Interpretation issues with “genomic vulnerability” arise from conceptual issues in local adaptation and maladaptation

Evolution Letters, Journal Year: 2024, Volume and Issue: 8(3), P. 331 - 339

Published: Feb. 8, 2024

Abstract As climate change causes the environment to shift away from local optimum that populations have adapted to, fitness declines are predicted occur. Recently, methods known as genomic offsets (GOs) become a popular tool predict population responses landscape data. Populations with high GO been interpreted “genomic vulnerability” change. GOs often implicitly offset, or in of an individual new compared reference. However, there several different types offset can be calculated, and appropriate choice depends on management goals. This study uses hypothetical empirical data explore situations which may not correlated each other GO. The examples reveal even when common garden experiment, this does necessarily validate their ability environmental Conceptual also used show how large arise under positive thus cannot vulnerability. These issues resolved robust validation experiments evaluate GOs.

Language: Английский

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When will a changing climate outpace adaptive evolution?

Wiley Interdisciplinary Reviews Climate Change, Journal Year: 2023, Volume and Issue: 14(6)

Published: June 28, 2023

Abstract Decades of research have illuminated the underlying ingredients that determine scope evolutionary responses to climate change. The field biology therefore stands ready take what it has learned about influences upon rate adaptive evolution—such as population demography, generation time, and standing genetic variation—and apply assess if how populations can evolve fast enough “keep pace” with Here, our review highlights contribute still needs learn provide more mechanistic predictions winners losers We begin by developing broad for contemporary evolution change based on theory. then discuss methods assessing climate‐driven evolution, including quantitative studies, experimental space‐for‐time substitutions. After providing this mechanism‐focused overview both evidence specifically, evolving keep pace change, we next consider factors limit actual responses. In context, dual role phenotypic plasticity in facilitating but also impeding Finally, detail a deeper consideration constraints improve forecasts inform conservation management decisions. This article is categorized under: Climate, Ecology, Conservation > Observed Ecological Changes Extinction Risk Assessing Impacts Climate Change Evaluating Future

Language: Английский

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Genomes reveal pervasive distant hybridization in nature among cyprinid fishes

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Genomic data have unveiled a fascinating aspect of the evolutionary past, showing that mingling different species through hybridization has left its mark on histories numerous life forms. However, relationship between events and origins cyprinid fishes remains unclear. In this study, we generated de novo assembled genomes 8 conducted phylogenetic analyses 24 species. Widespread allele sharing across boundaries was observed within 7 subfamilies fishes. Based systematic analysis multiple tissues, found testis exhibited conserved pattern divergence herbivorous Megalobrama amblycephala carnivorous Culter alburnus, suggesting potential link to incomplete reproductive isolation. Significant differences in expression 4 genes (dpp2, ctrl, psb7, ppce) liver intestine, accompanied by variations enzyme activities, indicated swift digestive secretion. Moreover, identified introgressed linked organ development sympatric with analogous feeding habits Cultrinae Leuciscinae subfamilies. Our findings highlight significant role played isolation frequent gene flow events, particularly those associated organs, driving speciation among diverse freshwater ecosystems.

Language: Английский

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Five millennia of mitonuclear discordance in Atlantic bluefin tuna identified using ancient DNA

Heredity, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Mitonuclear discordance between species is readily documented in marine fishes. Such may either be the result of past natural phenomena or recent introgression from previously seperated after shifts their spatial distributions. Using ancient DNA spanning five millennia, we here investigate long-term presence Pacific bluefin tuna (Thunnus orientalis) and albacore alalunga) -like mitochondrial (MT) genomes Atlantic thynnus), a with extensive exploitation history observed abundance age structure. Comparing (n = 130) modern 78) MT most its range, detect no significant temporal population structure, which implies ongoing gene flow populations large effective sizes over millennia. Moreover, identify discordant haplotypes specimens up to 5000 years old find that frequency these has remained similar through time. We therefore conclude not driven by introgression. Our observations provide oldest example directly environment, highlighting utility obtain insights persistence such phenomena.

