1
|
Rakotoarivelo AR, Rambuda T, Taron UH, Stalder G, O'Donoghue P, Robovský J, Hartmann S, Hofreiter M, Moodley Y. Complex patterns of gene flow and convergence in the evolutionary history of the spiral-horned antelopes (Tragelaphini). Mol Phylogenet Evol 2024; 198:108131. [PMID: 38909875 DOI: 10.1016/j.ympev.2024.108131] [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: 12/26/2023] [Revised: 05/19/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
The Tragelaphini, also known as spiral-horned antelope, is a phenotypically diverse mammalian tribe comprising a single genus, Tragelaphus. The evolutionary history of this tribe has attracted the attention of taxonomists and molecular geneticists for decades because its diversity is characterised by conflicts between morphological and molecular data as well as between mitochondrial, nuclear and chromosomal DNA. These inconsistencies point to a complex history of ecological diversification, coupled by either phenotypic convergence or introgression. Therefore, to unravel the phylogenetic relationships among spiral-horned antelopes, and to further investigate the role of divergence and gene flow in trait evolution, we sequenced genomes for all nine accepted species of the genus Tragelaphus, including a genome each for the highly divergent bushbuck lineages (T. s. scriptus and T. s. sylvaticus). We successfully reconstructed the Tragelaphus species tree, providing genome-level support for the early Pliocene divergence and monophyly of the nyala (T. angasii) and lesser kudu (T. imberbis), the monophyly of the two eland species (T. oryx and T. derbianus) and, importantly, the monophyly of kéwel (T. s. scriptus) and imbabala (T. s. sylvaticus) bushbuck. We found strong evidence for gene flow in at least four of eight nodes on the species tree. Among the six phenotypic traits assessed here, only habitat type mapped onto the species tree without homoplasy, showing that trait evolution was the result of complex patterns of divergence, introgression and convergent evolution.
Collapse
Affiliation(s)
- Andrinajoro R Rakotoarivelo
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa; Department of Zoology and Entomology, University of the Free State: QwaQwa Campus, Private Bag X13, Phuthaditjhaba 9866, Republic of South Africa
| | - Thabelo Rambuda
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa; Department of Genetics, University of Pretoria, Private Bag X20, Hatfield 0028, Republic of South Africa
| | - Ulrike H Taron
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Gabrielle Stalder
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstraße 1, A-1160 Wien, Austria
| | | | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Stefanie Hartmann
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa.
| |
Collapse
|
2
|
Dopman EB, Shaw KL, Servedio MR, Butlin RK, Smadja CM. Coupling of Barriers to Gene Exchange: Causes and Consequences. Cold Spring Harb Perspect Biol 2024; 16:a041432. [PMID: 38191516 PMCID: PMC11293547 DOI: 10.1101/cshperspect.a041432] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Coupling has emerged as a concept to describe the transition from differentiated populations to newly evolved species through the strengthening of reproductive isolation. However, the term has been used in multiple ways, and relevant processes have sometimes not been clearly distinguished. Here, we synthesize existing uses of the concept of coupling and find three main perspectives: (1) coupling as the build-up of linkage disequilibrium among loci underlying barriers to gene exchange, (2) coupling as the build-up of genome-wide linkage disequilibrium, and (3) coupling as the process generating a coincidence of distinct barrier effects. We compare and contrast these views, show the diverse processes involved and the complexity of the relationships among recombination, linkage disequilibrium, and reproductive isolation, and, finally, we emphasize how each perspective can guide new directions in speciation research. Although the importance of coupling for evolutionary divergence and speciation is well established, many theoretical and empirical questions remain unanswered.
Collapse
Affiliation(s)
- Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Kerry L Shaw
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York 14853, USA
| | - Maria R Servedio
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Roger K Butlin
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
- Department of Marine Sciences, University of Gothenburg, Gothenburg 40530, Sweden
| | - Carole M Smadja
- Institut des Sciences de l'Evolution de Montpellier ISEM, Universite de Montpellier, CNRS, IRD, Montpellier 34095, France
| |
Collapse
|
3
|
Kaminski M, Brown JI, Seibert SR, Hernández F, Duya MV, Fontanilla IKC, Roshier D, Miles A, Joseph L, Peters JL, Lavretsky P. Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data. Mol Phylogenet Evol 2024; 197:108085. [PMID: 38688441 DOI: 10.1016/j.ympev.2024.108085] [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: 12/04/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
AIM We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines. LOCATION Oceania, greater Indonesia, and the Philippines. TAXON Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) METHODS: Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species' range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species. RESULTS Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1-2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Papua New Guinea, and Timor-Leste, Indonesia. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu'u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples. MAIN CONCLUSIONS Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.
Collapse
Affiliation(s)
- Marissa Kaminski
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA; Upper Midwest Environmental Sciences Center, United States Geological Survey, La Crosse, WI, USA.
| | - Joshua I Brown
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA; Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Sara R Seibert
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Flor Hernández
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Melizar V Duya
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| | - Ian Kendrich C Fontanilla
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | - David Roshier
- School of Animal and Veterinary Science, University of Adelaide, Roseworthy SA, Australia
| | - Adam Miles
- Department of Marine and Wildlife Resources, Pago Pago, 96799, American Samoa
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australia
| | - Jeffrey L Peters
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX, USA
| |
Collapse
|
4
|
Reyna-Blanco CS, Caduff M, Galimberti M, Leuenberger C, Wegmann D. Inference of Locus-Specific Population Mixtures from Linked Genome-Wide Allele Frequencies. Mol Biol Evol 2024; 41:msae137. [PMID: 38958167 PMCID: PMC11255385 DOI: 10.1093/molbev/msae137] [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: 11/06/2023] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
Admixture between populations and species is common in nature. Since the influx of new genetic material might be either facilitated or hindered by selection, variation in mixture proportions along the genome is expected in organisms undergoing recombination. Various graph-based models have been developed to better understand these evolutionary dynamics of population splits and mixtures. However, current models assume a single mixture rate for the entire genome and do not explicitly account for linkage. Here, we introduce TreeSwirl, a novel method for inferring branch lengths and locus-specific mixture proportions by using genome-wide allele frequency data, assuming that the admixture graph is known or has been inferred. TreeSwirl builds upon TreeMix that uses Gaussian processes to estimate the presence of gene flow between diverged populations. However, in contrast to TreeMix, our model infers locus-specific mixture proportions employing a hidden Markov model that accounts for linkage. Through simulated data, we demonstrate that TreeSwirl can accurately estimate locus-specific mixture proportions and handle complex demographic scenarios. It also outperforms related D- and f-statistics in terms of accuracy and sensitivity to detect introgressed loci.
Collapse
Affiliation(s)
- Carlos S Reyna-Blanco
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Madleina Caduff
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| | - Marco Galimberti
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | | | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg 1700, Switzerland
- Swiss Institute of Bioinformatics, Fribourg 1700, Switzerland
| |
Collapse
|
5
|
Schneemann H, De Sanctis B, Welch JJ. Fisher's Geometric Model as a Tool to Study Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041442. [PMID: 38253415 PMCID: PMC11216183 DOI: 10.1101/cshperspect.a041442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Interactions between alleles and across environments play an important role in the fitness of hybrids and are at the heart of the speciation process. Fitness landscapes capture these interactions and can be used to model hybrid fitness, helping us to interpret empirical observations and clarify verbal models. Here, we review recent progress in understanding hybridization outcomes through Fisher's geometric model, an intuitive and analytically tractable fitness landscape that captures many fitness patterns observed across taxa. We use case studies to show how the model parameters can be estimated from different types of data and discuss how these estimates can be used to make inferences about the divergence history and genetic architecture. We also highlight some areas where the model's predictions differ from alternative incompatibility-based models, such as the snowball effect and outlier patterns in genome scans.
