Fu's Fs Tests Research Articles

Genetic structure of the Peruvian scallop Argopecten purpuratus inferred from mitochondrial and nuclear DNA variation

The population genetic structure of the Peruvian scallop Argopecten purpuratus from three different wild populations along the Peruvian coast was analyzed using nine microsatellite loci and a partial region (530bp) of the mitochondrial 16S rRNA gene. A total of 19 polymorphic sites in the 16S rRNA gene defined 18 unique haplotypes. High genetic diversity was presented in all populations. Statistical analysis of mitochondrial DNA revealed no significant genetic structure (ΦST=0.00511, P=0.32149) among the three localities. However, microsatellite analysis showed low (2.86%) but highly significant (P=0.0001) genetic differentiation among populations, most of the variation was found in Independencia Bay population, which is located in the Peruvian National Reserve of Paracas. Neutrality tests based on mitochondrial haplotypes were performed to assess signatures of recent historical demographic events. Overall results from Tajima's D and Fu's FS tests indicated significant deviations from neutrality. To our knowledge, this study constitutes the first investigation based on mitochondrial and microsatellite markers on the genetic structure of A. purpuratus.

Genetic difference of Chinese horseshoe crab (Tachypleus tridentatus) in southeast coast of China based on mitochondrial COI gene analysis

Population genetic structure and historical demography of Chinese horseshoe crab (T. tridentatus) along southeast coast of China were inferred from the sequence data of mitochondrial cytochrome c oxidase subunit I (COI) fragment. The sequence analysis for 964 bp COI fragment was conducted in 28 individuals collected from five localities: Ninghai in Zhejiang Province, Meizhou and Zhangpu in Fujian Province, Beihai of Guangxi Zhuang Autonomous Region and Danzhou of Hainan Province. Sequence variation was relatively low with a total of seven transitions observed. In all localities, :Haplotype H3 was the dominant type observed among eight haplotypes defined previously, and was at the center of radiation in Median-Joining network. The prolonged star-like network suggests a signature of population expansions. The level of diversity was low in total, with haplotype diversity (H-d) being equal to 0.765 and nucleotide diversity (pi) being equal to 0.001 18, respectively. The genetic structure analysis revealed the significant genetic difference between Ninghai and Danzhou populations. Both mismatch distribution analysis and Fu's Fs test provided consistent inference of historic population expansion. The low genetic diversity of horseshoe crab observed along China coast indicated that urgent measures should be taken to protect this rare marine animal.

The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis)

2 . Previous morphological and genetic studies have proposed the existence of at least two evolutionary significant units: one distributed across the Orinoco and Amazon basins and another confined to the Bolivian Amazon. The presence of barriers in the riverine environment has been suggested to play a significant role in shaping present-day patterns of ecological and genetic structure for this species. In the present study, we examined the phylogeographic structure, lineage divergence time and historical demography using mitochondrial (mt)DNA sequences in different pink dolphin populations distributed in large and small spatial scales, including two neighbouring Brazilian Amazon populations. mtDNA control region (CR) analysis revealed that the Brazilian haplotypes occupy an intermediate position compared to three previously studied geographic locations: the Colombian Amazon, the Colombian Orinoco, and the Bolivian Amazon. On a local scale, we have identified a pattern of maternal isolation between two neighbouring populations from Brazil. Six mtDNA CR haplotypes were identified in Brazil with no sharing between the two populations, as well as specific cytochrome b (cyt b) haplotypes identified in each locality. In addition, we analyzed autosomal microsatellites to investigate male-mediated gene flow and demographic changes within the study area in Brazil. Data analysis of 14 microsatellite loci failed to detect significant population subdivision, suggesting that male-mediated gene flow may maintain homogeneity between these two locations. Moreover, both mtDNA and microsatellite data indicate a major demographic collapse within Brazil in the late Pleistocene. Bayesian skyline plots (BSP) of mtDNA data revealed a stable population for Colombian and Brazilian Amazon lineages through time, whereas a population decline was demonstrated in the Colombian Orinoco lineage. Moreover, BSP and Tajima's D and Fu's Fs tests revealed a recent population expansion exclusively in the Bolivian sample. Finally, we estimated that the diversification of the Inia sp. lineage began in the Late Pliocene (approximately 3.1 Mya) and continued throughout the Pleistocene. Published 2011. This article is a US Government work and is in the public domain in the USA. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 812-827.

