A marine fish follows Wallace's Line: the phylogeography of the three-spot seahorse (Hippocampus trimaculatus, Syngnathidae, Teleostei) in Southeast Asia

Aim To test the potential of two contrasting biogeographical hypotheses (‘Indian/Pacific Ocean Basin’ vs. ‘Wallace's Line’) to explain the distribution of genetic diversity among populations of a marine fish in Southeast Asia. Location The marine waters of Asia and Southeast Asia: from India to Japan, and east to the Indonesian islands of Sulawesi and Flores. Methods We sequenced a 696 base pair fragment of cytochrome b DNA of 100 individuals of Hippocampus trimaculatus Leach 1814 (three‐spot seahorse), obtained from across its range. We tested our hypotheses using phylogenetic reconstructions and analyses of molecular variance. Results Significant genetic divergence was observed among the specimens. Two distinct lineages emerged that diverged by an average of 2.9%. The genetic split was geographically associated, but surprisingly it indicated a major east–west division similar to the terrestrial Wallace's Line (Φ_ST = 0.662, P < 0.001) rather than one consistent with an Indian‐Pacific ocean basin separation hypothesis (Φ_ST = 0.023, P = 0.153). Samples from east of Wallace's Line, when analysed separately, however, were consistent with an Indian/Pacific Ocean separation (Φ_ST = 0.461, P = 0.005). The degree of genetic and geographical structure within each lineage also varied. Lineage A, to the west, was evolutionarily shallow (star‐like), and the haplotypes it contained often occurred over a wide area. Lineage B to the east had greater genetic structure, and there was also some evidence of geographical localization of sublineages within B. Main conclusions Our results indicate that the genetic diversity of marine organisms in Southeast Asia may reflect a more complex history than the simple division between two major ocean basins that has been proposed by previous authors. In particular, the east–west genetic division observed here is novel among marine organisms examined to date. The high haplotype, but low nucleotide diversity to the west of Wallace's Line is consistent with post‐glacial colonization of the Sunda Shelf. Additional data are needed to test the generality of these patterns.     

A New Trichomycterus (Siluriformes: Trichomycteridae) from Aguarague National Park of the Bolivian Preandean Region, with Comments on Relationships within of the Genus

Synopsis The Andean and preandean regions are characterized by the presence of several endorheic drainage basins, each of which has evolved a characteristic fish fauna, some of which are poorly known or hitherto inaccessible. We describe here a new species of Trichomycterus from Aguarague National Park, Bolivia. Trichomycterus aguarague is considered to belong to a species assemblage comprised of T. alterus, T. boylei, T. ramosus, and T. belensis, a group diagnosed by three putative apomorphic conditions: (1) base of the maxillary barbel wide and engrossed like a skin flap or fold, (2) premaxillary bone smaller than maxilla, and (3) odontodes embedded in thick integument that covers interopercle. Alternatively, T. aguarague and T. alterus share an unusual number of five or fewer abdominal vertebrae, which is a synapomorphy for the group composed of Scleronema, Ituglanis, and the Stegophilinae+Tridentinae+Vandelliinae+Glanapteryginae+Sarcoglanidinae clade. The new species differs from all congeners in having the following combination of characters: caudal peduncle depth 13.5 – 16.0% SL, 15 or 16 pairs of ribs, 15 dorsal procurrent rays, 12 ventral procurrent rays, 8 pectoral fin rays; 9 anal fin rays; barbels and skin of trunk with numerous, minute thread-like papillae.     

Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus)

