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Lin H, Li W, Zhao Y. A Diverging Species within the Stewartia gemmata (Theaceae) Complex Revealed by RAD-Seq Data. PLANTS (BASEL, SWITZERLAND) 2024; 13:1296. [PMID: 38794366 PMCID: PMC11124813 DOI: 10.3390/plants13101296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
Informed species delimitation is crucial in diverse biological fields; however, it can be problematic for species complexes. Showing a peripatric distribution pattern, Stewartia gemmata and S. acutisepala (the S. gemmata complex) provide us with an opportunity to study species boundaries among taxa undergoing nascent speciation. Here, we generated genomic data from representative individuals across the natural distribution ranges of the S. gemmata complex using restriction site-associated DNA sequencing (RAD-seq). Based on the DNA sequence of assembled loci containing 41,436 single-nucleotide polymorphisms (SNPs) and invariant sites, the phylogenetic analysis suggested strong monophyly of both the S. gemmata complex and S. acutisepala, and the latter was nested within the former. Among S. gemmata individuals, the one sampled from Mt. Tianmu (Zhejiang) showed the closest evolutionary affinity with S. acutisepala (which is endemic to southern Zhejiang). Estimated from 2996 high-quality SNPs, the genetic divergence between S. gemmata and S. acutisepala was relatively low (an Fst of 0.073 on a per-site basis). Nevertheless, we observed a proportion of genomic regions showing relatively high genetic differentiation on a windowed basis. Up to 1037 genomic bins showed an Fst value greater than 0.25, accounting for 8.31% of the total. After SNPs subject to linkage disequilibrium were pruned, the principal component analysis (PCA) showed that S. acutisepala diverged from S. gemmata along the first and the second PCs to some extent. By applying phylogenomic analysis, the present study determines that S. acutisepala is a variety of S. gemmata and is diverging from S. gemmata, providing empirical insights into the nascent speciation within a species complex.
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Affiliation(s)
- Hanyang Lin
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China;
| | - Wenhao Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Yunpeng Zhao
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China;
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2
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Lewin PJ, Wynn J, Arcos JM, Austin RE, Blagrove J, Bond S, Carrasco G, Delord K, Fisher-Reeves L, García D, Gillies N, Guilford T, Hawkins I, Jaggers P, Kirk C, Louzao M, Maurice L, McMinn M, Micol T, Morford J, Morgan G, Moss J, Riera EM, Rodriguez A, Siddiqi-Davies K, Weimerskirch H, Wynn RB, Padget O. Climate change drives migratory range shift via individual plasticity in shearwaters. Proc Natl Acad Sci U S A 2024; 121:e2312438121. [PMID: 38285933 PMCID: PMC10861922 DOI: 10.1073/pnas.2312438121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/08/2023] [Indexed: 01/31/2024] Open
Abstract
How individual animals respond to climate change is key to whether populations will persist or go extinct. Yet, few studies investigate how changes in individual behavior underpin these population-level phenomena. Shifts in the distributions of migratory animals can occur through adaptation in migratory behaviors, but there is little understanding of how selection and plasticity contribute to population range shift. Here, we use long-term geolocator tracking of Balearic shearwaters (Puffinus mauretanicus) to investigate how year-to-year changes in individual birds' migrations underpin a range shift in the post-breeding migration. We demonstrate a northward shift in the post-breeding range and show that this is brought about by individual plasticity in migratory destination, with individuals migrating further north in response to changes in sea-surface temperature. Furthermore, we find that when individuals migrate further, they return faster, perhaps minimizing delays in return to the breeding area. Birds apparently judge the increased distance that they will need to migrate via memory of the migration route, suggesting that spatial cognitive mechanisms may contribute to this plasticity and the resulting range shift. Our study exemplifies the role that individual behavior plays in populations' responses to environmental change and highlights some of the behavioral mechanisms that might be key to understanding and predicting species persistence in response to climate change.
