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Dive into the research topics where Sally Potter is active.

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Featured researches published by Sally Potter.


Molecular Ecology | 2012

Multiple biogeographical barriers identified across the monsoon tropics of northern Australia: Phylogeographic analysis of the brachyotis group of rock-wallabies

Sally Potter; Mark D. B. Eldridge; David A. Taggart; Steven J.B. Cooper

The monsoon tropics of northern Australia are a globally significant biodiversity hotspot, but its phylogeography is poorly known. A major challenge for this region is to understand the biogeographical processes that have shaped the distribution and diversity of taxa, without detailed knowledge of past climatic and environmental fluctuations. Although molecular data have great potential to address these questions, only a few species have been examined phylogeographically. Here, we use the widely distributed and abundant short‐eared rock‐wallaby (Petrogale brachyotis; n = 101), together with the sympatric monjon (P. burbidgei; n = 11) and nabarlek (P. concinna; n = 1), to assess historical evolutionary and biogeographical processes in northern Australia. We sequenced ∼1000 bp of mitochondrial DNA (control region, ND2) and ∼3000 bp of nDNA (BRCA1, ω‐globin and two anonymous loci) to investigate phylogeographic structuring and delineate the time‐scale of diversification within the region. Our results indicate multiple barriers between the Top End (Northern Territory) and Kimberley (Western Australia), which have caused divergence throughout the Plio‐Pleistocene. Eight geographically discrete and genetically distinct lineages within the brachyotis group were identified, five of which are separated by major river valleys (Ord, Victoria, Daly), arid lowlands and discontinuous sandstone ranges. It is likely that these barriers have similarly influenced genetic structure in other monsoonal biota.


Molecular Ecology Resources | 2016

Exon capture phylogenomics: efficacy across scales of divergence

Jason G. Bragg; Sally Potter; Ke Bi; Craig Moritz

The evolutionary histories of species are not measured directly, but estimated using genealogies inferred for particular loci. Individual loci can have discordant histories, but in general we expect to infer evolutionary histories more accurately as more of the genome is sampled. High Throughput Sequencing (HTS) is now providing opportunities to incorporate thousands of loci in ‘phylogenomic’ studies. Here, we used target enrichment to sequence c.3000 protein‐coding exons in a group of Australian skink lizards (crown group age c.80 Ma). This method uses synthetic probes to ‘capture’ target exons that were identified in the transcriptomes of selected probe design (PD) samples. The target exons are then enriched in sample DNA libraries prior to performing HTS. Our main goal was to study the efficacy of enrichment of targeted loci at different levels of phylogenetic divergence from the PD species. In taxa sharing a common ancestor with PD samples up to c.20 Ma, we detected little reduction in efficacy, measured here as sequencing depth of coverage. However, at around 80 Myr divergence from the PD species, we observed an approximately two‐fold reduction in efficacy. A secondary goal was to develop a workflow for analysing exon capture studies of phylogenetically diverse samples, while minimizing potential bias. Our approach assembles each exon in each sample separately, by first recruiting short sequencing reads having homology to the corresponding protein sequence. In sum, custom exon capture provides a complement to existing, more generic target capture methods and is a practical and robust option across low‐moderate levels of phylogenetic divergence.


Australian Journal of Zoology | 2011

Biogeographic barriers in north-western Australia: an overview and standardisation of nomenclature

