ORCID Profile
0000-0002-7493-416X
Current Organisation
University of Queensland
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Research Topics
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.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Genetics | Population, Ecological and Evolutionary Genetics | Genomics | Ecology And Evolution Not Elsewhere Classified | Population And Ecological Genetics | Crop and pasture production | Animal reproduction and breeding | Horticultural crop improvement (incl. selection and breeding) | Crop and pasture improvement (incl. selection and breeding) | Biologically Active Molecules | Intellectual Property Law | Evolutionary Biology | Plant Biology | Speciation and Extinction | Biological Mathematics | Plant Physiology | Molecular Evolution |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Biological sciences | Expanding Knowledge in Law and Legal Studies | Flora, Fauna and Biodiversity of environments not elsewhere classified | Horticultural Crops not elsewhere classified | Expanding Knowledge in the Agricultural and Veterinary Sciences | Expanding Knowledge in the Mathematical Sciences
Related Links
Publications
Speciation: The Strength of Natural Selection Driving Reinforcement
Publisher: Elsevier BV
Date: 10-2014
DOI: 10.1016/J.CUB.2014.08.033
Abstract: Our understanding of how natural selection drives the speciation process remains a mystery. A recent study shows how selection for flower color differences causes the evolution of reproductive isolation between two plant species of the genus Phlox.
Homage to Felsenstein 1981, or why are there so few/many species?
Publisher: Wiley
Date: 05-2021
DOI: 10.1111/EVO.14235
Recombination Rate Evolution and the Origin of Species
Publisher: Elsevier BV
Date: 03-2016
DOI: 10.1016/J.TREE.2015.12.016
Abstract: A recipe for dissolving incipient species into a continuum of phenotypes is to recombine their genetic material. Therefore, students of speciation have become increasingly interested in the mechanisms by which recombination between locally adapted lineages is reduced. Evidence abounds that chromosomal rearrangements, via their suppression of recombination during meiosis in hybrids, play a major role in adaptation and speciation. By contrast, genic modifiers of recombination rates have been largely ignored in studies of speciation. We show how both types of reduction in recombination rates facilitate ergence in the face of gene flow, including the early stages of adaptive ergence, the persistence of species after secondary contact, and reinforcement.
CONVERGENCE AND DIVERGENCE DURING THE ADAPTATION TO SIMILAR ENVIRONMENTS BY AN AUSTRALIAN GROUNDSEL
Publisher: Wiley
Date: 22-05-2013
DOI: 10.1111/EVO.12136
Abstract: Adaptation to replicate environments is often achieved through similar phenotypic solutions. Whether selection also produces convergent genomic changes in these situations remains largely unknown. The variable groundsel, Senecio lautus, is an excellent system to investigate the genetic underpinnings of convergent evolution, because morphologically similar forms of these plants have adapted to the same environments along the coast of Australia. We compared range-wide patterns of genomic ergence in natural populations of this plant and searched for regions putatively affected by natural selection. Our results indicate that environmental adaptation followed complex genetic trajectories, affecting multiple loci, implying both the parallel recruitment of the same alleles and the ergence of completely different genomic regions across geography. An analysis of the biological functions of candidate genes suggests that adaptation to coastal environments may have occurred through the recruitment of different genes participating in similar processes. The relatively low genetic convergence that characterizes the parallel evolution of S. lautus forms suggests that evolution is more constrained at higher levels of biological organization.
The origin and maintenance of metabolic allometry in animals
Publisher: Springer Science and Business Media LLC
Date: 18-03-2019
DOI: 10.1038/S41559-019-0839-9
Abstract: Organisms vary widely in size, from microbes weighing 0.1 pg to trees weighing thousands of megagrams - a 10
Comparisons of chemosensory gene repertoires in human and non-human feeding Anopheles mosquitoes link olfactory genes to anthropophily
Publisher: Elsevier BV
Date: 07-2022
Receivers Limit the Prevalence of Deception in Humans: Evidence from Diving Behaviour in Soccer Players
Publisher: Public Library of Science (PLoS)
Date: 05-10-2011
Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex
Publisher: Wiley
Date: 25-05-2013
DOI: 10.1111/MEC.12311
Abstract: Instances of parallel ecotypic ergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel ergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection of Senecio species showed that members of the S. lautus complex form a distinct lineage that has ersified recently in Australasia. An inspection of thousands of polymorphisms in the genome of 27 natural populations from the S. lautus complex in Australia revealed a signal of strong genetic structure independent of habitat and phenotype. Additionally, genetic differentiation between populations was correlated with the geographical distance separating them, and the genetic ersity of populations strongly depended on geographical location. Importantly, coastal forms appeared in several independent phylogenetic clades, a pattern that is consistent with the parallel evolution of these forms. Analyses of the patterns of genomic differentiation between populations further revealed that adjacent populations displayed greater genomic heterogeneity than allopatric populations and are differentiated according to variation in soil composition. These results are consistent with a process of parallel ecotypic ergence in face of gene flow.
Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflower
Publisher: Proceedings of the National Academy of Sciences
Date: 17-11-2021
Abstract: New species originate as populations become reproductively isolated from one another. Despite recent progress in uncovering the genetic basis of reproductive isolation, it remains unclear whether intrinsic reproductive barriers, such as hybrid sterility, can evolve as a by-product of local adaptation to contrasting environments. Here, we show that differences in a plant’s response to the pull of gravity have repeatedly evolved amongst coastal populations of an Australian wildflower, thus implicating a role of natural selection in their evolution. We found a strong genetic association between variation in this adaptive trait and hybrid sterility, suggesting that intrinsic reproductive barriers contribute to the origin of new species as populations adapt to heterogeneous environments.
Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus
Publisher: Wiley
Date: 30-05-2016
DOI: 10.1111/EVO.12936
Abstract: Speciation proceeds when gene exchange is prevented between populations. Determining the different barriers preventing gene flow can therefore give insights into the factors driving and maintaining species boundaries. These reproductive barriers may result from intrinsic genetic incompatibilities between populations, from extrinsic environmental differences between populations, or a combination of both mechanisms. We investigated the potential barriers to gene exchange between three adjacent ecotypes of an Australian wildflower to determine the strength of in idual barriers and the degree of overall isolation between populations. We found almost complete isolation between the three populations mainly due to premating extrinsic barriers. Intrinsic genetic barriers were weak and variable among populations. There were asymmetries in some intrinsic barriers due to the origin of cytoplasm in hybrids. Overall, these results suggest that reproductive isolation between these three populations is almost complete despite the absence of geographic barriers, and that the main drivers of this isolation are ecologically based, consistent with the mechanisms underlying ecological speciation.
