ORCID Profile
0000-0001-8965-1042
Current Organisation
The University of Auckland
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Publisher: Elsevier BV
Date: 02-2018
Publisher: Wiley
Date: 12-09-2021
DOI: 10.1111/MEC.16141
Abstract: Structural variants (SVs) are large rearrangements ( bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on in idual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future‐focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP‐based approaches to enhance species recovery. We also leverage the existing literature–predominantly in human health, agriculture and ecoevolutionary biology–to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 27-05-2022
Abstract: The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in in idual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.
Publisher: Wiley
Date: 24-08-2017
DOI: 10.1111/MEC.14291
Abstract: Social interactions are rarely random. In some instances, animals exhibit homophily or heterophily, the tendency to interact with similar or dissimilar conspecifics, respectively. Genetic homophily and heterophily influence the evolutionary dynamics of populations, because they potentially affect sexual and social selection. Here, we investigate the link between social interactions and allele frequencies in foraging flocks of great tits (Parus major) over three consecutive years. We constructed co-occurrence networks which explicitly described the splitting and merging of 85,602 flocks through time (fission-fusion dynamics), at 60 feeding sites. Of the 1,711 birds in those flocks, we genotyped 962 in iduals at 4,701 autosomal single nucleotide polymorphisms (SNPs). By combining genomewide genotyping with repeated field observations of the same in iduals, we were able to investigate links between social structure and allele frequencies at a much finer scale than was previously possible. We explicitly accounted for potential spatial effects underlying genetic structure at the population level. We modelled social structure and spatial configuration of great tit fission-fusion dynamics with eigenvector maps. Variance partitioning revealed that allele frequencies were strongly affected by group fidelity (explaining 27%-45% of variance) as in iduals tended to maintain associations with the same conspecifics. These conspecifics were genetically more dissimilar than expected, shown by genomewide heterophily for pure social (i.e., space-independent) grouping preferences. Genomewide homophily was linked to spatial configuration, indicating spatial segregation of genotypes. We did not find evidence for homophily or heterophily for putative socially relevant candidate genes or any other SNP markers. Together, these results demonstrate the importance of distinguishing social and spatial processes in determining population structure.
Publisher: Wiley
Date: 22-10-2021
DOI: 10.1111/MEC.16192
Abstract: Over the past 50 years conservation genetics has developed a substantive toolbox to inform species management. One of the most long‐standing tools available to manage genetics—the pedigree—has been widely used to characterize ersity and maximize evolutionary potential in threatened populations. Now, with the ability to use high throughput sequencing to estimate relatedness, inbreeding, and genome‐wide functional ersity, some have asked whether it is warranted for conservation biologists to continue collecting and collating pedigrees for species management. In this perspective, we argue that pedigrees remain a relevant tool, and when combined with genomic data, create an invaluable resource for conservation genomic management. Genomic data can address pedigree pitfalls (e.g., founder relatedness, missing data, uncertainty), and in return robust pedigrees allow for more nuanced research design, including well‐informed s ling strategies and quantitative analyses (e.g., heritability, linkage) to better inform genomic inquiry. We further contend that building and maintaining pedigrees provides an opportunity to strengthen trusted relationships among conservation researchers, practitioners, Indigenous Peoples, and Local Communities.
Publisher: Wiley
Date: 13-07-2013
DOI: 10.1111/MEC.12375
Abstract: The underlying basis of genetic variation in quantitative traits, in terms of the number of causal variants and the size of their effects, is largely unknown in natural populations. The expectation is that complex quantitative trait variation is attributable to many, possibly interacting, causal variants, whose effects may depend upon the sex, age and the environment in which they are expressed. A recently developed methodology in animal breeding derives a value of relatedness among in iduals from high-density genomic marker data, to estimate additive genetic variance within livestock populations. Here, we adapt and test the effectiveness of these methods to partition genetic variation for complex traits across genomic regions within ecological study populations where in iduals have varying degrees of relatedness. We then apply this approach for the first time to a natural population and demonstrate that genetic variation in wing length in the great tit (Parus major) reflects contributions from multiple genomic regions. We show that a polygenic additive mode of gene action best describes the patterns observed, and we find no evidence of dosage compensation for the sex chromosome. Our results suggest that most of the genomic regions that influence wing length have the same effects in both sexes. We found a limited amount of genetic variance in males that is attributed to regions that have no effects in females, which could facilitate the sexual dimorphism observed for this trait. Although this exploratory work focuses on one complex trait, the methodology is generally applicable to any trait for any laboratory or wild population, paving the way for investigating sex-, age- and environment-specific genetic effects and thus the underlying genetic architecture of phenotype in biological study systems.
Publisher: Wiley
Date: 16-02-2015
DOI: 10.1111/MEC.13089
Abstract: Rapid adaptation of invasive species to novel habitats has puzzled evolutionary biologists for decades, especially as this often occurs in the face of limited genetic variability. Although some ecological traits common to invasive species have been identified, little is known about the possible genomic/genetic mechanisms that may underlie their success. A common scenario in many introductions is that small founder population sizes will often lead to reduced genetic ersity, but that invading populations experience large environmental perturbations, such as changes in habitat and environmental stress. Although sudden and intense stress is usually considered in a negative context, these perturbations may actually facilitate rapid adaptation by affecting genome structure, organization and function via interactions with transposable elements (TEs), especially in populations with low genetic ersity. Stress-induced changes in TE activity can alter gene action and can promote structural variation that may facilitate the rapid adaptation observed in new environments. We focus here on the adaptive potential of TEs in relation to invasive species and highlight their role as powerful mutational forces that can rapidly create genetic ersity. We hypothesize that activity of transposable elements can explain rapid adaptation despite low genetic variation (the genetic paradox of invasive species), and provide a framework under which this hypothesis can be tested using recently developed and emerging genomic technologies.