Mark D. B. Eldridge; Sally Potter; Steven J.B. Cooper

Within Australia, the biodiverse monsoon tropics are of considerable biogeographical interest. However, this vast and relatively undisturbed area with its high endemicity has only recently become the focus of phylogeographic research (Bowman et al. 2010; Fujita et al. 2010; Melville et al. 2011; Toon et al. 2010). A major challenge to understand the biogeographical processes that have shaped the distribution and diversity of taxa in this region is the lack of detailed fossil and palaeoecological data (Bowman et al. 2010). Although molecular data are able to contribute to our understanding of the biogeographic history of the region (e.g. Lee and Edwards 2008; Toon et al. 2010), relatively few studies have focussed on the geologically old and topographically complex northwest region of Australia (Jennings and Edwards 2005; Fujita et al. 2010; Melville et al. 2011). It is becoming increasingly clear that the biogeographic patterns of this region and the accompanying terminology are complex (Potter et al. 2012).Here we seek to provide an historical overview of the biogeographic nomenclature used for this region in order to bring greater clarity and concordance. We also propose a standard nomenclature that could beused in future biogeographic/phylogeographic studies of north-western Australia. The tropical monsoon region of north-western Australia represents a unique biome comprising a range of habitats. Proterozoic sandstone dominates the landscape and forms ranges and dissected escarpments set within widespread savannah woodlands. Smaller areas of monsoon rainforest, gallery forest and seasonally wet grasslands also occur. The monsoonal climate is characterised by dry winters and wet summers, which drives the vegetation type and associated distribution of taxa (Bowman et al. 2010). Tropical habitats contracted north during aridification in the Miocene and late Pliocene and the monsoonal conditions commenced following the rise of the Tibetan Plateau (3.4–7.2million years ago) and the closing of the Isthmus of Panama (see Bowman et al. 2010; Fujita et al. 2010). However, it was not until the Pleistocene that the monsoonal tropics experienced fluctuating environmental changes associated with global glacial cycles that developed the more contemporary arid-adapted vegetation (reviewed in Bowman et al. 2010; Fujita et al. 2010). The less topographically complex lowlands between the disjunct sandstone outcrops have been identified as potential biogeographic barriers for a wide variety of fauna (e.g. Bowman et al. 2010). Keast (1961) regarded north-west Australia (including both the Kimberley region and Top End of the Northern Territory, Fig. 1) as a single major mesic refuge area (North-West refuge) for Australian fauna. Earlier, Keast (1958) noted that the region of the Joseph Bonaparte Gulf formed a distributional barrier for some mangrove-dependent birds, due to a lack of habitat. After an examination of the North-West refuge bird fauna, Ford (1978) identified the presence of three ‘minor biogeographic barriers’ in the region between the Kimberley and northern Northern Territory (i.e. the Top End). These were identified as ‘arid country round the Joseph Bonaparte Gulf and the Victoria River valley, a discontinuity in sandstone ranges in the region of the Daly River drainage and a stretch of coastline poor in mangroves on western side of the Joseph Bonaparte Gulf’. More specifically, the lowlands of the Daly River drainage were identified as a significant barrier for many sandstone-rangeadapted taxa (Ford 1978). The arid country around the head of the Joseph Bonaparte Gulf (in the region of the Ord and Victoria Rivers) was considered a significant barrier for monsoon and gallery forest species, aswell as formoist grassland taxa,while the break in mangrove habitat in the western Joseph Bonaparte Gulf had significantly influenced mangrove specialists (Ford 1978). This later gap in the distribution of mangroves was subsequently examined in greater detail by Ford (1982), who identified it as a significant biogeographical barrier for mangrove birds, which he termed the ‘Bonaparte Gap’. Subsequently, ‘Bonaparte Gap’ has entered the literature as a more general term


Proceedings of the National Academy of Sciences of the United States of America | 2016

Reticulation, divergence, and the phylogeography–phylogenetics continuum

Scott V. Edwards; Sally Potter; Jonathan Jonathan Schmitt; Jason G. Bragg; Craig Moritz

Phylogeography, and its extensions into comparative phylogeography, have their roots in the layering of gene trees across geography, a paradigm that was greatly facilitated by the nonrecombining, fast evolution provided by animal mtDNA. As phylogeography moves into the era of next-generation sequencing, the specter of reticulation at several levels—within loci and genomes in the form of recombination and across populations and species in the form of introgression—has raised its head with a prominence even greater than glimpsed during the nuclear gene PCR era. Here we explore the theme of reticulation in comparative phylogeography, speciation analysis, and phylogenomics, and ask how the centrality of gene trees has fared in the next-generation era. To frame these issues, we first provide a snapshot of multilocus phylogeographic studies across the Carpentarian Barrier, a prominent biogeographic barrier dividing faunas spanning the monsoon tropics in northern Australia. We find that divergence across this barrier is evident in most species, but is heterogeneous in time and demographic history, often reflecting the taxonomic distinctness of lineages spanning it. We then discuss a variety of forces generating reticulate patterns in phylogeography, including introgression, contact zones, and the potential selection-driven outliers on next-generation molecular markers. We emphasize the continued need for demographic models incorporating reticulation at the level of genomes and populations, and conclude that gene trees, whether explicit or implicit, should continue to play a role in the future of phylogeography.


