo‐genetic monitoring to test 1) whether demographic declines were associated with genetic diversity declines and 2) whether the spatial structure of a metapopulation can weaken or reinforce these demographic and genetic temporal trends. We continuously surveyed, over time and across their entire range, two metapopulations of an endemic freshwater fish species Leuciscus burdigalensis: one metapopulation that had experienced a recent demographic decline and a second metapopulation that was stable over time. In the declining metapopulation, the number of alleles rapidly decreased, the inbreeding coefficient increased, and a genetic bottleneck emerged over time. In contrast, genetic indices were constant over time in the stable metapopulation. We further show that, in the declining metapopulation, demographic and genetic declines were not homogeneously distributed across the metapopulation. We notably identify one local population situated downstream as a ‘reservoir’ of individuals and genetic variability that dampens both the demographic and genetic declines measured at the metapopulation level. We demonstrate the usefulness of long‐term monitoring that combines both genetic and demographic parameters to understand and predict temporal population fluctuations of at‐risk species living in a metapopulation context.     

Extinction,recolonization, and the genetic structure of tidepool copepod populations

Summary Extinction and recolonization in metapopulations may either increase or decrease genetic differentiation among populations, but recent genetic models predict increased differentiation under most circumstances of recolonization. I examine this prediction empirically using tidepool populations of the marine tidepool copepodTigriopus californicus. The probability of extinction of tidepool populations was sufficiently high to invoke the model's predictions, but varied among populations. Nearly 75% of colonizing groups consisted of 10 or fewer individuals. The genetic effective size of colonizing groups might be as high as 18, depending on assumptions, but colonists probably originated from a subset of local populations. In contrast to my predictions, genetic differentiation was smaller among younger tidepool populations than among older populations on each of three rock outcrops, suggesting that genetic differentiation was reduced by metapopulation dynamics. The discrepancy between the prediction and the results may be explained by the unmet assumptions of classical metapopulation structure underlying the genetic models.     

Genetic variability in Chamaenerion angustifolium (L.) Scop. (Onagraceae) occurring on contrasting soils

Isoenzyme analysis of 5 populations of Chamaenerion angustifolium (L.) Scop. from different habitats revealed that only two of the nine enzymes scored were polymorphic. The estimated number of polymorphic loci was 2 out of 16. The only significant difference found was with regard to the gene and genotype frequencies of glucose-6-phosphate dehydrogenase (G6PDH). This difference could be demonstrated for established populations, occurring on contrasting soils but not for their seed populations.The genetic similarity between seed populations even in a sample obtained from only four established individuals was striking and its consequences for the life strategy and colonizing ability of the species are discussed. Genotypic differentiation due to age structure was not present. Genotype-dependent selection occurs in the seedling phase only.     

Isolation and characterization of highly polymorphic microsatellite markers in Hypochaeris radicata (Asteraceae)

We developed five highly polymorphic dinucleotide microsatellite loci for the grassland species Hypochaeris radicata (Asteraceae). Polymorphism of these markers was examined in six populations in the Netherlands. All loci were polymorphic in all populations. The number of alleles per locus varied between 18 and 43. Expected heterozygosity was between 0.86 and 0.91. Cross‐species amplification was tested in six Hypochaeris species and was successful for three different loci in four species. These microsatellites are a useful tool in population genetic, dispersal and metapopulation studies or in testing levels of inbreeding.     

Assessing changes in functional connectivity in a desert bighorn sheep metapopulation after two generations

Determining how species move across complex and fragmented landscapes and interact with human‐made barriers is a major research focus in conservation. Studies estimating functional connectivity from movement, dispersal or gene flow usually rely on a single study period and rarely consider variation over time. We contrasted genetic structure and gene flow across barriers for a metapopulation of desert bighorn sheep (Ovis canadensis nelsoni) using genotypes collected 2000–2003 and 2013–2015. Based on the recently observed but unexpected spread of a respiratory pathogen across an interstate highway previously identified as a barrier to gene flow, we hypothesized that bighorn sheep changed how they interacted with that barrier, and that shifts in metapopulation structure influenced gene flow, genetic diversity and connectivity. Population assignment tests, genetic structure and genetic recapture demonstrated that bighorn sheep crossed the interstate highway in at least one location in 2013–2015, sharply reducing genetic structure between two populations, but supported conclusions of an earlier study that such crossings were very infrequent or unknown in 2000–2003. A recently expanded population established new links and caused decreases in genetic structure among multiple populations. Genetic diversity showed only slight increases in populations linked by new connections. Genetic structure and assignments revealed other previously undetected changes in movements and distribution, but much was consistent. Thus, we observed changes in both structural and functional connectivity over just two generations, but only in specific locations. Movement patterns of species should be revisited periodically to enable informed management, particularly in dynamic and fragmented systems.     

