Allan Wilson Centre

Skinks (Family Scincidae) are the most diverse family of lizards (~1745 described species worldwide), and the Australasian region (Australia, New Caledonia, New Zealand) is a recognised global hotspot (>600 species) for skinks. Here we focus on determining the phylogenetic relationships and biogeography within the tribe Eugongylini, one of three lineages in the region. We used mtDNA (ND2) and nuclear (RAG-1, c-mos) DNA sequences and phylogenetic analyses to reveal the presence of three well-supported lineages of Australian Eugongylini. We found a sister relationship between the monotypic genera Eroticoscincus and Harrisoniascincus, and that the monotypic Anepischetosia has close affinities with Carinascincus coventryi and Pseudemoia. C. coventryi represents a separate lineage from the main Carinascincus radiation. Emoia was not found to be monophyletic, with Emoia s.s. part of an Australian lineage, and the remainder of the genus representing an older divergence within the tribe. The widespread and speciose Cryptoblepharus represented a well-supported lineage within an Australian lineage. Our analyses confirm previous suggestions that four Sphenomorphus species (louisiadensis, minutus, bignelli, and aignanus) are misplaced, and are part of the Eugongylini. Our phylogenetic analyses support the hypothesis that the origin of the tribe lies in Asia, with dispersal events to Africa, Australasia, and Oceania.

In a range of taxa, the relatedness between mates influences both pre- and post-mating processes of sexual selection. However, relatively little is known about the genetic loci facilitating such a bias, with the exception of the major histocompatibility complex. Here, we performed tightly controlled replicated in vitro fertilization trials to explore the impact of relatedness on two possible mechanisms of cryptic female choice (CFC) in Chinook salmon (Oncorhynchus tshawytscha). We tested (i) whether relatedness of mates, assessed using 682 single nucleotide polymorphisms (SNPs) on 29 SNP-linkage groups (LGs), biases a male's sperm velocity in ovarian fluid (a parameter previously shown to predict male fertilization success), and (ii) whether relatedness of mates governs fertilization success via other mechanisms, probably via sperm-egg interactions. We found that relatedness on three LGs explained the variation in sperm velocity, and relatedness on two LGs explained fertilization success, which might indicate the presence of genes important in sperm-ovarian fluid and sperm-egg interactions in these genomic regions. Mapping of the SNPs on these LGs to the rainbow trout genome revealed two genes that affect fertility in humans and represent candidate genes for further studies. Our results thereby provide a novel contribution to the understanding of the mechanism of CFC.

Archaeological, palaeontological and geological evidence shows that post-glacial warming released human populations from their various climate-bound refugia. Yet specific connections between these refugia and the timing and routes of post-glacial migrations that ultimately established modern patterns of genetic variation remain elusive. Here, we use Y-chromosome markers combined with autosomal data to reconstruct population expansions from regional refugia in Southwest Asia. Populations from three regions in particular possess distinctive autosomal genetic signatures indicative of likely refugia: one, in the north, centered around the eastern coast of the Black Sea, the second, with a more Levantine focus, and the third in the southern Arabian Peninsula. Modern populations from these three regions carry the widest diversity and may indeed represent the most likely descendants of the populations responsible for the Neolithic cultures of Southwest Asia. We reveal the distinct and datable expansion routes of populations from these three refugia throughout Southwest Asia and into Europe and North Africa and discuss the possible correlations of these migrations to various cultural and climatic events evident in the archaeological record of the past 15,000 years.

ABSTRACTPlanctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immuno-gold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.

Digenean parasites infecting four Cominella whelk species (C. glandiformis, C. adspersa, C. maculosa and C. virgata), which inhabit New Zealand's intertidal zone, were analysed using molecular techniques. Mitochondrial 16S and cytochrome oxidase 1 (COI) and nuclear rDNA ITS1 sequences were used to infer phylogenetic relationships amongst digenea. Host species were parasitized by a diverse range of digenea (Platyhelminthes, Trematoda), representing seven families: Echinostomatidae, Opecoelidae, Microphallidae, Strigeidae and three, as yet, undetermined families A, B and C. Each parasite family infected between one and three host whelk species, and infection levels were typically low (average infection rates ranged from 1·4 to 3·6%). Host specificity ranged from highly species-specific amongst the echinostomes, which were only ever observed infecting C. glandiformis, to the more generalist opecoelids and strigeids, which were capable of infecting three out of four of the Cominella species analysed. Digeneans displayed a highly variable geographic range; for example, echinostomes had a large geographic range stretching the length of New Zealand, from Northland to Otago, whereas Family B parasites were restricted to fairly small areas of the North Island. Our results add to a growing body of research identifying wide ranges in both host specificity and geographic range amongst intertidal, multi-host parasite systems.

