Comparative phylogeography of coastal limpets across a marine disjunction in New Zealand

Pre-domestication bottlenecks of the cultivated seaweed Gracilaria chilensis

Gracilaria chilensis is the main cultivated seaweed in Chile. The low genetic diversity observed in the Chilean populations has been associated with the over-exploitation of natural beds and/or the founder effect that occurred during post-glacial colonization from New Zealand. How these processes have affected its evolutionary trajectory before farming and incipient domestication is poorly understood. In this study, we used 2232 single nucleotide polymorphisms (SNPs) to assess how the species' evolutionary history in New Zealand (its region of origin), the founder effect linked to transoceanic dispersion and colonization of South America, and the recent over-exploitation of natural populations have influenced the genetic architecture of G. chilensis in Chile. The contrasting patterns of genetic diversity and structure observed between the two main islands in New Zealand attest to the important effects of Quaternary glacial cycles on G. chilensis. Approximate Bayesian Computation (ABC) analyses indicated that Chatham Island and South America were colonized independently near the end of the Last Glacial Maximum and emphasized the importance of coastal and oceanic currents during that period. Furthermore, ABC analyses inferred the existence of a recent and strong genetic bottleneck in Chile, matching the period of over-exploitation of the natural beds during the 1970s, followed by rapid demographic expansion linked to active clonal propagation used in farming. Recurrent genetic bottlenecks strongly eroded the genetic diversity of G. chilensis prior to its cultivation, raising important challenges for the management of genetic resources in this incipiently domesticated species.

Insights into the Deep Phylogeny and Novel Divergence Time Estimation of Patellogastropoda from Complete Mitogenomes

To further understand the origin and evolution of Patellogastropoda, we determined the mitochondrial genome sequence of Cellana toreuma, and compared its mitogenome characteristics with the other four limpets of Nacellidae. The ratio of Ka and Ks indicated that these Nacellidae species were suffering a purifying selection, with exception of the atp6 gene. The gene sequence is basically consistent among families, while there are great differences among Lottidae species. According to the mitogenome sequences of selected gastropod species, we reconstructed a new phylogenetic tree with two methods. The data complement the mitogenome database of limpets and is a favorable research tool for the phylogenetic analysis of Gastropoda. It is found that there is a long-branch attraction (LBA) artefact in the family Lottiidae of Patellogastropoda. Therefore, the Patellogastropoda was separated by Heterobranchia, and Lottiidae is located at the root of the whole phylogenetic tree. Furthermore, we constructed the divergence time tree according to the Bayesian method and discussed the internal historical dynamics, and divergence differences among the main lineages of 12 Patellogastropoda under an uncorrelated relaxed molecular clock. In turn, we made a more comprehensive discussion on the divergence time of limpets at the molecular level.

Concordant geographic and genetic structure revealed by genotyping-by-sequencing in a New Zealand marine isopod

Population genetic structure in the marine environment can be influenced by life-history traits such as developmental mode (biphasic, with distinct adult and larval morphology, and direct development, in which larvae resemble adults) or habitat specificity, as well as geography and selection. Developmental mode is thought to significantly influence dispersal, with direct developers expected to have much lower dispersal potential. However, this prediction can be complicated by the presence of geophysical barriers to dispersal. In this study, we use a panel of 8,020 SNPs to investigate population structure and biogeography over multiple spatial scales for a direct-developing species, the New Zealand endemic marine isopod Isocladus armatus. Because our sampling range is intersected by two well-known biogeographic barriers (the East Cape and the Cook Strait), our study provides an opportunity to understand how such barriers influence dispersal in direct developers. On a small spatial scale (20 km), gene flow between locations is extremely high, suggestive of an island model of migration. However, over larger spatial scales (600 km), populations exhibit a clear pattern of isolation-by-distance. Our results indicate that I. armatus exhibits significant migration across the hypothesized barriers and suggest that large-scale ocean currents associated with these locations do not present a barrier to dispersal. Interestingly, we find evidence of a north-south population genetic break occurring between Māhia and Wellington. While no known geophysical barrier is apparent in this area, it coincides with the location of a proposed border between bioregions. Analysis of loci under selection revealed that both isolation-by-distance and adaption may be contributing to the degree of population structure we have observed here. We conclude that developmental life history largely predicts dispersal in the intertidal isopod I. armatus. However, localized biogeographic processes can disrupt this expectation, and this may explain the potential meta-population detected in the Auckland region.

