Absence Of Phylogeographic Structure Research Articles

Does rafting promote contemporary gene flow? Global and regional patterns of population genetic diversity and structure on the false limpet Siphonaria lateralis in the Southern Ocean

Rafting has been proposed as an effective mechanism for species without free-living pelagic larvae to achieve long-distance dispersal, theoretically preventing population differentiation over wide distributional ranges. Moreover, rafting has been advocated as a main dispersal mechanism for marine invertebrates with sub-Antarctic distributions, because of abundant buoyant kelps, driven by the Antarctic Circumpolar Current. Nonetheless, little attention has been given to the role of rafting to establish regular gene flow across the sub-Antarctic, and the geographic and temporal scales at which it occurs. Aiming to unravel these major questions about the extent of genetic connectivity across the Southern Ocean (SO), we studied the pulmonate limpet Siphonaria lateralis, a benthic species with encapsulated larvae, found on the rocky intertidal of sub-Antarctic islands and southern South America. Since S. lateralis is closely associated with D. antarctica, dispersal by rafting is plausible, as revealed by the absence of phylogeographic structure across the sub-Antarctic. We sampled 116 individuals from eight localities across the SO, and used 5,515 SNPs obtained through Genotyping-by-Sequencing, to determine contemporary genetic diversity, structure, and gene flow at two spatial scales; global, across the SO, and regional, within Kerguelen. Results identified substantial genetic structure, differentiating Patagonia, Falklands/Malvinas Islands, South Georgia and the Kerguelen archipelago, and low levels of contemporary gene flow. The most notable genetic differentiation was found between Patagonia/Falklands and South Georgia/Kerguelen. Structure was also significant between Patagonia and the Falkland/Malvinas Islands. Conversely, South Georgia and Kerguelen exhibited closer genetic affinity, and indications of recent but limited gene flow. Moreover, historical gene flow estimates between the four populations were low. At regional scale, noteworthy genetic structure persisted, and gene flow was insufficient to prevent genetic differentiation within Kerguelen. Consequently, rafting’s potential may be overestimated as a contemporary mechanism promoting gene flow across the SO, as these events may be sporadic, irregular, and unpredictable for marine invertebrates lacking a larval dispersal stage, since contemporary dispersal events don’t seem to facilitate high gene flow at both scales. Accordingly, other oceanographic factors or processes may hinder the establishment of species associated with macroalgae, and as consequence, contemporary genetic connectivity in the sub-Antarctic.

Phylogeographic analysis of Thyrsites atun (Perciformes: Gempylidae) reveals connectivity between fish from South Africa and Chile

ABSTRACT The snoek, Thyrsites atun, is a pelagic fish of the family Gempylidae that inhabits cold waters of the southern hemisphere. It is an important fishing resource species (e.g. Chile, Namibia, New Zealand) linked mainly to the artisanal fisheries, however, its phylogeographic and population aspects are largely unknown. In this study we provide the first detailed analysis of the phylogeographic patterns and demographic processes of the snoek for the southern hemisphere using mitochondrial data of the Cytochrome c Oxidase subunit I gene. Our results indicate two lineages: (i) Australia-New Zealand, and (ii) Chile-South Africa-Namibia. The Australia-New Zealand clade shows partial isolation between populations associated with distinct biogeographic regions, likely driven by the region’s oceanography. The divergence between the lineages happened ∼800,000 years ago. On the other hand, analysis of the fish caught in the South-eastern Pacific (Chile) showed that the genetic diversity among localities (hT = 0.657) was lower than within localities (hS = 0.664), which was consistent with the pairwise comparisons results, suggesting the absence of phylogeographic structure. Based on our estimations, population expansion in T. atun would have occurred ∼7.5 ka (after LGM) under the Bayesian skyline plots approximation. We discuss the scope that this study could have in fisheries management of this important species.