Complex genetic patterns in the mangrove wood-borer Sphaeroma terebrans Bate, 1866 (Isopoda, Crustacea, Sphaeromatidae) generated by shoreline topography and rafting dispersal

A phylogeographic analysis of the widely distributed marine wood-boring isopod Sphaeroma terebrans Bate 1866 was carried out to test for potential genetic differentiation and geographical structure. The species spends its entire life cycle in mangrove roots and is characterized by low active dispersal ability and no early dispersal stages. As the species has a mainly circumtropical distribution, long-range dispersal mechanisms, such as rafting on floating wood, could have played important roles in the distribution of the species throughout the world. However, as high genetic diversity and very low gene flow levels have been found among very close localities, physical barriers related to changes in coastal topography could have contributed to the contemporary genetic structure. Mitochondrial (COI and 16S) and nuclear (Histone3) sequences were analysed from 13 populations of S. terebrans. High levels of genetic population differentiation (Φst=0.84) were observed among the 13 populations analysed and they were not explainable by an isolation by distance model (Mantel test: p>0.13). Four major lineages were recognized by phylogenetic and spatial genetic analyses. One lineage (Clade D), highly divergent from the others, was only found in one of the two populations from Mahè (Seychelles Is.) and it shows morphological affinities with South Asian populations. The other 12 populations are represented by three haplogroups. Clades B and C are not highly differentiated from each other, but both of them appear very distant from Clade A, probably representing a different species with significant departure from neutrality, as suggested by Mismatch distribution, Tajima's and Fu's Fs tests. Contrary to expectation, the cosmopolitian S. terebrans seems to comprise more than one species.

Phylogeography of Rhinella spinulosa (Anura: Bufonidae) in northern Chile

AbstractThe southern part of the Altiplano of the Andes Range is characterized by a complex hydrography, due to an intense geologic activity and the effects of the Pleistocene glaciations. This has produced a high degree of diversity at the species level in some aquatic taxa (e.g., fish and amphibians), which suggests that these same processes have produced divergence at the intraspecific level in co-distributed taxa. We investigated the genetic variation in populations of the anuran Rhinella spinulosa which represent its entire distribution in the extreme north of Chile (17°44′S-23°47′S). Haplotype networks of the mitochondrial control region recognized two main lineages, one of which is distributed from the northern boundary of Chile to the Salar de Alconcha and the other from the Salar de Carcote to the locality of Tilomonte. The northern lineage showed little phylogeographic structure; a few very frequent haplotypes are widely distributed. The southern lineage had greater structure, due principally to the high divergence of the populations from the eastern springs of the Salar de Atacama. Fu's Fs test and the mismatch distributions suggested that most of the populations of both lineages are in the process of demographic expansion. The spatial distribution of the genetic variability was correlated with the hydrography and the paleoclimatological data available for the region, which suggested that geographic expansions followed by periods of contraction of population ranges, together with sporadic floods may explain the observed phylogeographic patterns.

Phylogeography of the Rice Frog, Fejervarya multistriata (Anura: Ranidae), from China Based on mtDNA D-loop Sequences

The rice frog, Fejervarya multistriata, is an amphibian widely distributed in China. In this study, we sampled the species across its distributional area in China and sequenced the mtDNA D-loop to investigate the genetic diversity and geographical pattern of the frog population. The results revealed 38 haplotypes in the population, with K2P values varying from 0.19% to 4.22%. Both a phylogenetic analysis and a nested clade analysis (NCA) detected two geographically isolated lineages respectively distributed around the Yangtze drainage (Yangtze lineage) and the south of China (southern lineage). NCA inferred a contiguous range expansion within the Yangtze lineage and allopatric fragmentation within the southern lineage, which might be partly due to the limited samples from this lineage. Accordingly, Fu's Fs test also indicated a population expansion after glacial movement. Therefore, we assumed that the species history responding to glacial events shaped the present population pattern of F. multistriata on the Chinese mainland.

Long current to nowhere? — Genetic connectivity of Jasus tristani populations in the southern Atlantic Ocean

The commercially exploited spiny lobster Jasus tristani has a disjunct distribution in the southern Atlantic Ocean, with populations occurring at the Tristan da Cunha Archipelago, Gough Island and on Vema Seamount. A distance of 2 000km separates Vema and the Tristan Archipelago. In order to determine genetic connectivity of lobster between these locations, a region of the cytochrome oxidase II (COII) gene was sequenced for 193 individuals of J. tristani from five sampling sites (Tristan da Cunha, Nightingale, Inaccessible, Gough islands and Vema Seamount). Our results show that J. tristani in the southern Atlantic share a most recent common ancestry that dates back at least one million years. Analyses of molecular variance and pairwise Φst analyses reveal shallow but significant genetic partitioning between Vema Seamount and all other locations. No population differentiation was detected among any of the remaining sampling sites. Coalescent analyses show limited gene flow between Vema and the archipelago (including Gough Island), possibly mediated by larval dispersal in the South Atlantic gyre system. Population divergence between Vema and the other populations, using MDIV, was estimated to be approx. 270 000 years ago. Mismatch distributions, a haplotype network, and Fu's Fs test, all suggest that the J. tristani population underwent population expansion between 12 000 and 99 000 years ago.