Molecular Phylogenetics and Evolution | 2012

Phylogenetic relationships of rock-wallabies, Petrogale (Marsupialia: Macropodidae) and their biogeographic history within Australia

Sally Potter; Steven J.B. Cooper; Cushla J. Metcalfe; David A. Taggart; Mark D. B. Eldridge

The rock-wallaby genus Petrogale comprises a group of habitat-specialist macropodids endemic to Australia. Their restriction to rocky outcrops, with infrequent interpopulation dispersal, has been suggested as the cause of their recent and rapid diversification. Molecular phylogenetic relationships within and among species of Petrogale were analysed using mitochondrial (cytochrome oxidase c subunit 1, cytochrome b, NADH dehydrogenase subunit 2) and nuclear (omega-globin intron, breast and ovarian cancer susceptibility gene) sequence data with representatives that encompassed the morphological and chromosomal variation within the genus, including for the first time both Petrogale concinna and Petrogale purpureicollis. Four distinct lineages were identified, (1) the brachyotis group, (2) Petrogale persephone, (3) Petrogalexanthopus and (4) the lateralis-penicillata group. Three of these lineages include taxa with the ancestral karyotype (2n=22). Paraphyletic relationships within the brachyotis group indicate the need for a focused phylogeographic study. There was support for P. purpureicollis being reinstated as a full species and P. concinna being placed within Petrogale rather than in the monotypic genus Peradorcas. Bayesian analyses of divergence times suggest that episodes of diversification commenced in the late Miocene-Pliocene and continued throughout the Pleistocene. Ancestral state reconstructions suggest that Petrogale originated in a mesic environment and dispersed into more arid environments, events that correlate with the timing of radiations in other arid zone vertebrate taxa across Australia.


Molecular Ecology | 2016

Phylogenomics at the tips: inferring lineages and their demographic history in a tropical lizard, Carlia amax.

Sally Potter; Jason G. Bragg; Benjamin M. Peter; Ke Bi; Craig Moritz

High‐throughput sequencing approaches offer opportunities to better understand the evolutionary processes driving diversification, particularly in nonmodel organisms. In particular, the 100–1000s of loci that can now be sequenced are providing unprecedented power in population, speciation and phylogenetic studies. Here, we apply an exon capture approach to generate >99% complete sequence and SNP data across >2000 loci from a tropical skink, Carlia amax, and exploit these data to identify divergent lineages and infer their relationships and demographic histories. This is especially relevant to low‐dispersal tropical taxa that often have cryptic diversity and spatially dynamic histories. For C. amax, clustering of nuclear SNPs and coalescent‐based species delimitation analyses identify four divergent lineages, one fewer than predicted based on geographically coherent mtDNA clades (>9.4% sequence divergence). Three of these lineages are widespread and parapatric on the mainland, whereas the most divergent is restricted to islands off the northeast Northern Territory. Tests for population expansion reject an equilibrium isolation‐by‐distance model for two of the three widespread lineages and infer refugial expansion sources in the relatively mesic northeast Top End and northwest Kimberley. The latter is already recognized as a hotspot of endemism, but our results also suggest that a stronger focus on the northeast Top End, and adjacent islands is warranted. More generally, our results show how genome‐reduction methods such as exon capture can yield insights into the pattern and dynamics of biodiversity across complex landscapes with as yet poorly understood biogeographic history and how exon data can link between population and phylogenetic questions.


Molecular Ecology | 2016

Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

Craig Moritz; Matthew K. Fujita; Dan F. Rosauer; Rosa Agudo; Gayleen Bourke; Paul Doughty; Russell Palmer; Mitzy Pepper; Sally Potter; Renae C. Pratt; M. Scott; M. Tonione; Steve Donnellan

Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics include vast, ecologically intact savanna‐woodland plains interspersed with ancient sandstone uplands. Although recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock‐restricted taxa. To provide a baseline for ongoing comparative analyses, we tested for phylogeographic structure in an ecologically generalized and widespread taxon, the gecko Heteronotia binoei. We apply coalescent analyses to multilocus sequence data (mitochondrial DNA and eight nuclear DNA introns) from individuals sampled extensively and at fine scale across the region. The results demonstrate surprisingly deep and geographically nested lineage diversity. Several intra‐specific clades previously shown to be endemic to the region were themselves found to contain multiple, short‐range lineages. To infer landscapes with concentrations of unique phylogeographic diversity, we probabilistically estimate the ranges of lineages from point data and then, combining these estimates with the nDNA species tree, estimate phyloendemism across the region. Highest levels of phyloendemism occur in northern Top End, especially on islands, across the topographically complex Arnhem escarpment, and across the sandstone ranges of the western Gulf region. These results drive home that deep phylogeographic structure is prevalent in tropical low‐dispersal taxa, even ones that are ubiquitous across geography and habitats.


