Genetic analysis of hog deer (Axis porcinus) in Victoria, Australia, and its applications to invasive species and game management

Hog deer were introduced to Australia in the 1860s, where they have spread across the Gippsland region of Victoria. Due to its status as an introduced species and an important game animal within Victoria, management of the species is complex. Given this complexity, genetic studies can provide important information regarding population structure and diversity which can assist in controlling problematic populations of hog deer, while also ensuring viable game stock in sites managed as game reserves. The aim of this study was to investigate the population genetic structure and diversity of the Victorian hog deer 150 years after introduction using short tandem repeats (STRs). Hog deer samples were collected across 15 sites of differing management regimes in the Gippsland region of Victoria and genotyped for 13 polymorphic STR loci. Up to four distinct genetic clusters were identified across the sites sampled, suggesting that despite low observed genetic diversity, population structure is present across their range. It was also possible to detect evidence of recent translocations among populations. This study suggests that the presence of distinct genetic clusters may enable management of separate genetic units, considering invasive species and game management objectives

Long distance (>20 km) downstream detection of endangered stream frogs suggests an important role for eDNA in surveying for remnant amphibian populations

Background Globally, amphibian species have suffered drastic population declines over the past 40 years. Hundreds of species are now listed as Critically Endangered, with many of these considered “possibly extinct”. Most of these species are stream-dwelling frogs inhabiting remote, montane areas, where remnant populations are hard to find using traditional surveys. Environmental DNA (eDNA) could revolutionize surveys for ‘missing’ and endangered amphibian populations by screening water samples from downstream sections to assess presence in the upstream catchments. However, the utility of this survey technique is dependent on quantifying downstream detection probability and distances. Methods Here we tested downstream detection distances in two endangered stream frogs (Litoria lorica and L. nannotis) that co-occur in a remote stream catchment in north-east Australia, and for which we know precise downstream distributional limits from traditional surveys. Importantly, the two last populations of L. lorica persist in this catchment: one small (~1,000 frogs) and one very small (~100 frogs). We conducted eDNA screening at a series of sites kilometers downstream from the populations using precipitation from two fixed water volumes (15 and 100 mL) and via water filtering (mean 1,480 L). Results We detected L. nannotis and the small L. lorica population (~1,000 frogs) at most sampling sites, including 22.8 km downstream. The filtration method was highly effective for far-downstream detection, as was precipitation from 100 mL water samples, which also resulted in consistent detections at the far-downstream sites (including to 22.8 km). In contrast, we had limited downstream detection success for the very small L. lorica population (~100 frogs). Discussion The ecological aspects of our study system, coupled with thorough traditional surveys, enabled us to measure downstream eDNA detection distances with accuracy. We demonstrate that eDNA from a small population of approximately 1,000 frogs can be detected as far as 22.8 km downstream from the population. Water filtration is considered best for eDNA detection of rare aquatic species—indeed it was effective in this study—but we also achieved far-downstream detections when precipitating eDNA from 100 mL water samples. Collecting small water volumes for subsequent precipitation in the lab is more practical than filtration when surveying remote areas. Our downstream detection distances (>20 km) suggest eDNA is a valuable tool for detecting rare stream amphibians. We provide recommendations on optimal survey methods

Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

The black-lip rock oyster (Saccostrea echinata) has considerable potential for aquaculture throughout the tropics. Previous attempts to farm S. echinata failed due to an insufficient supply of wild spat; however, the prospect of hatchery-based aquaculture has stimulated renewed interest, and small-scale farming is underway across northern Australia and in New Caledonia. The absence of knowledge surrounding the population genetic structure of this species has raised concerns about the genetic impacts of this emerging aquaculture industry. This study is the first to examine population genetics of S. echinata and employs both mitochondrial cytochrome c oxidase subunit I gene (COI) and single nucleotide polymorphism (SNP) markers

Allopatric speciation within a cryptic species complex of Australasian octopuses

Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub- species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the ` tetricus complex'. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide

Dietary supplementation of astaxanthin modulates skin color and liver antioxidant status of giant grouper (Epinephelus lanceolatus)