Four distinct phylogeographical patterns across Southeast Asia were observed for four species of seahorse (genus Hippocampus) with differing ecologies. For all species, genetic differentiation (based on cytochrome b sequence comparisons) was significantly associated with sample site (Phi(ST) = 0.190-0.810, P < 0.0001) and with geographical distance (Mantel's r = 0.37-0.59, P < 0.019). Geographic locations of genetic breaks were inconsistent across species in 7/10 comparisons, although some similarities across species were also observed. The two shallow-water species (Hippocampus barbouri and Hippocampus kuda) have colonized the Sunda Shelf to a lesser degree than the two deeper-water species (Hippocampus spinosissimus and Hippocampus trimaculatus). In all species the presence of geographically restricted haplotypes in the Philippines could indicate past population fragmentation and/or long-distance colonization. A nested clade analysis (NCA) revealed that long-distance colonization and/or fragmentation were likely the dominant forces that structure populations of the two shallow-water species, whereas range expansion and restricted dispersal with isolation by distance were proportionally more important in the history of the two deeper-water species. H. trimaculatus has the most widespread haplotypes [average clade distance (D(c)) of nonsingleton haplotypes = 1169 km], indicating potentially high dispersal capabilities, whereas H. barbouri has the least widespread haplotypes (average D(c) = 67 km) indicating potentially lower dispersal capabilities. Pleistocene separation of marine basins and postglacial flooding of the Sunda Shelf are extrinsic factors likely to have contributed to the phylogeographical structure observed, whereas differences among the species appear to reflect their individual ecologies.     

Molecular systematics,taxonomy and biogeography of the genus Cavia (Rodentia: Caviidae)

Phylogenetic analyses were conducted on cytochrome b sequence data of the most geographically and taxonomically broad sampling of Cavia taxa to date. Primary objectives included providing the first extensive molecular phylogenetic framework for the genus, testing the taxonomic and systematic hypotheses of previous authors and providing insight into the evolutionary and biogeographic history of the genus. Support was found for the morphologically defined species C. aperea, C. tschudii, C. magna and C. fulgida and the taxonomic placement of taxa previously subject to conflicting taxonomic opinions (e.g. C. nana, C. anolaimae and C. guianae) was further resolved. Additionally, we elevate the Ecuadorian C. a. patzelti to species status, restrict the distributional limits and suggest taxonomic affiliations of some C. tschudii subspecies, and provide strong evidence for the geographic origin of guinea pig domestication. Finally, we provide an estimated evolutionary timeline for the genus Cavia, which appears to extend well into the late Miocene.     

Phylogeny and phylogeography of the Liolaemus darwinii complex (Squamata: Liolaemidae): evidence for introgression and incomplete lineage sorting

Although mitochondrial DNA markers have several properties that make them suitable for phylogeographic studies, they are not free of difficulties. Phylogeographic inferences within and between closely related species can be mislead by introgression and retention of ancestral polymorphism. Here we combine different phylogenetic, phylogeographic, and population genetic methods to extract the maximum information from the Liolaemus darwinii complex. We estimate the phylogeographic structure of L. darwinii across most of its distributional range, and we then estimate relationships between L. darwinii and the syntopic species L. laurenti and L. grosseorum. Our results suggest that range expansion of these lineages brought them into secondary contact in areas where they are presently in syntopy. Here we present the first evidence for introgression in lizards from temperate South America (of L. danwinii mitochondrial DNA into L. laurenti and L. grosseorum), and for incomplete lineage sorting (between L. darwinii and L. laurenti). We show that a combination of methods can provide additional support for inferences derived from any single method and thus provide more robust interpretations and narrow the range of plausible hypotheses about mechanisms and processes of divergence. Additional studies are needed in this group of lizards and in other codistributed groups to determine if Pleistocene climatic changes could be a general factor influencing the evolutionary history of a regional biota.     

Plio-Pleistocene history of West African Sudanian savanna and the phylogeography of the Praomys daltoni complex (Rodentia): the environment/geography/genetic interplay

Rodents of the Praomys daltoni complex are typical inhabitants of the Sudanian savanna ecosystem in western Africa and represent a suitable model for testing the effects of Quaternary climatic oscillations on extant genetic variation patterns. Phylogeographical analyses of mitochondrial DNA sequences (cytochrome b) across the distribution range of the complex revealed several well‐defined clades that do not support the division of the clade into the two species currently recognized on the basis of morphology, i.e. P. daltoni (Thomas, 1892) and Praomys derooi ( Van der Straeten & Verheyen 1978 ). The observed genetic structure fits the refuge hypothesis, suggesting that only a small number of populations repeatedly survived in distinct forest‐savanna mosaic blocks during the arid phases of the Pleistocene, and then expanded again during moister periods. West African rivers may also have contributed to genetic differentiation, especially by forming barriers after secondary contact of expanding populations. The combination of three types of genetic markers (mtDNA sequences, microsatellite loci, cytogenetic data) provides evidence for the presence of up to three lineages, which most probably represent distinct biological species. Furthermore, incongruence between nuclear and mtDNA markers in some individuals unambiguously points towards a past introgression event. Our results highlight the importance of combining different molecular markers for an accurate interpretation of genetic data.     

