Nested Clade Phylogeographic Analysis Research Articles

Population structure and genetic diversity of Sinibrama macrops from Ou River and Ling River based on mtDNA D-loop region analysis, China

In order to understand the influence of human activities such as habitat fragmentation on freshwater fish population evolution, we investigated and compared the genetic diversity and phylogeography of Sinibrama macrops populations in the Oujiang River and Ling River. Mitochondrial control region sequences (D-loop region) of 131 specimens from six populations were obtained and analyzed. The diversity of main stream in the Ou River was lower than that in Ling River. Changtan population showed the lowest diversity (H = 0.646 ± 0.077; π = 0.00060 ± 0.00820). Pairwise FST, gene flow (Nm), and genetic distance (Da) indicated that Longquan and Changtan significantly differentiate from other populations. Nested clade phylogeographical analysis (NCPA) showed some clades and total cladogram experienced isolation by distance. In conclusion, the populations from severely fragmented Ou River have the lower diversity and more intense differentiation than that from the mainstream of Ling River, Changtan population present the lowest diversity and were isolated by the dam construction.

Haplotype Structure and Phylogeographic Evolution of West African Populations of Sitophilus zeamais (Coleoptera, Curculionidae)

Knowledge of spatial and temporal distribution of genetic variability within and between populations is a crucial step for establishing strategies management of stored crops and commodities to assure food safety. The maize weevil, Sitophilus zeamais, is known because of his extraordinary potential for destruction of stored cereals; but little is known about its phylogeography and population structure in Africa in general. This study aimed to determine phylogenic relationships and Phylogeographic structuring of maize weevil populations in West and Central Africa. After alignments and corrections, a total of 112 and 109 samples were used for analysis of Cytochrome B and Cytochrome oxidase I, respectively. The standard indices of genetic diversity, analyses of hierarchical molecular variance (AMOVA), haplotypic network, phylogenetic relationships, demographic tests and Nested Clade Phylogeographic Analysis (NPCA) were computed. Analysis of sequences revealed, with the concatenated matrix, for example, the presence of 30 haplotypes and a high level of haplotype diversity and low nucleotide diversity were observed in West Africa (h = 0.922 ± 0.023; π = 0.0067 ± 0.00116); but these both parameters were twice lower in Central Africa’s populations (h=0.512 ± 0.085; π =0.0034 ± 0.00083). The majority haplotype represented 43% of the overall population and connected West Africa to Central Africa. Maize weevil populations showed a genetic structure but indicated a lack of phylogeographic signal. They also showed that most of molecular variance was due to individual characteristics in a population (~60%); while a proportion of molecular divergence (8-14%) was related to a differentiation between two biogeographical regions in Sub-Saharan Africa. The latters were characterized by the presence of endemic haplotypes as well as common haplotypes. Analysis of mismatch distribution, neutrality tests and Bayesian inferences suggested the existence of 4 to 5 main clusters that had separated themselves from a bottleneck followed by a moderate demographic expansion since Pleistocene period.

Phylogeography of northern Dolly Varden Salvelinus malma (Salmoniformes: Salmonidae) from Asia and North America: An analysis based on the mitochondrial DNA genealogy

Spawning in habitats affected by Pleistocene glacial advances over most of its natural range, northern Dolly Varden Salvelinus malma malma typifies Arctic fauna distributed in northeastern Asia and northwestern North America. We reconstructed a genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of historical events on the phylogeography and contemporary population genetic structure. Analysis of molecular variance partitioned most of the mtDNA variability to the intrapopulation component (72.5%) with much reduced differences between populations (21.1%) and regions (6.4%). Similar patterns of variation apparent from hierarchical diversity and nested clade phylogeographical analysis (NCPA) of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. These findings suggest (1) that demographic history has been influenced by historical range expansions and recent isolation by distance, (2) that present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon’s ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period. The genealogical and NCPA analyses, and mismatch distribution of S. m. malma mtDNA haplotypes do not confirm the assumptions about presence of the two refugia on the territories of the Beringian Land, in which allopatric S. m. malma ancestral populations evolved, and independent origin of the Sea of Okhotsk populations.

