Genetic Differentiation Of Species Research Articles

Regional environmental differences significantly affect the genetic structure and genetic differentiation of Carpinus tientaiensis Cheng, an endemic and extremely endangered species from China.

Differences in topography and environment greatly affect the genetic structure and genetic differentiation of species, and endemic or endangered species with limited geographic ranges seem to be more sensitive to changes in climate and other environmental factors. The complex topography of eastern China is likely to affect genetic differentiation of plants there. Carpinus tientaiensis Cheng is a native and endangered plants from China, and exploring its genetic diversity has profound significance for protection and the collection of germplasm resources. Based on AFLP markers, this study found that C. tientaiensis has low genetic diversity, which mainly came from within populations, while Shangshantou and Tiantai Mountain populations have relatively high genetic diversity. The Nei genetic distance was closely related to geographical distance, and temperature and precipitation notablely affected the genetic variation and genetic differentiation of C. tientaiensis. Based on cpDNA, this study indicated that C. tientaiensis exhibits a moderate level of genetic diversity, and which mainly came from among populations, while Tiantai Mountain population have the highest genetic diversity. It demonstrated that there was genetic differentiation between populations, which can be divided into two independent geographical groups, but there was no significant phylogeographic structure between them. The MaxEnt model showed that climate change significantly affects its distribution, and the suitable distribution areas in Zhejiang were primarily divided into two regions, eastern Zhejiang and southern Zhejiang, and there was niche differentiation in its suitable distribution areas. Therefore, this study speculated that the climate and the terrain of mountains and hills in East China jointly shape the genetic structure of C. tientaiensis, which gived rise to an obvious north-south differentiation trend of these species, and the populations located in the hilly areas of eastern Zhejiang and the mountainous areas of southern Zhejiang formed two genetic branches respectively.

Differentiated historical demography and ecological niche forming present distribution and genetic structure in coexisting two salamanders (Amphibia, Urodela, Hynobiidae) in a small island, Japan.

BackgroundThe climatic oscillations in the Quaternary period considerably shaped the distribution and population genetic structure of organisms. Studies on the historical dynamics of distribution and demography not only reflect the current geographic distribution but also allow us to understand the adaption and genetic differentiation of species. However, the process and factors affecting the present distribution and genetic structure of many taxa are still poorly understood, especially for endemic organisms to small islands.MethodsHere, we integrated population genetic and ecological niche modelling approaches to investigate the historical distribution and demographic dynamics of two co-existing salamanders on Tsushima Island, Japan: the true H. tsuensis (Group A), and Hynobius sp. (Group B). We also examined the hypothesis on the equivalency and similarity of niches of these groups by identity and background tests for ecological niche space.ResultsOur result showed that Group A is considered to have undergone a recent population expansion after the Last Glacial Maximum while it is unlikely to have occurred in Group B. The highest suitability was predicted for Group A in southern Tsushima Island, whereas the northern part of Tsushima Island was the potential distribution of Group B. The results also suggested a restricted range of both salamanders during the Last Interglacial and Last Glacial Maximum, and recent expansion in Mid-Holocene. The genetic landscape-shape interpolation analysis and historical suitable area of ecological niche modelling were consistent, and suggested refugia used during glacial ages in southern part for Group A, and in northern part of Tsushima Island for Group B. Additionally, we found evidence of nonequivalence for the ecological niche of the two groups of the salamanders, although our test could not show either niche divergence or conservatism based on the background tests. The environmental predictors affecting the potential distribution of each group also showed distinctiveness, leading to differences in selecting suitable areas. Finally, the combination of population genetics and ecological modeling has revealed the differential demographic/historical response between coexisting two salamanders on a small island.

Genomic data reveal similar genetic differentiation in aquifer species with different dispersal capabilities and life histories

Abstract Little is known about the life histories, genetic structure and population connectivity of shallow groundwater organisms. We used next-generation sequencing (RAD-seq) to analyse population genomic structure in two aquifer species: Paraperla frontalis (Banks, 1902), a stonefly with groundwater larvae and aerial (winged) adults; and Stygobromus sp., a groundwater-obligate amphipod. We found similar genetic differentiation in each species between floodplains separated by ~70 river km in the Flathead River basin of north-west Montana, USA. Given that Stygobromus lacks the above-ground life stage of P. frontalis, our findings suggest that connectivity and the magnitude of genetic structure cannot be definitively assumed from life history differences.

Molecular Phylogeography Analysis Reveals Population Dynamics and Genetic Divergence of a Widespread Tree Pterocarya stenoptera in China.

