ORCID Profile
0000-0002-8185-6091
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Environmental Science and Management | Forestry Sciences | Genetics | Terrestrial Ecology | Population And Ecological Genetics | Forestry Management and Environment | Conservation and Biodiversity | Conservation And Biodiversity | Photogrammetry and remote sensing | Wildlife and Habitat Management | Ecology | Developmental Genetics (incl. Sex Determination) | Population Ecology | Environmental management | Ecological Impacts of Climate Change | Marine And Estuarine Ecology (Incl. Marine Ichthyology) | Population ecology | Conservation and biodiversity | Behavioural Ecology |
ANZSRC Socio-Economic Objective (SEO)
Native Forests | Living resources (flora and fauna) | Land and water management | Flora, Fauna and Biodiversity at Regional or Larger Scales | Forest and Woodlands Flora, Fauna and Biodiversity | Ecosystem Adaptation to Climate Change | Native forests | Wind Energy | Environmental and resource evaluation not elsewhere classified | Living resources (flora and fauna) | Socio-cultural issues | Expanding Knowledge in the Biological Sciences | Farmland, Arable Cropland and Permanent Cropland Flora, Fauna and Biodiversity | Forest and Woodlands Land Management
Related Links
Publications
Under‐representation of avian studies in landscape genetics
Publisher: Wiley
Date: 20-09-2017
DOI: 10.1111/IBI.12532
Contrasting population manipulations reveal resource competition between two large marsupials: bare-nosed wombats and eastern grey kangaroos
Publisher: Springer Science and Business Media LLC
Date: 06-06-2021
Making the connection: expanding the role of restoration genetics in restoring and evaluating connectivity
Publisher: Wiley
Date: 12-03-2018
DOI: 10.1111/REC.12692
A hybrid zone and bidirectional introgression between two catadromous species: Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum
Publisher: Wiley
Date: 25-10-2011
DOI: 10.1111/J.1095-8649.2011.03105.X
Abstract: The presence and distribution of hybrid in iduals and the existence of a hybrid zone between the catadromous Australian bass Macquaria novemaculeata and estuary perch Macquaria colonorum were investigated throughout the range of both species in Australia. Bayesian analyses and genotypic simulations identified 140 putative hybrids (11·5% of the total s le) with varying levels of introgression. Most hybrids were observed in an area extending from the Snowy River to the Albert River suggesting a hybrid zone in the eastern Bass Strait region. Sixteen hybrids, however, were found outside this zone, possibly reflecting the movement of hybrid offspring between estuaries or their inadvertent release during fish stocking programmes. Biparental backcrossing was found to occur suggesting that hybrids were fertile. These results have implications for the management of the extensive stocking programme in M. novemaculeata and for understanding the potential role of habitat degradation and reduced water flow in facilitating hybridization in species with migratory life histories.
Trophic position determines functional and phylogenetic recovery after disturbance within a community
Publisher: Wiley
Date: 29-03-2017
Implications of macroalgal isolation by distance for networks of marine protected areas
Publisher: Wiley
Date: 26-12-2013
DOI: 10.1111/COBI.12203
Abstract: The global extent of macroalgal forests is declining, greatly affecting marine bio ersity at broad scales through the effects macroalgae have on ecosystem processes, habitat provision, and food web support. Networks of marine protected areas comprise one potential tool that may safeguard gene flow among macroalgal populations in the face of increasing population fragmentation caused by pollution, habitat modification, climate change, algal harvesting, trophic cascades, and other anthropogenic stressors. Optimal design of protected area networks requires knowledge of effective dispersal distances for a range of macroalgae. We conducted a global meta-analysis based on data in the published literature to determine the generality of relation between genetic differentiation and geographic distance among macroalgal populations. We also examined whether spatial genetic variation differed significantly with respect to higher taxon, life history, and habitat characteristics. We found clear evidence of population isolation by distance across a multitude of macroalgal species. Genetic and geographic distance were positively correlated across 49 studies a modal distance of 50-100 km maintained F(ST) < 0.2. This relation was consistent for all algal isions, life cycles, habitats, and molecular marker classes investigated. Incorporating knowledge of the spatial scales of gene flow into the design of marine protected area networks will help moderate anthropogenic increases in population isolation and inbreeding and contribute to the resilience of macroalgal forests.
Geological and biological evidence for drainage reorientation during uplift of alluvial basins, central Otago, New Zealand
Publisher: Informa UK Limited
Date: 12-2007
Persistence and dispersal in a Southern Hemisphere glaciated landscape: the phylogeography of the spotted snow skink (Niveoscincus ocellatus) in Tasmania
Publisher: Springer Science and Business Media LLC
Date: 26-06-2015
A practical guide to DNA metabarcoding for entomological ecologists
Publisher: Wiley
Date: 30-12-2019
DOI: 10.1111/EEN.12831
Geological Dates and Molecular Rates: Fish DNA Sheds Light on Time Dependency
Publisher: Oxford University Press (OUP)
Date: 14-02-2008
Abstract: Knowledge of DNA evolution is central to our understanding of biological history, but how fast does DNA change? Previously, pedigree and ancient DNA studies--focusing on evolution in the short term--have yielded molecular rate estimates substantially faster than those based on deeper phylogenies. It has recently been suggested that short-term, elevated molecular rates decay exponentially over 1-2 Myr to long-term, phylogenetic rates, termed "time dependency of molecular rates." This transition has potential to confound molecular inferences of demographic parameters and dating of many important evolutionary events. Here, we employ a novel approach--geologically dated changes in river drainages and isolation of fish populations--to document rates of mitochondrial DNA change over a range of temporal scales. This method utilizes precise spatiotemporal disruptions of linear freshwater systems and hence avoids many of the limitations associated with typical DNA calibration methods involving fossil data or island formation. Studies of freshwater-limited fishes across the South Island of New Zealand have revealed that genetic relationships reflect past, rather than present, drainage connections. Here, we use this link between drainage geology and genetics to calibrate rates of molecular evolution across nine events ranging in age from 0.007 Myr (Holocene) to 5.0 Myr (Pliocene). Molecular rates of change in galaxiid fishes from calibration points younger than 200 kyr were faster than those based on older calibration points. This study provides conclusive evidence of time dependency in molecular rates as it is based on a robust calibration system that was applied to closely related taxa, and analyzed using a consistent and rigorous methodology. The time dependency observed here appears short-lived relative to previous suggestions (1-2 Myr), which has bearing on the accuracy of molecular inferences drawn from processes operating within the Quaternary and mechanisms invoked to explain the decay of rates with time.
