Phylogeography of the olive sea snake, Aipysurus laevis (Hydrophiinae) indicates Pleistocene range expansion around northern Australia but low contemporary gene flow

Pleistocene sea-level fluctuations profoundly changed landmass configurations around northern Australia. The cyclic emergence of the Torres Strait land bridge and concomitant shifts in the distribution of shallow-water marine habitats repeatedly sundered east and west coast populations. These biogeographical perturbations invoke three possible scenarios regarding the directions of interglacial range expansion: west to east, east to west, or bidirectional. We evaluated these scenarios for the olive sea snake, Aipysurus laevis, by exploring its genetic structure around northern Australia based on 354 individuals from 14 locations in three regions (Western Australia, WA; Gulf of Carpentaria, GoC; Great Barrier Reef, GBR). A 726-bp fragment of the mitochondrial DNA ND4 region revealed 41 variable sites and 38 haplotypes, with no shared haplotypes among the three regions. Population genetic structure was strong overall, phiST=0.78, P<0.001, and coalescent analyses revealed no migration between regions. Genetic diversity was low in the GBR and GoC and the genetic signatures of these regions indicated range or population expansions consistent with their recent marine transgressions around 7000 years ago. By contrast, genetic diversity on most WA reefs was higher and there were no signals of recent expansion events on these reefs. Phylogenetic analyses indicated that GBR and GoC haplotypes were derived from WA haplotypes; however, statistical parsimony suggested that recent range expansion in the GBR-GoC probably occurred from east coast populations, possibly in the Coral Sea. Levels of contemporary female-mediated gene flow varied within regions and reflected potential connectivity among populations afforded by the different regional habitat types.     

Large–Scale Movement and Reef Fidelity of Grey Reef Sharks

Despite an Indo-Pacific wide distribution, the movement patterns of grey reef sharks (Carcharhinus amblyrhynchos) and fidelity to individual reef platforms has gone largely unstudied. Their wide distribution implies that some individuals have dispersed throughout tropical waters of the Indo-Pacific, but data on large-scale movements do not exist. We present data from nine C. amblyrhynchos monitored within the Great Barrier Reef and Coral Sea off the coast of Australia. Shark presence and movements were monitored via an array of acoustic receivers for a period of six months in 2008. During the course of this monitoring few individuals showed fidelity to an individual reef suggesting that current protective areas have limited utility for this species. One individual undertook a large-scale movement (134 km) between the Coral Sea and Great Barrier Reef, providing the first evidence of direct linkage of C. amblyrhynchos populations between these two regions. Results indicate limited reef fidelity and evidence of large-scale movements within northern Australian waters.     

Genetic population structure of the endemic fourline wrasse (Larabicus quadrilineatus) suggests limited larval dispersal distances in the Red Sea

The connectivity among marine populations is determined by the dispersal capabilities of adults as well as their eggs and larvae. Dispersal distances and directions have a profound effect on gene flow and genetic differentiation within species. Genetic homogeneity over large areas is a common feature of coral reef fishes and can reflect high dispersal capability resulting in high levels of gene flow. If fish larvae return to their parental reef, gene flow would be restricted and genetic differentiation could occur. Larabicus quadrilineatus (Labridae) is considered as an endemic fish species of the Red Sea and Gulf of Aden. The juveniles of this species are cleaner fish that feed on ectoparasites of other fishes. Here, we investigated the genetic population structure and gene flow in L. quadrilineatus among five locations in the Red Sea to infer connectivity among them. To estimate genetic diversity, we analysed 369 bp of 237 mitochondrial DNA control region sequences. Haplotype and nucleotide diversities were higher in the southern than in the northern Red Sea. Analysis of molecular variance (amova) detected the highest significant genetic variation between northern and central/southern populations (Phi(CT) = 0.01; P < 0.001). Migration analysis revealed a several fold higher northward than southward migration, which could be explained by oceanographic conditions and spawning season. Even though the Phi(ST) value of 0.01 is rather low and implies a long larval dispersal distance, estimates based on the isolation-by-distance model show a very low mean larval dispersal distance (0.44-5.1 km) compared to other studies. In order to enable a sustainable ornamental fishery on the fourline wrasse, the results of this study suggest that populations in the northern and southern Red Sea should be managed separately as two different stocks. The rather low larval dispersal distance of about 5 km needs to be considered in the design of marine protected areas to enable connectivity and self-seeding.     

Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographical features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two‐band anemonefish Amphiprion bicinctus across its entire geographical range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the southern coast of Oman. Both the Red Sea and the Arabian Sea are complex and environmentally heterogeneous marine systems that provide an ideal scenario to address these questions. Our findings confirm the presence of two genetic clusters previously reported for A. bicinctus in the Red Sea. Genetic structure analyses suggest a complex seascape configuration, with evidence of both isolation by distance (IBD) and isolation by environment (IBE). In addition to IBD and IBE, genetic structure among sites was best explained when two barriers to gene flow were also accounted for. One of these coincides with a strong oligotrophic–eutrophic gradient at around 16–20?N in the Red Sea. The other agrees with a historical bathymetric barrier at the straight of Bab al Mandab. Finally, these data support the presence of interspecific hybrids at an intermediate suture zone at Socotra and indicate complex patterns of genomic admixture in the Gulf of Aden with evidence of introgression between species. Our findings highlight the power of recent genomic approaches to resolve subtle patterns of gene flow in marine seascapes.     

Islands increase genetic subdivision and disrupt patterns of connectivity of intertidal snails in a complex archipelago

The view that marine species with planktonic dispersal have highly connected, demographically open populations is giving way to recognition that populations may often be largely self-recruiting, or demographically closed. This raises the question of what local conditions might favor isolation of populations. To test the importance of islands for local isolation in species with planktonic larvae, we examined allozyme variation among 35 populations of the intertidal snail Austrocochlea constricta in the Houtman Abrolhos Islands, Western Australia, spanning 60 km. Heterogeneity of allozyme frequencies among populations was high, with average F(ST) of 0.237, indicating highly localized populations. Increased subdivision was associated with islands at different scales: between island groups, separated by deep water gaps, and between disconnected sets of islands within groups. At short distances, up to two km, subdivision increased fivefold between islands compared with that between populations on the same island. Along 11 km of continuous, sheltered shore, there was isolation by distance but among a linear series of islands over similar distance, there was greater subdivision at short distances but no association with distance. These patterns had been seen previously in the direct-developing snail Bembicium vittatum, but its finding in A. constricta confirms for a planktonic disperser the importance of this complex archipelago for both retention of locally produced larvae and disruption of patterns of connectivity. Taken together, these results indicate that islands can increase both the "open" and the "closed" components of recruitment and that applicable models of genetic connectivity depend substantially on local conditions.     

Local assessments of marine mammals in cross-cultural environments

Biodiversity assessments by research scientists are often logistically difficult and expensive to implement in remote areas. Locally-based approaches have the potential to overcome some of these challenges by capitalising on the knowledge and capacity of local people. Many Indigenous people in northern Australia are custodians of coastal areas that support globally significant populations of tropical marine mammals, including coastal dolphins and dugongs. The objective of our study was to design and implement a locally-based approach in a cross-cultural environment to assess the distribution of marine mammals in the remote waters of the Gulf of Carpentaria, Northern Territory. The study was conducted as a partnership between Yanyuwa Aboriginal families, research scientists, government officers and the li-Anthawirriyarra Sea Rangers. We conducted a series of participatory mapping workshops to share and record local observations of dolphins and dugongs. These observations provided the longitudinal information required to inform the design of the first dedicated marine mammal vessel survey in the Gulf of Carpentaria. The vessel surveys found three species of dolphins present in the area (Australian snubfin, humpback and bottlenose dolphins), even though sightings were low; dugongs being much more common. We found that the integrative and locally-based approach built the capacity of both the li-Anthawirriyarra Sea Rangers and research scientists to assess the distribution of marine mammals. If replicated over longer time-frames and coordinated over broader spatial scales, information on distribution and abundance derived from locally-based approaches has the potential to inform the status of marine mammals.     

Looking back to go forward: genetics informs future management of captive and reintroduced populations of the black-footed rock-wallaby <Emphasis Type="Italic">Petrogale lateralis</Emphasis>

