Population genetics of the spotted seahorse (Hippocampus kuda) in Thai waters : implications for conservation

A population genetics approach was used to investigate the genetic diversity of the spotted seahorse (Hippocampus kuda) in Thai waters; specifically, the degree of genetic differentiation and species evolution was inferred from sequence analysis of 353 bp of the mitochondrial (mt)DNA control region. The data were then used to identify discrete populations in Thai waters for effective conservation and management. Spotted seahorses were collected from 4 regions on the east and west coasts of the Gulf of Thailand and a geographically separated region in the Andaman Sea. Of the 101 mtDNA sequences analyzed, 7 haplotypes were identified, 5 of which were shared among individuals from the east and west coasts of the Gulf of Thailand. The remaining haplotypes were restricted to individuals from the Andaman Sea. Nucleotide and haplotype diversities were similar within the Gulf of Thailand samples, whereas diversity was lower in the Andaman Sea sample. Genetic differentiation appeared between pairs of samples from the Gulf of Thailand and Andaman Sea (FST, p < 0.0001). A large genetic variance appeared among the 2 population groups (94.46%, ΦCT = 0.94464, p < 0.01). A Neighbor-joining tree indicated that individuals from the Gulf of Thailand and Andaman Sea formed 2 phylogenetically distinct groups, which were segregated into different population-based clades. While results reported here indicate that populations from the Gulf of Thailand and Andaman Sea should be treated as separate conservation units, a larger sample size from the Andaman Sea is required to confirm this genetic partitioning and low level of diversity observed in the present study.

Mitochondrial DNA offers unique insights into invasion history of the common starling

Mitochondrial DNA (mtDNA) can be a powerful genetic marker for tracing origins and history of invasive populations. Here, we use mtDNA to address questions relevant to the understanding of invasion pathways of common starlings (Sturnus vulgaris) into Western Australia (WA) and discuss the utility of this marker to provide information useful to invasive species management. Mitochondrial sequence data indicate two geographically restricted genetic groups within Australia. Evidence of dispersal from genetically distinct sources outside the sampled range of starlings in Australia suggests increased vigilance by management agencies may be required to prevent further incursions from widely separated localities. Overall, genetic diversity in Australia was lower than in samples from the native range. Within Australia, genetic diversity was lowest in the most recently colonized area in the west, indicating that demographic bottlenecks have occurred in this area. Evidence of restricted dispersal between localities on the edge of the range expansion (ERE) in WA and other Australian sampling localities suggests that localized control within the ERE may be effective in preventing further range expansion. Signatures of spatial and demographic expansion are present in mismatch analyses from sampling localities located at the ERE, but neutrality indices did not support this finding, suggesting that the former may be more sensitive to recent expansion. Additionally, mismatch analyses support the presence of admixture, which is likely to have occurred pre-introduction. We compare our findings with those from a microsatellite study of the same samples and discuss how the mtDNA analyses used here offer valuable and unique insights into the invasion history of introduced species.

Contrasting patterns of population connectivity between regions in a commercially important mollusc Haliotis rubra: integrating population genetics, genomics and marine LiDAR data

Estimating contemporary genetic structure and population connectivity in marine species is challenging, often compromised by genetic markers that lack adequate sensitivity, and unstructured sampling regimes. We show how these limitations can be overcome via the integration of modern genotyping methods and sampling designs guided by LIDAR and SONAR datasets. Here we explore patterns of gene flow and local genetic structure in a commercially harvested abalone species (Haliotis rubra) from South Eastern Australia, where the viability of fishing stocks is believed to be dictated by recruitment from local sources. Using a panel of microsatellite and genome-wide SNP markers we compare allele frequencies across a replicated hierarchical sampling area guided by bathymetric LIDAR imagery. Results indicate high levels of gene flow and no significant genetic structure within or between benthic reef habitats across 1400 km of coastline. These findings differ to those reported for other regions of the fishery indicating that larval supply is likely to be spatially variable, with implications for management and long-term recovery from stock depletion. The study highlights the utility of suitably designed genetic markers and spatially informed sampling strategies for gaining insights into recruitment patterns in benthic marine species, assisting in conservation planning and sustainable management of fisheries.

