Joanna Sumner

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.

Neighbourhood size, dispersal and density estimates in the prickly forest skink (Gnypetoscincus queenslandiae) using individual genetic and demographic methods.

Dispersal, or the amount of dispersion between an individual’s birthplace and that of its offspring, is of great importance in population biology, behavioural ecology and conservation, however, obtaining direct estimates from field data on natural populations can be problematic. The prickly forest skink, Gnypetoscincus queenslandiae, is a rainforest endemic skink from the wet tropics of Australia. Because of its log‐dwelling habits and lack of definite nesting sites, a demographic estimate of dispersal distance is difficult to obtain. Neighbourhood size, defined as 4πDσ2 (where D is the population density and σ2 the mean axial squared parent–offspring dispersal rate), dispersal and density were estimated directly and indirectly for this species using mark–recapture and microsatellite data, respectively, on lizards captured at a local geographical scale of 3 ha. Mark–recapture data gave a dispersal rate of 843 m2/generation (assuming a generation time of 6.5 years), a time‐scaled density of 13 635 individuals * generation/km2 and, hence, a neighbourhood size of 144 individuals. A genetic method based on the multilocus (10 loci) microsatellite genotypes of individuals and their geographical location indicated that there is a significant isolation by distance pattern, and gave a neighbourhood size of 69 individuals, with a 95% confidence interval between 48 and 184. This translates into a dispersal rate of 404 m2/generation when using the mark–recapture density estimation, or an estimate of time‐scaled population density of 6520 individuals * generation/km2 when using the mark–recapture dispersal rate estimate. The relationship between the two categories of neighbourhood size, dispersal and density estimates and reasons for any disparities are discussed.

Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae.

To examine the effects of recent habitat fragmentation, we assayed genetic diversity in a rain forest endemic lizard, the prickly forest skink (Gnypetoscincus queenslandiae), from seven forest fragments and five sites in continuous forest on the Atherton tableland of northeastern Queensland, Australia. The rain forest in this region was fragmented by logging and clearing for dairy farms in the early 1900s and most forest fragments studied have been isolated for 50–80 years or nine to 12 skink generations. We genotyped 411 individuals at nine microsatellite DNA loci and found fewer alleles per locus in prickly forest skinks from small rain forest fragments and a lower ratio of allele number to allele size range in forest fragments than in continuous forest, indicative of a decrease in effective population size. In contrast, and as expected for populations with small neighbourhood sizes, neither heterozygosity nor variance in allele size differed between fragments and sites in continuous forests. Considering measures of among population differentiation, there was no increase in FST among fragments and a significant isolation by distance pattern was identified across all 12 sites. However, the relationship between genetic (FST) and geographical distance was significantly stronger for continuous forest sites than for fragments, consistent with disruption of gene flow among the latter. The observed changes in genetic diversity within and among populations are small, but in the direction predicted by the theory of genetic erosion in recently fragmented populations. The results also illustrate the inherent difficulty in detecting genetic consequences of recent habitat fragmentation, even in genetically variable species, and especially when effective population size and dispersal rates are low.

Reproduction in shark-attacked sea turtles is supported by stress-reduction mechanisms.

Vertebrates exhibit varied behavioural and physiological tactics to promote reproductive success. We examined mechanisms that could enable female loggerhead turtles to undertake nesting activities and maintain seasonal reproduction despite recent shark injuries of varying severity. We proposed that endocrinal mechanisms that regulate both a turtles stress response and reproductive ability are modified to promote successful and continued reproduction. Irrespective of the degree of injury, females did not exhibit increased levels of the stress hormone corticosterone, nor decreased levels of the reproductive steroid testosterone; hormone responses consistent with stress. When exposed to a capture stressor, females with shark injury did not exhibit any greater corticosterone response than controls. In addition, breeding females showed a reduced corticosterone stress response compared to non–breeding females. Reduced endocrinal responses following shark injury, and during breeding in general may, in part, enable females to maintain behavioural and physiological commitment to reproduction.

Decreased relatedness between male prickly forest skinks (Gnypetoscincus queenslandiae) in habitat fragments

In species with low levels of dispersal the chance of closely related individuals breeding may be a potential problem; sex-biased dispersal is a mechanism that may decrease the possibility of cosanguineous mating. Fragmentation of the habitat in which a species lives may affect mechanisms such as sex-biased dispersal, which may in turn exacerbate more direct effects of fragmentation such as decreasing population size that may lead to inbreeding depression. Relatedness statistics calculated using microsatellite DNA data showed that rainforest fragmentation has had an effect on the patterns of dispersal in the prickly forest skink (Gnypetoscincus queenslandiae), a rainforest endemic of the Wet Tropics of north eastern Australia. A lower level of relatedness was found in fragments compared to continuous forest sites due to a significantly lower level of pairwise relatedness between males in rainforest fragments. The pattern of genetic relatedness between sexes indicates the presence of male-biased dispersal in this species, with a stronger pattern detected in populations in rainforest fragments. Male prickly forest skinks may have to move further in fragmented habitat in order to find mates or suitable habitat logs.

