Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration

Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F_ST up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F_ST above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat.     

Low genetic differentiation between populations of an endemic prairie katydid despite habitat loss and fragmentation

Tallgrass prairie habitats within North America have suffered severe fragmentation and habitat loss as land has been converted for agricultural purposes. Habitat loss and fragmentation can affect gene flow and the genetic structure of insect populations. Neoconocephalus bivocatus is a prairie obligate katydid found only in isolated prairie patches. We compared genetic diversity and population differentiation using AFLP markers in N. bivocatus and N. robustus, a grassland generalist that is not isolated to prairie fragments and occupies a more contiguous range. Similar levels of genetic diversity were present within populations of both species. While population genetic structure was found in both species, there was no relationship between assigned genotypes and sampling localities. This genetic structure may instead be evidence of a past barrier to gene flow that has since been removed. Genetic differentiation within both species was low, with no evidence of a correlation with geographic distance, indicating neither species is dispersal limited at these distances. We see no significant reduction in genetic diversity or genetic differentiation within N. bivocatus when compared to N. robustus. We therefore conclude that while N. bivocatus utilizes a fragmented landscape, long-distance dispersal likely maintains gene flow between isolated prairie patches.     

Morphological and genetic differentiation between allopatric populations of a freshwater amphipod

The morphological and isozyme variation in 17 populations of the freshwater amphipod genus Paramelita was investigated to see whether morphological differences were genetically based. On the whole, morphological and genetic differentiation coincided, and could be related to geographical distribution. Five distinct genetic groups, separated at Nei's (1978) genetic identity values below 0-35, and possessing diagnostic alleles, were identified. Discriminant functions and cluster analyses confirmed that these genetic clusters were phenotypically distinct. It was concluded that these groups were sufficiently different to warrant the recognition of five species, four of which were new, and as yet, undescribed.     

Regional genetic differentiation among northern high-latitude island populations of a broadcast-spawning coral

Knowledge of genetic connectivity is useful for understanding of the recovery potential of coral populations after various disturbances, such as coral mass bleaching. Population genetic studies in corals are mostly restricted to Australian and Caribbean species; studies in the northern Pacific are relatively limited. Using microsatellite markers, the population genetics of Acropora sp. 1 was examined between two regions in Japan, the Okinawa-Aka and Bonin Islands, which are separated by approximately 1,500 km of open water in a high-latitude area. Statistically significant but small genetic differentiation in Acropora sp. 1 was detected between and within these regions. Genetic diversity was not obviously reduced in populations of the Bonin Islands, which are relatively isolated. Thus, some level of connectivity appears to be maintained between the two regions, likely because of the high dispersal ability of this broadcast spawner.     

High levels of genetic differentiation between Ugandan Glossina fuscipes fuscipes populations separated by Lake Kyoga

Background

Glossina fuscipes fuscipes is the major vector of human African trypanosomiasis, commonly referred to as sleeping sickness, in Uganda. In western and eastern Africa, the disease has distinct clinical manifestations and is caused by two different parasites: Trypanosoma brucei rhodesiense and T. b. gambiense. Uganda is exceptional in that it harbors both parasites, which are separated by a narrow 160-km belt. This separation is puzzling considering there are no restrictions on the movement of people and animals across this region.

Methodology and Results

We investigated whether genetic heterogeneity of G. f. fuscipes vector populations can provide an explanation for this disjunct distribution of the Trypanosoma parasites. Therefore, we examined genetic structuring of G. f. fuscipes populations across Uganda using newly developed microsatellite markers, as well as mtDNA. Our data show that G. f. fuscipes populations are highly structured, with two clearly defined clusters that are separated by Lake Kyoga, located in central Uganda. Interestingly, we did not find a correlation between genetic heterogeneity and the type of Trypanosoma parasite transmitted.

Conclusions

The lack of a correlation between genetic structuring of G. f. fuscipes populations and the distribution of T. b. gambiense and T. b. rhodesiense indicates that it is unlikely that genetic heterogeneity of G. f. fuscipes populations explains the disjunct distribution of the parasites. These results have important epidemiological implications, suggesting that a fusion of the two disease distributions is unlikely to be prevented by an incompatibility between vector populations and parasite.     

Simulating allele frequencies in a population and the genetic differentiation of populations under mutation pressure

A method is developed for simulating the allele frequencies in an equilibrium or transient population under the effects of neutral mutation and random drift. The method is based on diffusion theory and is fast so that it can be used to study in detail the distribution of heterozygosity or any quantity that can be expressed as a function of allele frequencies. It has been applied to study the distribution of heterozygosity and the distributions of the frequencies of the first three most frequent alleles in a population. It also has been applied to study the distribution of the number of alleles shared by two populations that were derived from a common stock.     

