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  • 1
    In: Evolution, Oxford University Press (OUP), ( 2023-08-17)
    Abstract: Freshwater ecosystems frequently house diverse 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 the 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 (R2 = .43; p = .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.
    Type of Medium: Online Resource
    ISSN: 0014-3820 , 1558-5646
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2036375-8
    SSG: 12
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  • 2
    In: BMC Biology, Springer Science and Business Media LLC, Vol. 20, No. 1 ( 2022-08-30)
    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 and transcriptomic and methylome approaches, we use zebrafish as a model to investigate cross-generational acclimation to hypoxia. Results 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 6-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 other epigenetic mechanisms are responsible for alterations in gene expression. Conclusions Overall, our findings suggest that an epigenetic 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.
    Type of Medium: Online Resource
    ISSN: 1741-7007
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2133020-7
    SSG: 12
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  • 3
    In: Evolution Letters, Oxford University Press (OUP), Vol. 4, No. 5 ( 2020-10-01), p. 398-415
    Abstract: Sexually antagonistic (SA) genetic variation—in which alleles favored in one sex are disfavored in the other—is predicted to be common and has been documented in several animal and plant populations, yet we currently know little about its pervasiveness among species or its population genetic basis. Recent applications of genomics in studies of SA genetic variation have highlighted considerable methodological challenges to the identification and characterization of SA genes, raising questions about the feasibility of genomic approaches for inferring SA selection. The related fields of local adaptation and statistical genomics have previously dealt with similar challenges, and lessons from these disciplines can therefore help overcome current difficulties in applying genomics to study SA genetic variation. Here, we integrate theoretical and analytical concepts from local adaptation and statistical genomics research—including FST and FIS statistics, genome-wide association studies, pedigree analyses, reciprocal transplant studies, and evolve-and-resequence experiments—to evaluate methods for identifying SA genes and genome-wide signals of SA genetic variation. We begin by developing theoretical models for between-sex FST and FIS, including explicit null distributions for each statistic, and using them to critically evaluate putative multilocus signals of sex-specific selection in previously published datasets. We then highlight new statistics that address some of the limitations of FST and FIS, along with applications of more direct approaches for characterizing SA genetic variation, which incorporate explicit fitness measurements. We finish by presenting practical guidelines for the validation and evolutionary analysis of candidate SA genes and discussing promising empirical systems for future work.
    Type of Medium: Online Resource
    ISSN: 2056-3744
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2894293-0
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  • 4
    In: Journal of Biogeography, Wiley, Vol. 48, No. 2 ( 2021-02), p. 453-464
    Abstract: Understanding the genetic structure of plants in their native range is crucial when reconstructing the invasion history of weeds. This information allows researchers to pinpoint the provenance of invasive plants and to test the importance of genetic admixture in facilitating invasion success. We assessed genetic structuring across the native range of A. auriculiformis , to determine whether genetic admixture contributes to the success of this weed in its introduced range, and test for rapid adaptation to environmental conditions in the invasive lineage. Location Australia, Papua New Guinea, Florida. Taxon Earleaf acacia. Methods We sampled A. auriculiformis from across its entire native distribution (northern Australia, Papua New Guinea) and its invasive range in Florida, and used genotyping by sequencing (GBS) to assess population structuring. Results Principal component analysis, based on 9591 single‐nucleotide polymorphisms, indicated significant differentiation among samples from Papua New Guinea, the Northern Territory (Australia) and north Queensland (Australia). Florida samples also formed a distinct cluster, with these samples most closely related to samples from the Northern Territory. These results indicate that the Florida A. auriculiformis lineage most likely originates from the Northern Territory, with no evidence that plants were introduced from different parts of the native range. We found evidence of allelic shifts in the Florida population, suggesting rapid adaptation to environmental conditions may contribute the success of the invasive lineage. Main conclusions Two well‐known biogeographic barriers—the Carpentaria Gap and Torres Strait—have caused genome‐wide divergence among A. auriculiformis plants from north Queensland, Northern Territory and Papua New Guinea. The taxonomic status of these allopatric populations should be further assessed. As the Florida lineage originated in the Northern Territory, the search for potential biological control agents should be focused in this region. Our results also demonstrate how artificial selection and strong genetic drift may cause introduced plants to have a unique genetic make‐up not found in the native range.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2020428-0
    detail.hit.zdb_id: 188963-1
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Oxford University Press (OUP) ; 2021
    In:  Systematic Biology Vol. 70, No. 5 ( 2021-08-11), p. 863-876
    In: Systematic Biology, Oxford University Press (OUP), Vol. 70, No. 5 ( 2021-08-11), p. 863-876
    Abstract: Recent genomic analyses have highlighted parallel divergence 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 diversification. 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 divergence” 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.]
    Type of Medium: Online Resource
    ISSN: 1063-5157 , 1076-836X
    RVK:
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1482572-7
    detail.hit.zdb_id: 1123455-6
    SSG: 12
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  • 6
    In: Molecular Ecology, Wiley, Vol. 28, No. 20 ( 2019-10), p. 4552-4572
    Abstract: The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white‐chinned petrel ( Procellaria aequinoctialis ) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range‐wide comprehensive sampling, we applied genomic (genotyping‐by‐sequencing or GBS; 60,709 loci) and standard mitochondrial‐marker approaches (cytochrome b and first domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non‐neutral) loci. Our results supported the multi‐region hypothesis, with a range of analyses showing clear three‐region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly‐discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide‐ranging circumpolar species previously assumed to be panmictic.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 7
    In: Molecular Ecology, Wiley, Vol. 31, No. 2 ( 2022-01), p. 646-657
    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 diversity 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 amphipod 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.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Wiley ; 2020
    In:  Molecular Ecology Vol. 29, No. 1 ( 2020-01), p. 149-159
    In: Molecular Ecology, Wiley, Vol. 29, No. 1 ( 2020-01), p. 149-159
    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 ) samples 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 diverse lineages dispersing to the newly uplifted coastline, suggesting potential for establishment of “exotic” lineages following disturbance. Furthermore, we found that some drifting individuals of each species came from far‐distant regions, some 〉 1,200 km away. These results show that diverse 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 individuals.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    The Royal Society ; 2018
    In:  Philosophical Transactions of the Royal Society B: Biological Sciences Vol. 373, No. 1757 ( 2018-10-05), p. 20170423-
    In: Philosophical Transactions of the Royal Society B: Biological Sciences, The Royal Society, Vol. 373, No. 1757 ( 2018-10-05), p. 20170423-
    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 divergence 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'.
    Type of Medium: Online Resource
    ISSN: 0962-8436 , 1471-2970
    RVK:
    Language: English
    Publisher: The Royal Society
    Publication Date: 2018
    detail.hit.zdb_id: 1462620-2
    SSG: 12
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  • 10
    In: Molecular Ecology, Wiley, Vol. 27, No. 18 ( 2018-09), p. 3572-3581
    Abstract: see also the Perspective by Meisel
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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