Inferring demographic processes from the genetic structure of a metapopulation of <Emphasis Type="Italic">Boltonia decurrens</Emphasis>(Asteraceae)

Boltonia decurrens(Asteraceae), a federally listed, threatened floodplain species, requires regular flooding for suitable habitat and seed dispersal. Flood suppression and habitat destruction have resulted in fewer than 25 populations remaining throughout its 400 km range. Because individual populations are widely interspaced (>10 km) and subject to frequent extinction and colonization, seed dispersal along the river, not pollen flow, is likely the primary determinant of population genetic structure. We used neutral genetic markers (isozymes) assayed for fourteen populations to determine which demographic processes contribute to the genetic structure of B. decurrens. Significant genetic differentiation was detected among populations (F _ST=0.098, P< 0.05) but not among regions (F _RT=0.013, P> 0.05), suggesting that long-distance dispersal events occur and involve seed from a small number of populations. Correspondingly, we found no evidence of isolation by distance, and admixture analyses indicate that colonization events involve seed from 3 to 5 source populations. Individual populations exhibited high levels of fixation (mean F _IS=0.192, P< 0.05), yet mean population outcrossing rates were high (t _m=0.87–0.95) and spatial autocorrelation analyses revealed no fine-scale within population structure, indicating that inbreeding alone cannot explain the observed fixation. Rather, genetic bottlenecks, detected for 12 of 14 populations, and admixture at population founding may be important sources of fixation. These observations are consistent with a metapopulation model and confirm the importance of regular flooding events, capable of producing suitable habitat and dispersing seed long distances, to the long-term persistence of B. decurrens.     

Phylogeography of the temperate marine bivalve Cerastoderma edule (Linnaeus, 1758) (Bivalvia: Cardiidae) in the Subarctic: Unique diversity and strong population structuring at different spatial scales

Using mitochondrial COI sequencing, we explored the genetic diversity and population structuring of the common cockle Cerastoderma edule (Linnaeus, 1758) in the Norwegian and Barents Seas. Phylogeographic diversity and hence the evolutionary history of C. edule on the Scandinavian and Russian coastlines were found to be richer than expected for populations of temperate species in postglacially colonized seas. A major phylogeographic break at Lofoten Islands separated a group of subarctic populations dominated by a distinct star‐shaped clade of haplotypes from those to the south, extending to the North Sea and having highest gene diversities (h). At the northeastern edge of the range of C. edule, the Russian Murman coast, populations show a mosaic structure with considerable admixture of haplotypes from the south and high local‐scale variation in haplotype diversity (ranging between 0 and 0.8). To explain this mosaic we refer to the core‐satellite metapopulation model, with Norwegian populations as core, and Murman populations as satellites. Our results contradict the conventional biogeographic paradigm implying lack of metapopulation structuring in marine broadcast spawning invertebrates. Hypotheses considered to explain the origin of the unique variation in cockles from Northern Norway involve an early postglacial colonization and establishment of these populations (10–12 ka ago), a persistent oceanographic break at Lofoten, and a mitochondrial selective sweep associated with the postglacial recolonization of the subarctic seas by the boreal C. edule.     

