Oliver Berry

Can assignment tests measure dispersal

Individual‐based assignment tests are now standard tools in molecular ecology and have several applications, including the study of dispersal. The measurement of natal dispersal is vital to understanding the ecology of many species, yet the accuracy of assignment tests in situations where natal dispersal is common remains untested in the field. We studied a metapopulation of the grand skink, Oligosoma grande, a large territorial lizard from southern New Zealand. Skink populations occur on isolated, regularly spaced rock outcrops and are characterized by frequent interpopulation dispersal. We examined the accuracy of assignment tests at four replicate sites by comparing long‐term mark‐and‐recapture records of natal dispersal with the results of assignment tests based on microsatellite DNA data. Assignment tests correctly identified the natal population of most individuals (65–100%, depending on the method of assignment), even when interpopulation dispersal was common (5–20% dispersers). They also provided similar estimates of the proportions of skinks dispersing to those estimated by the long‐term mark‐and‐recapture data. Fully and partially Bayesian assignment methods were equally accurate but their accuracy depended on the stringency applied, the degree of genetic differentiation between populations, and the number of loci used. In addition, when assignments required high confidence, the method of assignment (fully or partially Bayesian) had a large bearing on the number of individuals that could be assigned. Because assignment tests require significantly less fieldwork than traditional mark‐and‐recapture approaches (in this study < 3 months vs. > 7 years), they will provide useful dispersal data in many applied and theoretical situations.

Faecal DNA detection of invasive species: the case of feral foxes in Tasmania.

Early detection of biological invasions is critical to reducing their impact, but because invading organisms are initially at low densities, detection and eradication can be challenging. Here, we demonstrate the utility of faecal DNA analysis for the detection of an elusive invasive species - the red fox, Vulpes vulpes, which was illegally introduced to the island of Tasmania in the late 1990s. Foxes are a devastating pest to both wildlife and agriculture on the Australian mainland, and would have a similarly serious impact in Tasmania if they became established. Attempts to eradicate foxes from Tasmania have been hampered by unreliable distribution data derived mostly from public sightings. In response, we developed a highly accurate and reliable DNA-based PCR-multiplex test that identifies foxes from field-collected faeces. We also developed a sexing test, but it was reliable only for faeces less than three weeks old. Faeces are a useful target for DNA-based diagnostics in foxes because they are deposited in prominent locations and are long-lasting. The species iden- tification test formed a key component of a Tasmania-wide detection and eradication program. In all, 1160 geo-referenced carnivore scats were analysed; of these, 78% contained DNA of sufficient quality for species identification. A single scat from the north-east of the island was identified as belonging to fox, as was a nine-week-old roadkill carcass from the north coast, and a blood sample from near Hobart, triggering increased control and surveillance in these regions. The accuracy, reliability, and cost-effectiveness of non-invasive tests make them a critical adjunct to traditional tools for monitoring cryptic invasive species that are at low density in the early stages of invasion and when eradication is still an option.

Cats (Felis catus) are more abundant and are the dominant predator of woylies (Bettongia penicillata) after sustained fox (Vulpes vulpes) control

Abstract. The control of foxes (Vulpes vulpes) is a key component of many fauna recovery programs in Australia. A question crucial to the success of these programs is how fox control influences feral cat abundance and subsequently affects predation upon native fauna. Historically, this question has been difficult to address because invasive predators are typically challenging to monitor. Here, non-invasive DNA analysis was used to determine the fate of radio-collared woylies (Bettongia penicillata) in two reserves in a mesic environment where foxes had been controlled intensively for over two decades. Woylie trap success had increased more than 20-fold after fox baiting commenced in the 1980s but decreased precipitously in 2000. Ninety-eight monitored woylies were killed between 2006 and 2009. DNA analysis of swabs taken from radio-collars and carcasses of these woylies indicated that predation by cats (Felis catus) caused most mortalities (65%) and was three times the fox predation rate (21%). Also, indices of cat abundance were higher in fox-baited sites where foxes were less abundant. Predation on woylies by cats was greater than previously recognised and, by implication, may significantly reduce the effectiveness of fox control programs throughout Australia. Integrated fox and cat control is essential to ensure the success of fauna recovery programs.

Larviposition, Host Cues, and Planidial Behavior in the Sound-Locating Parasitoid Fly Homotrixa alleni (Diptera: Tachinidae)

Some groups of tachinid flies deposit mobile first-instar larvae (or planidia) on or near their host. Flies within one such group, the tribe Ormiini, parasitize singing species of ensiferan Orthoptera and use sound for long distance host location. However, what induces tachinids to larviposit and whether planidia use any cues actively to locate their host remains poorly known. This paper examines the larviposition and planidial behavior of the ormiine Homotrixa alleni in relation to its bushcricket host, Sciarasaga quadrata. Sound alone was sufficient to elicit larviposition in gravid female H. alleni, where females arriving at an arena placed over a speaker broadcasting host song deposited an equal number of planidia in the presence or absence of a silent S. quadrata. Flies were observed to larviposit by forcibly expelling planidia up to 6 cm in a forward direction from the fly, with less than half of the trials with a host present resulting in physical contact between the host and the fly. In the hosts absence, flies walked around the arena significantly more often, remained on the arena for the experimental duration (10 min), and changed orientation frequently. In the hosts presence, flies generally maintained a position facing the host, stayed in the quadrant of first approach, and typically flew off the arena within 2 min of arrival. When the oncoming fly approached a forward facing host, more planidia were found in the arenas center (i.e., closer to the host) than in the no-host or rearward-facing host treatment. Planidia experimentally placed on a circular arena averaged 1 cm of movement in 15 min but none of the following cues–host song, host song with song-vibration transmission, a silent host, and a silent host with host movement-vibration transmission–significantly affected the direction or distance planidia traveled. At 20 ± 1°C, over half of the planidia died within 1 h and all died within 2 h of deposition. The significance of these results in relation to reproductive strategies and parasitism is discussed.

Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories

Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the worlds most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization time frame suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y‐chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long‐term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva.

Death by sex in an Australian icon: a continent-wide survey reveals extensive hybridization between dingoes and domestic dogs.

Hybridization between domesticated animals and their wild counterparts can disrupt adaptive gene combinations, reduce genetic diversity, extinguish wild populations and change ecosystem function. The dingo is a free‐ranging dog that is an iconic apex predator and distributed throughout most of mainland Australia. Dingoes readily hybridize with domestic dogs, and in many Australian jurisdictions, distinct management strategies are dictated by hybrid status. Yet, the magnitude and spatial extent of domestic dog–dingo hybridization is poorly characterized. To address this, we performed a continent‐wide analysis of hybridization throughout Australia based on 24 locus microsatellite DNA genotypes from 3637 free‐ranging dogs. Although 46% of all free‐ranging dogs were classified as pure dingoes, all regions exhibited some hybridization, and the magnitude varied substantially. The southeast of Australia was highly admixed, with 99% of animals being hybrids or feral domestic dogs, whereas only 13% of the animals from remote central Australia were hybrids. Almost all free‐ranging dogs had some dingo ancestry, indicating that domestic dogs could have poor survivorship in nonurban Australian environments. Overall, wild pure dingoes remain the dominant predator over most of Australia, but the speed and extent to which hybridization has occurred in the approximately 220 years since the first introduction of domestic dogs indicate that the process may soon threaten the persistence of pure dingoes.

Increased expression of Hsp70 and Hsp90 mRNA as biomarkers of thermal stress in loggerhead turtle embryos (Caretta Caretta).

The survival and viability of sea turtle embryos is dependent upon favourable nest temperatures throughout the incubation period. Consequently, future generations of sea turtles may be at risk from increasing nest temperatures due to climate change, but little is known about how embryos respond to heat stress. Heat shock genes are likely to be important in this process because they code for proteins that prevent cellular damage in response to environmental stressors. This study provides the first evidence of an expression response in the heat shock genes of embryos of loggerhead sea turtles (Caretta caretta) exposed to realistic and near-lethal temperatures (34°C and 36°C) for 1 or 3 hours. We investigated changes in Heat shock protein 60 (Hsp60), Hsp70, and Hsp90 mRNA in heart (n=24) and brain tissue (n=29) in response to heat stress. Under the most extreme treatment (36°C, 3h), Hsp70 increased mRNA expression by a factor of 38.8 in heart tissue and 15.7 in brain tissue, while Hsp90 mRNA expression increased by a factor of 98.3 in heart tissue and 14.7 in brain tissue. Hence, both Hsp70 and Hsp90 are useful biomarkers for assessing heat stress in the late-stage embryos of sea turtles. The method we developed can be used as a platform for future studies on variation in the thermotolerance response from the clutch to population scale, and can help us anticipate the resilience of reptile embryos to extreme heating events.

Microsatellite DNA markers for New Zealand skinks

Reptiles are a prominent part of the faunal diversity of New Zealand, but most species have suffered major range declines or extinctions in the past 2000 years. Nearly fifty percent of species (26 of 62) are now threatened or restricted to offshore islands and eight are subject to recovery programs (Towns and Daugherty 1994; Towns et al. 2001). Most declines can be attributed to loss or modification of habitat and predation by introduced mammals. Previous genetic studies of New Zealand reptiles have increased the number of recognised species (e.g. Daugherty et al. 1990), but provided little autecological or population-level genetic information that could be applied to management. Here we present the first microsatellite DNA markers to be developed for a New Zealand lizard. We are using these markers to study dispersal in the grand skink, Oligosoma grande, a large rock-dwelling lizard endemic to sub-alpine grasslands in southern New Zealand. This formerly widespread species now has a restricted range, and is listed as ‘vulnerable’ under IUCN criteria (HiltonTaylor 2000).

Cryptic genetic divergence within threatened species of Acropora coral from the Indian and Pacific Oceans

Most hard corals have broad distributions, and historically this was attributed to their capability for extensive dispersal leading to high evolutionary and demographic inter-dependence among regions. More recently there has been a paradigm shift in the understanding of coral dispersal, driven largely by genetic evidence, which has put greater emphasis on self-recruitment and larval retention. There is now a growing body of evidence that morphologically cryptic species exist within many recognized ‘species’ of stony corals. Here, we characterise levels of genetic divergence within and between five species of Acropora sampled from disparate populations spanning the Indo-Pacific Oceans. We find that strong regional genetic differentiation corresponding to the separation of the Indian and Pacific Ocean basins is a consistent pattern in three of the five species examined. Furthermore, the extent of allopatric divergence within species is similar to that observed between species, implying negligible contemporary gene flow between regions in four of the five species examined. This is consistent with the presence of numerous morphologically cryptic allopatric subspecies or incipient Acropora species. If this is confirmed, the conservation status of several species, which are already demonstrably threatened, would require re-evaluation so that risks including silent extinctions and inappropriate translocations are properly managed.

Forensic DNA confirms intraguild killing of a chuditch ( Dasyurus geoffroii ) by a feral cat ( Felis catus )

Because animals killed by predators are often found partially consumed or decomposed, identification of the predator is often unachievable by post mortem examination. Forensic DNA offers an alternative in such situations. Using a novel method to analyse DNA from bite wounds on a freshly-killed chuditch Dasyurus geoffroii, we describe the first confirmed instance in this species of intraguild killing by a feral cat. Unlike post mortem examination, our method of DNA melt curve analysis is highly accurate and requires less time and expense than DNA sequencing.