The geological events, past climatic fluctuations, and river systems played key roles in the spatial distribution, population dynamics, and genetic differentiation of species. In this work, we selected Pterocarya stenoptera, a widespread tree species in China, to test the roles of these factors. Four noncoding spacers, eight microsatellite (simple sequence repeat) markers, and species distribution modeling were used to examine the phylogeographical pattern of P. stenoptera. Based on chloroplast DNA data, populations of P. stenoptera were clearly clustered into three groups. The divergence time of these groups fell into the stage of the Qinghai–Tibet Movement, 1.7–2.6 Ma. For simple sequence repeat data, only one western marginal population YNYB could be separated from other populations, whereas other populations were mixed together. Our results indicated that the environmental heterogeneity resulting from the Qinghai–Tibet movement might be response for this genetic divergence. The climatic fluctuations in the Pleistocene did not cause the substantial range shift of P. stenoptera, while the fluctuations affected its population size. Moreover, we also confirmed the river systems did not act as channels or barrier of dispersal for P. stenoptera.

Differential gene expression of heat shock protein in response to thermal stress, in two Fundulus species endemic to the Gulf of Mexico

Expression of heat shock protein genes (Hsp) could be determinant for fish to survive an increase of water temperature due to global warming. Coastal lagoons, with their intrinsic high-water temperatures, test the resilience and adaptability of fish populations to environmental change. We analyze the variation in gene expression and genetic variation of 2 endemic Fundulus species in 2 lagoons to the north of the Yucatan Peninsula. We evaluated genetic distances between species using Hsp 70 gene sequences; our results showed low genetic differentiation between both Fundulus species and also showed individuals with high genetic variability, due to non-neutral polymorphisms. Expression of 2 isoforms of Hsp70 genes was higher in F. grandissimus than in F. persimilis. These variations are prompted by water temperature and genetic differentiation of species, induced in the fish thermal stress sensitivity. Our results suggest that both species are sensitive to thermal stress; however, populations exhibit wide genetic expression range and non-neutral polymorphisms, which could be an evidence of an adaptive process to thermal stress. This capacity of the fish populations to adapt to environmental variations could be affecting fish distribution.

What's stopping you? Variability of interstate highways as barriers for four species of terrestrial rodents

AbstractLandscape features that form a barrier for one species may not be a barrier for others, depending on how each species perceives the feature. Barriers may not be equivalent, due to unique characteristics at different locations, which may ameliorate barrier effects. In this study, we employed population genetics techniques to investigate how four Rodentia species with differing life history characteristics (fox squirrels [Sciurus niger], eastern gray squirrels [Sciurus carolinensis], eastern chipmunks [Tamias striatus], and white‐footed mice [Peromyscus leucopus]) responded to interstate highways as barriers to movement at seven locations with differing site‐specific landscape features. For comparative purposes, we included control sites that lacked heavily trafficked roads. We detected genetic differentiation relative to interstate highways among the gray squirrels, chipmunks, and white‐footed mice, but signals for differentiation among those three species varied by site, suggesting that site‐specific features are important considerations for species responses to high‐traffic roads. Chipmunk and gray squirrel populations, two forest specialist species that avoid open areas, exhibited more genetic structure corresponding with highways than either white‐footed mice (a nocturnal generalist) or fox squirrels (a larger‐bodied specialist that traverses open areas more readily than the other species in this study). Fox squirrels did not exhibit genetic differentiation at any site, whereas gray squirrel study populations evinced no population differentiation at sites with bridges spanning the interstate highway. Chipmunks also exhibited population differentiation at two of the control sites, indicating that less obvious barriers in the landscape may be as important as roads for sensitive species. We interpreted variation in genetic differentiation of species across sites in the context of how interstate highway features (i.e., the presence and condition of drainage culverts and bridges near study sites), combined with species‐specific life history characteristics, influence the barrier potential of highways. Culvert presence generally corresponded with a low or nonexistent barrier effect; however, an open, large culvert (>8 m in height) may create a semi‐permeable barrier for species that avoid open areas. Bridge presence appeared to facilitate gray squirrel and chipmunk dispersal across highways.

熱帯・亜熱帯域における沿岸域生態系の景観形成種の遺伝的分化

熱帯・亜熱帯域における沿岸域生態系の景観形成種の遺伝的分化

Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation in Busseola fusca (Lepidoptera: Noctuidae)