Population size and fragmentation thresholds for the maintenance of genetic diversity in the herbaceous endemic Scutellaria montana (Lamiaceae)

Abstract.-The level and distribution of genetic variation is thought to be affected primarily by the size of individual populations and by gene flow among populations. Although the effects of population size have frequently been examined, the contributions of regional gene flow to levels of genetic variation are less well known. Here I examine the effects of population size and the number of neighboring populations (metapopulation density) on the distribution and maintenance of genetic diversity in an endemic herbaceous perennial. Reductions in the proportion of polymorphic loci and the effective number of alleles per locus were apparent for many populations with a census size of less than 100 individuals, but no effects of population size on levels of inbreeding were detected. I assess the effects of regional population density on levels of diversity and inbreeding using stepwise regression analysis of metapopulation diameter (i.e., the size of a circle within which population density is estimated). This procedure provides a spatially explicit evaluation of the effects of metapopulation size on population genetic parameters and indicates the critical number of neighboring populations (fragmentation threshold) for the regional maintenance of genetic diversity. Stepwise regression analyses revealed fragmentation thresholds at two levels; at a scale of 2 km, where small metapopulations resulted in greater levels of selfing or sibling mating, and at a scale of 8 km, where metapopulation size was positively associated with higher levels of genetic diversity. I hypothesize that the smaller fragmentation threshold may reflect higher levels of selfing in isolated populations because of the absence of pollinators. The larger threshold probably indicates the maximum distance over which pollen dispersal rates are high enough to counteract genetic drift. This study demonstrates that the regional distribution of populations can be an important factor for the long-term maintenance of genetic variation.     

Spatial genetic structure in a metapopulation of the land snail Cepaea nemoralis (Gastropoda: Helicidae)

Habitat fragmentation is a major force affecting demography and genetic structure of wild populations, especially in agricultural landscapes. The land snail Cepaea nemoralis (L.) was selected to investigate the impact of habitat fragmentation on the spatial genetic structure of an organism with limited dispersal ability. Genetic and morphological patterns were investigated at a local scale of a 500 m transect and a mesoscale of 4 x 4 km in a fragmented agricultural landscape while accounting for variation in the landscape using least-cost models. Analysis of microsatellite loci using expected heterozygosity (HE), pairwise genetic distance (FST/1-FST) and spatial autocorrelograms (Moran's I) as well as shell characteristics revealed spatial structuring at both scales and provided evidence for a metapopulation structure. Genetic diversity was related to morphological diversity regardless of landscape properties. This pointed to bottlenecks caused by founder effects after (re)colonization. Our study suggests that metapopulation structure depended on both landscape features and the shape of the dispersal function. A range of genetic spatial autocorrelation up to 80 m at the local scale and up to 800 m at the mesoscale indicated leptokurtic dispersal patterns. The metapopulation dynamics of C. nemoralis resulted in a patchwork of interconnected, spatially structured subpopulations. They were shaped by gene flow which was affected by landscape features, the dispersal function and an increasing role of genetic drift with distance.     

Population genetics and reproductive strategies of two Notostraca (Crustacea) species from winter ponds in Israel

Fluorescent-amplified fragment length polymorphism (FAFLP) fingerprinting assay was used to compare the genetic diversity within and between tadpole shrimps (Notostraca) populations of Lepidurus apus (n=7) and Triops cancriformis (n=2) from rain pools in Israel. Each ephemeral water body has revealed a unique fingerprint pattern with an entailed genetic drift between nearby ponds. High similarity of genotypic diversity within each geographic area led to three clusters of water bodies, north, south and center of Israel. FAFLP assays on several newly hatched individuals of T. cancriformis revealed high identity amongst kin, as compared to L. apus where newly hatched from the same maternal source showed high diversity. Results indicate that T. cancriformis populations from Israel are probably parthenogenetic as indicated by clonal structures. The higher genetic variability in the L. apus populations and in laboratory-hatched specimens indicates the existence of sexual reproduction.     

Mitochondrial DNA variation among populations of Oedura reticulata (Gekkonidae) in remnant vegetation: implications for metapopulation structure and population decline

Restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA was used to examine the regional population structure of a species of gecko (Oedura reticulata) in vegetation remnants within the Western Australian wheatbelt. The species exhibited considerable polymorphism within and between populations with 22 haplotypes recognized among 12 populations. Phylogenetic analysis of haplotypes and clustering of nucleotide divergence among populations demonstrated little regional structure within the species with several haplotypes present in all three regions surveyed. This contrasted markedly with variation in haplotype frequency among populations which showed a high degree of independence between populations indicating that current levels of maternal gene flow are low and that the populations are too small to prevent genetic drift. This conclusion is supported by generally lower numbers of haplotypes in remnant populations than in nearby nature reserves. These findings, combined with demographic data from a previous study, suggest that post-fragmentation populations of O. reticulata are unable to form a metapopulation structure in the habitat that remains and that stochastic extinction forces alone will be sufficient to severely reduce the regional distribution of this species. This study demonstrates that mtDNA is a useful tool for detecting contemporary population phenomena and can provide qualitative information of practical importance to wildlife managers.     