Active management is essential to the survival of many threatened species globally. Captive breeding programmes can play an important role in facilitating the supplementation, translocation and reintroduction of wild populations. However, understanding the genetic dynamics within and among wild and captive populations is crucial to the planning and implementation of ex situ management, as adaptive potential is, in part, driven by genetic diversity. Here, we use 14 microsatellite loci and mitochondrial Control Region sequence to examine the population genetics of both wild populations and captive colonies of the endangered warru (the MacDonnell Ranges race of the black-footed rock-wallaby Petrogale lateralis) in central Australia, to understand how historical evolutionary processes have shaped current diversity and ensure effective ex situ management. Whilst microsatellite data reveal significant contemporary differentiation amongst remnant warru populations, evidence of contemporary dispersal and relatively weak isolation by distance, as well as a lack of phylogeographic structure suggests historical connectivity. Genetic diversity within current captive populations is lower than in the wild source populations. Based on our genetic data and ecological observations, we predict outbreeding depression is unlikely and hence make the recommendation that captive populations be managed as one genetic group. This will increase genetic diversity within the captive population and as a result increase the adaptive potential of reintroduced populations. We also identify a new site in the Musgrave Ranges which contains unique alleles but also connectivity with a population 6 km away. This novel genetic diversity could be used as a future source for supplementation.     

Pronounced genetic population structure in a potentially vagile fish species (Pristipomoides multidens, Teleostei; Perciformes; Lutjanidae) from the East Indies triangle

The East Indies triangle, bordered by the Phillipines, Malay Peninsula and New Guinea, has a high level of tropical marine species biodiversity. Pristipomoides multidens is a large, long-lived, fecund snapper species that is distributed throughout the East Indies and Indo-Pacific. Samples were analysed from central and eastern Indonesia and northern Australia to test for genetic discontinuities in population structure. Fish (n = 377) were collected from the Indonesian islands of Bali, Sumbawa, Flores, West Timor, Tanimbar and Tual along with 131 fish from two northern Australian locations (Arafura and Timor Seas) from a previous study. Genetic variation in the control region of the mitochondrial genome was assayed using restriction fragment length polymorphism and direct sequencing. Haplotype diversity was high (0.67-0.82), as was intraspecific sequence divergence (range 0-5.8%). F(ST) between pairs of populations ranged from 0 to 0.2753. Genetic subdivision was apparent on a small spatial scale; F(ST) was 0.16 over 191 km (Bali/Sumbawa) and 0.17 over 491 km (Bali/Flores). Constraints to dispersal that contribute to, and maintain, the observed degree of genetic subdivision are experienced presumably by all life history stages of this tropical marine finfish. The constraints may include (1) little or no movement of eggs or larvae, (2) little or no home range or migratory movement of adults and (3) loss of larval cohorts due to transport of larvae away from suitable habitat by prevailing currents.     

Phylogeography of Padina boryana (Dictyotales,Phaeophyceae) around the Thai-Malay Peninsula

The Indo-Pacific Ocean is a biodiversity hotspot for marine organisms. In this area, most of the research has focused on marine animals, such as reef fish, molluscs and other associated coral fauna, but very little has been done on macroalgae. The Thai-Malay Peninsula is an important north–south barrier in this area, which faces two different oceans – the Indian Ocean and the Pacific Ocean. This study aims to investigate genetic distribution patterns of Padina boryana Thivy around the Thai-Malay Peninsula, where it is common. Three DNA marker regions, the mitochondrion-encoded cytochrome c oxidase subunit 3 gene (cox3); the plastid rbcL, and the nuclear internal transcribed spacer 2 (ITS2) were used to evaluate genetic diversity and the relationships within and between populations. Samples were collected from both the Andaman Sea and Gulf of Thailand sides of the peninsula. Parsimony networks and maximum likelihood and Bayesian analyses showed clearly that there are two separated P. boryana lineages, one restricted to the Gulf of Thailand and the other to the Andaman Sea and other areas of the Indo-Pacific. The effect of different ocean currents along the Andaman Sea and Gulf of Thailand may have shaped these populations of P. boryana. This phylogeographic separation, based on persistent currents in the area, may affect other marine organisms along the Thai peninsula.     

Large‐scale,multidirectional larval connectivity among coral reef fish populations in the Great Barrier Reef Marine Park

Larval dispersal is the key process by which populations of most marine fishes and invertebrates are connected and replenished. Advances in larval tagging and genetics have enhanced our capacity to track larval dispersal, assess scales of population connectivity, and quantify larval exchange among no‐take marine reserves and fished areas. Recent studies have found that reserves can be a significant source of recruits for populations up to 40 km away, but the scale and direction of larval connectivity across larger seascapes remain unknown. Here, we apply genetic parentage analysis to investigate larval dispersal patterns for two exploited coral reef groupers (Plectropomus maculatus and Plectropomus leopardus) within and among three clusters of reefs separated by 60–220 km within the Great Barrier Reef Marine Park, Australia. A total of 69 juvenile P. maculatus and 17 juvenile P. leopardus (representing 6% and 9% of the total juveniles sampled, respectively) were genetically assigned to parent individuals on reefs within the study area. We identified both short‐distance larval dispersal within regions (200 m to 50 km) and long‐distance, multidirectional dispersal of up to ~250 km among regions. Dispersal strength declined significantly with distance, with best‐fit dispersal kernels estimating median dispersal distances of ~110 km for P. maculatus and ~190 km for P. leopardus. Larval exchange among reefs demonstrates that established reserves form a highly connected network and contribute larvae for the replenishment of fished reefs at multiple spatial scales. Our findings highlight the potential for long‐distance dispersal in an important group of reef fishes, and provide further evidence that effectively protected reserves can yield recruitment and sustainability benefits for exploited fish populations.     