Collapse
Affiliation(s)
- Hilde Schneemann
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Bianca De Sanctis
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| |
Collapse
|
6
|
Manthey JD, Spellman GM. Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana). Mol Phylogenet Evol 2024; 196:108088. [PMID: 38697377 DOI: 10.1016/j.ympev.2024.108088] [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: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
Abstract
The nonrandom distribution of chromosomal characteristics and functional elements-genomic architecture-impacts the relative strengths and impacts of population genetic processes across the genome. Due to this relationship, genomic architecture has the potential to shape variation in population genetic structure across the genome. Population genetic structure has been shown to vary across the genome in a variety of taxa, but this body of work has largely focused on pairwise population genomic comparisons between closely related taxa. Here, we used whole genome sequencing of seven phylogeographically structured populations of a North American songbird, the Brown Creeper (Certhia americana), to determine the impacts of genomic architecture on phylogeographic structure variation across the genome. Using multiple methods to infer phylogeographic structure-ordination, clustering, and phylogenetic methods-we found that recombination rate variation explained a large proportion of phylogeographic structure variation. Genomic regions with low recombination showed phylogeographic structure consistent with the genome-wide pattern. In regions with high recombination, we found strong phylogeographic structure, but with discordant patterns relative to the genome-wide pattern. In regions with high recombination rate, we found that populations with small effective population sizes evolve relatively more rapidly than larger populations, leading to discordant signatures of phylogeographic structure. These results suggest that the interplay between recombination rate variation and effective population sizes shape the relative impacts of selection and genetic drift in different parts of the genome. Overall, the combined interactions of population genetic processes, genomic architecture, and effective population sizes shape patterns of variability in phylogeographic structure across the genome of the Brown Creeper.
Collapse
Affiliation(s)
- Joseph D Manthey
- Department of Biological Sciences, Texas Tech University. Lubbock, TX, USA.
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO, USA
| |
Collapse
|
7
|
Morales P, Gajardo F, Valdivieso C, Valladares MA, Di Genova A, Orellana A, Gutiérrez RA, González M, Montecino M, Maass A, Méndez MA, Allende ML. Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes. BMC Genomics 2024; 25:614. [PMID: 38890559 PMCID: PMC11184842 DOI: 10.1186/s12864-024-10416-w] [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: 10/05/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. RESULTS We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. CONCLUSIONS The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
Collapse
Affiliation(s)
- Pamela Morales
- Millennium Institute Center for Genome Regulation, Santiago, Chile.
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Felipe Gajardo
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Moisés A Valladares
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Grupo de Biodiversidad y Cambio Global (GBCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alex Di Genova
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- DiGenoma-Lab, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
- Centro de Modelamiento Matemático UMI-CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Ariel Orellana
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- ANID Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Mauricio González
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Martin Montecino
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, 837001, Chile
| | - Alejandro Maass
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Modelamiento Matemático IRL 2807 CNRS, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Matemática, Universidad de Chile, Santiago, Chile
| | - Marco A Méndez
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Ecología Aplicada y Sustentabilidad (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Cape Horn International Center (CHIC), Parque Etnobotánico Omora, Universidad de Magallanes, Puerto Williams, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| |
Collapse
|
8
|
Xun H, Lv R, Yu Y, Yao J, Wang R, Sha Y, Wang H, Zhang D, Xu C, Wang T, Zhang Z, Liu B, Gong L. Evolutionary genomics of two diploid goat grass species belonging to the section Sitopsis of Aegilops, Aegilops longissima, and Aegilops sharonensis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38859560 DOI: 10.1111/tpj.16876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/23/2024] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Aegilops longissima and Ae. sharonensis, being classified into the Sitopsis section of genus Aegilops, are distinct species both taxonomically and ecologically. Nevertheless, earlier observations indicate that the two species are not reproductively isolated to full extent and can inter-bred upon secondary contact. However, the genomic underpinnings of the morpho-ecological differentiation between the two foci species remained unexplored. Here, we resequenced 31 representative accessions of the two species and conducted in-depth comparative genomic analyses. We demonstrate recurrent and ongoing natural hybridizations between Ae. longissima and Ae. sharonensis, and depict features of genome composition of the resultant hybrids at both individual and population levels. We also delineate genomic regions and candidate genes potentially underpinning the differential morphological and edaphic adaptations of the two species. Intriguingly, a binary morphology was observed in the hybrids, suggesting existence of highly diverged genomic regions that remain uneroded by the admixtures. Together, our results provide new insights into the molding effects of interspecific hybridization on genome composition and mechanisms preventing merge of the two species.
Collapse
Affiliation(s)
- Hongwei Xun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruili Lv
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yue Yu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jinyang Yao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ruisi Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Han Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Deshi Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| |
Collapse
|
9
|
Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
Collapse
Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| |
Collapse
|
10
|
Grupstra CGB, Gómez-Corrales M, Fifer JE, Aichelman HE, Meyer-Kaiser KS, Prada C, Davies SW. Integrating cryptic diversity into coral evolution, symbiosis and conservation. Nat Ecol Evol 2024; 8:622-636. [PMID: 38351091 DOI: 10.1038/s41559-023-02319-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/12/2023] [Indexed: 04/13/2024]
Abstract
Understanding how diversity evolves and is maintained is critical to predicting the future trajectories of ecosystems under climate change; however, our understanding of these processes is limited in marine systems. Corals, which engineer reef ecosystems, are critically threatened by climate change, and global efforts are underway to conserve and restore populations as attempts to mitigate ocean warming continue. Recently, sequencing efforts have uncovered widespread undescribed coral diversity, including 'cryptic lineages'-genetically distinct but morphologically similar coral taxa. Such cryptic lineages have been identified in at least 24 coral genera spanning the anthozoan phylogeny and across ocean basins. These cryptic lineages co-occur in many reef systems, but their distributions often differ among habitats. Research suggests that cryptic lineages are ecologically specialized and several examples demonstrate differences in thermal tolerance, highlighting the critical implications of this diversity for predicting coral responses to future warming. Here, we draw attention to recent discoveries, discuss how cryptic diversity affects the study of coral adaptation and acclimation to future environments, explore how it shapes symbiotic partnerships, and highlight challenges and opportunities for conservation and restoration efforts.
