Supergene origin and maintenance in Atlantic cod

Nature Ecology & Evolution, Journal Year: 2022, Volume and Issue: 6(4), P. 469 - 481

Published: Feb. 17, 2022

Abstract Supergenes are sets of genes that inherited as a single marker and encode complex phenotypes through their joint action. They identified in an increasing number organisms, yet origins evolution remain enigmatic. In Atlantic cod, four megabase-scale supergenes have been linked to migratory lifestyle environmental adaptations. Here we investigate the origin maintenance these analysis whole-genome-sequencing data, including new long-read-based genome assembly for non-migratory cod individual. We corroborate finding chromosomal inversions underlie all supergenes, show they originated at different times between 0.40 1.66 million years ago. reveal gene flux supergene haplotypes where stationary co-occur conclude this is driven by conversion, on basis increase GC content exchanged sites. Additionally, find evidence double crossover haplotypes, leading exchange ~275 kilobase fragment with potentially involved adaptation low salinity Baltic Sea. Our results suggest can be maintained over long timescales same way hybridizing species, selective purging introduced genetic variation.

Language: Английский

---

Important questions to progress science and sustainable management of anguillid eels

Fish and Fisheries, Journal Year: 2021, Volume and Issue: 22(4), P. 762 - 788

Published: May 6, 2021

Abstract Anguillid eels are found globally in fresh, transitional and saline waters have played an important role human life for centuries. The population status of several species is now significant concern. threats to populations include direct exploitation at different stages, blockages migratory routes by dams other structures, changes river basin management that impact habitat carrying capacity suitability, pollution, climate change, diseases parasites. While much has been done understand eel biology ecology, a major challenge identify the key research questions so effective targeted studies can be designed inform conservation, policy. We gathered 30 experts field review current state knowledge anguillid main topics research. identified fell into three themes: (a) Lifecycle Biology; (b) Impacts (c) Management. Although tropical far least well understood, gaps exist all species. Considerable progress made last 20 years, but many remains great concern, particularly northern temperate Without improved engagement coordination regional, national international level, situation unlikely improve. Further, adaptive mechanisms respond developments science, policy our potential required ensure future these enigmatic

Language: Английский

---

Empirical and philosophical problems with the subspecies rank

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(7)

Published: July 1, 2022

Species-level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species "concepts." These concepts determine if observed are independent given a particular methodology ontology, which relates metaphysical concept to what "kind" thing is in reality. Often, fail link epistemology back ontology. This lack coherence part responsible for persistence subspecies rank, modern usage often functions as placeholder between events divergence or collapse incipient species. Thus, prospective like merging diverging require information unknowable future information. also conditioned on evidence lineage already has detectably distinct history. Ranking these can seem attractive many do not exhibit intrinsic reproductive isolation. We argue using indefensible philosophical grounds. Ontologically, rank either identical undefined context representing spatiotemporally defined individuals. Some more inclined consider subspecies, Biological Species Concept, disconnected ontology genealogy. Even ignored, methods addressing isolation indirect capture range scenarios linking gene flow identity over space time. The use reliance basis an operational conflict with ethical issues governing protection provide way forward recognizing naming links theoretical regardless magnitude

Language: Английский

---

River Damming Impacts on Fish Habitat and Associated Conservation Measures

Reviews of Geophysics, Journal Year: 2023, Volume and Issue: 61(4)

Published: Dec. 1, 2023

Abstract River damming has brought great benefits to flood mitigation, energy and food production, will continue play a significant role in global supply, particularly Asia, Africa, South America. However, dams have extensively altered river dynamics, including riverine connectivity, hydrological, thermal, sediment solute regimes, the channel morphology. These alterations detrimental effects on quality quantity of fish habitat associated impacts aquatic life. Indeed, been implicated decline numerous fishes, emphasizing need for effective conservation measures. Here, we present synthesis critical issues concerning physical habitats, with particular focus key species across continents. We also consider current measures their applicability different contexts. Finally, identify future research needs. The information presented herein help support sustainable dam operation under constraints climate change human

Language: Английский

---

The Legacy of Recurrent Introgression during the Radiation of Hares

Systematic Biology, Journal Year: 2020, Volume and Issue: 70(3), P. 593 - 607

Published: Nov. 19, 2020

Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts introgression have seldom been evaluated in phylogenetic context a radiation. Hares (Lepus) represent widespread mammalian radiation 32 extant species characterized by striking ecological adaptations recurrent admixture. To understand relevance introgressive hybridization during diversification Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 hares (1-4 individuals per species), spanning global distribution genus, two outgroups. We used coalescent framework to infer relationships divergence times, despite extensive genealogical discordance. found high levels allele sharing among show that this reflects incomplete lineage sorting temporally layered hybridization. Our results revealed at all stages along Lepus radiation, including recent gene flow between since last glacial maximum also pervasive ancient occurring near origin hare lineages. northern hemisphere has resulted shared variation potential highly seasonal environments, genes involved circadian rhythm regulation, pigmentation, thermoregulation. illustrate how genetic legacy ancestral persist across leaving long-lasting signature contribute adaptation. [Adaptation; introgression; hybridization; Lepus; phylogenomics.].