Comparative phylogeography of Zacco platypus and Opsariichthys bidens (Teleostei, Cyprinidae) in China based on cytochrome b sequences

We compared the phylogenetic relationships and the population structure of the sympatric cyprinids Opsariichthys bidens and Zacco platypus across the Yangzte, Pearl and Hai He drainages in Mainland China. We used the mitochondrial cytochrome b gene to evaluate their phylogeographical structure and to discuss further systematic implications. We sequenced 71 new individuals of Z. platypus to add to a previous study and to construct a geographically comparable data set with O. bidens (Mol. Phylogenet. Evol. 31, 2004, 192; Mol. Phylogenet. Evol. 37, 2005, 920). Phylogeographic analysis of Z. platypus identified two additional mtDNA lineages (Zacco E and F) in addition to the previously recovered lineages (Zacco A–D). The geographical range of the Zacco A was extended across the Pearl drainage, broadening considerably the previous distribution that was circumscribed to the Yangtze drainage. Our results show high molecular divergence between all Zacco A–F mtDNA lineages (mean TrN + I + G distance 17.7%, range 4.4–30.8%), and the population analyses showed that most of the genetic variation was found among major river tributaries (90.2%). Values of θ_ST higher than 0.97 corroborated this interruption of gene flow between Zacco A–F mtDNA lineages. Nested clade analysis results were also concordant with the phylogenetic relationships recovered. We found similar phylogeographic patterns in Z. platypus and O. bidens: they exhibited two widespread and common lineages (Zacco A and Opsariichthys 1) ranging across the Yangtze and Pearl drainages, and both taxa had Northern lineages (Zacco F and Opsariichthys 5) clearly differentiated. Similar phylogeographic patterns suggest that common historical factors have shaped current Zacco and Opsariichthys diversity. High genetic distances and θ_ST values suggested that differentiation of Zacco A–F mtDNA lineages and Opsariichthys 1–5 was not recent and was probably favoured by old geological events. However, population parameters and low genetic differentiation inside Zacco A and Opsariichthys 1 suggest a recent gene flow across river drainages. Mitochondrial‐based phylogenies for the combined data sets of Zacco A–F and Opsariichthys 1–5 mtDNA lineages always recovered both taxa as paraphyletic, highlighting the notion that their current systematics need a revision.     

A catfish of the genus Trichomycterus from a thermal stream in southern South America (Teleostei, Siluriformes, Trichomycteridae), with comments on relationships within the genus

The first record of two trichomycterid species from the thermal waters of a small stream in Miraflores, north of Potosí, Bolivia is given. The reported species are Trichomycterus therma n. sp. and Trichomycterus tiraquae . The new species differ from all congeners in the possession of thickened transverse skin on the ventral surface of the head. They are further distinguished from all congeners by the following combination of characteristics: presence of spatulate incisiform premaxillary teeth; presence of large and rounded papilla-like structures on trunk of body; continuous segment of the laterosensory canal within the frontal with the presence of a segment between pores 2 and 6; long laterosensory canal with four to six pores; maxilla with a short anterior process that is smaller than the main axis of the bone, and has an anterior orientation; mesethmoid shaft narrower than the width of the lateral cornua; prepelvic length 58·7–61·0% of standard length ( L _S); head width 19·1–22·8% of L _S; submaxillary barbel length 23·9–37·5% of head length ( L _H). Two derived characters, namely the presence of spatulate incisiform premaxillary teeth and large and rounded papilla-like structures, define a monophyletic group within Trichomycterus , comprising T. therma , T. corduvensis and T. tiraquae .     