Montane refugia isolation and plateau population expansion: Phylogeography of Sino‐Himalayan endemic Spenceria ramalana (Rosaceae)

AbstractClimate oscillations and landscape heterogeneity make the historical population processes of organisms of the Qinghai–Tibet Plateau quite complex. We used chloroplast DNA sequences and amplified fragment length polymorphism (AFLPs) to study the phylogeography and genetic variation of the Qinghai–Tibet Plateau endemic Spenceria ramalana Trimen. The parsimony network contains two star‐like evolutionary units, nested into two nested clades, coinciding with geographic population groups indicated by SAMOVA software. The central group shows genetic homogeneity, indicating a bottleneck or founder effect of population dynamics. Margin groups contribute more haplotype diversity (CT), indicating potential refugia. Several expansion events during several interglacial periods were detected. The latest expansion of the eastern population contributed to the modern population structure of the central area. Four AFLP clusters were detected. Higher CT, a relict pattern of haplotype distribution and DW values of marginal populations, confirmed the location of potential montane refugia. Relict distribution pattern, nested clade phylogeographic analysis conclusions, and restricted gene flow detected by AFLPs indicated an isolation pattern of the populations of montane areas. Heterogeneity of landscape of the western and southern montane areas could be the main barrier for gene flow. Moisture conditions and ecotype transformation might help to build the phylogeographic pattern of this species. Neither chloroplast DNA markers nor AFLP was able to differentiate the two varieties of this species.

Nested clade phylogeographical analysis of the finless porpoise (Neophocaena phocaenoides) inhabiting Chinese and Japanese coasts

The finless porpoise (Neophocaena phocaenoides) is a small cetacean whose survival is largely affected by human activity. The characteristics and structures of 3 populations in China and 4 to 5 populations in Japan have been well documented, although their history and origins remain poorly understood. In this study, nested clade phylogeographical analysis was applied to mtDNA sequences from finless porpoises to delineate the historical factors shaping the divergence pattern of this species. The sampling range covered most habitats of the finless porpoise, including the Chinese and Japanese coasts and the Yangtze River. A nested cladogram was constructed, and all 3 (2-step) clades were linked together without interior or tip status. Our data indicated that haplotype C was the most common among most individuals and populations, which could be the most ancient haplotype among all of the sampled types. As populations expanded to reside in different areas, ancient types with haplotype C mutated to other haplotypes, which were kept endemic by geological barriers that changed during glacial cycles that retarded gene flow. Populations in Japanese Pacific coasts and inland sea and post-arc marginal seacoasts and the Yangtze River were formed by the residual individuals left when allopatric fragmentation occurred in the ancestral population. The existence of highly endemic haplotypes and high genetic diversity from the Ariake Sound, Tachibana Bay, and the Yellow Sea indicated a relatively isolated state in these areas during the evolutionary history of the finless porpoise. The phylogenetic pattern revealed in the present study provided a better understanding of the biogeographical events that affected the finless porpoise within this region.

Divergence and gene flow between the East Sea and the Southeast Atlantic populations of North Pacific light fish Maurolicus japonicus Ishikawa

In the present study, we examined the divergence time and the magnitude of gene flow between two distantly separated populations of North Pacific light fish Maurolicus japonicus, one in the southern part of the East Sea (off Korea) and the other in the Southeast Atlantic Ocean (off Namibia). The mitochondrial 16SrDNA sequences (524 base pairs) obtained from the two populations were analyzed using the isolation with migration (IM) coalescent method as well as the conventional F ST statistic and a phylogeographic method. A significant nonzero F ST value (0.176, P<0.05) indicated genetic differentiation between the two populations. The low level of nucleotide diversity compared to the moderately high level of haplotype diversity implied that the populations have experienced a bottleneck followed by rapid growth in both populations. IM analysis suggested that these two populations most likely split approximately 500–800 K years ago during the Pleistocene climatic oscillations and that gene flow has occurred unidirectionally from the Southeast Atlantic population to the East Sea population. Nested clade phylogeographic analysis supports restricted gene flow between the two populations.