Isolated populations of a rare alpine plant show high genetic diversity and considerable population differentiation

Background and Aims

Gene flow and genetic variability within and among alpine plant populations can be greatly influenced by the steep environmental gradients and heterogeneous topography of alpine landscapes. In this study, the effects are examined of natural isolation of alpine habitats on genetic diversity and geographic structure in populations of C. thyrsoides, a rare and isolated European Alpine monocarpic perennial with limited seed dispersal capacity.

Methods

Molecular diversity was analysed for 736 individuals from 32 populations in the Swiss Alps and adjacent Jura mountains using five polymorphic microsatellite loci. Pollen flow was estimated using pollen grain-sized fluorescent powder. In addition, individual-based Bayesian approaches were applied to examine population structure.

Key Results

High within-population genetic diversity (H_E = 0·76) and a relatively low inbreeding coefficient (F_IS = 0·022) were found. Genetic differentiation among populations measured with a standardized measure was considerable (G′_ST = 0·53). A significant isolation-by-distance relationship was found (r = 0·62, P < 0·001) and a significant geographic sub-structure, coinciding with proposed postglacial migration patterns. Altitudinal location and size of populations did not influence molecular variation. Direct measures of pollen flow revealed that insect-mediated pollen dispersal was restricted to short distances within a population.

Conclusions

The natural isolation of suitable habitats for C. thyrsoides restricts gene flow among the populations as expected for a monocarpic species with very limited seed dispersal capacities. The observed high within-population genetic diversity in this rare monocarpic perennial is best explained by its outcrossing behaviour, long-lived individuals and overlapping generations. Despite the high within-population genetic diversity, the considerable genetic differentiation and the clear western–eastern differentiation in this species merits consideration in future conservation efforts.Key words: Alpine plant, Campanula thyrsoides, genetic diversity, gene flow, genetic differentiation, glacial history, G′_ST, habitat isolation, microsatellites, monocarpy, SSR     

Subtle genetic structure reveals restricted connectivity among populations of a coral reef fish inhabiting remote atolls

We utilized a spatial and temporal analyses of genetic structure, supplemented with ecological and oceanographic analysis, to assess patterns of population connectivity in a coral reef fish Chromis margaritifer among the unique and remote atolls in the eastern Indian Ocean. A subtle, but significant genetic discontinuity at 10 microsatellite DNA loci was detected between atoll systems corresponding with a low (≤ 1%) probability of advection across the hundreds of kilometers of open ocean that separates them. Thus, although genetic connections between systems are likely maintained by occasional long-distance dispersal of C. margaritifer larvae, ecological population connectivity at this spatial scale appears to be restricted. Further, within one of these atoll systems, significant spatial differentiation among samples was accompanied by a lack of temporal pairwise differentiation between recruit and adult samples, indicating that restrictions to connectivity also occur at a local scale (tens of kilometers). In contrast, a signal of panmixia was detected at the other atoll system studied. Lastly, greater relatedness and reduced genetic diversity within recruit samples was associated with relatively large differences among them, indicating the presence of sweepstakes reproduction whereby a small proportion of adults contributes to recruitment in the next generation. These results are congruent with earlier work on hard corals, suggesting that local production of larvae drives population replenishment in these atoll systems for a range of coral reef species.     

Comparison of fish impingement by a thermal power station with fish populations in the Ems Estuary

On an annual basis >10 million individuals of c . 35 fish species are impinged at the EC20 unit of the Eems power station located on the Ems Estuary. The most abundant are: herring Clupea harengus , gobies ( Gobiidae ), Nilsson's pipefish Sygnathus rostellatus , three-spined stickleback Gasterosteus aculeatus and sprat Sprattus sprattus . The impingement shows a seasonal pattern which reflects the presence of the fishes in the estuary. The results are compared with other impingement studies at power stations on the Belgian and Dutch estuaries.
In 1995, the cooling water entrance was displaced from the shoreline to 300 m off the coast at the edge of the tidal channel. The effect of this relocation on the level of fish impingement, determined by comparing the ratio of fish density in the cooling water and in the estuary before (1992–1993) and after (1996–1997) the relocation of the intake canal is discussed.     

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation

We have determined the three-dimensional (3D) architecture of the Caulobacter crescentus genome by combining genome-wide chromatin interaction detection, live-cell imaging, and computational modeling. Using chromosome conformation capture carbon copy (5C), we derive ~13 kb resolution 3D models of the Caulobacter genome. The resulting models illustrate that the genome is ellipsoidal with periodically arranged arms. The parS sites, a pair of short contiguous sequence elements known to be involved in chromosome segregation, are positioned at one pole, where they anchor the chromosome to the cell and contribute to the formation of a compact chromatin conformation. Repositioning these elements resulted in rotations of the chromosome that changed the subcellular positions of most genes. Such rotations did not lead to large-scale changes in gene expression, indicating that genome folding does not strongly affect gene regulation. Collectively, our data suggest that genome folding is globally dictated by the parS sites and chromosome segregation.     

