Fine-scale effects of habitat loss and fragmentation despite large-scale gene flow for some regionally declining woodland bird species

Habitat loss and associated fragmentation effects are well-recognised threats to biodiversity. Loss of functional connectivity (mobility, gene flow and demographic continuity) could result in population decline in altered habitat, because smaller, isolated populations are more vulnerable to extinction. We tested whether substantial habitat reduction plus fragmentation is associated with reduced gene flow in three 'decliner' woodland-dependent bird species (eastern yellow robin, weebill and spotted pardalote) identified in earlier work to have declined disproportionately in heavily fragmented landscapes in the Box-Ironbark forest region in north-central Victoria, Australia. For these three decliners, and one 'tolerant' species (striated pardalote), we compared patterns of genetic diversity, relatedness, effective population size, sex-ratios and genic (allele frequency) differentiation among landscapes of different total tree cover, identified population subdivision at the regional scale, and explored fine-scale genotypic (individual-based genetic signature) structure. Unexpectedly high genetic connectivity across the study region was detected for 'decliner' and 'tolerant' species. Power analysis simulations suggest that moderate reductions in gene flow should have been detectable. However, there was evidence of local negative effects of reduced habitat extent and structural connectivity: slightly lower effective population sizes, lower genetic diversity, higher within-site relatedness and altered sex-ratios (for weebill and eastern yellow robin) in 10 x 10 km 'landscapes' with low vegetation cover. We conclude that reduced structural connectivity in the Box-Ironbark ecosystem may still allow sufficient gene flow to avoid the harmful effects of inbreeding in our study species. Although there may still be negative consequences of fragmentation for demographic connectivity, the high genetic connectivity of mobile bird species in this system suggests that reconnecting isolated habitat patches may be less important than increasing habitat extent and/or quality if these need to be traded off.

Biogeographic models of gene flow in two waterfowl of the Australo-Papuan tropics

There are many large, easy-to-observe anseriform birds (ducks, geese, and swans) in northern Australia and New Guinea and they often gather in large numbers. Yet, the structure of their populations and their regional movements are poorly understood. Lack of understanding of population structure limits our capacity to understand source-sink dynamics relevant to their conservation or assess risks associated with avian-borne pathogens, in particular, avian influenza for which waterfowl are the main reservoir species. We set out to assess present-day genetic connectivity between populations of two widely distributed waterfowl in the Australo-Papuan tropics, magpie goose Anseranas semipalmata (Latham, 1798) and wandering whistling-duck Dendrocygna arcuata (Horsfield, 1824). Microsatellite data were obtained from 237 magpie geese and 64 wandering whistling-duck. Samples were collected across northern Australia, and at one site each in New Guinea and Timor Leste. In the wandering whistling-duck, genetic diversity was significantly apportioned by region and sampling location. For this species, the best model of population structure was New Guinea as the source population for all other populations. One remarkable result for this species was genetic separation of two flocks sampled contemporaneously on Cape York Peninsula only a few kilometers apart. In contrast, evidence for population structure was much weaker in the magpie goose, and Cape York as the source population provided the best fit to the observed structure. The fine scale genetic structure observed in wandering whistling-duck and magpie goose is consistent with earlier suggestions that the west-coast of Cape York Peninsula is a flyway for Australo-Papuan anseriforms between Australia and New Guinea across Torres Strait.

Gene flow in east antarctic echinoderms and resilience to climate change

The spatial scales of population genetic structure in three species of Antarctic echinoderm, Sterechinus neumayeri, Abatus nimrodi and Abatus ingens was quantified using mitochondrial sequences and a novel set of microsatellite markers. Reduced fertilisation success in S. neumayeri resulting from increasing temperature and decreasing salinity was also identified.

Population genetic structure, gene flow and sex-biased dispersal in frillneck lizards (Chlamydosaurus kingii)

By using both mitochondrial and nuclear multiloci markers, we explored population genetic structure, gene flow and sex-specific dispersal of frillneck lizards (Chlamydosaurus kingii) sampled at three locations, separated by 10 to 50 km, in a homogenous savannah woodland in tropical Australia. Apart from a recombinant lizard, the mitochondrial analyses revealed two nonoverlapping haplotypes/populations, while the nuclear markers showed that the frillneck lizards represented three separate clusters/populations. Due to the small population size of the mtDNA, fixation may occur via founder effects and/or drift. We therefore suggest that either of these two processes, or a combination of the two, are the most likely causes of the discordant results obtained from the mitochondrial and the nuclear markers. In contrast to the nonoverlapping mitochondrial haplotypes, in 12 out of 74 lizards, mixed nuclear genotypes were observed, hence revealing a limited nuclear gene flow. Although gene flow should ultimately result in a blending of the populations, we propose that the distinct nuclear population structure is maintained by frequent fires resulting in local bottlenecks, and concomitant spatial separation of the frillneck lizard populations. Limited mark-recapture data and the difference in distribution of the mitochondrial and nuclear markers suggest that the mixed nuclear genotypes were caused by juvenile male-biased dispersal.

