Biology subjects

Keogh, J. S.

Publications and source records attributed to Keogh, J. S..

12 recordsLinked to original sources

bioRxiv2026

Pygopods are an exceptional radiation of snake-like geckos

Limb loss in vertebrate animals is surprisingly common despite imposing strong functional constraints. These pressures funnel species towards regions of limited ecological and phenotypic space. To date, snakes have been considered unique in having escaped this pattern. Using a new species-level phylogeny and comparative morphological and dietary datasets, we show that pygopods, a group of limbless Australo-Papuan geckos, have undergone a similar evolutionary trajectory to snakes. Our analyses provide evidence of exceptional morphological and diet evolution. This is exemplified by strong niche partitioning among genera through dietary specialization and greater than expected dietary disparity. Diversification in pygopods has also been driven by extreme phenotypic evolution, with pygopods encompassing much of the morphological space covered by all other limb-reduced lizards. Interestingly, the diversification of pygopods has resulted in only a modest number of species, emphasizing the decoupling of diversity and richness possible in adaptive radiations.

evolutionary biology↗

bioRxiv2026

Unlocking the venom vault: Museum venomics reveals an untapped biochemical archive in natural history collections

Venoms are powerful weapons that shape ecological interactions across the animal kingdom. They also have high medical importance, causing thousands of human fatalities annually, while offering a rich resource for drug discovery. Despite this, considerable logistical, safety and ethical challenges mean only a fraction of the worlds venoms have been profiled quantitatively. Natural history collections offer opportunities to greatly expand our knowledge of venom systems. We used quantitative proteomic mass spectrometry on preserved venom glands, spanning 0-57 years in age, from 37 venomous snake species (32 elapids and 5 viperids), alongside fresh venom samples from most of the same taxa. Preserved glands and fresh venoms from the same species showed strong concordance in venom composition across multiple metrics. Critically, specimen age did not degrade data quality, indicating that decades-old material yields reliable quantitative profiles, opening the possibility for vast quantities of existing museum specimens to be used. When we integrate our data with published profiles, we confirm known elapid vs viper broad diversity patterns while revealing substantial Australasian elapid venom diversity. Our findings demonstrate the potential of natural history collections as a vast, largely untapped biochemical archive for high-throughput "museum venomics," enabling evolutionary and temporal analyses of venom diversity at unprecedented scale.

molecular biology↗

bioRxiv2026

Aridification and habitat shifts drove diversification in Australian diplodactylid geckos

Continental radiations record the long-term interplay between environmental change, ecological opportunity, and lineage diversification across large geographic scales. The gecko family Diplodactyli-dae represents one such radiation with [~]200 species distributed across Australia, New Caledonia, and Aotearoa New Zealand, occupying ecological forms ranging from burrow-dwelling desert specialists to canopy climbers, and diversifying over a [~]45 Ma history shaped by dramatic continental environ-mental change. Using [~]5000 nuclear loci, we reconstructed phylogenetic relationships and divergence times, estimated ancestral ecology and biomes using newly generated biome-through-time maps for Australia, and modeled the effects of ecological states on diversification and morphology. Crown diplodactylids originated in the mid-Eocene ([~]45 Ma), with the core Australian clade radiating in the Oligocene ([~]28 Ma), substantially younger than previous estimates. Ancestral state estimation indicated arboreal origins in mesic environments, followed by repeated transitions into open habitats and expansion into semi-arid and arid biomes. Despite moderate differences in diversification rates among ecological states, rate variation was better explained by unmeasured hidden states than by observed ecological states, suggesting that our broad ecological categorization alone does not explain diversification dynamics within this radiation. Size varies with ecological state, while tail length shows no detectable ecological association and remains phylogenetically conserved. These patterns indicate that environmental change and biome transformation were associated with ecological opportunity, coinciding with diversification through repeated habitat transitions and morphological divergence, providing a macroevolutionary framework linking environmental change, ecological expansion, and trait evolution in a continental radiation.

evolutionary biology↗

bioRxiv2026

Phylogenomic assessment of microhylid frogs reveals widespread taxonomic confusion in the Asterophryinae and establishes the timing of diversification in Australia

