Genetic diversity and population structure of Schizopygopsis younghusbandi Regan in the Yarlung Tsangpo River inferred from mitochondrial DNA sequence analysis

The genetic diversity and population structure of Schizopygopsis younghusbandi from six sites in the middle reach of the Yarlung Tsangpo River were examined based on mitochondrial DNA cytochrome b (Cyt b) gene and control region (D-loop) sequences. 1141 bp of complete Cyt b sequences and 737 bp of partial D-loop sequences for 153 individuals of S. younghusbandi were obtained by using PCR amplification and sequencing. The results showed that S. younghusbandi populations had high haplotype diversity and low nucleotide diversity, and the population genetic diversity of this species was at a low level. Analysis of molecular variance revealed that most genetic variation occurred within populations, and that genetic differentiation was at low or moderate levels. The network of haplotypes based on Cyt b gene showed that there were two groups within the examined populations. Neutrality tests and mismatch distribution analysis suggested that this species might have undergone a population expansion and the expansion time was estimated to be 0.25–0.46 Ma BP. All these results would be crucial to establish scientific strategies for effective conservation and sustainable exploitation of wild resources of S. younghusbandi.     

Genetic variation in the kakerori (Pomarea dimidiata), an endangered endemic bird successfully recovering in the Cook Islands

The Cook Islands endemic kakerori (Pomarea dimidiata) underwent a severe population decline following the introduction of ship rats (Rattus rattus) in the late 1800s. By 1989, the sole population on Rarotonga consisted of 29 known birds. Subsequent intensive management efforts enabled this population to recover to around 250?C300 birds in recent years. This study, using microsatellite and mitochondrial DNA markers, assesses the level of genetic diversity and the genetic structure of the contemporary kakerori population on Rarotonga. No mitochondrial control region and cytochrome b haplotype diversity was found in the 11 samples examined at each locus. In 81 samples genotyped at 7 polymorphic microsatellite loci, an average of 4 alleles per locus were found, with an average observed heterozygosity of 0.65. No subpopulation division was found in this population. There was no evidence of inbreeding, but genetic bottleneck tests showed that the population had indeed experienced a significant genetic bottleneck. Recovery of the kakerori was successful in the past two decades despite low genetic diversity in terms of allelic diversity. Our data suggested that low allelic diversity did not hamper population expansion and the continued survival of this species, however, longer-term effects are still possible.     

Strong population genetic structure and its implications for the conservation and management of the endangered Itasenpara bitterling

To infer the population genetic structure and genetic diversity of Itasenpara bitterling (Acheilognathus longipinnis), a cyprinid species endemic to Japan and distributed in only three specific regions, we investigated mitochondrial DNA variation. The distribution of the haplotypes among the three regions showed distinct geographic structure, and no common haplotypes were observed among regions. Analysis of molecular variance revealed a significant proportion of the genetic variance was partitioned among regions (93.1 %, P < 0.001), and pairwise estimates of D_A and Φ_ST between regions also revealed strong population structure. Given the strong genetic structure and low genetic diversity within regions, we strongly suggest that each region should be treated as a separate unit in any conservation program and any inter-regional translocations should be avoided.     

Maintenance of genetic variation and panmixia in the commercially exploited western rock lobster (Panulirus cygnus)

Marine species with high fecundities and mortalities in the early life stages can have low effective population sizes, making them vulnerable to declines in genetic diversity when they are commercially harvested. Here, we compare levels of microsatellite and mitochondrial sequence variation in the western rock lobster (Panulirus cygnus) over a 14-year period to test whether genetic variation is being maintained. Panulirus cygnus is a strong candidate for loss of genetic variation because it is a highly fecund species that is likely to experience high variance in reproductive success due to an extended larval planktonic stage. It also supports one of the largest and most economically important fisheries in Australia, with landings of between 8,000 and 14,500 tons (~70 % of the total legal-sized biomass) being harvested in some years. We found remarkably high levels of genetic variation in all samples and no evidence of a decline in genetic diversity over the time interval we studied. Furthermore, there was no evidence of a recent genetic bottleneck, and effective population size estimates based on single sample and temporal methods were infinitely large. Analysis of molecular variance indicated no significant population structure along 960 km of coastline or genetic differentiation among temporal samples. Our results support the view that P. cygnus is a single, panmictic population, and suggest genetic drift is not strong enough to reduce neutral genetic diversity in this species if current management practices and breeding stock sizes are maintained.     