Comparative phylogeography of reef fishes from the Gulf of Aden to the Arabian Sea reveals two cryptic lineages

The Arabian Sea is a heterogeneous region with high coral cover and warm stable conditions at the western end (Djibouti), in contrast to sparse coral cover, cooler temperatures, and upwelling at the eastern end (southern Oman). We tested for barriers to dispersal across this region (including the Gulf of Aden and Gulf of Oman), using mitochondrial DNA surveys of 11 reef fishes. Study species included seven taxa from six families with broad distributions across the Indo-Pacific and four species restricted to the Arabian Sea (and adjacent areas). Nine species showed no significant genetic partitions, indicating connectivity among contrasting environments spread across 2000 km. One butterflyfish (Chaetodon melannotus) and a snapper (Lutjanus kasmira) showed phylogenetic divergences of d = 0.008 and 0.048, respectively, possibly indicating cryptic species within these broadly distributed taxa. These genetic partitions at the western periphery of the Indo-Pacific reflect similar partitions recently discovered at the eastern periphery of the Indo-Pacific (the Hawaiian and the Marquesan Archipelagos), indicating that these disjunctive habitats at the ends of the range may serve as evolutionary incubators for coral reef organisms.

     

Mitochondrial DNA Diversity of the Asian Moon Scallop, <Emphasis Type="Italic">Amusium pleuronectes</Emphasis> (Pectinidae), in Thailand

Sequence variation of the mitochondrial DNA 16S rRNA region of the Asian moon scallop, Amusium pleuronectes, was surveyed in seven populations along the coast of Thailand. A total of 16 unique haplotypes were detected among 174 individuals with a total 27 variable sites out of 534 bp sequenced. The mitochondrial haplotypes grouped into two distinct arrays (estimated to differ by about 2.62% to 2.99% nucleotide divergence) that characterized samples collected from the Gulf of Thailand versus the Andaman Sea. Low levels of intrapopulation variation were observed, while in contrast, significant divergence was observed between populations from the Gulf of Thailand and Andaman Sea. Results of AMOVA reveal a high F _ST value (0.765) and showed that the majority of the total genetic variance (76.03%) occurred among groups (i.e., Andaman Sea and the Gulf of Thailand) and little among populations within the group (0.52%) and within populations (23.45%). The genetic differentiation between the populations recorded in the present study is similar to that observed in a variety of marine species in the Indo-Pacific. The implications of the findings for management of A. pleuronectes genetic resources in Thailand are discussed.     

Genetic isolation by distance among populations of the netted dog whelk Nassarius reticulatus (L.) along the European Atlantic coastline

Estimates of the average distances by which marine larvae disperse are generally poorly described, despite the central role that larval dispersal plays in the demographic connectivity of populations across geographic space. Here, we describe the population genetic structure and average dispersal distance of the netted dog whelk Nassarius reticulatus (L.) (Mollusca, Gastropoda, Prosobranchia), a widespread member of European intertidal communities, using DNA sequence variation in a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI). An analysis of 156 individuals from 6 locations spread across approximately 1700 km of the European Atlantic coastline revealed weak and nonsignificant population structure (overall Phi(ST) = 0.00013). However, pairwise Phi(ST) values revealed a slight but significant increase in genetic isolation with geographic distance (IBD), suggesting that populations are not panmictic across the sampled geographic range. If we assume that the isolation by distance is maintained by a stable, stepping stone model of gene flow, then the slope of the IBD is consistent with an average larval dispersal distance of approximately 70 km per generation. The spatial scale of larval dispersal in N. reticulatus is consistent with the life cycle of the species (planktotrophic veliger lasting 30-60 days before competent to settle). A mismatch analysis of the COI sequences revealed a signature of an ancient demographic expansion that began 61 500-160,000 years ago, well before the most recent Pleistocene glaciation event. The greatest levels of genetic diversity occur within the middle latitudes of the whelk's geographic range, consistent with the notion that historic populations of N. reticulatus might have expanded northward and southward from the centrally located Bay of Biscay.     