Population-level perspectives on global change : genetic and demographic analyses indicate various scales, timing, and causes of scyphozoan jellyfish blooms

Whether a perceived increase in the abundance of jellyfishes is related to changing marine environments has been considered primarily using large-scale analyses of multi-species assemblages. Yet jellyfish blooms-rapid increases in the biomass of pelagic coelenterate species-are single-species demographic events. Using published and new genetic analyses and population surveys, we investigate whether there may be a critical knowledge gap between the scales of recent analyses and the scales of natural phenomena. We find that scyphomedusae may show population genetic structure over scales of tens to hundreds of kilometers, that environments vary regionally and locally, and that populations of medusae can display uncorrelated dynamics on these scales. These findings suggest genetic differences between populations and/or environmental differences between sites are important determinants of population dynamics in these jellyfishes. Moreover, the local abundance of medusae may be most strongly correlated with preceding rather than current local environmental conditions, indicating there is a cumulative time-course to the formation of 'blooms'. Broad-scale macro-ecological analyses will need to build from coordinated, long-term, fine-grained studies to synthesize, rather than mask, population-level phenomena in larger-scale analyses. © 2014 Springer International Publishing Switzerland.

Genetic analysis along an invasion pathway reveals endemic cryptic taxa, but a single species with little population structure in the introduced range

The invasion pathways of pest arthropods can be traced using genetic tools to develop an understanding of the processes that have shaped successful invasions and to inform both pest management and conservation strategies in their non-native and native ranges, respectively. The redlegged earth mite, Halotydeus destructor, is a major economic pest in Australia, successfully establishing and spreading after arrival from South Africa more than 100 years ago. Halotydeus destructor has recently expanded its range and evolved resistance to numerous pesticides in Australia, raising questions around its origin and spread. Location: South Africa and Australia. Methods: We sampled H. destructor populations in South Africa and Australia and developed a microsatellite marker library. We then examined genetic variation using mtDNA and microsatellite markers across both native and invasive ranges to determine endemic genetic diversity within South Africa, identify the likely origin of invasive populations and test genetic divergence across Australia. Results: The data show that H. destructor comprises a cryptic species complex in South Africa, with putative climatic/host plant associations that may correspond to regional variation. A lineage similar to that found near Cape Town has spread throughout Western and eastern Australia, where populations remain genetically similar. Main conclusions: Tracing the invasion pathway of this economically important pest revealed cryptic lineages in South Africa which points to the need for a taxonomic revision. The absence of significant genetic structure across the wide invasive range of H. destructor within Australia has implications for the development (and spread) of pesticide resistance and also points to recent local adaptation in physiological traits.

Multiple dispersal vectors drive range expansion in an invasive marine species

The establishment and subsequent spread of invasive species is widely recognised as one of the most threatening processes contributing to global biodiversity loss. This is especially true for marine and estuarine ecosystems, which have experienced significant increases in the number of invasive species with the increase in global maritime trade. Understanding the rate and mechanisms of range expansion is therefore of significant interest to ecologists and conservation managers alike. Using a combination of population genetic surveys, eDNA plankton sampling and hydrodynamic modelling we examined the patterns of introduction of the predatory Northern Pacific seastar (Asterias amurensis) and pathways of secondary spread within southeast Australia. Genetic surveys across the invasive range reveal some genetic divergence between the two main invasive regions and no evidence of ongoing gene flow; a pattern that is consistent with the establishment of the second invasive region via a human-mediated translocation event. In contrast hydrodynamic modelling combined with eDNA plankton sampling demonstrated that the establishment of range expansion populations within a region is consistent with natural larval dispersal and recruitment. Our results suggest that both anthropogenic and natural dispersal vectors have played an important role in the range expansion of this species in Australia. The multiple modes of spread combined with high levels of fecundity and a long larval duration in A. amurensis suggests it is likely to continue its range expansion and significantly impact Australian marine ecosystems.

Development of novel microsatellite markers for the invasive Northern Pacific seastar, Asterias amurensis

The Northern Pacific seastar, Asterias amurensis, is a benthic marine predator, which has recently established several invasive populations in Australian waters. To investigate population structure, diversity and patterns of connectivity, we isolated and characterised 27 microsatellite loci and tested their polymorphism based on 46 individuals from two invasive populations. The mean allelic richness was 4.33; observed heterozygosity was 0.42, while the percentage of polymorphic loci was 92.6%. The polymorphic markers will prove useful in the assessment of population genetic parameters, in both invasive and native A. amurensis populations.

