Oceanic dispersal in a sedentary reef shark (Triaenodon obesus): genetic evidence for extensive connectivity without a pelagic larval stage

Aim Most reef fishes are site‐attached, but can maintain a broad distribution through their highly dispersive larval stage. The whitetip reef shark (Triaenodon obesus) is site‐attached, yet maintains the largest Indo‐Pacific distribution of any reef shark while lacking the larval stage of bony (teleost) fishes. Here we use mitochondrial DNA (mtDNA) sequence data to evaluate the enigma of the sedentary reef shark that maintains a distribution across two‐thirds of the planet. Location Tropical Pacific and Indian Oceans. Methods We analysed 1025 base pairs of the mtDNA control region in 310 individuals from 25 locations across the Indian and Pacific Oceans. Phylogeographic and population genetic analyses were used to reveal the dispersal and recent evolutionary history of the species. Results We resolved 15 mtDNA control region haplotypes, but two comprised 87% of the specimens and were detected at nearly every location. Similar to other sharks, genetic diversity was low (h = 0.550 ± 0.0254 and π = 0.00213 ± 0.00131). Spatial analyses of genetic variation demonstrated strong isolation across the Indo‐Pacific Barrier and between western and central Pacific locations. Pairwise Φ_ST comparisons indicated high connectivity among archipelagos of the central Pacific but isolation across short distances of contiguous habitat (Great Barrier Reef) and intermittent habitat (Hawaiian Archipelago). In the eastern Pacific only a single haplotype (the most common one in the central Pacific) was observed, indicating recent dispersal (or colonization) across the East Pacific Barrier. Main conclusions The shallow haplotype network indicates recent expansion of modern populations within the last half million years from a common ancestor. Based on the distribution of mtDNA diversity, this began with an Indo‐West Pacific centre of origin, with subsequent dispersal to the Central Pacific and East Pacific. Genetic differences between Indian and Pacific Ocean populations are consistent with Pleistocene closures of the Indo‐Pacific Barrier associated with glacial cycles. Pairwise population comparisons reveal weak but significant isolation by distance, and notably do not indicate the high coastal connectivity observed in other shark species. The finding of population structure among semi‐contiguous habitats, but population connectivity among archipelagos, may indicate a previously unsuspected oceanic dispersal behaviour in whitetip reef sharks.     

Phylogeography of the humbug damselfish,Dascyllus aruanus (Linnaeus, 1758): evidence of Indo‐Pacific vicariance and genetic differentiation of peripheral populations

The phylogeographical structure of coral‐associated reef fishes may have been severely affected, more than species from deeper habitats, by habitat loss during periods of low sea level. The humbug damselfish, Dascyllus aruanus, is widely distributed across the Indo‐West Pacific, and exclusively inhabits branching corals. We used mitochondrial cytochrome b sequence and seven microsatellite loci on D. aruanus samples (260 individuals) from 13 locations across the Indo‐West Pacific to investigate its phylogeographical structure distribution‐wide. A major genetic partition was found between the Indian and Pacific Ocean populations, which we interpret as the result of geographical isolation on either side of the Indo‐Pacific barrier during glacial periods. The peripheral populations of the Red Sea and the Society Islands exhibited lower genetic diversity, and substantial genetic differences with the other populations, suggesting relative isolation. Thus, vicariance on either side of the Indo‐Pacific barrier and peripheral differentiation are considered to be the main drivers that have shaped the phylogeographical patterns presently observed in D. aruanus. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 931–942.     

Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?

The conservation of humpback dolphins, distributed in coastal waters of the Indo‐West Pacific and eastern Atlantic Oceans, has been hindered by a lack of understanding about the number of species in the genus (Sousa) and their population structure. To address this issue, we present a combined analysis of genetic and morphologic data collected from beach‐cast, remote‐biopsied and museum specimens from throughout the known Sousa range. We extracted genetic sequence data from 235 samples from extant populations and explored the mitochondrial control region and four nuclear introns through phylogenetic, population‐level and population aggregation frameworks. In addition, 180 cranial specimens from the same geographical regions allowed comparisons of 24 morphological characters through multivariate analyses. The genetic and morphological data showed significant and concordant patterns of geographical segregation, which are typical for the kind of demographic isolation displayed by species units, across the Sousa genus distribution range. Based on our combined genetic and morphological analyses, there is convincing evidence for at least four species within the genus (S. teuszii in the Atlantic off West Africa, S. plumbea in the central and western Indian Ocean, S. chinensis in the eastern Indian and West Pacific Oceans, and a new as‐yet‐unnamed species off northern Australia).     