Collapse
Affiliation(s)
| | | | - James E Fifer
- Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Sarah W Davies
- Department of Biology, Boston University, Boston, MA, USA.
| |
Collapse
|
11
|
Carvalho-Madrigal S, Sanín MJ. The role of introgressive hybridization in shaping the geographically isolated gene pools of wax palm populations (genus Ceroxylon). Mol Phylogenet Evol 2024; 193:108013. [PMID: 38195012 DOI: 10.1016/j.ympev.2024.108013] [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: 09/18/2023] [Revised: 12/22/2023] [Accepted: 01/06/2024] [Indexed: 01/11/2024]
Abstract
The speciation continuum is the process by which genetic groups diverge until they reach reproductive isolation. It has become common in the literature to show that this process is gradual and flickering, with possibly many instances of secondary contact and introgression after divergence has started. The level of divergence might vary among genomic regions due to, among others, the different forces and roles of selection played by the shared regions. Through hybrid capture, we sequenced ca. 4,000 nuclear regions in populations of six species of wax palms, five of which form a monophyletic group (genus Ceroxylon, Arecaceae: Ceroxyloideae). We show that in this group, the different populations show varying degrees of introgressive hybridization, and two of them are backcrosses of the other three 'pure' species. This is particularly interesting because these three species are dioecious, have a shared main pollinator, and have slightly overlapping reproductive seasons but highly divergent morphologies. Our work supports shows wax palms diverge under positive and background selection in allopatry, and hybridize due to secondary contact and inefficient reproductive barriers, which sustain genetic diversity. Introgressed regions are generally not under positive selection. Peripheral populations are backcrosses of other species; thus, introgressive hybridization is likely modulated by demographic effects rather than selective pressures. In general, these species might function as an 'evolutionary syngameon' where expanding, peripheral, small, and isolated populations maintain diversity by crossing with available individuals of other wax palms. In the Andean context, species can benefit from gained variation from a second taxon or the enhancement of population sizes by recreating a common genetic pool.
Collapse
Affiliation(s)
| | - María José Sanín
- School of Mathematical and Natural Sciences, Arizona State University, West Valley Campus, Glendale, United States.
| |
Collapse
|
12
|
Martins ARP, Warren NB, McMillan WO, Barrett RDH. Spatiotemporal dynamics in butterfly hybrid zones. INSECT SCIENCE 2024; 31:328-353. [PMID: 37596954 DOI: 10.1111/1744-7917.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.
Collapse
Affiliation(s)
- Ananda R Pereira Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Natalie B Warren
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Rowan D H Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| |
Collapse
|
13
|
Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Podsiadlowski L, Niehuis O, Ahrens D. Metazoa-level USCOs as markers in species delimitation and classification. Mol Ecol Resour 2024; 24:e13921. [PMID: 38146909 DOI: 10.1111/1755-0998.13921] [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: 10/15/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.
Collapse
Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eckart Stolle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Paris-Lodron-University, Salzburg, Austria
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lars Podsiadlowski
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| |
Collapse
|
14
|
Groh JS, Coop G. The temporal and genomic scale of selection following hybridization. Proc Natl Acad Sci U S A 2024; 121:e2309168121. [PMID: 38489387 PMCID: PMC10962946 DOI: 10.1073/pnas.2309168121] [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: 05/31/2023] [Accepted: 01/30/2024] [Indexed: 03/17/2024] Open
Abstract
Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the evolutionary dynamics within hybrid populations that underlie these patterns have been lacking. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of ancestry variation at varying spatial genomic scales through time. Here, we develop methods based on the Discrete Wavelet Transform to study the genomic scale of local ancestry variation and its association with recombination rates and show that these methods capture temporal dynamics of drift and genome-wide selection after hybridization. We apply these methods to published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio) and to inferred Neanderthal introgression in modern humans. Across systems, upward of 20% of variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. Signatures of selection at fine genomic scales suggest selection over longer time scales; however, we suggest that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from contiguous segments of genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available and can help shed light on generalities of the genomic consequences of interspecific hybridization.
Collapse
Affiliation(s)
- Jeffrey S. Groh
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA95616
| | - Graham Coop
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, CA95616
| |
Collapse
|
15
|
Stanojković A, Skoupý S, Johannesson H, Dvořák P. The global speciation continuum of the cyanobacterium Microcoleus. Nat Commun 2024; 15:2122. [PMID: 38459017 PMCID: PMC10923798 DOI: 10.1038/s41467-024-46459-6] [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: 07/10/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.
Collapse
Affiliation(s)
- Aleksandar Stanojković
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Svatopluk Skoupý
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Hanna Johannesson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Petr Dvořák
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic.
| |
Collapse
|
16
|
Berdan EL, Aubier TG, Cozzolino S, Faria R, Feder JL, Giménez MD, Joron M, Searle JB, Mérot C. Structural Variants and Speciation: Multiple Processes at Play. Cold Spring Harb Perspect Biol 2024; 16:a041446. [PMID: 38052499 PMCID: PMC10910405 DOI: 10.1101/cshperspect.a041446] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.
Collapse
Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, Gothenburg University, Gothenburg 40530, Sweden
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas G Aubier
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, 4485-661 Vairão, Portugal
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Claire Mérot
- CNRS, UMR 6553 Ecobio, OSUR, Université de Rennes, 35000 Rennes, France
| |
Collapse
|
17
|
Feng X, Merilä J, Löytynoja A. Secondary Contact, Introgressive Hybridization, and Genome Stabilization in Sticklebacks. Mol Biol Evol 2024; 41:msae031. [PMID: 38366566 PMCID: PMC10903534 DOI: 10.1093/molbev/msae031] [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: 09/19/2023] [Revised: 12/20/2023] [Accepted: 02/09/2024] [Indexed: 02/18/2024] Open
Abstract
Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data, we investigated the genetic introgression between 2 divergent lineages of 9-spined sticklebacks (Pungitius pungitius) in the Baltic Sea. We found that the intensity and direction of selection on the introgressed variation has varied across different genomic elements: while functionally important regions displayed reduced rates of introgression, promoter regions showed enrichment. Despite the general trend of negative selection, we identified specific genomic regions that were enriched for introgressed variants, and within these regions, we detected footprints of selection, indicating adaptive introgression. Geographically, we found the selection against the functional changes to be strongest in the vicinity of the secondary contact zone and weaken as a function of distance from the initial contact. Altogether, the results suggest that the stabilization of introgressed variation in the genomes is a complex, multistage process involving both negative and positive selection. In spite of the predominance of negative selection against introgressed variants, we also found evidence for adaptive introgression variants likely associated with adaptation to Baltic Sea environmental conditions.
Collapse
Affiliation(s)
- Xueyun Feng
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Area of Ecology and Biodiversity, The School of Biological Sciences, Kadoorie Biological Sciences Building, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Ari Löytynoja
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
18
|
Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
Collapse
Affiliation(s)
- Kira Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
| |
Collapse
|
19
|
Goebl AM, Kane NC, Doak DF, Rieseberg LH, Ostevik KL. Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes. Mol Ecol 2024; 33:e16785. [PMID: 36374153 DOI: 10.1111/mec.16785] [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: 07/12/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Conspecific populations living in adjacent but contrasting microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow is expected to force genetic homogeneity except at loci experiencing divergent selection. A history of reciprocal transplant and common garden studies in such systems, and a growing number of genomic studies, have contributed to understanding how selection operates in natural populations. While selection can vary across different fitness components and life stages, few studies have investigated how this ultimately affects allele frequencies and the maintenance of divergence between populations. Here, we study two sunflower ecotypes in distinct, adjacent habitats by combining demographic models with genome-wide sequence data to estimate fitness and allele frequency change at multiple life stages. This framework allows us to estimate that only local ecotypes are likely to experience positive population growth (λ > 1) and that the maintenance of divergent adaptation appears to be mediated via habitat- and life stage-specific selection. We identify genetic variation, significantly driven by loci in chromosomal inversions, associated with different life history strategies in neighbouring ecotypes that optimize different fitness components and may contribute to the maintenance of distinct ecotypes.