Ocean currents influence the genetic structure of an intertidal mollusc in southeastern Australia – implications for predicting the movement of passive dispersers across a marine biogeographic barrier

Major disjunctions among marine communities in southeastern Australia have been well documented, although explanations for biogeographic structuring remain uncertain. Converging ocean currents, environmental gradients, and habitat discontinuities have been hypothesized as likely drivers of structuring in many species, although the extent to which species are affected appears largely dependent on specific life histories and ecologies. Understanding these relationships is critical to the management of native and invasive species, and the preservation of evolutionary processes that shape biodiversity in this region. In this study we test the direct influence of ocean currents on the genetic structure of a passive disperser across a major biogeographic barrier. Donax deltoides (Veneroida: Donacidae) is an intertidal, soft-sediment mollusc and an ideal surrogate for testing this relationship, given its lack of habitat constraints in this region, and its immense dispersal potential driven by year-long spawning and long-lived planktonic larvae. We assessed allele frequencies at 10 polymorphic microsatellite loci across 11 sample locations spanning the barrier region and identified genetic structure consistent with the major ocean currents of southeastern Australia. Analysis of mitochondrial DNA sequence data indicated no evidence of genetic structuring, but signatures of a species range expansion corresponding with historical inundations of the Bassian Isthmus. Our results indicate that ocean currents are likely to be the most influential factor affecting the genetic structure of D. deltoides and a likely physical barrier for passive dispersing marine fauna generally in southeastern Australia.

Population genetic structure of the Australian caddisfly Lectrides varians Mosely (Trichoptera: Leptoceridae) and the identification of cryptic species in south-eastern Australia

Lectrides varians (Mosely) is a large, ecologically-important, caddisfly found in perennial and intermittent streams throughout much of eastern Australia. We conducted a population genetic analysis to investigate the dispersal potential of L. varians, building on previous works that have assessed life-history traits associated with drought resistance. Genetic analyses of L. varians from the Grampians region of Victoria, based on mitochondrial DNA sequence data, revealed extensive gene flow and a lack of genetic structure across the sample range (ΦST = 0.04). This suggests that the species is a strong disperser and is likely to be resilient to increased drying and habitat fragmentation under climate change considering other known resistance traits. However, during this study, two divergent genotypes were identified, indicating a potential species complex. A comprehensive phylogenetic analysis of L. varians across its current range was subsequently performed, confirming the species is indeed paraphyletic, consisting of one lineage that is restricted to the Grampians National Park and the other being widespread throughout south-eastern Australia. Further analyses revealed consistent morphological differences between these lineages supporting the notion that L. varians is a species complex. We discuss the implications of these findings with regard to conservation and taxonomy of this important invertebrate group.

Geographical variation and population structure in the White-rumped Sandpiper Calidris fuscicollis as shown by morphology, mitochondrial DNA and carbon isotope ratios

We studied the population structure of a high arctic breeding wader bird species, the White-rumped Sandpiper Calidris fuscicollis. Breeding adults, chicks and juveniles were sampled at seven localities throughout the species' breeding range in arctic Canada in 1999. The mitochondrial control region was analysed by DNA sequencing, feathers were analysed for carbon isotope ratios (C13/C12) by isotope ratio mass spectrometry, and morphological measurements were analysed using principal component analyses, taking the effect of sex into account (identified by molecular genetic methods). In general, our results support the notion that the White-rumped Sandpiper is a monotypic species with no subspecies, and most of the morphological and genetic variation occurs within sites. Nevertheless, some differences between sites were found. Birds from the two northernmost sites (Ellesmere and Devon Islands) had relatively longer bill and wing and shorter tarsus than birds sampled further south, possibly reflecting genetic differences between populations. The carbon isotope ratios were higher at the easternmost site (Baffin Island), revealing differences in the isotope content of the food. The mtDNA sequences showed no significant differentiation between sites and no pattern of isolation-by-distance was found. Based on the mtDNA variation, the species was estimated to have a long-term effective population size of approximately 9,000 females. The species shows no clear evidence of any population expansion or decline. Our results indicate that carbon isotope ratios, and possibly also certain mtDNA haplotypes, may be useful as tools for identifying the breeding origin of White-rumped Sandpipers on migration and wintering sites.