Marine dispersal as a pre‐requisite for Gondwanan vicariance among elements of the galaxiid fish fauna
Publisher: Wiley
Date: 15-09-2011
Sex reversal explains some, but not all, climate-mediated sex ratio variation within a viviparous reptile
Publisher: The Royal Society
Date: 06-2022
Abstract: Evolutionary transitions in sex-determining systems have occurred frequently yet understanding how they occur remains a major challenge. In reptiles, transitions from genetic to temperature-dependent sex determination can occur if the gene products that determine sex evolve thermal sensitivity, resulting in sex-reversed in iduals. However, evidence of sex reversal is limited to oviparous reptiles. Here we used thermal experiments to test whether sex reversal is responsible for differences in sex determination in a viviparous reptile, Carinascincus ocellatus, a species with XY sex chromosomes and population-specific sex ratio response to temperature. We show that sex reversal is occurring and that its frequency is related to temperature. Sex reversal was unidirectional (phenotypic males with XX genotype) and observed in both high- and low-elevation populations. We propose that XX-biased genotypic sex ratios could produce either male- or female-biased phenotypic sex ratios as observed in low-elevation C. ocellatus under variable rates of XX sex reversal. We discuss reasons why sex reversal may not influence sex ratios at high elevation. Our results suggest that the mechanism responsible for evolutionary transitions from genotypic to temperature-dependent sex determination is more complex than can be explained by a single process such as sex reversal.
Extreme Intraspecific Mitochondrial DNA Sequence Divergence inGalaxias maculatus(Osteichthys: Galaxiidae), One of the World's Most Widespread Freshwater Fish
Publisher: Elsevier BV
Date: 02-1999
Abstract: Biogeographic controversies surrounding the widespread freshwater fish, Galaxias maculatus, were addressed with DNA sequence data. Mitochondrial cytochrome b and 16S rRNA sequences were obtained from representatives of six populations of this species. Substantial levels of cytochrome b (maximum 14.6%) and 16S rRNA sequence ergence (maximum 6.0%) were detected between western Pacific (Tasmania-New Zealand) and South American (Chile-Falkland Islands) haplotypes. A considerable level of ergence was also detected between Tasmanian and New Zealand haplotypes (maximum 5.1%) and within and among Chilean and Falkland Island G. maculatus (maximum 3. 8%). The phylogenetic structure of haplotypes conflicts with the accepted pattern of continental fragmentation. Molecular clock calibrations suggest that haplotype ergences postdate the fragmentation of Gondwana. These findings point to marine dispersal rather than ancient vicariance as an explanation for the wide distribution. The phylogenetic structure of South American haplotypes was not consistent with their geographic distribution. We consider factors such as population ergence, population size, dispersal, secondary contact, and philopatry as potential causes of the high level of mtDNA nucleotide ersity in this species.
Evolution of the Taieri River catchment, East Otago, New Zealand
Publisher: Informa UK Limited
Date: 02-04-2016
Isolation via next‐generation sequencing of microsatellites from the Tasmanian macroalgae Lessonia corrugata (Lessoniaceae)
Publisher: Wiley
Date: 07-2015
DOI: 10.3732/APPS.1500042
From rivers to ocean basins: the role of ocean barriers and philopatry in the genetic structuring of a cosmopolitan coastal predator
Publisher: Wiley
Date: 02-2023
DOI: 10.1002/ECE3.9837
Abstract: The Bull Shark ( Carcharhinus leucas ) faces varying levels of exploitation around the world due to its coastal distribution. Information regarding population connectivity is crucial to evaluate its conservation status and local fishing impacts. In this study, we s led 922 putative Bull Sharks from 19 locations in the first global assessment of population structure of this cosmopolitan species. Using a recently developed DNA‐capture approach (DArTcap), s les were genotyped for 3400 nuclear markers. Additionally, full mitochondrial genomes of 384 Indo‐Pacific s les were sequenced. Reproductive isolation was found between and across ocean basins (eastern Pacific, western Atlantic, eastern Atlantic, Indo‐West Pacific) with distinct island populations in Japan and Fiji. Bull Sharks appear to maintain gene flow using shallow coastal waters as dispersal corridors, whereas large oceanic distances and historical land‐bridges act as barriers. Females tend to return to the same area for reproduction, making them more susceptible to local threats and an important focus for management actions. Given these behaviors, the exploitation of Bull Sharks from insular populations, such as Japan and Fiji, may instigate local decline that cannot readily be replenished by immigration, which can in turn affect ecosystem dynamics and functions. These data also supported the development of a genetic panel to ascertain the population of origin, which will be useful in monitoring the trade of fisheries products and assessing population‐level impacts of this harvest.
Intrinsic factors drive spatial genetic variation in a highly vagile species, the wedge‐tailed eagle Aquila audax, in Tasmania
Publisher: Wiley
Date: 10-05-2017
DOI: 10.1111/JAV.01326
Identifying mechanisms of genetic differentiation among populations in vagile species: historical factors dominate genetic differentiation in seabirds
Publisher: Wiley
Date: 05-02-2020
DOI: 10.1111/BRV.12580
Pleistocene divergence in the absence of gene flow among populations of a viviparous reptile with intraspecific variation in sex determination
Publisher: Wiley
Date: 25-03-2021
DOI: 10.1002/ECE3.7458
Abstract: Polymorphisms can lead to genetic isolation if there is differential mating success among conspecifics ergent for a trait. Polymorphism for sex‐determining system may fall into this category, given strong selection for the production of viable males and females and the low success of heterogametic hybrids when sex chromosomes differ (Haldane's rule). Here we investigated whether populations exhibiting polymorphism for sex determination are genetically isolated, using the viviparous snow skink Carinascincus ocellatus . While a comparatively high elevation population has genotypic sex determination, in a lower elevation population there is an additional temperature component to sex determination. Based on 11,107 SNP markers, these populations appear genetically isolated. “Isolation with Migration” analysis also suggests these populations erged in the absence of gene flow, across a period encompassing multiple Pleistocene glaciations and likely greater geographic proximity of populations. However, further experiments are required to establish whether genetic isolation may be a cause or consequence of differences in sex determination. Given the influence of temperature on sex in one lineage, we also discuss the implications for the persistence of this polymorphism under climate change.
Social structure and landscape genetics of the endemic New Caledonian ant Leptomyrmex pallens Emery, 1883 (Hymenoptera: Formicidae: Dolichoderinae), in the context of fire-induced rainforest fragmenta
Publisher: Springer Science and Business Media LLC
Date: 17-03-2016
The significance of past interdrainage connectivity for studies of diversity, distribution and movement of freshwater‐limited taxa within a catchment
Publisher: Wiley
Date: 03-10-2013
DOI: 10.1111/JBI.12207
Geological Dates and Molecular Rates: Rapid Divergence of Rivers and Their Biotas
Publisher: Oxford University Press (OUP)
Date: 04-2007
DOI: 10.1080/10635150701313855
Abstract: We highlight a novel molecular clock calibration system based on geologically dated river reversal and river capture events. Changes in drainage pattern may effect vicariant isolation of freshwater taxa, and thus provide a predictive framework for associated phylogeographic study. As a case in point, New Zealand's Pelorus and Kaituna rivers became geologically isolated from the larger Wairau River system 70 to 130 kyr BP. We conducted mitochondrial DNA phylogeographic analyses of two unrelated freshwater-limited fish taxa native to these river systems (Gobiomorphus breviceps, n = 63 Galaxias ergens, n = 95). Phylogenetic analysis of combined control region and cytochrome b sequences yielded reciprocally monophyletic clades of Pelorus-Kaituna and Wairau haplotypes for each species. Calibrated rates of molecular change based on this freshwater vicariant event are substantially faster than traditionally accepted rates for fishes but consistent with other recent inferences based on geologically young calibration points. A survey of freshwater phylogeographic literature reveals numerous ex les in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations. We recommend that--wherever possible--biologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.