Collapse
Affiliation(s)
- April M Goebl
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Daniel F Doak
- Environmental Studies Programme, University of Colorado, Boulder, Colorado, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, California, USA
| |
Collapse
|
20
|
Tensen L, Fischer K. Evaluating hybrid speciation and swamping in wild carnivores with a decision-tree approach. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14197. [PMID: 37811741 DOI: 10.1111/cobi.14197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/12/2023] [Accepted: 06/28/2023] [Indexed: 10/10/2023]
Abstract
Hybridization is an important evolutionary force with a principal role in the origin of new species, known as hybrid speciation. However, ongoing hybridization can create hybrid swamping, in which parental genomes are completely lost. This can become a biodiversity threat if it involves species that have adapted to certain environmental conditions and occur nowhere else. Because conservation scientists commonly have a negative attitude toward hybrids, it is important to improve understanding of the influence of interspecific gene flow on the persistence of species. We reviewed the literature on species hybridization to build a list of all known cases in the order Carnivora. To examine the relative impact, we also noted level of introgression, whether fertile offspring were produced, and whether there was mention of negative or positive evolutionary effects (hybrid speciation and swamping). To evaluate the conservation implications of hybrids, we developed a decision-making tree with which to determine which actions should be taken to manage hybrid species. We found 53 hybrids involving 68 unique taxa, which is roughly 23% of all carnivore species. They mainly involved monophyletic (83%) and sympatric species (75%). For 2 species, the outcome of the assessment was to eliminate or restrict the hybrids: Ethiopian wolf (Canis simensis) and Scottish wildcat (Felis silvestris silvestris). Both species hybridize with their domestic conspecifics. For all other cases, we suggest hybrids be protected in the same manner as native species. We found no evidence of genomic extinction in Carnivora. To the contrary, some species appear to be of hybrid origin, such as the Asiatic black bear (Ursus thibetanus) and African golden wolf (Canis lupaster). Other positive outcomes of hybridization are novel genetic diversity, adaptation to extreme environments, and increased reproductive fitness. These outcomes are particularly valuable for counterbalancing genetic drift and enabling adaptive introgression in a human-dominated world.
Collapse
Affiliation(s)
- Laura Tensen
- Institute for Integrated Natural Sciences, Department of Zoology, University of Koblenz, Koblenz, Germany
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, Department of Zoology, University of Koblenz, Koblenz, Germany
| |
Collapse
|
21
|
Delapieve MLS, Rocha LA, Reis RE. Phylogenomics of the narrowly endemic Eurycheilichthys (Siluriformes: Loricariidae): Sympatric species with non-sister relationships suggest mainly allopatric speciation. Mol Phylogenet Evol 2024; 190:107970. [PMID: 37995894 DOI: 10.1016/j.ympev.2023.107970] [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: 07/17/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Armored catfishes of the genus Eurycheilichthys are endemic to Southern Brazil and Misiones (Argentina) comprising nine species of small size, with a high degree of sympatry and species diversity distributed in two river basins. Here we use new genome-wide data to infer a species phylogeny and test species boundaries for this poorly known group. We estimate 1) the phylogenetic relationships of the species of Eurycheilichthys based on 29,350 loci in 65 individuals of nine species plus outgroups, and 2) the population structure and differentiation based on 43,712 loci and 62 individuals to estimate how geography may have acted on speciation and formation of the sympatric species groups. Analyses support the monophyly of the genus and suggest two species-inclusive clades (East and West) with high support and very recently diverged species. Western clade contains E. limulus (from upper Jacuí River basin) that is sister to Western species of the Taquari-Antas basin plus E. paucidens. The Eastern clade contains E. pantherinus (from Uruguay River basin) sister to the Eastern species of the Taquari-Antas basin E. coryphaenus, plus the central-distributed species E. planus and E. vacariensis, and the more widely-distributed species E. luisae. Eurycheilichthys luisae is not monophyletic and may contain one or more cryptic species or hybrid individuals. A stronger diversity on structure of lineages on the Taquari-Antas, when compared to upper Uruguay and Jacuí River basins, and the fact that most of the sympatrically distributed taxa have non-sister relationships suggest a scenario of mainly allopatric speciation and may indicate a more dynamic landscape with headwater capture events among these tributaries.
Collapse
Affiliation(s)
- Maria Laura S Delapieve
- Laboratory of Vertebrate Systematics, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga 6681, 90619-900 Porto Alegre, RS, Brazil.
| | - Luiz A Rocha
- Section of Ichthyology, California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118, USA
| | - Roberto E Reis
- Laboratory of Vertebrate Systematics, Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Av. Ipiranga 6681, 90619-900 Porto Alegre, RS, Brazil
| |
Collapse
|
22
|
Kou Y, Fan D, Cheng S, Yang Y, Wang M, Wang Y, Zhang Z. Peripatric speciation within Torreya fargesii (Taxaceae) in the Hengduan Mountains inferred from multi-loci phylogeography. BMC Ecol Evol 2023; 23:74. [PMID: 38087226 PMCID: PMC10714551 DOI: 10.1186/s12862-023-02183-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The Hengduan Mountains (HDM) are one of the major global biodiversity hotspots in the world. Several evolutionary scenarios, especially in-situ diversification, have been proposed to account for the high species richness of temperate plants. However, peripatric speciation, an important mode of allopatric speciation, has seldom been reported in this region. RESULTS Here, two chloroplast DNA regions and 14 nuclear loci were sequenced for 112 individuals from 10 populations of Torreya fargesii var. fargesii and 63 individuals from 6 populations of T. fargesii var. yunnanensis. Population genetic analyses revealed that the two varieties are well differentiated genetically (FST, 0.5765) and have uneven genetic diversity (π, 0.00221 vs. 0.00073 on an average of nuclear loci). The gene genealogical relationship showed that T. fargesii var. yunnanensis is inferred as derived from T. fargesii var. fargesii, which was further supported by the coalescent simulations (DIYABC, fastsimcoal2 and IMa2). By the coalescent simulations, the divergence time (~ 2.50-3.65 Ma) and the weak gene flow between the two varieties were detected. The gene flow was asymmetrical and only occurred in later stages of divergence, which is caused by second contact due to the population expansion (~ 0.61 Ma) in T. fargesii var. fargesii. In addition, niche modeling indicated that the two varieties are differentiated geographically and ecologically and have unbalanced distribution range. CONCLUSIONS Overall, T. fargesii var. fargesii is always parapatric with respect to T. fargesii var. yunnanensis, and the latter derived from the former in peripatry of the HDM following a colonization from central China during the late Pliocene. Our findings demonstrate that peripatric speciation following dispersal events may be an important evolutionary scenario for the formation of biodiversity hotspot of the HDM.