Moths use their sense of smell to find food sources, mating partners and oviposition sites. For this they possess a family of odorant receptors (ORs). Some ORs are used by both sexes whereas others have sex-specific roles. For example, male moths possess ORs specifically tuned to sex pheromones produced by conspecific females. Here we identify sets of ORs from the antennae of New Zealand endemic leafroller moths Planotortrix octo (48 ORs) and P. excessana (47 ORs) using an RNA-Seq approach. Two orthologous ORs show male-biased expression in the adult antennae of both species (OR7 and OR30) and one other OR in each species was female-biased in its expression (PoctOR25, PexcOR14) by qPCR. PAML analysis conducted on male-biased ORs indicated positive selection acting on the male-biased OR7. The fact that OR7 is likely under positive selection, that it is male-biased in its expression and that its orthologue in C. obliquana, CoblOR7, responds to sex pheromone components also utilised by Planotortrix species, suggests that this receptor may also be important in sex pheromone reception in Planotortrix species.

ABSTRACT General anaesthesia administered during the day has previously been shown to phase shift the honey bee clock. We describe a phase response curve for honey bees (n=105) to six hour isoflurane anaesthesia. The honey bee isoflurane PRC is “weak” with a delay portion (maximum shift of –1.88 hours, circadian time 0 – 3) but no advance zone. The isoflurane-induced shifts observed here are in direct opposition to those of light. Furthermore, concurrent administration of light and isoflurane abolishes the shifts that occur with isoflurane alone. Light may thus provide a means of reducing isoflurane–induced phase shifts.

Abstract AimTo determine which seascape features have shaped the spatial genetic patterns of coral reef fishes, and to identify common patterns among species related to dispersal traits [egg type and pelagic larval duration (PLD)].LocationIndian and Pacific Oceans, including the Indo‐Australian Archipelago.MethodsWe sampled coral reef fishes with differing dispersal traits (Pomacentrus coelestis, Dascyllus trimaculatus, Hailchoeres hortulanus and Acanthurus triostegus) and characterized spatial (mtDNA) genetic patterns using AMOVA‐clustering and measures of genetic differentiation. Similarity in the spatial genetic patterns among species was assessed using the congruence among distance matrices method and the seascape features associated with the genetic differentiation of each species were identified using multiple regression of distance matrices (MRDM) and stepwise model selection.ResultsSimilar spatial genetic patterns were found for P. coelestis and H. hortulanus, despite their differing egg type (benthic versus pelagic). MRDM indicated that geographical distance was underlying their correlated genetic patterns. Species with pelagic eggs (A. triostegus and H. hortulanus) also had correlated patterns of genetic differentiation (Dest); however, a common underlying seascape feature could not be inferred. Additionally, the common influence of the Torres Strait and the Lydekker/Weber's line was identified for the genetic patterns of differentiation for P. coelestis and A. triostegus, despite their differing dispersal traits, and the uncorrelated spatial genetic patterns of these species.Main conclusionsOur study demonstrates the value of a quantitative, hypothesis‐testing framework in comparative phylogeography. We found that dispersal traits (egg type and PLD) did not predict which species had similar spatial genetic patterns or which seascape features were associated with these patterns. Furthermore, even in the absence of visually similar, or correlated spatial genetic patterns, our approach enabled us to identify seascape features that had a common influence on the spatial genetic patterns of co‐distributed species.

Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human-driven faunal declines.

Few studies have examined core–periphery genetic patterns in tropical marine taxa. The core–periphery hypothesis (CPH) predicts that core populations will have higher genetic diversity and lower genetic differentiation than peripheral populations as a consequence of greater population sizes and population connectivity in the core. However, the applicability of the CPH to many tropical marine taxa may be confounded by their complex population histories and/or high (asymmetric) population connectivity. In this study we investigated genetic patterns (based on mtDNA) across the latitudinal range of the neon damselfish Pomacentrus coelestis (36°N, Japan – 37°S, east Australia). We suggest a novel hypothetical framework for core–periphery genetic patterns and extend typical analyses to include genealogical analyses, partitioned β‐diversity measures (total β SOR , turnover β SIM , and nestedness‐resultant β SNE ), and analyses of nestedness. We found that the existence of two divergent lineages of the neon damselfish led levels of genetic diversity to deviate from CPH expectations. When focusing on the widespread lineage (Pacific clade) nucleotide diversity was higher in the core, supporting the CPH. However, genetic patterns differed toward the northern and southern peripheries of the Pacific clade. The turnover of haplotypes (pairwise‐β sim ) increased over distance in the north, indicative of historical colonization with little contemporary migration. In contrast, although turnover was still dominant in the south (β SIM ), there was no relationship to distance (pairwise‐β sim ), suggesting the influence of more contemporary processes. Moreover, the haplotype compositions of populations in the south were nested according to latitude, indicating immigration from lower latitudes toward the southern periphery. By extending the typical characterizations of core–periphery genetic patterns we were able to identify the effects of lineage sympatry on measures of genetic diversity and contrasting demographic histories toward the latitudinal peripheries of the neon damselfish's range.