Comparative phylogeography of two Agarophyton species in the New Zealand archipelago

Molecular studies have reported the coexistence of two species of Agarophyton in New Zealand: the newly described A.transtasmanicum with an apparently restricted distribution to some sites in the North Island, and the more widespread A.chilense. Here, we compared the distribution, genetic diversity, and structure of both Agarophyton species throughout the archipelago using sequences of the nuclear Internal Transcribed Spacer 2 (ITS2) marker. Agarophyton chilense's distribution was continuous and extensive along the North and South Islands, Stewart Island, and Chatham Island, and the genetic clusters were mostly concordant with boundaries between biogeographic regions. In contrast, specimens of A.transtasmanicum were collected in four sites broadly distributed in both the North and South Islands, with no clear spatial structure of the genetic diversity. Populations, where the species co-occurred, tended to display similar levels in genetic diversity for the two species. Demographic inferences supported a postglacial demographic expansion for two A.chilense genetic clusters, one present in the South Island and the eastern coast of the North Island, and the other present in northern South Island. A third genetic cluster located on the western coast of the North Island had a signature of long-term demographic stability. For A.transtasmanicum, the skyline plot also suggested a postglacial demographic expansion. Last, we developed a new molecular tool to quickly and easily distinguish between the two Agarophyton species, which could be used to ease future fine-scale population studies, especially in areas where the two species coexist.

Population structure of the New Zealand whelk, Cominella glandiformis (Gastropoda: Buccinidae), suggests sporadic dispersal of a direct developer

We examined phylogeographic structure in the direct-developing New Zealand endemic intertidal mud whelk, Cominella glandiformis. Two hundred and ninety-six whelks from 12 sites were collected from sheltered shores around New Zealand’s four largest islands (North Island, South Island, Stewart Island and Chatham Island), encompassing the geographical range of this species. Despite being direct developers, gene flow among C. glandiformis populations may occur over short distances by adult floating, and over larger distances by rafting of egg masses. Primers were developed to amplify variable microsatellite regions at six loci. All loci were variable, with 8–34 alleles/loci. Observed and expected heterozygosities were high across all alleles, with minimal evidence of null alleles. The average number of alleles varied from 3.5 (Chatham Island) to 7.5 (Waitemata Harbour). Strong genetic structure was evident, with distinct ‘eastern’ and ‘western’ groups. Each group extended over a large geographic area, including regions of unsuitable habitat, but were linked by oceanic currents. We suggest that the intraspecific geographic genetic structure in C. glandiformis has arisen due a combination of ocean currents (promoting gene flow between geographically distant regions) and upwelling areas (limiting gene flow between certain regions).

Global phylogeography of toxic cyanobacteria Moorea producens reveals distinct genetic partitioning influenced by Proterozoic glacial cycles

Lyngbya majuscula is a marine filamentous cyanobacteria belonging to the family Oscillatoriaceae. Recent phylogenetic analyses of L. majuscula have reclassified a subset of this species into various genera such as Moorea, Okeania and Dapis. From the genus Moorea, Moorea producens is a toxic invasive cyanobacterium that produces bioactive secondary metabolites that can cause severe inflammation and blistering. Despite the global distribution of M. producens, little information is available on their origin, patterns of dispersal and population structure. In this study, the spatial population structure of M. producens was investigated using near-complete 16S rRNA sequences. Analysis of the global population of M. producens by Isolation by Distance and STRUCTURE revealed two significantly distinct cosmopolitan populations that were separated by a genetic break. Lineage-specific divergence estimates of 147 cyanobacterial taxa, based on a relaxed molecular clock indicated the first global emergence of M. producens during the Mesoarchean and a subsequent global recolonization during the Mesoproterozoic period. We conclude that the genetic discontinuity between both cosmopolitan populations is attributed to refugia associated with Proterozoic glacial cycles.