Hypergraphs and centrality measures identifying key features in gene expression data
Publisher: Cold Spring Harbor Laboratory
Date: 19-12-2022
DOI: 10.1101/2022.12.18.518108
Abstract: Multidisciplinary approaches can significantly advance our understanding of complex systems. For instance, gene co-expression networks align prior knowledge of biological systems with studies in graph theory, emphasising pairwise gene to gene interactions. In this paper, we extend these ideas, promoting hypergraphs as an investigative tool for studying multi-way interactions in gene expression data. Additional freedoms are achieved by representing in idual genes with hyperedges, and simultaneous testing each gene against many features/vertices. Further gene/hyperedge interactions can be captured and explored using the line graph representations, a techniques that also reduces the complexity of dense hypergraphs. Such an approach provides access to graph centrality measures, which in turn identify salient features within a data set, for instance dominant or hub-like hyperedges leading to key knowledge on gene expression. The validity of this approach is established through the study of gene expression data for the plant species Senecio lautus and results will be interpreted within this biological setting.
Species Concepts and Speciation
Publisher: Elsevier
Date: 2016
Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation
Publisher: Oxford University Press (OUP)
Date: 08-2020
DOI: 10.1002/EVL3.187
Abstract: Adaptation to contrasting environments occurs when advantageous alleles accumulate in each population, but it remains largely unknown whether these same advantageous alleles create genetic incompatibilities that can cause intrinsic reproductive isolation leading to speciation. Identifying alleles that underlie both adaptation and reproductive isolation is further complicated by factors such as dominance and genetic interactions among loci, which can affect both processes differently and obscure potential links between adaptation and speciation. Here, we use a combination of field and glasshouse experiments to explore the connection between adaptation and speciation while accounting for dominance and genetic interactions. We created a hybrid population with equal contributions from four contrasting ecotypes of Senecio lautus (Asteraceae), which produced hybrid genomes both before (F1 hybrid generation) and after (F4 hybrid generation) recombination among the parental ecotypes. In the glasshouse, plants in the second generation (F2 hybrid generation) showed reduced fitness as a loss of fertility. However, fertility was recovered in subsequent generations, suggesting that genetic variation underlying the fitness reduction was lost in subsequent generations. To quantify the effects of losing genetic variation at the F2 generation on the fitness of later generation hybrids, we used a reciprocal transplant to test for fitness differences between parental ecotypes, and F1 and F4 hybrids in all four parental habitats. Compared to the parental ecotypes and F1 hybrids, variance in F4 hybrid fitness was lower, and lowest in habitats that showed stronger native-ecotype advantage, suggesting that stronger natural selection for the native ecotype reduced fitness variation in the F4 hybrids. Fitness trade-offs that were present in the parental ecotypes and F1 hybrids were absent in the F4 hybrid. Together, these results suggest that the genetic variation lost after the F2 generation was likely associated with both adaptation and intrinsic reproductive isolation among ecotypes from contrasting habitats.
Reinforcement
Publisher: Oxford University Press
Date: 26-06-2019
DOI: 10.1093/OBO/9780199941728-0120
Abstract: Reinforcement, or the strengthening of reproductive isolation in response to hybridization costs, is a case in which natural selection directly contributes to the origin of new species. From its conception, reinforcement has enjoyed alternate periods of enthusiasm and rejection, in which powerful verbal arguments identified obstacles that were subsequently solved by novel theory. Empirical data has provided some of the strongest arguments for the plausibility of reinforcement and for its frequency in nature, indicating that it is likely to be a common aspect of species ergence and the completion of speciation.
Sharing and reporting benefits from biodiversity research
Publisher: Wiley
Date: 06-11-2020
DOI: 10.1111/MEC.15702
Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant
Publisher: Oxford University Press (OUP)
Date: 07-10-2010
DOI: 10.1093/AOB/MCQ201
Speciation: Splitting when together
Publisher: Springer Science and Business Media LLC
Date: 17-05-2006
Evidence for mutation-order speciation inSenecio lautus
Publisher: Cold Spring Harbor Laboratory
Date: 04-07-2019
DOI: 10.1101/692673
Abstract: In a number of animal species, ergent natural selection has repeatedly and independently driven the evolution of reproductive isolation between populations adapted to contrasting, but not to similar environments 1 . This process is known as parallel ecological speciation, and ex les in plants are enigmatically rare 2 . Here, we perform a comprehensive test of the ecological speciation hypothesis in an Australian wildflower where parapatric populations found in coastal sand dunes (Dune ecotype) and headlands (Headland ecotype) have repeatedly and independently erged in growth habit. Consistent with a role for ergent natural selection driving the evolution of reproductive isolation, we found that Dune populations with erect growth habit were easy to transplant across sand dunes, were largely interfertile despite half-a-million years of ergence, and were reproductively isolated from equally ergent Headland populations with prostrate growth habit. However, we unexpectedly discovered that both extrinsic and intrinsic reproductive isolation has evolved between prostrate Headland populations, suggesting that populations evolving convergent phenotypes can also rapidly become new species. Mutation-order speciation 2 , where the random accumulation of adaptive alleles create genetic incompatibilities between populations inhabiting similar habitats, provides a compelling explanation for these complex patterns of reproductive isolation. Our results suggest that natural selection can drive speciation effectively, but environmental and genetic complexity might make parallel ecological speciation uncommon in plants despite strong morphological convergence.
Environmentally induced development costs underlie fitness tradeoffs
Publisher: Wiley
Date: 06-2018
DOI: 10.1002/ECY.2234
Abstract: Local adaptation can lead to genotype-by-environment interactions, which can create fitness tradeoffs in alternative environments, and govern the distribution of bio ersity across geographic landscapes. Exploring the ecological circumstances that promote the evolution of fitness tradeoffs requires identifying how natural selection operates and during which ontogenetic stages natural selection is strongest. When organisms disperse to areas outside their natural range, tradeoffs might emerge when organisms struggle to reach key life history stages, or alternatively, die shortly after reaching life history stages if there are greater risks of mortality associated with costs to developing in novel environments. We used multiple populations from four ecotypes of an Australian native wildflower (Senecio pinnatifolius) in reciprocal transplants to explore how fitness tradeoffs arise across ontogeny. We then assessed whether the survival probability for plants from native and foreign populations was contingent on reaching key developmental stages. We found that fitness tradeoffs emerged as ontogeny progressed when native plants were more successful than foreign plants at reaching seedling establishment and maturity. Native and foreign plants that failed to reach seedling establishment died at the same rate, but plants from foreign populations died quicker than native plants after reaching seedling establishment, and died quicker regardless of whether they reached sexual maturity or not. Development rates were similar for native and foreign populations, but changed depending on the environment. Together, our results suggest that natural selection for environment-specific traits early in life history created tradeoffs between contrasting environments. Plants from foreign populations were either unable to develop to seedling establishment, or they suffered increased mortality as a consequence of reaching seedling establishment. The observation of tradeoffs together with environmentally dependent changes in development rate suggest that foreign environments induce organisms to develop at a rate different from their native habitat, incurring consequences for lifetime fitness and population ergence.
