ORCID Profile
0000-0002-0164-9878
Current Organisations
Beijing University of Posts and Telecommunications
,
University of Otago
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Publisher: Cold Spring Harbor Laboratory
Date: 19-08-2021
DOI: 10.1101/2021.08.18.456742
Abstract: Understanding how wild populations respond to climatic shifts is a fundamental goal of biological research in a fast-changing world. The Southern Ocean represents a fascinating system for assessing large-scale climate-driven biological change, as it contains extremely isolated island groups within a predominantly westerly, circumpolar wind and current system. The blue-eyed shags ( Leucocarbo spp.) represent a paradoxical Southern Ocean seabird radiation a circumpolar distribution implies strong dispersal capacity yet their speciose nature suggests local adaptation and isolation. Here we use genetic tools in an attempt to resolve this paradox. Southern Ocean. 17 species and subspecies of blue-eyed shags ( Leucocarbo spp.) across the geographical distribution of the genus. Here we use mitochondrial and nuclear sequence data to conduct the first global genetic analysis of this group using a temporal phylogenetic framework to test for rapid speciation. Our analysis reveals remarkably shallow evolutionary histories among island-endemic lineages, consistent with a recent high-latitude circumpolar radiation. This rapid sub-Antarctic expansion contrasts with significantly deeper lineages detected in more temperate regions such as South America and New Zealand that may have acted as glacial refugia. The dynamic history of high-latitude expansions is further supported by ancestral demographic and biogeographic reconstructions. The circumpolar distribution of blue-eyed shags, and their highly dynamic evolutionary history, potentially make Leucocarbo a strong sentinel of past and ongoing Southern Ocean ecosystem change given their sensitivity to climatic impacts.
Publisher: Cold Spring Harbor Laboratory
Date: 09-12-2020
DOI: 10.1101/2020.12.09.416727
Abstract: In a time of rapid environmental change, understanding how the challenges experienced by one generation can influence the fitness of future generations is critically needed. Using tolerance assays, transcriptomic and methylome approaches, we use zebrafish as a model to investigate transgenerational acclimation to hypoxia. We show that short-term paternal exposure to hypoxia endows offspring with greater tolerance to acute hypoxia. We detected two hemoglobin genes that are significantly upregulated by more than 7-fold in the offspring of hypoxia exposed males. Moreover, the offspring which maintained equilibrium the longest showed greatest upregulation in hemoglobin expression. We did not detect differential methylation at any of the differentially expressed genes, suggesting that another epigenetic mechanism is responsible for alterations in gene expression. Overall, our findings suggest that a ‘memory’ of past hypoxia exposure is maintained and that this environmentally induced information is transferred to subsequent generations, pre-acclimating progeny to cope with hypoxic conditions.
Publisher: Wiley
Date: 07-11-2022
DOI: 10.1111/JBI.14516
Abstract: Genotyping‐by‐sequencing (GBS) and similar reduced‐representation sequencing methods, such as restriction site‐associated DNA sequencing (RADseq), have been revolutionary for genetic analyses in biogeography. However, navigating the many different methodological and analytical approaches and numerous sources of potential error can be overwhelming. We provide an overview of key considerations for biogeographical research using GBS, from s le design through data filtering to the sharing of data, which should particularly assist new users. All taxa. Worldwide. We review recent advances for GBS and compare differences among GBS methods and analytical approaches. We highlight the concerns most relevant for biogeographical research, and emphasise practical limitations for studies on non‐model organisms. GBS methods vary substantially and recent literature demonstrates the need for careful study design and data filtering relevant to the study organism and hypothesis under investigation. Biogeographical research using non‐model organisms or long‐term s ling are likely to face some practical limitations compared to ideal GBS study designs. The methodological information recorded in published manuscripts often varies. We outline a general framework for planning and undertaking biogeographical research using GBS. GBS and similar approaches have grown rapidly in popularity for biogeographical research. Evaluating, recording and justifying decisions throughout a GBS workflow—across s ling, library preparation and sequencing, identifying and filtering s les and loci, biogeographical analyses, and sharing data—is crucial for improving scientific reproducibility and compatibility among GBS datasets. This review outlines ways to improve and simplify GBS research, thereby enhancing our capacity to use genomic data to address broad‐scale biogeographical questions.