Comparative Analysis of Genetic Diversity and Population Structure of Sipunculus nudus as Revealed by Mitochondrial COI Sequences

Genetic diversity and population structure of Sipunculus nudus were evaluated using a 652 base pair fragment of the mitochondrial cytochrome oxidase I gene. The populations were collected from Beihai, Sanya, and Xiamen. A total of 71 polymorphic sites defined 16 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the three populations were 0.9354 ± 0.0168 and 0.0035 ± 0.0018, respectively. Analysis at the intrapopulation level showed that the Beihai population had the greatest haplotype and nucleotide diversity, followed by the Xiamen and Sanya populations. Analysis of molecular variance showed significant genetic differentiation among the three populations (Fst = 0.0796, P < 0.05). The present results revealed that S. nudus populations had a high level of genetic diversity and distinct population structures.     

Mitochondrial and nuclear markers reveal a lack of genetic structure in the entocommensal nemertean Malacobdella arrokeana in the Patagonian gulfs

Malacobdella arrokeana is an entocommensal nemertean exclusively found in the bivalve geoduck Panopea abbreviata, and it is the only representative of the genus in the southern hemisphere. To characterize its genetic diversity, population structure and recent demographic history, we conducted the first genetic survey on this species, using sequence data for the cytochrome oxidase I gene (COI), 16S rRNA (16S) and the internal transcribed spacer (ITS2). Only four different ITS2 genotypes were found in the whole sample, and the two main haplotypes identified in the mitochondrial dataset were present among all localities with a diversity ranging from 0.583 to 0.939. Nucleotide diversity was low (π = 0.001–0.002). No significant genetic structure was detected between populations, and mismatch distribution patterns and neutrality tests results are consistent with a population in expansion or under selection. Analysis of molecular variance (AMOVA) revealed that the largest level of variance observed was due to intrapopulation variation (100, 100 and 94.39 % for 16S, COI and ITS2, respectively). F _st values were also non-significant. The observed lack of population structure is likely due to high levels of genetic connectivity in combination with the lack or permeability of biogeographic barriers and episodes of habitat modification.     

Demographic History and Population Structure of Blackfin Flounder (Glyptocephalus stelleri) in Japan Revealed by Mitochondrial Control Region Sequences

The demographic history and population genetic structure of the blackfin flounder (Glyptocephalus stelleri) along coastal regions of Japan were investigated. Genetic variation in DNA sequences was examined from the first hypervariable region of the mitochondrial DNA control region. A high level of haplotypic diversity (h = 0.99 ± 0.004) was detected, indicating a high level of intrapopulation genetic diversity. The starburst structure of the minimum spanning tree suggested a very recent origin for most haplotypes. The demographic history of G. stelleri was examined using neutrality tests and mismatch distribution analysis, which also indicated a Pleistocene population expansion at about 124,100–413,400 years ago. Hierarchical molecular variance analysis and conventional population Fst comparisons revealed no significant genetic differentiation throughout the range examined.     