Evolution of genetic variance during adaptive radiation
Publisher: Cold Spring Harbor Laboratory
Date: 02-01-2017
DOI: 10.1101/097642
Abstract: Genetic correlations between traits can bias adaptation away from optimal phenotypes and constrain the rate of evolution. If genetic correlations between traits limit adaptation to contrasting environments, rapid adaptive ergence across a heterogeneous landscape may be difficult. However, if genetic variance can evolve and align with the direction of natural selection, then abundant allelic variation can promote rapid ergence during adaptive radiation. Here, we explored adaptive ergence among ecotypes of an Australian native wildflower by quantifying ergence in multivariate phenotypes of populations that occupy four contrasting environments. We investigated differences in multivariate genetic variance underlying morphological traits and examined the alignment between ergence in phenotype and ergence in genetic variance. We found that ergence in mean multivariate phenotype has occurred along two major axes represented by different combinations of plant architecture and leaf traits. Ecotypes also showed ergence in the level of genetic variance in in idual traits, and the multivariate distribution of genetic variance among traits. Divergence in multivariate phenotypic mean aligned with ergence in genetic variance, with most of the ergence in phenotype among ecotypes associated with a change in trait combinations that had substantial levels of genetic variance in each ecotype. Overall, our results suggest that ergent natural selection acting on high levels of standing genetic variation might fuel ecotypic differentiation during the early stages of adaptive radiation.
Senecio as a model system for integrating studies of genotype, phenotype and fitness.
Publisher: Wiley
Date: 17-03-2020
DOI: 10.1111/NPH.16434
Abstract: Two major developments have made it possible to use ex les of ecological radiations as model systems to understand evolution and ecology. First, the integration of quantitative genetics with ecological experiments allows detailed connections to be made between genotype, phenotype, and fitness in the field. Second, dramatic advances in molecular genetics have created new possibilities for integrating field and laboratory experiments with detailed genetic sequencing. Combining these approaches allows evolutionary biologists to better study the interplay between genotype, phenotype, and fitness to explore a wide range of evolutionary processes. Here, we present the genus Senecio (Asteraceae) as an excellent system to integrate these developments, and to address fundamental questions in ecology and evolution. Senecio is one of the largest and most phenotypically erse genera of flowering plants, containing species ranging from woody perennials to herbaceous annuals. These Senecio species exhibit many growth habits, life histories, and morphologies, and they occupy a multitude of environments. Common within the genus are species that have hybridized naturally, undergone polyploidization, and colonized erse environments, often through rapid phenotypic ergence and adaptive radiation. These erse experimental attributes make Senecio an attractive model system in which to address a broad range of questions in evolution and ecology.
The Genetics and Ecology of Reinforcement
Publisher: Wiley
Date: 06-2009
DOI: 10.1111/J.1749-6632.2009.04919.X
Abstract: Reinforcement, the evolution of prezygotic reproductive barriers by natural selection in response to maladaptive hybridization, is one of the most debated processes in speciation. Critics point to "fatal" conceptual flaws for sympatric evolution of prezygotic isolation, but recent theoretical and empirical work on genetics and ecology of reinforcement suggests that such criticisms can be overcome. New studies provide evidence for reinforcement in frogs, fish, insects, birds, and plants. While such evidence lays to rest the argument over reinforcement's existence, our understanding remains incomplete. We lack data on (1) the genetic basis of female preferences and the links between genetics of pre- and postzygotic isolation, (2) the ecological basis of reproductive isolation, (3) connections between prezygotic isolation between species and within-species sexual selection (potentially leading to a "cascade" of effects on reproductive isolation), (4) the role of habitat versus mate preference in reinforcement, and (5) additional detailed comparative studies. Here, we review data on these issues and highlight why they are important for understanding speciation.
An association study of bipolar mood disorder (type I) with the 5-HTTLPR serotonin transporter polymorphism in a human population isolate from Colombia
Publisher: Elsevier BV
Date: 10-2000
DOI: 10.1016/S0304-3940(00)01464-6
Abstract: The short variant of a functional length polymorphism in the promoter region of the serotonin transporter has been associated with several behavioural and psychiatric traits, including bipolar mood disorder. The same short allele has also been implicated as a modifier of the bipolar phenotype. Here we evaluate the etiologic/modifier role of this polymorphism in a case (N=103) / control (N=112) s le for bipolar mood disorder (type I) collected from an isolated South American population. We did not detect an association between bipolar disorder and the 5-HTT promoter polymorphism in this s le. However, an excess of the short allele was seen in younger cases and in cases with psychotic symptoms. When combined with data from the literature, the increased frequency of the short allele in patients with psychotic symptoms was statistically significant.
Modelling selection response in plant breeding programs using crop models as mechanistic gene-to-phenotype (CGM-G2P) multi-trait link functions
Publisher: Cold Spring Harbor Laboratory
Date: 14-10-2020
DOI: 10.1101/2020.10.13.338301
Abstract: Plant breeding programs are designed and operated over multiple cycles to systematically change the genetic makeup of plants to achieve improved trait performance for a Target Population of Environments (TPE). Within each cycle, selection applied to the standing genetic variation within a structured reference population of genotypes (RPG) is the primary mechanism by which breeding programs make the desired genetic changes. Selection operates to change the frequencies of the alleles of the genes controlling trait variation within the RPG. The structure of the RPG and the TPE has important implications for the design of optimal breeding strategies. The breeder’s equation, together with the quantitative genetic theory behind the equation, informs many of the principles for design of breeding programs. The breeder’s equation can take many forms depending on the details of the breeding strategy. Through the genetic changes achieved by selection, the cultivated varieties of crops (cultivars) are improved for use in agriculture. From a breeding perspective, selection for specific trait combinations requires a quantitative link between the effects of the alleles of the genes impacted by selection and the trait phenotypes of plants and their breeding value. This gene-to-phenotype link function provides the G2P map for one to many traits. For complex traits controlled by many genes, the infinitesimal model for trait genetic variation is the dominant G2P model of quantitative genetics. Here we consider motivations and potential benefits of using the hierarchical structure of crop models as CGM-G2P trait link functions in combination with the infinitesimal model for the design and optimisation of selection in breeding programs.
Ecological selection maintains cytonuclear incompatibilities in hybridizing sunflowers
Publisher: Wiley
Date: 09-2008
Archipelagos of the Anthropocene: rapid and extensive differentiation of native terrestrial vertebrates in a single metropolis
Publisher: Wiley
Date: 06-03-2017
DOI: 10.1111/MEC.14042
Abstract: Some of the best evidence for rapid evolutionary change comes from studies of archipelagos and oceanic islands. City parks are analogous systems as they create geographically isolated green spaces that differ in size, structure and complexity. Very little, however, is known about whether city parks within a single urban centre drive selection and result in the ersification of native species. Here, we provide evidence for the rapid genetic and morphological differentiation of a native lizard (Intellagama lesueurii) at four geographically close yet unconnected parks within one city. Year of establishment of each city park varied from 1855 (oldest) to 2001 (youngest) equating to a generation time range of 32 to three generations. Genetic ergence among city park populations was large despite the small pairwise geographic distances (<5 km) and found to be two to three times higher for microsatellites and three to 33 times higher for mtDNA relative to nonurban populations. Patterns of morphological differentiation were also found to be most extensive among the four city park populations. In contrast to nonurban populations, city park populations showed significant differentiation in relative body size, relative head and limb morphology and relative forelimb and hindlimb length. Crucially, we show that these patterns of differentiation are unlikely to have been caused by founder events and/or drift alone. Our results suggest that city park 'archipelagos' could represent theatres for rapid evolution that may, in time, favour adaptive ersification.