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Affiliation(s)
- Patrick J. Lewin
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Joe Wynn
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
- Institut für Vogelforschung “Vogelwarte Helgoland”, Wilhelmshaven26386, Germany
| | - José Manuel Arcos
- Programa Marino, Sociedad Española de Ornitología/BirdLife, Delegació de Catalunya, Barcelona08026, Spain
| | - Rhiannon E. Austin
- National Oceanography Centre–Southampton, SouthamptonSO14 3ZH, United Kingdom
- Earth Ocean and Ecological Sciences, School of Environmental Sciences, University of Liverpool, LiverpoolL69 3GP, United Kingdom
| | - Josephine Blagrove
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Sarah Bond
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
- School of Ocean Sciences, College of Science and Engineering, Bangor University, Menai BridgeLL59 5AB, United Kingdom
| | - Gemma Carrasco
- Iniciativa de Recerca de la Biodiversitat de les Illes, Alaior, Balearic Islands07730, Spain
| | - Karine Delord
- Centre d’Etudes Biologiques de Chizé, Laboratoire des Sciences de l'Environnement Marin, UMR 7372, Centre National de la Recherche Scientifique, Villiers en Bois79360, France
| | | | - David García
- Iniciativa de Recerca de la Biodiversitat de les Illes, Alaior, Balearic Islands07730, Spain
| | - Natasha Gillies
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
- Earth Ocean and Ecological Sciences, School of Environmental Sciences, University of Liverpool, LiverpoolL69 3GP, United Kingdom
| | - Tim Guilford
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Isobel Hawkins
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Paris Jaggers
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Christian Kirk
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Maite Louzao
- AZTI, Marine Research, Basque Research and Technology Alliance, Pasaia20110, Spain
| | - Lou Maurice
- British Geological Survey, WallingfordOX10 8ED, United Kingdom
| | - Miguel McMinn
- Grupo Biogeografía, geodinámica y sedimentación del Mediterráneo occidental, Ciències i Tecnologies Mediambientals, Universitat de les Illes Balears,Palma, Balearic IslandsE07122, Spain
| | - Thierry Micol
- Ligue pour la Protection des Oiseaux, BirdLife International Partner in France, Rochefort Cedex17305, France
| | - Joe Morford
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Greg Morgan
- Royal Society for the Protection of Birds, Ramsey Island, St. Davids, PembrokeshireSA62 6PY, United Kingdom
| | - Jason Moss
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Elisa Miquel Riera
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
| | - Ana Rodriguez
- Grupo Biogeografía, geodinámica y sedimentación del Mediterráneo occidental, Ciències i Tecnologies Mediambientals, Universitat de les Illes Balears,Palma, Balearic IslandsE07122, Spain
| | | | - Henri Weimerskirch
- Centre d’Etudes Biologiques de Chizé, Laboratoire des Sciences de l'Environnement Marin, UMR 7372, Centre National de la Recherche Scientifique, Villiers en Bois79360, France
| | - Russell B. Wynn
- National Oceanography Centre–Southampton, SouthamptonSO14 3ZH, United Kingdom
| | - Oliver Padget
- Department of Biology, University of Oxford, OxfordOX1 3SZ, United Kingdom
- Earth Ocean and Ecological Sciences, School of Environmental Sciences, University of Liverpool, LiverpoolL69 3GP, United Kingdom
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3
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Schüßler D, Blanco MB, Guthrie NK, Sgarlata GM, Dammhahn M, Ernest R, Evasoa MR, Hasiniaina A, Hending D, Jan F, le Pors B, Miller A, Olivieri G, Rakotonanahary AN, Rakotondranary SJ, Rakotondravony R, Ralantoharijaona T, Ramananjato V, Randrianambinina B, Raoelinjanakolona NN, Rasoazanabary E, Rasoloarison RM, Rasolofoson DW, Rasoloharijaona S, Rasolondraibe E, Roberts SH, Teixeira H, van Elst T, Johnson SE, Ganzhorn JU, Chikhi L, Kappeler PM, Louis EE, Salmona J, Radespiel U. Morphological variability or inter-observer bias? A methodological toolkit to improve data quality of multi-researcher datasets for the analysis of morphological variation. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:60-78. [PMID: 37607125 DOI: 10.1002/ajpa.24836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 07/21/2023] [Accepted: 08/01/2023] [Indexed: 08/24/2023]
Abstract
OBJECTIVES The investigation of morphological variation in animals is widely used in taxonomy, ecology, and evolution. Using large datasets for meta-analyses has dramatically increased, raising concerns about dataset compatibilities and biases introduced by contributions of multiple researchers. MATERIALS AND METHODS We compiled morphological data on 13 variables for 3073 individual mouse lemurs (Cheirogaleidae, Microcebus spp.) from 25 taxa and 153 different sampling locations, measured by 48 different researchers. We introduced and applied a filtering pipeline and quantified improvements in data quality (Shapiro-Francia statistic, skewness, and excess kurtosis). The filtered dataset was then used to test for genus-wide sexual size dimorphism and the applicability of Rensch's, Allen's, and Bergmann's rules. RESULTS Our pipeline reduced inter-observer bias (i.e., increased normality of data distributions). Inter-observer reliability of measurements was notably variable, highlighting the need to reduce data collection biases. Although subtle, we found a consistent pattern of sexual size dimorphism across Microcebus, with females being the larger (but not heavier) sex. Sexual size dimorphism was isometric, providing no support for Rensch's rule. Variations in tail length but not in ear size were consistent with the predictions of Allen's rule. Body mass and length followed a pattern contrary to predictions of Bergmann's rule. DISCUSSION We highlighted the usefulness of large multi-researcher datasets for testing ecological hypotheses after correcting for inter-observer biases. Using genus-wide tests, we outlined generalizable patterns of morphological variability across all mouse lemurs. This new methodological toolkit aims to facilitate future large-scale morphological comparisons for a wide range of taxa and applications.