Publisher: Oxford University Press (OUP)
Date: 21-12-2020
Abstract: Recent genomic analyses have highlighted parallel ergence in response to ecological gradients, but the extent to which altitude can underpin such repeated speciation remains unclear. Wing reduction and flight loss have apparently evolved repeatedly in montane insect assemblages and have been suggested as important drivers of hexapod ersification. We test this hypothesis using genomic analyses of a widespread wing-polymorphic stonefly species complex in New Zealand. We identified over 50,000 polymorphic genetic markers generated across almost 200 Zelandoperla fenestrata stonefly specimens using a newly generated plecopteran reference genome, to reveal widespread parallel speciation between sympatric full-winged and wing-reduced ecotypes. Rather than the existence of a single, widespread, flightless taxon (Zelandoperla pennulata), evolutionary genomic data reveal that wing-reduced upland lineages have speciated repeatedly and independently from full-winged Z. fenestrata. This repeated evolution of reproductive isolation between local ecotype pairs that lack mitochondrial DNA differentiation suggests that ecological speciation has evolved recently. A cluster of outlier single-nucleotide polymorphisms detected in independently wing-reduced lineages, tightly linked in an approximately 85 kb genomic region that includes the developmental “supergene” doublesex, suggests that this “island of ergence” may play a key role in rapid ecological speciation. [Ecological speciation genome assembly genomic island of differentiation genotyping-by-sequencing incipient species plecoptera wing reduction.]
Publisher: Cold Spring Harbor Laboratory
Date: 05-07-2022
DOI: 10.1101/2022.07.04.498769
Abstract: Freshwater fish radiations are often characterized by multiple closely-related species in close proximity, which can lead to introgression and associated discordance of mitochondrial and nuclear characterizations of species ersity. As a case in point, single locus nuclear versus mitochondrial analyses of New Zealand’s stream-resident Galaxias vulgaris complex have yielded conflicting phylogenies. We generate and analyze a genome-wide data set comprising 52,352 SNPs across 187 Galaxias specimens to resolve the phylogeny of this recent fish radiation. We conduct phylogenetic, PCA, STRUCTURE, and ABBA-BABA analyses to evaluate the evolutionary relationships of lineages in the context of natural and anthropogenic river drainage alterations. In addition to the 11 previously recognized stream-resident lineages, genome-wide data reveal a twelfth candidate species ( G . ‘Pomahaka’), apparently obscured by introgressive mitochondrial capture. We identify additional ex les of mito-nuclear discordance and putative mitochondrial capture, likely mediated by geological and anthropogenic modification of drainage boundaries. Our study highlights the need for genome-wide approaches for delimiting freshwater bio ersity. Genetic data also reveal the influence of drainage history on freshwater bio ersity, including the rapid ergence of recently fragmented fish populations, and the conservation genetic risks of anthropogenic translocations events.
Publisher: Wiley
Date: 21-11-2020
DOI: 10.1111/JBI.14013
Publisher: Authorea, Inc.
