ORCID Profile
0000-0003-0472-9299
Current Organisations
University of Western Australia
,
University of Sheffield
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.
Genomics | Population, Ecological and Evolutionary Genetics | Biologically Active Molecules | Genetics
Flora, Fauna and Biodiversity of environments not elsewhere classified | Horticultural Crops not elsewhere classified |
Publisher: Wiley
Date: 06-2020
DOI: 10.1111/MEC.15460
Publisher: Wiley
Date: 05-05-2021
DOI: 10.1111/EVO.14215
Publisher: Wiley
Date: 21-09-2022
DOI: 10.1111/EVO.14632
Abstract: Hybrid speciation-the origin of new species resulting from the hybridization of genetically ergent lineages-was once considered rare, but genomic data suggest that it may occur more often than once thought. In this study, Noguerales and Ortego found genomic evidence supporting the hybrid origin of a grasshopper that is able to exploit a broader range of host plants than either of its putative parents.
Publisher: Oxford University Press (OUP)
Date: 06-09-2018
Publisher: Oxford University Press (OUP)
Date: 14-05-2015
DOI: 10.1111/ZOJ.12238
Publisher: Oxford University Press (OUP)
Date: 19-10-2011
Publisher: Wiley
Date: 15-12-2022
DOI: 10.1111/MEC.16793
Abstract: The term “haplotype block” is commonly used in the developing field of haplotype‐based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a s le. We use simulated ex les to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked‐read sequencing technologies.
Publisher: Wiley
Date: 10-06-2017
DOI: 10.1111/MEC.13645
Abstract: A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological ergence, but they do not incorporate spatial, phenotypic or environmental data that might enhance outlier detection. Geographic cline analysis provides a potential framework for integrating erse forms of data in a spatially explicit framework, but has not been used to study genome-wide patterns of ergence. Aided by a first-draft genome assembly, we combined an F
Publisher: Oxford University Press (OUP)
Date: 21-07-2015
DOI: 10.1111/ZOJ.12307
Publisher: Wiley
Date: 03-04-2019
DOI: 10.1111/JEB.13442
Abstract: Many forms of reproductive isolation contribute to speciation, and early-acting barriers may be especially important, because they have the first opportunity to limit gene flow. Ecogeographic isolation occurs when intrinsic traits of taxa contribute to disjunct geographic distributions, reducing the frequency of intertaxon mating. Characterizing this form of isolation requires knowledge of both the geographic arrangement of suitable habitats in nature and the identification of phenotypes involved in shaping geographic distributions. In Mimulus aurantiacus, red- and yellow-flowered ecotypes are incompletely isolated by ergent selection exerted by different pollinators. However, these emerging taxa are largely isolated spatially, with a hybrid zone occurring along a narrow region of contact. In order to assess whether responses to abiotic conditions contribute to the parapatric distribution of ecotypes, we measured a series of ecophysiological traits from populations along a transect, including drought sensitivity, leaf area and the concentrations of vegetative flavonoids. In contrast to the abrupt transitions in floral phenotypes, we found that ecophysiological traits exhibited a continuous geographic transition that largely mirrors variation in climatological variables. These traits may impede gene flow across a continuous environmental gradient, but they would be unlikely to result in ecotypic ergence alone. Nevertheless, we found a genetic correlation between vegetative and floral traits, providing a potential link between the two forms of isolation. Although neither barrier appears sufficient to cause ergence on its own, the combined impacts of local adaptation to abiotic conditions and regional adaptation to pollinators may interact to drive discontinuous variation in the face of gene flow in this system.
Publisher: Wiley
Date: 29-10-2008
DOI: 10.1111/J.1755-0998.2008.02256.X
Abstract: Atriplex nummularia is a polyploid Australian saltbush which has been identified as a suitable species for use in the rehabilitation of agricultural land affected by salinity. We isolated 12 polymorphic loci for a preliminary assessment of genetic variability and structure within the species as a basis for a breeding programme. Preliminary screening of loci in 40 in iduals from two populations revealed multibanded genotypes consisting of up to seven alleles in a single in idual, with up to 29 alleles observed at a single locus. The multibanded patterns are consistent with the polyploid status of this species.