Historical translocations by Māori may explain the distribution and genetic structure of a threatened surf clam in Aotearoa (New Zealand)

The population genetic structure of toheroa (Paphies ventricosa), an Aotearoa (New Zealand) endemic surf clam, was assessed to determine levels of inter-population connectivity and test hypotheses regarding life history, habitat distribution and connectivity in coastal vs. estuarine taxa. Ninety-eight toheroa from populations across the length of New Zealand were sequenced for the mitochondrial cytochrome c oxidase I gene with analyses suggesting a population genetic structure unique among New Zealand marine invertebrates. Toheroa genetic diversity was high in Te Ika-a Māui (the North Island of New Zealand) but completely lacking in the south of Te Waipounamu (the South Island), an indication of recent isolation. Changes in habitat availability, long distance dispersal events or translocation of toheroa to southern New Zealand by Māori could explain the observed geographic distribution of toheroa and their genetic diversity. Given that early-Māori and their ancestors, were adept at food cultivation and relocation, the toheroa translocation hypothesis is plausible and may explain the disjointed modern distribution of this species. Translocation would also explain the limited success in restoring what may in some cases be ecologically isolated populations located outside their natural distributions and preferred niches.

Contrasting gene flow at different spatial scales revealed by genotyping-by-sequencing in Isocladus armatus, a massively colour polymorphic New Zealand marine isopod

Understanding how genetic diversity is maintained within populations is central to evolutionary biology. Research on colour polymorphism (CP), which typically has a genetic basis, can shed light on this issue. However, because gene flow can homogenise genetic variation, understanding population connectivity is critical in examining the maintenance of polymorphisms. In this study we assess the utility of genotyping-by-sequencing to resolve gene flow, and provide a preliminary investigation into the genetic basis of CP in Isocladus armatus, an endemic New Zealand marine isopod. Analysis of the genetic variation in 4,000 single nucleotide polymorphisms (SNPs) within and among populations and colour morphs revealed large differences in gene flow across two spatial scales. Marine isopods, which lack a pelagic larval phase, are typically assumed to exhibit greater population structuring than marine invertebrates possessing a biphasic life cycle. However, we found high gene flow rates and no genetic subdivision between two North Island populations situated 8 km apart. This suggests that I. armatus is capable of substantial dispersal along coastlines. In contrast, we identified a strong genetic disjunction between North and South Island populations. This result is similar to those reported in other New Zealand marine species, and is congruent with the presence of a geophysical barrier to dispersal down the east coast of New Zealand. We also found some support for a genetic basis to colouration evidenced by positive FST outlier tests, with two SNPs in particular showing strong association to the expression of a striped morph. Our study provides one of the first population genomic studies of a marine organism in New Zealand, and suggests that genotyping-by-sequencing can be a good alternative to more traditional investigations based on traditional markers such as microsatellites. Our study provides a foundation for further development of a highly tractable system for research on the evolutionary maintenance of CP.

Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand

Pleurobranchaea maculata is a rarely studied species of the Heterobranchia found throughout the south and western Pacific-and recently recorded in Argentina-whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history of P. maculata populations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and the COI and CytB regions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence sea slugs from Argentina did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.

Genetics, Gene Flow, and Glaciation: The Case of the South American Limpet Nacella mytilina