Species integrity in trees
Publisher: Wiley
Date: 25-08-2014
DOI: 10.1111/MEC.12867
Abstract: From California sequoia, to Australian eucalyptus, to the outstanding ersity of Amazonian forests, trees are fundamental to many processes in ecology and evolution. Trees define the communities that they inhabit, are host to a multiplicity of other organisms and can determine the ecological dynamics of other plants and animals. Trees are also at the heart of major patterns of bio ersity such as the latitudinal gradient of species ersity and thus are important systems for studying the origin of new plant species. Although the role of trees in community assembly and ecological succession is partially understood, the origin of tree ersity remains largely opaque. For instance, the relative importance of differing habitats and phenologies as barriers to hybridization between closely related species is still largely uncharacterized in trees. Consequently, we know very little about the origin of trees species and their integrity. Similarly, studies on the interplay between speciation and tree community assembly are in their infancy and so are studies on how processes like forest maturation modifies the context in which reproductive isolation evolves. In this issue of Molecular Ecology, Lindtke et al. (2014) and Lagache et al. (2014) overcome some traditional difficulties in studying mating systems and sexual isolation in the iconic oaks and poplars, providing novel insights about the integrity of tree species and on how ecology leads to variation in selection on reproductive isolation over time and space.
Divergent selection and heterogeneous genomic divergence
Publisher: Wiley
Date: 19-01-2009
Empowering Latina scientists
Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-02-2019
RECONCILING EXTREMELY STRONG BARRIERS WITH HIGH LEVELS OF GENE EXCHANGE IN ANNUAL SUNFLOWERS
Publisher: Wiley
Date: 03-01-2012
DOI: 10.1111/J.1558-5646.2011.01537.X
Abstract: In several cases, estimates of gene flow between species appear to be higher than we might predict given the strength of interspecific barriers separating these species pairs. However, as far as we are aware, detailed measurements of reproductive isolation have not previously been compared with a coalescent-based assessment of gene flow. Here, we contrast these two measures in two species of sunflower, Helianthus annuus and H. petiolaris. We quantified the total reproductive barrier strength between these species by compounding the contributions of the following prezygotic and postzygotic barriers: ecogeographic isolation, reproductive asynchrony, niche differentiation, pollen competition, hybrid seed formation, hybrid seed germination, hybrid fertility, and extrinsic postzygotic isolation. From this estimate, we calculated the probability that a reproductively successful hybrid is produced: estimates of P(hyb) range from 10(-4) to 10(-6) depending on the direction of the cross and the degree of independence among reproductive barriers. We then compared this probability with population genetic estimates of the per generation migration rate (m). We showed that the relatively high levels of gene flow estimated between these sunflower species (N(e) m= 0.34-0.76) are mainly due to their large effective population sizes (N(e) > 10(6)). The interspecific migration rate (m) is very small ( 0.999) may produce genomic mosaics.
Evolution of Genetic Variance during Adaptive Radiation
Publisher: University of Chicago Press
Date: 04-2018
DOI: 10.1086/696123
Abstract: Genetic correlations between traits can concentrate genetic variance into fewer phenotypic dimensions that can bias evolutionary trajectories along the axis of greatest genetic variance and away from optimal phenotypes, constraining the rate of evolution. If genetic correlations limit adaptation, rapid adaptive ergence between multiple contrasting environments may be difficult. However, if natural selection increases the frequency of rare alleles after colonization of new environments, an increase in genetic variance in the direction of selection can accelerate adaptive ergence. Here, we explored adaptive ergence of an Australian native wildflower by examining the alignment between ergence in phenotype mean and ergence in genetic variance among four contrasting ecotypes. We found ergence in mean multivariate phenotype along two major axes represented by different combinations of plant architecture and leaf traits. Ecotypes also showed ergence in the level of genetic variance in in idual traits and the multivariate distribution of genetic variance among traits. Divergence in multivariate phenotypic mean aligned with ergence in genetic variance, with much of the ergence in phenotype among ecotypes associated with changes in trait combinations containing substantial levels of genetic variance. Overall, our results suggest that natural selection can alter the distribution of genetic variance underlying phenotypic traits, increasing the amount of genetic variance in the direction of natural selection and potentially facilitating rapid adaptive ergence during an adaptive radiation.
Phenotypic and genotypic parallel evolution in parapatric ecotypes ofSenecio
Publisher: Cold Spring Harbor Laboratory
Date: 07-02-2020
DOI: 10.1101/2020.02.05.936450
Abstract: The independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred to as parallel evolution. However, we are still largely unaware of the dynamics of parallel evolution, as well as the interplay between phenotype and genotype within natural systems. Here, we examined phenotypic and genotypic parallel evolution in multiple parapatric Dune-Headland coastal ecotypes of an Australian wildflower, Senecio lautus . We observed a clear trait-environment association within the system, with all replicate populations having evolved along the same phenotypic evolutionary trajectory. Similar phenotypes have arisen via mutational changes occurring in different genes, although many share the same biological functions. Our results shed light on how replicated adaptation manifests at the phenotypic and genotypic levels within populations, and highlights S. lautus as one of the most striking cases of phenotypic parallel evolution in nature.
Evolution of recombination rates and the genomic landscape of speciation
Publisher: Wiley
Date: 08-2017
DOI: 10.1111/JEB.13116
Evolutionary Origins of a Bioactive Peptide Buried within Preproalbumin
Publisher: Oxford University Press (OUP)
Date: 03-2014
Abstract: The de novo evolution of proteins is now considered a frequented route for biological innovation, but the genetic and biochemical processes that lead to each newly created protein are often poorly documented. The common sunflower (Helianthus annuus) contains the unusual gene PawS1 (Preproalbumin with SFTI-1) that encodes a precursor for seed storage albumin however, in a region usually discarded during albumin maturation, its sequence is matured into SFTI-1, a protease-inhibiting cyclic peptide with a motif homologous to unrelated inhibitors from legumes, cereals, and frogs. To understand how PawS1 acquired this additional peptide with novel biochemical functionality, we cloned PawS1 genes and showed that this dual destiny is over 18 million years old. This new family of mostly backbone-cyclic peptides is structurally erse, but the protease-inhibitory motif was restricted to peptides from sunflower and close relatives from its subtribe. We describe a widely distributed, potential evolutionary intermediate PawS-Like1 (PawL1), which is matured into storage albumin, but makes no stable peptide despite possessing residues essential for processing and cyclization from within PawS1. Using sequences we cloned, we retrodict the likely stepwise creation of PawS1's additional destiny within a simple albumin precursor. We propose that relaxed selection enabled SFTI-1 to evolve its inhibitor function by converging upon a successful sequence and structure.
Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower
Publisher: Wiley
Date: 28-05-2017
DOI: 10.1111/MEC.14150
Abstract: The build-up of the phenotypic differences that distinguish species has long intrigued biologists. These differences are often inherited as stable polymorphisms that allow the cosegregation of adaptive variation within species, and facilitate the differentiation of complex phenotypes between species. It has been suggested that the clustering of adaptive loci could facilitate this process, but evidence is still scarce. Here, we used QTL analysis to study the genetic basis of phenotypic differentiation between coastal populations of the Australian wildflower Senecio lautus. We found that a genomic region consistently governs variation in several of the traits that distinguish these contrasting forms. Additionally, some of the taxon-specific traits controlled by this QTL cluster have evolved repeatedly during the adaptation to the same habitats, suggesting that it could mediate ergence between locally adapted forms. This cluster contains footprints of ergent natural selection across the range of S. lautus, which suggests that it could have been instrumental for the rapid ersification of this species.
Divergent natural selection drives the evolution of reproductive isolation in an Australian wildflower
Publisher: Wiley
Date: 08-08-2016
DOI: 10.1111/EVO.12994
Abstract: Ecological speciation occurs when reproductive isolation evolves between populations adapting to contrasting environments. A key prediction of this process is that the fitness of hybrids between ergent populations should be reduced in each parental environment as a function of the proportion of local genes they carry, a process resulting in ecologically dependent reproductive isolation (RI). To test this prediction, we use reciprocal transplant experiments between adjacent populations of an Australian wildflower, Senecio lautus, at two locations to distinguish between ecologically dependent and intrinsic genetic reproductive barriers. These barriers can be distinguished by observing the relative fitness of reciprocal backcross hybrids, as they differ in the contribution of genes from either parent while controlling for any intrinsic fitness effects of hybridization. We show ecologically dependent fitness effects in establishment and survival of backcrosses in one transplant experiment, and growth performance in the second transplant experiment. These results suggest natural selection can create strong reproductive barriers that maintain differentiation between populations with the potential to interbreed, and implies a significant role for ecology in the evolutionary ergence of S. lautus.
Evidence for a One-Allele Assortative Mating Locus
Publisher: American Association for the Advancement of Science (AAAS)
Date: 02-12-2005
Abstract: Theoretical models have shown that speciation with gene flow can occur readily via a “one-allele mechanism,” where the spread of the same allele within both of two erging species reduces their subsequent hybridization. Here we present direct genetic evidence for such an allele in Drosophila pseudoobscura . Alleles conferring high or low assortative mating in D. pseudoobscura produce the same effects when inserted into D. persimilis . This observation suggests that the type of genetic variation that is most conducive to controversial modes of speciation with gene flow, such as reinforcement or sympatric speciation, is present in nature.
The evolution of recombination rates in finite populations during ecological speciation
Publisher: The Royal Society
Date: 26-10-2016
Abstract: Recombination can impede ecological speciation with gene flow by mixing locally adapted genotypes with maladapted migrant genotypes from a ergent population. In such a scenario, suppression of recombination can be selectively favoured. However, in finite populations evolving under the influence of random genetic drift, recombination can also facilitate adaptation by reducing Hill–Robertson interference between loci under selection. In this case, increased recombination rates can be favoured. Although these two major effects on recombination have been studied in idually, their joint effect on ecological speciation with gene flow remains unexplored. Using a mathematical model, we investigated the evolution of recombination rates in two finite populations that exchange migrants while adapting to contrasting environments. Our results indicate a two-step dynamic where increased recombination is first favoured (in response to the Hill–Robertson effect), and then disfavoured, as the cost of recombining locally with maladapted migrant genotypes increases over time (the maladaptive gene flow effect). In larger populations, a stronger initial benefit for recombination was observed, whereas high migration rates intensify the long-term cost of recombination. These dynamics may have important implications for our understanding of the conditions that facilitate incipient speciation with gene flow and the evolution of recombination in finite populations.
Strong extrinsic reproductive isolation between parapatric populations of an Australian groundsel
Publisher: Wiley
Date: 28-03-2014
DOI: 10.1111/NPH.12779
Abstract: Speciation with gene flow, or the evolution of reproductive isolation between interbreeding populations, remains a controversial problem in evolution. This is because gene flow erodes the adaptive differences that selection creates between populations. Here, we use a combination of common garden experiments in the field and in the glasshouse to investigate what ecological and genetic mechanisms prevent gene flow and maintain morphological and genetic differentiation between coastal parapatric populations of the Australian groundsel Senecio lautus . We discovered that in each habitat extrinsic reproductive barriers prevented gene flow, whereas intrinsic barriers in F 1 hybrids were weak. In the field, herbivores played a major role in preventing gene flow, but glasshouse experiments demonstrated that soil type also created variable selective pressures both locally and on a greater geographic scale. Our experimental results demonstrate that interfertile plant populations adapting to contrasting environments may erge as a consequence of concurrent natural selection acting against migrants and hybrids through multiple mechanisms. These results provide novel insights into the consequences of local adaptation in the origin of strong barriers to gene flow in plants, and suggest that herbivory may play an important role in the early stages of plant speciation.
Diversification across a heterogeneous landscape
Publisher: Wiley
Date: 08-08-2016
DOI: 10.1111/EVO.13009
Abstract: Adaptation to contrasting environments across a heterogeneous landscape favors the formation of ecotypes by promoting ecological ergence. Patterns of fitness variation in the field can show whether natural selection drives local adaptation and ecotype formation. However, to demonstrate a link between ecological ergence and speciation, local adaptation must have consequences for reproductive isolation. Using contrasting ecotypes of an Australian wildflower, Senecio lautus in common garden experiments, hybridization experiments, and reciprocal transplants, we assessed how the environment shapes patterns of adaptation and the consequences of adaptive ergence for reproductive isolation. Local adaptation was strong between ecotypes, but weaker between populations of the same ecotype. F1 hybrids exhibited heterosis, but crosses involving one native parent performed better than those with two foreign parents. In a common garden experiment, F2 hybrids exhibited reduced fitness compared to parentals and F1 hybrids, suggesting that few genetic incompatibilities have accumulated between populations adapted to contrasting environments. Our results show how ecological differences across the landscape have created complex patterns of local adaptation and reproductive isolation, suggesting that ergent natural selection has played a fundamental role in the early stages of species ersification.
Natural selection drives leaf divergence in experimental populations of Senecio lautus under natural conditions
Publisher: Wiley
Date: 06-2019
DOI: 10.1002/ECE3.5263
Abstract: Leaf morphology is highly variable both within and between plant species. This study employs a combination of common garden and reciprocal transplant experiments to determine whether differences in leaf shape between Senecio lautus ecotypes has evolved as an adaptive response to ergent ecological conditions. We created a synthetic population of hybrid genotypes to segregate morphological variation between three ecotypes and performed reciprocal transplants where this hybrid population was transplanted into the three adjacent native environments. We measured nine leaf morphology traits across the experimental and natural populations at these sites. We found significant ergence in multivariate leaf morphology toward the native character in each environment, suggesting environmental conditions at each site exert selective pressure that results in a phenotypic shift toward the local phenotype of the wild populations. These associations suggest that differences in leaf morphology between S. lautus ecotypes have arisen as a result of ergent selection on leaf shape or associated traits that confer an adaptive advantage in each environment, which has led to the formation of morphologically distinct ecotypes.
