W. Jason Kennington

Patterns of diversity and linkage disequilibrium within the cosmopolitan inversion in(3R)payne in Drosophila melanogaster are indicative of coadaptation

The cosmopolitan inversion In(3R)Payne in Drosophila melanogaster decreases in frequency with increasing distance from the equator on three continents, indicating it is subject to strong natural selection. We investigated patterns of genetic variation and linkage disequilibrium (LD) in 24 molecular markers located within and near In(3R)Payne to determine if different parts of the inversion responded to selection the same way. We found reduced variation in the markers we used compared to others distributed throughout the genome, consistent with the inversion having a relatively recent origin (<Ne generations). LD between markers and In(3R)Payne varied significantly among markers within the inversion, with regions of high association interspersed by regions of low association. Several factors indicate that these patterns were not due to demographic factors such as admixture and bottlenecks associated with colonization, but instead reflected strong epistatic selection. Furthermore, we found that nonadjacent regions with high association to the inversion contained markers with the strongest clinal patterns in allele frequency; in most cases, the level of clinal variation was beyond what could be explained by hitchhiking with In(3R)Payne, indicating that genes within these regions are targets of selection. Our results provide some support for the hypothesis that inversions persist in natural populations because they hold together favorable combinations of alleles that act together to facilitate adaptive shifts.

Polyandry in the wild: temporal changes in female mating frequency and sperm competition intensity in natural populations of the tettigoniid Requena verticalis

Empirical tests of sexual selection theory generally utilize model systems under laboratory settings, and extend conclusions to evolutionary processes occurring in nature. The biological significance of laboratory findings will depend largely on the mating rates of females and patterns of paternity in natural populations, information on which is generally lacking. Here we use microsatellite markers to provide rare estimates of female mating rates and patterns of parentage in a species of tettigoniid, Requena verticalis, which has been used extensively to test theory on the evolution of male parental investment and its influence on the direction of sexual selection. We found that although the number of males having a genetic representation in the females sperm stores was higher for females collected late in the breeding season than those collected early in the season, overall the female mating rate was lower than that expected from laboratory observations. Analysis of parentage of offspring produced by females at the end of the breeding season revealed that all males represented in the sperm stores fathered offspring, although paternity was biased away from that expected from random sperm utilization. The data show that the complete first male sperm precedence documented in laboratory studies of this species does not persist in natural populations. Our data provide a solid underpinning for conclusions drawn from laboratory studies of this species.

Mapping regions within cosmopolitan inversion In(3R)Payne associated with natural variation in body size in Drosophila melanogaster.

Associations between genotypes for inversions and quantitative traits have been reported in several organisms, but little has been done to localize regions within inversions controlling variation in these traits. Here, we use an association mapping technique to identify genomic regions controlling variation in wing size within the cosmopolitan inversion In(3R)Payne in Drosophila melanogaster. Previous studies have shown that this inversion strongly influences variation in wing size, a trait highly correlated with body size. We found three alleles from two separate regions within In(3R)Payne with significant additive effects on wing size after the additional effect of the inversion itself had been taken into account. There were also several alleles with significant genotype-by-inversion interaction effects on wing size. None of the alleles tested had a significant additive effect on development time, suggesting different genes control these traits and that clinal patterns in them have therefore arisen independently. The presence of multiple regions within In(3R)Payne controlling size is consistent with the idea that inversions persist in populations because they contain multiple sets of locally adapted alleles, but more work needs to be done to test if they are indeed coadapted.

Phylogeography and population genetic structure of the Ornate Dragon Lizard, Ctenophorus ornatus.

Species inhabiting ancient, geologically stable landscapes that have been impacted by agriculture and urbanisation are expected to have complex patterns of genetic subdivision due to the influence of both historical and contemporary gene flow. Here, we investigate genetic differences among populations of the granite outcrop-dwelling lizard Ctenophorus ornatus, a phenotypically variable species with a wide geographical distribution across the south-west of Western Australia. Phylogenetic analysis of mitochondrial DNA sequence data revealed two distinct evolutionary lineages that have been isolated for more than four million years within the C. ornatus complex. This evolutionary split is associated with a change in dorsal colouration of the lizards from deep brown or black to reddish-pink. In addition, analysis of microsatellite data revealed high levels of genetic structuring within each lineage, as well as strong isolation by distance at multiple spatial scales. Among the 50 outcrop populations’ analysed, non-hierarchical Bayesian clustering analysis revealed the presence of 23 distinct genetic groups, with outcrop populations less than 4 km apart usually forming a single genetic group. When a hierarchical analysis was carried out, almost every outcrop was assigned to a different genetic group. Our results show there are multiple levels of genetic structuring in C. ornatus, reflecting the influence of both historical and contemporary evolutionary processes. They also highlight the need to recognise the presence of two evolutionarily distinct lineages when making conservation management decisions on this species.