Patterns of population genetic variation in sympatric chiltoniid amphipods within a calcrete aquifer reveal a dynamic subterranean environment

Calcrete aquifers from the Yilgarn region of arid central Western Australia contain an assemblage of obligate groundwater invertebrate species that are each endemic to single aquifers. Fine-scale phylogeographic and population genetic analyses of three sympatric and independently derived species of amphipod (Chiltoniidae) were carried out to determine whether there were common patterns of population genetic structure or evidence for past geographic isolation of populations within a single calcrete aquifer. Genetic diversity in amphipod mitochondrial DNA (cytochrome c oxidase subunit I gene) and allozymes were examined across a 3.5 km² region of the Sturt Meadows calcrete, which contains a grid of 115 bore holes (=wells). Stygobiont amphipods were found to have high levels of mitochondrial haplotype diversity coupled with low nucleotide diversity. Mitochondrial phylogeographic structuring was found between haplogroups for one of the chiltoniid species, which also showed population structuring for nuclear markers. Signatures of population expansion in two of the three species, match previous findings for diving beetles at the same site, indicating that the system is dynamic. We propose isolation of populations in refugia within the calcrete, followed by expansion events, as the most likely source of intraspecific genetic diversity, due to changes in water level influencing gene flow across the calcrete.     

Bucking the trend: genetic analysis reveals high diversity,large population size and low differentiation in a deep ocean cetacean

Understanding the genetic structure of a population is essential to its conservation and management. We report the level of genetic diversity and determine the population structure of a cryptic deep ocean cetacean, the Gray''s beaked whale (Mesoplodon grayi). We analysed 530 bp of mitochondrial control region and 12 microsatellite loci from 94 individuals stranded around New Zealand and Australia. The samples cover a large area of the species distribution (~6000 km) and were collected over a 22-year period. We show high genetic diversity (h=0.933–0.987, π=0.763–0.996% and R_s=4.22–4.37, H_e=0.624–0.675), and, in contrast to other cetaceans, we found a complete lack of genetic structure in both maternally and biparentally inherited markers. The oceanic habitats around New Zealand are diverse with extremely deep waters, seamounts and submarine canyons that are suitable for Gray''s beaked whales and their prey. We propose that the abundance of this rich habitat has promoted genetic homogeneity in this species. Furthermore, it has been suggested that the lack of beaked whale sightings is the result of their low abundance, but this is in contrast to our estimates of female effective population size based on mitochondrial data. In conclusion, the high diversity and lack of genetic structure can be explained by a historically large population size, in combination with no known exploitation, few apparent behavioural barriers and abundant habitat.     

Genetic Diversity in Endangered Guizhou Snub-Nosed Monkeys (Rhinopithecus brelichi): Contrasting Results from Microsatellite and Mitochondrial DNA Data

To evaluate the conservation status of a species or population it is necessary to gain insight into its ecological requirements, reproduction, genetic population structure, and overall genetic diversity. In our study we examined the genetic diversity of Rhinopithecus brelichi by analyzing microsatellite data and compared them with already existing data derived from mitochondrial DNA, which revealed that R. brelichi exhibits the lowest mitochondrial diversity of all so far studied Rhinopithecus species. In contrast, the genetic diversity of nuclear DNA is high and comparable to other Rhinopithecus species, i.e. the examined microsatellite loci are similarly highly polymorphic as in other species of the genus. An explanation for these differences in mitochondrial and nuclear genetic diversity could be a male biased dispersal. Females most likely stay within their natal band and males migrate between bands, thus mitochondrial DNA will not be exchanged between bands but nuclear DNA via males. A Bayesian Skyline Plot based on mitochondrial DNA sequences shows a strong decrease of the female effective population size (N_ef) starting about 3,500 to 4,000 years ago, which concurs with the increasing human population in the area and respective expansion of agriculture. Given that we found no indication for a loss of nuclear DNA diversity in R. brelichi it seems that this factor does not represent the most prominent conservation threat for the long-term survival of the species. Conservation efforts should therefore focus more on immediate threats such as development of tourism and habitat destruction.     