Gene Trees versus Species Trees: Reassessing Life-History Evolution in a Freshwater Fish Radiation
Publisher: Oxford University Press (OUP)
Date: 05-07-2010
Abstract: Mechanisms of speciation are best understood in the context of phylogenetic relationships and as such have often been inferred from single gene trees, typically those derived from mitochondrial DNA (mtDNA) markers. Recent studies, however, have noted the potential for phylogenetic discordance between gene trees and underlying species trees (e.g., due to stochastic lineage sorting, introgression, or selection). Here, we employ a variety of nuclear DNA loci to reassess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation. New Zealand's freshwater-limited Galaxias vulgaris complex is thought to have evolved from G. brevipinnis, a widespread migratory species that retains a plesiomorphic marine juvenile phase. A well-resolved tree, based on four mtDNA regions, previously suggested that marine migratory ability has been lost on 3 independent occasions in the evolution of this species flock (assuming that loss of diadromy is irreversible). Here, we use pseudogene (galaxiid Numt: 1801 bp), intron (S: 903 bp), and exon (RAG-1: 1427 bp) markers, together with mtDNA, to reevaluate this hypothesis of parallel evolution. Interestingly, partitioned Bayesian analysis of concatenated nuclear sequences (3141 bp) and concatenated nuclear and mtDNA (4770 bp) both recover phylogenies implying a single loss of diadromy, not three parallel losses as previously inferred from mtDNA alone. This phylogenetic result is reinforced by a multilocus analysis performed using Bayesian estimation of species trees (BEST) software that estimates the posterior distribution of species trees under a coalescent model. We discuss factors that might explain the apparently misleading phylogenetic inferences generated by mtDNA.
The lasting biological signature of Pliocene tectonics: Reviewing the re‐routing of Australia's largest river drainage system
Publisher: Wiley
Date: 02-06-2019
DOI: 10.1111/JBI.13612
Geology shapes biogeography: Quaternary river-capture explains New Zealand's biologically 'composite' Taieri River
Publisher: Elsevier BV
Date: 07-2015
Fine-scale habitat preferences influence within-river population connectivity: a case-study using two sympatric New Zealand Galaxias fish species
Publisher: Wiley
Date: 10-09-2016
DOI: 10.1111/FWB.12675
Nonequilibrium Conditions Explain Spatial Variability in Genetic Structuring of Little Penguin (Eudyptula minor)
Publisher: Oxford University Press (OUP)
Date: 04-2015
Understanding age-specifc dispersal in fishes through hydrodynamic modelling, genetic simulations and microsatellite DNA analysis
Publisher: Wiley
Date: 25-02-2012
Seascape habitat patchiness and hydrodynamics explain genetic structuring of kelp populations
Publisher: Inter-Research Science Center
Date: 25-01-2018
DOI: 10.3354/MEPS12447
DOES FISH ECOLOGY PREDICT DISPERSAL ACROSS A RIVER DRAINAGE DIVIDE?
Publisher: Wiley
Date: 06-2008
DOI: 10.1111/J.1558-5646.2008.00377.X
Abstract: Obligate freshwater taxa are frequently distributed among catchments isolated by marine and terrestrial barriers. Such distributions can arise through vicariant changes in drainage geometry, or dispersal via intermittent freshwater connections. We employed two adjacent rivers in southern New Zealand to test for interdrainage dispersal while controlling for historical drainage geometry, and analyzed four ecologically distinct freshwater-limited fish taxa to assess any relationship with habitat preference. In iduals from the Mararoa and Oreti catchments (n >100 per species) were sequenced for a minimum of 1297 bp of mitochondrial DNA (cytochrome b and control region). Phylogeographic relationships were consistent with ecological expectations of interdrainage dispersal capability, with the two obligate riverine taxa each exhibiting reciprocal monophyly between catchments, whereas the two facultative sw dwellers revealed paraphyletic relationships, one of which shared a haplotype between catchments. Statistical phylogeography, accommodating taxon-specific mutation rates and the known age of the last major riverine connection between these catchments, rejected complete isolation of populations for one of the sw dwellers. Therefore, dispersal across a young (145-240 kyr) drainage ide is inferred for one species, and can be predicted to some extent by species ecology. Moreover, our study highlights the importance of historical drainage geometry when assessing the causes of contemporary genetic structuring in freshwater taxa.
Using ancient DNA to quantify losses of genetic and species diversity in seabirds: a case study of Pterodroma petrels from a Pacific island
Publisher: Springer Science and Business Media LLC
Date: 03-04-2020
Ancient
DNA
tracks the mainland extinction and island survival of the Tasmanian devil
Publisher: Wiley
Date: 04-2018
DOI: 10.1111/JBI.13214
Evolution of biological dispersal corridors through a tectonically active mountain range in New Zealand
Publisher: Wiley
Date: 15-09-2008
Optimizing the use of shed feathers for genetic analysis
Publisher: Wiley
Date: 05-2008
DOI: 10.1111/J.1471-8286.2007.02044.X
Abstract: Shed feathers obtained by noninvasive genetic s ling (NGS) are a valuable source of DNA for genetic studies of birds. They can be collected across a large geographical range and facilitate research on species that would otherwise be extremely difficult to study. A limitation of this approach is uncertainty concerning the quality of the extracted DNA. Here we investigate the relationship between feather type, feather condition and DNA quality ( lification success) in order to provide a simple, cost-effective method for screening s les prior to genetic analysis. We obtained 637 shed feathers of the powerful owl (Ninox strenua) from across its range in southeastern Australia. The extracted DNA was lified using polymerase chain reaction for a range of markers including mitochondrial DNA, ND3 and nuclear DNA, a simple sequence repeat (Nst02) and a portion of the CHD-1 gene (P2/P8). We found that feather condition significantly influenced the lification success of all three loci, with feathers characterized as 'good' having greater success. Feather type was found to be of lower importance, with good quality feathers of all types consistently producing high success for all three loci. We also found that the successful lification of multilocus genotypes was dependant on the condition of the starting material and was highly correlated with successful lification of the sex-linked CHD-1 locus. S les with low DNA quality have a higher probability of lification failure and are more likely to produce incorrect genotypes therefore, identifying s les with high DNA quality can save substantial time and cost associated with the genetic analysis of NGS. As a result, we propose a method for screening shed feathers in order to provide a subset of s les which will have a greater probability of containing high quality DNA suitable for the lification of multilocus genotypes.