Introgression from cultivated rice influences genetic differentiation of weedy rice populations at a local spatial scale

Hybridization and introgression can play an important role in genetic differentiation and adaptive evolution of plant species. For example, a conspecific feral species may frequently acquire new alleles from its coexisting crops via introgression. However, little is known about this process. We analyzed 24 weedy rice (Oryza sativa f. spontanea) populations and their coexisting rice cultivars from northern Italy to study their genetic differentiation, outcrossing, and introgression based on microsatellite polymorphisms. A total of 576 maternal plants representing 24 weedy populations were used to estimate their genetic differentiation, and 5,395 progeny (seedlings) derived from 299 families of 15 selected populations were included to measure outcrossing rates. Considerable genetic differentiation (F _st = 0.26) was detected among weedy rice populations, although the differentiation was not associated with the spatial pattern of the populations. Private alleles (28%) were identified in most populations that exhibited a multiple cluster assignments, indicating stronger genetic affinities of some weedy populations. Outcrossing rates were greatly variable and positively correlated (R ² = 0.34, P = 0.02) with the private alleles of the corresponding populations. Paternity analysis suggested that ~15% of paternal specific alleles, a considerable portion of which was found to be crop-specific, were acquired from the introgression of the coexisting rice cultivars. Frequent allelic introgression into weedy populations resulting from outcrossing with nearby cultivars determines the private alleles of local feral populations, possibly leading to their genetic differentiation. Introgression from a crop may play an important role in the adaptive evolution of feral populations.     

A single mitochondrial haplotype and nuclear genetic differentiation in sympatric colour morphs of a riverine cichlid fish

Some of the diversity of lacustrine cichlid fishes has been ascribed to sympatric divergence, whereas diversification in rivers is generally driven by vicariance and geographic isolation. In the riverine Pseudocrenilabrus philander species complex, several morphologically highly distinct populations are restricted to particular river systems, sinkholes and springs in southern Africa. One of these populations consists of a prevalent yellow morph in sympatry with a less frequent blue morph, and no individuals bear intermediate phenotypes. Genetic variation in microsatellites and AFLP markers was very low in both morphs and one single mtDNA haplotype was fixed in all samples, indicating a very young evolutionary age and small effective population size. Nevertheless, the nuclear markers detected low but significant differentiation between the two morphs. The data suggest recent and perhaps sympatric divergence in the riverine habitat.     

Use of a multivariate model using allele frequency distributions to analyse patterns of genetic differentiation among populations

Very few studies have attempted to relate the properties of some ordination techniques to classical tools of population genetics as F -statistics. A multivariate model to analyse population genetics data based on the properties of 'joint scaling' of populations and loci is developed. The design of population genetics data means that this model deals with a modified version of the classical Multiple Correspondence Analysis which is called Constant Row Total-Multiple Correspondence Analysis (CRT-MCA) and is an original tool in population genetics. Such a model allows estimates of the degree of population differentiation by studying the variability of the distribution of allele frequencies in different samples. Some clear relationships exist between some model parameters and the classical F_st statistics. The CRT-MCA also allows all the studied loci to be considered simultaneously and the role of each locus in patterns of population differentiation to be expressed. Such a multivariate approach prevents the use of any pooling strategy as is classically used in studies of hierarchical F -statistics. The relevance of the CRT-MCA model is illustrated by the analysis of population structure of 15 dogwhelk ( Nucella lapillus ) populations in south-west England. The advantages and limitations of CRT-MCA are presented.     

Lack of genetic structure among ecologically adapted populations of an Australian rainforest Drosophila species as indicated by microsatellite markers and mitochondrial DNA sequences

Although fragmented rainforest environments represent hotspots for invertebrate biodiversity, few genetic studies have been conducted on rainforest invertebrates. Thus, it is not known if invertebrate species in rainforests are highly genetically fragmented, with the potential for populations to show divergent selection responses, or if there are low levels of gene flow sufficient to maintain genetic homogeneity among fragmented populations. Here we use microsatellite markers and DNA sequences from the mitochondrial ND5 locus to investigate genetic differences among Drosophila birchii populations from tropical rainforests in Queensland, Australia. As found in a previous study, mitochondrial DNA diversity was low with no evidence for population differentiation among rainforest fragments. The pattern of mitochondrial haplotype variation was consistent with D. birchii having undergone substantial past population growth. Levels of nuclear genetic variation were high in all populations while F(ST) values were very low, even for flies from geographically isolated areas of rainforest. No significant differentiation was observed between populations on either side of the Burdekin Gap (a long-term dry corridor), although there was evidence for higher gene diversity in low-latitude populations. Spatial autocorrelation coefficients were low and did not differ significantly from random, except for one locus which revealed a clinal-like pattern. Comparisons of microsatellite differentiation contrasted with previously established clinal patterns in quantitative traits in D. birchii, and indicate that the patterns in quantitative traits are likely to be due to selection. These results suggest moderate gene flow in D. birchii over large distances. Limited population structure in this species appears to be due to recent range expansions or cycles of local extinctions followed by recolonizations/expansions. Nevertheless, patterns of local adaptation have developed in D. birchii that may result in populations showing different selection responses when faced with environmental change.     