Population genetic structuring in Acanthopagrus butcheri (Pisces: Sparidae): does low gene flow among estuaries apply to both sexes?

Acanthopagrus butcheri completes its entire life history within estuaries and coastal lakes of southern Australia, although adults occasionally move between estuaries via the sea. Consequently, it is expected that populations of A. butcheri in different estuaries will be genetically distinct, with the magnitude of genetic divergence increasing with geographic isolation. However, previous genetic studies of A. butcheri from southeast Australia yielded conflicting results; allozyme variation exhibited minimal spatial structuring (θ = 0.012), whereas mitochondrial DNA distinguished the majority of populations analyzed (θ = 0.263) and genetic divergence was positively correlated with geographic isolation. This discrepancy could reflect high male gene flow, which impacts nuclear but not mitochondrial markers. Here we estimated allele frequencies at five nuclear microsatellite loci across 11 southeast Australian populations (595 individuals). Overall structuring of microsatellite variation was weaker (θ = 0.088) than that observed for mitochondrial DNA, but was able to distinguish a greater number of populations and was positively correlated with geographic distance. Therefore, we reject high male gene flow and invoke a stepping-stone model of infrequent gene flow among estuaries for both sexes. Likewise, management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries for both sexes. The lack of allozyme structuring in southeast Australia reflects either the large variance in structuring expected among loci under neutral conditions and the low number of allozymes surveyed or a recent colonization of estuaries such that some but not all nuclear loci have approached migration-drift equilibrium.

Conservation genetic studies of the endangered Cape Fear Shiner, Notropis mekistocholas (Teleostei: Cyprinidae)

Genetic variation at ten microsatellite lociand one anonymous-nuclear locus was assayed for three geographic samples of the criticallyendangered North American cyprinid Notropis mekistocholas (Cape Fear shiner). Despite low abundance of this species, there was little suggestion of small population effects; allele diversity and heterozygosity were relatively high, F_IS values within samples were non-significant, and genotypes were distributed in frequencies according to Hardy-Weinberg expectations. Genetic divergence among samples was minimal despite the presence of dams, constructed in the early1900s, that separate the sample sites. This suggests that recent gene flow has been sufficient to inhibit genetic divergence or that gene flow has been reduced but there has been insufficient time for genetic divergence to develop. Tests of heterozygosity excess were non-significant, suggesting that N.mekistocholas in the localities sampled have not undergone recent reductions ineffective population size. Future studies employing larger sample sizes to provide more robust tests of population structure and temporally separated samples to estimate contemporaneous N_e are warranted.

No outbreeding depression at a regional scale for a habitat-forming intertidal alga with limited dispersal

Hormosira banksii is distributed throughout southern Australasia, but dispersal of propagules is thought to be limited. In the present study, the hypothesis that outbreeding depression occurs in H. banksii was tested by assessing fertilisation success and early development of embryos in crosses between populations at local to regional spatial scales. Hierarchical experiments were conducted at three spatial scales with nesting present within each scale: small scale (within a rocky shore population), intermediate scale (regions separated by 70 km) and large scale (450-km separation between two states: Victoria and Tasmania). In each experiment, eggs and sperm were crossed within and between each population located in the spatial scale of interest. There were no consistent patterns of variable fertilisation success and subsequent development within a population or at different spatial scales. It was concluded that outbreeding depression is not detected in analyses of fertilisation success or early development processes in H. banksii. The results suggest one of the following to be likely: (1) H. banksii is capable of longer distance dispersal than previously considered, thus maintaining gene flow between distant populations, (2) gene flow is restricted by limited dispersal, but populations have not been isolated for a sufficient length of time to cause genetic divergence or (3) outbreeding depression is manifested as effects on later life-history stages.

Dispersal of Hormosira banksii (phaeophyceae) via detached fragments : reproductive viability and longevity

Drifting, fertile thalli are well documented to be the primary long-distance dispersal vector for many marine macroalgae, but little information about reproductive viability of drift is known. This study examined the reproductive viability and longevity of floating fragments of the intertidal Australasian fucoid Hormosira banksii (Turner) Decne. Beach wrack surveys and field experiments were conducted to test the model that long-distance dispersal is achieved in H. banksii via floating, fertile fronds. High densities of beach wrack fragments were evident during summer compared to autumn. The majority of beach wrack occurred on sandy beaches rather than rocky shores. Both male and female fragments were present in the beach wrack. Detached fronds were capable of releasing gametes up to 8 weeks after detachment. Beach wrack produced high fertilization rates and recruited successfully onto artificial panels. Results suggest that detached fragments are reproductively viable and that floating, fertile fronds may be an important mechanism for facilitating long-distance dispersal in this species. Nevertheless, the frequency of fronds reaching a suitable habitat and contributing to gene flow between populations, or colonizing new populations, may not be proportional to the total density of beach wrack.