Giant grouper (Epinephelus lanceolatus) is an emerging aquaculture species in Southeast Asia and Australia with limited knowledge of its nutrient requirements and effects of supplements on its physiology. The present study investigated the effects of astaxanthin, vitamin E, and combinations on growth performance, body coloration, and the antioxidant status of juvenile giant grouper. Nine isonitrogenous (crude protein = 65 % ± 0.7 %) and isolipidic (crude lipid = 10 % ± 0.3 %) diets were formulated using a 3 × 3 factorial design, including three levels astaxanthin (0, 75, and 150 mg/kg) and vitamin E (0, 250, and 500 mg/kg), respectively. Each of the nine diets was fed to triplicate groups of 15 giant grouper (18.04 ± 0.92 g) for 30 days. Giant grouper fed the different diets exhibited no significant differences (p > 0.05) in specific growth rate (4.87 %/day - 5.21 %/day). However, dietary astaxanthin supplementation significantly enhanced the redness (a*), yellowness (b*b*), chroma, and hue values of the fin, regardless of the dose supplemented. Giant grouper fed astaxanthin at 75 and 150 mg/kg diet were more yellow and had three times higher b* values than fish fed non-supplemented diets. Further, total antioxidant capacity (TAC; mmol Trolox equivalent) in liver tissues was significantly increased in fish fed any of the astaxanthin-supplemented diets (p ≤ 0.05). In contrast, TAC levels were not affected by vitamin E supple-mentation. Malondialdehyde (MDA) levels were not significantly (p > 0.05) affected by astaxanthin or vitamin E. Findings from this study will contribute toward a better understanding of the dietary effects of antioxidant and pigment in juvenile giant grouper. We present that dietary treatment can modulate giant grouper pigmentation and may be used in the live fish trade. Further, this study contributes to narrowing the knowledge gap in formulating appropriate diets for giant grouper, which to date is fed diets formulated for other species

A biogeographic framework of octopod species diversification: the role of the Isthmus of Panama

The uplift of the Isthmus of Panama (IP) created a land bridge between Central and South America and caused the separation of the Western Atlantic and Eastern Pacific oceans, resulting in profound changes in the environmental and oceanographic conditions. To evaluate how these changes have influenced speciation processes in octopods, fragments of two mitochondrial (Cytochrome oxidase subunit I, COI and 16S rDNA) and two nuclear (Rhodopsin and Elongation Factor-1 alpha, EF-1 alpha) genes were amplified from samples from the Atlantic and Pacific oceans. One biogeographical and four fossil calibration priors were used within a relaxed Bayesian phylogenetic analysis framework to estimate divergence times among dadogenic events. Reconstruction of the ancestral states in phylogenies was used to infer historical biogeography of the lineages and species dispersal routes. The results revealed three well-supported Glades of transisthmian octopus sister species pair/complex (TSSP/TSSC) and two additional clades showing a low probability of species diversification, having been influenced by the IP. Divergence times estimated in the present study revealed that octopod TSSP/TSSC from the Atlantic and Pacific diverged between the Middle Miocene and Early Pliocene (mean range = 5-18 Ma). Given that oceanographic changes caused by the uplift of the IP were so strong as to affect the global climate, we suggest that octopod TSSP/TSSC diverged because of these physical and environmental barriers, even before the complete uplift of the IP 3 Ma, proposed by the Late Pliocene model. The results obtained in this phylogenetic reconstruction also indicate that the octopus species pairs in each ocean share a recent common ancestor from the Pacific Ocean

The complete mitochondrial genome of Axis porcinus (Mammalia: Cervidae) from Victoria, Australia, using MiSeq sequencing

The mitochondrial genome of the hog deer (Axis porcinus) was sequenced using an Illumina MiSeq. The assembled genome consists of 16,351 bp, and shared a 99.8% similarity to the published chital deer (Axis axis) genome, suggesting that they belong to the same species. Further research is ongoing to understand why these mitochondrial genomes are highly similar