Barcoding of mygalomorph spiders (Araneae : Mygalomorphae) in the Pilbara bioregion of Western Australia reveals a highly diverse biota

Abstract. The Pilbara bioregion of Western Australia is an area that contains vast mineral deposits and unique ecosystems. To ensure that mineral deposits are mined with minimal impact on the natural environment, impact assessment surveys are required to determine what fauna and flora species are located within proposed development areas, in particular, by determining the distributions of short-range endemic species (SREs). One infraorder of Arachnida, the Mygalomorphae (trapdoor spiders and their kin), are frequently identified as SREs. These identifications are traditionally performed using morphological techniques; however, only males can be reliably identified to species. Furthermore, the majority of species have not been formally described and males comprise only ∼5% of specimens collected. To assess mygalomorph diversity and the distribution of species in the Pilbara, we employed a molecular barcoding approach. Sequence data from the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene were obtained from 1134 specimens, and analysed using Bayesian methods. Only a fraction of the total mygalomorph fauna of the Pilbara has been documented, and using a species boundary cut-off of 9.5% sequence divergence, we report an increase in species richness of 191%. Barcoding provides a rapid, objective method to help quantify mygalomorph species identifications and their distributions, and these data, in turn, provide crucial information that regulatory authorities can use to assess the environmental impacts of large-scale developments.

Patterns of genetic variation across inversions: geographic variation in the In(2L)t inversion in populations of Drosophila melanogaster from eastern Australia

BackgroundChromosomal inversions are increasingly being recognized as important in adaptive shifts and are expected to influence patterns of genetic variation, but few studies have examined genetic patterns in inversion polymorphisms across and within populations. Here, we examine genetic variation at 20 microsatellite loci and the alcohol dehydrogenase gene (Adh) located within and near the In(2L)t inversion of Drosophila melanogaster at three different sites along a latitudinal cline on the east coast of Australia.ResultsWe found significant genetic differentiation between the standard and inverted chromosomal arrangements at each site as well as significant, but smaller differences among sites in the same arrangement. Genetic differentiation between pairs of sites was higher for inverted chromosomes than standard chromosomes, while inverted chromosomes had lower levels of genetic variation even well away from inversion breakpoints. Bayesian clustering analysis provided evidence of genetic exchange between chromosomal arrangements at each site.ConclusionsThe strong differentiation between arrangements and reduced variation in the inverted chromosomes are likely to reflect ongoing selection at multiple loci within the inverted region. They may also reflect lower effective population sizes of In(2L)t chromosomes and colonization of Australia, although there was no consistent evidence of a recent bottleneck and simulations suggest that differences between arrangements would not persist unless rates of gene exchange between them were low. Genetic patterns therefore support the notion of selection and linkage disequilibrium contributing to inversion polymorphisms, although more work is needed to determine whether there are spatially varying targets of selection within this inversion. They also support the idea that the allelic content within an inversion can vary between geographic locations.

Isolation by resistance across a complex coral reef seascape.

A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance surface to predict the spatial genetic structure of populations and explain deviations from the widely applied isolation-by-distance model. The majority of seascape approaches to date have been applied to linear coastal systems or at large spatial scales (more than 250 km), with very few applied to complex systems at regional spatial scales (less than 100 km). Here, we apply a seascape genetics approach to a peripheral population of the broadcast-spawning coral Acropora spicifera across the Houtman Abrolhos Islands, a high-latitude complex coral reef system off the central coast of Western Australia. We coupled population genetic data from a panel of microsatellite DNA markers with a biophysical dispersal model to test whether oceanographic processes could explain patterns of genetic divergence. We identified significant variation in allele frequencies over distances of less than 10 km, with significant differentiation occurring between adjacent sites but not between the most geographically distant ones. Recruitment probabilities between sites based on simulated larval dispersal were projected into a measure of resistance to connectivity that was significantly correlated with patterns of genetic divergence, demonstrating that patterns of spatial genetic structure are a function of restrictions to gene flow imposed by oceanographic currents. This study advances our understanding of the role of larval dispersal on the fine-scale genetic structure of coral populations across a complex island system and applies a methodological framework that can be tailored to suit a variety of marine organisms with a range of life-history characteristics.