Population Genetic Structuring in Acanthopagrus butcheri (Pisces: Sparidae): Does Low Gene Flow Among Estuaries Apply to Both Sexes?
Publisher: Springer Science and Business Media LLC
Date: 22-08-2006
DOI: 10.1007/S10126-006-6023-7
Abstract: Acanthopagrus butcheri completes its entire life history within estuaries and coastal lakes of southern Australia, although adults occasionally move between estuaries via the sea. Consequently, it is expected that populations of A. butcheri in different estuaries will be genetically distinct, with the magnitude of genetic ergence increasing with geographic isolation. However, previous genetic studies of A. butcheri from southeast Australia yielded conflicting results allozyme variation exhibited minimal spatial structuring (theta = 0.012), whereas mitochondrial DNA distinguished the majority of populations analyzed (theta = 0.263) and genetic ergence was positively correlated with geographic isolation. This discrepancy could reflect high male gene flow, which impacts nuclear but not mitochondrial markers. Here we estimated allele frequencies at five nuclear microsatellite loci across 11 southeast Australian populations (595 in iduals). Overall structuring of microsatellite variation was weaker (theta = 0.088) than that observed for mitochondrial DNA, but was able to distinguish a greater number of populations and was positively correlated with geographic distance. Therefore, we reject high male gene flow and invoke a stepping-stone model of infrequent gene flow among estuaries for both sexes. Likewise, management of A. butcheri within the study range should be conducted at the scale of in idual or geographically proximate estuaries for both sexes. The lack of allozyme structuring in southeast Australia reflects either the large variance in structuring expected among loci under neutral conditions and the low number of allozymes surveyed or a recent colonization of estuaries such that some but not all nuclear loci have approached migration-drift equilibrium.
Open access solutions for biodiversity journals: Do not replace one problem with another
Publisher: Wiley
Date: 2019
DOI: 10.1111/DDI.12885
Isolation and characterization of microsatellite loci to DNA fingerprint the Powerful Owl (Ninox strenua)
Publisher: Wiley
Date: 11-06-2007
Development of 13 microsatellite loci in the spotted snow skink Niveoscincus ocellatus (Squamata: Scincidae)
Publisher: Springer Science and Business Media LLC
Date: 11-11-2010
Historic divergence with contemporary connectivity in a catadromous fish, the estuary perch (Macquaria colonorum)
Publisher: Canadian Science Publishing
Date: 02-2011
DOI: 10.1139/F10-139
Abstract: The estuary perch ( Macquaria colonorum ) represents an important model for assessing how historical changes in coastal geomorphology and current oceanographic and estuarine conditions may have impacted connectivity in a catadromous fish. A fragment of the mitochondrial control region and six microsatellite DNA markers were used to clarify connectivity in 17 populations (n = 354) of estuary perch from the southeast and southern coasts of Australia. The mtDNA data showed a latitudinal disjunction in haplotype frequencies that ided populations into two groups (Φ ST = 0.419), in a pattern suggestive of isolation by geographic distance. However, no marked structure or correlation with distance was apparent within each group, a result consistent with microsatellite data that showed high contemporary population connectivity across large distances. This was contrary to expectations that the species would exhibit moderate to strong genetic structure consistent with a one-dimensional stepping stone pattern. Coalescent phylogeographic and population genetic analyses provided support for a historical ergence probably due to the emergence of the Bassian Isthmus in southern Australia. Current connectivity appears to be maintained by both large- and fine-scale oceanographic currents and processes, highlighting the important role of the marine environment for an estuarine resident species.
Shallow phylogeographic histories of key species in a biodiversity hotspot
Publisher: Informa UK Limited
Date: 11-2015
DOI: 10.2216/15-24.1
Does the virus cross the road? Viral phylogeographic patterns among bobcat populations reflect a history of urban development
Publisher: Wiley
Date: 20-02-2020
DOI: 10.1111/EVA.12927
Biogeography Off the Tracks
Publisher: Oxford University Press (OUP)
Date: 15-03-2013
Genetic distinctiveness of Masked Booby (Sula dactylatra) on Bedout Island, Western Australia
Publisher: Informa UK Limited
Date: 12-09-2020
Late Quaternary river drainage and fish evolution, Southland, New Zealand
Publisher: Elsevier BV
Date: 02-2007
Rainfall and topography predict gene flow among populations of the declining northern quoll (Dasyurus hallucatus)
Publisher: Springer Science and Business Media LLC
Date: 25-06-2016
Development of eight polymorphic microsatellite loci in the cephalopod Octopus pallidus
Publisher: Springer Science and Business Media LLC
Date: 16-07-2012
Rapid biological speciation driven by tectonic evolution in New Zealand
Publisher: Springer Science and Business Media LLC
Date: 14-12-2016
DOI: 10.1038/NGEO2618
Twenty microsatellite loci for population and conservation genetic studies of the wedge-tailed eagle (Aquila audax)
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/ZO14030
Abstract: Twenty di- to pentanucleotide microsatellites are reported for the wedge-tailed eagle (Aquila audax), a large raptor from Australia, Tasmania, and New Guinea. These loci were tested for variation among 49 in iduals. All loci are polymorphic with 2–14 alleles per locus, and observed heterozygosities ranged between 0.021 and 0.898. Genotype frequencies for all loci did not differ significantly from Hardy–Weinberg equilibrium and there was no evidence of linkage disequilibrium. These markers will be used to assess population structure and conservation genetics of this species, focusing on population differentiation and gene flow between Tasmanian and mainland populations and conservation genetics of the endangered Tasmanian population.
An empirical test of freshwater vicariance via river capture
Publisher: Wiley
Date: 13-04-2007
Microsatellite loci for studies of wild and hatchery Australian Murray cod Maccullochella peelii peelii (Percichthyidae)
Publisher: Wiley
Date: 08-06-2004
Differences in homomorphic sex chromosomes are associated with population divergence in sex determination in Carinascincus ocellatus (Scincidae: Lygosominae)
Publisher: MDPI AG
Date: 02-2021
Abstract: Sex determination directs development as male or female in sexually reproducing organisms. Evolutionary transitions in sex determination have occurred frequently, suggesting simple mechanisms behind the transitions, yet their detail remains elusive. Here we explore the links between mechanisms of transitions in sex determination and sex chromosome evolution at both recent and deeper temporal scales ( Myr ~79 Myr). We studied a rare ex le of a species with intraspecific variation in sex determination, Carinascincus ocellatus, and a relative, Liopholis whitii, using c-banding and mapping of repeat motifs and a custom Y chromosome probe set to identify the sex chromosomes. We identified both unique and conserved regions of the Y chromosome among C. ocellatus populations differing in sex determination. There was no evidence for homology of sex chromosomes between C. ocellatus and L. whitii, suggesting independent evolutionary origins. We discuss sex chromosome homology between members of the subfamily Lygosominae and propose links between sex chromosome evolution, sex determination transitions, and karyotype evolution.