Language: Английский

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Genomic Insights Into Introgression Between Quercus aquifolioides and Its Sympatric Relatives Across Elevational Gradients

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: April 4, 2025

Geographically widespread species tend to have more opportunities hybridise with different related species. However, the evolutionary consequences of such multi-species hybridisation are still poorly understood. In Hengduan Mountains southwest China, Quercus aquifolioides and its closely form two types elevational hybrid zone in geographical areas (i.e., Q. aquifolioides-Q. guyavaefolia-Q. longispica spinosa). Here, we investigated genome-wide patterns introgression between sympatric relatives assess hybridisation. A new assembled genome as a reference whole-genome resequencing data these focal oaks were used this study. Our results showed that bidirectional gene flow occurred relatives, candidate genomic regions derived from broadly distributed across oak genome. Local has fuelled intraspecific divergence compositions. We found signatures positive selection some introgressed regions. Putative adaptation signals detected genes diverse functions, including stress response organism development growth. addition, identified targets environment-associated aquifolioides, which located sum, study demonstrates local is non-negligible mechanism facilitating reveals putative adaptive relatives.

Language: Английский

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The ecological importance of hybridization

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 38(11), P. 1097 - 1108

Published: Aug. 22, 2023

Hybridization as an evolutionary process has been studied in depth over the past few decades. Research focused on its role shaping reproductive barriers, adaptive value, and genomic consequences. In contrast, our knowledge of ecological dimensions hybridization is still infancy, despite being inherently interaction. Using examples from various organisms, we show that can affect be affected by non-reproductive interactions, including predation, competition, parasitism, mutualism, commensalism, organism–environment with significant implications for community structure ecosystem functioning. However, since these have mostly revealed studies designed to decipher other processes, argue much eco-evolutionary importance yet discovered.

Language: Английский

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The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(12)

Published: March 11, 2024

Introgression is pervasive across the tree of life but varies taxa, geography, and genomic regions. However, factors modulating this variation how they may be affected by global change are not well understood. Here, we used 200 genomes a 15-y site-specific environmental dataset to investigate effects mating system divergence on magnitude introgression between recently diverged outcrosser-selfer pair annual plants in genus Clarkia . These sister taxa very subsequently came into secondary sympatry where form replicated contact zones. Consistent with observations other pairs, found that was asymmetric substantially more from selfer outcrosser. This asymmetry caused bias direction initial F1 hybrid formation subsequent backcrossing. We also extensive outcrosser’s admixture proportion among zones, which predicted nearly entirely interannual variance spring precipitation. Greater fluctuations precipitation resulted higher proportions, likely mediated expression traits determine premating reproductive isolation. Climate-driven hybridization dynamics particularly change, potentially reshaping species boundaries adaptation novel environments.

Language: Английский

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Post‐glacial recolonization and multiple scales of secondary contact contribute to contemporary Atlantic salmon (Salmo salar) genomic variation in North America

Journal of Biogeography, Journal Year: 2024, Volume and Issue: 51(9), P. 1767 - 1782

Published: April 24, 2024

Abstract Aim In northern environments, periods of isolation during Pleistocene glaciations and subsequent recolonization secondary contact have had a significant influence on contemporary diversity many species. The recent advent high‐resolution genomic analyses allows unprecedented power to resolve signatures such events in Here, we provide the highest resolution characterization Atlantic salmon North America date infer glacial refugia geographic scales post‐glacial contact. Location America. Taxon salmon, Salmo salar . Methods Samples were collected for 5455 individuals from 148 populations, encompassing majority salmon's native range America, Labrador Maine. Individuals genotyped using 220K single nucleotide polymorphism array aligned ( ) genome. Spatial genetic structure (principal component analysis, k ‐means clustering, admixture) was evaluated conjunction with comparisons these identified lineages last maximum regions following recolonization. Results three phylogeographic groups, consistent northward two southern (a western Maritime lineage an eastern Newfoundland lineage), differentiation into separate groups. Secondary among American groups observed within Gulf St. Lawrence, evidence trans‐Atlantic detected lineage. Comparison insular those mainland suggests displaying high characterized by elevated European admixture, suggesting possible role population divergence. Main Conclusions These findings present first that extant populations has resulted allopatric followed both regional demonstrate tools historical drivers wild populations.

