J. Scott Keogh

J. Scott Keogh
Australian National University | ANU · Division of Ecology and Evolution - Research School of Biology

About

299
Publications
105,059
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9,746
Citations
Additional affiliations
March 1993 - May 1997
The University of Sydney
Position
  • PostDoc Position
May 1998 - June 2021
Australian National University
Position
  • Professor

Publications

Publications (299)
Article
Full-text available
Aim We review the biogeography of the Kimberley, with a particular focus on the geological and landscape history of the region. We identified broad geological and biogeographical discontinuities across the Kimberley, and propose a number of testable hypotheses concerning how the evolution of these land‐forms may have harboured and structured geneti...
Article
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Body shape is predicted to differ among species for functional reasons and in relation to environmental niche and phylogenetic history. We quantified morphological differences in shape and size among 98.5% of the 129 species and all 21 genera of the Australo-Papuan endemic myobatrachid frogs to test the hypothesis that habitat type predicts body sh...
Article
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Abstract Alternative reproductive tactics (ARTs) are predicted to be the result of disruptive correlational selection on suites of morphological, physiological, and behavioral traits. ARTs are most obvious when they occur in discrete morphs with concomitant behavioral tactics. However, ARTs driven by behavior in species lacking obvious phenotypic d...
Article
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Sexual selection theory predicts different optima for multiple mating in males and females. We used mating experiments and genetic paternity testing to disentangle pre- and postcopulatory mechanisms of sexual selection and alternate reproductive tactics in the highly promiscuous lizard Eulamprus heatwolei. Both sexes mated multiply: 30–60 % of clut...
Article
We review the biogeography of the Pilbara, synthesize information on the geological and landscape history of this region and surrounds, and assess fine-scale genetic structure across multiple taxa to examine hypotheses concerning the distribution of genetic lineages. We use this to provide a baseline for future biological studies in an ancient area...
Article
Understanding how continental radiations are assembled across space and time is a major question in macroevolutionary biology. Here, we use a phylogenomic-scale phylogeny, a comprehensive morphological dataset and environmental niche models to evaluate the relationship between trait and environment, and assess the role of geography and niche conser...
Preprint
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The accurate characterization of species diversity is a vital prerequisite for ecological and evolutionary research, as well as conservation. Thus, it is necessary to generate robust hypotheses of species limits based on the inference of evolutionary processes. Integrative species delimitation, the inference of species limits based on multiple sour...
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Recent phylogenetic studies have shown that the affinities of the two currently recognised species of Neelaps Günther, 1863, Neelaps bimaculatus (Duméril, Bibron & Duméril, 1854) and Neelaps calonotos (Duméril, Bibron & Duméril, 1854), are unresolved. Here we provide an expanded molecular phylogeny and new morphology data to clarify generic boundar...
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The Australian continent’s size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia’s plants and animals are unique and endemic, including the continent’s frogs. Australian frogs comprise a remarkable ecological and morphological...
Article
Aim Shifts in diversification rates of Australian flora and fauna have been associated with aridification, but the relationship between diversification rates and aridity has never been quantified. We employed multiple approaches to reconstruct paleoenvironments of Australia for the first time. We used this information, and phylogenetic‐based analys...
Preprint
Full-text available
The Australian continent’s size and isolation make it an ideal place for studying the accumulation and evolution of biodiversity. Long separated from the ancient supercontinent Gondwana, most of Australia’s plants and animals are unique and endemic, including the continent’s frogs. Australian frogs comprise a remarkable ecological and morphological...
Article
Full-text available
Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collisio...
Preprint
Selective processes act on phenotypic variation yet the evolutionary potential of any given trait relies on underlying heritable variation. Developmental plasticity is an important source of phenotypic variation, but it can also promote changes in heritability by modifying environmental sources of variability. Here, we quantified the influence of d...
Article
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Abstract When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favor traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD freq...
Article
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Conspicuous social and sexual signals are predicted to experience pronounced character release when natural selection via predation is relaxed. However, we have few good examples of this phenomenon in the wild and none in species with dynamic color change. Here, we show that Jackson's chameleons inadvertently introduced from Kenya to Hawaii (Oahu),...
Article
Genomic data are a powerful tool for the elucidation of evolutionary patterns at the population level and above. The combined analysis of genomic and morphological data can result in species delimitation hypotheses that reflect evolutionary history better than traditional taxonomy or any individual source of evidence. Here, we used thousands of sin...
Article
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Background Heterochrony, change in the rate or timing of development, is thought to be one of the main drivers of morphological evolution, and allometry, trait scaling patterns imposed by size, is traditionally thought to represent an evolutionary constraint. However, recent studies suggest that the ontogenetic allometric trajectories describing ho...
Article
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The habenula is a small structure in the brain that acts as a relay station for neural information, helping to modulate behaviour in response to variable and unpredictable stimuli. Broadly, it is evolutionarily conserved in structure and connectivity across vertebrates, and is the most prominent bilaterally asymmetric structure in the brain. Noneth...
