BIODIVERSITY RESEARCH: Genetic diversity in two introduced biofouling amphipods (Ampithoe valida & Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversity

Aim We investigated patterns of genetic diversity among invasive populations of Ampithoe valida and Jassa marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute to the contemporary distribution of these species in the region. Location Native range: Atlantic North American coast; Invaded range: Pacific North American coast. Methods We assessed indices of genetic diversity based on DNA sequence data from the mitochondrial cytochrome c oxidase subunit I (COI) gene, determined the distribution of COI haplotypes among populations in both the invasive and putative native ranges of A. valida and J. marmorata and reconstructed phylogenetic relationships among COI haplotypes using both maximum parsimony and Bayesian approaches. Results Phylogenetic inference indicates that inaccurate species‐level identifications by morphological criteria are common among Jassa specimens. In addition, our data reveal the presence of three well supported but previously unrecognized clades of A. valida among specimens in the north‐eastern Pacific. Different species of Jassa and different genetic lineages of Ampithoe exhibit striking disparity in geographic distribution across the region as well as substantial differences in genetic diversity indices. Main conclusions Molecular genetic methods greatly improve the accuracy and resolution of identifications for invasive benthic marine amphipods at the species level and below. Our data suggest that multiple cryptic introductions of Ampithoe have occurred in the north‐eastern Pacific and highlight uncertainty regarding the origin and invasion histories of both Jassa and Ampithoe species. Additional morphological and genetic analyses are necessary to clarify the taxonomy and native biogeography of both amphipod genera.     

Comparative phylogeography of two seastars and their ectosymbionts within the Coral Triangle

Repeated exposure and flooding of the Sunda and Sahul shelves during Pleistocene sea‐level fluctuations is thought to have contributed to the isolation and diversification of sea‐basin populations within the Coral Triangle. This hypothesis has been tested in numerous phylogeographical studies, recovering an assortment of genetic patterns that the authors have generally attributed to differences in larval dispersal capability or adult habitat specificity. This study compares phylogeographical patterns from mitochondrial COI sequences among two co‐distributed seastars that differ in their adult habitat and dispersal ability, and two seastar ectosymbionts that differ in their degree of host specificity. Of these, only the seastar Linckia laevigata displayed a classical pattern of Indian‐Pacific divergence, but with only moderate genetic structure (Φ_CT = 0.067). In contrast, the seastar Protoreaster nodosus exhibited strong structure (Φ_CT = 0.23) between Teluk Cenderawasih and the remainder of Indonesia, a pattern of regional structure that was echoed in L. laevigata (Φ_CT = 0.03) as well as its obligate gastropod parasite Thyca crystallina (Φ_CT = 0.04). The generalist commensal shrimp, Periclimenes soror showed little genetic structuring across the Coral Triangle. Despite species‐specific phylogeographical patterns, all four species showed departures from neutrality that are consistent with massive range expansions onto the continental shelves as the sea levels rose, and that date within the Pleistocene epoch. Our results suggest that habitat differences may affect the manner in which species responded to Pleistocene sea‐level fluctuations, shaping contemporary patterns of genetic structure and diversity.     

