Jane Hughes

a b s t r a c t Atyid freshwater shrimps are globally distributed and form an important part of freshwater ecosystems, particularly in the tropics and subtropics. Despite theirwidespread distribution and ecological importance, their phylogenetic relationships are largely unresolved. Herewepresent thefirst comprehensivemolecular phylogeny of the Atyidae investigating the evolutionary relationships among 32 of the 42 genera using mitochondrial and nuclear markers. Our data indicate that the established classification of the Atyidae is in need of substantial taxonomic revision at all taxonomic levels. We suggest a new suprageneric systematization of atyids and discuss problematic issues at the generic level, particularly in the most speciose genus, Caridina. Molecular clock based divergence time estimates for atyids vary widely, but invariably support the assumption that atyids are an ancient freshwater lineage with an origin in the mid-Cretaceous at the very latest. Atyid distribution...

The genetic basis of plumage color variation has already been determined for many model species; however, the genetic mechanisms responsible for intraspecific color variation in the majority of wild-bird species are yet to be uncovered. The Australian magpie (Cracticus tibicen) is a large black and white passerine which is widely distributed across the Australian continent. The proportion of melanized back plumage varies between regionally delineated subspecies; where back-color forms overlap, intermediate color phenotypes ...

Anthropogenic disturbance regimes in areas that were once large continuous habitats have been major drivers of habitat fragmentation and loss which in turn form the largest worldwide threat to avian biodiversity. Studies suggest that functional trait based approaches provide better understanding of fragmentation effects on ecological processes in human-modified landscapes. However, research on these thematic areas is limited in many tropical regions, such as Ethiopia. In this study, we evaluated sensitivity of bird communities and functional groups to fragmentation processes in Ethiopia. Standard point counts were used to survey birds in 16 remnant forest patches of variable sizes and degrees of isolation. The information theoretic model selection approach was used for precise understanding of avian functional group responses to habitat loss and fragmentation. Results showed strong impacts of forest loss and fragmentation on forest specialists, insectivores, frugivores, open nesters...

Much controversy still seems to surround the role of molecular data in general, and DNA barcoding in particular, within the taxonomic community. This has lead to numerous “call and response” pairs of papers, most recently Ebach (2011) and Mitchell (2011), but preceded by many other pairs, such as Packer et al. (2009) and Hołyński (2010). There have been numerous calls for a more “integrative” approach to taxonomy (Mitchell 2011; Stevens et al. 2011), which itself has generated point and counterpoint papers (Dayrat 2005; Valdecasas et al. 2008). This of course is how science progresses (although Max Planck suggested that science advances “one funeral at a time”, en.wikiquote.org/wiki/Max_Planck, accessed 20 March 2011).

Mud crabs (Portunidae; Scylla spp.) have become established recently in some south-west Australian estuaries – almost 1000 km south of their recorded distribution. Colonisation may have occurred by a natural range expansion from the north-west or by translocation from source(s) within the Indo-West Pacific. To identify the species and the potential source population(s), genetic analyses was used to compare south-west crabs (N = 32) to other populations. Levels of diversity at two independent genetic markers were also compared to obtain relative estimates of effective population size between colonist and suspected source population(s). Comparisons of mitochondrial DNA sequences (COI) indicated that all south-west crabs were Scylla serrata. Indeed, the sole haplotype found among colonists was identical to one prevalent but endemic to more diverse north-west Australian populations. In contrast, source and colonist populations had equally high levels of genetic diversity at two microsat...

The Caridina indistincta complex is a group of closely related atyid shrimps that inhabit coastal freshwater streams throughout north-eastern Australia. Using mitochondrial DNA sequence data (cytochrome oxidase 1, CO1), we (1) inferred the timing of speciation in the C. indistincta group and (2) examined the intraspecific phylogeographic patterns within the group. Assuming a shrimp-specific rate of CO1 evolution, the level of sequence divergence among species suggests that speciation took place during the Miocene epoch. Within one widespread mainland species, phylogeographic patterns suggest strong geographic 'regionalisation' of mtDNA lineages that are most likely of Pleistocene origin. By contrast, another species comprises two highly divergent mtDNA lineages that occur in sympatry. We suggest that although Pleistocene sea-level regressions appear important in generating population-level phylogeographic patterns, these events were largely unimportant in the formation of sp...

