{"title":"Can We Use Genomic Data to Predict Maladaptation to Environmental Change?","authors":"Christian Rellstab, Stephen R Keller","doi":"10.1111/1755-0998.14059","DOIUrl":"https://doi.org/10.1111/1755-0998.14059","url":null,"abstract":"<p><p>Climate change is happening fast, maybe too fast for some species and populations to adapt in time. Therefore, practice and science are highly interested in predicting how populations may react to future changes. Such information could be used to identify populations at risk or sources for assisted gene flow. Ideally, such predictions account for intraspecific genetic variation and adaptation. A promising approach is genomic offset, which aims at predicting the disruption to adaptation arising from environmental change. In this issue of Molecular Ecology Resources, Lind and Lotterhos (2024) perform an enormous simulation effort to test the performance of genomic offset under various evolutionary and ecological settings. They show that genomic offset is a valuable approach for predicting fitness under changed environments, but that performance can be reduced under certain conditions, especially under highly novel environments.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14059"},"PeriodicalIF":5.5,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142890745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Robert Kesälahti, Timo A. Kumpula, Sandra Cervantes, Sonja T. Kujala, Tiina M. Mattila, Jaakko S. Tyrmi, Alina K. Niskanen, Pasi Rastas, Outi Savolainen, Tanja Pyhäjärvi
{"title":"Optimising Exome Captures in Species With Large Genomes Using Species-Specific Repetitive DNA Blocker","authors":"Robert Kesälahti, Timo A. Kumpula, Sandra Cervantes, Sonja T. Kujala, Tiina M. Mattila, Jaakko S. Tyrmi, Alina K. Niskanen, Pasi Rastas, Outi Savolainen, Tanja Pyhäjärvi","doi":"10.1111/1755-0998.14053","DOIUrl":"10.1111/1755-0998.14053","url":null,"abstract":"<p>Large and highly repetitive genomes are common. However, research interests usually lie within the non-repetitive parts of the genome, as they are more likely functional, and can be used to answer questions related to adaptation, selection and evolutionary history. Exome capture is a cost-effective method for providing sequencing data from protein-coding parts of the genes. C0t-1 DNA blockers consist of repetitive DNA and are used in exome captures to prevent the hybridisation of repetitive DNA sequences to capture baits or bait-bound genomic DNA. Universal blockers target repetitive regions shared by many species, while species-specific c0t-1 DNA is prepared from the DNA of the studied species, thus perfectly matching the repetitive DNA contents of the species. So far, the use of species-specific c0t-1 DNA has been limited to a few model species. Here, we evaluated the performance of blocker treatments in exome captures of <i>Pinus sylvestris</i>, a widely distributed conifer species with a large (> 20 Gbp) and highly repetitive genome. We compared treatment with a commercial universal blocker to treatments with species-specific c0t-1 (30,000 and 60,000 ng). Species-specific c0t-1 captured more unique exons than the initial set of targets leading to increased SNP discovery and reduced sequencing of tandem repeats compared to the universal blocker. Based on our results, we recommend optimising exome captures using at least 60,000 ng of species-specific c0t-1 DNA. It is relatively easy and fast to prepare and can also be used with existing bait set designs.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anusha P. Bishop, Drew E. Terasaki Hart, Ian J. Wang
{"title":"Optimising Sampling Design for Landscape Genomics","authors":"Anusha P. Bishop, Drew E. Terasaki Hart, Ian J. Wang","doi":"10.1111/1755-0998.14052","DOIUrl":"10.1111/1755-0998.14052","url":null,"abstract":"<div>\u0000 \u0000 <p>Landscape genomic approaches for detecting genotype-environment associations (GEA), isolation by distance (IBD) and isolation by environment (IBE) have seen a dramatic increase in use, but there have been few thorough analyses of the influence of sampling strategy on their performance under realistic genomic and environmental conditions. We simulated 24,000 datasets across a range of scenarios with complex population dynamics and realistic landscape structure to evaluate the effects of the spatial distribution and number of samples on common landscape genomics methods. Our results show that common analyses are relatively robust to sampling scheme as long as sampling covers enough environmental and geographic space. We found that for detecting adaptive loci and estimating IBE, sampling schemes that were explicitly designed to increase coverage of available environmental space matched or outperformed sampling schemes that only considered geographic space. When sampling does not cover adequate geographic and environmental space, such as with transect-based sampling, we detected fewer adaptive loci and had higher error when estimating IBD and IBE. We found that IBD could be detected with as few as nine sampling sites, while large sample sizes (e.g., greater than 100 individuals) were crucial for detecting adaptive loci and IBE. We also demonstrate that, even with optimal sampling strategies, landscape genomic analyses are highly sensitive to landscape structure and migration—when spatial autocorrelation and migration are weak, common GEA methods fail to detect adaptive loci.</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142845344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Seafha C. Ramos, Andrew P. Kinziger, Alana Alexander