Genetic structure and origin of Busseola fusca populations in Cameroon

AbstractThe cereal stem borer Busseola fusca Fuller (Lepidoptera: Noctuidae) is a species endemic to sub‐Saharan Africa. It is a major pest of maize and cultivated sorghum, the main cereal crops on the African mainland. Previous studies using mitochondrial markers revealed the presence of three clades of haplotypes (W, KI, KII) among B. fusca populations. Previous preliminary studies based on a few B. fusca individuals collected from three localities within the Guineo‐Congolian rain forest in Cameroon demonstrated a matching with clade KII, a fairly surprising result because the putative centre of origin of that clade is located 3 000 km away in East Africa. To check this finding, 120 individuals of B. fusca covering several Cameroonian sites belonging to both Guineo‐Congolian rain forest and Afromontane vegetation mosaics were collected. Comparison of cytochrome b sequences using the same marker revealed low mitochondrial diversity (h = 0.483 ± 0.054, π = 0.073 ± 0.061%). Moreover, molecular diversity in the Guineo‐Congolian rain forest zone was lower than that in Afromontane vegetation, which is therefore thought to be the likely starting point for the colonization of other zones in Cameroon. The study showed a moderate but significant structuring between populations (ΦST = 0.034, P&lt;0.001) as well as within and among the two Cameroonian phytogeographical groups considered (ΦSC = 0.000 and ΦCT = 0.051, respectively, both P&lt;0.001). Nested clade phylogeographic analysis indicated that all Cameroonian clades with significant geographical associations were interpreted as a phenomenon of contiguous range expansion. All results suggest that the Cameroonian population of B. fusca is relatively recent and originates from the recent geographical expansion of clade KII.

Phylogeography and conservation genetics of the relic Gymnocarpos przewalskii (Caryophyllaceae) restricted to northwestern China

Gymnocarpos przewalskii is restricted mainly to the arid desert areas of northwestern China, and is listed as a rare and endangered species of second conservation priority in the China Red Data Book. A phylogeographic study was conducted using two chloroplast regions (psbA–trnH and ycf6–psbM), together with various population genetic analyses, to examine genetic variation, population structure, and evolutionary history of the species. In all, 25 haplotypes were detected, 14 of which were found in the northwestern Tarim Basin of southern Xinjiang Autonomous Region. G. przewalskii showed high levels of total genetic diversity (h T = 0.849) and average gene diversity within populations (h S = 0.350). A higher N ST than G ST (P < 0.001) indicated significant phylogeographic structure across the species range. Nested clade phylogeographic analysis (NCPA) suggested that genetic structure in G. przewalskii has been heavily affected by past fragmentation, which likely resulted from aridity and the expansion of desert in northwestern China during the Quaternary. Mismatch analyses were consistent with NCPA in additionally suggesting contiguous range expansion for populations in the northern Tarim Basin and the Yumen region of Gansu Province, which may have occurred during a less arid interval. Human disturbance was identified as the greatest current threat to the species.

Population genetic structure of Simulium degrangei (Diptera: Simuliidae) from Western Carpathians

Simulium degrangei Dorier & Grenier, 1960 was recorded in southern and central Europe and in the Crimea and Caucasus. Its distribution pattern is scattered. The variability of the mtDNA gene encoding cytochrome oxidase I was studied in populations of S. degrangei from the Western Carpathians in Slovakia and in the northern Hellenides of Greece. In the analyzed samples, 21 haplotypes were recorded, of which twenty were private and occurred in only one mountain range, but one haplotype was found in all three studied populations from the Western Carpathians. Both haplotypes from the Hellenides were private, but these were not isolated and they fit into the haplotype network of the Western Carpathians. Statistics of genetic variability, different designs of analysis of molecular variation with non-significant differences and the pair-wise genetic distances support the hypothesis that there are no differences between the analyzed populations. Similarly, using nested clade phylogeographical analysis, no genetic-geographical structure was found.

Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation

BackgroundAs one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species.ResultsHere, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; π = 0.00314) were almost as high as at PAL (h = 0.836; π = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P < 0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel’s test of nrDNA haplotypes (r = 0.234, P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species.ConclusionsWe found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.

Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis.