Population genetic structure of annual and perennial populations of Zostera marina L. along the Pacific coast of Baja California and the Gulf of California

The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using θ_ST values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest θ_ST (0.13–0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (θ_ST = 0.04–0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Niño Southern Oscillation (ENSO) events along the Pacific coast.     

Rapid recovery of genetic diversity of stomatopod populations on Krakatau: temporal and spatial scales of marine larval dispersal

Although the recovery of terrestrial communities shattered by the massive eruption of Krakatau in 1883 has been well chronicled, the fate of marine populations has been largely ignored. We examined patterns of genetic diversity in populations of two coral reef-dwelling mantis shrimp, Haptosquilla pulchella and Haptosquilla glyptocercus (Stomatopoda: Protosquillidae), on the islands of Anak Krakatau and Rakata. Genetic surveys of mitochondrial cytochrome oxidase c (subunit 1) in these populations revealed remarkably high levels of haplotypic and nucleotide diversity that were comparable with undisturbed populations throughout the Indo-Pacific. Recolonization and rapid recovery of genetic diversity in the Krakatau populations indicates that larval dispersal from multiple and diverse source populations contributes substantially to the demographics of local populations over intermediate temporal (tens to hundreds of years) and spatial scales (tens to hundreds of kilometres). Natural experiments such as Krakatau provide an excellent mechanism to investigate marine larval dispersal and connectivity. Results from stomatopods indicate that marine reserves should be spaced no more than 50-100 km apart to facilitate ecological connectivity via larval dispersal.     

Evidence for long-distance dispersal in a sedentary passerine, Gymnorhina tibicen (Artamidae)

Australian magpies (Gymnorhina tibicen) are group-living birds found across much of mainland Australia. Adults commonly remain in a breeding territory until death. Young of the year either remain on the natal (birth) site or are forced by their parents to disperse. Observational studies in south-eastern Australia suggest that most dispersing juveniles settle within 7 km of their natal territory. Therefore, despite potential for considerable gene flow (via flight), social organization predisposes magpies towards local population structuring. In this study, we measured genetic variation at both nuclear (allozyme) and mitochondrial loci and found evidence of substantial gene flow over very large distances (up to 1599 km). Thus, some juvenile magpies may disperse much greater distances than was previously thought. For mtDNA, geographic and genetic distance were strongly correlated, consistent with a pattern of isolation by distance. Therefore, although female gene flow is substantial it is apparently geographically restricted over large distances, in approximately a stepping-stone fashion. We conclude that a strong relationship between gene flow and geographic distance can develop even over large distances if populations have experienced no major historical disturbances to gene flow.     

Reconciling geography and genealogy: phylogeography of giant freshwater prawns from the Lake Carpentaria region

There is convincing geological evidence for the historical existence of an ancient lake on the Australian-New Guinea continental shelf during the late Pleistocene. Lake Carpentaria was a vast fresh- to brackishwater lake that would presumably have provided habitat for, and facilitated gene flow among, aquatic taxa that tolerate low to moderate salinities in this region. Moreover, it has been argued that the outflow of Papua New Guinea's Fly River was diverted westward into Lake Carpentaria during this period, although this hypothesis is controversial. We predicted that these events, if a true history, would have promoted gene flow and population growth via range-expansion events in the giant freshwater prawn (Macrobrachium rosenbergii) and restricted gene flow subsequently by way of a vicariant event as sea levels rose during the late Pleistocene, and a marine environment replaced Lake Carpentaria. We tested these hypotheses using phylogeographical and phylogenetic analyses of mitochondrial DNA variation in M. rosenbergii populations sampled from the Lake Carpentaria region. Our results support the hypothesis that Lake Carpentaria facilitated gene flow among populations of M. rosenbergii that are today isolated, but contest claims of a westward diversion of the Fly River. We inferred the timing of initial expansion in the 'Lake Carpentaria lineage' and found the timing of this event to be broadly concordant with geological dating of the formation of Lake Carpentaria. Reconciling geological and molecular data, as presented here, provides a powerful framework for investigating the influence of historical earth history events on the distribution of biological (i.e. molecular) diversity.     