The study of hybrid zones advances understanding of the speciation process, and approaches incorporating genomic data are increasingly used to draw significant conclusions about the impact of hybridisation. Despite the progress made, the complex interplay of factors that can lead to substantially variable hybridisation outcomes are still not well understood, and many systems and/or groups remain comparatively poorly studied. Our study aims to broaden the literature on avian hybrid zones, investigating a potentially geographically and temporally complex putative hybrid zone between two native Australian non-sister parrot species, the pale-headed and eastern rosellas (Platycercus adscitus and Platycercus eximius, respectively). We analysed six plumage traits and >1400 RADseq loci and detected hybrid individuals and an unexpectedly complex geographic structure. The hybrid zone is larger than previously described due to either observer bias or its movement over recent decades. It com...

Tiger (Panthera tigris) populations are in danger across their entire range due to habitat loss, poaching and the demand for tiger parts. The Bengal tiger (Panthera tigris tigris) is an endangered apex predator with a population size estimated to be less than 200 in Nepal. In spite of strict wildlife protection laws, illegal trade of tiger parts is increasing; and Nepal has become one of the major sources and transit routes for poached wildlife parts. Identification of wildlife parts is often challenging for law enforcement officials due to inadequate training and lack of available tools. Here, we describe a molecular forensic approach to gain insight into illegally trafficked tiger parts seized across Nepal. We created Nepal's first comprehensive reference genetic database of wild tigers through the Nepal Tiger Genome Project (2011-2013). This database has nuclear DNA microsatellite genotype and sex profiles, including geo-spatial information, of over 60% (n = 120) of the wild ...

An important challenge for conservation science is to detect declines in intraspecific diversity so that management action can be guided towards populations or species at risk. The lifespan of Australian lungfish (Neoceratodus forsteri) exceeds 80 years, and human impacts on breeding habitat over the last half century may have impeded recruitment, leaving populations dominated by old post-reproductive individuals, potentially resulting in a small and declining breeding population. Here we conduct a "single-sample" evaluation of genetic erosion within contemporary populations of the Australian lungfish. Genetic erosion is a temporal decline in intraspecific diversity due to factors such as reduced population size and inbreeding. We examined whether young individuals showed signs of reduced genetic diversity and/or inbreeding using a novel bomb-radiocarbon dating method to age lungfish non-lethally, based on C ratios of scales. A total of 15,201 single nucleotide polymorphic...

Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: ) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species' distribution, using ten microsatellite loci and sequences of the mitochondrial cyt gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of disp...

The utility of restriction-site associated DNA sequencing (RADseq) to resolve fine-scale population structure was tested on an abundant and vagile fish species in a tropical river. Australia's most widespread freshwater fish, the "extreme disperser" Leiopotherapon unicolor was sampled from 6 locations in an unregulated system, the Daly River in Australia's Northern Territory. Despite an expectation of high connectivity based on life history knowledge of this species derived from arid zone habitats, L. unicolor was not a panmictic population in the tropical lower Daly. Using ~14000 polymorphic RADseq loci, we found a pattern of upstream versus downstream population subdivision and evidence for differentiation among tributary populations. The magnitude of population structure was low with narrow confidence intervals (global FST = 0.014; 95% CI = 0.012-0.016). Confidence intervals around pairwise FST estimates were all nonzero and consistent with the results of cluste...

Spiders of the infraorder Mygalomorphae are fast becoming model organisms for the study of biogeography and speciation. However, these spiders can be difficult to study in the absence of fundamental life history information. In particular, their cryptic nature hinders comprehensive sampling, and linking males with conspecific females can be challenging. Recently discovered differences in burrow entrance architecture and male morphology indicated that these challenges may have impeded our understanding of the trapdoor spider genus Euoplos in Australia's eastern mesic zone. We investigated the evolutionary significance of these discoveries using a multi-locus phylogenetic approach. Our results revealed the existence of a second, previously undocumented, lineage of Euoplos in the eastern mesic zone. This new lineage occurs in sympatry with a lineage previously known from the region, and the two are consistently divergent in their burrow entrance architecture and male morphology, re...

... Quick Search All fields Author Search tips (Opens new window) Journal/book title. Volume Issue Page Clear all fields ... Using recently detected cryptic species in atyid shrimps from eastern Australia (Atyidae: Paratya australiensis, Caridina mccullochi and C. indistinca), we tested ...