Evolutionary history of the oriental fire‐bellied toad (Bombina orientalis) in Northeast China

The evolutionary history of a species is generally affected by the combination of geological events and climate fluctuations. By analyzing the population features, genetic structure and the effective population historical dynamics of existing species, the population evolutionary history can be reestablished. In recent years, geological evidence shows that the Yilan–Yitong fault zone located in Northeast Asia experienced strong and frequent geological changes in the late Quaternary period. Species population history has been shaped by the combination of the complex climatic conditions of the Quaternary and Pleistocene glacial interglacial cycles and palaeogeological events in Northeast Asia and it has become a research focus for evolutionary biology researchers. In this study, mitochondrial and microsatellite molecular markers were used to reveal the population features, genetic structure, and the effective population historical dynamics of the Oriental fire‐bellied toad (Bombina orientalis). The results showed that the strong seismic activity of the Yilan–Yitong fault zone in the late Quaternary period was the main reason for the population differentiation of Oriental fire‐bellied toad in northeast China. The Quaternary Pleistocene glacial interglacial cycles led to the significant bottleneck effect of the western population located in the Maoer mountain area. As a result, the western population has low genetic diversity. Recent gene flow between eastern and western populations and historical evidence of population expansion proved that the dispersal behavior of the western populations was the main cause of the low genetic diversity and mitochondrial and nuclear discordance. Human economic activity may be the mainly driving factor. These evidences showed that the comprehensive influence of geology, climate, human activities and other factors should be considered in the process of exploring the evolutionary history of species.     

Conservation study of an endangered stingless bee (Melipona capixaba—Hymenoptera: Apidae) with restricted distribution in Brazil

Melipona capixaba, popularly known as “uruçu preta”, is a stingless bee restricted to the mountainous Atlantic Rainforest areas of Espírito Santo State, Brazil. Due to the endemism and small population size, this species discovered in 1994 is now considered “vulnerable to extinction”. Using ISSR, PCR–RFLP and microsatellites markers, we studied the genetic variability and structure of M. capixaba from 88 colonies collected throughout the distribution area of the species within Espírito Santo State. The microsatellite, ISSR and mitochondrial haplotype analyses showed that M. capixaba has low genetic variability compared to other insect species. The molecular analyses also indicated a high genetic similarity among the M. capixaba samples, with no clear pattern of structuring. The analyses of molecular variance results indicated that most of the total genetic variation in M. capixaba was explained by the genetic diversity within local populations. Results suggest that the analyzed samples could be treated as a single population for preservation purposes. Thus, given its endemism, local adaptation and low number of natural colonies, efforts for the conservation of M. capixaba should focus on preservation and increasing the number of colonies in the wild, so that M. capixaba can support constant captures and the effects of habitat deforestation in Espírito Santo State.     

Population genetic structure and historical demography of Oratosquilla oratoria revealed by mitochondrial DNA sequences

Genetic diversity, population genetic structure and molecular phylogeographic pattern of mantis shrimp Oratosquilla oratoria in Bohai Sea and South China Sea were analyzed by mitochondrial DNA sequences. Nucleotide and haplotype diversities were 0.00409?C0.00669 and 0.894?C0.953 respectively. Neighbor-Joining phylogenetic tree clustered two distinct lineages. Both phylogenetic tree and median-joining network showed the consistent genetic structure corresponding to geographical distribution. Mismatch distributions, negative neutral test and ??star-like?? network supported a sudden population expansion event. And the time was estimated about 44000 and 50000 years ago.     

Persistence,Isolation and Diversification of a Naturally Fragmented Species in Local Refugia: The Case of Hydromantes strinatii

The study of the European plethodontid salamander Hydromantes strinatii using allozyme and mitochondrial markers showed a strong geographical genetic structure. This was likely the outcome of different evolutionary mechanisms leaving their signature despite the effects of the genetic drift due to the low population size typical of this species. Two highly divergent clades were identified in the eastern and central-western part of the range, with further geographic sub-structure. Nuclear and mitochondrial markers substantially recovered the same population groups but were conflicting in reconstructing their relationships. This apparent incongruence highlighted the action of different mechanisms such as secondary contacts and incomplete lineage sorting in originating the observed genetic variation. The troglophilic habit of this species provided the opportunity to show the importance of caves as local refugia in maintaining the genetic diversity through the persistence of local populations. Accordingly, high nucleotide and haplotype diversity, strong geographic genetic structuring and lack of expansion were evidenced. This signature was found in the populations from the Ligurian and Maritime Alps, in agreement with the complex orography and paleoclimatic history of this Mediterranean hotspot.     