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How biotic and abiotic factors act together to shape biological diversity is a major question in evolutionary biology. The recent availability of large datasets and development of new methodological approaches provide new tools to evaluate the predicted effects of ecological interactions and geography on lineage diversification and phenotypic evolu...
Article
There is a high rate of recent species discovery in remote regions of northern Australia, especially for amphibians and reptiles. The Wessel Islands, located in the northeastern corner of the Northern Territory, has recently been identified as a region of high species and phylogenetic endemism based on samples collected during the sole reptile and...
Article
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Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to de...
Article
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Global biodiversity loss is a profound consequence of human activity. Disturbingly, biodiversity loss is greater than realized because of the unknown number of undocumented species. Conservation fundamentally relies on taxonomic recognition of species, but only a fraction of biodiversity is described. Here, we provide a new quantitative approach fo...
Article
Our knowledge of the conservation status of reptiles, the most diverse class of terrestrial vertebrates, has improved dramatically over the past decade, but still lags behind that of the other tetrapod groups. Here, we conduct the first comprehensive evaluation (~92% of the world's ~1714 described species) of the conservation 1 Joint senior authors...
Article
Advances from empirical studies in phylogeography, systematics and species delimitation highlight the importance of integrative approaches for quantifying taxonomic diversity. Genomic data have greatly improved our ability to discern both systematic diversity and evolutionary history. Here we combine analyses of mitochondrial DNA sequences, thousan...
Article
Significance The mechanisms by which genomes become smaller in lineages with large genomes, such as many frogs, are poorly understood. Here, we present the sequence of a very small genome from a frog—that of the ornate burrowing frog, Platyplectrum ornatum , whose genome is smaller than that of many birds, a group well known for small genomes. Our...
Article
The sublethal effects of infectious disease on reproductive behaviour and mating success are not well understood. Here, we investigated predictors of male mating success in one of Australia's most critically endangered vertebrates: the northern corroboree frog, Pseudophryne pengilleyi. Using a genomic approach to assign parentage, we explored wheth...
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Aim The Australian deserts are home to a remarkable diversity of taxa that might appear to have evolved in the absence of topographic and physical barriers to dispersal. In fact this is a biogeographical illusion, as the dunefields of the modern arid zone obscure the fossil landscapes of the wet desert that existed for much of the Cenozoic. As the...
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Hybridization between species occurs more frequently in vertebrates than traditionally thought but distinguishing ancient hybridization from other phenomena that generate similar evolutionary patterns remains challenging. Here, we used a comprehensive workflow to discover evidence of ancient hybridization between the Komodo dragon (Varanus komodoen...
Article
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Mate choice for genetic benefits remains controversial, largely because few studies have estimated the relative contributions of additive and non‐additive sources of genetic variation to offspring fitness. Moreover, there remains a deficit of these estimates for species where female‐mate preferences have been quantified in the wild, especially spec...
Article
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Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrich...
Article
Full-text available
Sexual selection shapes the adaptive landscape in complex ways that lead to trait integration. Much of our understanding of selection comes from studies of morphological traits. However, few studies attempt to quantify the form and direction of selection on performance even though it is predicted to be a more direct target of selection in nature. W...
Article
The large and enigmatic New Guinean pythons in the genus Leiopython are harvested from the wild to supply the international trade in pets. Six species are currently recognized (albertisii, biakensis, fredparkeri, huonensis, meridionalis, montanus) but the taxonomy of this group has been controversial. We combined analysis of 421 nuclear loci and co...
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Australia hosts approximately 10% of the world’s reptile species, the largest number of any country. Despite this and evidence of widespread decline, the first comprehensive assessment of the conservation status of Australian terrestrial squamates (snakes and lizards) was undertaken only recently. Here we apply structured expert elicitation to the...
Article
Full-text available
Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly o...
Article
Full-text available
Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid...
Article
Full-text available
Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrich...
Article
Full-text available
Ecological opportunities can be provided to organisms that cross stringent biogeographic barriers towards environments with new ecological niches. Wallace's and Lyddeker's lines are arguably the most famous biogeographic barriers, separating the Asian and Australo-Papuan biotas. One of the most ecomorphologically diverse groups of reptiles, the pyt...
Article
The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered fro...
Preprint
Full-text available
Organismal interactions drive the accumulation of diversity by influencing species ranges, morphology, and behavior. Interactions vary from agonistic to cooperative and should result in predictable patterns in trait and range evolution. However, despite a conceptual understanding of these processes, they have been difficult to model, particularly o...
Article
Full-text available
Genomics is narrowing uncertainty in the phylogenetic structure for many amniote groups. For one of the most diverse and species-rich groups, the squamate reptiles (lizards and snakes, amphisbaenians), an inverse correlation between the number of taxa and loci sampled still persists across all publications using DNA sequence data and reaching a con...
Article
Full-text available