Ecological genetics of the cave beetle Neaphaenops tellkampfii (Coleoptera: Carabidae)

Summary Genetic variability and similarity were examined in eight populations of the Kentucky cave beetle Neaphaenops tellkampfii (Coleoptera: Carabidae) using the technique of polyacrylamide gel electrophoresis. Results indicate that N. tellkampfii has high genetic variation within and high genetic similarity among local populations. These results are in sharp contrast to the patterns of low variability and similarity reported for other cave dwelling species in the same region. It is concluded that the differences in genetical population structure among cave species in the Central Kentucky Karst are related to ecological differences among the species.     

A genetic analysis of dragonfly population structure

Dragonflies reside in both aquatic and terrestrial environments, depending on their life stage, necessitating the conservation of drastically different habitats; however, little is understood about how nymph and adult dragonflies function as metapopulations within connected habitat. We used genetic techniques to examine nymphs and adults within a single metapopulation both spatially and temporally to better understand metapopulation structure and the processes that might influence said structure. We sampled 97 nymphs and 149 adult Sympetrum obtrusum from eight locations, four aquatic, and four terrestrial, at the Pierce Cedar Creek Institute in Southwest Michigan over two summers. We performed AFLP genetic analysis and used the Bayesian analysis program STRUCTURE to detect genetic clusters from sampled individuals. STRUCTURE detected k = u4 populations, in which nymphs and adults from the same locations collected in different years did not necessarily fall into the same clusters. We also evaluated grouping using the statistical clustering analyses NMDS and MRPP. The results of these confirmed findings from STRUCTURE and emphasized differences between adults collected in 2012 and all other generations. These results suggest that both dispersal and a temporal cycle of emergence of nymphs from unique clusters every other year could be influential in structuring dragonfly populations, although our methods were not able to fully distinguish the influences of either force. This study provides a better understanding of local dragonfly metapopulation structure and provides a starting point for future studies to investigate the spatial and temporal mechanisms controlling metapopulation structure. The results of the study should prove informative for managers working to preserve genetic diversity in connected dragonfly metapopulations, especially in the face of increasing anthropogenic landscape changes.     

Spatiotemporal analysis of gene flow in Chesapeake Bay Diamondback Terrapins (Malaclemys terrapin)

There is widespread concern regarding the impacts of anthropogenic activities on connectivity among populations of plants and animals, and understanding how contemporary and historical processes shape metapopulation dynamics is crucial for setting appropriate conservation targets. We used genetic data to identify population clusters and quantify gene flow over historical and contemporary time frames in the Diamondback Terrapin (Malaclemys terrapin). This species has a long and complicated history with humans, including commercial overharvesting and subsequent translocation events during the early twentieth century. Today, terrapins face threats from habitat loss and mortality in fisheries bycatch. To evaluate population structure and gene flow among Diamondback Terrapin populations in the Chesapeake Bay region, we sampled 617 individuals from 15 localities and screened individuals at 12 polymorphic microsatellite loci. Our goals were to demarcate metapopulation structure, quantify genetic diversity, estimate effective population sizes, and document temporal changes in gene flow. We found that terrapins in the Chesapeake Bay region harbour high levels of genetic diversity and form four populations. Effective population sizes were variable. Among most population comparisons, estimates of historical and contemporary terrapin gene flow were generally low (m ≈ 0.01). However, we detected a substantial increase in contemporary gene flow into Chesapeake Bay from populations outside the bay, as well as between two populations within Chesapeake Bay, possibly as a consequence of translocations during the early twentieth century. Our study shows that inferences across multiple time scales are needed to evaluate population connectivity, especially as recent changes may identify threats to population persistence.     