Autosomal, mtDNA, and Y-Chromosome Diversity in Amerinds: Pre- and Post-Columbian Patterns of Gene Flow in South America
Publisher: Elsevier BV
Date: 11-2000
easyfm: An easy software suite for file manipulation of Next Generation Sequencing data on desktops
Publisher: Cold Spring Harbor Laboratory
Date: 30-09-2021
DOI: 10.1101/2021.09.29.462291
Abstract: Storing and manipulating Next Generation Sequencing (NGS) file formats is an essential but difficult task in biological data analysis. The easyfm ( easy f ile m anipulation) toolkit ( github.com/TaekAndBrendan/easyfm ) makes manipulating commonly used NGS files more accessible to biologists. It enables them to perform end-to-end reproducible data analyses using a free standalone desktop application (available on Windows, Mac and Linux). Unlike existing tools (e.g. Galaxy), the Graphical User Interface (GUI)-based easyfm is not dependent on any high-performance computing (HPC) system and can be operated without an internet connection. This specific benefit allow easyfm to seamlessly integrate visual and interactive representations of NGS files, supporting a wider scope of bioinformatics applications in the life sciences. The analysis and manipulation of NGS data for understanding biological phenomena is an increasingly important aspect in the life sciences. Yet, most methods for analysing, storing and manipulating NGS data require complex command-line tools in HPC or web-based servers and have not yet been implemented in comprehensive, easy-to-use software. This is a major hurdle preventing more general application in the field of NGS data analysis and file manipulation. Here we present easyfm , a free standalone Graphical User Interface (GUI) software with Python support that can be used to facilitate the rapid discovery of target sequences (or user’s interest) in NGS datasets for novice users. For user-friendliness and convenience, easyfm was developed with four work modules and a secondary GUI window (herein secondary window), covering different aspects of NGS data analysis (mainly focusing on FASTA files), including post-processing, filtering, format conversion, generating results, real-time log, and help. In combination with the executable tools (BLAST+ and BLAT) and Python, easyfm allows the user to set analysis parameters, select/extract regions of interest, examine the input and output results, and convert to a wide range of file formats. To help augment the functionality of existing web-based and command-line tools, easyfm , a self-contained program, comes with extensive documentation (hosted at github.com/TaekAndBrendan/easyfm ) including a comprehensive step-by-step guide.
The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool
Publisher: Cold Spring Harbor Laboratory
Date: 06-09-2022
DOI: 10.1101/2022.09.04.506567
Abstract: Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica cultivars to explore whether the genetic structure of the Australian mango gene pool explained variation in tree size, fruit blush colour and intensity. Our results show that genetic structure is weak, but cultivars imported from Southeast Asia (mainly those from Thailand) were genetically differentiated across multiple population genetic analyses. We find that genetic structure was strongly associated with phenotypic ersity in M. indica , suggesting that the history of these cultivars could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype has the potential to improve the accuracy of genomic selection, which can assist the development of new cultivars.
Highly replicated evolution of parapatric ecotypes
Publisher: Cold Spring Harbor Laboratory
Date: 07-02-2020
DOI: 10.1101/2020.02.05.936401
Abstract: Parallel evolution of ecotypes occurs when selection independently drives the evolution of similar traits across similar environments. The multiple origin of ecotypes is often inferred on the basis of a phylogeny which clusters populations according to geographic location and not by the environment they occupy. However, the use of phylogenies to infer parallel evolution in closely related populations is problematic because gene flow and incomplete lineage sorting can uncouple the genetic structure at neutral markers from the colonization history of populations. Here, we demonstrate multiple origins within ecotypes of an Australian wildflower, Senecio lautus . We observed strong genetic structure as well as phylogenetic clustering by geography and show that this is unlikely due to gene flow between parapatric ecotypes, which is surprisingly low. We further confirm this analytically by demonstrating that phylogenetic distortion due to gene flow often requires higher levels of migration than those observed in S. lautus . Our results imply that selection can repeatedly create similar phenotypes despite the perceived homogenizing effects of gene flow.
Gene flow between island populations of the malaria mosquito, Anopheles hinesorum, may have contributed to the spread of divergent host preference phenotypes
Publisher: Wiley
Date: 23-08-2021
DOI: 10.1111/EVA.13288
Abstract: Anopheles hinesorum is a mosquito species with variable host preference. Throughout New Guinea and northern Australia, An . hinesorum feeds on humans (it is opportunistically anthropophagic) while in the south‐west Pacific's Solomon Archipelago, the species is abundant but has rarely been found biting humans (it is exclusively zoophagic in most populations). There are at least two ergent zoophagic (nonhuman biting) mitochondrial lineages of An . hinesorum in the Solomon Archipelago representing two independent dispersals. Since zoophagy is a derived (nonancestral) trait in this species, this leads to the question: has zoophagy evolved independently in these two populations? Or conversely: has nuclear gene flow or connectivity resulted in the transfer of zoophagy? Although we cannot conclusively answer this, we find close nuclear relationships between Solomon Archipelago populations indicating that recent nuclear gene flow has occurred between zoophagic populations from the ergent mitochondrial lineages. Recent work on isolated islands of the Western Province (Solomon Archipelago) has also revealed an anomalous, anthropophagic island population of An . hinesorum . We find a common shared mitochondrial haplotype between this Solomon Island population and another anthropophagic population from New Guinea. This finding suggests that there has been recent migration from New Guinea into the only known anthropophagic population from the Solomon Islands. Although currently localized to a few islands in the Western Province of the Solomon Archipelago, if anthropophagy presents a selective advantage, we may see An . hinesorum emerge as a new malaria vector in a region that is now working on malaria elimination.