Glacial episodes of the Quaternary, and particularly the Last Glacial Maximum (LGM) drastically altered the distribution of the Southern-Hemisphere biota, principally at higher latitudes. The irregular coastline of Patagonia expanding for more than 84.000 km constitutes a remarkable area to evaluate the effect of Quaternary landscape and seascape shifts over the demography of near-shore marine benthic organisms. Few studies describing the biogeographic responses of marine species to the LGM have been conducted in Patagonia, but existing data from coastal marine species have demonstrated marked genetic signatures of post-LGM recolonization and expansion. The kelp-dweller limpet Nacella mytilina is broadly distributed along the southern tip of South America and at the Falkland/Malvinas Islands. Considering its distribution, abundance, and narrow bathymetry, N. mytilina represents an appropriate model to infer how historical and contemporary processes affected the distribution of intraspecific genetic diversity and structure along the southern tip of South America. At the same time, it will be possible to determine how life history traits and the ecology of the species are responsible for the current pattern of gene flow and connectivity across the study area. We conducted phylogeographic and demographic inference analyses in N. mytilina from 12 localities along Pacific Patagonia (PP) and one population from the Falkland/Malvinas Islands (FI). Analyses of the mitochondrial gene COI in 300 individuals of N. mytilina revealed low levels of genetic polymorphism and the absence of genetic differentiation along PP. In contrast, FI showed a strong and significant differentiation from Pacific Patagonian populations. Higher levels of genetic diversity were also recorded in the FI population, together with a more expanded genealogy supporting the hypothesis of glacial persistence of the species in these islands. Haplotype genealogy, and mismatch analyses in the FI population recognized an older and more complex demographic history than in PP. Demographic reconstructions along PP suggest a post-LGM expansion process (7.5 ka), also supported by neutrality tests, mismatch distribution and maximum parsimony haplotype genealogies. Migration rate estimations showed evidence of asymmetrical gene flow from PP to FI. The absence of genetic differentiation, the presence of a single dominant haplotype, high estimated migration rates, and marked signal of recent demographic growth, support the hypothesis of rapid post-glacial expansion in N. mytilina along PP. This expansion could have been sustained by larval and rafting-mediated dispersal of adults from northernmost populations following the Cape Horn Current System. Marked genetic differentiation between PP and FI could be explained through differences in their respective glacial histories. During the LGM, Pacific Patagonia (PP) was almost fully covered by the Patagonian Ice Sheet, while sheet coverage in the FI ice was restricted to small cirques and valleys. As previously recorded in the sister-species N. magellanica, the FI rather than represent a classical glacial refugium for N. mytilina, seems to represent a sink area and/or a secondary contact zone. Accordingly, historical and contemporary processes, contrasting glacial histories between the analyzed sectors, as well as life history traits constitute the main factors explaining the current biogeographical patterns of most shallow Patagonian marine benthic organisms.

Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae

Both historical and contemporary processes influence the genetic structure of species, but the relative roles of such processes are still difficult to access. Population genetic studies of species with recent evolutionary histories such as the New Zealand endemic scallop Pecten novaezelandiae (<1 Ma) permit testing of the effects of recent processes affecting gene flow and shaping genetic structure. In addition, studies encompassing the entire distributional range of species can provide insight into colonization processes. Analyses of genetic variation in P. novaezelandiae (952 individuals from 14 locations, genotyped at 10 microsatellite loci) revealed a weak but significant regional structure across the distributional range of the species, as well as latitudinal gradients of genetic diversity and differentiation: estimates of migration rates supported these patterns. Our results suggest that the observed genetic structure and latitudinal gradients reflect a stepping-stone model of colonization (north to south) and emerging divergence of populations as a result of ongoing limitations to gene flow and insufficient time to reach migration-drift equilibrium. The low levels of interpopulation and interregional genetic differentiation detected over hundreds of kilometres reflect the recent evolutionary history of P. novaezelandiae and stand in contrast to patterns reported for other evolutionary older species at the same spatial scale. The outcomes of this study contribute to a better understanding of evolutionary processes influencing the genetic variation of species and provide vital information on the genetic structure of P. novaezelandiae.

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees

BACKGROUND

There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously.

RESULTS

Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes.

CONCLUSIONS

Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

Phylogeography in Galaxias maculatus (Jenyns, 1848) along Two Biogeographical Provinces in the Chilean Coast

Major geologic and climatic changes during the Quaternary exerted a major role in shaping past and contemporary distribution of genetic diversity and structure of aquatic organisms in southern South America. In fact, the northern glacial limit along the Pacific coast, an area of major environmental changes in terms of topography, currents, and water salinity, represents a major biogeographic transition for marine and freshwater species. We used mitochondrial DNA sequences (D-loop) to investigate the consequences of Quaternary glacial cycles over the pattern of genetic diversity and structure of G. maculatus (Pisces: Galaxiidae) along two biogeographical provinces in the Chilean coast. Extreme levels of genetic diversity and strong phylogeographic structure characterize the species suggesting a low amount of influence of the last glacial cycle over its demography. However, we recognized contrasting patterns of genetic diversity and structure between main biogeographical areas here analyzed. Along the Intermediate Area (38°-41° S) each estuarine population constitutes a different unit. In contrast, Magellanic populations (43°-53° S) exhibited low levels of genetic differentiation. Contrasting patterns of genetic diversity and structure recorded in the species between the analyzed biogeographic areas are consistent with the marked differences in abiotic factors (i.e., different coastal configurations, Quaternary glacial histories, and oceanographic regimes) and to inherent characteristics of the species (i.e., salt-tolerance, physiology, and reproductive behavior).

Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae, Rhodophyta) from New Zealand

Spatial patterns of genetic diversity provide insight into the demography and history of species. Morphologically similar but genetically distinct "cryptic" species are increasingly being recognized in marine organisms through molecular analyses. Such species are, on closer inspection, often discovered to display contrasting life histories or occasionally minor morphological differences; molecular tools can thus be useful indicators of diversity. Bostrychia intricata, a marine red alga, is widely distributed throughout the Southern Hemisphere and comprises many cryptic species. We used mitochondrial cytochrome c oxidase I gene sequences to assess the genetic variation, population genetic structure, and demographic history of B. intricata in New Zealand. Our results supported the existence of three cryptic species of B. intricata (N2, N4, and N5) in New Zealand. Cryptic species N4, which was found throughout New Zealand, showed a higher genetic diversity and wider distribution than the other two species, which were only found in the North Island and northern South Island. Our analyses showed low to moderate genetic differentiation among eastern North Island populations for cryptic species N2, but high differentiation among North and South Island populations for N4, suggesting different population structure between these cryptic species. Data also indicated that N2 has recently undergone population expansion, probably since the Last Glacial Maximum (LGM), while the higher genetic diversity in N4 populations suggests persistence in situ through the LGM. The contrasting population structures and inferred demographic histories of these species highlight that life history can vary greatly even among morphologically indistinguishable taxa.

The genetic architecture of hybridisation between two lineages of greenshell mussels

A multidisciplinary approach has identified sigmoidal genetic clines on the east and west coasts in central New Zealand where low-density ecological interactions occur between northern and southern lineages of the endemic greenshell mussel, Perna canaliculus. The sigmoidal clines indicate the existence of a mussel hybrid zone in a region of genetic discontinuities for many continuously distributed coastal taxa, in particular marine invertebrates. Examination of the genetic architecture of the hybrid zone revealed the differential contribution of individual microsatellite loci and/or alleles to defining the zone of interaction and no evidence of increased allelic richness or heterozygosity inside versus outside the hybrid zone. Genomics cline analysis identified one locus in particular (Pcan1-27) as being different from neutral expectations, thereby contributing to lineage differentiation. Estimates of contemporary gene flow revealed very high levels of within-lineage self-recruitment and a hybrid zone composed mostly (~85%) of northern immigrants. Broad scale interpretation of these results is consistent with a zone of genetic interaction that was generated between 0.3 and 1.3 million years before present at a time of pronounced global sea-level change. At that time, the continuous distribution of the greenshell mussel was split into northern and southern groups, which differentiated to become distinct lineages, and which have subsequently been reunited (secondary contact) resulting in the generation of the hybrid zone at ~42°S.

Phylogeographic structure in benthic marine invertebrates of the southeast Pacific coast of Chile with differing dispersal potential

The role of dispersal potential on phylogeographic structure, evidenced by the degree of genetic structure and the presence of coincident genetic and biogeographic breaks, was evaluated in a macrogeographic comparative approach along the north-central coast of Chile, across the biogeographic transition zone at 30°S. Using 2,217 partial sequences of the mitochondrial Cytochrome Oxidase I gene of eight benthic invertebrate species along ca. 2,600 km of coast, we contrasted dispersal potential with genetic structure and determined the concordance between genetic divergence between biogeographic regions and the biogeographic transition zone at 30°S. Genetic diversity and differentiation highly differed between species with high and low dispersal potential. Dispersal potential, sometimes together with biogeographic region, was the factor that best explained the genetic structure of the eight species. The three low dispersal species, and one species assigned to the high dispersal category, had a phylogeographic discontinuity coincident with the biogeographic transition zone at 30°S. Furthermore, coalescent analyses based on the isolation-with-migration model validate that the split between biogeographic regions north and south of 30°S has a historic origin. The signatures of the historic break in high dispersers is parsimoniously explained by the homogenizing effects of gene flow that have erased the genetic signatures, if ever existed, in high dispersers. Of the four species with structure across the break, only two had significant albeit very low levels of asymmetric migration across the transition zone. Historic processes have led to the current biogeographic and phylogeographic structure of marine species with limited dispersal along the north-central coast of Chile, with a strong lasting impact in their genetic structure.