Genetic diversity and population connectivity of the Asian green mussel Perna viridis in South China Sea,inferred from mitochondria DNA markers

The Asian green mussel Perna viridis is ecologically and economically important in the coastal regions of China. In order to characterize the genetic diversity and population connectivity of P. viridis in South China Sea, a 664 bp region of mitochondrial COI gene and a 293 bp region of 16S rRNA gene were sequenced and analyzed for 78 and 92 individuals from four populations in South China Sea, respectively. A total of 15 haplotypes were defined by 14 variable nucleotide sites in COI gene, and 7 haplotypes by 6 variable nucleotide sites in 16S rRNA gene. High haplotype diversity and low nucleotide diversity were observed in COI gene, while moderate haplotype diversity and low nucleotide diversity were observed in 16S rRNA gene. Pairwise F_ST values of COI gene were all negative and those of 16S rRNA gene ranged from −0.01409 to 0.10289. The results showed that no significant genetic divergence (or shallow genetic structure) and high levels of population connectivity among the four populations of P. viridis in South China Sea.     

Population genetic structure of banana corm weevil Cosmopolites sordidus (Germar) in India

The population genetic structure of Cosmopolites sordidus (Germar), an economically important pest of bananas, was studied using the sequence data of the internal transcribed rDNA (ITS1+ITS2) and the mitochondrial ‘COI-tRNA^Leu-COII’ region from seventy nine individuals collected from six sampling locations in India. The ITS data revealed 70% within population variation and non-significant genetic differentiation estimates suggesting lack of phylogeographic sub-structuring. 49% within population variation and highly significant genetic differentiation values were obtained with the mitochondrial data. The Mantel test revealed lack of correlation between genetic and geographic distance with both the markers. Demographic expansion of the populations was confirmed by the star shaped haplotype networks, demographic tests and mismatch distribution curves using both the markers. Molecular diversity indices show a high haplotype diversity (Hd) but low nucleotide diversity (π) suggesting that the populations are closely related. Considering the low self-dispersal ability of the weevils, these results suggest that the range expansion of this banana pest in India has taken place mainly through transport of infested corms and plant material resulting in the weevils forming localised populations which are not genetically distinct from each other. The high gene diversity (Hd) has enabled the weevils to adapt to varying environmental conditions which could explain the range expansion of this pest in India. The observed discrepancy in the genetic differentiation estimates using these two markers can be attributed to the evolutionary dynamics of the nuclear and mitochondrial genomes.     

Population genetic structure and history of a generalist parasite infecting multiple sympatric host species

Host specificity is predicted to shape patterns of parasite gene flow between host species; specialist parasites should have low gene flow between host species, while generalists are predicted to have high gene flow between species. However, even for generalist parasites external forces, including ecological differences between host species may sometimes intervene to limit gene flow and create genetic structure. To investigate the potential for cryptic parasite genetic structure to arise under such circumstances, we examined the population genetic structure and history of the generalist nematode, Trichostrongylus axei, infecting six sympatric wild ungulate species in North America. Using genotypes for 186 T. axei larvae at two mitochondrial genes, cox1 and nad4, we found that T. axei was completely panmictic across host species, with 0% of genetic variation structured between host species and 97% within individual hosts. In addition, T. axei showed no evidence of recent genetic bottlenecks, had high nucleotide diversities (above 2%), and an effective population size estimated to be in the tens of millions. Our result that T. axei maintains high rates of gene flow between multiple sympatric host species adds to a growing body of information on trichostrongylid population genetic structure in different ecological contexts. Furthermore, the high rates of gene flow, coupled with high levels of genetic diversity and large effective population size which we observed in T. axei, point to a potentially broad capacity for rapid evolutionary change in this parasite.     