Date: 03-02-2023
DOI: 10.22541/AU.167541666.62966770/V1
Abstract: Landlocking is a process whereby a population of normally diadromous fish becomes limited to freshwater, potentially leading to behavioural, morphological, and genetic changes, and occasionally speciation. The study of recently landlocked populations can shed light on how populations adapt to environmental change, and how such life-history shifts affect population-genetic structure. Kōaro (Galaxias brevipinnis) is a facultatively diadromous Southern Hemisphere galaxiid fish that frequently becomes landlocked in inland lakes. This study compares seven landlocked kōaro populations to diadromous populations from main and offshore islands of New Zealand. Genotyping-by-sequencing was used to obtain genotypes at 18,813 single nucleotide polymorphism sites for each population. Analyses of population structure revealed that most landlocked populations were genetically highly distinct from one another, as well as from diadromous populations. A few particularly isolated island and lake populations were particularly strongly genetically differentiated. Landscape characteristics were measured to test whether lake elevation, size, or distance from the sea predicted genetic ersity or differentiation from diadromous kōaro. While there were no significant relationships indicating isolation-by-distance or isolation-by-environment, we detected a trend toward lower genetic ersity in lakes at higher elevations. Our findings illustrate the critical role that landlocking can play in the structure of intraspecific genetic ersity within and between populations.
Publisher: Wiley
Date: 11-10-2021
DOI: 10.1111/MEC.16204
Abstract: Natural selection along elevational gradients has potential to drive predictable adaptations across distinct lineages, but the extent of such repeated evolution remains poorly studied for many widespread alpine taxa. We present parallel genomic analyses of two recently evolved flightless alpine insect lineages to test for molecular signatures of repeated alpine adaptation. Specifically, we compare low‐elevation vs. alpine stonefly ecotypes from parallel stream populations in which flightless upland ecotypes have been independently derived. We map 67,922 polymorphic genetic markers, generated across 176 Zelandoperla fenestrata specimens from two independent alpine stream populations in New Zealand's Rock and Pillar Range, to a newly developed plecopteran reference genome. Genome‐wide scans revealed 31 regions with outlier single nucleotide polymorphisms (SNPs) differentiating lowland vs. alpine ecotypes in Lug Creek, and 37 regions with outliers differentiating ecotypes in Six Mile Creek. Of these regions, 13% (8/60) yielded outlier SNPs across both within‐stream ecotype comparisons, implying comparable genomic shifts contribute to this repeated alpine adaptation. Candidate genes closely linked to repeated outlier regions include several with documented roles in insect wing‐development (e.g., dishevelled ), suggesting that they may contribute to repeated alpine wing reduction. Additional candidate genes have been shown to influence insect fecundity (e.g., ovo ) and lifespan (e.g., Mrp4 ), implying that they might contribute to life history differentiation between upland and lowland ecotypes. Additional outlier genes have potential roles in the evolution of reproductive isolation among ecotypes ( hedgehog and Desaturase 1). These results demonstrate how replicated outlier tests across independent lineages can potentially contribute to the discovery of genes underpinning repeated adaptation.
Publisher: Wiley
Date: 04-12-2019
DOI: 10.1111/MEC.15303
Abstract: In species that form dense populations, major disturbance events are expected to increase the chance of establishment for immigrant lineages. Real-time tests of the impact of disturbance on patterns of genetic structure are, however, scarce. Central to testing these concepts is determining the pool of potential immigrants dispersing into a disturbed area. In 2016, a 7.8 magnitude earthquake occurred on the South Island of New Zealand. Affecting approximately 100 km of coastline, this quake caused extensive uplift (several metres high), extirpating many intertidal populations, including keystone intertidal kelp species. Following the uplift, we set out to determine the geographic origins of detached kelp specimens which rafted into the disturbed zone. Specifically, we used genotyping-by-sequencing (GBS) approaches to compare beach-cast southern bull-kelp (Durvillaea antarctica and Durvillaea poha) s les to established populations throughout the species' ranges, and thus infer the geographic origins of potential colonists reaching the disturbed coast. Our findings revealed an ongoing supply of erse lineages dispersing to the newly uplifted coastline, suggesting potential for establishment of "exotic" lineages following disturbance. Furthermore, we found that some drifting in iduals of each species came from far-distant regions, some >1,200 km away. These results show that erse lineages - in many cases from very distant sources - can compete for new space in the wake of an exceptional disturbance event, illustrating the potential of long-distance dispersal as a key mechanism for reassembly of coastal ecosystems. Furthermore, our findings demonstrate that high-resolution genomic baselines can be used to robustly assign the provenance of dispersing in iduals.