Pleistocene refugia and recolonization routes in the southern Andes: insights from Hypochaeris palustris (Asteraceae, Lactuceae)

Hypochaeris palustris (Phil.) De Wild. is a species growing in the southern Andean chain. To elucidate potential Pleistocene refugia and recolonization routes in the southern Andes, we analysed amplified fragment length polymorphisms (AFLPs) in 206 individuals in 21 populations of H. palustris from the coastal Cordillera, the central, northern, and eastern ranges of the southern Andes, and Patagonia. Populations from the coastal Cordillera harboured more private AFLP fragments, and exhibited a higher frequency of polymorphic fragments as well as higher Shannon diversity than all other areas investigated. The comparison among pooled AFLP profiles of each region revealed that the central Andean ranges shared most fragments with populations from the margins of the distributional area in the Andes, in the N, E, and S (Patagonia). Phenetic analysis indicated close relationships among populations of the central ranges. Populations of the coastal Cordillera were shown to be highly differentiated from the Andean populations. It is very likely therefore that (1) H. palustris recolonized the central ranges of the southern Andes from nearby refugia, possibly unglaciated areas N, E, and/or S of its present distributional area; (2) the postglacial spread of H. palustris in the central ranges of the southern Andes occurred rapidly; and (3) the coastal Cordillera served as a refugium for H. palustris, but these populations did not contribute to the recolonization of the central Andean ranges.     

Effects of Pleistocene climatic and geomorphological changes on the population structure of the restricted-range catfish Trichogenes longipinnis (Siluriformes: Trichomycteridae)

Trichogenes longipinnis Britski & Ortega is a narrowly distributed endemic and phenotypically variable catfish from the coastal basins of the Serra do Mar range in southeast Brazil. We examined patterns of mtDNA variation of this species in coastal basins of the Serra do Mar to determine the influences of past climatic and geomorphological processes in connection with the currently isolated basins. Allozyme data were also used to test the hypothesis that the different spotting patterns in the different areas could be the result of cryptic speciation. Regardless of body pigmentation, T. longipinnis specimens from across the basins were found to belong to a single species, but the populations were structured in accordance with the current hydrological watersheds, in four management units across the three distinct basins of its geographic distribution. Thus, the current genetic distribution may be best explained by both marine regressions and orogeny. Based on the low levels of genetic variation and high population structure observed, we suggest that T. longipinnis should be classified as “vulnerable” in the Brazilian red list of threatened fauna. Furthermore, we propose that the headwaters of the Parati-Mirim River basin should be incorporated as an extension of the Bocaina National Park to protect its genetically differentiated lineages.     

Multiple refugia and barriers explain the phylogeography of the Valais shrew,Sorex antinorii (Mammalia: Soricomorpha)

The aim of the present study was to investigate the genetic structure of the Valais shrew (Sorex antinorii) by a combined phylogeographical and landscape genetic approach, and thereby to infer the locations of glacial refugia and establish the influence of geographical barriers. We sequenced part of the mitochondrial cytochrome b (cyt b) gene of 179 individuals of S. antinorii sampled across the entire species' range. Six specimens attributed to S. arunchi were included in the analysis. The phylogeographical pattern was assessed by Bayesian molecular phylogenetic reconstruction, population genetic analyses, and a species distribution modelling (SDM)‐based hindcasting approach. We also used landscape genetics (including isolation‐by‐resistance) to infer the determinants of current intra‐specific genetic structure. The phylogeographical analysis revealed shallow divergence among haplotypes and no clear substructure within S. antinorii. The starlike structure of the median‐joining network is consistent with population expansion from a single refugium, probably located in the Apennines. Long branches observed on the same network also suggest that another refugium may have existed in the north‐eastern part of Italy. This result is consistent with SDM, which also suggests several habitable areas for S. antinorii in the Italian peninsula during the LGM. Therefore S. antinorii appears to have occupied disconnected glacial refugia in the Italian peninsula, supporting previous data for other species showing multiple refugia within southern refugial areas. By coupling genetic analyses and SDM, we were able to infer how past climatic suitability contributed to genetic divergence of populations. The genetic differentiation shown in the present study does not support the specific status of S. arunchi. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 864–880.     