BackgroundMultiple loci and population genetic methods were employed to study the phylogeographic history of the Patagonian freshwater crab Aegla neuquensis (Aeglidae: Decopoda). This taxon occurs in two large river systems in the Patagonian Steppe, from the foothills of the Andes Mountains east to the Atlantic Ocean.Methodology/Principal FindingsA nuclear phylogeny and multilocus nested clade phylogeographic analysis detected a fragmentation event between the Negro and Chico-Chubut river systems. This event occurred approximately 137 thousand years ago. An isolation-with-migration analysis and maximum-likelihood estimates of gene flow showed asymmetrical exchange of genetic material between these two river systems exclusively in their headwaters. We used information theory to determine the best-fit demographic history between these two river systems under an isolation-with-migration model. The best-fit model suggests that the Negro and the ancestral populations have the same effective population sizes; whereas the Chico-Chubut population is smaller and shows that gene flow from the Chico-Chubut into the Negro is four times higher than in the reverse direction. Much of the Chico-Chubut system appears to have only been recently colonized while the Negro populations appear to have been in place for most of the evolutionary history of this taxon.Conclusions/SignificanceDue to mitochondrial introgression, three nuclear loci provided different phylogeographic resolution than the three mitochondrial genes for an ancient fragmentation event observed in the nuclear phylogeny. However, the mitochondrial locus provided greater resolution on more recent evolutionary events. Our study, therefore, demonstrates the need to include both nuclear and mitochondrial loci for a more complete understanding of evolutionary histories and associated phylogeographic events. Our results suggest that gene flow between these systems, before and after fragmentation was through periodic paleolakes that formed in the headwaters region. Fragmentation between the Negro and Chico-Chubut systems was driven by the disappearance of these paleolakes during the Patagonian Glaciation.

Divergence and biogeography of the recently evolved Macaronesian red Festuca (Gramineae) species inferred from coalescence‐based analyses

Studying the biogeography and the phylogeography of the endemic Macaronesian red Festuca species (Loliinae, Poaceae) is of prime interest in understanding the speciation and colonization patterns of recently evolved groups in oceanic archipelagos. Coalescence-based analyses of plastid trnLF sequences were employed to estimate evolutionary parameters and to test different species-history scenarios that model the pattern of species divergence. Bayesian IM estimates of species divergence times suggested that ancestral lineages of diploid Macaronesian and Iberian red fescues could have diverged between 1.2 and 1.57 Ma. When empirical data were compared to coalescence-based simulated distributions of discordance and p-distance statistics, two species-history models were chosen in which the first branching lineage derived in Canarian Festuca agustinii. Its sister lineage could have involved a recent polytomy leading to the Madeiran Festuca jubata, the Azorean Festuca francoi + Festuca petraea and the continental Festuca rivularis lineages (Canarian model) or the sequential branching of lineages leading to F. jubata and finally to the sister clades of F.rivularis and F.francoi + F.petraea (Sequential model). Nested clade phylogeographic analysis (NCPA) and a first adapted host-parasite co-evolutionary ParaFit method were used to detect the phylogeographic signal. NCPA inferred long-distance colonizations for the entire diploid red Festuca complex, but allopatric-fragmentation and isolation-by-distance (IBD) patterns were inferred within archipelagos. In addition, the ParaFit method suggested a generalized pattern of a stepping-stone model at all hierarchical levels. Maximum-likelihood-based dispersal-extinction-cladogenesis (DEC) models were superimposed on the Sequential model species tree. The three-independent-colonization (3IC) model was the best supported biogeographic scenario, concurring with previous analysis based on multilocus AFLP data.