Genetic Connectivity among Populations of an Endangered Snake Species from Southeastern Australia (Hoplocephalus bungaroides, Elapidae)

For endangered species that persist as apparently isolated populations within a previously more extensive range, the degree of genetic exchange between those populations is critical to conservation and management. A lack of gene flow can exacerbate impacts of threatening processes and delay or prevent colonization of sites after local extirpation. The broad-headed snake, Hoplocephalus bungaroides, is a small venomous species restricted to a handful of disjunct reserves near Sydney, Australia. Mark-recapture studies have indicated low vagility for this ambush predator, suggesting that gene flow also may be low. However, our analyses of 11 microsatellite loci from 163 snakes collected in Morton National Park, from six sites within a 10-km diameter, suggest relatively high rates of gene flow among sites. Most populations exchange genes with each other, with one large population serving as a source area and smaller populations apparently acting as sinks. About half of the juvenile snakes, for which we could reliably infer parentage, were collected from populations other than those in which we collected their putative parents. As expected from the snakes’ reliance on rocky outcrops during cooler months of the year, most gene flow appears to be along sandstone plateaux rather than across the densely forested valleys that separate plateaux. The unexpectedly high rates of gene flow on a landscape scale are encouraging for future conservation of this endangered taxon. For example, wildlife managers could conserve broad-headed snakes by restoring habitats near extant source populations in areas predicted to be least affected by future climate change.

Fauna-rescue programs highlight unresolved scientific, ethical and animal welfare issues

In response to a paper advocating large-scale, multi-species ‘fauna-rescue’ programs when habitat is being destroyed, we urge caution by highlighting the lack of evidence of success in such programs. We argue that any benefits are likely to be outweighed by ecological and animal welfare risks, and that any conservation gains are likely to be illusionary.

Geographic variation in hybridization and ecological differentiation between three syntopic, morphologically similar species of montane lizards.

To understand factors shaping species boundaries in closely related taxa, a powerful approach is to compare levels of genetic admixture at multiple points of contact and determine how this relates to intrinsic and extrinsic factors, such as genetic, morphological and ecological differentiation. In the Australian Alps, the threatened alpine bog skink Pseudemoia cryodroma co‐occurs with two morphologically and ecologically similar congeners, P. entrecasteauxii and P. pagenstecheri, and all three species are suspected to hybridize. We predicted that the frequency of hybridization should be negatively correlated with genetic divergence, morphological differentiation and microhabitat separation. We tested this hypothesis using a mitochondrial locus, 13 microsatellite loci, morphological and microhabitat data and compared results across three geographically isolated sites. Despite strong genetic structure between species, we detected hybridization between all species pairs, including evidence of backcrossed individuals at the two sites where all three species are syntopic. Hybridization frequencies were not consistently associated with genetic, morphological or ecological differentiation. Furthermore, P. entrecasteauxii and P. pagenstecheri only hybridized at the two sites where they are syntopic with P. cryodroma, but not at the largest site where P. cryodroma was not recorded, suggesting that P. cryodroma may serve as a bridging species. This study reveals the complex dynamics within a three species hybrid zone and provides a baseline for assessing the impact of climate change and anthropogenic habitat modification on future hybridization frequencies.

Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region

Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog (Litoria raniformis) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbournes urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis. However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.

Assessment of environmental and host dependent factors correlated with tick abundance on Komodo dragons

In this study we assessed interactions among Komodo dragon Varanus komodoensis populations, individual Komodo dragons and two tick parasites Amblyomma robinsoni and Aponomma komodoense to assess variation in host-parasite aggregations. Prevalence of ticks was uniformly high (> 98%) but median tick abundance varied 3.52 fold among 9 host lizard populations. There was no evidence to suggest that average tick abundances were correlated with genetic similarities (Rm = 0.133, P = 0.446) or geographic proximities (Rm = 0.175 P=0.303) among host populations. Temporal concordance in tick abundance was measured for host populations between two different years but not for the individual hosts within these populations. General linearized modelling indicated that ≈ 23% of host variation in tick abundance was positively correlated to a multivariate function incorporating lizard body size, body condition, their interactions, and habitat differences. The covariates of host population density and inbreeding coefficients,...