The presence of a cryptic barrier in the West Pacific Ocean suggests the effect of glacial climate changes on a widespread sea‐dispersed plant,Vigna marina (Fabaceae)

Ocean currents are an important driver of evolution for sea‐dispersed plants, enabling them to maintain reciprocal gene flow via sea‐dispersed diaspores and obtain wide distribution ranges. Although geographic barriers are known to be the primary factors shaping present genetic structure of sea‐dispersed plants, cryptic barriers which form clear genetic structure within oceanic regions are poorly understood. To test the presence of a cryptic barrier, we conducted a phylogeographic study together with past demographic inference for a widespread sea‐dispersed plant, Vigna marina, using 308 individuals collected from the entire Indo‐West Pacific (IWP) region. Chloroplast DNA variation showed strong genetic structure that separated populations into three groups: North Pacific (NP), South Pacific (SP) and Indian Ocean (IN) (F′_CT among groups = 0.954–1.000). According to the Approximate Bayesian computation inference, splitting time between NP and SP was approximately 20,200 years (95%HPD, 4,530–95,400) before present. Moreover, a signal of recent population expansion was detected in the NP group. This study clearly showed the presence of a cryptic barrier in the West Pacific region of the distributional range of V. marina. The locations of the cryptic barrier observed in V. marina corresponded to the genetic breaks found in other plants, suggesting the presence of a common cryptic barrier for sea‐dispersed plants. Demographic inference suggested that genetic structure related to this cryptic barrier has been present since the last glacial maximum and may reflect patterns of past population expansion from refugia.     

Pleistocene sea level fluctuations and the phylogeography of the dugong in Australian waters

We investigated phylogeography, demography, and population connectivity of the dugong (Dugong dugon) in Australian waters using mitochondrial control region DNA sequences from 177 Australian dugongs and 11 from elsewhere. The dugong is widespread in shallow Indo‐West Pacific waters suitable for growth of its main food, seagrass. We hypothesized that the loss of habitat and creation of a land barrier (the Torres Strait landbridge) during low sea level stands associated with Pleistocene glacial cycles have left a persisting genetic signature in the dugong. The landbridge was most recently flooded about 7,000 yr ago. Individual dugongs are capable of traveling long distances, suggesting an alternative hypothesis that there might now be little genetic differentiation across the dugong's Australian range. We demonstrated that Australian dugongs fall into two distinct maternal lineages and exhibit a phylogeographic pattern reflecting Pleistocene sea‐level fluctuations. Within each lineage, genetic structure exists, albeit at large spatial scales. We suggest that these lineages diverged following the last emergence of the Torres Strait landbridge (ca. 115 kya) and remained geographically separated until after 7 kya when passage through Torres Strait again became possible for marine animals. Evidence for population growth in the widespread lineage, especially after the last glacial maximum, was detected.     

Glacial refuges and cryptic speciation in a Southern Palearctic tiger beetle (Coleoptera: Cicindelidae)

Pleistocene glaciations had a determining role for shaping the current distribution and diversity of organisms, especially in the Palearctic region. In this work, we carry out a phylogeographic analysis of Iberian and two Eastern European populations of the tiger beetle Calomera littoralis (Fabricius, 1787) in order to infer the processes that may have affected their evolutionary history. According to our results, the genetic diversity of central Iberian C. littoralis populations is very low. The haplotype networks also suggest that these populations experienced a genetic bottleneck in the past, possibly related to the last glacial maxima, similar to that observed in other cicindelid taxa. These results highlight the remarkable dispersal capacity of this species, being able to move freely from one locality to another, despite the relatively long distances of sub-optimal habitat that separates them. The genetic data of central Iberian populations contrast with those of the Eastern European populations, with higher genetic diversity and no hints of any past bottleneck. This can be explained by the different characteristics of both (Iberian and Pontic) glacial refuges. The high degree of genetic differentiation between the three C. littoralis clades, and the inclusion of C. lunulata between them, suggests that the three analysed populations could be considered as different cryptic species. In that case, C. littoralis may correspond to a species complex that is still undergoing a process of speciation, similar to that observed in Cicindela campestris.     