The upland mesic rainforests of eastern Australia have been described as a "mesothermal archipelago" where a chain of cool mountain "islands" arise from a warm "sea" of tropical and subtropical lowlands. An endemic freshwater crayfish belonging to the genus Euastacus is found on each of these mountain "islands." The Euastacus are particularly suitable for the study of evolution because each mountain harbors a unique species, there are many taxa present providing replication within the group and, most importantly, their distribution is linear, extending along a south-north axis. This group could have evolved by "simultaneous vicariance" where there was one vicariant separation event of a widespread ancestor, or by "south to north stepping stone dispersal" where there were long distance dispersal events from neighboring mountain islands, starting in the south and proceeding north in a dispersal-colonization wave. We used pairwise genetic distances between nearest geographic neighbors as a novel way to test the two hypotheses. If diversification was due to "south to north stepping stone dispersal," then pairwise genetic distances between nearest geographic neighbors should decrease progressively the farther north the taxon pairs are found, reflecting the decreasing periods of isolation. In this case there should be a negative correlation between the south to north rank order of nearest neighbors and pairwise genetic distances. A Spearman's correlation on 16S mtDNA pairwise genetic distances and geographic rank order was not significant, indicating there was no support for the south to north stepping stone dispersal hypothesis. If simultaneous vicariance was responsible for diversification then all nearest geographic neighbor taxon pairs should have similar genetic distances and, therefore, the variance in nearest neighbor distances should be zero, or close to it. To test if the observed variance was tending towards zero we developed a randomization test where nearest neighbor taxon pairs were assigned random genetic distances and the variances calculated. The observed variance lay in the < 0.05 range of the simulated variances, providing support for the simultaneous vicariance hypothesis. The data also suggest there was simultaneous vicariance of at least two ancestral Queensland lineages. The timing of this vicariant event was probably in the Pliocene, which is consistent with the divergence times reported for other Australian mesic rainforest restricted taxa.

In 1993, a population of freshwater glass shrimp (Paratya australiensis) was translocated from Kilcoy Creek to Branch Creek in the Conondale Range, Queensland. Subsequent genetic analysis revealed that the translocated and resident shrimp belonged to different mitochondrial DNA lineages (mtDNA) that were capable of hybridising. Monitoring of the pools along Branch Creek up until 2002 suggested that the translocated lineage had an advantage in upstream pools, and the resident lineage dominated downstream. Differential temperature tolerance and hybridisation barriers such as hybrid inviability and mate selection were factors proposed to explain hybrid zone structure.The major objective of this study was to combine nuclear and mtDNA markers to identify the structure of the hybrid zone in 2013 and identify any changes that had occurred since 2002. Specifically, we used genetic data to test for evidence of hybrid zone movement, and used FIS values to investigate whether mating was random...

The contemporary and historical colonization capacity of an Australian freshwater fish, north-west glassfish Ambassis sp., was tested using mtDNA sequence data and six newly developed microsatellite loci in an endoreic basin in central Australia. Overall, Ambassis sp. exhibited weak genetic structure within catchments, suggesting some capacity to recolonize extirpated waterholes after disturbance. Genetic structure revealed that the historical pattern of connectivity among catchments in the Lake Eyre Basin was dramatically different from other species studied in this region. Two highly divergent clades were detected in separate catchments in the basin. mtDNA from individuals sampled in catchments north of the Lake Eyre Basin suggest that Ambassis sp. has colonized on two separate occasions from catchments in northern Australia, subsequently generating two highly divergent lineages.

Rivers in north-western Australia have been long isolated systems and several of them, including those in the central north Kimberley (CNK) and Pilbara (PIL) regions, are known for their endemism in freshwater fishes. Furthermore, some species of freshwater fish are ...

Understanding the patterns of connectivity among natural populations is critical for making predictions concerning impacts of anthropogenic influences that cause local extinctions. Based on genetic studies, four main models of connectivity have been proposed for animals that inhabit stream systems. These are the death valley model, the stream hierarchy model, the headwater model and panmixia. Each of these models has specific predictions as to the spatial structuring of genetic variation and the subsequent effects of local extinctions. We will present predictions from each of the models. Then we will present analysis of molecular data from our lab and recently published studies to test the idea that a knowledge of a species' life-history, its habitat requirements and the architecture of the rivers in which it lives can be used to predict the model of connectivity it will best fit. We will present analysis on fish, insects crustaceans and molluscs.

Bactrocera (Bactrocera) musae (Tryon) is a major pest species of some banana varieties in northern Queensland, the Torres Strait Islands, Papua New Guinea and associated islands. It is the only pest species in a complex of 17 species described herein. Five of these are new species and are described and illustrated: Bactrocera (Bactrocera) balagawii, B. (B.) parabancroftii, B. (B.) ramuensis, B. (B.) rufi vitta, B. (B.) uvariae. The remaining 12 species have been previously described and are revised with up-to-date information on host plants, attractant records and geographic distributions. Further, a molecular study was able to explore the distinction between six of the described species. A phylogeney based on 562 base pairs of the CO1 gene showed strong agreement between morphological and molecular data. Furthermore, for three of the species that occurred in sympatry and were represented by suffi cient sample numbers (namely, B. contermina, B. musae, B. rufi vitta), analysis of eig...