Evolution in populations of Swedish sand lizards: genetic differentiation and loss of variability revealed by multilocus DNA fingerprinting

The Swedish sand lizard (Lacerta agilis) is a relict species from the period of warmth following the last glacial episode and has a fragmented distribution in central Sweden and a more continuous distribution in the southern part of the country. We used this model system of colonization–extinction for a study of genetic variability within and among Swedish populations from different parts of the distribution range using multilocus DNA fingerprinting. The results from the Swedish populations are then contrasted with those from a large Hungarian population in the centre of the species geographical distribution range, which is likely to closely resemble the ancestral founding population of Sweden. Swedish populations have a low level of genetic variability compared with the Hungarian reference population, which showed a genetic variability within the range described for outbred populations. Within the Swedish populations, the average bandsharing was 0.61, the mean heterozygosity 0.45 and the estimated number of alleles 2.7. The figures for the Hungarian population were a bandsharing of 0.19, a heterozygosity of 0.89 and an estimated number of alleles of 9.8. A population bottleneck, common to all Swedish sand lizards, is indicated by less than 20% of the alleles in the Hungarian population being retained in the Swedish populations, and higher bandsharing similarity between different Swedish populations (0.33) as opposed to the Hungarian population (0.19). The limited variability found in Swedish sand lizards is strongly subdivided between populations, with an average F_ST of 0.32, indicating a very limited gene flow between the isolated populations, as well as between populations in the region where the sand lizard has a more or less continuous distribution (F_ST = 0.41).     

Patterns of differentiation in a colour polymorphism and in neutral markers reveal rapid genetic changes in natural damselfly populations

The existence and mode of selection operating on heritable adaptive traits can be inferred by comparing population differentiation in neutral genetic variation between populations (often using F(ST) values) with the corresponding estimates for adaptive traits. Such comparisons indicate if selection acts in a diversifying way between populations, in which case differentiation in selected traits is expected to exceed differentiation in neutral markers [F(ST )(selected) > F(ST )(neutral)], or if negative frequency-dependent selection maintains genetic polymorphisms and pulls populations towards a common stable equilibrium [F(ST) (selected) < F(ST) (neutral)]. Here, we compared F(ST) values for putatively neutral data (obtained using amplified fragment length polymorphism) with estimates of differentiation in morph frequencies in the colour-polymorphic damselfly Ischnura elegans. We found that in the first year (2000), population differentiation in morph frequencies was significantly greater than differentiation in neutral loci, while in 2002 (only 2 years and 2 generations later), population differentiation in morph frequencies had decreased to a level significantly lower than differentiation in neutral loci. Genetic drift as an explanation for population differentiation in morph frequencies could thus be rejected in both years. These results indicate that the type and/or strength of selection on morph frequencies in this system can change substantially between years. We suggest that an approach to a common equilibrium morph frequency across all populations, driven by negative frequency-dependent selection, is the cause of these temporal changes. We conclude that inferences about selection obtained by comparing F(ST) values from neutral and adaptive genetic variation are most useful when spatial and temporal data are available from several populations and time points and when such information is combined with other ecological sources of data.     

Strong genetic differentiation on a fragmentation gradient among populations of the heterocarpic annual Catananche lutea L. (Asteraceae)

In landscapes which are predominately characterised by agriculture, natural ecosystems are often reduced to a mosaic of scattered patches of natural vegetation. Species with formerly connected distribution ranges now have restricted gene flow among populations. This has isolating effects upon population structure, because species are often confined by their limited dispersal capabilities. In this study, we test the effects of habitat fragmentation, precipitation, and isolation of populations on the genetic structure (AFLP) and fitness of the Asteraceae Catananche lutea. Our study area is an agro-dominated ecosystem in the desert–Mediterranean transition zone of the Southern Judea Lowlands in Israel. Our analysis revealed an intermediate level of intra-population genetic diversity across the study site with reduced genetic diversity on smaller scale. Although the size of the whole study area was relatively small (20?×?45?km), we found isolation by distance to be effective. We detected a high level of genetic differentiation among populations but genetic structure did not reflect spatial patterns. Population genetic diversity was correlated neither with position along the precipitation gradient nor with different seed types or other plant fitness variables in C. lutea.