Collapse
Affiliation(s)
- Yixuan Kou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Dengmei Fan
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Shanmei Cheng
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yi Yang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Meixia Wang
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China
| | - Yujin Wang
- State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, China.
| | - Zhiyong Zhang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Guangxi Normal University, Ministry of Education, Guilin, China.
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, China.
- Laboratory of Subtropical Biodiversity, Jiangxi Agricultural University, Nanchang, China.
| |
Collapse
|
23
|
Firneno TJ, Semenov G, Dopman EB, Taylor SA, Larson EL, Gompert Z. Quantitative Analyses of Coupling in Hybrid Zones. Cold Spring Harb Perspect Biol 2023; 15:a041434. [PMID: 37739809 PMCID: PMC10691479 DOI: 10.1101/cshperspect.a041434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then reanalyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time.
Collapse
Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Georgy Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erica L Larson
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah 84321, USA
| |
Collapse
|
24
|
Deville D, Kawai K, Fujita H, Umino T. Genetic divergences and hybridization within the Sebastes inermis complex. PeerJ 2023; 11:e16391. [PMID: 38025733 PMCID: PMC10656903 DOI: 10.7717/peerj.16391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
The Sebastes inermis complex includes three sympatric species (Sebastes cheni, viz Sebastes inermis, and Sebastes ventricosus) with clear ecomorphological differences, albeit incomplete reproductive isolation. The presence of putative morphological hybrids (PMH) with plausibly higher fitness than the parent species indicates the need to confirm whether hybridization occurs within the complex. In this sense, we assessed the dynamics of genetic divergence and hybridization within the species complex using a panel of 10 microsatellite loci, and sequences of the mitochondrial control region (D-loop) and the intron-free rhodopsin (RH1) gene. The analyses revealed the presence of three distinct genetic clusters, large genetic distances using D-loop sequences, and distinctive mutations within the RH1 gene. These results are consistent with the descriptions of the three species. Two microsatellite loci had signatures of divergent selection, indicating that they are linked to genomic regions that are crucial for speciation. Furthermore, nonsynonymous mutations within the RH1 gene detected in S. cheni and "Kumano" (a PMH) suggest dissimilar adaptations related to visual perception in dim-light environments. The presence of individuals with admixed ancestry between two species confirmed hybridization. The presence of nonsynonymous mutations within the RH1 gene and the admixed ancestry of the "Kumano" morphotype highlight the potential role of hybridization in generating novelties within the species complex. We discuss possible outcomes of hybridization within the species complex, considering hybrid fitness and assortative mating. Overall, our findings indicate that the genetic divergence of each species is maintained in the presence of hybridization, as expected in a scenario of speciation-with-gene-flow.
Collapse
Affiliation(s)
- Diego Deville
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japón
| | - Kentaro Kawai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japón
| | - Hiroki Fujita
- Seto Marine Biological Laboratory, Field Science Education and Research Center, Kyoto University, Shirahama, Wakayama, Japan
| | - Tetsuya Umino
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japón
| |
Collapse
|
25
|
Rutherford S, Rossetto M, Bragg JG, Wan JSH. Where to draw the boundaries? Using landscape genomics to disentangle the scribbly gum species complex. AMERICAN JOURNAL OF BOTANY 2023; 110:e16245. [PMID: 37747108 DOI: 10.1002/ajb2.16245] [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: 02/10/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
PREMISE Species delimitation is an integral part of evolution and ecology and is vital in conservation science. However, in some groups, species delimitation is difficult, especially where ancestral relationships inferred from morphological or genetic characters are discordant, possibly due to a complicated demographic history (e.g., recent divergences between lineages). Modern genetic techniques can take into account complex histories to distinguish species at a reasonable cost and are increasingly used in numerous applications. We focus on the scribbly gums, a group of up to five closely related and morphologically similar "species" within the eucalypts. METHODS Multiple populations of each recognized scribbly gum species were sampled over a wide region across climates, and genomewide scans were used to resolve species boundaries. RESULTS None of the taxa were completely divergent, and there were two genetically distinct entities: the inland distributed Eucalyptus rossii and a coastal conglomerate consisting of four species forming three discernible, but highly admixed groups. Divergence among taxa was likely driven by temporal vicariant processes resulting in partial separation across biogeographic barriers. High interspecific gene flow indicated separated taxa reconnected at different points in time, blurring species boundaries. CONCLUSIONS Our results highlight the need for genetic screening when dealing with closely related taxonomic entities, particularly those with modest morphological differences. We show that high-throughput sequencing can be effective at identifying species groupings and processes driving divergence, even in the most taxonomically complex groups, and be used as a standard practice for disentangling species complexes.
Collapse
Affiliation(s)
- Susan Rutherford
- Department of Environmental Science, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Department of Environmental and Sustainability Sciences, The Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, Union, NJ, USA
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
| | - Justin S H Wan
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
| |
Collapse
|
26
|
Fukutani K, Matsui M, Nishikawa K. Population genetic structure and hybrid zone analyses for species delimitation in the Japanese toad ( Bufo japonicus). PeerJ 2023; 11:e16302. [PMID: 37901459 PMCID: PMC10607272 DOI: 10.7717/peerj.16302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated during isolation. The Japanese toad, Bufo japonicus, is distributed on the main islands of Japan. In the present study, we applied multiplexed inter-simple sequence repeat genotyping by sequencing to achieve the fine-scale resolution of the genetic cluster in B. j. japonicus and B. j. formosus. We also elucidated hybridization patterns and gene flow degrees across contact zones between the clusters identified. Using SNP data, we found four genetic clusters in B. j. japonicus and B. j. formosus and three contact zones of the cluster pairs among these four clusters. The two oldest diverged lineages, B. j. japonicus and B. j. formosus, formed a narrow contact zone consistent with species distinctiveness. Therefore, we recommend that these two subspecies be elevated to the species level. In contrast, the less diverged pairs of two clusters in B. j. japonicus and B. j. formosus, respectively, admixed over a hundred kilometers, suggesting that they have not yet developed strong reproductive isolation and need to be treated as conspecifics. These results will contribute to resolving taxonomic confusion in Japanese toads.
Collapse
Affiliation(s)
- Kazumi Fukutani
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| |
Collapse
|
27
|
Laetsch DR, Bisschop G, Martin SH, Aeschbacher S, Setter D, Lohse K. Demographically explicit scans for barriers to gene flow using gIMble. PLoS Genet 2023; 19:e1010999. [PMID: 37816069 PMCID: PMC10610087 DOI: 10.1371/journal.pgen.1010999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/27/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Identifying regions of the genome that act as barriers to gene flow between recently diverged taxa has remained challenging given the many evolutionary forces that generate variation in genetic diversity and divergence along the genome, and the stochastic nature of this variation. Progress has been impeded by a conceptual and methodological divide between analyses that infer the demographic history of speciation and genome scans aimed at identifying locally maladaptive alleles i.e. genomic barriers to gene flow. Here we implement genomewide IM blockwise likelihood estimation (gIMble), a composite likelihood approach for the quantification of barriers, that bridges this divide. This analytic framework captures background selection and selection against barriers in a model of isolation with migration (IM) as heterogeneity in effective population size (Ne) and effective migration rate (me), respectively. Variation in both effective demographic parameters is estimated in sliding windows via pre-computed likelihood grids. gIMble includes modules for pre-processing/filtering of genomic data and performing parametric bootstraps using coalescent simulations. To demonstrate the new approach, we analyse data from a well-studied pair of sister species of tropical butterflies with a known history of post-divergence gene flow: Heliconius melpomene and H. cydno. Our analyses uncover both large-effect barrier loci (including well-known wing-pattern genes) and a genome-wide signal of a polygenic barrier architecture.