Detecting glacial refugia in the Southern Ocean

Throughout the Quaternary, the continental‐based Antarctic ice sheets expanded and contracted repeatedly. Evidence suggests that during glacial maxima, grounded ice eliminated most benthic (bottom‐dwelling) fauna across the Antarctic continental shelf. However, paleontological and molecular evidence indicates most extant Antarctica benthic taxa have persisted in situ throughout the Quaternary. Where and how the Antarctic benthic fauna survived throughout repeated glacial maxima remain mostly hypothesised. If understood, this would provide valuable insights into the ecology and evolution of Southern Ocean biota over geological timescales. Here we synthesised and appraised recent studies and presented an approach to demonstrate how genetic data can be effective in identifying where and how Antarctic benthic fauna survived glacial periods. We first examined the geological and ecological evidence for how glacial periods influenced past species demography in order to provide testable frameworks for future studies. We outlined past ice‐free areas from Antarctic ice sheet reconstructions that could serve as glacial refugia and discussed how benthic fauna with pelagic or non‐pelagic dispersal strategies moved into and out of glacial refugia. We also reviewed current molecular studies and collated proposed locations of Southern Ocean glacial refugia on the continental shelf around Antarctica, in the deep sea, and around sub‐Antarctic islands. Interestingly, the proposed glacial refugia based on molecular data generally do not correspond to the ice‐free areas identified by Antarctic ice sheet reconstructions. The potential biases in sampling and in the choice of molecular markers in current literature are discussed, along with the future directions for employing testable frameworks and genomic methods in Southern Ocean molecular studies. Continued data syntheses will elucidate greater understanding of where and how Southern Ocean benthic fauna persisted throughout glacial periods and provide insights into their resilience against climate changes in the future

Distribution of Palinuridae and Scyllaridae phyllosoma larvae within the East Australian Current: a climate change hot spot

Many marine species are predicted to shift their ranges poleward due to rising ocean temperatures driven by climate change. For benthic marine species with pelagic larval stages, poleward range shifts are often facilitated through pelagic larval transport via western boundary currents (WBC). By surveying pelagic larval distributions within WBCs, species advected poleward of their known distributions can be identified and monitored. Palinurid and scyllarid lobster larvae (phyllosoma) have long pelagic larval durations, providing high potential for poleward advection. We surveyed spatial distribution of phyllosoma within the western-boundary East Australian Current. Due to difficulties morphologically identifying phyllosoma, we tested the utility of molecular identification using cytochrome c oxidase I (COI). From COI sequences of 56 phyllosoma and one postlarva, 65% of sequences consisted of good-quality mitochondrial DNA. Across water types sampled, scyllarid phyllosoma exhibited relatively homogeneous distribution, whereas palinurid phyllosoma exhibited heterogeneous distribution with greatest abundance inside a warm core eddy on the south coast of eastern Australia. Two tropical and one subtropical palinurid species were detected ~75–1800 km to the south or south-west of their known species distribution. Our results indicate tropical lobster species are reaching temperate regions, providing these species the opportunity to establish in temperate regions if or when environmental conditions become amenable to settlement

Epipodial tentacle gene expression and predetermined resilience to summer mortality in the commercially important greenlip abalone, Haliotis laevigata

"Summer mortality" is a phenomenon that occurs during warm water temperature spikes that results in the mass mortality of many ecologically and economically important mollusks such as abalone. This study aimed to determine whether the baseline gene expression of abalone before a laboratory-induced summer mortality event was associated with resilience to summer mortality. Tentacle transcriptomes of 35 greenlip abalone (Haliotis laevigata) were sequenced prior to the animals being exposed to an increase in water temperature — simulating conditions which have previously resulted in summer mortality. Abalone derived from three source locations with different environmental conditions were categorized as susceptible or resistant to summer mortality depending on whether they died or survived after the water temperature was increased. We detected two genes showing significantly higher expression in resilient abalone relative to susceptible abalone prior to the laboratory-induced summer mortality event. One of these genes was annotated through the NCBI non-redundant protein database using BLASTX to an anemone (Exaiptasia pallida) Transposon Ty3-G Gag Pol polyprotein. Distinct gene expression signatures were also found between resilient and susceptible abalone depending on the population origin, which may suggest divergence in local adaptation mechanisms for resilience. Many of these genes have been suggested to be involved in antioxidant and immune-related functions. The identification of these genes and their functional roles have enhanced our understanding of processes that may contribute to summer mortality in abalone. Our study supports the hypothesis that prestress gene expression signatures are indicative of the likelihood of summer mortality