DECOUPLING OF SHORT- AND LONG-DISTANCE DISPERSAL PATHWAYS IN THE ENDEMIC NEW ZEALAND SEAWEED CARPOPHYLLUM MASCHALOCARPUM (PHAEOPHYCEAE, FUCALES)(1)

The processes that produce and maintain genetic structure in organisms operate at different timescales and on different life-history stages. In marine macroalgae, gene flow occurs through gamete/zygote dispersal and rafting by adult thalli. Population genetic patterns arise from this contemporary gene flow interacting with historical processes. We analyzed spatial patterns of mitochondrial DNA variation to investigate contemporary and historical dispersal patterns in the New Zealand endemic fucalean brown alga Carpophyllum maschalocarpum (Turner) Grev. Populations bounded by habitat discontinuities were often strongly differentiated from adjoining populations over scales of tens of kilometers and intrapopulation diversity was generally low, except for one region of northeast New Zealand (the Bay of Plenty). There was evidence of strong connectivity between the northern and eastern regions of New Zealand's North Island and between the North and South Islands of New Zealand and the Chatham Islands (separated by 650 km of open ocean). Moderate haplotypic diversity was found in Chatham Islands populations, while other southern populations showed low diversity consistent with Last Glacial Maximum (LGM) retreat and subsequent recolonization. We suggest that ocean current patterns and prevailing westerly winds facilitate long-distance dispersal by floating adult thalli, decoupling genetic differentiation of Chatham Island populations from dispersal potential at the gamete/zygote stage. This study highlights the importance of encompassing the entire range of a species when inferring dispersal patterns from genetic differentiation, as realized dispersal distances can be contingent on local or regional oceanographic and historical processes.

The impact of Yangtze River discharge, ocean currents and historical events on the biogeographic pattern of Cellana toreuma along the China coast

AIM

Genetic data were used to measure the phylogeographic distribution of the limpet, Cellana toreuma along the China coast in order to acsertain impacts of historic events, ocean currents and especially freshwater discharge from the Yangtze River on the connectivity of intertidal species with limited larval dispersal capability.

METHODOLOGY/PRINCIPAL FINDINGS

Genetic variation in 15 populations of C. toreuma (n = 418), ranging from the Yellow Sea (YS), East China Sea (ECS) and South China Sea (SCS), were determined from partial mitochondrial cytochrome c oxidase subunit I gene. Genetic diversity and divergence based on haplotype frequencies were analyzed using CONTRIB, and AMOVA was used to examine genetic population structure. Historic demographic expansions were evaluated from both neutrality tests and mismatch distribution tests. Among the 30 haplotypes identified, a dominant haplotype No. 1 (H1) existed in all the populations, and a relatively abundant private haplotype (H2) in YS. Pairwise F(ST) values between YS and the other two groups were relatively high and the percentage of variation among groups was 10.9%.

CONCLUSIONS

The high nucleotide and gene diversity in the YS, with large pairwise genetic distances and relatively high percentages of variation among groups, suggests that this group was relatively isolated from ECS and SCS. This is likely driven by historic events, ocean currents, and demographic expansion. We propose that freshwater discharge from the Yangtze River, which may act as physical barrier limiting the southward dispersal of larvae from northern populations, is especially important in determining the separation of the YS group from the rest of the Chinese populations of C. toreuma.