Population‐scale treatment informs solutions for control of environmentally transmitted wildlife disease
Publisher: Wiley
Date: 23-07-2019
Abstract: Long‐term pathogen control or eradication in wildlife is rare and represents a major challenge in conservation. Control is particularly difficult for environmentally transmitted pathogens, including some of the most conservation‐critical wildlife diseases. We undertook a treatment programme aimed at population‐scale eradication of the environmentally transmitted Sarcoptes scabiei mite (causative agent of sarcoptic mange) during an epizootic in bare‐nosed wombats ( Vombatus ursinus ). Field trial results were used to parameterize a mechanistic host‐disease model that explicitly described indirect transmission, host behaviour and viable disease intervention methods. Model analysis shows that elimination of S. scabiei in the wild is most sensitive to the success of treatment delivery, and duration of the programme. In addition, we found the frequency that wombats switch burrows was an important positive driver of mite persistence. Synthesis and applications . This research emphasizes the utility of applying model‐guided management techniques in order to achieve practical solutions for controlling disease in the field. We find that control efforts of Sarcoptes scabiei are most successful when simultaneous improvements are made to the current best‐practice protocol, specifically the implementation of better treatment application methods in combination with a longer lasting treatment. These suggested management changes may also reduce the resources and field effort required to implement a successful regime. Furthermore, our approach and findings have applicability to other species affected by S. scabiei (e.g. wolves, red foxes, Spanish ibex and American black bear), as well as other conservation‐critical systems involving environmental transmission (e.g. bat white‐nose syndrome and hibian chytridiomycosis).
Genetic ages for Quaternary topographic evolution: A new dating tool
Publisher: Geological Society of America
Date: 2008
DOI: 10.1130/G24126A.1
Pathogens in space: Advancing understanding of pathogen dynamics and disease ecology through landscape genetics
Publisher: Wiley
Date: 28-07-2018
DOI: 10.1111/EVA.12678
The effects of weather variability on patterns of genetic diversity in Tasmanian bettongs
Publisher: Wiley
Date: 15-03-2021
DOI: 10.1111/MEC.15847
Abstract: While the effects of climate (long‐term, prevailing weather) on species abundance, range and genetic ersity have been widely studied, short‐term, localized variations in atmospheric conditions (i.e., weather) can also rapidly alter species’ geographical ranges and population sizes, but little is known about how they affect genetic ersity. We investigated the relationship between weather and range‐wide genetic ersity in a marsupial, Bettongia gaimardi , using dynamic species distribution models (SDMs). Genetic ersity was lower in parts of the range where the weather‐based SDM predicted high variability in probability of B. gaimardi occurrence during 1950–2009. This is probably an effect of lower population sizes and extinction–recolonization cycles in places with highly variable weather. Spatial variation in genetic ersity was also better predicted by mean probabilities of B. gaimardi occurrence from weather‐ than climate‐based SDMs. Our results illustrate the importance of weather in driving population dynamics and species distributions on decadal timescales and thereby in affecting genetic ersity. Modelling the links between changing weather patterns, species distributions and genetic ersity will allow researchers to better forecast biological impacts of climate change.
Genome-wide analysis resolves the radiation of New Zealand's freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture
Publisher: Wiley
Date: 26-08-2022
DOI: 10.1111/DDI.13629
Abstract: Freshwater fish radiations are often characterized by multiple closely related species in close proximity, which can lead to introgression and associated discordance of mitochondrial and nuclear characterizations of species ersity. As a case in point, single locus nuclear versus mitochondrial analyses of New Zealand's stream‐resident Galaxias vulgaris complex have yielded conflicting phylogenies. Our goal is to use genome‐wide ergence patterns among these fishes to evaluate the potential role of mitochondrial capture in obscuring species ersity, and to understand how ancient and anthropogenic drainage modification explain this ersity. Freshwater ecosystems of New Zealand. We generate and analyse a genome‐wide dataset comprising 52,352 SNPs across 187 Galaxias specimens to resolve the phylogeny of this recent fish radiation. We conduct phylogenetic, PCA, STRUCTURE, and ABBA‐BABA analyses to evaluate the evolutionary relationships of lineages in the context of natural and anthropogenic river drainage alterations. In addition to the 11 previously recognized stream‐resident lineages, genome‐wide data reveal a twelfth candidate species ( G. ‘Pomahaka’), apparently obscured by introgressive mitochondrial capture. We identify additional ex les of mito‐nuclear discordance and putative mitochondrial capture, likely mediated by geological and anthropogenic modification of drainage boundaries. Our study highlights the need for genome‐wide approaches for delimiting freshwater bio ersity. Genetic data also reveal the influence of drainage history on freshwater bio ersity, including the rapid ergence of recently fragmented fish populations, and the conservation genetic risks of anthropogenic translocations events.
Does phylogeny explain bias in quantitative DNA metabarcoding?
Publisher: Pensoft Publishers
Date: 13-06-2023
Abstract: Estimating species biomass or abundance from the number of high-throughput sequencing (HTS) reads is an aspirational goal for DNA metabarcoding, yet studies have found varied correlations. Performance varies depending on the gene marker and taxonomic group and, in part, may be related to primer-template mismatches, which are likely to exhibit phylogenetic signals. In this study, we compared commonly used fragments of two gene markers for beetles, the mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S), which have similar lengths, but different propensity for primer-template mismatches. We tested whether primer-template mismatches influence the relationship between species biomass and HTS read abundance and whether the effect of mismatches was explained by phylogeny. A significant correlation between species biomass and HTS read abundance existed for 16S, but not for COI, which had more primer-template mismatches. Models incorporating the effects of mismatch type or number improved the estimation of species biomass from HTS read abundance for COI and strong phylogenetic signals were identified. Researchers seeking to quantify biomass from metabarcoding studies should consider the effect of primer-template mismatches for the taxonomic group of interest and, for beetles, 16S appears a good candidate. Phylogenetic correction can also improve biomass estimation when using gene markers with higher primer mismatching.
Sarcoptic mange changes bacterial and fungal microbiota of bare-nosed wombats (Vombatus ursinus)
Publisher: Springer Science and Business Media LLC
Date: 13-09-2022
DOI: 10.1186/S13071-022-05452-Y
Abstract: Sarcoptes scabiei is globally distributed and one of the most impactful mammalian ectoparasites. Sarcoptic mange, caused by infection with S. scabiei , causes disruption of the epidermis and its bacterial microbiota, but its effects on host fungal microbiota and on the microbiota of marsupials in general have not been studied. Here, we (i) examine bacterial and fungal microbiota changes associated with mange in wild bare-nosed wombats (BNWs) and (ii) evaluate whether opportunistic pathogens are potentiated by S. scabiei infection in this species. Using Amplicon Sequencing of the 16S rRNA and ITS2 rDNA genes, we detected skin microbiota changes of the bare-nosed wombat ( Vombatus ursinus ). We compared the alpha and beta ersity among healthy, moderate, and severe disease states using ANOVA and PERMANOVA with nesting. Lastly, we identified taxa that differed between disease states using analysis of composition of microbes (ANCOM) testing. We detected significant changes in the microbial communities and ersity with mange in BNWs. Severely affected BNWs had lower licon sequence variant (ASV) richness compared to that of healthy in iduals, and the microbial communities were significantly different between disease states with higher relative abundance of potentially pathogenic microbial taxa in mange-affected BNWs including Staphylococcus sciuri , Corynebacterium spp., Brevibacterium spp., Brachybacterium spp., and Pseudogymnascus spp. and Debaryomyces spp. This study represents the first investigation of microbial changes in association with sarcoptic mange in a marsupial host, as well as the first investigation of fungal microbial changes on the skin of any host suffering from sarcoptic mange. Our results are broadly consistent with bacterial microbiota changes observed in humans, pigs, canids, and Iberian ibex, suggesting the epidermal microbial impacts of mange may be generalisable across host species. We recommend that future studies investigating skin microbiota changes include both bacterial and fungal data to gain a more complete picture of the effects of sarcoptic mange.
