Levels Of Genetic Subdivision Research Articles

Assessment of Genetic Diversity of the Salangid, Neosalanx taihuensis, Based on the Mitochondrial COI Gene in Different Chinese River Basins.

Simple SummaryIn the current study, we estimate the genetic diversity of the salangid Neosalanx taihuensis sampled from 11 populations in the six typical river basins of China. Using the COI gene sequencing technology, the N. taihuensis population’s genetic difference within and between river basins was investigated. Significant levels of genetic subdivision were detected among populations within basins rather than between basins. Population history dynamics showed that N. taihuensis populations experienced a population expansion during the glacial period in the late Pleistocene. These results suggest that different populations should be considered as different management units to achieve effective conservation and management purposes.The salangid Neosalanx taihuensis (Salangidae) is a commercially important economical fish endemic to China and restricted to large freshwater systems with a wide-ranging distribution. This fish species has continuous distribution ranges and a long-introduced aquaculture history in Chinese basins. However, the research on its population genetic differentiation within and between basins is very limited. In this regard, 197 individuals were sampled from 11 populations in the Nenjiang River Basin (A1–A4), Songhua River Basin (B1), Yellow River Basin (C1–C2), Yangtze River Basin (D1), Lanchang River Basin (E1–E2) and Huaihe River Basin (F1). Based on the COI sequence, the N. taihuensis population’s genetic difference within and between river basins was investigated. The haplotypes and their frequency distributions were strongly skewed, with most haplotypes (n = 13) represented only in single samples each and thus restricted to a single population. The most common haplotype (H4, 67/197) was found in all individuals. The analysis of molecular variance (AMOVA) revealed a random pattern in the distribution of genetic diversity, which is inconsistent with contemporary hydrological structure. The mismatch between the distribution and neutrality tests supported the evidence of a population expansion, which occurred during the late Pleistocene (0.041–0.051 million years ago). Significant levels of genetic subdivision were detected among populations within basins rather than between the six basins. Population history dynamics showed that N. taihuensis experienced an expansion during the glacial period in the late Pleistocene. Therefore, different populations should be considered as different management units to achieve effective conservation and management purposes. These results have great significance for the evaluation and exploitation of the germplasm resources of N. taihuensis.

Genetic and morphological heterogeneity among populations of Eurytemora affinis (Crustacea: Copepoda: Temoridae) in European waters

Our understanding of the systematics of the Eurytemora affinis complex developed at a fast pace over the last decades. Formerly considered as a complex of cryptic species, it is now believed to include three valid species: E. affinis, Eurytemora carolleeae, and Eurytemora caspica. American and European representatives have been studied in detail with respect to fine-scale geographic distribution, levels of genetic subdivision, evolutionary and demographic histories. Morphological components have been less explored. In this study, an analysis of the phylogeny and morphology of E. affinis was done, with a special focus on European populations. A total of 447 individuals of E. affinis from Europe were analyzed with genetic tools and 170 individuals according to morphological criteria. Common and new morphological and genetic features were analyzed. For this, we used ML and Bayesian methods to analyze the bar coding mt-DNA gene cytochrome c oxidase I subunit. Both genetic and morphological analyses showed high heterogeneities among the E. affinis populations from Europe. As a result, three local populations of E. affinis in Western Europe, including the European part of Russia, were established. Their genetic and morphological heterogeneity corresponded to the subspecies level.

Genetic heterogeneity among Eurytemora affinis populations in Western Europe

Evolutionary diversification of the broadly distributed copepod sibling species complex Eurytemora affinis has been documented in the northern hemisphere. However, the fine scale geographic distribution, levels of genetic subdivision, evolutionary, and demographic histories of European populations have been less explored. To gain information on genetic subdivision and to evaluate heterogeneity among European populations, we analyzed samples from 8 locations from 58° to 45°N and 0° to 23°E, using 549 base pairs of the mitochondrial cytochrome oxidase subunit I (COI) gene. We discovered three distinct lineages of E. affinis in Western Europe, namely the East Atlantic lineage, the North Sea/English Channel (NSEC) lineage, and the Baltic lineage. These geographically separated lineages showed sequences divergence of 1.7–2.1%, dating back 1.9 million years (CI: 0.9–3.0 My) with no indication of isolation by distance. Genetic divergence in Europe was much lower than among North American lineages. Interestingly, genetic structure varied distinctively among the three lineages: the East Atlantic lineage was divided between the Gironde and the Loire populations, the NSEC lineage comprised one single population unit spanning the Seine, Scheldt and Elbe rivers and the third lineage was restricted to the Baltic Proper (Sweden). We revealed high haplotype diversity in the East Atlantic and the Baltic lineages, whereas in the NSEC lineage haplotype diversity was comparatively low. All three lineages showed signs of at least one demographic expansion event during Pleistocene glaciations that marked their genetic structure. These results provide a preliminary overview of the genetic structure of E. affinis in Europe.

