Evolutionary journal of the Linnean Society最新文献

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Recombination and phylogenetic inference. 重组和系统发育推断。

Evolutionary journal of the Linnean Society Pub Date : 2025-08-21 eCollection Date: 2025-01-01 DOI: 10.1093/evolinnean/kzaf016

Bruce Rannala

{"title":"Recombination and phylogenetic inference.","authors":"Bruce Rannala","doi":"10.1093/evolinnean/kzaf016","DOIUrl":"10.1093/evolinnean/kzaf016","url":null,"abstract":"I explore the problem of inferring phylogenetic trees in the presence of recombination. Two widely used approaches are considered: concatenation methods assume all loci have one underlying gene tree; and species tree inference methods assume one gene tree underlies each locus (no intralocus recombination) and loci have independent gene trees (high interlocus recombination). The impact of recombination is different under these two approaches. Three strategies for addressing the impacts of recombination are considered: (i) studies of the statistical robustness of phylogenetic inference methods when recombination occurs and is not accounted for (if impacts are minimal, recombination can be safely ignored); (ii) methods that accommodate recombination by identifying recombinant regions to either eliminate recombinant loci (to reduce intralocus recombination) or to choose loci that are separated by multiple recombinations (to increase interlocus recombination); and (iii) methods for phylogenetic inference that aim to accommodate recombination by inferring breakpoints between regions of sequences with different gene trees or allow varying topology along a sequence. I conclude that recombination is likely to be more detrimental for concatenation methods, having little impact on topology or divergence time estimates for species tree inference methods. Recombination detection may not be necessary when performing species tree inference, and eliminating recombinant loci may bias parameter estimates. Methods allowing gene trees to vary across the genome still lack theory-based criteria for combining inferred gene trees to estimate a species tree; this could in principle be done using a multispecies coalescent model with recombination but is a considerable technical challenge.","PeriodicalId":520301,"journal":{"name":"Evolutionary journal of the Linnean Society","volume":"4 1","pages":"kzaf016"},"PeriodicalIF":0.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12448323/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145115869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The evolution and genetic basis of a functionally critical skull bone, the parasphenoid, among Lake Malawi cichlids. 马拉维湖鲷中一个功能关键的颅骨，副类骨的进化和遗传基础。

Evolutionary journal of the Linnean Society Pub Date : 2024-12-05 eCollection Date: 2024-01-01 DOI: 10.1093/evolinnean/kzae039

Andrew J Conith, Sarah M Pascarella, Sylvie A Hope, R Craig Albertson

{"title":"The evolution and genetic basis of a functionally critical skull bone, the parasphenoid, among Lake Malawi cichlids.","authors":"Andrew J Conith, Sarah M Pascarella, Sylvie A Hope, R Craig Albertson","doi":"10.1093/evolinnean/kzae039","DOIUrl":"10.1093/evolinnean/kzae039","url":null,"abstract":"Adaptive radiation, whereby a clade pairs rapid speciation with rapid phenotypic evolution, can result in an uneven distribution of biodiversity across the Metazoan tree. The cichlid fishes of East Africa have undergone multiple adaptive radiations within the major rift lakes. Cichlid radiations are marked by divergence across distinct habitat gradients producing many morphological and behavioural adaptations. Here, we characterize the shape of the parasphenoid, a bone in the neurocranium that dissipates forces generated during feeding. We examine Tropheops, a group that has transitioned between deep and shallow habitats multiple times, to examine habitat-specific differences in parasphenoid shape. We find differences in the depth and length of the parasphenoid between Tropheops residing in each habitat, variation that may impact the ability of the cranium to resist force. We next use a hybrid cross between two cichlid species that differ in parasphenoid shape, Labeotropheus and Tropheops, to examine the genetic basis of these morphological differences. We perform genetic mapping and identify two genomic regions responsible for variation in parasphenoid shape. These regions are implicated in other functional traits including the oral jaws and neurocranium, indicating that the genetic landscape for adaptive evolution may be limited to a few loci with broad effects. Repurposing the same gene(s) for multiple traits via regulatory evolution may be sufficient for selection to drive transitions between habitats important for incipient stages of adaptive radiations.","PeriodicalId":520301,"journal":{"name":"Evolutionary journal of the Linnean Society","volume":"3 1","pages":"kzae039"},"PeriodicalIF":0.0,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142934410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Common misconceptions of speciation. 对物种形成的常见误解。

Evolutionary journal of the Linnean Society Pub Date : 2024-10-28 eCollection Date: 2024-01-01 DOI: 10.1093/evolinnean/kzae029

Jonah M Walker, Eva S M van der Heijden, Arif Maulana, Nicol Rueda-M, Karin Näsvall, Patricio A Salazar, Marco Meyer, Joana I Meier

{"title":"Common misconceptions of speciation.","authors":"Jonah M Walker, Eva S M van der Heijden, Arif Maulana, Nicol Rueda-M, Karin Näsvall, Patricio A Salazar, Marco Meyer, Joana I Meier","doi":"10.1093/evolinnean/kzae029","DOIUrl":"10.1093/evolinnean/kzae029","url":null,"abstract":"Speciation is a complex process that can unfold in many different ways. Speciation researchers sometimes simplify core principles in their writing in a way that implies misconceptions about the speciation process. While we think that these misconceptions are usually inadvertently implied (and not actively believed) by the researchers, they nonetheless risk warping how external readers understand speciation. Here we highlight six misconceptions of speciation that are especially widespread. First, species are implied to be clearly and consistently defined entities in nature, whereas in reality species boundaries are often fuzzy and semipermeable. Second, speciation is often implied to be 'good', which is two-fold problematic because it implies both that evolution has a goal and that speciation universally increases the chances of lineage persistence. Third, species-poor clades with species-rich sister clades are considered 'primitive' or 'basal', falsely implying a ladder of progress. Fourth, the evolution of species is assumed to be strictly tree-like, but genomic findings show widespread hybridization more consistent with network-like evolution. Fifth, a lack of association between a trait and elevated speciation rates in macroevolutionary studies is often interpreted as evidence against its relevance in speciation-even if microevolutionary case studies show that it is relevant. Sixth, obvious trait differences between species are sometimes too readily assumed to be (i) barriers to reproduction, (ii) a stepping-stone to inevitable speciation, or (iii) reflective of the species' whole divergence history. In conclusion, we call for caution, particularly when communicating science, because miscommunication of these ideas provides fertile ground for misconceptions to spread.","PeriodicalId":520301,"journal":{"name":"Evolutionary journal of the Linnean Society","volume":"3 1","pages":"kzae029"},"PeriodicalIF":0.0,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11590199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142735509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0