High genetic diversity and absence of phylogeographic structure in breeding populations of vulnerable Saundersilarus saundersi (Charadriiformes: Laridae) in Bohai Bay, China

Genetic diversity is an important consideration in developing effective conservation strategies for threatened species. The Saunders’s Gull (Saundersilarus saundersi) is a globally vulnerable species, which breeds in coastal wetlands in eastern China and western South Korea. Approximately 85% of the world population breeds at three sites along Bohai Bay in eastern China: Nanxiaohe in Liaohekou National Nature Reserve of Liaoning Province, and Yiqianer and Dawenliu in Yellow River Delta National Nature Reserve of Shandong Province. We examined mitochondrial and nuclear markers to detect genetic diversity and phylogeographic structure of the three Bohai Bay subpopulations. Unexpectedly high genetic diversity was observed in both mitochondrial and nuclear markers for every subpopulation. There was no evidence of phylogeographic structure among the three breeding subpopulations, indicating high levels of gene flow in the recent past, possibly continuing into the present day. These results reveal high levels of genetic diversity and evolutionary potential among the current populations of S. saundersi in Bohai Bay. If timely conservation measures are implemented, this gull species would has excellent prospects for long-term survival.

Genetic diversity and population structure of Taxus cuspidata in the Changbai Mountains assessed by chloroplast DNA sequences and microsatellite markers

Taxus cuspidata, a tree species with high economic value because of its anticancer properties, is experiencing severe reduction in populations across its range in China. We examined one chloroplast DNA (cpDNA) region (petA-psbE) and 9 nuclear simple sequence repeats (SSRs) loci variations among seven populations in the Changbai Mountains of China to investigate the levels of genetic diversity and population structure. A moderate level of haplotype diversity (HT = 0.625), low nuclear microsatellite diversity (HE = 0.261 ± 0.028), significant genetic differences (FST = 0.065) and substantial gene flow (Nm = 2.806) were observed. Most of the total genetic variation was partitioned within the population (87.8% and 94.0% for cpDNA and SSRs, respectively). Our haplotype identification permutation tests revealed that GST > NST, indicating an absence of phylogeographic structure in T. cuspidata. Neither STRUCTURE nor UPGMA analyses showed any geographic pattern in T. cuspidata populations. By comparatively analyzing the genetic diversity and survival situation of T. cuspidata, our results provide a theoretical foundation for the resource protection, utilization cultivation and breeding of this valuable plant.

Differences in population genetic structure of two ethnomedicinal herbs of the genus Phyllanthus from India: a consequence of anthropogenic intervention?

Phyllanthus amarus and Phyllanthus fraternus are important ethnomedicinal herbs used as traditional medicines in many parts of the world. The increasing popularity of these green medicines and almost no studies on structuring of genetic diversity in these herbs, led to this investigation. Keeping this in view, our main objective was to analyze the structuring of chloroplast DNA diversity in wild populations of the two herbs from Northern India, using chloroplast DNA (cpDNA) markers. PCR–RFLP of cpDNA regions was carried out to detect intraspecific polymorphisms. The study revealed differences in cpDNA diversity in the two ethnomedicinal herbs. Lower cpDNA diversity, lesser number of haplotypes and absence of correlation between phylogeny and geographical distribution of haplotypes were observed in P. amarus. Absence of phylogeographic structure in P. amarus may be attributed partly to higher anthropogenic intervention, owing to its commercialization for export and raw drug trade. The investigation identified populations with high haplotype diversity and unique haplotypes in both the herbs, which will be useful while formulating future conservation strategies. As there are comparatively less number of studies on structure of cpDNA diversity in annuals, the present analyses also add to the available data on population genetic structure in annual plants.