Contrasting genetic structuring between colonies of the world's smallest penguin, Eudyptula minor (Aves: Spheniscidae)

The Little Penguin, Eudyptula minor, is a seabird that nests in colonies throughout New Zealand and southern Australia. Individuals from different colonies in southeast Australia differ significantly in morphology and ecology, suggesting that some genetic structuring may exist among colonies. In contrast, the marking of individuals with flipper bands has revealed some, albeit infrequent, movement between colonies. To determine the extent of genetic structuring, we tested the null hypothesis of substantial gene flow within southeast Australia by examining patterns of genetic variation across seven colonies separated by up to 1,500 km. Phylogeographic structuring was absent for mitochondrial control region sequences (2–3 individuals per colony). Microsatellite allele frequencies at five loci and mitochondrial haplotype frequencies (50 individuals per colony) were also homogenous among the majority of colonies sampled, although two colonies at the western periphery of the sampling range were distinct from those to the east. The genetic homogeneity among the majority of colonies can be explained by low but consistent contemporary gene flow among them, or a recent founder event in Bass Strait following the last marine transgression. The genetic break towards the western end of the sampling distribution appears best explained by differences in sea surface temperature and, consequentially breeding phenology, the latter hindering genetically effective migration.

Population structure in the highly fragmented range of Tor douronensis (Cyprinidae) in Sarawak, Malaysia revealed by microsatellite DNA markers

1. Understanding the structure of threatened populations, particularly those that exist in degraded or fragmented habitats is crucial for their effective management and conservation. Recently developed methods of individual-based analysis of genetic data provide an unprecedented opportunity to understand the relationships amongst fragmented populations.

2. In the present study, population structure of an important cyprinid species (Tor douronensis), which is indigenous to Sarawak, Malaysia, is investigated as part of an ongoing conservation effort to restore threatened wild populations of the species. The population structure inferred using data from seven autosomal microsatellite loci was generally consistent with geography and habitat fragmentation.

3. The results indicate that there are two well-defined clusters of T. douronensis in Sarawak, namely the 'northeastern' and the 'southwestern' clusters. In addition, a further subdivision was observed in each of the clusters distributed between river systems. Low levels of gene flow were also observed and migrants between habitat fragments were identified, possibly resulting from human-mediated translocations.

4. Implications of the findings for management and conservation of T. douronensis are discussed.

A tangled tale of two teal : population history of the grey Anas gracilis and chestnut teal A. castanea of Australia

Two Australian species of teal (Anseriformes: Anatidae: Anas), the grey teal Anas gracilis and the chestnut teal A. castanea, are remarkable for the zero or near-zero divergence recorded between them in earlier surveys of mitochondrial DNA (mtDNA) diversity. We confirmed this result through wider geographical and population sampling as well as nucleotide sampling in the more rapidly evolving mtDNA control region. Any data set where two species share polymorphism as is the case here can be explained by a model of gene flow through hybridization on one hand or by incomplete lineage sorting on the other hand. Ideally, analysis of such shared polymorphism would simultaneously estimate the likelihood of both phenomena. To do this, we used the underlying principle of the IMa package to explore ramifications to understanding population histories of A. gracilis and A. castanea. We cannot reject that hybridization occurs between the two species but an equally or more plausible finding for their nearly zero divergence is incomplete sorting following very recent divergence between the two, probably in the mid-late Pleistocene. Our data add to studies that explore intermediate stages in the evolution of reciprocal monophyly and paraphyletic or polyphyletic relationships in mtDNA diversity among widespread Australian birds.

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.

Polymorphic microsatellite loci in the Australian tree frog, Litoria peronii

Eleven novel polymorphic microsatellite loci developed from a microsatellite enriched genomic library, are presented for the Australian tree frog <i>Litoria peroniii>. We screened 29 individuals from a single population and detected high levels of polymorphism for all 11 loci with the number of alleles/locus ranging from 9 to 24. Values of expected and observed heterozygosities ranged from 0.789–0.955 and 0.207–1.00, respectively. These microsatellite markers should prove useful in determining levels of genetic diversity, measuring gene flow and migration, assigning individuals to their most likely population of origin, and in the assignment of paternity.

Genetic status of an endemic marine mammal, the Australian fur seal, following historical harvesting

Genetic variation, and the way in which it is partitioned among populations, has implications for a species’ survival and evolutionary potential. Such information is particularly important for the successful conservation and management of species that have experienced past human impacts and potential losses of genetic diversity. Overharvesting of the Australian fur seal Arctocephalus pusillus doriferus in the 18th and 19th centuries resulted in severe population reductions and elimination of an estimated 17 of 26 colonies. Currently, the subspecies is recovering and c. 20 000 pups are produced annually at 13 colony sites, most of which are situated in Bass Strait in south-eastern Australia. Genetic analysis of samples collected from pups captured at nine colonies revealed no difference in allelic diversity or heterozygosity at five microsatellite loci and no differences in haplotype diversity within a 344 bp region of the mitochondrial DNA control region. There was some evidence for isolation by distance but the program STRUCTURE predicted a single cluster of individuals. Gene flow among colonies appears to be substantial at present, indicating that the Australian fur seal is currently a single, panmictic unit.