Chloroplast phylogeography of Helianthemum songaricum (Cistaceae) from northwestern China: implications for preservation of genetic diversity

Two chloroplast intergenic spacers (trnD-trnT and rps16-trnK) were used to study the phylogeographical structure of Helianthemumsongaricum in northwestern China, with 12 haplotypes detected. Phylogenetic analysis showed that H. songaricum comprised two lineages, one distributed in the Yili Valley and the other in the western Ordos Plateau. Nested clade phylogeographic analysis likewise indicated that haplotypes in the Yili Valley and those in the western Ordos Plateau formed sister monophyletic clades. This lineage split was also supported by AMOVA analysis and the Mantel test. AMOVA showed that 99.41% of variance in H. songaricum occurred between the two distribution regions, and correlation between genetic differentiation and geographical distances was significant (r2 = 0.877, P < 0.0001). All populations in the Yili Valley shared haplotype A with high frequency, and range expansion was detected by nested clade analysis and strongly supported by negative Fu’s FS-values, Tajima’s D-values, and mismatch distribution analysis. We speculate that aggravation of the dry and cold climate during the early Quaternary, combined with plant physiological features, were determining factors contributing to the lineage split, and climate oscillations most likely led to the Yili range expansion. The high drift load (FST = 0.9923, GST = 0.663) and inbreeding load (HS = 0.219) of H. songaricum indicate a significant extinction risk, and protective measures should be taken immediately.

Population genetic structure of the point-head flounder, Cleisthenes herzensteini, in the Northwestern Pacific

Intraspecific phylogenies can provide useful insights into how populations have been shaped by historical and contemporary processes. To determine the population genetic structure and the demographic and colonization history of Cleisthenes herzensteini in the Northwestern Pacific, one hundred and twenty-one individuals were sampled from six localities along the coastal regions of Japan and the Yellow Sea of China. Mitochondrial DNA variation was analyzed using DNA sequence data from the 5' end of control region. High levels of haplotype diversity (>0.96) were found for all populations, indicating a high level of genetic diversity. No pattern of isolation by distance was detected among the population differentiation throughout the examined range. Analyses of molecular variance (AMOVA) and the conventional population statistic Fst revealed no significant population genetic structure among populations. According to the exact test of differentiation among populations, the null hypothesis that C. herzensteini within the examined range constituted a non-differential mtDNA gene pool was accepted. The demographic history of C. herzensteini was examined using neutrality test and mismatch distribution analyses and results indicated Pleistocene population expansion (about 94-376kya) in the species, which was consistent with the inference result of nested clade phylogeographical analysis (NCPA) showing contiguous range expansion for C. herzensteini. The lack of phylogeographical structure for the species may reflect a recent range expansion after the glacial maximum and insufficient time to attain migration-drift equilibrium.

DIM SUM: demography and individual migration simulated using a Markov chain

An increasing number of studies seek to infer demographic history, often jointly with genetic relationships. Despite numerous analytical methods for such data, few simulations have investigated the methods' power and robustness, especially when underlying assumptions have been violated. DIM SUM (Demography and Individual Migration Simulated Using a Markov chain) is a stand-alone Java program for the simulation of population demography and individual migration while recording ancestor-descendant relationships. It does not employ coalescent assumptions or discrete population boundaries. It is extremely flexible, allowing the user to specify border positions, reactions of organisms to borders, local and global carrying capacities, individual dispersal kernels, rates of reproduction and strategies for sampling individuals. Spatial variables may be specified using image files (e.g., as exported from gis software) and may vary through time. In combination with software for genetic marker simulation, DIM SUM will be useful for testing phylogeographic (e.g., nested clade phylogeographic analysis, coalescent-based tests and continuous-landscape frameworks) and landscape-genetic methods, specifically regarding violations of coalescent assumptions. It can also be used to explore the qualitative features of proposed demographic scenarios (e.g. regarding biological invasions) and as a pedagogical tool. DIM SUM (with user's manual) can be downloaded from http://code.google.com/p/bio-dimsum.

Phylogeography, genetic diversity and structure of the poecilosclerid sponge Phorbas fictitius at oceanic islands

