Ecology, Evolution and Landscape Science
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Ecology, Evolution and Landscape Science is concerned with understanding, managing and conserving the natural systems of the Australian continent. Our natural resources are declining due to increasing pressures, including more intensive agriculture, urbanisation, invasive species and climate change. Study within Ecology, Evolution and Landscape Science includes the assessment, monitoring and prediction of the environment and resources and covers marine and coastal systems, natural and constructed wetlands, estuaries, woodlands and the arid zone. Research interests are focussed on marine biology, terrestrial and freshwater ecology, the study of taxonomy and systematics of organisms and their evolution, spatial technology, and natural resource systems.
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Browsing Ecology, Evolution and Landscape Science by Author "Adams, M."
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Item Open Access Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families(Elsevier, 2023) Thacker, C.E.; Tyler McCraney, W.; Harrington, R.C.; Near, T.J.; Shelley, J.J.; Adams, M.; Hammer, M.P.; Unmack, P.J.Eleotridae (sleepers) and five smaller families are the earliest diverging lineages within Gobioidei. Most inhabit freshwaters in and around the Indo-Pacific, but Eleotridae also includes species that have invaded the Neotropics as well as several inland radiations in the freshwaters of Australia, New Zealand, and New Guinea. Previous efforts to infer phylogeny of these families have been based on sets of mitochondrial or nuclear loci and have yielded uncertain resolution of clades within Eleotridae. We expand the taxon sampling of previous studies and use genomic data from nuclear ultraconserved elements (UCEs) to infer phylogeny, then calibrate the hypothesis with recently discovered fossils. Our hypothesis clarifies ambiguously resolved relationships, provides a timescale for divergences, and indicates the core crown Eleotridae diverged over a short period 24.3-26.3 Ma in the late Oligocene. Within Eleotridae, we evaluate diversification dynamics with BAMM and find evidence for an overall slowdown in diversification over the past 35 Ma, but with a sharp increase 3.5 Ma in the genus Mogurnda, a clade of brightly colored species found in the freshwaters of Australia and New Guinea.Item Metadata only Evolutionary processes and biodiversity(CSIRO Publishing, 2013) Hammer, M.; Adams, M.; Hughes, J.; Humphries, P.; Walker, K.Item Open Access Perspectives on the clonal persistence of presumed ‘ghost’ genomes in unisexual or allopolyploid taxa arising via hybridization(Springer Nature, 2019) Unmack, P.J.; Adams, M.; Bylemans, J.; Hardy, C.M.; Hammer, M.P.; Georges, A.Although hybridization between non-sibling species rarely results in viable or fertile offspring, it occasionally produces self-perpetuating or sexually-parasitic lineages in which ancestral genomes are inherited clonally and thus may persist as 'ghost species' after ancestor extinction. Ghost species have been detected in animals and plants, for polyploid and diploid organisms, and across clonal, semi-clonal, and even sexual reproductive modes. Here we use a detailed investigation of the evolutionary and taxonomic status of a newly-discovered, putative ghost lineage (HX) in the fish genus Hypseleotris to provide perspectives on several important issues not previously explored by other studies on ghost species, but relevant to ongoing discussions about their detection, conservation, and artificial re-creation. Our comprehensive genetic (allozymes, mtDNA) and genomic (SNPs) datasets successfully identified a threatened sexual population of HX in one tiny portion of the extensive distribution displayed by two hemi-clonal HX-containing lineages. We also discuss what confidence should be placed on any assertion that an ancestral species is actually extinct, and how to assess whether any putative sexual ancestor represents a pure remnant, as shown here, or a naturally-occurring resurrection via the crossing of compatible clones or hemi-clones.Item Open Access Phylogeny, diversification, and biogeography of a hemiclonal hybrid system of native Australian freshwater fishes (Gobiiformes: Gobioidei: Eleotridae: Hypseleotris)(Springer Nature, 2022) Thacker, C.E.; Shelley, J.J.; McCraney, W.T.; Adams, M.; Hammer, M.P.; Unmack, P.J.Background: Carp gudgeons (genus Hypseleotris) are a prominent part of the Australian freshwater fish fauna, with species distributed around the western, northern, and eastern reaches of the continent. We infer a calibrated phylogeny of the genus based on nuclear ultraconserved element (UCE) sequences and using Bayesian estimation of divergence times, and use this phylogeny to investigate geographic patterns of diversification with GeoSSE. The southeastern species have hybridized to form hemiclonal lineages, and we also resolve relationships of hemiclones and compare their phylogenetic placement in the UCE