Comparison of population structuring in sympatric octopus species with and without a pelagic larval stage
Publisher: Inter-Research Science Center
Date: 12-07-2013
DOI: 10.3354/MEPS10330
Within-river genetic connectivity patterns reflect contrasting geomorphology
Publisher: Wiley
Date: 09-2015
DOI: 10.1111/JBI.12608
Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease
Publisher: The Royal Society
Date: 11-2014
Abstract: The Tasmanian devil ( Sarcophilus harrisii ) was widespread in Australia during the Late Pleistocene but is now endemic to the island of Tasmania. Low genetic ersity combined with the spread of devil facial tumour disease have raised concerns for the species’ long-term survival. Here, we investigate the origin of low genetic ersity by inferring the species' demographic history using temporal s ling with summary statistics, full-likelihood and approximate Bayesian computation methods. Our results show extensive population declines across Tasmania correlating with environmental changes around the last glacial maximum and following unstable climate related to increased ‘El Niño–Southern Oscillation’ activity.
Allozyme diversity in Australian rainbow trout, Oncorhynchus mykiss
Publisher: Wiley
Date: 05-03-2004
Does migration promote or inhibit diversification? A case study involving the dominant radiation of temperate Southern Hemisphere freshwater fishes
Publisher: Wiley
Date: 13-08-2020
DOI: 10.1111/EVO.14066
River Capture and Freshwater Biological Evolution: A Review of Galaxiid Fish Vicariance
Publisher: MDPI AG
Date: 29-05-2020
DOI: 10.3390/D12060216
Abstract: Geological processes can strongly affect the distribution and ersification of freshwater-limited species. In particular, a combination of geological and biological data has suggested that Earth history processes can drive vicariant isolation and speciation in non-migratory freshwater fishes. Here, we synthesise recently published geological and freshwater phylogeographic data to illustrate that changes in river drainage geometry are important drivers of galaxiid ersification, both in New Zealand and elsewhere. Major river capture events have led to the isolation and ergence of unique and geographically-restricted lineages, including taxa that are now of prime conservation concern. The parallel phylogeographic effects of drainage shifts have been verified by observations of concordant patterns in co-distributed species. Broadly, this study highlights the dynamic interplay between physical and biological processes in geologically active settings.
Research supporting restoration aiming to make a fragmented landscape ‘functional’ for native wildlife
Publisher: Wiley
Date: 12-2021
DOI: 10.1111/EMR.12504
Abstract: Temperate woodlands are amongst the most threatened ecosystems in Australia because the land on which they occur is highly suited to agriculture. Two hundred years of habitat loss and fragmentation in the Midlands agricultural region in Tasmania have led to widespread declines in native vertebrates and landscapes with populations of predators including feral Cat ( Felis catus ) and the native‐invasive Noisy Miner ( Manorina melanocephala ). Ecologists at the University of Tasmania co‐designed mechanistic animal‐centric research on mammals and birds in the Midlands to inform vegetation restoration carried out by Greening Australia that would support the recovery of wildlife species. We used species‐appropriate technologies to assess the decisions made by in idual animals to find food and shelter and to disperse across this fragmented landscape, and linked these, together with patterns of occupancy, across multiple spatial and temporal scales. We focussed on a native (Spotted‐tailed Quoll, Dasyurus maculatus ) and an invasive (feral Cat, Felis catus ) carnivore, a woodland‐specialist herbivore (Eastern Bettong, Bettongia gaimardi ) and woodland birds including the native‐invasive Noisy Miner. Our results, which show intense predatory and competitive pressure of cats and populations of Noisy Miner on native fauna, highlight how grounding restoration in the context of ecological interactions is essential to success in managing the impacts of invasive species in restored landscapes. Successful restoration will require innovative approaches in plantings and field experimentation with artificial refuges, to reduce habitat suitability for the Noisy Miner and cats and provide refuges for native mammals and birds to live in the landscape where cats also occur. Our results emphasise the significance of structural complexity of restoration plantings for supporting the recolonisation and persistence of native fauna. At large landscape‐scale, we demonstrate the importance of retaining small habitat elements, including ancient paddock trees, pivot irrigation corners and small, degraded remnants, in facilitating occupancy and dispersal and, therefore, persistence of wild animals across this agricultural region.
Tectonic controls on the evolution of the Clutha River catchment, New Zealand
Publisher: Informa UK Limited
Date: 12-2012
Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads.
Publisher: Wiley
Date: 25-09-2022
DOI: 10.1111/MEC.16680
Abstract: Mammal declines across northern Australia are one of the major bio ersity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic ersity. To address this, we conducted a species-wide assessment of genomic ersity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 in iduals from across a 3220-km length of the continent, investigating patterns of population genomic structure and ersity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic ersity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in ersity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic ersity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic ersity after 16 years. By mapping patterns of genomic ersity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic ersity, and the characterization of putative evolutionarily significant units.
Invasive pathogen drives host population collapse: Effects of a travelling wave of sarcoptic mange on bare-nosed wombats
Publisher: Wiley
Date: 23-08-2017
Global Biodiversity Assessment and Hyper-Cryptic Species Complexes: More Than One Species of Elephant in the Room?
Publisher: Oxford University Press (OUP)
Date: 13-03-2014
Abstract: Several recent estimates of global bio ersity have concluded that the total number of species on Earth lies near the lower end of the wide range touted in previous decades. However, none of these recent estimates formally explore the real "elephant in the room", namely, what proportion of species are taxonomically invisible to conventional assessments, and thus, as undiagnosed cryptic species, remain uncountable until revealed by multi-gene molecular assessments. Here we explore the significance and extent of so-called "hyper-cryptic" species complexes, using the Australian freshwater fish Galaxias olidus as a proxy for any organism whose taxonomy ought to be largely finalized when compared to those in little-studied or morphologically undifferentiated groups. Our comprehensive allozyme (838 fish for 54 putative loci), mtDNA (557 fish for 605 bp of cytb), and morphological (1963-3389 vouchers for 17-58 characters) assessment of this species across its broad geographic range revealed a 1500% increase in species-level bio ersity, and suggested that additional taxa may remain undiscovered. Importantly, while all 15 candidate species were morphologically diagnosable a posteriori from one another, single-gene DNA barcoding proved largely unsuccessful as an a priori method for species identification. These results lead us to draw two strong inferences of relevance to estimates of global bio ersity. First, hyper-cryptic complexes are likely to be common in many organismal groups. Second, no assessment of species numbers can be considered "best practice" in the molecular age unless it explicitly includes estimates of the extent of cryptic and hyper-cryptic bio ersity. [Galaxiidae global estimates hyper- erse mountain galaxias species counts species richness.].
