Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex)

Pavón‐Vázquez, Carlos J.; Esquerré, Damien; Fitch, Alison J.; Maryan, Brad; Doughty, Paul; Donnellan, Stephen C.; Keogh, J. Scott

doi:10.1016/j.ympev.2022.107516

Cited by 8 publications

(8 citation statements)

References 96 publications

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“…This suggests that these four geographically distinct populations likely represent four genetically distinct conservation units, similar to what was shown in the study of the Komodo dragon (V. komodoensis), where three genetically distinct conservation units were identified from the five main Indonesian islands (Iannucci et al 2021). A recent phylogeographic study on V. acanthurus that utilized SNP markers, morphometric data and weather data, identified a need for taxonomic revisions and considered V. acanthurus a species complex with at least one undescribed species from the Cape Crawford area, which is sympatric with our north population (Pavón-vázquez et al 2022). It is therefore of significant interest that here we have shown the population structure of these widespread dwarf goannas was essentially "islands" in various stages of divergence similar to the observations of other species of varanids on the many islands of Indonesia (Welton et al 2014;Weijola et al 2019) but without any obvious geographical barriers.…”

Section: Absence Of Gene Flow Between Populationssupporting

confidence: 77%

Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae)

et al. 2023

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Chromosomal rearrangements are often associated with local adaptation and speciation because they suppress recombination, and as a result, rearrangements have been implicated in disrupting gene flow. Although there is strong evidence to suggest that chromosome rearrangements are a factor in genetic isolation of divergent populations, the underlying mechanism remains elusive. Here, we applied an integrative cytogenetics and genomics approach testing whether chromosomal rearrangements are the initial process, or a consequence, of population divergence in the dwarf goanna, Varanus acanthurus. Specifically, we tested whether chromosome rearrangements are indicators of genetic barriers that can be used to identify divergent populations by looking at gene flow within and between populations with rearrangements. We found that gene flow was present between individuals with chromosome rearrangements within populations, but there was no gene flow between populations that had similar chromosome rearrangements. Moreover, we identified a correlation between reduced genetic variation in populations with a higher frequency of homozygous submetacentric individuals. These findings suggest that chromosomal rearrangements were widespread prior to divergence, and because we found populations with higher frequencies of submetacentric chromosomes were associated with lower genetic diversity, this could indicate that polymorphisms within populations are early indicators of genetic drift.

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Section: Absence Of Gene Flow Between Populationssupporting

confidence: 77%

Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae)

et al. 2023

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“…SE appears to be the most highly differentiated population. The Carpentarian Gap, Simpson Desert, and Lake Eyre are all major barriers that probably restrict gene flow between SE and other populations (Austin et al 2013; Pepper and Keogh 2021; Pavón-Vázquez et al 2022). However, occasional gene flow is apparently possible (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Tissue samples were sourced from several Australian biological collections (Table S1). DArTseq data have been used successfully for phylogeographic inference and species delimitation in numerous taxa (e.g., Georges et al 2018; Chaplin et al 2020; Esquerré et al 2021; Binks and Byrne 2022; Mahony et al 2022), including other Varanus (Pavón-Vázquez et al 2022).…”

Section: Methodsmentioning

confidence: 99%

“…orientalis Fry 1913. We processed the data following Pavón-Vázquez et al (2022). Briefly, missing measurements (i.e., from incomplete tails) were imputed using random forest training (Stekhoven and Bühlmann 2012).…”

Section: Methodsmentioning

confidence: 99%

“…Specimens convey information about the genotype, gene interactions, epigenetic regulation, and environmental demands in the form of morphological data. The approaches used to collect and analyze morphological data have advanced in parallel to molecular methods, providing unique insight into species limits (Pavón-Vázquez et al 2018, 2022; Chaplin et al 2020). Furthermore, museum specimens link specific phenotypes (and genotypes, if molecular resources are available) with particular temporal, geographic, and environmental conditions (Edwards et al 2005; Schmitt et al 2019).…”

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confidence: 99%

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

Pavón-Vázquez,

Fitch,

Doughty

et al. 2023

Preprint

Self Cite

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Abstract—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 inVaranus 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.

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Dragons in the tropics – Phylogeography and speciation in Diporiphora lizards and common geographic breaks in co-distributed taxa

Fenker,

Melville,

Moritz

2024

Molecular Phylogenetics and Evolution

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Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex)

Cited by 8 publications

References 96 publications

Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae)

Widespread chromosomal rearrangements preceded genetic divergence in a monitor lizard, Varanus acanthurus (Varanidae)

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

Dragons in the tropics – Phylogeography and speciation in Diporiphora lizards and common geographic breaks in co-distributed taxa

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