PHYLOGEOGRAPHY OF THE PANTROPICAL SEA URCHIN EUCIDARIS IN RELATION TO LAND BARRIERS AND OCEAN CURRENTS

The pantropical sea urchin genus Eucidaris contains four currently recognized species, all of them allopatric: E. metularia in the Indo-West Pacific, E. thouarsi in the eastern Pacific, E. tribuloides in both the western and eastern Atlantic, and E. clavata at the central Atlantic islands of Ascension and St. Helena. We sequenced a 640-bp region of the cytochrome oxidase I (COI) gene of mitochondrial DNA to determine whether this division of the genus into species was confirmed by molecular markers, to ascertain their phylogenetic relations, and to reconstruct the history of possible dispersal and vicariance events that led to present-day patterns of species distribution. We found that E. metularia split first from the rest of the extant species of the genus. If COI divergence is calibrated by the emergence of the Isthmus of Panama, the estimated date of the separation of the Indo-West Pacific species is 4.7–6.4 million years ago. This date suggests that the last available route of genetic contact between the Indo-Pacific and the rest of the tropics was from west to east through the Eastern Pacific Barrier, rather than through the Tethyan Sea or around the southern tip of Africa. The second cladogenic event was the separation of eastern Pacific and Atlantic populations by the Isthmus of Panama. Eucidaris at the outer eastern Pacific islands (Galapagos, Isla del Coco, Clipperton Atoll) belong to a separate clade, so distinct from mainland E. thouarsi as to suggest that this is a different species, for which the name E. galapagensis is revived from the older taxonomic literature. Complete lack of shared alleles in three allozyme loci between island and mainland populations support their separate specific status. Eucidaris galapagensis and E. thouarsi are estimated from their COI divergence to have split at about the same time that E. thouarsi and E. tribuloides were being separated by the Isthmus of Panama. Even though currents could easily convey larvae between the eastern Pacific islands and the American mainland, the two species do not appear to have invaded each other's ranges. Conversely, the central Atlantic E. clavata at St. Helena and Ascension is genetically similar to E. tribuloides from the American and African coasts. Populations on these islands are either genetically connected to the coasts of the Atlantic or have been colonized by extant mitochondrial DNA lineages of Eucidaris within the last 200,000 years. Although it is hard to explain how larvae can cross the entire width of the Atlantic within their competent lifetimes, COI sequences of Eucidaris from the west coast of Africa are very similar to those of E. tribuloides from the Caribbean. F_ST statistics indicate that gene flow between E. metularia from the Indian Ocean and from the western and central Pacific is restricted. Low gene flow is also evident between populations of E. clavata from Ascension and St. Helena. Rates of intraspecific exchange of genes in E. thouarsi, E. galapagensis, and E. tribuloides, on the other hand, are high. The phylogeny of Eucidaris confirms Ernst Mayr's conclusions that major barriers to the dispersal of tropical echinoids have been the wide stretch of deep water between central and eastern Pacific, the cold water off the southwest coast of Africa, and the Isthmus of Panama. It also suggests that a colonization event in the eastern Pacific has led to speciation between mainland and island populations.     

A molecular phylogenetic framework for the subfamily Ocenebrinae (Gastropoda,Muricidae)

The Ocenebrinae is a subfamily of marine predatory gastropods known as oyster and mussel drills. Their current phylogenetic framework is traditionally based on shell and radular characters, but a consensus on relationships among genera is still lacking. We investigated the molecular phylogeny of Ocenebrinae using 50 species and DNA data from one nuclear (28S) and two mitochondrial (COI and 16S) genes, the largest data set so far assembled for this subfamily. We found support for the monophyly of the Ocenebrinae, and species were divided into four major lineages. Within groups, genera had similar geographic distributions, suggesting that except in a few cases, species diversification within clades occurred without range expansions. We discuss the phylogenetic distribution of a labral tooth and a sealed siphonal canal, two characteristic ocenebrine features. We also show that Ocinebrina species in the north‐eastern Pacific are not monophyletic with north‐eastern Atlantic and Mediterranean species, and that the Ocinebrina edwardsii species complex belongs to Ocenebra.     

Longtail tuna Thunnus tonggol (Bleeker, 1851) shows genetic partitioning across,but not within,basins of the Indo‐Pacific based on mitochondrial DNA

Genetic stock structure is atypical in tuna species, with most species demonstrating geographically‐broad, panmictic populations. Here, genetic data suggest a distinct pattern for Thunnus tonggol across the Indo‐Pacific region. The genetic variation in the coastal tuna T. tonggol sampled from across the South China Sea was examined using the highly variable mitochondrial DNA displacement loop (D‐loop) gene region. One hundred and thirty‐nine specimens were sampled from four locations in Indonesia, Vietnam and the Philippines. Phylogenetic reconstruction of genetic relationships revealed no significant ?_ST statistics and hence no population structure within the South China Sea. However, subsequent analysis with sequence data from coastal northwest India infers discrete genetic stocks between the Indian Ocean and the South China Sea. Consistent with previous genetic analyses of tuna species in the Indo‐Pacific, the findings in this study infer no population structure within each basin, but rather show a significant partitioning across the wider region. Furthermore, these results have implications for the management of the commercially valuable Thunnus tonggol across national boundaries, and thus requiring collaboration among countries to ensure its sustainable use.     

Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematode Thoracostoma trachygaster (Nematoda,Leptosomatidae)

Derycke, S., De Ley, P., De Ley, I.T., Holovachov, O., Rigaux, A. & Moens, T. (2010). Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematode Thoracostoma trachygaster (Nematoda, Leptosomatidae).—Zoologica Scripta, 39, 276–289. Recent taxonomic and population genetic studies have revealed the presence of substantial cryptic diversity through sequence analysis of nematode morphospecies classified in different major clades. Correct interpretations of intra‐ and interspecific genetic variation require certainty about the conspecificity of the sequenced specimens, which in turn must depend on appropriate protocols with built‐in verifiability procedures. In this study, we performed a population genetic study in the free‐living marine nematode Thoracostoma trachygaster, a member of one of the earliest major clades to diverge in nematode phylogeny. We collected 367 nematodes from 11 populations located in the Californian Bight, all of which were video captured before DNA extraction to document and verify their individual morphology. Sequences for the cytochrome c oxidase subunit 1 (COI), D2D3 and 18S genes showed eight deeply divergent clades, and using a reverse taxonomy approach, six of these clades proved to be other morphospecies than T. trachygaster. Phylogenetic analyses of COI, internal transcribed spacer and D2D3 showed evidence for two sympatrically distributed cryptic species within the morphospecies T. trachygaster. Population genetic analyses of the most widespread cryptic species showed a moderate genetic structuring (Φ_ST = 0.28), and 18% of this genetic variation was caused by differences between populations north and south of Point Conception. Within the southern Californian Bight, some genetic differentiation could be attributed to differences between populations north and south of Malibu, supporting the idea of a barrier to gene flow near Los Angeles region. The results for T. trachygaster support the contention that species diversity within free‐living nematodes is underestimated, and that dispersal of marine nematodes from tidal environments associated with kelp holdfasts is substantial at scales of a few 100 km.     

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.     

High genetic diversity in the harvestman Geraeocormobius sylvarum (Arachnida,Opiliones, Gonyleptidae) from subtropical forests in north‐eastern Argentina revealed by mitochondrial DNA sequences

This research was aimed to analyse the genetic diversity of Geraeocormobius sylvarum, a forest‐dwelling Neotropical harvestman with a disjunct distribution, separated by approximately 630 km of semi‐arid environments. The usefulness of a fragment of the cytochrome c oxidase subunit I (COI) mitochondrial gene as molecular marker was tested in 109 individuals. Results showed high levels of both haplotype and nucleotide diversity in populations corresponding to north‐eastern Argentina, the core area of the species range. A strong genetic structuring was detected, supported by both the phylogenetic trees and the haplotype network, with six identifiable haplogroups. Populations of the Yungas ecoregion did not show significant diversity levels, suggesting a putative recent introduction of the species into that region. The overall results suggest that the present genetic diversity of the species is consistent with past fragmentation events of the species range (in refuges?), probably during the Last Glacial Maximum. The COI gene was concluded to be a well‐suited marker to associate past environmental events with the high genetic diversity observed in this species.     

First record of an epibiosis between the sand crab Emerita analoga (Stimpson, 1857) (Decapoda: Hippidae) and the mussel Semimytilus algosus (Gould, 1850) (Bivalvia, Mytilidae) in southern Peru

Coastal zones of the Humboldt Current Upwelling System (HCUS) are composed both of rocky and sandy beaches inhabited by macrozoobenthic communities. These show oscillating changes in the dominance of species; the abundance of the sand crab Emerita analoga is linked to phases of the El Niño Southern Oscillation (ENSO). The biogenic surfaces of these crabs serve as substrate for opportunistic colonizers. This study is the first record of an epibiosis between E. analoga and the rock mussel Semimytilus algosus, detected at a southern Peruvian sandy beach. Mussels fouled a wide size-range of adult E. analoga (7.3%) but they themselves belonged to small-size classes. The largest S. algosus was 17.4 mm in length. Highest permanence of epibionts was found on larger sand crabs (maximum between 24 and 27 mm). Significantly more mussels were found on the ventral surface (39.4%) compared to 10 other surface areas of the sand crab. Possible benefits and disadvantages of the observed epibiosis for both the basibiont and the epibiont are discussed.     