Language: Английский

---

Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species

Ichthyology & Herpetology, Journal Year: 2021, Volume and Issue: 109(3)

Published: Sept. 28, 2021

Species delimitation is a first step for realizing the extent of biodiversity and relevant all downstream applications in biology. The production large genome-scale datasets non-model organisms combined with development methodological tools have allowed researchers to examine fine-scale processes speciation such as timing origin, degree migration, population-size changes, selection, drift, recombination. Studies using reptiles amphibians have, part, paved way use methods exploring delimitation. While these methodologies improved our understanding diversification, are far from agreeing upon set criteria delimit species. In cases where genetic lineages discovered that unique geographic areas, usually agree two entities exist. Disagreement about taxonomic status often centers on reproductive isolation between taxa probability remaining distinct. However, frequently inferred without examining gene flow, nature hybrid zones, or determining amount type introgression. Here, we review some vexing problems delimiting amphibians, which include by distance, flow differential allelic introgression, zone dynamics, genomic islands divergence. We also respond recent literature criticizing model-based species North American snakes context advancements address how scientists can move forward studies speciation.

Language: Английский

---

River network rearrangements promote speciation in lowland Amazonian birds

Science Advances, Journal Year: 2022, Volume and Issue: 8(14)

Published: April 8, 2022

Large Amazonian rivers impede dispersal for many species, but lowland river networks frequently rearrange, thereby altering the location and effectiveness of barriers through time. These rearrangements may promote biotic diversification by facilitating episodic allopatry secondary contact among populations. We sequenced genome-wide markers to evaluate histories divergence introgression in six avian species complexes. first tested assumption that are these taxa found even relatively small facilitate divergence. then whether diverged with gene flow recovered reticulate all including one potential case hybrid speciation. Our results support hypothesis speciation reveal rainforest micro-endemic, unrecognized, thus threatened imminent extinction. propose hyper-diversity originates partly from fine-scale barrier displacement processes—including dynamics—which allow populations differentiate disperse into contact.

Language: Английский

---

Candidate‐species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(2)

Published: Feb. 1, 2022

Dusky Salamanders (genus

---

Rapid Radiation and Rampant Reticulation: Phylogenomics of South AmericanLiolaemusLizards

Systematic Biology, Journal Year: 2021, Volume and Issue: 71(2), P. 286 - 300

Published: July 7, 2021

Understanding the factors that cause heterogeneity among gene trees can increase accuracy of species trees. Discordant signals across genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn result reticulate evolution. Species tree inference using multispecies coalescent is designed to deal with ILS robust low levels but extensive introgression violates fundamental assumption relationships strictly bifurcating. In this study, we explore phylogenomics iconic Liolaemus subgenus South American lizards, a group over 100 mostly distributed around Andes mountains. Using mitochondrial DNA (mtDNA) genome-wide restriction site-associated sequencing (RADseq; nDNA hereafter), inferred time-calibrated mtDNA tree, trees, phylogenetic networks. We found high discordance between nDNA, attribute part resulting from rapid diversification. These data also reveal deep combined diversification, explain level discordance. discuss these findings context Andean orogeny glacial cycles fragmented, expanded, contracted distributions. Finally, use new phylogeny resolve long-standing taxonomic issues one most studied lizard groups New World.[Andes; ddRADSeq; introgression; lizards; mtDNA; reptiles; SNPs.].

Language: Английский

---

The genomic revolution and species delimitation in birds (and other organisms): Why phenotypes should not be overlooked

Ornithology, Journal Year: 2021, Volume and Issue: 138(2)

Published: March 1, 2021

Abstract Given the availability of genomic data to identify separately evolving groups organisms, many researchers establish species limits based on assessments extent gene flow among populations and often use analytical approaches in which is explicitly disallowed. Strictly considering lack of—or limited—gene as main or only criterion delimit involves two complications practice. First, used analyze genome-wide cannot by themselves distinguish from within-species population structure, particularly allopatric organisms. Second, recognizing those lineages one can using such fails embrace role other evolutionary forces (i.e. various forms selection) defining lineages. Using examples birds, we call for importance additional delimitation explain why commonly taxonomic studies may be insufficient properly uncover limits. By processes that structure genotypic phenotypic variation during speciation, argue rigorous analyses remain crucial genomics era because phenotypes uniquely inform us about selection maintaining cohesion Evolutionary theory describing roles flow, genetic drift natural sexual origin maintenance calls an integration with phenomics avian delimitation.

Language: Английский

---