Taxonomic review of genus Sooretamys Weksler,Percequillo & Voss (Rodentia: Cricetidae: Sigmodontinae): an integrative approach

Sooretamys is a monotypic genus of the family Cricetidae, subfamily Sigmodontinae, that is distributed throughout eastern South America in the Atlantic Forest Biome, including Argentina, Brazil, and Paraguay. The taxonomic history of the forms associated with this genus is long and relatively complex, and few studies have evaluated the taxonomic problems of this genus. To this end, our goal was to describe the degree and geographical pattern of morphological and molecular variation in this genus to test the current hypothesis that the genus is monotypic, and, as a consequence, to determine the status of the nominal forms associated with Sooretamys. Accordingly, we employed morphometric, morphological, and molecular tools, according to an integrative taxonomy approach. The results show that some level of morphometric discontinuity is present between the individuals from Paraguay and those from adjacent localities in Brazil and Argentina; sharp discontinuities were not observed in qualitative traits. Molecular analyses of the mitochondrial cytochrome b gene showed that the Paraguayan populations have some degree of genetic differentiation, but the haplotypic variants do not form a monophyletic group. Thus, the evidence so far suggests a difference in the genes and morphology of the Paraguayan population, but there is no consistent resolution (e.g. lack of monophyly) to show that specimens from Paraguay represent a distinct population that would merit taxonomic recognition. Thus, we recognize a single species within the genus Sooretamys, named Sooretamys angouya. The pattern of morphological and genetic differentiation of Sooretamys could be the result of divergence with gene flow. However, our data also correspond in some aspects with the model advanced by Carnaval & Moritz, which claims the existence of stable Atlantic Forest areas where the forest biota persisted during the Quaternary climatic fluctuations. Whatever process has occurred, S. angouya represents one species with a complex evolutionary history, and the analysis of additional samples would be welcome to further elucidate the process of diversification of this taxon. © 2014 The Linnean Society of London     

Adult habitat preferences, larval dispersal, and the comparative phylogeography of three Atlantic surgeonfishes (Teleostei: Acanthuridae)

Although many reef fishes of the tropical Atlantic are widely distributed, there are large discontinuities that may strongly influence phylogeographical patterns. The freshwater outflow of the Amazon basin is recognized as a major barrier that produces a break between Brazilian and Caribbean faunas. The vast oceanic distances between Brazil and the mid-Atlantic ridge islands represent another formidable barrier. To assess the relative importance of these barriers, we compared a fragment of the mitochondrial DNA (mtDNA) cytochrome b gene among populations of three species of Atlantic surgeonfishes: Acanthurus bahianus, A. chirurgus and A. coeruleus. These species have similar life histories but different adult habitat preferences. The mtDNA data show no population structure between Brazil and the mid-Atlantic islands, indicating that this oceanic barrier is readily traversed by the pelagic larval stage of all three surgeonfishes, which spend approximately 45-70 days in the pelagic environment. The Amazon is a strong barrier to dispersal of A. bahianus (d = 0.024, phiST = 0.724), a modest barrier for A. coeruleus (phiST = 0.356), and has no discernible effect as a barrier for A. chirurgus. The later species has been collected on soft bottoms with sponge habitats under the Amazon outflow, indicating that relaxed adult habitat requirements enable it to readily cross that barrier. A limited ability to use soft bottom habitats may also explain the low (but significant) population structure in A. coeruleus. In contrast, A. bahianus has not been collected over deep sponge bottoms, and rarely settles outside shallow reefs. Overall, adult habitat preferences seem to be the factor that differentiates phylogeographical patterns in these reef-associated species.     

Phylogeography and post-glacial colonization patterns of the rainbow darter, Etheostoma caeruleum (Teleostei: Percidae)