Collapse
Affiliation(s)
- Dominik R. Laetsch
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Gertjan Bisschop
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon H. Martin
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Derek Setter
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Konrad Lohse
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
28
|
Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [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: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
Collapse
Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
29
|
Wang XF, Zhang YX, Niu YQ, Sha Y, Wang ZH, Zhang ZB, Yang J, Liu B, Li LF. Post-hybridization introgression and natural selection promoted genomic divergence of Aegilops speltoides and the four S*-genome diploid species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1500-1513. [PMID: 37313760 DOI: 10.1111/tpj.16334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 05/22/2023] [Accepted: 05/24/2023] [Indexed: 06/15/2023]
Abstract
Understanding how different driving forces have promoted biological divergence and speciation is one of the central issues in evolutionary biology. The Triticum/Aegilops species complex contains 13 diploid species belonging to the A-, B- and D-lineages and offers an ideal system to address the evolutionary dynamics of lineage fusion and splitting. Here, we sequenced the whole genomes of one S-genome species (Aegilops speltoides) of the B-lineage and four S*-genome diploid species (Aegilops bicornis, Aegilops longissima, Aegilops sharonensis and Aegilops searsii) of the D-lineage at the population level. We performed detailed comparisons of the five species and with the other four representative A-, B- and D-lineage species. Our estimates identified frequent genetic introgressions from A- and B-lineages to the D-lineage species. A remarkable observation is the contrasting distributions of putative introgressed loci by the A- and B-lineages along all the seven chromosomes to the extant D-lineage species. These genetic introgressions resulted in high levels of genetic divergence at centromeric regions between Ae. speltoides (B-lineage) and the other four S*-genome diploid species (D-lineage), while natural selection is a potential contributor to divergence among the four S*-genome species at telomeric regions. Our study provides a genome-wide view on how genetic introgression and natural selection acted together yet chromosome-regionally divided to promote genomic divergence among the five S- and S*-genome diploid species, which provides new and nuanced insights into the evolutionary history of the Triticum/Aegilops species complex.
Collapse
Affiliation(s)
- Xin-Feng Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu-Xin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu-Qian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yan Sha
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, 130118, China
| | - Zhi-Bin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| |
Collapse
|
30
|
Katemo Manda B, Snoeks J, Decru E, Brecko J, Vreven EJWMN. Revision of Nannocharax luapulae Boulenger, 1915 (Characiformes: Distichodontidae) from the Upper Congo basin: Evidence for a species pair. JOURNAL OF FISH BIOLOGY 2023; 103:557-573. [PMID: 37026429 DOI: 10.1111/jfb.15400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
For many decades, Nannocharax luapulae has been considered to be widespread in the southern part of the Upper Congo basin. However, meristic, morphometric and cytochrome c oxidase subunit I (COI) barcoding evidence revealed that its geographical distribution is restricted to the Luapula-Moero basin. The populations of the Upper Lualaba are assigned to a new species, N. chochamandai. This new species, though highly similar to N. luapulae, can readily be distinguished from it by its lower number of lateral line scales, 41-46 (vs. 49-55), its pectoral fin reaching the pelvic-fin insertion (vs. not reaching the pelvic-fin insertion) and its pelvic fin reaching the base of the anal fin (vs. not reaching the base of the anal fin). Specimens of N. chochamandai display thickened pads on the first three pelvic-fin rays that exhibit intraspecific variation in development, which appears to be related to the flow-strength of the river in which these Nannocharax specimens occur. Nannocharax luapulae is redescribed and an updated identification key to the Nannocharax species of the Congo basin sensu lato is provided as well. Some fish conservation issues related to N. luapulae and N. chochamandai are also highlighted.
Collapse
Affiliation(s)
- Bauchet Katemo Manda
- Unité de Recherche en Biodiversité et Exploitation durable des Zones Humides, Faculty of Agricultural Sciences, University of Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Jos Snoeks
- Ichthyology, Section Vertebrates, Royal Museum for Central Africa, Tervuren, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Leuven, Belgium
| | - Eva Decru
- Biology Department, Fish Diversity and Conservation, KU Leuven, Leuven, Belgium
| | - Jonathan Brecko
- Biological Collection and Data Management, Section Biology, Royal Museum for Central Africa, Tervuren, Belgium
- Scientific Service of Heritage, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Emmanuel J W M N Vreven
- Ichthyology, Section Vertebrates, Royal Museum for Central Africa, Tervuren, Belgium
- Biology Department, Fish Diversity and Conservation, KU Leuven, Leuven, Belgium
| |
Collapse
|
31
|
Giesen A, Blanckenhorn WU, Schäfer MA, Shimizu KK, Shimizu-Inatsugi R, Misof B, Podsiadlowski L, Niehuis O, Lischer HEL, Aeschbacher S, Kapun M. Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species. Evol Biol 2023; 50:395-412. [PMID: 37854269 PMCID: PMC10579158 DOI: 10.1007/s11692-023-09612-5] [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: 01/16/2023] [Accepted: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The extent of interspecific gene flow and its consequences for the initiation, maintenance, and breakdown of species barriers in natural systems remain poorly understood. Interspecific gene flow by hybridization may weaken adaptive divergence, but can be overcome by selection against hybrids, which may ultimately promote reinforcement. An informative step towards understanding the role of gene flow during speciation is to describe patterns of past gene flow among extant species. We investigate signals of admixture between allopatric and sympatric populations of the two closely related European dung fly species Sepsis cynipsea and S. neocynipsea (Diptera: Sepsidae). Based on microsatellite genotypes, we first inferred a baseline demographic history using Approximate Bayesian Computation. We then used genomic data from pooled DNA of natural and laboratory populations to test for past interspecific gene flow based on allelic configurations discordant with the inferred population tree (ABBA-BABA test with D-statistic). Comparing the detected signals of gene flow with the contemporary geographic relationship among interspecific pairs of populations (sympatric vs. allopatric), we made two contrasting observations. At one site in the French Cevennes, we detected an excess of past interspecific gene flow, while at two sites in Switzerland we observed lower signals of past microsatellite genotypes gene flow among populations in sympatry compared to allopatric populations. These results suggest that the species boundaries between these two species depend on the past and/or present eco-geographic context in Europe, which indicates that there is no uniform link between contemporary geographic proximity and past interspecific gene flow in natural populations. Supplementary Information The online version contains supplementary material available at 10.1007/s11692-023-09612-5.