Coordination between the legs and tail during digging and swimming in sand crabs

Rhythmic leg movements and tailflipping are mutually exclusive behaviours in most decapod crustaceans, but sand crabs (Anomura: Hippoidea) combine leg movements with simultaneous tailflipping or uropod beating for both digging and swimming. We examined the coordination between the legs and tail (abdomen and tailfan) of Blepharipoda occidentalis, Lepidopa californica (Albuneidae), and Emerita analoga (Hippidae). When either albuneid swims, the tail cycles at a higher frequency than the legs, and the two rhythms are not coupled. When albuneids begin digging, the tail's frequency drops to that of the legs, and its rhythm becomes phase coupled to the legs. In E. analoga the legs seldom move during swimming by uropod beating. During digging the frequency of the uropods and fourth legs starts at about double that of the second and third legs, but drops to that of the second and third legs as digging progresses. The fourth legs in E. analoga are coupled with the uropods; their outward movement (= power stroke) is concurrent with the uropod return stroke. The familial differences in leg coordination and in the coordination of the legs and tail account for the smooth descent of E. analoga beneath sand compared to the stepwise descent of the albuneids. Accepted: 23 August 1996     

Factors influencing aggregation patterns in the sand crab Emerita analoga (Crustacea: Hippidae)

Summary Aggregation patterns in Emerita analoga (in southern California) are delineated with respect to their spatial, daily, and seasonal components. Both abiotic and biotic factors are found to be associated with patterns of aggregation. Spatially, E. analoga aggregates from March through September to a significantly greater degree in the upper one-third area of the wash zone where exposure to wave shock and fish predation are probably decreased. Sand crabs are more aggregated on a daily basis during low tides than at high tides. This may be due to differential rates of migration caused by a decrease in the beach slope angle. Two seasonal peak periods of aggregation are present, one in the early spring, and one in the late summer. These periods occur during the times of highest reproductive female abundance. High seasonal intensities of aggregation probably function to facilitate mating through the maintenance of close proximity between males and females. Visual methods and/or quantitative sampling based on visual observations do not adequately reflect patterns of aggregation in E. analoga.     

Genetic diversity and structure of circumtropical almaco jack,Seriola rivoliana: tool for conservation and management

The almaco jack, Seriola rivoliana, is a circumtropical pelagic fish of importance both in commercial fisheries and in aquaculture. To understand levels of genetic diversity within and among populations in the wild, population genetic structure and the relative magnitude of migration were assessed using mtDNA sequence data and single nucleotide polymorphisms (SNPs) from individuals sampled from locations in the Pacific and Atlantic Oceans. A total of 25 variable sites of cytochrome c oxidase subunit 1 and 3678 neutral SNPs were recovered. Three genetic groups were identified, with both marker types distributed in different oceanic regions: Pacific-1 in central Pacific, Pacific-2 in eastern Pacific and Atlantic in western Atlantic. Nonetheless, the analysis of SNP identified a fourth population in the Pacific coast of Baja California Sur, Mexico (Pacific-3), whereas that of mtDNA did not. This mito-nuclear discordance is likely explained by a recently diverged Pacific-3 population. In addition, two mtDNA haplogroups were found within the western Atlantic, likely indicating that the species came into the Atlantic from the Indian Ocean with historical gene flow from the eastern Pacific. Relative gene flow among ocean basins was low with _rm < 0.2, whereas in the eastern Pacific it was asymmetric and higher from south to north (_rm > 0.79). The results reflect the importance of assessing genetic structure and gene flow of natural populations for the purposes of sustainable management.     