Microhylid frogs are a hyper-diverse family thought to have radiated explosively around the Cretaceous-Paleogene boundary. Roughly half of microhylid species richness is concentrated into a single subfamily, the Asterophryinae, which is centered in New Guinea and surrounds, and has been a rich source for species discovery over the past 50 years. However, resolving Asterophryinae phylogenetics has remained a challenge, with frequent taxonomic reshuffling. To address this instability, we generated a sequence-capture molecular dataset to investigate the phylogenetics of the group. This included 71 species of Asterophryinae, across 13 of 17 recognized genera representing extensive sampling of the New Guinea radiation and full sampling of Australian microhylid species. Our dated species tree supports an explosive diversification of microhylids in New Guinea near the start of the Miocene, approximately 20 million years ago. Asterophryinae expansion into northern Australia occurred much later ([~]10 ma) and is marked by well supported clades of Austrochaperina and Cophixalus that show temporally consistent splits from their New Guinea sister taxa. Our phylogeny allows us to identify several instances of polyphyly, which are at odds with our current understanding of intergeneric relationships within the Asterophryinae. We suggest that this confusion is a result of rapid radiation and morphological variability across some poorly defined genera. This work establishes a reliable phylogenetic framework that can form a foundation for a more stable taxonomy of the Asterophryinae. HighlightsO_LIA phylogenomic assessment of the globally distributed frog family Microhylidae C_LIO_LIThe subfamily Asterophryinae radiated explosively in New Guinea C_LIO_LIAustralian species represent two distinct clades C_LIO_LIAssignments of species to genera by morphological means are often unreliable C_LI

evolutionary biology↗

bioRxiv2025

Generalists link peaks in the shifting adaptive landscape of Australia's dragon lizards

The adaptive landscape is a flexible concept in biology which helps map entities onto an eco-evolutionary topography. A common practice is clustering species to identify adaptive peaks but the pathways that allow movement into new adaptive zones remain poorly understood. Here we integrate new sequence-capture (>5,000 nuclear markers) and multivariate morphological data to investigate the adaptive landscape of Amphibolurinae dragon lizards (Agamidae). Our well-supported, time-calibrated phylogeny includes over 360 specimens from 176 species, including iconic taxa such as the frilled-neck lizard, thorny devil, and bearded dragon. We show that arrival in Australia was followed by rapid expansion of morphological diversity facilitated by generalist habitat use. Ancestral dragons were likely arboreal, but species with broad niche breadths and intermediate morphologies provided pathways to subsequent specialization. These findings reveal an evolutionary pathway for adaptive diversification in a major continental radiation.

evolutionary biology↗

bioRxiv2024

The first complete mitochondrial genome of tjakura (Great Desert Skink, Liopholis kintorei)

The complete mitochondrial genome (mitogenome) of the tjaku{square}a, Liopholis kintorei was obtained using next-generation sequencing, making it the first recorded mitogenome of the genus Liopholis and the Tiliquini. The mitogenome is 16,844bp in length with a base composition of A (31.7%), T (24.4%), G (14.6%), and C (29.3%) and a G + C content of 43.9%. The genome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (12S and 16S), and three non-coding fragments, consisting of the putative control region and two mitochondrially encoded heavy strand origin of replication region (OriH). The gene order is identical to that of typical skink mitogenomes. This genomic resource will provide valuable information for genetic studies of this genus and contribute to the growing collection of mitogenomes within the family Scincidae.

genomics↗

bioRxiv2024

Evolutionary bursts drive morphological novelty in the world's largest skinks

Animal phenotypes evolve and diverge as a result of differing selective pressures and drift. These processes leave unique signatures in patterns of trait evolution, impacting the tempo and mode of morphological macroevolution. While there is a broad understanding of the history of some organismal traits (e.g. body size), there is little consensus about the evolutionary mode of most others. This includes the relative contribution of prolonged (Darwinian gradualist) and episodic (Simpsonian jump) changes towards the evolution of novel morphologies. Here we use new exon-capture and linear morphological datasets to investigate the tempo and mode of morphological evolution in Australo-Melanesian Tiliquini skinks. We generate a well-supported time-calibrated phylogenomic tree from [~]400 nuclear markers for more than 100 specimens including undescribed diversity, and provide unprecedented resolution of the rapid Miocene diversification of these lizards. By collecting a morphological dataset that encompasses the lizard body plan (19 traits across the head, body, limb, and tail) we are able to identify that most traits evolve conservatively but infrequent evolutionary bursts result in morphological novelty. These phenotypic discontinuities occur via rapid rate increases along individual branches, inconsistent with both gradualistic and punctuated equilibrial evolutionary modes. Instead, this punctuated gradualism has resulted in the rapid evolution of blue-tongued giants and armored dwarves in the [~]20 million years since colonizing Australia. These results outline the evolutionary pathway towards new morphologies and highlight the heterogeneity of evolutionary tempo and mode, even within individual traits.