Mate choice for genetic benefits is assumed to be widespread in nature, yet very few studies have comprehensively examined relationships between female mate choice and male genetic quality in wild populations. Here, we use exhaustive sampling and single nucleotide polymorphisms to provide a partial test of the “good genes as heterozygosity” hypothe...
Preprint
Full-text available
Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less well-understood. The Australian burrowing frog genus Neobatrachus is comprised of six di...
Book
Lizards and snakes (squamate reptiles) are the most diverse vertebrate group in Australia, with approximately 1000 described species, representing about 10% of the global squamate diversity. Squamates are a vital part of the Australian ecosystem, but their conservation has been hindered by a lack of knowledge of their diversity, distribution, biolo...
Article
Full-text available
Testing hypotheses on the drivers of clade evolution and trait diversification provides insight into many aspects of evolutionary biology. Often, studies investigate only the intrinsic biological properties of organisms as the causes of diversity, however extrinsic properties of a clade's environment, particularly geological history, may also offer...
Article
Full-text available
Ecomorphology is the association between an organism's morphology and its ecology. Larval anuran amphibians (tadpoles) are classified into distinct ecomorphological guilds based upon morphological features and observations of their ecology. The extent to which guilds comprise distinct morphologies resulting from convergent evolution, the degree of...
Article
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On deep time scales, changing climatic trends can have a predictable influence on macroevolution. From evidence of mass extinctions, we know that rapid climatic oscillations can indirectly open niche space and precipitate adaptive radiation, changing the course of ecological diversification. These dramatic shifts in the global climate, however, are...
Article
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The methods used to detect and describe morphologically cryptic species have advanced in recent years, owing to the integrative nature of molecular and morphological techniques required to elucidate them. Here we integrate recent phylogenomic work that sequenced many genes but few individuals, with new data from mtDNA and morphology from hundreds o...
Data
Raw genetic data and GenBank accession numbers.
Data
Table S1. Morphological summary. Covers all species treated herein, divided by sex (M or F). Sample sizes are provided after the species name and sex. Abbreviations and definitions of characters: SVL (snout-vent length)–from tip of snout to anterior edge of cloaca; TailL (tail length)–from posterior edge of cloaca to tip of tail, original tails onl...
Data
Table S2. Specimen information for species treated here. All specimens are from the Western Australian Museum (R prefixes omitted from the registration numbers). ‘Genotyped’ means mtDNA was sequenced, and ‘Morphology’ refers to specimens included in the morphological analyses.
Data
Brief redescriptions of arid zone variegata group species that have been previously described. Below we briefly redescribe species within the arid clade of the variegata group. Tables 2 and S1 provide further information. The redescriptions are based on the specimens we examined in Table S2, and also the previous work of Hutchinson et al. (2014).
Article
Full-text available
Aim To develop a robust phylogeny for the iconic Australian water skinks (Eulamprus) and to explore the influence of landscape evolution of eastern Australia on phylogeographic patterns. Location Eastern and south‐eastern Australia. Methods We used Sanger methods to sequence a mitochondrial DNA (mtDNA) locus for 386 individuals across the five Eu...
Article
Magnetic resonance imaging (MRI) is an established technique for neuroanatomical analysis, being particularly useful in the medical sciences. However, the application of MRI to evolutionary neuroscience is still in its infancy. Few magnetic resonance brain atlases exist outside the standard model organisms in neuroscience and no magnetic resonance...
Article
Molecular technologies have revolutionised our classification of animal mating systems, yet we still know very little about the genetic mating systems of many vertebrate groups. It is widely believed that anuran amphibians have the highest reproductive diversity of all vertebrates, yet genetic mating systems have been studied in less than one perce...
Article
Full-text available
The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered fro...
Preprint
The quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered fro...
Article
Full-text available
Targeting phylogenetic diversity (PD) in systematic conservation planning is an efficient way to minimize losses across the Tree of Life. Considering representation of genetic diversity below and above species level, also allows robust analyses within systems where taxonomy is in flux. We use dense sampling of phylogeographic diversity for eleven l...
Article
Full-text available
Background Quantifying morphological diversity across taxa can provide valuable insight into evolutionary processes, yet its complexities can make it difficult to identify appropriate units for evaluation. One of the challenges in this field is identifying the processes that drive morphological evolution, especially when accounting for shape divers...
Article
High throughput sequencing methods promise to improve our ability to infer the evolutionary histories of lineages and to delimit species. These are exciting prospects for the study of Australian vertebrates, a group comprised of many globally unique lineages with a long history of isolation. The evolutionary relationships within many of these linea...
Article
Understanding the joint evolutionary and ecological underpinnings of sympatry among close relatives remains a key challenge in biology. This problem can be addressed through joint phylogenomic and phenotypic analysis of complexes of closely related lineages within, and across, species and hence representing the speciation continuum. For a complex o...
Article
Full-text available
Ontogenetic allometry, how species change with size through their lives, and heterochony, a decoupling between shape, size and age, are major contributors to biological diversity. However, macro-evolutionary allometric and heterochronic trends remain poorly understood because previous studies have focused on small groups of closely related species....
Article
Full-text available
The brain plays a critical role in a wide variety of functions including behaviour, perception, motor control, and homeostatic maintenance. Each function can undergo different selective pressures over the course of evolution, and as selection acts on the outputs of brain function, it necessarily alters the structure of the brain. Two models have be...