Genome-wide analysis resolves the radiation of New Zealand’s freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture
Publisher: Cold Spring Harbor Laboratory
Date: 05-07-2022
DOI: 10.1101/2022.07.04.498769
Abstract: Freshwater fish radiations are often characterized by multiple closely-related species in close proximity, which can lead to introgression and associated discordance of mitochondrial and nuclear characterizations of species ersity. As a case in point, single locus nuclear versus mitochondrial analyses of New Zealand’s stream-resident Galaxias vulgaris complex have yielded conflicting phylogenies. We generate and analyze a genome-wide data set comprising 52,352 SNPs across 187 Galaxias specimens to resolve the phylogeny of this recent fish radiation. We conduct phylogenetic, PCA, STRUCTURE, and ABBA-BABA analyses to evaluate the evolutionary relationships of lineages in the context of natural and anthropogenic river drainage alterations. In addition to the 11 previously recognized stream-resident lineages, genome-wide data reveal a twelfth candidate species ( G . ‘Pomahaka’), apparently obscured by introgressive mitochondrial capture. We identify additional ex les of mito-nuclear discordance and putative mitochondrial capture, likely mediated by geological and anthropogenic modification of drainage boundaries. Our study highlights the need for genome-wide approaches for delimiting freshwater bio ersity. Genetic data also reveal the influence of drainage history on freshwater bio ersity, including the rapid ergence of recently fragmented fish populations, and the conservation genetic risks of anthropogenic translocations events.
Conservation of sex-linked markers among conspecific populations of a viviparous skink, Niveoscincus occllatus, exhibiting genetic and temperature-dependent sex determination
Publisher: Oxford University Press (OUP)
Date: 05-03-2018
DOI: 10.1093/GBE/EVY042
River capture, range expansion, and cladogenesis: The genetic signature of freshwater vicariance
Publisher: The Society for the Study of Evolution
Date: 2006
DOI: 10.1554/05-439.1
Disease induced changes in gene flow patterns among Tasmanian devil populations
Publisher: Elsevier BV
Date: 09-2013
Lack of detectable genetic isolation in the cyclic rodent Microtus arvalis despite large landscape fragmentation owing to transportation infrastructures
Publisher: Springer Science and Business Media LLC
Date: 15-06-2021
DOI: 10.1038/S41598-021-91824-W
Abstract: Although roads are widely seen as dispersal barriers, their genetic consequences for animals that experience large fluctuations in population density are poorly documented. We developed a spatially paired experimental design to assess the genetic impacts of roads on cyclic voles ( Microtus arvalis ) during a high-density phase in North-Western Spain. We compared genetic patterns from 15 paired plots bisected by three different barrier types, using linear mixed models and computing effect sizes to assess the importance of each type, and the influence of road features like width or the age of the infrastructure. Evidence of effects by roads on genetic ersity and differentiation were lacking. We speculate that the recurrent (each 3–5 generations) episodes of massive dispersal associated with population density peaks can homogenize populations and mitigate the possible genetic impact of landscape fragmentation by roads. This study highlights the importance of developing spatially replicated experimental designs that allow us to consider the large natural spatial variation in genetic parameters. More generally, these results contribute to our understanding of the not well explored effects of habitat fragmentation on dispersal in species showing “boom-bust” dynamics.
DNA metabarcoding captures subtle differences in forest beetle communities following disturbance
Publisher: Wiley
Date: 10-10-2020
DOI: 10.1111/REC.13236
Abstract: DNA metabarcoding is an emerging approach for monitoring bio ersity, but uncertainties remain about its capacity to detect subtle differences in invertebrate community composition comparable to those achievable based on conventional morphological identification. In this study, DNA metabarcoding and morphology‐based approaches were compared as tools for investigating whether logging history impacted beetle communities in Tasmanian wet eucalypt forests. We compared 12 unlogged mature forest sites with 12 neighboring regeneration sites that had been logged approximately 55 years previously. The number of species identified based on morphology (173) was close to the number of zero‐radius operational taxonomic units (ZOTUs) identified by DNA metabarcoding of cytochrome c oxidase subunit I (COI, 176) and 16S ribosomal RNA (16S, 156) markers. Subtle but significant differences in beetle species composition between regeneration and unlogged mature forests were captured by both morphology‐based and COI DNA metabarcoding approaches, but not by 16S DNA metabarcoding. Our results support the suitability of mitochondrial COI for studying invertebrate bio ersity. A slight loss of signal compared to the morphology‐based approach may be resolved by developing more comprehensive DNA reference databases. While confirming forest recovery of 48–58 years did not fully restore mature forest beetle communities, we suggest that DNA metabarcoding can be used for monitoring bio ersity and probing subtle differences in community composition.
Australian lizards are outstanding models for reproductive biology research
Publisher: CSIRO Publishing
Date: 28-09-2020
DOI: 10.1071/ZO21017
Abstract: Australian lizards are a erse group distributed across the continent and inhabiting a wide range of environments. Together, they exhibit a remarkable ersity of reproductive morphologies, physiologies, and behaviours that is broadly representative of vertebrates in general. Many reproductive traits exhibited by Australian lizards have evolved independently in multiple lizard lineages, including sociality, complex signalling and mating systems, viviparity, and temperature-dependent sex determination. Australian lizards are thus outstanding model organisms for testing hypotheses about how reproductive traits function and evolve, and they provide an important basis of comparison with other animals that exhibit similar traits. We review how research on Australian lizard reproduction has contributed to answering broader evolutionary and ecological questions that apply to animals in general. We focus on reproductive traits, processes, and strategies that are important areas of current research, including behaviours and signalling involved in courtship mechanisms involved in mating, egg production, and sperm competition nesting and gestation sex determination and finally, birth in viviparous species. We use our review to identify important questions that emerge from an understanding of this body of research when considered holistically. Finally, we identify additional research questions within each topic that Australian lizards are well suited for reproductive biologists to address.
Genetic divergence between colonies of Flesh-footed Shearwater Ardenna carneipes exhibiting different foraging strategies
Publisher: Springer Science and Business Media LLC
Date: 07-07-2017
Phylogeographic parallelism: Concordant patterns in closely related species illuminate underlying mechanisms in the historically glaciated Tasmanian landscape
Publisher: Wiley
Date: 16-04-2020
DOI: 10.1111/JBI.13831
Did postglacial sea-level changes initiate the evolutionary divergence of a Tasmanian endemic raptor from its mainland relative?