evolutionary biology↗

bioRxiv2023

Integrating Genomics, Collections, and Community Science to Reveal Speciation in a Variable Monitor Lizard (Varanus tristis)

--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 sources of evidence, can provide unique insight into species diversity and the processes behind it. However, the application of integrative approaches in non-model organisms is often limited by the amount of data that is available. Here, we show how data relevant for species delimitation can be bolstered by incorporating information from tissue collections, museum specimens, and observations made by the wider community. We show how to integrate these data under a hypothesis-driven, integrative framework by identifying the processes generating genetic and phenotypic variation in Varanus tristis, a widespread and variable complex of Australian monitor lizards. Using genomic, morphometric (linear and geometric), coloration, spatial, and environmental data we show that disparity in this complex is inconsistent with intraspecific variation and instead suggests that speciation has occurred. Based on our results, we identify the environmental factors that may have been responsible for the geographic sorting of variation. Our workflow provides a guideline for the integrative analysis of several types of data to identify the occurrence and causes of speciation. Furthermore, our study highlights how community science and machine learning--two tools used here--can be used to accelerate taxonomic research.

evolutionary biology↗

bioRxiv2023

Populating a Continent: Phylogenomics Reveal the Timing of Australian Frog Diversification

The Australian continents 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 Australias plants and animals are unique and endemic, including the continents frogs. Australian frogs comprise a remarkable ecological and morphological diversity categorized into a small number of distantly related radiations. We present a phylogenomic hypothesis based on an exon-capture dataset that spans the main clades of Australian myobatrachoid, pelodryadid hyloid, and microhylid frogs. Our time-calibrated phylogenomic-scale phylogeny identifies great disparity in the relative ages of these groups which vary from Gondwanan relics to recent immigrants from Asia and include arguably the continents oldest living vertebrate radiation. This age stratification provides insight into the colonization of, and diversification on, the Australian continent through deep time, during periods of dramatic climatic and community changes. Contemporary Australian frog diversity highlights the adaptive capacity of anurans, particularly in response to heat and aridity, and explains why they are one of the continents most visible faunas.

evolutionary biology↗

bioRxiv2020

Phylogenomics of monitor lizards and the role of competition in dictating body size disparity

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 on macroevolutionary timescales and across broad geographic spaces. Here we investigate the influence of biotic interactions on trait evolution and community assembly in monitor lizards (Varanus). Monitors are an iconic radiation with a cosmopolitan distribution and the greatest size disparity of any living terrestrial vertebrate genus. Between the colossal Komodo dragon Varanus komodoensis and the smallest Australian dwarf goannas, Varanus length and mass vary by multiple orders of magnitude. To test the hypothesis that size variation in this genus was driven by character displacement, we extended existing phylogenetic comparative methods which consider lineage interactions to account for dynamic biogeographic history and apply these methods to Australian monitors and marsupial predators. We use a phylogenomic approach to estimate the relationships among living and extinct varaniform lizards, incorporating both exon-capture molecular and morphological datasets. Our results suggest that communities of Australian Varanus show high functional diversity as a result of continent-wide interspecific competition among monitors but not with faunivorous marsupials. We demonstrate that patterns of trait evolution resulting from character displacement on continental scales are recoverable from comparative data and highlight that these macroevolutionary patterns may develop in parallel across widely distributed sympatric groups.

evolutionary biology↗

bioRxiv2019

Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus

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 diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We resolve the phylogenetic relationships among Neobatrachus species and provide further support that the three polyploid species have independent autotetraploid origins. We document higher genetic diversity in tetraploids, resulting from widespread gene flow specifically between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and current isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate variation on frogs with differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which in turn corresponds to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow into tetraploid lineages specifically. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.

evolutionary biology↗

bioRxiv2017

ShapeRotator: an R package for standardised rigid rotations of articulated Three-Dimensional structures with application for geometric morphometrics

O_LIThe 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 from these structures are difficult to incorporate in to modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures.\nC_LIO_LIWhile there are existing methods for analysing shape variation in articulated structures in Two-Dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research.\nC_LIO_LIHere we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space so it can be applied to any morphometric problem that also uses 3D coordinates (e.g. spherical harmonics). We demonstrate the method by applying it to a landmark-based data set for analysing shape variation using geometric morphometrics.\nC_LIO_LIWe have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.\nC_LI

evolutionary biology↗