The accuracy of predicting maladaptation to new environments with genomic data

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 30, 2024

Rapid environmental change poses unprecedented challenges to species persistence. To understand the extent that continued could have, genomic offset methods have been used forecast maladaptation of natural populations future change. However, while their use has become increasingly common, little is known regarding predictive performance across a wide array realistic and challenging scenarios. Here, we evaluate currently available (gradientForest, Risk-Of-Non-Adaptedness, redundancy analysis with without structure correction LFMM2) using an extensive set simulated data sets vary demography, adaptive architecture number spatial patterns environments. For each set, train models either all, or neutral marker in silico common gardens by correlating fitness projected offset. Using over 4,849,600 such evaluations, find (1) method largely due degree local adaptation metapopulation (LA), (2) provide minimal advantages, (3) within range variable declines when are trained additional non-adaptive environments (4) despite more rapidly globally novel climates (i.e. climate analogue range) for metapopulations greater LA than lesser LA. We discuss implications these results management, assisted gene flow migration.

Language: Английский

---

The limits of predicting maladaptation to future environments with genomic data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 31, 2024

Abstract Anthropogenically driven changes in land use and climate patterns pose unprecedented challenges to species persistence. To understand the extent of these impacts, genomic offset methods have been used forecast maladaptation natural populations future environmental change. However, while their has become increasingly common, little is known regarding predictive performance across a wide array realistic challenging scenarios. Here, we evaluate four (Gradient Forests, Risk-Of-Non-Adaptedness, redundancy analysis, LFMM2) using an extensive set simulated datasets that vary demography, adaptive architecture, number spatial environments. For each dataset, train models either all, , or neutral marker sets silico common gardens by correlating fitness with projected offset. Using over 4,850,000 such evaluations, find 1) method largely due degree local adaptation metapopulation ( LA ΔSA ), 2) provide minimal advantages, 3) within-landscape variable declines when are trained additional non-adaptive environments, 4) despite (1), more rapidly novel climates for metapopulations higher than lower . We discuss implications results management, assisted gene flow, migration.

Language: Английский

---

Evaluating genomic offset predictions in a forest tree with high population genetic structure

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 20, 2024

Abstract Predicting how tree populations will respond to climate change is an urgent societal concern. An increasingly popular way make such predictions the genomic offset (GO) approach, which aims use and data identify that may experience maladaptation in near future. More precisely, GO tries represent allele frequencies required maintain current gene-climate relationships under change. However, approach has major limitations and, despite promising validation of its using height from common gardens, it still lacks broad empirical testing. In present study, we evaluated consistency validity maritime pine ( Pinus pinaster Ait.), a species southwestern Europe North Africa with marked population genetic structure. First, were estimated 9,817 SNPs genotyped 454 trees 34 populations; candidate potentially involved adaptation identified. Second, was predicted four methods, namely Gradient Forest (GF), Redundancy Analysis (RDA), latent factor mixed model (LFMM) Generalised Dissimilarity Modeling (GDM), two sets (candidate control SNPs) five general circulation models (GCMs) account for uncertainty future predictions. Last, within Bayesian framework by estimating associations between independent sources: mortality National Inventories (NFI), gardens contrasting environments. We found high variability across SNP GCMs. Regarding validation, GDM GF (and lesser extent RDA) based on showed strongest most consistent rates NFI plots. almost no association likely due overwhelming effect structure this species. Our study demonstrates imperative validate range sources before they can be used as informative reliable metrics conservation or management strategies.

Language: Английский

---

Predicting species invasiveness with genomic data: Is genomic offset related to establishment probability?

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(6)

Published: June 1, 2024

Abstract Predicting the risk of establishment and spread populations outside their native range represents a major challenge in evolutionary biology. Various methods have recently been developed to estimate population (mal)adaptation new environment with genomic data via so‐called Genomic Offset (GO) statistics. These approaches are particularly promising for studying invasive species but still rarely used this context. Here, we evaluated relationship between GO probability using both silico empirical data. First, designed invasion simulations evaluate ability predict two computation (Geometric Gradient Forest) under several conditions. Additionally, aimed interpretability absolute Geometric values, which theoretically represent adaptive genetic distance from distinct environments. Second, utilizing public crop pest Bactrocera tryoni , fruit fly Northern Australia, computed “source” diverse locations within invaded areas. This practical application context biological underscores its potential providing insights guiding recommendations future assessment. Overall, our results suggest that statistics good predictors may thus inform risk, although influence factors on prediction performance (e.g., propagule pressure or admixture) will need further investigation.