In this study we assessed the sequence variation in the I3-M11 partition of the mtDNA cytochrome c oxidase subunit I gene (COI) in ten populations of the Atlanto-Mediterranean demosponge Phorbas fictitius (Porifera: Poecilosclerida) at two spatial scales: a regional scale comparing mainland (Iberian) and insular (Macaronesian) populations, and a local (Archipelagic) scale focusing on different island populations of the Azores archipelago. A multiple approach combining diversity measures, FST estimates, phylogenetic inference and nested clade phylogeographic analysis was used to assess the genetic structure and elucidate the evolutionary history of this species. Genetic differentiation, based of FST estimates, was found among most populations at both scales revealing highly structured populations. This results of a presumably low dispersal potential and bathymetric range of the species, and the geographical isolation of the studied populations. However we found evidence of long distance dispersal events between some populations. Phylogenetic and network analyses indicate a separation of insular (Macaronesian) and mainland (Iberian) clades with only two haplotypes shared between these areas. The high genetic diversity and prevalence of ancestral haplotypes suggest the Macaronesian islands as the likely place of origin of this species with posterior expansion to mainland locations via current-mediated dispersal of larvae or sponge fragments. This study adds to the growing evidence of structured populations in the marine realm and highlights the importance of the Macaronesian islands on the evolutionary history of the Northeast Atlantic marine biota.

Inferring dispersal of aquatic invertebrates from genetic variation: a comparative study of an amphipod and mayfly in Great Basin springs

AbstractWhether active or passive, dispersal accompanied by gene flow shapes the genetic makeup of populations and ultimately the evolutionary divergence of species. Our objective was to determine if 2 very different aquatic invertebrates with overlapping distributions show similar dispersal histories in their phylogeographic patterns and genetic uniqueness. Two spring-dwelling invertebrates, Hyalella azteca and Callibaetis americanus, were collected from 6 adjacent closed basins in the Great Basin of western North America. Cytochrome c oxidase subunit I (COI) and the 28S ribosomal subunit were used as genetic markers in Hyalella, and COI with the 16S ribosomal subunit of the mitochondrial genome were examined in Callibaetis. Maximum parsimony (MP) and likelihood (ML) analyses, FST values, analysis of molecular variance (AMOVA), Mantel tests, and nested clade phylogeographical analysis (NCPA) were used to evaluate geographical associations. Hyalella azteca appears to have been in the adjacent basins much ...

Little shrimp left on the shelf: the roles that sea‐level change, ocean currents and continental shelf width play in the genetic connectivity of a seagrass‐associated species

AbstractAim Caridean shrimp are diverse and abundant inhabitants of seagrass beds. Anthropogenic disturbances have already reduced and fragmented seagrass habitat, and the rate of change is likely to increase in the future. It is therefore becoming increasingly important to build a basis of understanding of connectivity among populations of seagrass‐associated fauna. Phycomenes zostericola is closely associated with seagrass and makes an ideal study species with which to explore patterns of connectivity and the influence of biogeographic boundaries and historical sea‐level changes on seagrass‐associated species. We hypothesized that strong currents and the high potential of P. zostericola for dispersal and adult movement would result, for the most part, in panmixia. We also hypothesized that if structure was evident, it would occur close to known biogeographic boundaries in Queensland.Location Phycomenes zostericola is an abundant shrimp species distributed throughout Queensland’s seagrass habitats. Nineteen seagrass sites from the Torres Strait Islands and Queensland coastlines were sampled.Methods Molecular sequence data for a 590 base pair fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI) was analysed for 279 specimens of P. zostericola. Phylogeographic patterns were analysed using nested clade phylogeographic analysis (NCPA); an isolation‐by‐distance effect was tested using a Mantel test; the effect of biogeographic boundaries was tested using an analysis of molecular variance (AMOVA), and also a spatial analysis of molecular variance (SAMOVA); demographic expansions were tested for using Tajima’s D, Fu’s FS and timing estimated using mismatch analysis; the timing of vicariant events was estimated using coalescent analysis (im program).Results Contrary to our original hypothesis, the strong marine currents are not a connective influence among populations of P. zostericola. Regional genetic structure and an isolation‐by‐distance effect are enhanced by existing coastal biogeographic boundaries. Population genetic structure and demographic history are intricately linked to the effects of a tumultuous Pleistocene sea‐level history on the Queensland continental shelf.Main conclusions Connectivity diminishes among populations of P. zostericola over scales larger than a few hundred kilometres. As seagrass habitats world‐wide become increasingly fragmented, low levels of connectivity will result in an isolated future for P. zostericola and other species reliant on seagrass as habitat.