Collapse
Affiliation(s)
- Athene Giesen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin A. Schäfer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Heidi E. L. Lischer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| |
Collapse
|
32
|
Burbrink FT, Ruane S, Rabibisoa N, Raselimanana AP, Raxworthy CJ, Kuhn A. Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes. Ecol Evol 2023; 13:e10344. [PMID: 37529593 PMCID: PMC10375368 DOI: 10.1002/ece3.10344] [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: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Speciation rates vary substantially across the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary patterns exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have been shown to be either correlated or uncorrelated depending on the group, but no study has yet examined the relationship between speciation rates and population structure in a young group that is constrained spatially to a single-island system. We examine this correlation in 109 gemsnakes (Pseudoxyrhophiidae) endemic to Madagascar and originating in the early Miocene, which helps control for extinction variation across time and space. We find no relationship between rates of speciation and the formation rates of population structure over space in 33 species of gemsnakes. Rates of speciation show low variation, yet population structure varies widely across species, indicating that speciation rates and population structure are disconnected. We suspect this is largely due to the persistence of some lineages not susceptible to extinction. Importantly, we discuss how delimiting populations versus species may contribute to problems understanding the continuum between shallow and deep evolutionary processes.
Collapse
Affiliation(s)
- Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Nirhy Rabibisoa
- Sciences de la Vie et de l'Environnement, Faculté des Sciences, de Technologies et de l'EnvironnementUniversité de MahajangaMahajangaMadagascar
| | - Achille P. Raselimanana
- Zoologie et Biodiversité Animale, Faculté des SciencesUniversité d'AntananarivoAntananarivoMadagascar
| | | | - Arianna Kuhn
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
- Virginia Museum of Natural HistoryMartinsvilleVirginiaUSA
| |
Collapse
|
33
|
Groh J, Coop G. The temporal and genomic scale of selection following hybridization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542345. [PMID: 37337589 PMCID: PMC10276902 DOI: 10.1101/2023.05.25.542345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the dynamics underlying these patterns within hybrid populations have been lacking. Here, we develop methods based on the Wavelet Transform to understand the spatial genomic scale of local ancestry variation and its association with recombination rates. We present theory and use simulations to show how wavelet-based decompositions of ancestry variance along the genome and the correlation between ancestry and recombination reflect the joint effects of recombination, genetic drift, and genome-wide selection against introgressed alleles. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of local ancestry variation at varying spatial genomic scales through time. Using wavelet approaches to identify the genomic scale of variance in ancestry and its correlates, we show that these methods can detect temporally localized effects of drift and selection. We apply these methods to previously published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio), and to inferred Neanderthal introgression in modern humans. Across systems, we find that upwards of 20% of the variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. We also see signals of selection at fine genomic scales and much longer time scales. However, we show that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available, and can help shed light on generalities of the genomic consequences of interspecific hybridization.
Collapse
Affiliation(s)
- Jeffrey Groh
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616
| | - Graham Coop
- Department of Evolution and Ecology, and Center for Population Biology, University of California, Davis, CA 95616
| |
Collapse
|
34
|
Freedman AH, Harrigan RJ, Zhen Y, Hamilton AM, Smith TB. Evidence for ecotone speciation across an African rainforest-savanna gradient. Mol Ecol 2023; 32:2287-2300. [PMID: 36718952 DOI: 10.1111/mec.16867] [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: 06/03/2022] [Revised: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Abstract
Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly probably driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.
Collapse
Affiliation(s)
- Adam H Freedman
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan J Harrigan
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
| | - Ying Zhen
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Alison M Hamilton
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Thomas B Smith
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| |
Collapse
|
35
|
Zhang W, Wang H, Zhang T, Fang X, Liu M, Xiao H. Geographic-genomic and geographic-phenotypic differentiation of the Aquilegia viridiflora complex. HORTICULTURE RESEARCH 2023; 10:uhad041. [PMID: 37159802 PMCID: PMC10163360 DOI: 10.1093/hr/uhad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/05/2023] [Indexed: 05/11/2023]
Abstract
How species diverge into different lineages is a central issue in evolutionary biology. Despite the increasing evidence indicating that such divergences do not need geographic isolation, the correlation between lineage divergence and the adaptive ecological divergence of phenotype corresponding to distribution is still unknown. In addition, gene flow has been widely detected during and through such diverging processes. We used one widely distributed Aquilegia viridiflora complex as a model system to examine genomic differentiation and corresponding phenotypic variations along geographic gradients. Our phenotypic analyses of 20 populations from northwest to northeast China identified two phenotypic groups along the geographic cline. All examined traits are distinct from each other, although a few intermediate individuals occur in their contacting regions. We further sequenced the genomes of representative individuals of each population. However, four distinct genetic lineages were detected based on nuclear genomes. In particular, we recovered numerous genetic hybrids in the contact regions of four lineages. Gene flow is widespread and continuous between four lineages but much higher between contacting lineages than geographically isolated lineages. Gene flow and natural selection might result in inconsistency between heredity and phenotype. Moreover, many genes with fast lineage-specific mutations were identified to be involved in local adaptation. Our results suggest that both geographic isolation and local selection exerted by the environment and pollinators may together create geographic distributions of phenotypic variations as well as the underlying genomic divergences in numerous lineages.
Collapse
Affiliation(s)
- Wei Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | | | - Tengjiao Zhang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Xiaoxue Fang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Meiying Liu
- Key Laboratory of Molecular Epigenetics of Ministry of Education, College of Life Sciences, Northeast Normal University, Changchun 130024, China
| | | |
Collapse
|
36
|
Guo JF, Zhao W, Andersson B, Mao JF, Wang XR. Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau. PLANT COMMUNICATIONS 2023:100574. [PMID: 36906801 PMCID: PMC10363505 DOI: 10.1016/j.xplc.2023.100574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/09/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Most species have clearly defined distribution ranges and ecological niches. The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are, however, less clearly defined. This study investigated the genetic structure and clines in Pinus densata, a pine of hybrid origin on the southeastern Tibetan Plateau, to gain an understanding of the contemporary dynamics of species barriers. We analyzed genetic diversity in a range-wide collection of P. densata and representative populations of its progenitors, Pinus tabuliformis and Pinus yunnanensis, using exome capture sequencing. We detected four distinct genetic groups within P. densata that reflect its migration history and major gene-flow barriers across the landscape. The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories. Interestingly, population sizes rebounded rapidly during interglacial periods, suggesting persistence and resilience of the species during the Quaternary ice age. In the contact zone between P. densata and P. yunnanensis, 3.36% of the analyzed loci (57 849) showed exceptional patterns of introgression, suggesting their potential roles in either adaptive introgression or reproductive isolation. These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation. This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition. Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.
