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.     

Effects of a single intensive harvest event on fish populations inside a customary marine closure

In September 2008, the villagers of Kia Island, Fiji, opened their customary managed closure (Cakaulevu tabu) to fishing for a fundraiser that lasted for 5 weeks. We report on opportunistic before-after-control-impact surveys describing changes to coral reef communities both 4 weeks into the harvest and 1 year later compared with pre-harvest conditions. Prior to the harvest, there was a gradient in mean fish abundance and biomass per transect, with highest levels in the north of the closure (250 fish transect⁻¹, 8,145.8 kg ha⁻¹), intermediate levels in the south of the closure (159 fish transect⁻¹, 4,672.1 kg ha⁻¹) and lowest levels in the control area open to fishing (109 fish transect⁻¹, 594.0 kg ha⁻¹). During the harvest, there were extensive depletions in large-bodied, primary targeted fish species, with significant loss in biomass of Acanthuridae and Carangidae in the north and Lutjanidae and Serranidae in the south. We also observed significant increases in Acanthuridae, Lethrinidae and Scaridae in the control, suggesting a “bail-out” effect whereby fish left the closure in response to a rapid increase in fishing pressure. These changes were coupled with a large increase in turf algal cover at all survey areas, despite a large numerical increase in small, roving acanthurids (e.g., Ctenochaetus striatus) and scarids (e.g., Chlorurus sordidus). By 1 year later, fish biomass was significantly lower within the closure than before the harvest, while values in the control returned to pre-harvest levels, suggesting non-compliance with the reinstated fishing ban. We use the lessons learned from this event to suggest recommendations for promoting effective management of periodically harvested customary closures that are a common feature across much of Oceania.     

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.     

Ethanol resistance in Drosophila melanogaster has increased in parallel cold‐adapted populations and shows a variable genetic architecture within and between populations

Understanding the genetic properties of adaptive trait evolution is a fundamental crux of biological inquiry that links molecular processes to biological diversity. Important uncertainties persist regarding the genetic predictability of adaptive trait change, the role of standing variation, and whether adaptation tends to result in the fixation of favored variants. Here, we use the recurrent evolution of enhanced ethanol resistance in Drosophila melanogaster during this species’ worldwide expansion as a promising system to add to our understanding of the genetics of adaptation. We find that elevated ethanol resistance has evolved at least three times in different cooler regions of the species’ modern range—not only at high latitude but also in two African high‐altitude regions. Applying a bulk segregant mapping framework, we find that the genetic architecture of ethanol resistance evolution differs substantially not only between our three resistant populations, but also between two crosses involving the same European population. We then apply population genetic scans for local adaptation within our quantitative trait locus regions, and we find potential contributions of genes with annotated roles in spindle localization, membrane composition, sterol and alcohol metabolism, and other processes. We also apply simulation‐based analyses that confirm the variable genetic basis of ethanol resistance and hint at a moderately polygenic architecture. However, these simulations indicate that larger‐scale studies will be needed to more clearly quantify the genetic architecture of adaptive evolution and to firmly connect trait evolution to specific causative loci.     

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.     

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     

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.     

Leading-edge populations do not show low genetic diversity or high differentiation in a wind-pollinated tree

Climate changes can shift species’ ranges. Knowledge on genetic variation of the leading-edge populations provides critical information to understand responses and adaptation of plants to projected climate warming. To date, the research into genetic variation of leading-edge populations has been limited, particularly in the role of wind-mediated pollen flow in maintaining high genetic variation. Castanopsis sclerophylla (Fagaceae) is a wind-pollinated and gravity-dispersed tree. In the present study, we used seven polymorphic microsatellites to genotype 482 samples from five leading-edge and 12 non-edge populations. Significant effects of recent population bottleneck events were found in three of the five leading-edge populations, indicating that the leading-edge populations might have been recolonized after the Last Glacial Maximum. Genetic diversity was higher, though not significantly, in leading-edge than in non-edge populations. Relationship between genetic diversity and latitude indicated an increasing trend of genetic diversity towards leading-edge populations. No significant difference in genetic differentiation was found between leading-edge and non-edge populations. The inconsistence with the general predictions by leading-edge colonization model could be explained by high gene flow via pollen grains. Pollen-mediated gene flow could maintain high genetic diversity within and low differentiation among leading-edge populations. In response to climate warming, high genetic variation may provide leading-edge populations raw materials for evolutionary adaptation to future environmental conditions.     

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.     

Limited genetic differentiation in Labeo rohita (Hamilton 1822) populations as revealed by microsatellite markers

Labeo rohita, popularly known as rohu is a widely cultured species in the whole Indian subcontinent. Knowledge of the genetic diversity of this species is important to support management and conservation programs which will subsequently help in sustainable production of this species. DNA markers, mostly microsatellite markers are excellent tool to evaluate genetic variation of populations. Genetic variation of three wild and one farm population was assessed using eleven microsatellite loci. In analyzing 192 samples, the number of alleles ranged from 4 to 23; observed heterozygosity 0.500 to 0.870 and expected heterozygosity from 0.389 to 0.878. Exact test for Hardy Weinberg disequilibrium revealed that each riverine sample had at least one locus not in equilibrium except one river. Negative inbreeding coefficients (F_IS) were observed across populations indicating very high level of genetic diversity but little genetic differentiation among populations.     

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.     

Population size is weakly related to quantitative genetic variation and trait differentiation in a stream fish

How population size influences quantitative genetic variation and differentiation among natural, fragmented populations remains unresolved. Small, isolated populations might occupy poor quality habitats and lose genetic variation more rapidly due to genetic drift than large populations. Genetic drift might furthermore overcome selection as population size decreases. Collectively, this might result in directional changes in additive genetic variation (V_A) and trait differentiation (Q_ST) from small to large population size. Alternatively, small populations might exhibit larger variation in V_A and Q_ST if habitat fragmentation increases variability in habitat types. We explored these alternatives by investigating V_A and Q_ST using nine fragmented populations of brook trout varying 50‐fold in census size N (179–8416) and 10‐fold in effective number of breeders, N_b (18–135). Across 15 traits, no evidence was found for consistent differences in V_A and Q_ST with population size and almost no evidence for increased variability of V_A or Q_ST estimates at small population size. This suggests that (i) small populations of some species may retain adaptive potential according to commonly adopted quantitative genetic measures and (ii) populations of varying sizes experience a variety of environmental conditions in nature, however extremely large studies are likely required before any firm conclusions can be made.     

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.