Comparative phylogeography and species boundaries in Echinolittorina snails in the central Indo-West Pacific

Aim This study aimed to test monophyly and geographical boundaries in five marine intertidal snail species from the central Indo‐West Pacific. We tested the prediction that phylogenetic breaks between the Indian and Pacific Ocean basins should be more pronounced in continental than oceanic settings, and sought common geographical patterns of interspecific boundaries and intraspecific phylogenetic breaks in the region. Location The tropical seas of the Indo‐West Pacific. Methods We sequenced over 1200 bp of the mitochondrial cytochrome oxidase subunit I gene (COI) from 18–92 individuals sampled from throughout the ranges of each of five species of Echinolittorina (Littorinidae): three members of the Echinolittorina trochoides species complex; Echinolittorina reticulata; and Echinolittorina vidua, together with sister species, in order to test species boundaries. In addition, 630 bp of the nuclear 28S rRNA gene were sequenced from E. reticulata and its sister Echinolittorina millegrana. Phylogenetic structure was assessed using neighbour‐joining and parsimony analyses. Results COI data confirmed species boundaries and geographical distributions for all species except the pair E. reticulata and E. millegrana, which were nevertheless reciprocally monophyletic for 28S rRNA. The species from ecologically ‘continental’ habitats (E. trochoides A and E. vidua, but not E. trochoides B) mostly showed strong interoceanic breaks (with age estimates 0.58–4.4 Ma), while the ecologically ‘oceanic’E. trochoides D and E. reticulata did not. The sister species E. trochoides A and B occupy the shores of the continental shelves of Southeast Asia and Australasia respectively; between them lies the oceanic ‘eastern Indonesian corridor’ occupied by E. trochoides D and E. reticulata. The widespread continental species E. vidua showed a complex pattern of deep division into six haplotype clades with apparently parapatric distributions. Main conclusions Our results show that ecological differences (in this case continental vs. oceanic habitat) influence both intraspecific phylogenetic structure and interspecific boundaries in these snails of intertidal rocky shores. Two of the three species restricted to continental shelves show phylogenetic breaks between the Indian and Pacific Oceans, consistent with vicariant separation during Plio‐Pleistocene low sea levels. The two oceanic species do not show breaks, suggesting that they maintained interoceanic connections through the eastern Indonesian corridor. The geographical location of the interspecific boundary between continental E. trochoides A and oceanic E. trochoides D mirrors intraspecific breaks reported in other species. The sister relationship of E. trochoides A and B in Asia and Australasia, respectively, is an example of a ‘marine Wallace's line’ distribution, and we suggest that it is the result of separation of two continental species by a barrier of unsuitable oceanic habitat.     

Phylogeography of a mite,Halozetes fulvus,reflects the landscape history of a young volcanic island in the sub‐Antarctic

Previous studies of the microarthropods of Marion Island, Southern Ocean, documented high mitochondrial COI (cytochrome c oxidase subunit I) haplotype diversity and significant genetic structure, which were ascribed to landscape subdivision. In this paper we revisit these ideas in light of new geomorphological evidence indicating a major lineament orientated along N26.5°E. Using the microarthropod Halozetes fulvus, we test the hypothesis that the eastern and western sides of the island show different population genetic patterns, corresponding to the previously unrecognized geological separation of these regions, and perhaps also with differences in climates across the island and further landscape complexity. Mitochondrial COI data were collected for 291 H. fulvus individuals from 30 localities across the island. Notwithstanding our sampling effort, haplotype diversity was under‐sampled as indicated by rarefaction analyses. Overall, significant genetic structure was found across the island as indicated by Φ_ST analyses. Nested clade phylogeographical analyses suggested that restricted gene flow (with isolation‐by‐distance) played a role in shaping current genetic patterns, as confirmed by Mantel tests. At the local scale, coalescent modelling revealed two different genetic patterns. The first, characterizing populations on the south‐western corner of the island, was that of low effective population size and high gene flow. The converse was found on the eastern side of Marion Island. Taken together, substantial differences in spatial genetic structure characterize H. fulvus populations across Marion Island, in keeping with the hypothesis that the complex history of the island, including the N26.5°E geological lineament, has influenced population genetic structure. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 131–145.     