Phylogeography of the Hypnea musciformis species complex (Gigartinales,Rhodophyta) with the recognition of cryptic species in the western Atlantic Ocean

Populations of the marine benthic red macroalgae Hypnea musciformis and Hypnea pseudomusciformis along the Atlantic and Pacific Oceans were tested for phylogeographic structure using the DNA barcode COI‐5P combined with rbcL for the construction of the phylogenetic tree. Strong patterns of genetic structure were detected across 210 COI‐5P DNA sequences, and 37 COI‐5P haplotypes were found, using multiple statistical approaches. Hypnea musciformis was found in the Northeast and Northwest Atlantic, the Mediterrean Sea, Namibia, and along the Pacific coast of Mexico. Two new putative species were detected, Hypnea sp. 1 in the Caribbean Sea and Hypnea sp. 2 in the Dominican Republic. Three distinct marine phylogeographic provinces were recognized in the Southern Hemisphere for H. pseudomusciformis: Uruguay, South‐Southeast Brazil, and Northeast Brazil. The degree of genetic isolation and distinctness among these provinces varied considerably. The Uruguay province was the most genetically distinct, as characterized by four unique haplotypes not shared with any of the Brazilian populations. Statistically significant results support both, isolation by distance and isolation by environment hypotheses, explaining the formation and mantainance of phylogeographic structuring along the Uruguay‐Brazil coast. Geographic, taxonomic and molecular marker concordances were found between our H. pseudomusciformis results and published studies. Furthermore, our data indicate that the Hawaiian introduced populations of H. musciformis contain Hypnea sp. 1 haplotypes, the current known distribution of which is restricted to the Caribbean.     

Long‐term panmixia in a cosmopolitan Indo‐Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species

Phylogeographical studies have shown that some shallow‐water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long‐term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long‐term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo‐Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two‐fold: first, to test for broad‐scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo‐Pacific and a range‐wide, long‐term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged.     

Multilocus phylogeography of the sea snake Hydrophis curtus reveals historical vicariance and cryptic lineage diversity

The Indo‐Australian archipelago (IAA) supports the world's highest diversity of marine fish, invertebrates and reptiles. Many of the marine fish and invertebrates show congruent phylogeographic patterns, supporting a view that the region's complex geo‐climatic history has played an important role in generating its exceptional biodiversity. Here, we examine population genetic structure of the viviparous sea snake, Hydrophis curtus, to assess how past and present barriers to gene flow in the IAA have contributed to genetic and species diversity in a fully marine reptile. Mitochondrial and anonymous nuclear sequences and ten microsatellite loci were used to identify patterns of historical genetic structure and population expansion, reconstruct dated genealogies and assess levels of recent gene flow. These markers revealed strong concordant geographic structure within H. curtus with a prominent genetic break between populations broadly distributed in the Indian Ocean and the West Pacific. These populations were estimated to have diverged in the late Pliocene or early Pleistocene, and microsatellite admixture analyses suggested limited recent gene flow between them despite the current lack of barriers to dispersal, indicating possible cryptic species. Subsequent divergence in the mid–late Pleistocene was detected within the West Pacific clade among the populations in the Phuket‐Thailand region, South‐East Asia and Australia, and two of these populations also showed genetic signals of recent range expansions. Our results show that climatic fluctuations during the Plio‐Pleistocene generated high levels of cryptic genetic diversity in H. curtus, and add to similar findings for diverse other marine groups in the IAA.     

Spatiotemporal analyses suggest the role of glacial history and the ice‐free corridor in shaping American badger population genetic variation

Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The “southerly refugia model” has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star‐like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice‐free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range‐wide patterns and identifies unique genetic units that can likely be used to inform conservation of at‐risk populations at the northern periphery.     