Publisher: The Royal Society
Date: 22-12-2013
Abstract: Populations on continental islands are often distinguishable from mainland conspecifics with respect to body size, appearance, behaviour or life history, and this is often congruent with genetic patterns. It is commonly assumed that such differences developed following the complete isolation of populations by sea-level rise following the Last Glacial Maximum (LGM). However, population ergence may predate the LGM, or marine dispersal and colonization of islands may have occurred more recently in both cases, populations may have also erged despite ongoing gene flow. Here, we test these alternative hypotheses for the ergence between wedge-tailed eagles from mainland Australia ( Aquila audax audax ) and the threatened Tasmanian subspecies ( Aquila audax fleayi ), based on variation at 20 microsatellite loci and mtDNA. Coalescent analyses indicate that population ergence appreciably postdates the severance of terrestrial habitat continuity and occurred without any subsequent gene flow. We infer a recent colonization of Tasmania by marine dispersal and cannot discount founder effects as the cause of differences in body size and life history. We call into question the general assumption of post-LGM marine transgression as the initiator of ergence of terrestrial lineages on continental islands and adjacent mainland, and highlight the range of alternative scenarios that should be considered.
Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra– and interpopulation spatial scales
Publisher: Wiley
Date: 12-11-2019
DOI: 10.1111/MEC.15274
Abstract: Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing in idual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.
Genome-wide analyses reveal drivers of penguin diversification
Publisher: Proceedings of the National Academy of Sciences
Date: 17-08-2020
Abstract: Penguins have long been of interest to scientists and the general public, but their evolutionary history remains unresolved. Using genomes, we investigated the drivers of penguin ersification. We found that crown-group penguins erged in the early Miocene in Australia/New Zealand and identified Aptenodytes (emperor and king penguins) as the sister group to all other extant penguins. Penguins first occupied temperate environments and then radiated to cold Antarctic waters. The Antarctic Circumpolar Current’s (ACC) intensification 11.6 Mya promoted penguin ersification and geographic expansion. We detected interspecies introgression among penguins, in some cases following the direction of the ACC, and identified genes acting on thermoregulation, oxygen metabolism, and ing capacity that underwent adaptive evolution as they progressively occupied more challenging thermal niches.
Detecting selection on temporal and spatial scales: A genomic time-series assessment of selective responses to devil facial tumor disease
Publisher: Public Library of Science (PLoS)
Date: 03-2016
Coalescent Modelling Suggests Recent Secondary-Contact of Cryptic Penguin Species
Publisher: Public Library of Science (PLoS)
Date: 14-12-2015
Population structure and long-term decline in three species of heart urchins Abatus spp. near-shore in the Vestfold Hills region, East Antarctica
Publisher: Inter-Research Science Center
Date: 08-03-2016
DOI: 10.3354/MEPS11573
Habitat connectivity and host relatedness influence virus spread across an urbanising landscape in a fragmentation-sensitive carnivore
Publisher: Oxford University Press (OUP)
Date: 21-12-2022
DOI: 10.1093/VE/VEAC122
Abstract: Spatially heterogeneous landscape factors such as urbanisation can have substantial effects on the severity and spread of wildlife diseases. However, research linking patterns of pathogen transmission to landscape features remains rare. Using a combination of phylogeographic and machine learning approaches, we tested the influence of landscape and host factors on feline immunodeficiency virus (FIVLru) genetic variation and spread among bobcats (Lynx rufus) s led from coastal southern California. We found evidence for increased rates of FIVLru lineage spread through areas of higher vegetation density. Furthermore, single-nucleotide polymorphism (SNP) variation among FIVLru sequences was associated with host genetic distances and geographic location, with FIVLru genetic discontinuities precisely correlating with known urban barriers to host dispersal. An effect of forest land cover on FIVLru SNP variation was likely attributable to host population structure and differences in forest land cover between different populations. Taken together, these results suggest that the spread of FIVLru is constrained by large-scale urban barriers to host movement. Although urbanisation at fine spatial scales did not appear to directly influence virus transmission or spread, we found evidence that viruses transmit and spread more quickly through areas containing higher proportions of natural habitat. These multiple lines of evidence demonstrate how urbanisation can change patterns of contact-dependent pathogen transmission and provide insights into how continued urban development may influence the incidence and management of wildlife disease.
Molecular discrimination of shelf-spawned eggs of two co-occurring Trachurus spp. (Carangidae) in southeastern Australia: a key step to future egg-based bio
Publisher: Oxford University Press (OUP)
Date: 11-09-2014
Abstract: A molecular approach was successfully developed to discriminate between spawned eggs of the pelagic carangids Trachurus declivis and Trachurus novaezelandiae collected during ichthyoplankton surveys conducted in October 2002 and 2003 along shelf waters of Queensland (Qld) and New South Wales (NSW), in southeastern Australia (25o50′–37o30′S). Visually identified Trachurus eggs were subjected to mtDNA analysis by targeting specific fragments of the cytochrome oxidase subunit 1 (CO1) and cytochrome b (Cyt b) genes, with three diagnostic sites (single-nucleotide polymorphisms) within a 297 bp segment of Cyt b (558, 588, 825) providing the best approach to discriminate between species. Polymerase chain reaction lification and sequencing of 608 suspected Trachurus eggs resulted in 586 (96.4%) high-quality sequences that unequivocally identified 315 and 207 eggs as T. declivis and T. novaezelandiae, respectively, as well as 18 “variant haplotype” eggs that exhibited a base substitution at one of the diagnostic sites the remaining 46 sequences aligned to three different genera in GenBank including two carangids, thus highlighting the effectiveness of molecular methods for egg identification. Rehydrated, mtDNA-verified eggs of T. declivis were significantly larger (0.97 ± 0.01 mm) than those of T. novaezelandiae (0.82 ± 0.01 mm), though still proved problematic to identify to species when relying on morphology alone. Egg distributions showed main spawning areas of T. declivis and T. novaezelandiae confined mostly to southern NSW (& °S) and northern NSW/southern Qld (& °S), respectively, with T. novaezelandiae likely to continue spawning further south during summer with the gradual temperature increase associated with the south-flowing East Australian Current. Overall findings support the adoption of comparable molecular protocols to verify identification of wild spawned eggs to species level, especially eggs collected during the application of the daily egg production method to estimate spawning biomass of pelagic species, as well as biological fish studies.
Isolation, marine transgression and translocation of the bare‐nosed wombat ( Vombatus ursinus )
Publisher: Wiley
Date: 21-03-2019
DOI: 10.1111/EVA.12785
Population genetic and behavioural variation of the two remaining colonies of Providence petrel (Pterodroma solandri)
Publisher: Springer Science and Business Media LLC
Date: 19-09-2016
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View Funded ActivityEvolution, Disease And Extinction - Using Ancient And Modern Deoxyribonucleic Acid (DNA) To Investigate Molecular Evolution In The Tasmanian Devil
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