Aim To examine the effects of historical climate change and drainage isolation on the distribution of mitochondrial DNA cytochrome b genetic variation within the rainbow darter, Etheostoma caeruleum (Percidae: Etheostomatinae). Location Eastern North American streams including tributaries to the Mississippi River, Great Lakes, Potomac River and Hudson Bay drainages. Methods Parsimony analyses, Bayesian analyses and haplotype networks of mitochondrial DNA sequences. Results Four major clades were recovered from sampled populations of E. caeruleum. Three of four clades are distributed in the western portion of the species’ range (primarily west of the Mississippi River). Samples from this region do not form a monophyletic group, and sequences often vary greatly between samples from adjacent stream systems (up to 7.2% divergence). A basal clade includes samples from the White River system in the Ozark Highlands. The northern Ozarks–upper Midwest clade includes samples from Missouri River tributaries and the upper Midwest (Hudson Bay, upper Mississippi River, and western Lake Michigan drainage). The eastern clade is composed of individuals from the Ohio River, Great Lakes and Potomac River. The Mississippi River corridor clade includes samples from middle and lower Mississippi River tributaries. Main conclusions The four major clades of E. caeruleum are deep allopatric lineages with well‐defined boundaries and have additional phylogeographical structure within each clade. The Ozark Highlands have the greatest levels of diversity relative to distributional area, with marked cytochrome b subdivisions between adjacent stream systems. Samples from previously glaciated areas do not have a subset of the cytochrome b diversity found in unglaciated areas, but four separate source areas are identified based on phylogenetic analyses. Dispersal into previously glaciated areas followed several known glacial outlets and, based on sequence divergence between populations, may have occurred during different glacial or interglacial stages. The disjunct distribution and cytochrome b pattern of E. caeruleum in the Mississippi River corridor clade is consistent with late Pleistocene and Recent changes in the course and characteristics of the middle and lower Mississippi River. Phylogeographical boundaries between clades of E. caeruleum correspond to independent sources of biogeographical information and provide insight into historical stream drainage relationships, post‐glacial colonization and drainage isolation patterns.     

Revision of the rhinoceros beetle genus Oryctophileurus Kolbe with description of a new species,the male of O. varicosus Prell,and notes on biogeography (Scarabaeoidea,Dynastinae, Phileurini)

The genus Oryctophileurus is reviewed and its validity is supported by a combination of the following apomorphic characters: a single cephalic horn with lateral carina, pronotal cavity with ocellate punctures and two teeth or tubercles close behind the anterior pronotal margin. The male of Oryctophileurus varicosus Prell, 1934, is described for the first time. A new species, Oryctophileurus guerrai Perger & Grossi sp. n., from subhumid Tucuman-Bolivian forest in the Southern Bolivian Andes is described. The new species is distinguished from its closest relative, O. armicollis Prell, 1911, by a narrower distance between the inner teeth of the dorsal pronotal protuberances and a reduced area of weakly developed ocellate punctures above the posterolateral pronotal margin. The occurrence of Oryctophileurus species in areas of endemism along the eastern slope of the tropical Andes suggests that these populations represent biogeographic “relicts”, and the discovery of Oryctophileurus guerrai sp. n. in the southern Bolivian Andes suggests that this area is underrated with respect to insect diversity and endemism.     

Genetic differentiation of the Thorn‐tailed Rayadito Aphrastura spinicauda (Furnariidae: Passeriformes) revealed by ISSR profiles suggests multiple palaeorefugia and high recurrent gene flow

Nucleotide sequence data (cytochrome b) and ISSR genomic fingerprints were used to analyse the genetic variation and population differentiation in Thorn‐tailed Rayadito, a widespread Patagonian forest bird. We included samples from eight populations of Thorn‐tailed Rayadito covering most of the distribution range of the species: from fragmented patches of Olivillo forest in northern Chile to Isla Navarino forests in the extreme south of South America. Low levels of genetic diversity were found among populations, with a large within‐population molecular variance indicating high levels of gene flow. The multivariate and cluster analyses based on ISSR markers show that the subspecies bullocki (from Mocha Island) differs significantly from all other populations. The subspecies fulva (Chiloé Island) shows less differentiation than bullocki, sharing several alleles with continental populations. Bayesian analyses suggest that the Mocha Island population contributes most to the total genetic diversity observed in the species. Mantel tests revealed no significant correlation between geographical distance and pairwise genetic distance and cytochrome b sequence analyses failed to detect differentiation among subspecies. Mocha Island might have been a palaeorefuge and this population may have diversified by genetic drift after the last glacial maximum. There is also the possibility of a postglacial colonization of the Thorn‐tailed Rayadito from an austral palaeorefugium, supporting a multiple refugia hypothesis. This study illustrates the usefulness of the rarely used ISSR genomic fingerprint method in avian phylogeography.     

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

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