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Affiliation(s)
- Dominik Schüßler
- Institute of Biology and Chemistry, University of Hildesheim, Hildesheim, Germany
| | | | - Nicola K Guthrie
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | | | | | | | - Mamy Rina Evasoa
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Alida Hasiniaina
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
- School for International Training, Antananarivo, Madagascar
| | | | - Fabien Jan
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Alex Miller
- Perth Zoo, South Perth, Western Australia, Australia
| | - Gillian Olivieri
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | | | | | - Romule Rakotondravony
- Faculté des Sciences, de Technologies et de l'Environnement, Ecole Doctorale Ecosystèmes Naturels, Université de Mahajanga, Mahajanga, Madagascar
| | - Tantely Ralantoharijaona
- Faculté des Sciences, de Technologies et de l'Environnement, Ecole Doctorale Ecosystèmes Naturels, Université de Mahajanga, Mahajanga, Madagascar
| | - Veronarindra Ramananjato
- Department of Integrative Biology, University of California Berkeley, Berkeley, California, USA
- Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Blanchard Randrianambinina
- Faculté des Sciences, de Technologies et de l'Environnement, Ecole Doctorale Ecosystèmes Naturels, Université de Mahajanga, Mahajanga, Madagascar
| | - Nancia N Raoelinjanakolona
- Mention Zoologie et Biodiversité Animale, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | | | - Rodin M Rasoloarison
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - David W Rasolofoson
- Groupe d'Etude et de Recherche sur les Primates de Madagascar (GERP), Antananarivo, Madagascar
| | - Solofonirina Rasoloharijaona
- Faculté des Sciences, de Technologies et de l'Environnement, Ecole Doctorale Ecosystèmes Naturels, Université de Mahajanga, Mahajanga, Madagascar
| | - Emmanuel Rasolondraibe
- Faculté des Sciences, de Technologies et de l'Environnement, Ecole Doctorale Ecosystèmes Naturels, Université de Mahajanga, Mahajanga, Madagascar
| | | | - Helena Teixeira
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
- UMR ENTROPIE, Université de La Réunion, La Réunion, France
| | - Tobias van Elst
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, Alberta, Canada
| | - Jörg U Ganzhorn
- Animal Ecology and Conservation, University of Hamburg, Hamburg, Germany
| | - Lounès Chikhi
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Laboratoire Évolution et Diversité Biologique, UMR5174, IRD, CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Peter M Kappeler
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Department of Anthropology/Sociobiology, University of Göttingen, Göttingen, Germany
| | - Edward E Louis
- Madagascar Biodiversity Partnership (MBP), Antananarivo, Madagascar
| | - Jordi Salmona
- Laboratoire Évolution et Diversité Biologique, UMR5174, IRD, CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Hannover, Germany
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4
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Khan M, Joshi M, Espeland M, Huemer P, Lopez-Vaamonde C, Mutanen M. Patterns of speciation in a parapatric pair of Saturnia moths as revealed by target capture. Mol Ecol 2024; 33:e17194. [PMID: 37933590 DOI: 10.1111/mec.17194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
The focus of this study has been to understand the evolutionary relationships and taxonomy of a widely distributed parapatric species pair of wild silk moths in Europe: Saturnia pavonia and Saturnia pavoniella (Lepidoptera: Saturniidae). To address species delimitation in these parapatric taxa, target enrichment and mtDNA sequencing was employed alongside phylogenetic, admixture, introgression, and species delimitation analyses. The dataset included individuals from both species close to and farther away from the contact zone as well as two hybrids generated in the lab. Nuclear markers strongly supported both S. pavonia and S. pavoniella as two distinct species, with hybrids forming a sister group to S. pavoniella. However, the Maximum Likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency is likely attributable to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization and/or incomplete lineage sorting). Our analyses indicate that past introgressions have taken place, but that there is no evidence to suggest an ongoing admixture between the two species, demonstrating that the taxa have reached full postzygotic reproductive isolation and hence represent two distinct biological species. Finally, we discuss our results from an evolutionary point of view taking into consideration the past climatic oscillations that have likely shaped the present dynamics between the two species. Overall, our study demonstrates the effectiveness of the target enrichment approach in resolving shallow phylogenetic relationships under complex evolutionary circumstances and that this approach is useful in establishing robust and well-informed taxonomic delimitations involving parapatric taxa.