Publisher: Oxford University Press (OUP)
Date: 17-08-2023
Abstract: Freshwater ecosystems frequently house erse assemblages of closely-related fish taxa, which can be particularly prone to hybridization and introgression. While extensive introgression may be expected among biogeographically proximate lineages, recent analyses imply that contemporary distributions do not always accurately predict hybridization history. Here we use the ABBA-BABA approach to test biogeographic hypotheses regarding the extent of hybridization in recent evolution of New Zealand’s species-rich freshwater Galaxias vulgaris fish complex. Genome-wide comparisons reveal significant increases in introgression associated with increasing geographic overlap of taxa. The estimator DP, which assesses the net proportion of a genome originating from introgression, shows a particularly strong relationship with biogeographic overlap (R 2 = 0.43 p = 0.005). Our analyses nevertheless reveal surprisingly substantial signatures of introgression among taxa that currently have disjunct distributions within drainages (e.g. separate subcatchments). These ‘anomalies’ imply that current biogeography is not always an accurate predictor of introgression history. Our study suggests that both modern and ancient biogeographic shifts, including recent anthropogenic range fragmentation and tectonically-driven riven capture events, have influenced introgression histories in this dynamic freshwater fish radiation.
Publisher: Wiley
Date: 25-05-2019
DOI: 10.1111/MEC.15114
Abstract: Alpine ecosystems are frequently characterized by an abundance of wing-reduced insect species, but the drivers of this bio ersity remain poorly understood. Insect wing reduction in these environments has variously been attributed to altitude, temperature, isolation, habitat stability or decreased habitat size. We used fine-scale ecotypic and genomic analyses, along with broad-scale distributional analyses of ecotypes, to unravel the ecological drivers of wing reduction in the wing-dimorphic stonefly Zelandoperla fenestrata complex. Altitudinal transects within populations revealed dramatic wing reduction over very fine spatial scales, tightly linked to the alpine treeline. Broad biogeographical analyses confirm that the treeline has a much stronger effect on these ecotype distributions than altitude per se. Molecular analyses revealed parallel genomic ergence between vestigial-winged (high altitude) and full-winged (low altitude) ecotypes across distinct streams. These data thus highlight the role of the alpine treeline as a key driver of rapid speciation, providing a new model for ecological ersification along exposure gradients.
Publisher: Oxford University Press (OUP)
Date: 31-08-2021
DOI: 10.1093/G3JOURNAL/JKAB307
Abstract: Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one in idual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between erse lineages.
Publisher: Informa UK Limited
Date: 24-03-2022
Publisher: Wiley
Date: 05-11-2022
DOI: 10.1111/MEC.16245
Abstract: Major ecological disturbance events can provide opportunities to assess multispecies responses to upheaval. In particular, catastrophic disturbances that regionally extirpate habitat‐forming species can potentially influence the genetic ersity of large numbers of codistributed taxa. However, due to the rarity of such disturbance events over ecological timeframes, the genetic dynamics of multispecies recolonization processes have remained little understood. Here, we use single nucleotide polymorphism (SNP) data from multiple coastal species to track the dynamics of cocolonization events in response to ancient earthquake disturbance in southern New Zealand. Specifically, we use a comparative phylogeographic approach to understand the extent to which epifauna (with varying ecological associations with their macroalgal hosts) share comparable spatial and temporal recolonization patterns. Our study reveals concordant disturbance‐related phylogeographic breaks in two intertidal macroalgal species along with two associated epibiotic species (a chiton and an isopod). By contrast, two codistributed species, one of which is an epibiotic hipod and the other a subtidal macroalga, show few, if any, genetic effects of palaeoseismic coastal uplift. Phylogeographic model selection reveals similar post‐uplift recolonization routes for the epibiotic chiton and isopod and their macroalgal hosts. Additionally, codemographic analyses support synchronous population expansions of these four phylogeographically similar taxa. Our findings indicate that coastal paleoseismic activity has driven concordant impacts on multiple codistributed species, with concerted recolonization events probably facilitated by macroalgal rafting. These results highlight that high‐resolution comparative genomic data can help reconstruct concerted multispecies responses to recent ecological disturbance.