Current population genetic models fail to cope with genetic differentiation for species with large, contiguous and heterogeneous distribution. We show that in such a case, genetic differentiation can be predicted at equilibrium by circuit theory, where conductance corresponds to abundance in species distribution models (SDMs). Circuit-SDM approach was used for the phylogeographic study of the lepidopteran cereal stemborer Busseola fuscaFüller (Noctuidae) across sub-Saharan Africa. Species abundance was surveyed across its distribution range. SDMs were optimized and selected by cross-validation. Relationship between observed matrices of genetic differentiation between individuals, and between matrices of resistance distance was assessed through Mantel tests and redundancy discriminant analyses (RDAs). A total of 628 individuals from 130 localities in 17 countries were genotyped at seven microsatellite loci. Six population clusters were found based on a Bayesian analysis. The eastern margin of Dahomey gap between East and West Africa was the main factor of genetic differentiation. The SDM projections at present, last interglacial and last glacial maximum periods were used for the estimation of circuit resistance between locations of genotyped individuals. For all periods of time, when using either all individuals or only East African individuals, partial Mantel r and RDA conditioning on geographic distance were found significant. Under future projections (year 2080), partial r and RDA significance were different. From this study, it is concluded that analytical solutions provided by circuit theory are useful for the evolutionary management of populations and for phylogeographic analysis when coalescence times are not accessible by approximate Bayesian simulations.

Genetic Differentiation in Species of Anopheles from the Subgenera Nyssorhynchus Based on Mitochondrial DNA

Our group analyzed species of Anopheles of the subgenus Nyssorhynchus (An. darlingi, An. marajoara, An. oswaldoi, An. benarrochi, An. triannulatus and An. rangeli) and a single species of the subgenus Anopheles (An. mattogrossensis), originating in the Amazon, based on the mitochondrial DNA control region. The fragment had 381 pb and the nucleotide composition in A+T ranged from 85.8 to 89.5%. DNA polymorphism analysis of the species detected 15 haplotypes, with the presence of 81 polymorphic loci, 95 mutations, haplotypic divergence of 0.879, nucleotide diversity of 0.06507, nucleotide differences pair the pair mean of 23.1749, and the observed and expected variances of 113.840 and 8.33, respectively. The genetic distance among the Anopheles species varied from 0.06 to 1.37%. An. oswaldoi and An. rangeli were the most similar, with nucleotide divergence of 0.17%. The An. benarrochi populations of Ji-Parana and Bolivia showed nucleotide divergence of 0.06%. An. darlingi, An. marajoara and An. triannulatus presented nucleotide divergences of 0.35% between An. triannulatus and An. darlingiand of 0.47% between An. darlingi and An. marajoara. This data showed ample interspecific nucleotide variation, though with low nucleotide divergence. The cladogram separated the species of the subgenus Nyssorhynchus and those of the subgenera Cellia and Anopheles, with 98% bootstrap. The region control data did not show strong phylogenetic support, as indicated by the transition/transversion mean rate (0.4643), which is necessary for increasing fragment size and using other more conservative genes for greater inference concerning the phylogeny of the Anopheles species of the subgenus Nyssorhynchus.

Differences in spatial genetic structure and diversity in two mosses with different dispersal strategies in a fragmented landscape

The Thousand-Island Lake (Zhejiang Province, China) was artificially isolated 50 years ago and provides an interesting model for investigating the impact of fragmentation on the spatial genetic structure in plant populations. Using variation from inter-simple sequence repeat markers and DNA sequences in two moss species with contrasting reproductive strategies, Hypnum plumaeforme and Pogonatum inflexum, we investigate the effect of sexual and asexual reproduction on molecular diversity and spatial genetic structure in this fragmented landscape. In H. plumaeforme, which mostly reproduces asexually, genetic diversity of island populations was significantly higher than that of lakeside populations. In the frequently fertile P. inflexum, conversely, genetic diversity was not significantly different between island and lakeside populations. Furthermore, a clear island versus lakeshore structure emerged from the spatial analysis of genetic variation in H. plumaeforme, but not in P. inflexum. We conclude that differences in reproductive strategies have a substantial effect on spatial genetic structure. In addition, landscape fragmentation may lead to the exacerbation of genetic differentiation in species with limited dispersal abilities at this scale, causing substantial spatial genetic structure.

Eutrophication causes speciation reversal in whitefish adaptive radiations

Species diversity can be lost through two different but potentially interacting extinction processes: demographic decline and speciation reversal through introgressive hybridization. To investigate the relative contribution of these processes, we analysed historical and contemporary data of replicate whitefish radiations from 17 pre-alpine European lakes and reconstructed changes in genetic species differentiation through time using historical samples. Here we provide evidence that species diversity evolved in response to ecological opportunity, and that eutrophication, by diminishing this opportunity, has driven extinctions through speciation reversal and demographic decline. Across the radiations, the magnitude of eutrophication explains the pattern of species loss and levels of genetic and functional distinctiveness among remaining species. We argue that extinction by speciation reversal may be more widespread than currently appreciated. Preventing such extinctions will require that conservation efforts not only target existing species but identify and protect the ecological and evolutionary processes that generate and maintain species.