Hidden endemism,deep polyphyly,and repeated dispersal across the Isthmus of Tehuantepec: Diversification of the White‐collared Seedeater complex (Thraupidae: Sporophila torqueola)

Phenotypic and genetic variation are present in all species, but lineages differ in how variation is partitioned among populations. Examining phenotypic clustering and genetic structure within a phylogeographic framework can clarify which biological processes have contributed to extant biodiversity in a given lineage. Here, we investigate genetic and phenotypic variation among populations and subspecies within a Neotropical songbird complex, the White‐collared Seedeater (Sporophila torqueola) of Central America and Mexico. We combine measurements of morphology and plumage patterning with thousands of nuclear loci derived from ultraconserved elements (UCEs) and mitochondrial DNA to evaluate population differentiation. We find deep levels of molecular divergence between two S. torqueola lineages that are phenotypically diagnosable: One corresponds to S. t. torqueola along the Pacific coast of Mexico, and the other includes S. t. morelleti and S. t. sharpei from the Gulf Coast of Mexico and Central America. Surprisingly, these two lineages are strongly differentiated in both nuclear and mitochondrial markers, and each is more closely related to other Sporophila species than to one another. We infer low levels of gene flow between these two groups based on demographic models, suggesting multiple independent evolutionary lineages within S. torqueola have been obscured by coarse‐scale similarity in plumage patterning. These findings improve our understanding of the biogeographic history of this lineage, which includes multiple dispersal events out of South America and across the Isthmus of Tehuantepec into Mesoamerica. Finally, the phenotypic and genetic distinctiveness of the range‐restricted S. t. torqueola highlights the Pacific Coast of Mexico as an important region of endemism and conservation priority.     

Nuclear and chloroplast DNA phylogeography reveals Pleistocene divergence and subsequent secondary contact of two genetic lineages of the tropical rainforest tree species Shorea leprosula (Dipterocarpaceae) in South‐East Asia

Tropical rainforests in South‐East Asia have been affected by climatic fluctuations during past glacial eras. To examine how the accompanying changes in land areas and temperature have affected the genetic properties of rainforest trees in the region, we investigated the phylogeographic patterns of a widespread dipterocarp species, Shorea leprosula. Two types of DNA markers were used: expressed sequence tag‐based simple sequence repeats and chloroplast DNA (cpDNA) sequence variations. Both sets of markers revealed clear genetic differentiation between populations in Borneo and those in the Malay Peninsula and Sumatra (Malay/Sumatra). However, in the south‐western part of Borneo, genetic admixture of the lineages was observed in the two marker types. Coalescent simulation based on cpDNA sequence variation suggested that the two lineages arose 0.28–0.09 million years before present and that following their divergence migration from Malay/Sumatra to Borneo strongly exceeded migration in the opposite direction. We conclude that the genetic structure of S. leprosula was largely formed during the middle Pleistocene and was subsequently modified by eastward migration across the subaerially exposed Sunda Shelf.     

Spatial Patterns of Haplotype Variation in the Epiphytic Bromeliad Catopsis nutans

Identifying factors governing the origin, distribution, and maintenance of Neotropical plant diversity is an enduring challenge. To explore the complex and dynamic historical processes that shaped contemporary genetic patterns for a Central American plant species, we investigated the spatial distribution of chloroplast haplotypes of a geographically and environmentally widespread epiphytic bromeliad with wind‐dispersed seeds, Catopsis nutans, in Costa Rica. We hypothesized that genetic discontinuities occur between northwestern and southwestern Pacific slope populations, resembling patterns reported for other plant taxa in the region. Using non‐coding chloroplast DNA from 469 individuals and 23 populations, we assessed the influences of geographic and environmental distance as well as historical climatic variation on the genetic structure of populations spanning >1200 m in elevation. Catopsis nutans revealed seven haplotypes with low within‐population diversity (mean haplotype richness = 1.2) and moderate genetic structure (F_ST = 0.699). Pairwise F_ST was significantly correlated with both geographic and environmental distance. The frequency of dominant haplotypes was significantly correlated with elevation. A cluster of nine Pacific lowland populations exhibited a distinct haplotype profile and contained five of the seven haplotypes, suggesting historical isolation and limited seed‐mediated gene flow with other populations. Paleodistribution models indicated lowland and upland habitats in this region were contiguous through past climatic oscillations. Based on our paleodistribution analysis and comparable prior phylogeographic studies, the genetic signature of recent climatic oscillations are likely superimposed upon the distribution of anciently divergent lineages. Our study highlights the unique phylogeographic history of a Neotropical plant species spanning an elevation gradient.     