Publisher: Authorea, Inc.
Date: 24-02-2023
DOI: 10.22541/AU.167725803.35894964/V1
Abstract: Landlocking of diadromous fish in freshwater systems can have significant genomic consequences. For instance, the loss of the migratory life stage can dramatically reduce gene flow across populations, leading to increased genetic structuring, and stronger effects of local adaptation. These genomic consequences have been well-studied in some mainland systems, but the evolutionary impacts of landlocking in island ecosystems are largely unknown. In this study, we used a genotyping-by-sequencing (GBS) approach to examine the evolutionary history of landlocking in common smelt ( Retropinna retropinna ) on Chatham Island, a small isolated oceanic island 650 km southeast of mainland New Zealand. We examined the relationship among the Chatham Island and mainland smelt, and used coalescent analyses to test the number and timing of landlocking events on Chatham Island. Our genomic analysis, based on 21,135 SNPs across 169 in iduals, revealed that the Chatham Island smelt were genomically distinct from the mainland New Zealand fish, consistent with a single ancestral colonisation event of Chatham Island in the Pleistocene. Significant genetic structure was also evident within the Chatham Island smelt, with a diadromous Chatham Island smelt group, along with three geographically structured landlocked groups. Coalescent demographic analysis supported three independent landlocking events, with this loss of diadromy significantly pre-dating human colonisation. Our results illustrate how landlocking of diadromous fish can occur repeatedly across a narrow spatial scale, and highlight a unique system to study the genomic basis of repeated adaptation.
Publisher: Wiley
Date: 03-2023
DOI: 10.1111/NPH.18802
Abstract: Mechanisms of ersification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host–symbiont selection may be an important driver of fungal ersification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus. We use metabarcoding of ectomycorrhizal fungi collected with hyphal ingrowth bags from Nothofagus forests across southern New Zealand to investigate host–symbiont specialisation and correlated evolution. We examine how ectomycorrhizal communities differ between host species and look for patterns of host–symbiont cophylogeny. We found substantial differences in ectomycorrhizal communities associated with different host taxa, particularly between hosts from different subgenera ( Lophozonia and Fuscospora ), but also between more closely related hosts. Twenty‐four per cent of fungal taxa tested showed affiliations to particular hosts, and tests for cophylogeny revealed significant correlations between host relatedness and the fungal phylogeny that extended to substantial evolutionary depth. These results provide new evidence of correlated evolution in ectomycorrhizal systems, indicating that preferences among closely related host species may represent an important evolutionary driver for local lineage ersification in ectomycorrhizal fungi.
Publisher: Proceedings of the National Academy of Sciences
Date: 16-12-2019
Abstract: Climate shifts are key drivers of ecosystem change. Despite the critical importance of Antarctica and the Southern Ocean for global climate, the extent of climate-driven ecological change in this region remains controversial. In particular, the biological effects of changing sea ice conditions are poorly understood. We hypothesize that rapid postglacial reductions in sea ice drove biological shifts across multiple widespread Southern Ocean species. We test for demographic shifts driven by climate events over recent millennia by analyzing population genomic datasets spanning 3 penguin genera ( Eudyptes , Pygoscelis , and Aptenodytes ). Demographic analyses for multiple species (macaroni/royal, eastern rockhopper, Adélie, gentoo, king, and emperor) currently inhabiting southern coastlines affected by heavy sea ice conditions during the Last Glacial Maximum (LGM) yielded genetic signatures of near-simultaneous population expansions associated with postglacial warming. Populations of the ice-adapted emperor penguin are inferred to have expanded slightly earlier than those of species requiring ice-free terrain. These concerted high-latitude expansion events contrast with relatively stable or declining demographic histories inferred for 4 penguin species (northern rockhopper, western rockhopper, Fiordland crested, and Snares crested) that apparently persisted throughout the LGM in ice-free habitats. Limited genetic structure detected in all ice-affected species across the vast Southern Ocean may reflect both rapid postglacial colonization of subantarctic and Antarctic shores, in addition to recent genetic exchange among populations. Together, these analyses highlight dramatic, ecosystem-wide responses to past Southern Ocean climate change and suggest potential for further shifts as warming continues.