Relationships and species limits among the colourful Australian parrots known as rosellas (Platycercus) are contentious because of poorly understood patterns of parapatry, sympatry and hybridization as well as complex patterns of geographical replacement of phenotypic forms. Two subgenera are, however, conventionally recognised: Platycercus comprises the blue-cheeked crimson rosella complex (Crimson Rosella P. elegans and Green Rosella P. caledonicus), and Violania contains the remaining four currently recognised species (Pale-headed Rosella P. adscitus, Eastern Rosella P. eximius, Northern Rosella P. venustus, and Western Rosella P. icterotis). We used phylogenetic analysis of ten loci (one mitochondrial, eight autosomal and one z-linked) and several individuals per nominal species primarily to examine relationships within the subgenera, especially the relationships and species limits within Violania. Of these, P. adscitus and P. eximius have long been considered sister species or ...

Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that...

Understanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of biodiversity and ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate change. Using a series of case studies, we show that the insight needed to understand the nature and implications of connectivity, and to underpin conservation and management, is best achieved via data synthesis from multiple analytical approaches. We identify four key knowledge requirements for progressing our understanding of the effects of anthropogenic impacts on ecological connectivity: autecology; population structure; movement characteristics; and environmental tolerance/phenotypic plasticity. Structuring empirical research around these four broad data requirements, and using this inf...

We assessed levels of mitochondrial genetic spatial structuring in the hydropsychid caddisfly Cheumatopsyche sp. AV1 in southeastern New South Wales, Australia. No significant spatial structuring was detected within or between catchments using analysis of molecular variance, and nested clade contingency analysis suggested no strong relationship between haplotypes and geographical location, at any clade level. However, tests for association among haplotypes incorporating geographical distance in the nested clade analysis, revealed patterns of historical range expansion and recent restricted gene flow. Most likely, population fragmentation preceded range expansion, although subsequent recontact and gene flow among the previously sundered populations has apparently obscured the geographical signature of the former fragmentation. Taken together, our analyses suggest that a number of populations fragmented during the Pleistocene evolved in isolation for a time and subsequently expanded i...

Most butterflies in the family Lycaenidae associate with ants but fewer than 3% are myrmecophagous. Larvae of the Australian endemic butterfly genus Acrodipsas parasitise the nests of ants from two subfamilies and, thus, constitute an interesting and uncommon myrmecophagous radiation within the Lepidoptera. Phylogenetic relationships among Acrodipsas species were inferred from fragments of mitochondrial cytochrome oxidase subunits I and II totalling 1155 bp using maximum parsimony and a neighbour joining method. Monophyly of the genus was confirmed, as was the sister genus status of Lucia. Acrodipsas myrmecophila was established as the plesiotypic Acrodipsas species, which together with Acrodipsas brisbanensis parasitises the ancestral dolichoderine host-ants. A speciation event associated with a radical host-ant shift to Myrmicinae occurred in an ancestor of Acrodipsas cuprea but subsequent speciation events may have been driven by climatic fluctuations during the Pleistocene. Modifications to leg morphology in several species were found to be a synapomorphic state, which arose subsequent to the host-shift to Myrmicinae. Minimal genetic variation detected in allopatric species exhibiting divergent morphology suggests that phenotypic variability has been driven by strong environmental selective pressures. As a result, morphological differences between closely related allopatric species have evolved faster than genetic differences, most notably between Acrodipsas arcana and Acrodipsas illidgei. In contrast, sympatric lineages of A. brisbanensis across similar habitats show considerable genetic differentiation, yet have remained phenotypically indistinguishable. Successful amplification of short overlapping fragments of DNA from museum specimens confirms their utility for phylogenetic analysis when the availability of fresh tissue is limited.

Mitochondrial DNA sequences were used to investigate phylogenetic and biogeographic relationships among Australian freshwater shrimp from the genus Caridina H. Milne Edwards, 1837 (Atyidae) and congeners from potential source populations throughout the Indo-West Pacific region. Numerous Australian taxa have close evolutionary relationships with non-Australian taxa from locations throughout the region, indicating a diverse origin of the Australian freshwater fauna. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. Interestingly, a study on Australia's other main genus of atyid shrimp, Paratya Miers, 1882, inferred only a single colonisation. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater t...