Differentiation between populations of Japanese grenadier anchovy (Coilia nasus) in Northwestern Pacific based on ISSR markers: Implications for biogeography

Northwestern Pacific provides unique scenarios for studying the roles of geography and ecology in driving population divergence and speciation. To elucidate the phylogeographic pattern of Coilia nasus in Northwestern Pacific, we examined ninety individuals from five localities along the coastal regions of China and the Ariake Bay of Japan by using seven ISSR markers. Analyses of molecular variance (AMOVA) showed that genetic differentiation among groups is relatively high (F_CT = 0.1904; P = 0.000). Bayesian analysis of ISSR data also revealed significant population structuring between Chinese and Japanese locations. Phylogenetic reconstructions show reciprocal monophyly in populations between China and the Ariake Bay of Japan. We conclude that the present-day phylogeographic pattern is the result of genetic isolation between Japanese and Chinese populations in the Northwestern Pacific following the glacial retreat, and that life-history traits and ecology may play a pivotal role in shaping the realized geographical distribution pattern of this species.     

Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia

The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species’ range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re‐examine these results to (1) determine phylogeographic patterns across the range of M. antilopinus and (2) infer the biogeographic barriers associated with these patterns. The tropical savannahs of northern Australia: from the Cape York Peninsula in the east, to the Kimberley in the west. We examined phylogeographic patterns in M. antilopinus using a larger number of samples and three mtDNA genes: NADH dehydrogenase subunit 2, cytochrome b, and the control region. Two datasets were generated and analyzed: (1) a subset of samples with all three mtDNA regions concatenated together and (2) all samples for just control region sequences that included samples from the previous study. Analysis included generating phylogenetic trees based on Bayesian analysis and intraspecific median‐joining networks. The contemporary spatial structure of M. antilopinus mtDNA lineages revealed five shallow clades and a sixth, divergent lineage. The genetic differences that we found between Queensland and Northern Territory M. antilopinus samples confirmed the split in the geographic distribution of the species. We also found weak genetic differentiation between Northern Territory samples and those from the Kimberley region of Western Australia, possibly due to the Kimberley Plateau–Arnhem Land barrier. Within the Northern Territory, two clades appear to be parapatric in the west, while another two clades are broadly sympatric across the Northern Territory. MtDNA diversity of M. antilopinus revealed an unexpectedly complex evolutionary history involving multiple sympatric and parapatric mtDNA clades across northern Australia. These phylogeographic patterns highlight the importance of investigating genetic variation across distributions of species and integrating this information into biodiversity conservation.     

Phylogeography and ecological niche modeling unravel the evolutionary history of the African green toad,Bufotes boulengeri boulengeri (Amphibia: Bufonidae), through the Quaternary

Recent integration of ecological niche models in phylogeographic studies is improving our understanding of the processes structuring genetic variation across landscapes. Previous studies on the amphibian Bufotes boulengeri boulengeri uncovered a surprisingly weak intraspecific differentiation across the Maghreb region. We widely sampled this species from Morocco to Egypt and sequenced one nuclear and three mitochondrial (mtDNA) genes to determine the level of genetic variability across its geographic range. We evaluated these data with ecological niche modeling to reveal its evolutionary history in response to climate change during the Quaternary. Our results highlight some mtDNA phylogeographic structure within this species, with one haplogroup endemic to coastal Morocco, and one haplogroup widely distributed throughout North Africa. No or little genetic differentiation is observed between isolated populations from the Hoggar Mountains, the Sabha district and the islands of Kerkennah and Lampedusa, compared to others populations. This can be explained by the expansion of the distribution range of B. b. boulengeri during glacial periods. This might have facilitated the species’ dispersal and subsequent gene flow between most North African localities.     