Extreme population subdivision throughout a continuous range: phylogeography of Batrachoseps attenuatus (Caudata: Plethodontidae) in western North America

Low-vagility species with deep evolutionary histories are key to our understanding of the biogeographical history of geologically complex areas, such as the west coast of North America. We present a detailed study of the phylogeography of the salamander Batrachoseps attenuatus (Caudata: Plethodontidae) using sequences of the mitochondrial gene cob from 178 individuals sampled from throughout the species' range. Sequences of three other mitochondrial genes (16S, cox1, nad4) and a nuclear gene (RAG-1) were used to investigate the deeper evolutionary history of the species. We found high levels of genetic diversity and deep divergences within a mostly continuous distribution, with five genetically well-differentiated and geographically structured mitochondrial DNA clades. Significant association between geographical and genetic distances within these clades suggests demographic stability, whereas Fu's FS tests suggest demographic expansions in three of them. Mantel tests identify two biogeographical barriers, the San Andreas Fault and the Sacramento-San Joaquin Delta, as important in the diversification of lineages. The timing of the main splitting events between intraspecific lineages was estimated by applying relaxed molecular clock methods combining several mutation rates and a fossil calibration. The earliest splitting events are old (Pliocene/Miocene), with more recent (Pleistocene) subdivisions in some clades. Disjunct populations distributed along the western foothills of the Sierra Nevada colonized this area relatively recently from a single refugium east of San Francisco Bay. The combination of fine-scale, comprehensive sampling with phylogenetic, historical demographic and hypothesis-based tests allowed delineation of a complex biogeographical scenario with general implications for the study of codistributed taxa.

Population structure and historical demography of eastern North Atlantic harbour porpoises inferred through mtDNA sequences

The harbour porpoise Phocoena phocoena experiences high rates of incidental mortal- ity in commercial fisheries, and in some areas these rates are sufficiently high to justify concern over population sustainability. Given this high mortality, conservation efforts may be facilitated by an understanding of how present-day population structure has been shaped by historical demographic changes. To investigate the demographic history of porpoises in the eastern North Atlantic, variation in the mitochondrial DNA (mtDNA) control region of 115 porpoises was compared among 4 sampling locations (North Sea, France, Portugal, and West Africa). Genetic variation was investigated by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA). To put the present study in context within the eastern Atlantic, previously published sequence data from Norway (n = 87) and the Black Sea (n = 9) were included. All areas showed substantial geographic structure as indicated by AMOVA and SAMOVA, and there was significant isolation by distance among sampling areas. The haplotype network, mismatch distribution and Fu's FS test of population equilibrium suggest there has been a relatively recent range expansion into the northernmost area (Norway), probably as a result of re-colonisation into regions previously iced over during Quaternary glaciation events. In all, these results suggest that harbour porpoises within the eastern North Atlantic show geographic structuring as a consequence of limited gene flow along the coast, and their historical biogeography can be interpreted in light of demographic changes that have influenced the evolutionary patterns observed in the mtDNA sequences.

PHYLOGEOGRAPHY OF THE SUBTERRANEAN RODENT CTENOMYS AUSTRALIS IN SAND-DUNE HABITATS: EVIDENCE OF POPULATION EXPANSION

In this work we examined the geographic genetic structure of the subterranean herbivorous rodent Ctenomys australis (sand-dune tuco-tuco) using mitochondrial DNA (mtDNA) control region (D-loop) sequences. We found 24 haplotypes in the analysis of 70 individual 403-base pair sequences; most were restricted to single populations, although a few haplotypes were shared broadly across the species' range. Genetic differentiation was not consistent with a simple model of isolation by distance, possibly evidencing a lack of equilibrium between gene flow and local genetic drift. The analysis of mismatch distributions, Fu's Fs-test of neutrality and the “starlike” topology of the gene genealogy showed a pattern consistent with a recent population expansion event. However, we could not rule out an alternative explanation based on departures from strict neutrality of mtDNA.