The genomic revolution and species delimitation in birds (and other organisms): Why phenotypes should not be overlooked DOI Open Access
Carlos Daniel Cadena, Felipe Zapata

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

The Role of Hybridization in Species Formation and Persistence DOI
Joshua V. Peñalba, Anna Runemark, Joana I. Meier

et al.

Cold Spring Harbor Perspectives in Biology, Journal Year: 2024, Volume and Issue: 16(12), P. a041445 - a041445

Published: March 4, 2024

Joshua V. Peñalba1, Anna Runemark2, Joana I. Meier3,4, Pooja Singh5,6, Guinevere O.U. Wogan7, Rosa Sánchez-Guillén8, James Mallet9, Sina J. Rometsch10,11, Mitra Menon12, Ole Seehausen5,6, Jonna Kulmuni13,14,16 and Ricardo Pereira15,16 1Museum für Naturkunde, Leibniz Institute for Evolution Biodiversity Science, Center Integrative Discovery, 10115 Berlin, Germany 2Department of Biology, Lund University, 22632 Lund, Sweden 3Tree Life, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom 4Department Zoology, University Cambridge, CB2 3EJ, 5Department Aquatic Ecology, Ecology Evolution, Bern, 3012 Switzerland 6Center & Biogeochemistry, Swiss Federal Science Technology (EAWAG), CH-8600 Kastanienbaum, 7Department Oklahoma State Stillwater, 74078, USA 8Red de Biología Evolutiva, INECOL, Xalapa, Veracruz, CP 91073, Mexico 9Organismal Evolutionary Harvard Massachusetts 02138, 10Department Yale New Haven, Connecticut 06511, 11Yale Biospheric Studies, 12Department California Davis, 95616, 13Department Population Ecosystem Dynamics, Amsterdam, 1098 XH The Netherlands 14Organismal Biology Research Programme, Helsinki, Biocenter 3, Finland 15Department Museum Natural History Stuttgart, Stuttgart 70191, Correspondence: ricardojn.pereira{at}gmail.com ↵16 These authors contributed equally to this work.

Language: Английский

Citations

18
Assessing the impacts of forest cover change on carbon stock and soil moisture dynamics using geospatial techniques: a case study of Nensebo forest, Southern Ethiopia DOI Creative Commons
Zenebe Reta Roba, Mitiku Badasa Moisa, Sanju Purohit

et al.

Environmental Monitoring and Assessment, Journal Year: 2025, Volume and Issue: 197(2)

Published: Jan. 14, 2025

Language: Английский

Citations

4
Reading Yule in light of the history and present of macroevolution DOI Creative Commons
Matthew W. Pennell, Ailene MacPherson

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1919)

Published: Feb. 13, 2025

Yule’s 1925 paper introducing the branching model that bears his name was a landmark contribution to biodiversity sciences. In paper, Yule developed stochastic models explain observed distribution of species across genera and test hypotheses about relationship between clade age, diversity geographic range. Here, we discuss intellectual context in which produced this work, highlight key mathematical conceptual contributions using both more modern derivations critically examine some assumptions work through lens. We then document strange trajectory history macroevolutionary thought how fundamental challenges he grappled with—such as defining higher taxa, linking microevolutionary population dynamics rates, accounting for inconsistent taxonomic practices—remain with us century later. This article is part theme issue ‘"A theory evolution": phylogenetic dating back 100 years’.

Language: Английский

Citations

3
Speciation completion rates have limited impact on macroevolutionary diversification DOI Creative Commons
Pierre Veron, Jérémy Andréoletti, Tatiana Giraud

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1919)

Published: Feb. 13, 2025

Standard birth–death (BD) processes used in macroevolutionary studies assume instantaneous speciation, an unrealistic premise that limits the interpretation of speciation and extinction rates. The protracted (PBD) model instead assumes involves two steps: initiation completion. In order to understand their respective influence on rates, we compute a standard time-varying BD scenario is ‘equivalent’ PBD terms probabilities. First, find sharp decline equivalent birth rate near present, indicating rates estimated at tips phylogenies may not accurately reflect underlying process. Second, completion controls timing decay rather than asymptotic past scales with rate, scaling factor depending mostly population rate. Our results suggest formation often play larger role speed accumulation reproductive isolation modulating study establishes theoretical framework for understanding how microevolutionary combine explain diversification species time scales. This article part theme issue ‘“A mathematical theory evolution”: phylogenetic models dating back 100 years’.

Language: Английский

Citations

2
Avian Diversity: Speciation, Macroevolution, and Ecological Function DOI
Joseph A. Tobias, Jente Ottenburghs, Alex L. Pigot

et al.

Annual Review of Ecology Evolution and Systematics, Journal Year: 2020, Volume and Issue: 51(1), P. 533 - 560

Published: Aug. 28, 2020

The origin, distribution, and function of biological diversity are fundamental themes ecology evolutionary biology. Research on birds has played a major role in the history development these ideas, yet progress was for many decades limited by focus patterns current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from recent wave integrative studies combining comprehensive phylogenetic, environmental, functional trait data at unprecedented scales. We review empirical advances describe how they reshaping our understanding global bird processes which it arises, with implications avian biogeography ecology. Further expansion integration sets may help resolve longstanding debates about origins biodiversity offer framework predicting response ecosystems environmental change.