Patterns of genetic isolation in a widely distributed pelagic fish,the narrow‐barred Spanish mackerel (Scomberomorus commerson)

Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow‐barred Spanish mackerel (Scomberomorus commerson Lacepède, 1800), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo‐West Pacific range using control‐region sequences (including previously published data sets), cytochrome b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo‐Malay‐Papua archipelago (IMPA) and the south‐western Pacific coalesced into a clade (clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (clade I). Such a high level of genetic divergence suggested the occurrence of two sister species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele‐frequency differences were found between local populations in the south‐western Pacific, both at the mitochondrial locus (Φ_st = 0.282–0.609) and at microsatellite loci ( = 0.202–0.313). Clade II consisted of four deeply divergent subclades (9.0–11.8% nucleotide divergence for the control region; 0.3–2.5% divergence at the cytochrome b locus). Mitochondrial subclades within clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within clade II was present throughout the central Indo‐West Pacific: this haplogroup was found to be the sister group to a haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 886–902.     

Isolation and characterization of 23 polymorphic microsatellite markers for diversity and stock analysis in tiger shrimp (Penaeus monodon)

The tiger shrimp (Penaeus monodon) is an important marine crustacean in terms of biological diversity and aquaculture resource. The shrimp is widespread across the Indo‐Pacific region and shows apparent genetic differentiation among geographical populations. It is common practice to transport female brooders between different countries to seed the shrimp farms, posing potential problems of unwanted population admixture. We developed 23 polymorphic microsatellites for P. monodon (average H_E = 0.936) and these microsatellites were applicable for studying population differentiation, identifying valid stocks and tagging nonindigenous farmed shrimps.     

Present and past genetic connectivity of the Indo‐Pacific tropical eel Anguilla bicolor

Aim The objective of this study was to reveal the present population structure and infer the gene‐flow history of the Indo‐Pacific tropical eel Anguilla bicolor. Location The Indo‐Pacific region. Methods The entire mitochondrial control region sequence and the genotypes at six microsatellite loci were analysed for 234 specimens collected from eight representative localities where two subspecies have been historically designated. In order to infer the population structure, genetic differentiation estimates, analysis of molecular variance and gene‐tree reconstruction were performed. The history of migration events and population growth was assessed using neutrality tests based on allelic frequency spectrum, coalescent‐based estimation of gene flow and Bayesian demographic analysis using control region sequences. Results Population structure analysis showed genetic divergence between eels from the Indian and Pacific oceans (F_ST = 0.0174–0.0251, P < 0.05 for microsatellites; Φ_ST = 0.706, P < 0.001 for control region), while no significant variation was observed within each ocean. Two mitochondrial sublineages that do not coincide with geographical regions were found in the Indian Ocean clade of a gene tree. However, these two sublineages were not differentiated at the microsatellite markers. The estimation of mitochondrial gene‐flow history suggested allopatric isolation between the Indian and Pacific oceans, and a possible secondary contact within the Indian Ocean after an initial population splitting. Bayesian demographic history reconstruction and neutrality tests indicated population growth in each ocean after the Indo‐Pacific divergence. Main conclusions Anguilla bicolor has diverged between the Indian and Pacific oceans, which is consistent with the classical subspecies designation, but is apparently genetically homogeneous in the Indian Ocean. The analysis of gene‐flow and demographic history indicated that the two mitochondrial sublineages observed in the Indian Ocean probably represent the haplotype groups of relict ancestral populations. A comparison with a sympatric congener suggested that absolute physical barriers to gene flow may not be necessary for population divergence in eels.     

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system,influence of marine currents,and footprints of postglacial recolonization routes

Understanding the factors that contribute to population genetic divergence across a species' range is a long‐standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present‐day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic‐Mediterranean refugia after the last glacial period, with leading‐edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long‐distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life‐history and major geographic features interact to shape the distribution of genetic diversity.