Advances in the molecular analysis of fish population structure

The characteristics of high population and species biodiversity, taken together with the major anthropogenic threats arising from exploitation, introductions and habitat alterations, have ensured that fishes have received major attention from molecular biologists in the study of wild populations. Foremost among the various challenges has been the development of techniques to estimate population discreteness and associated patterns of dispersal and gene flow, so‐called stock structure analysis. Here, we review some recent developments in molecular technology, especially microsatellite analysis, and consider critically how such markers can be employed to estimate genetic differentiation in species exhibiting high mobility in open waters. Comparisons are made between microsatellites and other genetic markers (protein and DNA) in their ability to detect population structuring. Particular emphasis is placed on the need to design sampling programmes that take account of aspects of the biology of the species under study, and the scale and nature of sample collection. Recent novel applications of PCR‐based technology in the analysis of population structure are considered, including the detection of micro‐geographic differentiation, the analysis of historical fish populations using recovered DNA, and the molecular characterization of allelic variants among populations in relation to function.

DEPENDENCE OF GENE FLOW ON GEOGRAPHIC DISTANCE IN TWO SOLITARY CORALS WITH DIFFERENT LARVAL DISPERSAL CAPABILITIES.

When the level of gene flow among populations depends upon the geographic distance separating them, genetic differentiation is relatively enhanced. Although the larval dispersal capabilities of marine organisms generally correlate with inferred levels of average gene flow, the effect of different modes of larval development on the association between gene flow and geographic distance remains unknown. In this paper, I examined the relationship between gene flow and distance in two co-occurring solitary corals. Balanophyllia elegans broods large, nonfeeding planulae that generally crawl only short distances from their place of birth before settling. In contrast, Paracyathus stearnsii free-spawns and produces small planktonic larvae presumably capable of broad dispersal by oceanic currents. I calculated F-statistics using genetic variation at six (P. stearnsii) or seven (B. elegans) polymorphic allozyme loci revealed by starch gel electrophoresis, and used these F-statistics to infer levels of gene flow. Average levels of gene flow among twelve Californian localities agreed with previous studies: the species with planktonic, feeding larvae was less genetically subdivided than the brooding species. In addition, geographic isolation between populations appeared to affect gene flow between populations in very different ways in the two species. In the brooding B. elegans, gene flow declined with increasing separation, and distance explained 31% of the variation in gene flow. In the planktonically dispersed P. stearnsii distance of separation between populations at the scale studied (10-1000 km) explained only 1% of the variation in gene flow between populations. The mechanisms generating geographic genetic differentiation in species with different modes of larval development should vary fundamentally as a result of these qualitative differences in the dependence of gene flow on distance.

DNA homology and taxonomy of Pseudomonas and Xanthomonas.

SUMMARY: The relatedness between several nomen species of the Pseudomonas-Xanthomonas group and some other organisms was numerically fixed through DNA homology and DNA base composition. For Pseudomonas the numerically analysed strains proposed by Lysenko as neotypes were used. The mean % (G+C) was in the range 60-67.5. 14C-DNA from either Pseudomonas fluorescens or P. putida was hybridized with DNA from 17 different species centres and the DNA homology was in the range 50-100%. Genetic species differentiation in the genus Pseudomonas seems justified. In three border cases (P. iodinum, P. diminuta and P. atlantica) DNA homology was only 28-50%, so the inclusion of these organisms in the genus Pseudomonas is uncertain. The species centres P. pavonacea and P. rubescens are omitted from the genus Pseudomonas because of their very low DNA homology and aberrant DNA base composition. Twenty-eight nomen species of Xanthomonas all form a narrow group in the range 63.5-69% (G+C). With two exceptions DNA homology with a median strain Xanthomonas pelargonii was always over 75% and frequently nearly complete. 14C-DNA from P. fluorescens hybridized with Xanthomonas-DNA to the same extent as with the pseudomonads proper. The Xanthomonas cluster overlapped perfectly with part of the Pseudomonas group. It is proposed therefore to gather all xanthomonads in a single genetic species P. campestris. This is such a dense cluster that the preservation of separate species names for the border cases seems undesirable. About one half to two-thirds of Pseudomonas- and Xanthomonas-DNA is identical. The genera Rhizobium, Azotobacter and Azomonas appeared to be rather closely related to Pseudomonas since they shared some 40-50% of their DNA. The genus Serratia appeared to be more closely related to Pseudomonas than to Escherichia. The genera Gluconobacter, Acetobacter, Serratia and Escherichia shared some 20-30% DNA with Pseudomonas, but Bacillus-DNA was almost entirely different. From a comparison between DNA homology and taximetric similarity, it appeared that most pseudomonads would not contain unused genes. The advantages of a classification based on % (G+C) and DNA homology are obvious.