Language: Английский

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Facilitated introgression from domestic goat into Alpine ibex at immune loci

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(14)

Published: June 7, 2024

Abstract Hybridization can result in the transfer of adaptive genetic material from one species to another, known as introgression. Bottlenecked (and hence genetically depleted) are expected be particularly receptive introgression, since introgression introduce new or previously lost variation. The Alpine ibex ( Capra ), which recently recovered near extinction, is hybridize with domestic goat aegagrus hircus and signals found at major histocompatibility complex were suggested potentially adaptive. Here, we combine two ancient whole genomes 29 modern 31 representing six related investigate genome‐wide patterns confirm potential relevance immune loci. We identified low rates admixture through various F statistics screening for putative introgressed tracts. Further results based on demographic modelling consistent have occurred during last 300 years, coinciding bottleneck, that each generation, 1–2 out 100 had a parent. putatively haplotypes enriched immune‐related genes, where value alternative alleles may give individuals otherwise depleted diversity selective advantage. While interbreeding prevalent issue conservation, this specific case, it resulted Our findings highlight interplay between hybridization, evolution, risks benefits associated anthropogenic influences wild species.

Language: Английский

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Smaller microorganisms outcompete larger ones in resistance and functional effects under disturbed agricultural ecosystems

iMeta, Journal Year: 2024, Volume and Issue: 3(4)