Publisher: CSIRO Publishing
Date: 2020
DOI: 10.1071/MF20044
Abstract: Barriers to dispersal can disrupt gene flow between populations, resulting in genetically distinct populations. Although many marine animals have potential for long-distance dispersal via a planktonic stage, gene flow among populations separated by large geographic distances is not always evident. Polychaetes are ecologically important and have been used as biological surrogates for marine bio ersity. Some polychaete species are used as bait for recreational fisheries, with this demand supporting commercial fisheries for polychaetes to service the retail bait market. However, despite their ecological and economic importance, very little is known about the life history or population dynamics of polychaetes, and few studies have used genetic or genomic approaches to understand polychaete population connectivity. Here, we investigate the population structure of one commonly collected beachworm species used for bait on the eastern coast of Australia, namely, Australonuphis teres, by using genome-wide single-nucleotide polymorphism data. We s led A. teres from hierarchical nested spatial scales along 900km of the coast in New South Wales. We identified six genetic groups, but there was no clear geographic pattern of distribution. Our results suggest that there is considerable gene flow among the s led populations. These high-resolution genomic data support the findings of previous studies, and we infer that oceanographic processes promote genetic exchange among polychaete populations in south-eastern Australia.
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 2023
Publisher: Oxford University Press (OUP)
Date: 03-2022
DOI: 10.1093/ISD/IXAC009
Abstract: Range-restricted upland taxa are prone to population bottlenecks and thus typically have low genetic ersity, making them particularly vulnerable to environmental change. In this study, we used a combination of genotyping-by-sequencing (10,419 SNPs) and mitochondrial COI sequencing to test for population genetic structure within the narrow-range flightless sub-alpine stonefly Zelandoperla maungatuaensis Foster. This species is restricted to only a handful of upland streams along a 4 km stretch of the isolated Maungatua range in southeast New Zealand. We identified striking genetic structure across the narrow range of Z. maungatuaensis, with three deeply ergent allopatric lineages detected. These distinct lineages likely erged in the early-mid Pleistocene, apparently persisting in separate microrefugia throughout subsequent glacial cycles. Our results illustrate how secondary flight loss can facilitate insect ersification across fine spatial scales, and demonstrate that intraspecific phylogenetic ersity cannot necessarily be predicted from range-size alone. Additional demographic analyses are required to better understand the conservation status of these ergent Z. maungatuaensis lineages, and to assess their potential susceptibility to climate change and other anthropogenic impacts.
Publisher: Cold Spring Harbor Laboratory
Date: 09-09-2015
Abstract: Speciation is a continuous process during which genetic changes gradually accumulate in the genomes of erging species. Recent studies have documented highly heterogeneous differentiation landscapes, with distinct regions of elevated differentiation (“differentiation islands”) widespread across genomes. However, it remains unclear which processes drive the evolution of differentiation islands how the differentiation landscape evolves as speciation advances and ultimately, how differentiation islands are related to speciation. Here, we addressed these questions based on population genetic analyses of 200 resequenced genomes from 10 populations of four Ficedula flycatcher sister species. We show that a heterogeneous differentiation landscape starts emerging among populations within species, and differentiation islands evolve recurrently in the very same genomic regions among independent lineages. Contrary to expectations from models that interpret differentiation islands as genomic regions involved in reproductive isolation that are shielded from gene flow, patterns of sequence ergence ( d xy and relative node depth) do not support a major role of gene flow in the evolution of the differentiation landscape in these species. Instead, as predicted by models of linked selection, genome-wide variation in ersity and differentiation can be explained by variation in recombination rate and the density of targets for selection. We thus conclude that the heterogeneous landscape of differentiation in Ficedula flycatchers evolves mainly as the result of background selection and selective sweeps in genomic regions of low recombination. Our results emphasize the necessity of incorporating linked selection as a null model to identify genome regions involved in adaptation and speciation.