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Affiliation(s)
- Maria Khan
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Mukta Joshi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Marianne Espeland
- Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Peter Huemer
- Tiroler Landesmuseen Betriebsges.m.b.H., Naturwissenschaftliche Sammlungen, Hall, Austria
| | | | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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5
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Congrains C, Dupuis JR, Rodriguez EJ, Norrbom AL, Steck G, Sutton B, Nolazco N, de Brito RA, Geib SM. Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex. Evol Appl 2023; 16:1598-1618. [PMID: 37752958 PMCID: PMC10519418 DOI: 10.1111/eva.13589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 09/28/2023] Open
Abstract
Insect pests cause tremendous impact to agriculture worldwide. Species identification is crucial for implementing appropriate measures of pest control but can be challenging in closely related species. True fruit flies of the genus Anastrepha Schiner (Diptera: Tephritidae) include some of the most serious agricultural pests in the Americas, with the Anastrepha fraterculus (Wiedemann) complex being one of the most important due to its extreme polyphagy and wide distribution across most of the New World tropics and subtropics. The eight morphotypes described for this complex as well as other closely related species are classified in the fraterculus species group, whose evolutionary relationships are unresolved due to incomplete lineage sorting and introgression. We performed multifaceted phylogenomic approaches using thousands of genes to unravel the evolutionary relationships within the A. fraterculus complex to provide a baseline for molecular diagnosis of these pests. We used a methodology that accommodates variable sources of data (transcriptome, genome, and whole-genome shotgun sequencing) and developed a tool to align and filter orthologs, generating reliable datasets for phylogenetic studies. We inferred 3031 gene trees that displayed high levels of discordance. Nevertheless, the topologies of the inferred coalescent species trees were consistent across methods and datasets, except for one lineage in the A. fraterculus complex. Furthermore, network analysis indicated introgression across lineages in the fraterculus group. We present a robust phylogeny of the group that provides insights into the intricate patterns of evolution of the A. fraterculus complex supporting the hypothesis that this complex is an assemblage of closely related cryptic lineages that have evolved under interspecific gene flow. Despite this complex evolutionary scenario, our subsampling analysis revealed that a set of as few as 80 loci has a similar phylogenetic resolution as the genome-scale dataset, offering a foundation to develop more efficient diagnostic tools in this species group.
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Affiliation(s)
- Carlos Congrains
- U.S. Department of Agriculture‐Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research UnitHiloHawaiiUSA
- Department of Plant and Environmental Protection ServicesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Julian R. Dupuis
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | - Erick J. Rodriguez
- Division of Plant Industry, Florida Department of Agriculture and Consumer ServicesGainesvilleFloridaUSA
| | - Allen L. Norrbom
- Systematic Entomology LabUSDA, ARS c/o Smithsonian InstitutionWashington DCUSA
| | - Gary Steck
- Division of Plant Industry, Florida Department of Agriculture and Consumer ServicesGainesvilleFloridaUSA
| | - Bruce Sutton
- Department of Entomology (Research Associate), National Museum of Natural HistorySmithsonian InstitutionGainesvilleFloridaUSA
| | - Norma Nolazco
- Centro de Diagnóstico de Sanidad Vegetal, Servicio Nacional de Sanidad AgrariaPeru
| | - Reinaldo A. de Brito
- Departamento de Genética e EvoluçãoUniversidade Federal de São CarlosSão CarlosSão PauloBrazil
| | - Scott M. Geib
- U.S. Department of Agriculture‐Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research UnitHiloHawaiiUSA
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Powell DM. Losing the forest for the tree? On the wisdom of subpopulation management. Zoo Biol 2023; 42:591-604. [PMID: 37218348 DOI: 10.1002/zoo.21776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/24/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
Animal habitats are changing around the world in many ways, presenting challenges to the survival of species. Zoo animal populations are also challenged by small population sizes and limited genetic diversity. Some ex situ populations are managed as subpopulations based on presumed subspecies or geographic locality and related concerns over genetic purity or taxonomic integrity. However, these decisions can accelerate the loss of genetic diversity and increase the likelihood of population extinction. Here I challenge the wisdom of subpopulation management, pointing out significant concerns in the literature with delineation of species, subspecies, and evolutionarily significant units. I also review literature demonstrating the value of gene flow for preserving adaptive potential, the often-misunderstood role of hybridization in evolution, and the likely overstated concerns about outbreeding depression, and preservation of local adaptations. I argue that the most effective way to manage animal populations for the long term be they in human care, in the wild, or if a captive population is being managed for reintroduction, is to manage for maximum genetic diversity rather than managing subpopulations focusing on taxonomic integrity, genetic purity, or geographic locale because selection in the future, rather than the past, will determine what genotypes and phenotypes are the most fit. Several case studies are presented to challenge the wisdom of subpopulation management and stimulate thinking about the preservation of genomes rather than species, subspecies, or lineages because those units evolved in habitats that are likely very different from those habitats today and in the future.
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Affiliation(s)
- David M Powell
- Department of Reproductive & Behavioral Sciences, Saint Louis Zoo, Saint Louis, Missouri, USA
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