Population genetic structure of Sorex unguiculatus and Sorex caecutiens (Soricidae, Mammalia) in Hokkaido, based on microsatellite DNA polymorphism

We investigated the genetic structure of Sorex unguiculatus and Sorex caecutiens populations in Hokkaido, Japan, using hypervariable microsatellite DNA markers. We used five microsatellite loci to type 475 S. unguiculatus individuals from 20 localities on the Hokkaido mainland and four localities from each of four offshore islands (and 11 shrews from one locality in southern Sakhalin for a particular analysis). We used six microsatellite loci to type 240 S. caecutiens individuals from 13 localities on the Hokkaido mainland. Genetic variation was high in mainland populations of both species and low in the island populations of S. unguiculatus. Allelic richness and island size were positively correlated for S. unguiculatus, suggesting that genetic drift occurred on those islands due to small population size. In addition, four insular populations of S. unguiculatus were genetically differentiated from the mainland populations, although clear phylogeographic clustering was not confirmed among populations on the Hokkaido mainland for either S. unguiculatus or S. caecutiens. Heterozygosity excess was observed in more than half of the populations including the mainland populations of the two species, suggesting recent bottleneck events in these populations. Population dynamics of the shrews might be explained by a metapopulation scheme. According to autocorrelation analysis, the extent of non-random spatial genetic structure was approximately 100 km. Isolation by distance was observed in S. unguiculatus, but not in S. caecutiens although there is a positive trend. The lack of correlation for S. caecutiens might have been due to small sample size. Thus, no obvious differences in population genetic structure were found between the two species on the Hokkaido mainland in the present study, while previous investigations using mitochondrial DNA sequences inferred that these two species might have rather different biogeographic histories.     

Structure and dynamic of a natterjack toad metapopulation (Bufo calamita)

Summary The migratory and reproductive behaviour ofBufo calamita was studied at four neighbouring breeding sites in the northern Rhineland, Germany, from 1986 to 1991. Radio telemetry and marking systems based on toe-clipping and on microchips were used to follow the tracks of toads and for individual recognition. Emphasis lay on estimates of (1) the exchange of reproductive individuals between neighbouring sites, and (2) the reproductive success at each site. Allozyme electrophoresis served to assess the genetic diversity of local populations. More than 90% of all reproductive males showed a lifelong fidelity to the site of first breeding, whereas females did not prefer certain breeding sites. Due to the female-biased exchange of individuals among neighbouring sites the genetic distance between local populations was generally low but increased with geographical distance. This pattern of spatial relations is consistent with the structure of a metapopulation. Morever, up to three mass immigrations of males per breeding period, replacing previously reproductive individuals, suggested the existence of temporal populations successively reproducing at the same locality. Genetic distances were considerably greater between temporal populations than between local ones, indicating partial reproductive isolation. In fact, an exchange of reproductive individuals between the temporal populations at each site was not detected, but gene flow due to the recruitment of first-breeders originating from offspring other than their own seems probable. Thus, natterjack metapopulations consist of interacting local and temporal populations. The reproductive success differed considerably among the four sites and also between the temporal populations. Three out of four local populations had low reproductive success as well as the latest temporal population. The persistence of these populations depended entirely on the recruitment of juveniles from the only self-sustaining local population. This rescue-effect impeded local extinction. The discussion focuses on the modifications required to fit the classical metapopulation concept to the empirical findings and their consequences for the dynamics of amphibian metapopulations.     

Metapopulation genetic structure of two coexisting parasitoids of the Glanville fritillary butterfly

We investigated the metapopulation genetic structure of two specialist parasitoids, Cotesia melitaearum and Hyposoter horticola, attacking the Glanville fritillary butterfly (Melitaea cinxia) in the Åland Islands south-western Finland. The host butterfly persists as a classic metapopulation in a network of 4,000 small habitat patches within an area of 50 by 70 km . The two parasitoids are known to differ greatly in their population dynamics and spatial pattern of occupancy in local host populations. Analysis of genetic population structure using F_ST and clustering of multilocus genotypes revealed a distinct large-scale spatial structure in C. melitaearum but a very weak pattern in H. horticola. This result is consistent with the known difference in the dispersal range (much longer in H. horticola) and population size (much greater in H. horticola) of the two parasitoids.