Language: Английский

Citations

118
Comparative studies on speciation: 30 years since Coyne and Orr DOI Creative Commons
Daniel R. Matute, Brandon S. Cooper

Evolution, Journal Year: 2021, Volume and Issue: 75(4), P. 764 - 778

Published: Jan. 25, 2021

Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly hundred years geneticists have characterized reproductive isolation (RI) mechanisms specific barriers to gene flow required for species formation. The seminal work Coyne Orr provided first comprehensive comparative analysis speciation. By combining phylogenetic hypotheses range data with estimates genetic multiple RI across Drosophila, Orr's influential meta-analyses answered fundamental questions motivated new analyses that continue push field forward today. Now 30 later, we revisit five addressed by Orr, identifying results remain well supported others seem less robust data. We then consider future research, emphasis on areas where novel methods motivate potential progress. While literature biased towards Drosophila other model systems, are enthusiastic about field.

Language: Английский

Citations

75
Global patterns of population genetic differentiation in seed plants DOI
Diana Gamba, Nathan Muchhala

Molecular Ecology, Journal Year: 2020, Volume and Issue: 29(18), P. 3413 - 3428

Published: Aug. 3, 2020

Evaluating the factors that drive patterns of population differentiation in plants is critical for understanding several biological processes such as local adaptation and incipient speciation. Previous studies have given conflicting results regarding significance pollination mode, seed dispersal mating system, growth form latitudinal region shaping genetic structure, estimated by FST values, no study to date has tested their relative importance together across a broad scale. Here, we assembled 337-species data set from publications with on nuclear markers species traits, including variables pertaining sampling scheme each study. We used while accounting variables, perform phylogenetic multiple regressions. Results demonstrated values were higher tropical, mixed-mating, non-woody pollinated small insects, indicating greater differentiation, lower temperate, outcrossing trees wind. Among tested, explained largest portion variance, followed system form, mode did not significantly relate . Our analyses provide most robust comprehensive evaluation main ecological predicted plants, important implications basis divergence. supports previous findings showing tropical regions first are aware robustly demonstrate insects.

Language: Английский

Citations

71
The latitudinal taxonomy gradient DOI
Benjamin G. Freeman, Matthew W. Pennell

Trends in Ecology & Evolution, Journal Year: 2021, Volume and Issue: 36(9), P. 778 - 786

Published: May 31, 2021

Language: Английский

Citations

68
The Evolution of Comparative Phylogeography: Putting the Geography (and More) into Comparative Population Genomics DOI Creative Commons
Scott V. Edwards, V. V. Robin, Nuno Ferrand

et al.

Genome Biology and Evolution, Journal Year: 2021, Volume and Issue: 14(1)

Published: Aug. 3, 2021

Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. phylogeography, by contrast, focuses on the shared lineage histories of codistributed geographically and decidedly organismal in perspective. phylogeography approximately 35 years old, and, some metrics, showing signs reduced growth. Here, we contrast goals methods comparative argue that offers important perspective evolutionary history succeeds integrating with landscape evolution ways complement suprageographic genomics. Focusing primarily terrestrial vertebrates, review its milestones ongoing conceptual innovations, increasingly global focus, status as a bridge process speciation. We also that, science strong "sense place," abundant "place-based" educational opportunities focus geography natural history, well for collaboration local communities indigenous peoples. Although does not yet require whole-genome sequencing many goals, conclude it nonetheless plays role grounding our interpretation variation fundamentals Earth history.

Language: Английский

Citations

59
The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution DOI Open Access
Kay Lucek,

Mabel D. Giménez,

Mathieu Joron

et al.

Cold Spring Harbor Perspectives in Biology, Journal Year: 2023, Volume and Issue: 15(11), P. a041447 - a041447

Published: Aug. 21, 2023

Kay Lucek1, Mabel D. Giménez2,3, Mathieu Joron4, Marina Rafajlović5,6, Jeremy B. Searle7, Nora Walden8, Anja Marie Westram9,10 and Rui Faria11,12 1Biodiversity Genomics Laboratory, Institute of Biology, University Neuchâtel, 2000 Switzerland 2Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto Genética Humana Misiones (IGeHM), Parque la Salud Provincia "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina 3Facultad Ciencias Exactas Químicas Naturales, Universidad N3300LQH 4Centre d'Ecologie Fonctionnelle et Evolutive, Université Montpellier, CNRS, EPHE, IRD, 34293 France 5Department Marine Sciences, Gothenburg, 405 30 Sweden 6Centre for Evolutionary 7Department Ecology Cornell University, Ithaca, New York 14853, USA 8Centre Organismal Studies, Heidelberg, 69117 Germany 9Institute Science Technology Austria (ISTA), 3400 Klosterneuburg, 10Faculty Biosciences Aquaculture, Nord 8026 Bodø, Norway 11CIBIO, Centro Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, CIBIO, Campus Vairão, Universidade do Porto, 4485-661 Portugal 12BIOPOLIS Program in Genomics, Biodiversity Land Planning, Correspondence: kay.lucek{at}unine.ch; ruifaria{at}cibio.up.pt

Language: Английский

Citations

25