Phylogeography of a pearl oyster (Pinctada maxima) across the Indo‐Australian Archipelago: evidence of strong regional structure and population expansions but no phylogenetic breaks

This study investigates the genetic structure and phylogeography of a broadcast spawning bivalve mollusc, Pinctada maxima, throughout the Indo‐West Pacific and northern Australia. DNA sequence variation of the mitochondrial cytochrome oxidase subunit I (COI) gene was analysed in 367 individuals sampled from nine populations across the Indo‐West Pacific. Hierarchical AMOVA indicated strong genetic structuring amongst populations (Φ_ST = 0.372, P < 0.001); however, sequence divergence between the 47 haplotypes detected was low (maximum 1.8% difference) and no deep phylogenetic divergence was observed. Results suggest the presence of genetic barriers isolating populations of the South China Sea and central Indonesian regions, which, in turn, show patterns of historical separation from northern Australian regions. In P. maxima, historical vicariance during Pleistocene low sea levels is likely to have restricted planktonic larval transport, causing genetic differentiation amongst populations. However, low genetic differentiation is observed where strong ocean currents are present and is most likely due to contemporary larval transport along these pathways. Geographical association with haplotype distributions may indicate signs of early lineage sorting arising from historical population separations, yet an absence of divergent phylogenetic clades related to geography could be the consequence of periodic pulses of high genetic exchange. We compare our results with previous microsatellite DNA analysis of these P. maxima populations, and discuss implications for future conservation management of this species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 632–646.     

Across the southern Andes on fin: glacial refugia,drainage reversals and a secondary contact zone revealed by the phylogeographical signal of Galaxias platei in Patagonia

We employed DNA sequence variation at two mitochondrial (control region, COI) regions from 212 individuals of Galaxias platei (Pisces, Galaxiidae) collected throughout Patagonia (25 lakes/rivers) to examine how Andean orogeny and the climatic cycles throughout the Quaternary affected the genetic diversity and phylogeography of this species. Phylogenetic analyses revealed four deep genealogical lineages which likely represent the initial division of G. platei into eastern and western lineages by Andean uplift, followed by further subdivision of each lineage into separate glacial refugia by repeated Pleistocene glacial cycles. West of the Andes, refugia were likely restricted to the northern region of Patagonia with small relicts in the south, whereas eastern refugia appear to have been much larger and widespread, consisting of separate northern and southern regions that collectively spanned most of Argentinean Patagonia. The retreat of glacial ice following the last glacial maximum allowed re‐colonization of central Chile from nonlocal refugia from the north and east, representing a region of secondary contact between all four glacial lineages. Northwestern glacial relicts likely followed pro‐glacial lakes into central Chilean Patagonia, whereas catastrophic changes in drainage direction (Atlantic → Pacific) for several eastern palaeolakes were the likely avenues for invasions from the east. These mechanisms, combined with evidence for recent, rapid and widespread population growth could explain the extensive contemporary distribution of G. platei throughout Patagonia.     

Phylogeography of the mottled spinefoot Siganus fuscescens: Pleistocene divergence and limited genetic connectivity across the Philippine archipelago

Historical isolation during Pleistocene low sea level periods is thought to have contributed to divergence among marine basin populations across the Coral Triangle. In the Philippine archipelago, populations in the South China Sea, Sulu Sea–inland seas, and Philippine Sea‐Celebes Sea basins might have been partially isolated. Meanwhile, present‐day broadscale oceanographic circulation patterns suggest connectivity between these basins. To evaluate hypotheses regarding the influence of historical and contemporary factors on genetic structure, phylogeographic patterns based on mitochondrial control region sequences for a reef‐associated fish, Siganus fuscescens, were analysed. Three distinct lineages were recovered. One lineage was identified as the morphologically similar species Siganus canaliculatus, while two lineages are monophyletic with S. fuscescens. Clade divergence and demographic expansion in S. fuscescens occurred during the Pleistocene. A strong signal of latitudinal structure was detected (Φ_CT = 0.188), driven by marked differences in clade distribution: one clade is widely distributed (clade A), while a second clade (clade B) has a restricted northern distribution. Regional structure of clade A is consistent with the basin isolation hypothesis (Φ_CT = 0.040) and suggests isolation of the South China Sea (Φ_CT = 0.091). Fine‐scale structure was observed in the South China Sea and south Philippine Sea, while Sulu Sea and inland seas were unstructured. Genetic structure across multiple spatial scales (archipelagic, regional, and fine‐scale within basins) suggests the influence of vicariant barriers and contemporary limits to gene flow in S. fuscescens that may be influenced by oceanographic circulation, geographical distance between available habitats, and latitudinal temperature differences.     