Parallel phylogeographic structure in ecologically similar sympatric sister taxa

Present-day phylogeographic patterns have been shaped by the dual histories of lineages and places, producing a diversity of relationships that may challenge discovery of general rules. For example, the predicted positive correlation between dispersal ability and gene flow has been supported inconsistently, suggesting unaccounted complexity in theory or the comparative framework. Here, I extend the sympatric sister-species approach, in which variance between lineages and places is minimized, to sister clades and test a fundamental assumption of comparative genetic studies of dispersal: that taxa which evolved at the same time and in the same place will, if they have similar life histories and ecologies, have essentially the same phylogeographic structure. Phylogenetic analyses of 197 Stigmatopora pipefishes using two nuclear (creatine kinase intron 6, α-tropomyosin) and two mitochondrial (16S, noncoding region) loci revealed largely synchronous parallel diversification of sister clades that are codistributed from Western Australia to New Zealand, supporting the null hypothesis. Only one comparison, however, yielded a sympatric sister-species pair (the two stem species), so I also explored the potential for extant species sharing a substantial proportion of their evolutionary histories in sympatry to substitute for sister taxon comparisons. In eastern Australia, where strong environmental structure is lacking, phylogeographic differences between species that have been codistributed for ~85% of their evolutionary histories were consistent with tendencies favoured by their modest life-history differences, that is the larger, rarer species had lower genetic diversity. In contrast, in New Zealand, two species codistributed for ~70% of their evolutionary histories were both structured similarly by a strong biogeographic filter despite differences in life history. Rigorously quantifying the influence of intrinsic and extrinsic factors on phylogeographic structure may advance most efficiently through meta-analyses of contemporaneously codistributed taxa, including but not limited to sympatric sister species.

Identification of genes directly involved in shell formation and their functions in pearl oyster, Pinctada fucata

Mollusk shell formation is a fascinating aspect of biomineralization research. Shell matrix proteins play crucial roles in the control of calcium carbonate crystallization during shell formation in the pearl oyster, Pinctada fucata. Characterization of biomineralization-related genes during larval development could enhance our understanding of shell formation. Genes involved in shell biomineralization were isolated by constructing three suppression subtractive hybridization (SSH) libraries that represented genes expressed at key points during larval shell formation. A total of 2,923 ESTs from these libraries were sequenced and gave 990 unigenes. Unigenes coding for secreted proteins and proteins with tandem-arranged repeat units were screened in the three SSH libraries. A set of sequences coding for genes involved in shell formation was obtained. RT-PCR and in situ hybridization assays were carried out on five genes to investigate their spatial expression in several tissues, especially the mantle tissue. They all showed a different expression pattern from known biomineralization-related genes. Inhibition of the five genes by RNA interference resulted in different defects of the nacreous layer, indicating that they all were involved in aragonite crystallization. Intriguingly, one gene (UD_Cluster94.seq.Singlet1) was restricted to the ‘aragonitic line’. The current data has yielded for the first time, to our knowledge, a suite of biomineralization-related genes active during the developmental stages of P.fucata, five of which were responsible for nacreous layer formation. This provides a useful starting point for isolating new genes involved in shell formation. The effects of genes on the formation of the ‘aragonitic line’, and other areas of the nacreous layer, suggests a different control mechanism for aragonite crystallization initiation from that of mature aragonite growth.

Multigene phylogeny of the southern bull-kelp genus Durvillaea (Phaeophyceae: Fucales)

Durvillaea (southern bull-kelp) is an economically and ecologically important brown algal genus that dominates many exposed, rocky coasts in the cold-temperate Southern Hemisphere. Of its five currently-recognized species, four are non-buoyant and restricted to the south-western Pacific, whereas one is both buoyant and widely distributed. Durvillaea has had an unsettled taxonomic history. Although its position within the brown algae (Phaeophyceae) has now been largely resolved through the use of molecular techniques, the taxonomic status of several Durvillaea species/morphotypes remains unresolved. Previous molecular phylogenetic studies of phaeophycean taxa have included few Durvillaea samples, and have consequently paid little or no attention to variation within this genus. The current study presents phylogenetic analyses of four genetic markers (mitchondrial: COI; chloroplast: rbcL; and nuclear: 18S and 28S) to resolve phylogenetic relationships within Durvillaea. Results support the monophyly of solid-bladed taxa D. willana, D. potatorum, and D. sp. A (an undescribed species from the Antipodes Islands), whereas the widespread, buoyant D. antarctica is paraphyletic, with solid-bladed D.chathamensis placed sister to a D. antarctica clade from northern NZ but within D. antarctica sensu lato. The phylogenetic and ecological diversity detected within D. antarctica indicate that it is a species complex of five deeply divergent clades. Under a phylogenetic species concept, Durvillaea can be interpreted as a complex of nine distinct evolutionary lineages, only one of which has an intercontinental distribution ('subantarctic'D. antarctica).