The mango seed weevil Sternochetus mangiferae (Fabricius) (Coleoptera: Curculionidae) is characterized by low genetic diversity and lack of genetic structure

1. The mango seed weevil Sternochetus mangiferae (Fabricius) is distributed across the major mango-producing areas of the world and causes significant economic losses of mango fruit. Despite its importance as a crop pest, we have only limited information on the population genetics of the mango seed weevil.
2. Here, we examined the genetic diversity of this important pest using specimens intercepted by Beijing Customs District P. R. in China from 41 countries and regions. We used segments of the mitochondrial gene cytochrome c oxidase subunit I and the nuclear gene elongation factor 1-alpha to examine population genetic structure in this species.
3. Our results showed that genetic diversity is low in S. mangiferae, with a mean genetic distance of 0.095–0.14%. Other population genetic parameters also indicated a low level of genetic diversity among samples from a large geographic range. Analysis of molecular variance revealed little population genetic structure, and mismatch distribution analyses provided evidence of a population expansion, although other demographic metrics of population expansion were nonsignificant.
4. We suggest that the observed low level of genetic diversity and population genetic structure in S. mangiferae supports the hypothesis that the population genetics of this species has been impacted by anthropogenic transportation of mangoes and weevils.

     

Genetic differentiation between Apis cerana cerana populations from Damen Island and adjacent mainland in China

Geographic isolation interrupted gene flow between populations leading to population differentiation during the long evolutionary period. In this paper, 33 colonies from Damen Island and 100 colonies from adjacent mainland populations, Juxi and Chixi, were analyzed with both mitochondrial tRNA^leu-COII sequences and five microsatellite loci. The results showed that Apis cerana cerana population from Damen Island significantly differentiated from its adjacent mainland populations. In addition, Damen Island population showed a lower level of genetic diversity in terms of the number of mitochondrial haplotypes while both island and mainland populations showed a low level of genetic diversity with mutilocus analysis. The divergent small island population A.c. cerana might probably have suffered inbreeding and genetic drift as well as limited gene flow across the strait. Our data provides useful information for management and preservation for the Damen Island population.     

Should I Stay or Should I Go? Dispersal and Population Structure in Small,Isolated Desert Populations of West African Crocodiles

The maintenance of both spatial and genetic connectivity is paramount to the long-term persistence of small, isolated populations living in environments with extreme climates. We aim to identify the distribution of genetic diversity and assess population sub-structuring and dispersal across dwarfed desert populations of Crocodylus suchus, which occur in isolated groups, usually less than five individuals, along the mountains of Mauritania (West Africa). We used both invasive and non-invasive sampling methods and a combination of mitochondrial DNA (12 S and ND4) and microsatellite markers (32 loci and a subset of 12 loci). Our results showed high genetic differentiation and geographic structure in Mauritanian populations of C. suchus. We identified a metapopulation system acting within four river sub-basins (high gene flow and absence of genetic structure) and considerable genetic differentiation between sub-basins (F _ST range: 0.12–0.24) with rare dispersal events. Effective population sizes tend to be low within sub-basins while genetic diversity is maintained. Our study suggests that hydrographic networks (temporal connections along seasonal rivers during rainy periods) allow C. suchus to disperse and maintain metapopulation dynamics within sub-basins, which attenuate the loss of genetic diversity and the risk of extinction. We highlight the need of hydrographic conservation to protect vulnerable crocodiles isolated in small water bodies. We propose C. suchus as an umbrella species in Mauritania based on ecological affinities shared with other water-dependent species in desert environments.