Genetic variation in populations of Populus davidiana Dode based on microsatellite marker analysis

Populus davidiana Dode, the only aspen in Korea, is useful for restoration because of its fast growth and vigorous reproduction. This study was conducted to estimate the genetic diversity and subdivision in populations of P. davidiana in South Korea using microsatellite markers. DNA from 113 individuals from five populations was amplified using five microsatellite primers. Fifty-three alleles were detected, and the expected heterozygosity was 0.603. The populations of P. davidiana in Korea have high genetic variation despite their peripheral distribution. RST (0.213) indicated a significant level of genetic subdivision among populations compared to the differentiation among other aspen populations. The high conservation value of the populations is attributed to its ecological and commercial importance.

Estimation of Genetic Diversity within and among Populations of Oncorhynchus mykiss in a Coastal River Experiencing Spatially Variable Hatchery Augmentation

AbstractThe allelic variation at 10 microsatellite loci was assayed in potentially wild rainbow trout Oncorhynchus mykiss and steelhead (anadromous rainbow trout) collected from 11 tributaries and three upper main‐stem river sites (n = 547) in the Kitimat River, central British Columbia, and compared with the variation in steelhead from areas within the lower river (n = 333), where a hatchery has operated since 1984. The objective was to see whether the genetic structure of O. mykiss in the upper river was influenced by hatchery‐reared fish stocked in the lower river. Measures of genetic diversity indicated that tributary and upper‐river diversity were similar to what has previously been documented for wild populations. The level of genetic subdivision (θ) was significant (θ = 0.031), indicating that genetic structure exists, and was higher than that among sites located in the lower main‐stem river where the hatchery operates (θ = 0.004). Bayesian assignment clustering suggested the existence of a genetic structure (K = 3) in O. mykiss in the upper river. The overall spatial pattern, however, identified no clearly separate genetic populations; rather, the genetic structure appeared to be an overlapping mosaic of modestly genetically divergent localities. We conclude that indigenous wild O. mykiss populations exist in the tributaries and the upper main‐stem river and its tributaries. These upper‐river populations appear to have retained genetic diversity and differentiation despite extensive releases of hatchery fish in the lower river.

Ecologically relevant dispersal of corals on isolated reefs: implications for managing resilience

Coral reefs are in decline worldwide, and marine reserve networks have been advocated as a powerful management tool for maximizing the resilience of coral communities to an increasing variety, number, and severity of disturbances. However, the effective design of reserves must account for the spatial scales of larval dispersal that affect the demography of communities over ecological time frames. Ecologically relevant distances of dispersal were inferred from DNA microsatellite data in a broadcast-spawning (Acropora tenuis) and a brooding (Seriatopora hystrix) coral at isolated reef systems off northwest Australia. Congruent with expectations based on life histories, levels of genetic subdivision among populations were markedly higher in the brooder than in the broadcast spawner. Additionally, significant subdivision for both species between systems (>100 km), and between (>10 km) or within reefs (<10 km) within systems, indicated that many reefs or reef patches are demographically independent. There was also a clear distinction in the scale of genetic structure between the different systems; at the more geographically complex of the systems, a much finer scale structure was detected in both species. This suggested that the hydrodynamics associated with these complex reefs restrict distances regularly traveled by larvae. The primary implication is that short-term recovery of these coral communities after severe disturbance requires the input of larvae from viable communities kilometers to a few tens of kilometers away. Therefore, to be self-sustaining, we suggest that coral reef protected areas need to be large enough to encompass these routine dispersal distances. Further, to facilitate recovery from severe disturbances, protected areas need to be replicated over these spatial scales. However, specific designs also need to account for size, complexity, and isolation of reefs, which will either restrict or enhance dispersal within this range.

MtDNA phylogeography and postglacial patterns of subdivision in the meadow grasshopper Chorthippus parallelus.

A 300 bp portion of the mitochondrial cytochrome oxidase subunit I (COI) gene was used to investigate the intraspecific genetic structure of the European meadow grasshopper Chorthippus parallelus. Levels of genetic subdivision between geographical regions in Europe were assessed using the KST statistic and revealed patterns indicative of the postglacial history of this organism. Northern European populations are shown to share a very recent common ancestor with, and hence originate from, a Balkan expansion. Genetic distances between these areas and both southern Italy and central Spain are shown to be approximately equal, even though only the Spanish form is recognized as a distinct subspecies. Distance estimates indicate that the common ancestor of the two subspecies lived more than one glacial cycle ago, and the refugial populations have probably been diverging in isolation for five or six glacial cycles (approximately equal to 550,000 years). Comparisons are made to the analysis of a similar data set using an anonymous nuclear DNA marker (Cooper et al., 1995). Although the structure revealed is generally very similar, differences in the location of transition zones between different genetic forms of C. parallelus may reflect the different historical assortment of these molecules.