Published: June 23, 2024

Body size is a key ecological trait of soil microorganisms related to their adaptation environmental changes. In this study, we reveal that the smaller show stronger community resistance than larger organisms in both maize and rice soil. Compared with organisms, have higher diversity broader niche breadth deploy survival strategies, because which they are less affected by selection thus survive complex various kinds environments. addition, strong correlation between ecosystem functions reflects greater metabolic flexibility illustrates significant roles continuously changing This research highlights importance body maintaining stability microbiome forecasting agroecosystem dynamics under disturbances. Natural man-made climate changes, such as warming excessive use fertilizers, seriously threaten services agricultural ecosystems [1, 2]. The biotic communities has been proven be great for multifunctionality [3]. Recent studies revealed can species' life-history traits [4]. However, still lack comprehensive understanding how species traits, size, influence among distinct groups ongoing determinant reproductive capacity survival, directly organism's changes [5, 6]. Since highly flexible metabolism [6], hypothesize microorganisms, underlying mechanisms phenomenon may result composite effect many factors. Current microbial ecology generally reports high more desirable scenario [7]. Thus, it tempting speculate species-rich maintain against disturbances effectively. Furthermore, tolerance range defines an niche, reflecting community's sensibility through scope resources living conditions [8]. Microorganisms narrow certain conditions, whereas other taxa tolerate ubiquitous probability stable abundance [9]. Meanwhile, diverse sizes assembly processes (deterministic stochastic process) due differences adaptability. Larger tend encounter stringent growth while able withstand filtering [10]. Given on critical biogeochemical (e.g., nutrient cycling) [11], mechanistic relations differentially sized essential accurate predictions future stability. Therefore, elucidating from multiple angles, particularly considering different sizes, crucial precise management resource-efficient disturbance-resistant sustainable agroecosystems. empirical evidence supporting above hypotheses these views explanatory factors induced limited lacks consensus. Here, considered two crop types, including (dryland) (wetland), investigate mechanism ecosystems. Soils collected 50 fields throughout eastern southeastern areas China were incubated simulate expected impacts addition (nitrogen, phosphorus). Following incubation, acquired bacterial, fungal, protistan information based high-throughput sequencing 16S 18S ribosomal RNA genes identified some basis literature. We also measured 11 activities, correspond carbon, nitrogen, phosphorus cycling. aimed address following question: resistant disturbed environments? Does maintenance depend largely when cease? first determined 24 organism (12 bacterial groups, seven fungal five groups) previous study [12]. These accounted at least 60% total sequences (Figure S1), span was quite considerable S2). Then, estimated significantly negatively across selected (Figures 1A S3A,D). Besides, disturbance further examined evaluating widths nonsynchronization responses level [13]. observed had width S4). combination, findings suggested arguably adaptive organisms. But what makes perturbations? Possible explanations observation discussed. It Shannon index markedly correlated 1B,C S3B,C,E,F), positively S5). confirmed our hypothesis wider lead resistance. Smaller faster rate, potentially increases rate mutation evolution results [14]. More coexisting provide buffer protect functional decline faced concept focus estimating risk whole-community collapse ever-changing environments, environmentally Soil generalists specialists amplicon sequence variants species–environment association pattern [15]. linear fitting model showed negative proportion 1D), means often play role ecosystem. quantified relative deterministic neutral normalized stochasticity ratio estimate mechanics [16]. Our gradually decreased increasing is, smallest (bacteria) regulated processes, ones (fungi protists) influenced S6). mostly consisting better cope mediate fluctuating Finally, functions. Similar patterns all treatments 1E). control group, R value, characterizes strength link 1F). meant before disturbances, weaker relationship After calculated D value (R treated group minus group) values. Interestingly, found positive 1G); shows improves, but decreases clearly. An interesting interpretation samples without any treatment involved increase incubation time. Under adverse become dormant themselves [17]. rapidly revived simulated warmth addition. Accordingly, conclude potential dormancy thereby ensuring widespread persistent ability switch active modes helps so promote perturbations Notably, response variables seems absent within taxonomic S7, S8, S9). limitations collecting data solely literature yield incomplete inaccurate do not consider generic variables. important note varies widely species, deviation might alleviated much intergroup intragroup [18]. discovery relationships diversity, breadth, reliable. Of course, keep mind caution must exercised inferring using unverified data. Further experimental analytical necessary corroborate gradients. Overall, demonstrates environments outcompete ecotypes (individuals occupying niches) wide its Although required confirm main finding outside scenario, likely pivotal factor affects could contribute in-depth responsible ecosystems, well contributions functioning global Gehong Wei, Shuo Jiao, Chunling Liang, Jiejun Qi conceived designed study. Qi, Wenyuan Wu, Xingyu Chen, Mingyu Li, Yu Liu, Ziheng Peng, Shi Haibo Pan, Beibei Jiai Yihe Wang samples. Liang performed experiments, analyzed data, wrote manuscript. Sanfeng Sen Du, revised All authors read final manuscript approved publication. work supported National Science Foundation Excellent Young Scholars (Grant No.: 42122050), 42077222), Fundamental Research Funds Central Universities Joint Fund U21A2029). declare no conflict interest. deposited Genome Sequence Archive (Genomics, Proteomics & Bioinformatics 2017) BIG Data Center (Nucleic Acids 2018), Beijing Institute Genomics (BIG), Chinese Academy Sciences, accession number PRJCA010837 set PRJCA010862 set, publicly accessible at: http://bigd.big.ac.cn/gsa. scripts used saved GitHub https://github.com/ChunlingLiang/Body-size. Supplementary Materials (methods, figures, graphical abstract, slides, videos, translated version, updated materials) online DOI or iMeta http://www.imeta.science/. Figure S1: Selected groups. S2: Taxa species. S3: Relationships resistance, index, soils. S4: Resistance S5: S6: Effects processes. S7: S8: S9: generalists, specialists, Please note: publisher content functionality supplied authors. Any queries (other missing content) should directed corresponding author article.

Language: Английский

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