Evolutionary systematics of the Australian Eocyzicus fauna (Crustacea: Branchiopoda: Spinicaudata) reveals hidden diversity and phylogeographic structure

Although ‘large branchiopods’ are an important faunal element of the temporary water bodies in Australia's vast (semi)arid regions, knowledge of their diversity, distribution and ecology is still poor. Here, on the basis of one mitochondrial [cytochrome oxidase subunit I (COI)] and three nuclear (EF1α, ITS2 and 28S) markers, we present new data relating to the diversity and phylogeography of eastern and central Australian Eocyzicus (Spinicaudata) fauna. Using a combination of phylogenetic, haplotype network and DNA barcoding analyses of COI, 312 individuals were grouped into eleven main lineages. To infer whether these lineages are reproductively isolated from each other (the prerequisite for species delineation according to the Biological or Hennigian Species Concepts), separate analyses of each nuclear marker were performed on a subset of specimens. Although some lineages are non‐monophyletic in the analysis of one nuclear marker, this is mostly attributed to processes such as incomplete lineage sorting rather than ongoing reproduction. The eleven lineages translate into at least seven species whose reproductive isolation is additionally indicated by sympatry, including both Australian Eocyzicus species previously described. Another three lineages may constitute further species, but their clear allopatric distribution rendered the test for reproductive isolation inapplicable. One lineage appears not to be reproductively isolated and is therefore considered a genetically distinct lineage within one of the other species, and one divergent lineage within E. argillaquus may constitute an additional species. Although sympatry is very common – six species occur in the central Paroo River catchment in eastern Australia, for instance – syntopic occurrence is rare. It is possible that a combination of differing habitat preferences and priority effects inhibits the presence of more than one Eocyzicus species per water body. There is little to no genetic differentiation between certain populations of the species found in eastern and central Australia (e.g. the Murray–Darling Basin, the Bulloo River catchment and the eastern and northern Lake Eyre Basin; LEB), suggesting high dispersal rates within this large area. Between the central Australian populations themselves, however (e.g. those inhabiting the central and western LEB), genetic differentiation is pronounced, probably as a result of the lack of abundance of important dispersal vectors (aquatic birds) and the lower diversity and density of suitable habitats in the area. The most prominent biogeographical break exists towards north‐eastern Australia (north‐east LEB), which does not share species with any other region studied.     

A parapatric propensity for breeding precludes the completion of speciation in common teal (Anas crecca, sensu lato)

Speciation is a process in which genetic drift and selection cause divergence over time. However, there is no rule dictating the time required for speciation, and even low levels of gene flow hinder divergence, so that taxa may be poised at the threshold of speciation for long periods of evolutionary time. We sequenced mitochondrial DNA (mtDNA) and eight nuclear introns (nuDNA) to estimate genomic levels of differentiation and gene flow between the Eurasian common teal (Anas crecca crecca) and the North American green‐winged teal (Anas crecca carolinensis). These ducks come into contact in Beringia (north‐eastern Asia and north‐western North America) and have probably done so, perhaps cyclically, since the Pliocene–Pleistocene transition, ～2.6 Ma, when they apparently began diverging. They have diagnosable differences in male plumage and are 6.9% divergent in the mtDNA control region, with only 1 of 58 crecca and 2 of 86 carolinensis having haplotypes grouping with the other. Two nuclear loci were likewise strongly structured between these teal (Φ_st ≥ 0.35), but six loci were undifferentiated or only weakly structured (Φ_st = 0.0–0.06). Gene flow between crecca and carolinensis was ～1 individual per generation in both directions in mtDNA, but was asymmetrical in nuDNA, with ～1 and ～20 individuals per generation immigrating into crecca and carolinensis, respectively. This study illustrates that species delimitation using a single marker oversimplifies the complexity of the speciation process, and it suggests that even with divergent selection, moderate levels of gene flow may stall the speciation process short of completion.