Asymmetric dispersal of southern bull-kelp (Durvillaea antarctica) adults in coastal New Zealand: testing an oceanographic hypothesis

Coastal populations are often connected by unidirectional current systems, but the biological effects of such asymmetric oceanographic connectivity remain relatively unstudied. We used mtDNA analysis to determine the phylogeographic origins of beach-cast bull-kelp (Durvillaea antarctica) adults in the Canterbury Bight, a 180 km coastal region devoid of rocky-reef habitat in southern New Zealand. A multi-year, quantitative analysis supports the oceanographically derived hypothesis of asymmetric dispersal mediated by the north-flowing Southland Current. Specifically, 92% of beach-cast specimens examined had originated south of the Bight, many drifting north for hundreds of kilometres, and some traversing at least 500 km of ocean from subantarctic sources. In contrast, only 8% of specimens had dispersed south against the prevailing current, and these counter-current dispersers likely travelled relatively small distances (tens of kilometres). These data show that oceanographic connectivity models can provide robust estimates of passive biological dispersal, even for highly buoyant taxa. The results also indicate that there are no oceanographic barriers to kelp dispersal across the Canterbury Bight, indicating that other ecological factors explain the phylogeographic disjunction across this kelp-free zone. The large number of long-distance dispersal events detected suggests drifting macroalgae have potential to facilitate ongoing connectivity between otherwise isolated benthic populations.

Advances in biosecurity to 2010 and beyond: towards integrated detection, analysis and response to exotic pest invasions

In order to limit the number and impact of exotic pest invasions, leading-edge technologies must be embraced and embedded within integrated national and international biosecurity systems. Outlined here are recent advances in the detection of exotic pests, and prospects for the early recognition of disease. Applications of new tools are described, using our understanding of the genomes of pathogens and vectors. In addition, the role of mathematical and simulation models to aid both biosecurity planning, and decision making in the face of an epidemic, are discussed, and recent attempts to unify epidemiology and evolutionary dynamics are outlined. Given the importance of emerging diseases and zoonoses, the need to align human and veterinary surveillance within fully integrated systems is underlined.

Contrasting phylogeography in three endemic Hawaiian limpets (Cellana spp.) with similar life histories

The marine environment offers few obvious barriers to dispersal for broadcast-spawning species, yet population genetic structure can occur on a scale much smaller than the theoretical limits of larval dispersal. Comparative phylogeographical studies of sympatric sister species can illuminate how differences in life history, behaviour, and habitat affinity influence population partitioning. Here we use a mitochondrial DNA marker (612 bp of cytochrome c oxidase subunit I) to investigate population structure of three endemic Hawaiian broadcast-spawning limpets (Cellana spp.) with planktonic larvae that are competent to settle within 4 days. All three species exhibit significant population structure and isolation by distance, but the spatial scales of partitioning differ among the species. Cellana talcosa (n = 105) exhibits strong population structure between Kauai and the other main Hawaiian Islands (MHI) where the maximum channel width is 117 km, and no shared haplotypes were observed (Phi(CT) = 0.30, P < 0.001). In contrast, populations of Cellana exarata (n = 149) and Cellana sandwicensis (n = 109) exhibit weaker population structure within the MHI (Phi(ST) = 0.03-0.04, P < 0.05), and between the MHI and the Northwestern Hawaiian Islands (Phi(ST) = 0.03-0.09, P < 0.01), where the maximum channel width is 260 km. Biogeographical range and microhabitat use were correlated with estimates of dispersal, while phylogenetic affiliation and minimum pelagic larval duration were poor predictors of population partitioning. Despite similar life histories, these closely related limpets have contrasting patterns of population structure, illustrating the danger of relying on model species in management initiatives to predict population structure and dispersal in the context of marine protected area delineation.