Publisher: Cold Spring Harbor Laboratory
Date: 13-02-2023
DOI: 10.1101/2023.02.13.528213
Abstract: Key innovations are fundamental to biological ersification, but their genetic architecture is poorly understood. A recent transition from egg-laying to live-bearing in Littorina snails provides the opportunity to study the architecture of an innovation that has evolved repeatedly in animals. S les do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous genomic regions where all live-bearers carry the same core haplotype. Associated regions show evidence for live-bearer-specific positive selection, and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest live-bearing alleles accumulated gradually, involving selection at different times in the past. Our results suggest that innovation can have a polygenic basis, and that novel functions can evolve gradually, rather than in a single step.
Publisher: Oxford University Press (OUP)
Date: 05-06-2015
DOI: 10.1111/BIJ.12594
Publisher: Springer Science and Business Media LLC
Date: 25-09-2013
DOI: 10.1038/HDY.2013.89
Publisher: Springer Science and Business Media LLC
Date: 2014
Publisher: The Royal Society
Date: 07-09-2015
Abstract: A primary goal in evolutionary biology is to identify the historical events that have facilitated the origin and spread of adaptations. When these adaptations also lead to reproductive isolation, we can learn about the evolutionary mechanisms contributing to speciation. We reveal the complex history of the gene MaMyb2 in shaping flower colour ergence within a recent radiation of monkeyflowers. In the Mimulus aurantiacus species complex, red-flowered M. a. ssp . puniceus and yellow-flowered M. a. ssp. australis are partially isolated because of differences in pollinator preferences. Phylogenetic analyses based on genome-wide variation across the complex suggest two origins of red flowers from a yellow-flowered ancestor: one in M. a. ssp . puniceus and one in M. a. ssp. flemingii . However, in both cases, red flowers are caused by cis -regulatory mutations in the gene MaMyb2 . Although this could be due to distinct mutations in each lineage, we show that the red allele in M. a. ssp. puniceus did not evolve de novo or exist as standing variation in its yellow-flowered ancestor. Rather, our results suggest that a single red MaMyb2 allele evolved during the radiation of M. aurantiacus that was subsequently transferred to the yellow-flowered ancestor of M. a. ssp. puniceus via introgressive hybridization. Because gene flow is still possible among taxa, we conclude that introgressive hybridization can be a potent driver of adaptation at the early stages of ergence that can contribute to the origins of bio ersity.
Publisher: Wiley
Date: 18-03-2013
DOI: 10.1111/MEC.12287
Abstract: Speciation is the process by which reproductive isolation evolves between populations. Two general models of speciation have been proposed: ecological speciation, where reproductive barriers evolve due to ecologically based ergent selection, and mutation-order speciation, where populations fix different mutations as they adapt to similar selection pressures. I evaluate these alternative models and determine the progress of speciation in a erse group of land snails, genus Rhagada, inhabiting Rosemary Island. A recently derived keeled-flat morphotype occupies two isolated rocky hills, while globose-shelled snails inhabit the surrounding plains. The study of one hill reveals that they are separated by a narrow hybrid zone. As predicted by ecological speciation theory, there are local and landscape level associations between shell shape and habitat, and the morphological transition coincides with a narrow ecotone between the two distinct environments. Microsatellite DNA revealed a cline of hybrid index scores much wider than the morphological cline, further supporting the ecological maintenance of the morphotypes. The hybrid zone does not run through an area of low population density, as is expected for mutation-order hybrid zones, and there is a unimodal distribution of phenotypes at the centre, suggesting that there is little or no prezygotic isolation. Instead, these data suggest that the ecotypes are maintained by ecologically dependent postzygotic isolation (i.e. ecological selection against hybrids). Mitochondrial and Microsatellite DNA indicate that the keeled-flat form evolved recently, and without major historical disruptions to gene flow. The data also suggest that the two keeled-flat populations, inhabiting similar rocky hills, have evolved in parallel. These snails provide a complex ex le of ecological speciation in its early stages.