Hierarchical structure of mitochondrial DNA gene flow among humpback whales Megaptera novaeangliae, world-wide

The genetic structure of humpback whale populations and subpopulation divisions is described by restriction fragment length analysis of the mitochondrial (mt) DNA from samples of 230 whales collected by biopsy darting in 11 seasonal habitats representing six subpopulations, or 'stocks', world-wide. The hierarchical structure of mtDNA haplotype diversity among population subdivisions is described using the analysis of molecular variance (AMOVA) procedure, the analysis of gene identity, and the genealogical relationship of haplotypes as constructed by parsimony analysis and distance clustering. These analyses revealed: (i) significant partitioning of world-wide genetic variation among oceanic populations, among subpopulations or 'stocks' within oceanic populations and among seasonal habitats within stocks; (ii) fixed categorical segregation of haplotypes on the south-eastern Alaska and central California feeding grounds of the North Pacific; (iii) support for the division of the North Pacific population into a central stock which feeds in Alaska and winters in Hawaii, and an eastern or 'American' stock which feeds along the coast of California and winters near Mexico; (iv) evidence of genetic heterogeneity within the Gulf of Maine feeding grounds and among the sampled feeding and breeding grounds of the western North Atlantic; and (v) support for the historical division between the Group IV (Western Australia) and Group V (eastern Australia, New Zealand and Tonga) stocks in the Southern Oceans. Overall, our results demonstrate a striking degree of genetic structure both within and between oceanic populations of humpback whales, despite the nearly unlimited migratory potential of this species. We suggest that the humpback whale is a suitable demographic and genetic model for the management of less tractable species of baleen whales and for the general study of gene flow among long-lived, mobile vertebrates in the marine ecosystem.     

A role for nonphysical barriers to gene flow in the diversification of a highly vagile seabird, the masked booby (Sula dactylatra)

To test the hypothesis that nonphysical barriers to gene flow play a role in the divergence of low-latitude seabird populations, we applied phylogeographic methods to mitochondrial control region sequence variation in a global sample of masked boobies (Sula dactylatra). In accord with previous studies, we found that Indo-Pacific and Atlantic haplotypes form two divergent lineages, excluding one haplotype previously attributed to secondary contact between the Indian Ocean and the Caribbean Sea. Within the Indo-Pacific and the Atlantic, we found a relatively large number of haplotypes, many of which were unique to a single population. Although haplotypes from most populations were found in more than one higher-level clade, nested clade analysis revealed a significant association between clades and geography for the majority of higher-level clades, most often interpreted as a consequence of isolation by distance. We found low levels of gene flow within Indo-Pacific and Atlantic populations, and a significant correlation between gene flow and geographical distance among Indo-Pacific populations. We estimate that Indo-Pacific masked boobies experienced rapid population growth approximately 180,000 years ago and that the majority of Indo-Pacific and Atlantic populations diverged within the last approximately 115,000 years. These combined data suggest that the predominant pattern between Indo-Pacific and Atlantic populations is long-term isolation by physical barriers to gene flow. In contrast, populations within these regions appear to have diverged despite few obvious physical barriers to gene flow, perhaps as a consequence of limited natal dispersal combined with local adaptation and/or genetic drift.     

Genetic structure of Indian scad mackerel Decapterus russelli: Pleistocene vicariance and secondary contact in the Central Indo-West Pacific Seas

Major genetic breaks between the Indian and Pacific oceans have been reported for marine fishes and invertebrates. The genetic structure and history of the Indian scad mackerel, Decapterus russelli, in the Indo-Malay archipelago were investigated using the cytochrome b gene sequence as mitochondrial marker and two length-polymorphic introns as nuclear markers. The existence of two major mitochondrial lineages separated by 2.2% average nucleotide divergence, and their heterogeneous geographical distributions, were confirmed. This indicated past geographic isolation, possibly caused by a Pleistocene drop in sea level. The presence, in sympatry, of the two mitochondrial lineages was thought to result from secondary contact. A recent population bottleneck and subsequent rapid population expansion were indicated by low genetic diversities and strongly negative Tajima's D-values. This evidence supports the hypothesis that the habitat available to D. russelli in the Pleistocene was restricted. Taking into account both mitochondrial and nuclear-DNA data, three geographically distinct populations were identified: one sampled in the Makassar Strait and Sulawesi Sea, one in the Arafura Sea and the third from the entire western region of the Indo-Malay archipelago. Considering the high hydrological connectivity of this region of the Indo-Pacific and the species pelagic life-history, the population structure may be maintained by homing behaviour and, perhaps, the association of spawning with retention zones.