Publisher: The Royal Society
Date: 27-08-2018
Abstract: Spatially varying selection with gene flow can favour the evolution of inversions that bind locally adapted alleles together, facilitate local adaptation and ultimately drive genomic ergence between species. Several studies have shown that the rates of spread and establishment of new inversions capturing locally adaptive alleles depend on a suite of evolutionary factors, including the strength of selection for local adaptation, rates of gene flow and recombination, and the deleterious mutation load carried by inversions. Because the balance of these factors is expected to differ between X (or Z) chromosomes and autosomes, opportunities for inversion evolution are likely to systematically differ between these genomic regions, though such scenarios have not been formally modelled. Here, we consider the evolutionary dynamics of X-linked and autosomal inversions in populations evolving at a balance between migration and local selection. We identify three factors that lead to asymmetric rates of X-linked and autosome inversion establishment: (1) sex-biased migration, (2) dominance of locally adapted alleles and (3) chromosome-specific deleterious mutation loads. This theory predicts an elevated rate of fixation, and depressed opportunities for polymorphism, for X-linked inversions. Our survey of data on the genomic distribution of polymorphic and fixed inversions supports both theoretical predictions. This article is part of the theme issue ‘Linking local adaptation with the evolution of sex differences'.
Publisher: Oxford University Press (OUP)
Date: 11-2022
DOI: 10.1093/ISD/IXAC027
Abstract: Flight loss is a common feature of upland insect assemblages, with recent studies detecting parallel wing reduction events across independent alpine lineages. However, the geographic scale over which such repeated evolution can operate remains unclear. In this study, we use genotyping-by-sequencing to assess the genomic relationships among vestigial-winged and full-winged populations of the widespread New Zealand stonefly Nesoperla fulvescens, to test for repeated wing loss events over small spatial scales. Biogeographic analyses indicate that alpine wing loss in this widespread species is restricted to a single, narrow mountain range. Intriguingly, our coalescent analyses indicate that upland vestigial-winged N. fulvescens populations are not sister to one another, suggesting wings have been lost independently in disjunct populations of this species, over a & km scale. Our results suggest that selection against flight above the alpine treeline can drive rapid and repeated adaptation even across narrow spatial scales. We propose that such repetitive processes may represent a far more pervasive feature of alpine insect adaptation than is currently recognized.
Publisher: The Royal Society
Date: 08-07-2020
Abstract: Theory suggests that catastrophic earth-history events can drive rapid biological evolution, but empirical evidence for such processes is scarce. Destructive geological events such as earthquakes can represent large-scale natural experiments for inferring such evolutionary processes. We capitalized on a major prehistoric (800 yr BP) geological uplift event affecting a southern New Zealand coastline to test for the lasting genomic impacts of disturbance. Genome-wide analyses of three co-distributed keystone kelp taxa revealed that post-earthquake recolonization drove the evolution of novel, large-scale intertidal spatial genetic ‘sectors’ which are tightly linked to geological fault boundaries. Demographic simulations confirmed that, following widespread extirpation, parallel expansions into newly vacant habitats rapidly restructured genome-wide ersity. Interspecific differences in recolonization mode and tempo reflect differing ecological constraints relating to habitat choice and dispersal capacity among taxa. This study highlights the rapid and enduring evolutionary effects of catastrophic ecosystem disturbance and reveals the key role of range expansion in reshaping spatial genetic patterns.
No related grants have been discovered for Ludovic Dutoit.