Clarifying an ambiguous evolutionary history: range‐wide phylogeography of an Australian freshwater fish, the golden perch (Macquaria ambigua)

AbstractAim We conducted a range‐wide phylogeographic study of a common Australian freshwater fish, the golden perch (Macquaria ambigua), to investigate the relationship between environmental processes and evolutionary history in drainage basins.Location Inland [Lake Eyre (LEB), Murray–Darling (MDB) and Bulloo (BULL)] and coastal basins [Fitzroy (FITZ)] of eastern Australia.Methods A total of 590 samples were collected from across the entire species’ distribution and a section of the mitochondrial DNA control region was sequenced. In order to reconstruct the evolutionary history of M. ambigua a comprehensive suite of phylogeographic analyses was conducted, including nested clade phylogeographic analysis, mismatch analysis and isolation‐with‐migration model simulations.Results Three major lineages corresponding to the major drainage basins, FITZ, MDB and LEB/BULL, were identified (ΦST = 0.92). Lineages from the coastal basin (FITZ) were highly divergent from those of the inland basins (up to 6%). Levels of genetic diversity in the inland basins were relatively low and our analyses indicate that these populations experienced both demographic and range expansions during the Pleistocene.Main conclusions Investigation of the range‐wide phylogeography of M. ambigua has revealed new insights into the biogeography of the Australian arid zone, particularly with regard to evolutionary events chronologically associated with cyclical moist and dry conditions. We propose that M. ambigua originated on the east coast (FITZ) and crossed a major geographic barrier, the Great Dividing Range (GDR), to colonize the inland basins (MDB, LEB and BULL). We infer a series of demographic and range expansion events for M. ambigua consistent with a scenario of moister Pleistocene conditions and increased connectivity of freshwater environments, both within and among drainage basins. Major lineages then diversified following isolation of freshwater environments under increasingly arid climate conditions. We suggest that management priorities for M. ambigua should include the resolution of taxonomic uncertainties and the maintenance of genetic diversity of both stocked populations in the MDB and native populations of the LEB that may be at risk of further isolation and reduced gene flow due to increased aridification under future climate change scenarios.

Evaluating Nested Clade Phylogeographic Analysis under Models of Restricted Gene Flow

Nested clade phylogeographic analysis (NCPA) is a widely used method that aims to identify past demographic events that have shaped the history of a population. In an earlier study, NCPA has been fully automated, allowing it to be tested with simulated data sets generated under a null model in which samples simulated from a panmictic population are geographically distributed. It was noted that NCPA was prone to inferring false positives, corroborating earlier findings. The present study aims to evaluate both single-locus and multilocus NCPA under the scenario of restricted gene flow among spatially distributed populations. We have developed a new program, ANeCA-ML, which implements multilocus NCPA. Data were simulated under 3 models of gene flow: a stepping stone model, an island model, and a stepping stone model with some long-distance dispersal. Results indicate that single-locus NCPA tends to give a high frequency of false positives, but, unlike the random-mating scenario presented previously, inferences are not limited to restricted gene flow with isolation by distance or contiguous range expansion. The proportion of single-locus data sets that contained false inferences was 76% for the panmictic case, 87% for the stepping stone model, 79% for the stepping stone model with long-distance dispersal, and more than 99% for the island model. The frequency of inferences is inversely related to the amount of gene flow between demes. We performed multilocus NCPA by grouping the simulated loci into data sets of 5 loci. The false-positive rate was reduced in multilocus NCPA for some inferences but remained high for others. The proportion of multilocus data sets that contained false inferences was 17% for the panmictic case, 30% for the stepping stone model, 4% for the stepping stone model with long-distance dispersal, and 54% for the island model. Multilocus NCPA reduces the false-positive rate by restricting the sensitivity of the method but does not appear to increase the accuracy of the approach. Three classical tests-the analysis of molecular variance method, Fu's Fs, and the Mantel test-show that there is information in the data that gives rise to explicable results using these standard approaches. In conclusion, for the scenarios that we have examined, our simulation study suggests that the NCPA method is unreliable and its inferences may be misleading. We suggest that the NCPA method should not be used without objective simulation-based testing by independent researchers.