Language: Английский

---

Integrating evolutionary genomics of forest trees to inform future tree breeding amidst rapid climate change

Plant Communications, Journal Year: 2024, Volume and Issue: 5(10), P. 101044 - 101044

Published: Aug. 7, 2024

Global climate change is leading to rapid and drastic shifts in environmental conditions, posing threats biodiversity nearly all life forms worldwide. Forest trees serve as foundational components of terrestrial ecosystems play a crucial role combating mitigating the adverse effects extreme events, despite their own vulnerability these threats. Therefore, understanding monitoring how natural forests respond key priority for conservation. Recent progress evolutionary genomics, driven primarily by cutting-edge multi-omics technologies, offers powerful new tools address several issues. These include precise delineation species units, inference past histories demographic fluctuations, identification environmentally adaptive variants, measurement genetic load levels. As urgency deal with more stresses grows, genomics history, local adaptation, future responses change, conservation restoration forest will be critical research at nexus global population biology. In this review, we explore application assess using approaches discuss outlook breeding climate-adapted trees.

Language: Английский

---

The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids

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

Published: April 18, 2025

ABSTRACT The increasing feasibility of whole‐genome sequencing has been highly anticipated, promising to transform our understanding the biology nonmodel species. Notably, dramatic cost reductions beginning around 2007 with advent high‐throughput inspired publications heralding ‘genomics revolution’, predictions about its future impacts. Although such served as useful guideposts, value is added when statements are evaluated benefit hindsight. Here, we review 10 key made early in genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on concerning applied aspects and examples involving salmonid species which, due their socioeconomic ecological significance, have frontrunners applications Predicted outcomes included enhanced analytical power, deeper insights into genetic basis phenotype fitness variation, disease management breeding program advancements. many materialised, several expectations remain unmet technological, knowledge barriers. Additionally, largely unforeseen advancements, including identification applicability large‐effect loci, close‐kin mark–recapture, environmental DNA gene editing under‐anticipated value. Finally, emerging innovations artificial intelligence bioinformatics offer new directions. This retrospective evaluation impacts genomic revolution offers for

Language: Английский

---

Breeding Without Breeding: Enabling Indirect Selection Schemes for Tropical Tree Improvement

Published: Jan. 1, 2025

Language: Английский

---

Principles in experimental design for evaluating genomic forecasts

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(9), P. 1466 - 1482

Published: July 10, 2024

Abstract Over the past decade, there has been a rapid increase in development of predictive models at intersection molecular ecology, genomics, and global change. The common goal these ‘genomic forecasting’ is to integrate genomic data with environmental ecological model make quantitative predictions about vulnerability populations climate Despite methodological growing number systems which forecasts are made, themselves rarely evaluated rigorous manner ground‐truth experiments. This study reviews evaluation experiments that have done, introduces important terminology regarding forecasting models, discusses elements design reporting To date, experimental evaluations found high variation accuracy forecasts, but it difficult compare studies on ground due different approaches designs. Additionally, some may be biased toward higher performance because training testing not independent. In addition independence between data, an experiment include construction parameterization model, choice fitness proxies measure for test metric(s), degree extrapolation novel environments or genotypes, sensitivity, uncertainty reproducbility forecasts. Although methods becoming more accessible, evaluating their limitations particular system requires careful planning experimentation. Meticulously designed can clarify robustness application management. Clear basic will improve rigour evaluations, turn our understanding why work cases others.

Language: Английский

---

Local adaptation of Pinus leiophylla under climate and land use change models in the Avocado Belt of Michoacán

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(13)

Published: May 30, 2024

Abstract Climate change and land use are two main drivers of global biodiversity decline, decreasing the genetic diversity that populations harbour altering patterns local adaptation. Landscape genomics allows measuring effect these anthropogenic disturbances on adaptation populations. However, both factors have rarely been considered simultaneously. Based a set 3660 SNPs from which 130 were identified as outliers by genome–environment association analysis (LFMM), we modelled spatial turnover allele frequencies in 19 localities Pinus leiophylla across Avocado Belt Michoacán state, Mexico. Then, evaluated climate scenarios, addition to evaluating assisted gene flow strategies connectivity metrics landscape identify priority conservation areas for species. We found centre‐east would be more vulnerable change, while western area threatened conversion avocado orchards. Assisted actions could aid mitigating threats. Connectivity among forest patches will also modified future habitat loss, with central eastern parts maintaining highest connectivity. These results suggest part Belt, including Monarch Butterfly Biosphere Reserve. This work is useful framework incorporates distinct layers information provide robust representation response tree disturbances.

Language: Английский

---

Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 913, P. 169679 - 169679

Published: Dec. 30, 2023

Language: Английский

---