ORCID Profile
0000-0002-4719-6640
Current Organisation
Instituto de Biología Evolutiva
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Biological adaptation | Genomics and transcriptomics | Molecular evolution | Genetics |
Publisher: Springer Science and Business Media LLC
Date: 08-01-2018
DOI: 10.1038/S41598-017-18562-W
Abstract: The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an ex le of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). In contrast, several molecular datasets have contradicted the Diplopoda–Pauropoda grouping (named Dignatha), often recovering a Symphyla–Pauropoda group (named Edafopoda). Here we present the first transcriptomic data including a pauropod and both families of symphylans, allowing myriapod interrelationships to be inferred from phylogenomic data from representatives of all main lineages. Phylogenomic analyses consistently recovered Dignatha with strong support. Taxon removal experiments identified outgroup choice as a critical factor affecting myriapod interrelationships. Diversification of millipedes in the Ordovician and centipedes in the Silurian closely approximates fossil evidence whereas the deeper nodes of the myriapod tree date to various depths in the Cambrian-Early Ordovician, roughly coinciding with recent estimates of terrestrialisation in other arthropod lineages, including hexapods and arachnids.
Publisher: Springer Science and Business Media LLC
Date: 29-06-2023
DOI: 10.1038/S41467-023-39603-1
Abstract: Adaptation to life in caves is often accompanied by dramatically convergent changes across distantly related taxa, epitomized by the loss or reduction of eyes and pigmentation. Nevertheless, the genomic underpinnings underlying cave-related phenotypes are largely unexplored from a macroevolutionary perspective. Here we investigate genome-wide gene evolutionary dynamics in three distantly related beetle tribes with at least six instances of independent colonization of subterranean habitats, inhabiting both aquatic and terrestrial underground systems. Our results indicate that remarkable gene repertoire changes mainly driven by gene family expansions occurred prior to underground colonization in the three tribes, suggesting that genomic exaptation may have facilitated a strict subterranean lifestyle parallelly across beetle lineages. The three tribes experienced both parallel and convergent changes in the evolutionary dynamics of their gene repertoires. These findings pave the way towards a deeper understanding of the evolution of the genomic toolkit in hypogean fauna.
Publisher: Elsevier BV
Date: 03-2022
DOI: 10.1016/J.TREE.2021.11.008
Abstract: Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global bio ersity. These genomes provide unique insights into genomic ersity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
Publisher: Oxford University Press (OUP)
Date: 18-04-2016
DOI: 10.1111/ZOJ.12419
Publisher: The Royal Society
Date: 10-07-2019
Abstract: Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa—or fail when such key taxa are not s led. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon s ling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.
Publisher: Oxford University Press (OUP)
Date: 09-05-2016
Publisher: Oxford University Press (OUP)
Date: 26-03-2014
Abstract: Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on s les of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to s le all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 25-10-2019
Abstract: Earthworms are key components of soil ecological communities, performing vital functions in decomposition and nutrient cycling through ecosystems. Using data from more than 7000 sites, Phillips et al. developed global maps of the distribution of earthworm ersity, abundance, and biomass (see the Perspective by Fierer). The patterns differ from those typically found in aboveground taxa there are peaks of ersity and abundance in the mid-latitude regions and peaks of biomass in the tropics. Climate variables strongly influence these patterns, and changes are likely to have cascading effects on other soil organisms and wider ecosystem functions. Science , this issue p. 480 see also p. 425
Publisher: Cold Spring Harbor Laboratory
Date: 12-12-2022
DOI: 10.1101/2022.12.08.519422
Abstract: Chemical cues in subterranean habitats differ highly from those on the surface due to the contrasting environmental conditions, such as absolute darkness, high humidity or food scarcity. Subterranean animals underwent changes to their sensory systems to facilitate the perception of essential stimuli for underground lifestyles. Despite representing unique systems to understand biological adaptation, the genomic basis of chemosensation across cave-dwelling species remains unexplored from a macroevolutionary perspective. Here, we explore the evolution of chemoreception in three beetle tribes that underwent at least six independent transitions to the underground through a phylogenomics spyglass. Our findings suggest that the chemosensory gene repertoire varies dramatically between species. Overall, no parallel changes in the net rate of evolution of chemosensory gene families were detected prior, during, or after the habitat shift among subterranean lineages. Contrarily, we found evidence of lineage-specific changes within surface and subterranean lineages. Our results reveal key duplications and losses shared between some of the lineages transitioning to the underground, including the loss of sugar receptors and gene duplications of the highly conserved ionotropic receptors IR25a and IR8a, involved in thermal and humidity sensing among other olfactory roles in insects. These duplications were detected both in independent subterranean lineages and their surface relatives, suggesting parallel evolution of these genes across lineages giving rise to cave-dwelling species. Overall, our results shed light on the genomic basis of chemoreception in subterranean beetles and contribute to deepen our understanding of the genomic underpinnings of adaptation to the subterranean lifestyle at a macroevolutionary scale.
Start Date: 2023
End Date: 12-2025
Amount: $426,591.00
Funder: Australian Research Council
View Funded Activity