The origins of reproductive isolation in plants
Publisher: Wiley
Date: 05-05-2015
DOI: 10.1111/NPH.13424
Abstract: Reproductive isolation in plants occurs through multiple barriers that restrict gene flow between populations, but their origins remain uncertain. Work in the past decade has shown that postpollination barriers, such as the failure to form hybrid seeds or sterility of hybrid offspring, are often less strong than prepollination barriers. Evidence implicates multiple evolutionary forces in the origins of reproductive barriers, including mutation, stochastic processes and natural selection. Although adaptation to different environments is a common element of reproductive isolation, genomic conflicts also play a role, including female meiotic drive. The genetic basis of some reproductive barriers, particularly flower colour influencing pollinator behaviour, is well understood in some species, but the genetic changes underlying many other barriers, especially pollen–stylar interactions, are largely unknown. Postpollination barriers appear to accumulate at a faster rate in annuals compared with perennials, due in part to chromosomal rearrangements. Chromosomal changes can be important isolating barriers in themselves but may also reduce the recombination of genes contributing to isolation. Important questions for the next decade include identifying the evolutionary forces responsible for chromosomal rearrangements, determining how often prezygotic barriers arise due to selection against hybrids, and establishing the relative importance of genomic conflicts in speciation. Contents Summary 968 I. Introduction 968 II. Reproductive barriers in plants 970 III. Geographic patterns and the origin of reproductive isolation 971 IV. Genetic changes and evolutionary drivers behind reproductive isolation 973 V. The timing of reproductive barriers 979 VI. Synthesis and future directions 980 Acknowledgements 981 References 981
The delimitation and evolutionary history of the Australasian Lautusoid group of Senecio (Asteraceae: Senecioneae)
Publisher: Wiley
Date: 02-2018
DOI: 10.12705/671.8
Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio
Publisher: Wiley
Date: 08-11-2021
DOI: 10.1111/EVO.14387
A recombinational portrait of the Drosophila pseudoobscura genome
Publisher: Hindawi Limited
Date: 02-2006
DOI: 10.1017/S0016672306007932
Abstract: Drosophila pseudoobscura has been intensively studied by evolutionary biologists for over 70 years. The recent publication of the genome sequence not only permits studies of comparative genomics with other dipterans but also opens the door to identifying genes associated with adaptive traits or speciation or testing for the signature of natural selection across the genome. Information on regional rates of recombination, localization of inversion breakpoints distinguishing it from its sibling species D. persimilis , and known polymorphic markers may be useful in such studies. Here, we present a molecular linkage map of four of the five major chromosome arms of D. pseudoobscura . In doing so, we order and orient several sequence contig groups, localize the inversion breakpoints on chromosome 2 to intervals of 200 kilobases, and identify one error in the published sequence assembly. Our results show that regional recombination rates in D. pseudoobscura are much higher than in D. melanogaster and significantly higher even than in D. persimilis . Furthermore, we detect a non-significant positive correlation between recombination rate and published DNA sequence variation. Finally, the online Appendix presents 200 primer sequence pairs for molecular markers that can be used for mapping of quantitative trait loci, of which 125 are known to be polymorphic within or between species.
Meeting review: American Genetics Association Symposium on the genetics of speciation
Publisher: Wiley
Date: 07-2007
Metabolic scaling has diversified among species, despite an evolutionary constraint within species
Publisher: Cold Spring Harbor Laboratory
Date: 29-05-2020
DOI: 10.1101/2020.05.26.117846
Abstract: Metabolic rate scales disproportionally with body mass, such that the energetic cost of living is relatively lower in larger organisms. Theory emphasises the importance of fixed physical constraints on metabolic scaling, yet empirical data are lacking with which to assess how evolutionary processes (e.g. mutation, drift, selection) contribute to the observed variation in metabolic scaling across the tree of life. Using a large-scale quantitative genetic study of growth in cockroaches, we show that ontogenetic metabolic scaling is evolutionarily constrained due to an absence of additive genetic variation in juvenile metabolic rate and mass. Using a phylogenetic analysis, we also show that ontogenetic metabolic scaling is more similar among closely related species than among distant relatives, suggesting that the constraints on metabolic scaling are subject to change during lineage ersification. Our results are consistent with growing evidence that there is strong stabilising selection on combinations of mass and metabolic rate within species.
Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflower
Publisher: Cold Spring Harbor Laboratory
Date: 17-11-2019
DOI: 10.1101/845354
Abstract: Natural selection is a significant driver of speciation. Yet it remains largely unknown whether local adaptation can drive speciation through the evolution of hybrid sterility between populations. Here, we show that adaptive ergence in shoot gravitropism, the ability of a plant’s shoot to bend upwards in response to the downward pull of gravity, contributes to the evolution of hybrid sterility in an Australian wildflower, Senecio lautus . We find that shoot gravitropism has evolved multiple times in association with plant height between adjacent populations inhabiting contrasting environments, suggesting that these traits have evolved by natural selection. We directly tested this prediction using a hybrid population subjected to eight rounds of recombination and three rounds of selection in the field. It revealed that shoot gravitropism responds to natural selection in the expected direction of the locally adapted population. This provided an ideal platform to test whether genetic differences in gravitropism contribute to hybrid sterility in S. lautus . Using this advanced hybrid population, we discovered that crossing in iduals with extreme differences in gravitropism reduce their ability to produce seed by 21%, providing strong evidence that this adaptive trait is genetically correlated with hybrid sterility. Our results suggest that natural selection can drive the evolution of locally adaptive traits that also create hybrid sterility, thus indicating an evolutionary connection between local adaptation and the origin of new species. New species originate as populations become reproductively isolated from one another. Despite recent progress in uncovering the genetic basis of reproductive isolation, it remains unclear whether intrinsic reproductive barriers, such as hybrid sterility, evolve as a by-product of local adaptation to contrasting environments or evolve through non-ecological processes, such as meiotic drive. Here, we show that differences in a plant’s response to the pull of gravity have repeatedly evolved amongst coastal populations of an Australian wildflower, thus implicating a role of natural selection in their evolution. We found a strong genetic correlation between variation in this adaptive trait and hybrid sterility, suggesting that intrinsic reproductive barriers contribute to the origin of new species as populations adapt to heterogeneous environments.
Gene expression divergence and the origin of hybrid dysfunctions
Publisher: Springer Science and Business Media LLC
Date: 17-10-2006
DOI: 10.1007/S10709-006-0034-1
Abstract: Hybrids between closely related species are often sterile or inviable as a consequence of failed interactions between alleles from the different species. Most genetic studies have focused on localizing the alleles associated with these failed interactions, but the mechanistic/biochemical nature of the failed interactions is poorly understood. This review discusses recent studies that may contribute to our understanding of these failed interactions. We focus on the possible contribution of failures in gene expression as an important contributor to hybrid dysfunctions. Although regulatory pathways that share elements in highly ergent taxa may contribute to hybrid dysfunction, various studies suggest that misexpression may be disproportionately great in regulatory pathways containing rapidly evolving, particularly male-biased, genes. We describe three systems that have been analyzed recently with respect to global patterns of gene expression in hybrids versus pure species, each in Drosophila. These studies reveal that quantitative misexpression of genes is associated with hybrid dysfunction. Misexpression of genes has been documented in sterile hybrids relative to pure species, and variation in upstream factors may sometimes cause the over- or under-expression of genes resulting in hybrid sterility or inviability. Studying patterns of evolution between species in regulatory pathways, such as spermatogenesis, should help in identifying which genes are more likely to be contributors to hybrid dysfunction. Ultimately, we hope more functional genetic studies will complement our understanding of the genetic disruptions leading to hybrid dysfunctions and their role in the origin of species.