MtDNA phylogeography and postglacial patterns of subdivision in the meadow grasshopper Chorthippus parallelus

A 300 bp portion of the mitochondrial cytochrome oxidase subunit I (COI) gene was used to investigate the intraspecific genetic structure of the European meadow grasshopper Chorthippus parallelus. Levels of genetic subdivision between geographical regions in Europe were assessed using the KST statistic and revealed patterns indicative of the postglacial history of this organism. Northern European populations are shown to share a very recent common ancestor with, and hence originate from, a Balkan expansion. Genetic distances between these areas and both southern Italy and central Spain are shown to be approximately equal, even though only the Spanish form is recognized as a distinct subspecies. Distance estimates indicate that the common ancestor of the two subspecies lived more than one glacial cycle ago, and the refugial populations have probably been diverging in isolation for five or six glacial cycles (≈550 000 years). Comparisons are made to the analysis of a similar data set using an anonymous nuclear DNA marker (Cooper et al., 1995). Although the structure revealed is generally very similar, differences in the location of transition zones between different genetic forms of C. parallelus may reflect the different historical assortment of these molecules.

The genetic effects of larval dispersal depend on spatial scale and habitat characteristics

The intertidal gastropods Bembicium vittatum and Austrocochlea constricta, which have direct and planktonic larval development, respectively, occur sympatrically at sites across a number of islands at the Houtman Abrolhos archipelago and two harbours at Albany in Western Australia. Their distribution provide an opportunity to examine the effect of dispersal ability on levels of genetic subdivision at a number of spatial scales. F ST (standardised variance in allelic frequencies) values in the range 0.361 to 0.396, determined from allozyme frequencies at 12 to 13 polymorphic loci, confirm isolation of Abrolhos and Albany populations, which are separated by 900 km of coastline, in both species. Within the Abrolhos and Albany, levels of subdivision in B. vittatum were high, but similar, as indicated by F ST values of 0.091 and 0.090, respectively. In A. constricta, a mean value of 0.160 at the Abrolhos suggests severe restrictions to gene flow, while 0.021 at Albany indicates much stronger connections among populations. F ST values at the Abrolhos support previous suggestions that this archipelago favours genetic subdivision in both direct and planktonic-developing species. The Albany harbours favoured subdivision only in B. vittatum, the low values of F ST in A. constricta being attributed to strong mixing between the harbours, thus facilitating gene flow via planktonic larvae. The isolation of A. constricta populations at the Abrolhos can be explained in terms of highly localised recruitment, the result of limited water movement in complex intertidal habitats. The study illustrates the value of examining sympatric direct and planktonic developers in assessing the role of larval dispersal in patterns of genetic subdivision, and concludes that planktonic larvae may not promote gene flow over broad or even some fine spatial scales.

Geographic cohesiveness versus associations with habitat: genetic subdivision of Bembicium vittatum Philippi (Gastropoda: Littorinidae) in the Houtman Abrolhos Islands

Abstract The littorine snail Bembicium vittatum has direct development and associated high levels of genetic subdivision. In the Houtman Abrolhos Islands, Western Australia, this species occupies a wide range of habitats. Replication of habitat types across the three major groups of islands, which are separated by water gaps of 10 to 15 km, separates patterns of genetic divergence related to gene flow from those expected from localised selection related to habitat. Allozyme frequencies at 14 loci were examined in samples of B. vittatum from 81 sites in the Abrolhos archipelago, at 72 of which descriptions of the physical and biological characteristics were made. Although shell shape and population density of B. vittatum varied with habitat, none of the allozymes showed such associations. Instead, there was spatial coherence of the allozyme variation, indicating connections among populations at two levels. On a larger scale, nearly half the interpopulation diversity was due to differences between island groups, including the association of rare alleles with island group. At a smaller scale, variation within island groups showed coherence in the form of isolation by distance, the extent and intensity of which were related to expected patterns of gene flow. This spatial coherence, independent of the mosaic of habitats, strongly favours the interpretation of patterns of genetic subdivision in B. vittatum in the Houtman Abrolhos as reflecting primarily the patterns of past and present gene flow. Contrasts with some results of an earlier study emphasise the importance of adequate sampling of sites and polymorphic loci.

High levels of genetic subdivision in peripherally isolated populations of the atherinid fish Craterocephalus capreoli in the Houtman Abrolhos Islands, Western Australia

The atherinid fish Craterocephalus capreoli Rendahl is abundant in the Houtman Abrolhos Islands, 70 km off the Western Australia coast and ≃250 km south of the southern limit of the range of the species along the mainland. Electrophoretic examination of 7 allozyme loci at 17 sites in the Houtman Abrolhos revealed a substantially lower level of polymorphism than found in an earlier study of the species in its mainland distribution, with many of the uncommon alleles and some common ones missing. There is a very high degree of genetic subdivision among the populations in the Houtman Abrolhos, measured by a mean F ST of 0.437 over a distance of 35 km. This F ST (standardized variance in allelic frequencies) is six times that found previously among populations along the mainland coast over distances up to 850 km. The subdivision of populations in the Houtman Abrolhos is similar within one island group on a scale up to 12 km, and between two groups that are separated by 15 km of deep water. Significant differences in allelic frequencies were found between populations from the open shore and enclosed lagoons less than 800 m apart, but the overall levels of subdivision were similar for the two types of environment. Previous work had shown high levels of genetic subdivision in the Houtman Abrolhos for a gastropod with direct development. The results for C. capreoli demonstrate that the archipelago favours subdivision even for a species with potentially much greater mobility and different life history.