{"title":"Hīkina te mānuka: Advancing Indigenous Leadership in Molecular Ecology","authors":"Seafha C. Ramos, Andrew P. Kinziger, Alana Alexander","doi":"10.1111/1755-0998.14049","DOIUrl":"10.1111/1755-0998.14049","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 2","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ellie E. Armstrong, Chenyang Li, Michael G. Campana, Tessa Ferrari, Joanna L. Kelley, Dmitri A. Petrov, Katherine A. Solari, Jazlyn A. Mooney
{"title":"A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species","authors":"Ellie E. Armstrong, Chenyang Li, Michael G. Campana, Tessa Ferrari, Joanna L. Kelley, Dmitri A. Petrov, Katherine A. Solari, Jazlyn A. Mooney","doi":"10.1111/1755-0998.14048","DOIUrl":"10.1111/1755-0998.14048","url":null,"abstract":"<p>Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14048","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ya Wang, Wei Dong, Yufan Liang, Weiwei Lin, Junhao Chen, Robert Henry, Fei Chen
{"title":"PhyloForge: Unifying Micro- and Macroevolution With Comprehensive Genomic Signals","authors":"Ya Wang, Wei Dong, Yufan Liang, Weiwei Lin, Junhao Chen, Robert Henry, Fei Chen","doi":"10.1111/1755-0998.14050","DOIUrl":"10.1111/1755-0998.14050","url":null,"abstract":"<div>\u0000 \u0000 <p>The dimensions of phylogenetic research have expanded to encompass the study of large-scale populations at the microevolutionary level and comparisons between different species or taxonomic units at the macroevolutionary level. Traditional phylogenetic tools often struggle to handle the diverse and complex data required for these different evolutionary scales. In response to this challenge, we introduce PhyloForge, a robust tool designed to seamlessly integrate the demands of both micro- and macroevolution, comprehensively utilising diverse phylogenomic signals, such as genes, SNPs, and structural variations, as well as mitochondrial and chloroplast genomes. PhyloForge's innovation lies in its capability to seamlessly integrate multiple phylogenomic signals, enabling the unified analysis of multidimensional genomic data. This unique feature empowers researchers to gain a more comprehensive understanding of diverse aspects of biological evolution. PhyloForge not only provides highly customisable analysis tools for experienced researchers but also features an intuitively designed interface, facilitating effortless phylogenetic analysis for beginners. Extensive testing across various domains, including animals, plants and fungi, attests to its broad applicability in the field of phylogenetics. In summary, PhyloForge has significant potential in the era of large-scale genomics, offering a new perspective and toolset for a deeper understanding of the evolution of life. PhyloForge codes could be found in GitHub (https://github.com/wangyayaya/PhyloForge/), and the program could be installed in Conda (https://anaconda.org/wangxiaobei/phyloforge).</p>\u0000 </div>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714806","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Daniel E. Ruzzante, Gregory R. McCracken, Dylan J. Fraser, John MacMillan, Colin Buhariwalla, Joanna Mills Flemming
{"title":"Temporal Variability in Effective Size (\u0000 \u0000 \u0000 \u0000 \u0000 N\u0000 ̂\u0000 \u0000 e\u0000 \u0000 \u0000 ) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance","authors":"Daniel E. Ruzzante, Gregory R. McCracken, Dylan J. Fraser, John MacMillan, Colin Buhariwalla, Joanna Mills Flemming","doi":"10.1111/1755-0998.14047","DOIUrl":"10.1111/1755-0998.14047","url":null,"abstract":"<p>Although efforts to estimate effective population size, census size and their ratio in wild populations are expanding, few empirical studies investigate interannual changes in these parameters. Hence, we do not know how repeatable or representative many estimates may be. Answering this question requires studies of long-term population dynamics. Here we took advantage of a rich dataset of seven brook trout (<i>Salvelinus fontinalis</i>) populations, 5 consecutive years and 5400 individuals genotyped at 33 microsatellites to examine variation in estimates of effective and census size and in their ratio. We first estimated the annual effective number of breeders (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mover>\u0000 <mi>N</mi>\u0000 <mo>̂</mo>\u0000 </mover>\u0000 </mrow>\u0000 </semantics></math><sub><i>b</i></sub>) using individuals aged 1+. We then adjusted these estimates using two life history traits, to obtain <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mover>\u0000 <mi>N</mi>\u0000 <mo>̂</mo>\u0000 </mover>\u0000 <mrow>\u0000 <mi>b</mi>\u0000 <mfenced>\u0000 <mrow>\u0000 <mi>adj</mi>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </mfenced>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math> and subsequently, <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mover>\u0000 <mi>N</mi>\u0000 <mo>̂</mo>\u0000 </mover>\u0000 <mrow>\u0000 <mi>e</mi>\u0000 <mfenced>\u0000 <mrow>\u0000 <mi>adj</mi>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </mfenced>\u0000 </mrow>\u0000 </msub>\u0000 </mrow>\u0000 </semantics></math> following Waples et al. (2013). <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mover>\u0000 <mi>N</mi>\u0000 <mo>̂</mo>\u0000 </mover>\u0000 <mrow>\u0000 <mi>e</mi>\u0000 <mfenced>\u0000 <mrow>\u0000 <mi>adj</mi>\u0000 <mn>2</mn>\u0000 </mrow>\u0000 </mfenced>\u0000 ","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"25 3","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.14047","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}