Modelling selection response in plant-breeding programs using crop models as mechanistic gene-to-phenotype (CGM-G2P) multi-trait link functions
Publisher: Oxford University Press (OUP)
Date: 28-12-2021
DOI: 10.1093/INSILICOPLANTS/DIAA016
Abstract: Plant-breeding programs are designed and operated over multiple cycles to systematically change the genetic makeup of plants to achieve improved trait performance for a Target Population of Environments (TPE). Within each cycle, selection applied to the standing genetic variation within a structured reference population of genotypes (RPG) is the primary mechanism by which breeding programs make the desired genetic changes. Selection operates to change the frequencies of the alleles of the genes controlling trait variation within the RPG. The structure of the RPG and the TPE has important implications for the design of optimal breeding strategies. The breeder’s equation, together with the quantitative genetic theory behind the equation, informs many of the principles for design of breeding programs. The breeder’s equation can take many forms depending on the details of the breeding strategy. Through the genetic changes achieved by selection, the cultivated varieties of crops (cultivars) are improved for use in agriculture. From a breeding perspective, selection for specific trait combinations requires a quantitative link between the effects of the alleles of the genes impacted by selection and the trait phenotypes of plants and their breeding value. This gene-to-phenotype link function provides the G2P map for one to many traits. For complex traits controlled by many genes, the infinitesimal model for trait genetic variation is the dominant G2P model of quantitative genetics. Here we consider motivations and potential benefits of using the hierarchical structure of crop models as CGM-G2P trait link functions in combination with the infinitesimal model for the design and optimization of selection in breeding programs.
Simulating Natural Conditions in the Laboratory: A Re-Examination of Sexual Isolation between Sympatric and Allopatric Populations of Drosophila pseudoobscura and D. persimilis
Publisher: Springer Science and Business Media LLC
Date: 24-02-2006
DOI: 10.1007/S10519-005-9033-8
Abstract: Simulating natural conditions in the laboratory poses one of the most significant challenges to behavioral studies. Some authors have argued that laboratory "choice" experiments reflect mate choice in nature more accurately than "no-choice" experiments. A recent choice experiment study questioned the conclusions of several earlier studies by failing to detect a published difference in sexual isolation between populations of Drosophila pseudoobscura, and suggested their result was more robust because of the more realistic design. Here, we re-examine the methods and analyses of this recent study, and we find there was indeed a difference in sexual isolation between populations of D. pseudoobscura. We also conduct a more rigorously controlled choice experiment and, in agreement with previous studies, note that D. pseudoobscura females from populations sympatric to their sibling species, D. persimilis, exhibit greater sexual isolation than those from allopatric populations. Our results confirm the existence of a geographic pattern in sexual isolation in D. pseudoobscura, and we discuss differences in experimental designs in light of the biology of this species.
Microsatellites provide evidence for Y chromosome diversity among the founders of the New World
Publisher: Proceedings of the National Academy of Sciences
Date: 25-05-1999
Abstract: Recently, Y chromosome markers have begun to be used to study Native American origins. Available data have been interpreted as indicating that the colonizers of the New World carried a single founder haplotype. However, these early studies have been based on a few, mostly complex polymorphisms of insufficient resolution to determine whether observed ersity stems from admixture or ersity among the colonizers. Because the interpretation of Y chromosomal variation in the New World depends on founding ersity, it is important to develop marker systems with finer resolution. Here we evaluate the hypothesis of a single-founder Y haplotype for Amerinds by using 11 Y-specific markers in five Colombian Amerind populations. Two of these markers (DYS271, DYS287) are reliable indicators of admixture and detected three non-Amerind chromosomes in our s le. Two other markers (DYS199, M19) are single-nucleotide polymorphisms mostly restricted to Native Americans. The relatedness of chromosomes defined by these two markers was evaluated by constructing haplotypes with seven microsatellite loci (DYS388 to 394). The microsatellite backgrounds found on the two haplogroups defined by marker DYS199 demonstrate the existence of at least two Amerind founder haplotypes, one of them (carrying allele DYS199 T) largely restricted to Native Americans. The estimated age and distribution of these haplogroups places them among the founders of the New World.
GENETICS OF INCIPIENT SPECIATION INDROSOPHILA MOJAVENSIS. I. MALE COURTSHIP SONG, MATING SUCCESS, AND GENOTYPE X ENVIRONMENT INTERACTIONS
Publisher: Wiley
Date: 24-04-2007
DOI: 10.1111/J.1558-5646.2007.00104.X
Abstract: Few studies have examined genotype by environment (GxE) effects on premating reproductive isolation and associated behaviors, even though such effects may be common when speciation is driven by adaptation to different environments. In this study, mating success and courtship song differences among erging populations of Drosophila mojavensis were investigated in a two-environment quantitative trait locus (QTL) analysis. Baja California and mainland Mexico populations of D. mojavensis feed and breed on different host cacti, so these host plants were used to culture F2 males to examine host-specific QTL effects and GxE interactions influencing mating success and courtship songs. Linear selection gradient analysis showed that mainland females mated with males that produced songs with significantly shorter L(long)-IPIs, burst durations, and interburst intervals. Twenty-one microsatellite loci distributed across all five major chromosomes were used to localize effects of mating success, time to copulation, and courtship song components. Male courtship success was influenced by a single detected QTL, the main effect of cactus, and four GxE interactions, whereas time to copulation was influenced by three different QTLs on the fourth chromosome. Multiple-locus restricted maximum likelihood (REML) analysis of courtship song revealed consistent effects linked with the same fourth chromosome markers that influenced time to copulation, a number of GxE interactions, and few possible cases of epistasis. GxE interactions for mate choice and song can maintain genetic variation in populations, but alter outcomes of sexual selection and isolation, so signal evolution and reproductive isolation may be slowed in erging populations. Understanding the genetics of incipient speciation in D. mojavensis clearly depends on cactus-specific expression of traits associated with courtship behavior and sexual isolation.
Uncovering the genetic architecture of parallel evolution
Publisher: Wiley
Date: 23-09-2023
DOI: 10.1111/MEC.17134
The Genetics of Speciation by Reinforcement
Publisher: Public Library of Science (PLoS)
Date: 23-11-2004
The Color Genes of Speciation in Plants
Publisher: Oxford University Press (OUP)
Date: 05-2013
Sexual selection in hermaphrodites, sperm and broadcast spawners, plants and fungi
Publisher: The Royal Society
Date: 19-10-2016
Abstract: Darwin was the first to recognize that sexual selection is a strong evolutionary force. Exaggerated traits allow same-sex in iduals to compete over access to mates and provide a mechanism by which mates are selected. It is relatively easy to appreciate how inter- and intrasexual selection work in organisms with the sensory capabilities to perceive physical or behavioural traits that signal mate quality or mate compatibility, and to assess the relative quality of competitors. It is therefore not surprising that most studies of sexual selection have focused on animals with separate sexes and obvious adaptations that function in the context of reproductive competition. Yet, many sexual organisms are both male and female at the same time, often lack sexual dimorphism and never come into direct contact at mating. How does sexual selection act in such species, and what can we learn from them? Here, we address these questions by exploring the potential for sexual selection in simultaneous hermaphrodites, sperm- and broadcast spawners, plants and fungi. Our review reveals a range of mechanisms of sexual selection, operating primarily after gametes have been released, which are common in many of these groups and also quite possibly in more familiar (internally fertilizing and sexually dimorphic) organisms. This article is part of the themed issue ‘Weird sex: the underappreciated ersity of sexual reproduction’.
Recombination and the divergence of hybridizing species.
Publisher: Springer Science and Business Media LLC
Date: 2002
Strong Amerind/White Sex Bias and a Possible Sephardic Contribution among the Founders of a Population in Northwest Colombia
Publisher: Elsevier BV
Date: 11-2000
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