Publisher: The Royal Society
Date: 13-07-2020
Abstract: The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological ersity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of ergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed in iduals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially erged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Publisher: Cold Spring Harbor Laboratory
Date: 11-06-2018
DOI: 10.1101/342352
Abstract: Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic ‘landscape’ of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a recent radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine taxa in this radiation, we show that highly similar ersity (π) and differentiation ( F ST ) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying ergence times between pairs of taxa, we show that the correlations between F ST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Thus, combined with existing evidence for adaptation in this system, we conclude that the correlation in F ST among these taxa informs us about the genomic basis of adaptation and speciation in this system. What can patterns of genome-wide variation tell us about the speciation process? The answer to this question depends upon our ability to infer the evolutionary processes underlying these patterns. This, however, is difficult, because many processes can leave similar footprints, but some have nothing to do with speciation per se . For ex le, many studies have found highly heterogeneous levels of genetic differentiation when comparing the genomes of emerging species. These patterns are often referred to as differentiation ‘landscapes’ because they appear as a rugged topography of ‘peaks’ and ‘valleys’ as one scans across the genome. It has often been argued that selection against deleterious mutations, a process referred to as background selection, is primarily responsible for shaping differentiation landscapes early in speciation. If this hypothesis is correct, then it is unlikely that patterns of differentiation will reveal much about the genomic basis of speciation. However, using genome sequences from nine emerging species of monkeyflower coupled with simulations of genomic ergence, we show that it is unlikely that background selection is the primary architect of these landscapes. Rather, differentiation landscapes have probably been shaped by adaptation and gene flow, which are processes that are central to our understanding of speciation. Therefore, our work has important implications for our understanding of what patterns of differentiation can tell us about the genetic basis of adaptation and speciation.
Publisher: Wiley
Date: 17-11-2015
DOI: 10.1111/EVO.12807
Abstract: Ecological adaptation is the driving force during ergence with gene flow and generates reproductive isolation early in speciation. Although gene flow opposes ergence, local adaptation can be facilitated by factors that prevent the breakup of favorable allelic combinations. We investigated how selection, genetic architecture, and geography have contributed to the maintenance of floral trait ergence and pollinator isolation between parapatric ecotypes of Mimulus aurantiacus. Combining greenhouse, field, and genomic studies, we show that sharp clines in floral traits are maintained by spatially varying selection. Although adaptation breaks down where the ecotypes co-occur, leading to the formation of a hybrid zone, the largely non-overlapping distributions of the ecotypes shield them from immigrant genes, facilitating ergence across most of the range. In contrast to the sharp genetic discontinuities observed across most hybrid zones, we observed a gradual cline in genome-wide ergence and a pattern of isolation by distance across the landscape. Thus, contrary to a long period of allopatry followed by recent re-contact, our data suggest that floral trait ergence in M. aurantiacus may have evolved with locally restricted, but ongoing gene flow. Therefore, our study reveals how the geographic distribution of an organism can contribute to the evolution of premating isolation in the early stages of ergence with gene flow.
Publisher: Oxford University Press (OUP)
Date: 2023
DOI: 10.1093/EVOLINNEAN/KZAD002
Abstract: Understanding the factors that have shaped the current distributions and ersity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and ersified across a broad range of coastal environments in the northern hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among s les spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about ersification of four ecotypes of L. saxatilis (the crab, wave, barnacle and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.
Publisher: Wiley
Date: 09-2022
DOI: 10.1111/JEB.14082
Publisher: CSIRO Publishing
Date: 2016
DOI: 10.1071/IS15046
Abstract: Phylogenetic ersity of Rhagada land snails is high on the Burrup Peninsula, Western Australia, with four distinct clades, representing three of the four major clades of the Pilbara region. Detailed s ling indicated little geographic overlap of the four clades, conforming to the general rarity of congeneric sympatry in Australian camaenids. The ersity on the Burrup Peninsula includes three previously unclassified morphotypes. One of these lies within the broad endemic clade of the adjacent D ier Archipelago, and is provisionally assigned to the island species R. perprima, based on phylogenetic evidence. The two other undescribed morphotypes constitute an endemic clade that is the sister group of the broader D ier Archipelago clade. All COI p-distances within clades are less than 6%, whereas nearly all distances between clades exceed 10%, the gap corresponding to differences among species of Rhagada generally. One morphotype in the Burrup Peninsula endemic clade has a low spire and a distinctive keel, and is restricted to a single rockpile. Detailed local s ling revealed gradation between this form and the more widely distributed globose morphotype. On the basis of genetic similarity and morphological continuity, we describe the morphologically variable endemic Burrup Peninsula clade as Rhagada ngurrana, sp. nov., which has a distribution spanning only 9 km.