phylogeny with a hypothesis based on complete mitochondrial genomes. We then use phased SNPs extracted from the UCE sequences for population structure analysis among the southeastern species and hemiclones. Results: Hypseleotris cyprinoides, a widespread euryhaline species known from throughout the Indo-Pacific, is resolved outside the remainder of the species. Two Australian radiations comprise the bulk of Hypseleotris, one primarily in the northwestern coastal rivers and a second inhabiting the southeastern region including the Murray–Darling, Bulloo-Bancannia and Lake Eyre basins, plus coastal rivers east of the Great Dividing Range. Our phylogenetic results reveal cytonuclear discordance between the UCE and mitochondrial hypotheses, place hemiclone hybrids among their parental taxa, and indicate that the genus Kimberleyeleotris is nested within the northwestern Hypseleotris radiation along with three undescribed species. We infer a crown age for Hypseleotris of 17.3 Ma, date the radiation of Australian species at roughly 10.1 Ma, and recover the crown ages of the northwestern (excluding H. compressa) and southeastern radiations at 5.9 and 7.2 Ma, respectively. Range-dependent diversification analyses using GeoSSE indicate that speciation and extinction rates have been steady between the northwestern and southeastern Australian radiations and between smaller radiations of species in the Kimberley region and the Arnhem Plateau. Analysis of phased SNPs confirms inheritance patterns and reveals high levels of heterozygosity among the hemiclones. Conclusions: The northwestern species have restricted ranges and likely speciated in allopatry, while the southeastern species are known from much larger areas, consistent with peripatric speciation or allopatric speciation followed by secondary contact. Species in the northwestern Kimberley region differ in shape from those in the southeast, with the Kimberley species notably more elongate and slender than the stocky southeastern species, likely due to the different topographies and flow regimes of the rivers they inhabit.Item Metadata only Species boundaries in carp gudgeons (Eleotrididae : Hypseleotris) from the River Murray, South Australia: evidence for multiple species and extensive hybridization(C S I R O Publishing, 2000) Bertozzi, T.; Adams, M.; Walker, K.Allozyme analyses of carp gudgeons (Hypseleotris) from five sites in the lower River Murray revealed three distinctive taxa designated HA, HB and HC, diagnosable from one another by fixed differences at 3–5 loci, and three apparent F 1 hybrid forms, HA¥HB, HA¥HX and HB¥HX, where HX denotes a taxon not sampled in its ‘pure’ form. Of all fish sampled, 25% were hybrids, although only one hybrid form was found at any one site, and never in company with both parental taxa. No hybrids involving HC were found, although this was the most common taxon, and no HA¥HB hybrids were present at the one site of demonstrated sympatry between the parental taxa. Morphological analysis and the lack of introgression confirm that HA, HB, and HC are distinct biological species. Partial meristic data suggest that HC corresponds to H. klunzingeri s.l., ‘Midgley’s carp gudgeon’ is a composite of HA, HB and HA¥HB hybrids, and ‘Lake’s carp gudgeon’ may be a composite of HX and one of its hybrids (HB¥HX). We speculate that one or more of the hybrid classes may be ‘unisexual lineages’ (clonally reproducing, usually all-female forms derived from hybridization between congeners).Item Metadata only The forensic application of allozyme electrophoresis to the identification of blowfly larvae (Diptera : Calliphoridae) in southern Australia(Amer Soc Testing Materials, 2001) Wallman, J.; Adams, M.Most known carrion-breeding species of blowflies in southern Australia are of the genus Calliphora. The morphological similarity of the immatures of these species means that correctly identifying them poses a challenge for forensic entomologists. This study investigates the potential of allozyme analysis to assist with this task. Molecular profiles of third-instar larvae and adults representing four of these carrion-breeding species, Calliphora stygia, C. dubia, C. hilli hilli, and C. vicina, were compared at 42 allozyme loci. The two life stages were found to display almost identical allozyme profiles in each species (93% of loci were expressed in both life history stages), enabling the reliable identification of larvae in these four species. Integration of these results with data from a previous study indicates that allozyme analysis would also be suitable for rapid, species-level identification of the larvae of six other carrion- breeding Calliphora species occurring in southern Australia. This is the first report of the application of allozyme data to the identification of forensically important blowflies.Item Metadata only Thresholds for morphological response to light reduction for four tropical seagrass species(Elsevier, 2016) Collier, C.; Adams, M.; Langlois, L.; Waycott, M.; O'Brien, K.; Maxwell, P.; McKenzie, L.Abstract not available