Restricted gene flow and local adaptation highlight the vulnerability of high-latitude reefs to rapid environmental change

Global climate change poses a serious threat to the future health of coral reef ecosystems. This calls for management strategies that are focused on maximizing the evolutionary potential of coral reefs. Fundamental to this is an accurate understanding of the spatial genetic structure in dominant reef-building coral species. In this study, we apply a genotyping-by-sequencing approach to investigate genome-wide patterns of genetic diversity, gene flow, and local adaptation in a reef-building coral, Pocillopora damicornis, across 10 degrees of latitude and a transition from temperate to tropical waters. We identified strong patterns of differentiation and reduced genetic diversity in high-latitude populations. In addition, genome-wide scans for selection identified a number of outlier loci putatively under directional selection with homology to proteins previously known to be involved in heat tolerance in corals and associated with processes such as photoprotection, protein degradation, and immunity. This study provides genomic evidence for both restricted gene flow and local adaptation in a widely distributed coral species, and highlights the potential vulnerability of leading-edge populations to rapid environmental change as they are locally adapted, reproductively isolated, and have reduced levels of genetic diversity.

MORE THAN BINDIN DIVERGENCE: REPRODUCTIVE ISOLATION BETWEEN SYMPATRIC SUBSPECIES OF A SEA URCHIN BY ASYNCHRONOUS SPAWNING

The evolution of reproductive barriers is crucial to the process of speciation. In the Echinoidea, studies have focused on divergence in the gamete recognition protein, bindin, as the primary isolating mechanism among species. As such, the capacity of alternate mechanisms to be effective reproductive barriers and the phylogenetic context in which they arise is unclear. Here, we examine the evolutionary histories and factors limiting gene exchange between two subspecies of Heliocidaris erythrogramma that occur sympatrically in Western Australia. We found low, but significant differentiation between the subspecies in two mitochondrial genes. Further, coalescent analyses suggest that they diverged in isolation on the east and west coasts of Australia, with a subsequent range expansion of H. e. erythrogramma into Western Australia. Differentiation in bindin was minimal, indicating gamete incompatibility is an unlikely reproductive barrier. We did, however, detect strong asynchrony in spawning seasons; H. e. erythrogramma spawned over summer whereas H. e. armigera spawned in autumn. Taken together, we provide compelling evidence for a recent divergence of these subspecies and their reproductive isolation without gamete incompatibility. Western Australian H. erythrogramma may therefore present an intriguing case of incipient speciation, which depends on long‐term persistence of the factors underlying this spawning asynchrony.

Population recovery of the New Zealand fur seal in Southern Australia: A molecular DNA analysis

Abstract Commercial harvest severely reduced the abundance of New Zealand fur seals (NZFSs; Arctocephalus australis forsteri), and the subspecies may have become regionally extinct in Western Australia (WA). NZFS populations are now expanding in WA and this study aimed to determine the origin of these populations and distinguish local recruitment from external recolonization. Mitochondrial cytochrome-b gene sequences were obtained from 137 NZFSs from breeding colonies in WA and South Australia (SA), and analyzed with sequences from Tasmania and New Zealand. Genetic differentiation among WA and SA populations was low, indicating extensive genetic exchange throughout this large region. Three unique haplotypes, however, were recorded from WA, supporting the local recruitment hypothesis. Moreover, a test for asymmetrical gene flow identified a predominance of migration from WA to SA, suggesting a role of WA NZFSs in the recovery of more heavily exploited SA NZFS populations. Significant genetic differentiation was evident between SA and Tasmania, indicating limited genetic exchange despite the close proximity of these populations. Examination of our data suggests NZFSs were not extirpated from WA, have retained unique genetic variants, and that peripheral, low-density populations may have had a role in the recolonization of heavily exploited populations.