Publisher: Wiley
Date: 12-2015
DOI: 10.1111/MEC.13452
Publisher: Cold Spring Harbor Laboratory
Date: 23-08-2023
DOI: 10.1101/2023.08.22.554353
Abstract: In an era of global climate change and massive environmental disturbance, bio ersity conservation is receiving increased attention. Conservation efforts are being greatly aided by genetic tools and approaches, which seek to understand patterns of genetic ersity and how they impact species health and ability to persist under future climate regimes. Invasive species offer vital model systems in which to investigate questions around adaptive potential, with a particular focus on how changes in genetic ersity and effective population size interact with the novel selection regime of the invaded range to drive rapid evolution. The common myna ( Acridotheres tristis ) is a globally invasive passerine, which has undergone multiple concurrent and sequential bottlenecks across its globally invasive range, and yet has established itself across a erse array of ecological conditions. It is therefore an excellent model species for research both into the persistence of low- ersity populations and the mechanics of biological invasion. To underpin research on the invasion genetics of this species, we present the genome assembly of the common myna, assembled using a backbone of Oxford Nanopore Technologies long reads, alongside an RNA-seq based transcriptome and genome annotation. To provide genomic context for future studies, we describe the genomic landscape of this species, including genome wide allelic ersity, methylation, repeats, and recombination rate, as well as an examination of gene family expansions and contractions. Finally, we use demographic analysis to identify that some native regions underwent a dramatic population increase between the two most recent periods of glaciation, but also reveal artefactual impacts of genetic bottlenecks on demographic analysis.
Publisher: Wiley
Date: 25-07-2013
DOI: 10.1111/MEC.12376
Abstract: Clutch size and egg mass are life history traits that have been extensively studied in wild bird populations, as life history theory predicts a negative trade-off between them, either at the phenotypic or at the genetic level. Here, we analyse the genomic architecture of these heritable traits in a wild great tit (Parus major) population, using three marker-based approaches - chromosome partitioning, quantitative trait locus (QTL) mapping and a genome-wide association study (GWAS). The variance explained by each great tit chromosome scales with predicted chromosome size, no location in the genome contains genome-wide significant QTL, and no in idual SNPs are associated with a large proportion of phenotypic variation, all of which may suggest that variation in both traits is due to many loci of small effect, located across the genome. There is no evidence that any regions of the genome contribute significantly to both traits, which combined with a small, nonsignificant negative genetic covariance between the traits, suggests the absence of genetic constraints on the independent evolution of these traits. Our findings support the hypothesis that variation in life history traits in natural populations is likely to be determined by many loci of small effect spread throughout the genome, which are subject to continued input of variation by mutation and migration, although we cannot exclude the possibility of an additional input of major effect genes influencing either trait.
Publisher: Oxford University Press (OUP)
Date: 18-06-2020
DOI: 10.1093/BIOLINNEAN/BLAA073
Abstract: Onithochiton neglectus is a morphologically variable, brooding chiton inhabiting coastal reefs throughout New Zealand and its Sub-Antarctic Islands. Southern O. neglectus populations are typically associated with buoyant kelp (Durvillaea spp.) and are potentially connected via kelp-rafting. Northern O. neglectus populations are less likely to raft, due to lower numbers of Durvillaea in northern New Zealand. To test for the impact of kelp-rafting on the spatial distribution of variation in O. neglectus, we undertook a combined analysis of morphological and genetic variation across the range of the species. Geometric morphometrics were used to assess shell shape. We detected a northern vs. southern split in shell shape, corresponding to the frequency of the O. neglectus/Durvillaea spp. association. To assess O. neglectus genetic patterns across New Zealand, we estimated phylogenetic trees with nuclear (ITS) and mitochondrial (COI and 16S) markers, which revealed distinct northern and southern lineages, and an additional lineage in central New Zealand. Neither the morphological nor genetic groups match existing O. neglectus subspecies, but are concordant with the patterns of association of O. neglectus with Durvillaea. We suggest that shell shape may be linked to O. neglectus’ regionally variable ecological association with kelp holdfasts.
Publisher: Springer Science and Business Media LLC
Date: 28-08-2023
Publisher: Cold Spring Harbor Laboratory
Date: 24-10-2022
DOI: 10.1101/2022.10.22.513130
Abstract: The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analyzed whole-genome sequence data for nearly all in iduals living in early 2018 (169 in iduals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide ersity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size, and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide ersity and ersity in breeding values, and hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing in iduals for translocation and monitoring in iduals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of small s le size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.
Publisher: Elsevier BV
Date: 06-2010
DOI: 10.1016/J.TIG.2010.03.005
Abstract: Over the past decade, long-term studies of vertebrate populations have been the focus of many quantitative genetic studies. As a result, we have a clearer understanding of why some fitness-related traits are heritable and under selection, but are apparently not evolving. An exciting extension of this work is to identify the genes underlying phenotypic variation in natural populations. The advent of next-generation sequencing and high-throughput single nucleotide polymorphism (SNP) genotyping platforms means that mapping studies are set to become widespread in those wild populations for whom appropriate phenotypic data and DNA s les are available. Here, we highlight the progress made in this area and define evolutionary genetic questions that have become tractable with the arrival of these new genomics technologies.
Publisher: Springer Science and Business Media LLC
Date: 02-06-2011
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Start Date: 2023
End Date: 2028
Funder: Ministry of Business, Innovation and Employment
View Funded ActivityStart Date: 2020
End Date: 2024
Funder: Marsden Fund
View Funded Activity