Deep divergences and extensive phylogeographic structure in a clade of lowland tropical salamanders

BackgroundThe complex geological history of Mesoamerica provides the opportunity to study the impact of multiple biogeographic barriers on population differentiation. We examine phylogeographic patterns in a clade of lowland salamanders (Bolitoglossa subgenus Nanotriton) using two mitochondrial genes and one nuclear gene. We use several phylogeographic analyses to infer the history of this clade and test hypotheses regarding the geographic origin of species and location of genetic breaks within species. We compare our results to those for other taxa to determine if historical events impacted different species in a similar manner.ResultsDeep genetic divergence between species indicates that they are relatively old, and two of the three widespread species show strong phylogeographic structure. Comparison of mtDNA and nuclear gene trees shows no evidence of hybridization or introgression between species. Isolated populations of Bolitoglossa rufescens from Los Tuxtlas region constitute a separate lineage based on molecular data and morphology, and divergence between Los Tuxtlas and other areas appears to predate the arrival of B. rufescens in other areas west of the Isthmus of Tehuantepec. The Isthmus appears responsible for Pliocene vicariance within B. rufescens, as has been shown for other taxa. The Motagua-Polochic fault system does not appear to have caused population vicariance, unlike in other systems.ConclusionsSpecies of Nanotriton have responded to some major geological events in the same manner as other taxa, particularly in the case of the Isthmus of Tehuantepec. The deep divergence of the Los Tuxtlas populations of B. rufescens from other populations highlights the contribution of this volcanic system to patterns of regional endemism, and morphological differences observed in the Los Tuxtlas populations suggests that they may represent an undescribed species of Bolitoglossa. The absence of phylogeographic structure in B. nympha, in contrast to the other widespread species in the subgenus, may be due to historical forest contraction and more recent range expansion in the region. Phylogeographic data provide substantial insight into the evolutionary history of these morphologically similar species of salamanders, and contribute to our understanding of factors that have generated the high biodiversity of Mesoamerica.

Different Post-Pleistocene Histories of Eurasian Parids

Previous phylogeographic studies of the great tit (Parus major) and the willow tit (Parus montanus) found a general absence of phylogeographic structure for both species and suggested that each species underwent range contraction during the last Ice Age and survived in relatively low numbers, P. major in southern Europe and P. montanus in southeastern Asia. However, prior studies did not sample the entire range of either species. We analyzed sequence data for the complete mitochondrial ND2 gene from 87 P. major and 139 P. montanus from 15 new Eurasian localities, both to test prior conclusions and to provide better coverage of each species' range. Our analyses confirmed the absence of phylogeographic structure in P. major and P. montanus and supported the prior refuge hypothesis for P. major. For P. montanus, we concluded that besides surviving the Ice Age in southeastern Asia, as previously hypothesized, it apparently sustained a relatively large population in northern Eurasian riverine thickets and then expanded eastward. Genetic diversity was low in P. major (pi = 0.0012, h = 0.64) and moderate in P. montanus (pi = 0.0021, h = 0.88), suggesting higher long-term effective population sizes and the older ages of populations in P. montanus. If molecular substitution rates are similar, P. montanus colonized its current Eurasian range earlier than P. major. Differences between prior studies and ours likely result from sampling gaps in earlier studies.

A population genetic analysis of chloroplast DNA in wild populations of Prunus avium L. in Europe.

A population genetic study of chloroplast DNA was carried out in 23 wild populations of Prunus avium sampled from several European deciduous forests. An analysis of approx. 9% of the chloroplast genome detected mostly insertion-deletion mutations and one point mutation. In all, 16 haplotypes were detected. Six haplotypes were shared by two or more populations and 10 were unique. One haplotype was present in 21 of the 23 populations and 161 of 211 individuals, which probably indicates its ancient origin. The level of population subdivision, using unordered and ordered alleles, was low, GSTC=0.29 and NSTC=0.33, respectively. The difference between GSTC and NSTC is nonsignificant, indicating an absence of correlation between haplotype phylogeny and geographical distribution. The absence of phylogeographic structure in wild cherry may be attributed to long distance gene flow among populations by birds, animals and anthropogenic activities. The minimum-length spanning tree depicting the phylogenetic relationships between the haplotypes indicates the possible existence of two lineages represented by the haplotypes H3 and H4. The information about homogeneity or heterogeneity of populations in terms of haplotype constitution and detection of rare haplotypes in some populations will be useful for formulation of conservation and management strategies of wild cherry.