Publisher: Public Library of Science (PLoS)
Date: 24-07-2019
Publisher: Wiley
Date: 09-2022
DOI: 10.1111/JEB.14005
Abstract: Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches.
Publisher: Wiley
Date: 10-2017
DOI: 10.3732/AJB.1700234
Abstract: Evolutionary radiations provide excellent opportunities to study the origins of bio ersity, but rapid ergence and ongoing gene flow make inferring evolutionary relationships among taxa difficult. Consequently, combining morphological and genomic analyses will be necessary to clarify the evolutionary history of radiations. We used an integrative approach to shed light on relationships within a erse radiation of monkeyflowers (Mimulus section Diplacus) with a controversial taxonomic history. We used genomewide single nucleotide polymorphism data and a combination of phylogenetic and population genomic analyses to infer the evolutionary relationships within the group. Tests for hybridization were performed to reveal sources of shared variation, and multivariate analyses of floral trait data were conducted to examine the correspondence between phenotypic and phylogenetic data. We identified four primary clades with evidence for some shared variation among them. We also detected evidence for recent gene flow between closely related subclades and populations. Strong discordance between floral trait and molecular data provides evidence for ergent and convergent phenotypic evolution. Mimulus section Diplacus has all the hallmarks of a rapid radiation, including erse taxa that are at different stages of ergence, extensive shared variation among taxa, and complex patterns of phenotypic evolution. Our findings will direct future evolutionary research and have important taxonomic implications that highlight the need for a new revision of section Diplacus.
Publisher: Cold Spring Harbor Laboratory
Date: 29-09-2023
Publisher: Informa UK Limited
Date: 11-07-2014
Publisher: Cold Spring Harbor Laboratory
Date: 20-09-2023
Publisher: Authorea, Inc.
Date: 05-12-2022
Publisher: Cold Spring Harbor Laboratory
Date: 28-01-2022
DOI: 10.1101/2022.01.28.478139
Abstract: Understanding the phenotypic and genetic architecture of reproductive isolation is a longstanding goal of speciation research. In many systems, candidate barrier traits and loci have been identified, but causal connections between them are rarely made. In this study, we combine ‘top-down’ and ‘bottom-up’ approaches with demographic modeling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work in this system suggests that pollinator-mediated reproductive isolation is a primary barrier to gene flow between two ergent red- and yellow-flowered ecotypes of Mimulus aurantiacus . Several candidate floral traits contributing to pollinator isolation have been identified, including a difference in flower color, which is caused primarily by a single large-effect locus ( MaMyb2 ). Other anonymous SNP loci, potentially contributing to pollinator isolation, also have been identified, but their causal relationships remain untested. Here, we performed demographic analyses, which indicate that this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted in a large fraction of the genome by barrier loci. Using a cline-based genome scan (our bottom-up approach), we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few ‘islands of speciation.’ A QTL analysis (our top-down approach) revealed most floral traits are highly polygenic, with little evidence that QTL co-localize, indicating that most traits are largely genetically independent. Finally, we find little convincing evidence for the overlap of QTL and candidate barrier loci, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow aside from pollinator isolation may play an important role in this system.
Publisher: Wiley
Date: 11-2020
DOI: 10.1111/EVO.14111
Publisher: The Royal Society
Date: 11-01-2017
Abstract: Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently erged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly erged lineages of the phylogenetic marker PaxC . Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora , including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC , provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 10-2022
End Date: 10-2025
Amount: $499,654.00
Funder: Australian Research Council
View Funded Activity