Population genetic studies on Australian freshwater crayfish, Cherax destructor (Crustacea: Parastacidae) using allozyme and RAPD markers

Allozyme and Random Amplified Polymorphic DNA (RAPD) variation was surveyed in the freshwater crayfish Cherax destructor Clark, an ecologically and commercially important species that is widespread throughout the freshwater systems of central Australia. At the intra-population level, allozymes revealed a similar level of variation to that found in other freshwater crayfish; RAPDs showed less diversity than allozymes, which was unexpected. At the inter-population level, both techniques revealed significant population structure, both within and between drainages. RAPD results were consistent with phylogeographic patterns previously identified using mtDNA. Although allozyme data showed little geographic pattern in relation to genetic variation based on multidimensional-scaling (MDS) plots on matrices of genetic distance, results of AMOVA and Mantel tests indicated significant population structuring. Each of the mtDNA lineages proposed in a previous study also showed significant genetic structure at similar levels as revealed by RAPDs but different levels by allozymes. These results reject hypotheses previously put forward on genetic homogenisation within the species due to wide-scale translocation. The implications of the findings for conservation and aquaculture of C. destructor are also discussed.

Manual on application of molecular tools in aquaculture and inland fisheries management. Part I : conceptual basis of population genetic approaches

The aim of this manual is to provide a comprehensive practical tool for the generation and analysis of genetic data for subsequent application in aquatic resources management in relation to genetic stock identification in inland fisheries and aquaculture. The material only covers general background on genetics in relation to aquaculture and fisheries resource management, the techniques and relevant methods of data analysis that are commonly used to address questions relating to genetic resource characterisation and population genetic analyses. No attempt is made to include applications of genetic improvement techniques e.g. selective breeding or producing genetically modified organisms (GMOs). The manual includes two ‘stand-alone’ parts, of which this is the first volume: Part 1 – Conceptual basis of population genetic approaches: will provide a basic foundation on genetics in general, and concepts of population genetics. Issues on the choices of molecular markers and project design are also discussed. Part 2 – Laboratory protocols, data management and analysis: will provide step-by-step protocols of the most commonly used molecular genetic techniques utilised in population genetics and systematic studies. In addition, a brief discussion and explanation of how these data are managed and analysed is also included. This manual is expected to enable NACA member country personnel to be trained to undertake molecular genetic studies in their own institutions, and as such is aimed at middle and higher level technical grades. The manual can also provide useful teaching material for specialised advanced level university courses in the region and postgraduate students. The manual has gone through two development/improvement stages. The initial material was tested at a regional workshop and at the second stage feedback from participants was used to improve the contents.

Where and when does a ring start and end? Testing the ring-species hypothesis in a species complex of Australian parrots

Speciation, despite ongoing gene flow can be studied directly in nature in ring species that comprise two reproductively isolated populations connected by a chain or ring of intergrading populations. We applied three tiers of spatio-temporal analysis (phylogeny/historical biogeography, phylogeography and landscape/population genetics) to the data from mitochondrial and nuclear genomes of eastern Australian parrots of the Crimson Rosella Platycercus elegans complex to understand the history and present genetic structure of the ring they have long been considered to form. A ring speciation hypothesis does not explain the patterns we have observed in our data (e.g. multiple genetic discontinuities, discordance in genotypic and phenotypic assignments where terminal differentiates meet). However, we cannot reject that a continuous circular distribution has been involved in the group's history or indeed that one was formed through secondary contact at the 'ring's' east and west; however, we reject a simple ring-species hypothesis as traditionally applied, with secondary contact only at its east. We discuss alternative models involving historical allopatry of populations. We suggest that population expansion shown by population genetics parameters in one of these isolates was accompanied by geographical range expansion, secondary contact and hybridization on the eastern and western sides of the ring. Pleistocene landscape and sea-level and habitat changes then established the birds' current distributions and range disjunctions. Populations now show idiosyncratic patterns of selection and drift. We suggest that selection and drift now drive evolution in different populations within what has been considered the ring.

Assessment of fracture risk : value of random population-based samples - the Geelong Osteoporosis Study

Fracture risk is determined by bone mineral density (BMD). The T-score, a measure of fracture risk, is the position of an individual's BMD in relation to a reference range. The aim of this study was to determine the magnitude of change in the T-score when different sampling techniques were used to produce the reference range. Reference ranges were derived from three samples, drawn from the same region: (1) an age-stratified population-based random sample, (2) unselected volunteers, and (3) a selected healthy subset of the population-based sample with no diseases or drugs known to affect bone. T-scores were calculated using the three reference ranges for a cohort of women who had sustained a fracture and as a group had a low mean BMD (ages 35-72 yr; n = 484). For most comparisons, the T-scores for the fracture cohort were more negative using the population reference range. The difference in T-scores reached 1.0 SD. The proportion of the fracture cohort classified as having osteoporosis at the spine was 26, 14, and 23% when the population, volunteer, and healthy reference ranges were applied, respectively. The use of inappropriate reference ranges results in substantial changes to T-scores and may lead to inappropriate management.