Molecular Ecology | 2013

The importance of an evolutionary perspective in conservation policy planning

Craig Moritz; Sally Potter

Prioritization of taxa for conservation must rest on a foundation of correctly identified species boundaries, enhanced by an understanding of evolutionary history and phylogenetic relationships. Therefore, we can incorporate both evolutionary and ecological processes into efforts to sustain biodiversity. In this issue of Molecular Ecology, Malaney & Cook ( ) highlight the critical value of an evolutionary biogeographical approach, combining multilocus phylogeography with climatic niche modelling to infer phylogenetically weighted conservation priorities for evolutionary lineages of jumping mice across North America. Remarkably, they find that the Prebles meadow jumping mouse (Zapus hudsonius preblei), long debated as a threatened taxon, in fact represents the southern terminus of a relatively uniform lineage that expanded well into Alaska during the Holocene. By contrast, some other relictual and phylogenetically divergent taxa of jumping mice likely warrant greater conservation priority. This study highlights the value of integrative approaches that place current taxonomy in a broader evolutionary context to identify taxa for conservation assessment, but also highlights the challenges in maintaining potential for adaptive responses to environmental change.


Ecology and Evolution | 2014

Differing impact of a major biogeographic barrier on genetic structure in two large kangaroos from the monsoon tropics of Northern Australia

Mark D. B. Eldridge; Sally Potter; Christopher N. Johnson; Euan G. Ritchie

Tropical savannas cover 20–30% of the worlds land surface and exhibit high levels of regional endemism, but the evolutionary histories of their biota remain poorly studied. The most extensive and unmodified tropical savannas occur in Northern Australia, and recent studies suggest this region supports high levels of previously undetected genetic diversity. To examine the importance of barriers to gene flow and the environmental history of Northern Australia in influencing patterns of diversity, we investigated the phylogeography of two closely related, large, vagile macropodid marsupials, the antilopine wallaroo (Macropus antilopinus; n = 78), and the common wallaroo (Macropus robustus; n = 21). Both species are widespread across the tropical savannas of Australia except across the Carpentarian Barrier (CB) where there is a break in the distribution of M. antilopinus. We determined sequence variation in the hypervariable Domain I of the mitochondrial DNA control region and genotyped individuals at 12 polymorphic microsatellite loci to assess the historical and contemporary influence of the CB on these species. Surprisingly, we detected only limited differentiation between the disjunct Northern Territory and QueenslandM. antilopinus populations. In contrast, the continuously distributedM. robustus was highly divergent across the CB. Although unexpected, these contrasting responses appear related to minor differences in species biology. Our results suggest that vicariance may not explain well the phylogeographic patterns in Australias dynamic monsoonal environments. This is because Quaternary environmental changes in this region have been complex, and diverse individual species’ biologies have resulted in less predictable and idiosyncratic responses.


Systematic Biology | 2016

Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards.

Mozes P. K. Blom; Jason G. Bragg; Sally Potter; Craig Moritz

Abstract Accurate gene tree inference is an important aspect of species tree estimation in a summary‐coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary‐coalescent species tree inference by screening ∼2000 exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well‐supported topology based on all loci and find that a relatively small number of high‐resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent‐based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low‐resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated in the analysis of empirical phylogenomic data sets. This will ultimately increase our confidence in species tree estimation using summary‐coalescent methods and enable us to exploit genomic data for phylogenetic inference.

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Craig Moritz

Australian National University

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Jason G. Bragg

Australian National University

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Dan F. Rosauer

Australian National University

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Paul M. Oliver

Australian National University

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Ke Bi

University of California

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Ana C. Afonso Silva

Australian National University

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Gayleen Bourke

Australian National University

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