Collapse
Affiliation(s)
- Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration; State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden
| | - Bea Andersson
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden
| | - Jian-Feng Mao
- National Engineering Research Center of Tree Breeding and Ecological Restoration; State Key Laboratory of Tree Genetics and Breeding; Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education; College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, 90187 Umeå, Sweden.
| |
Collapse
|
37
|
McDiarmid CS, Finch F, Peso M, van Rooij E, Hooper DM, Rowe M, Griffith SC. Experimentally testing mate preference in an avian system with unidirectional bill color introgression. Ecol Evol 2023; 13:e9812. [PMID: 36825134 PMCID: PMC9942114 DOI: 10.1002/ece3.9812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 02/23/2023] Open
Abstract
Mating behavior can play a key role in speciation by inhibiting or facilitating gene flow between closely related taxa. Hybrid zones facilitate a direct examination of mating behavior and the traits involved in establishing species barriers. The long-tailed finch (Poephila acuticauda) has two hybridizing subspecies that differ in bill color (red and yellow), and the yellow bill phenotype appears to have introgressed ~350 km eastward following secondary contact. To examine the role of mate choice on bill color introgression, we performed behavioral assays using natural and manipulated bill colors. We found an assortative female mating preference for males of their own subspecies when bill color was not manipulated. However, we did not find this assortative preference in trials based on artificially manipulated bill color. This could suggest that assortative preference is not fixed entirely on bill color and instead may be based on a different trait (e.g., song) or a combination of traits, or alternatively may be due to lower statistical power alongside the bill manipulations being unconvincing to the female choosers. Intriguingly, we find a bias in the inheritance of bill color in captive bred F1 hybrid females. Previous modeling suggests that assortative mate preference and this kind of partial dominance in the underlying genes may together contribute to introgression, making the genetic architecture of bill color in this system a priority for future research.
Collapse
Affiliation(s)
- Callum S. McDiarmid
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Fiona Finch
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Marianne Peso
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Erica van Rooij
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Daniel M. Hooper
- Department of Biological SciencesColumbia UniversityNew YorkNew YorkUSA,Institute for Comparative GenomicsAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - Melissah Rowe
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Simon C. Griffith
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| |
Collapse
|
38
|
|
39
|
Feder JL, Nosil P. Beyond dichotomies in species and speciation. Natl Sci Rev 2023; 9:nwad018. [PMID: 36778105 PMCID: PMC9905644 DOI: 10.1093/nsr/nwad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
|
40
|
Martin CH. Is sympatric speciation in nature only possible with micro-parapatry? A new case study of glacial lake cyprinid fishes. Natl Sci Rev 2023; 9:nwad006. [PMID: 36751304 PMCID: PMC9894001 DOI: 10.1093/nsr/nwad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
|
41
|
Ottenburghs J, Honka J, Heikkinen ME, Madsen J, Müskens GJDM, Ellegren H. Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex. BMC Ecol Evol 2023; 23:2. [PMID: 36658479 PMCID: PMC9854053 DOI: 10.1186/s12862-023-02103-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Reconstructing phylogenetic relationships with genomic data remains a challenging endeavor. Numerous phylogenomic studies have reported incongruent gene trees when analyzing different genomic regions, complicating the search for a 'true' species tree. Some authors have argued that genomic regions of increased divergence (i.e. differentiation islands) reflect the species tree, although other studies have shown that these regions might produce misleading topologies due to species-specific selective sweeps or ancient introgression events. In this study, we tested the extent to which highly differentiated loci can resolve phylogenetic relationships in the Bean Goose complex, a group of goose taxa that includes the Taiga Bean Goose (Anser fabalis), the Tundra Bean Goose (Anser serrirostris) and the Pink-footed Goose (Anser brachyrhynchus). RESULTS First, we show that a random selection of genomic loci-which mainly samples the undifferentiated regions of the genome-results in an unresolved species complex with a monophyletic A. brachyrhynchus embedded within a paraphyletic cluster of A. fabalis and A. serrirostris. Next, phylogenetic analyses of differentiation islands converged upon a topology of three monophyletic clades in which A. brachyrhynchus is sister to A. fabalis, and A. serrirostris is sister to the clade uniting these two species. Close inspection of the locus trees within the differentiated regions revealed that this topology was consistently supported over other phylogenetic arrangements. As it seems unlikely that selection or introgression events have impacted all differentiation islands in the same way, we are convinced that this topology reflects the 'true' species tree. Additional analyses, based on D-statistics, revealed extensive introgression between A. fabalis and A. serrirostris, which partly explains the failure to resolve the species complex with a random selection of genomic loci. Recent introgression between these taxa has probably erased the phylogenetic branching pattern across a large section of the genome, whereas differentiation islands were unaffected by the homogenizing gene flow and maintained the phylogenetic patterns that reflect the species tree. CONCLUSIONS The evolution of the Bean Goose complex can be depicted as a simple bifurcating tree, but this would ignore the impact of introgressive hybridization. Hence, we advocate that the evolutionary relationships between these taxa are best represented as a phylogenetic network.
Collapse
Affiliation(s)
- Jente Ottenburghs
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.
| | - Johanna Honka
- grid.10858.340000 0001 0941 4873Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Marja E. Heikkinen
- grid.10858.340000 0001 0941 4873Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Jesper Madsen
- grid.7048.b0000 0001 1956 2722Department of Ecoscience, Aarhus University, C. F. Møllers Allé 8, 8000 Aarhus C, Denmark
| | - Gerhard J. D. M. Müskens
- grid.4818.50000 0001 0791 5666Team Animal Ecology, Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3-3A, 6708 PB Wageningen, The Netherlands
| | - Hans Ellegren
- grid.8993.b0000 0004 1936 9457Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden
| |
Collapse
|
42
|
Nikelski E, Rubtsov AS, Irwin D. High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression. Heredity (Edinb) 2023; 130:1-13. [PMID: 36463372 PMCID: PMC9814147 DOI: 10.1038/s41437-022-00580-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.
Collapse
Affiliation(s)
- Ellen Nikelski
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada.
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
| | | | - Darren Irwin
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd., University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
43
|
Sun N, Yang L, Tian F, Zeng H, He Z, Zhao K, Wang C, Meng M, Feng C, Fang C, Lv W, Bo J, Tang Y, Gan X, Peng Z, Chen Y, He S. Sympatric or micro-allopatric speciation in a glacial lake? Genomic islands support neither. Natl Sci Rev 2022; 9:nwac291. [PMID: 36778108 PMCID: PMC9905650 DOI: 10.1093/nsr/nwac291] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 12/19/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation. One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence, wherein divergent DNA segments are interspersed with low-divergence segments. Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow. Sympatric divergence of endemic fishes is known from isolated saline, crater, postglacial, and ancient lakes. Two morphologically distinct cyprinid fishes, Gymnocypris eckloni scoliostomus (GS) and G. eckloni eckloni (GE), in a small glacial lake on the Qinghai-Tibet Plateau, Lake Sunmcuo, match the biogeographic criteria of sympatric speciation. In this study, we examined genome-wide variation in 46 individuals from these two groups. The divergence time between the GS and GE lineages was estimated to be 20-60 Kya. We identified 54 large genomic islands (≥100 kb) of speciation, which accounted for 89.4% of the total length of all genomic islands. These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes. Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation, they were too large to support the hypothesis of sympatric speciation. Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands (as small as a few kilobases in size). Thus, the observed pattern is consistent with the extensive evidence on parapatric speciation, in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation. We suggest that many, if not most, of the reported cases of sympatric speciation are likely to be micro-parapatric speciation.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minghui Meng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Chenguang Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China,School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710129, China
| | - Chengchi Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wenqi Lv
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Bo
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongtao Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing 400700, China
| | | | | |
Collapse
|
44
|
Wang X, He Z, Guo Z, Yang M, Xu S, Chen Q, Shao S, Li S, Zhong C, Duke NC, Shi S. Extensive gene flow in secondary sympatry after allopatric speciation. Natl Sci Rev 2022; 9:nwac280. [PMID: 36694801 PMCID: PMC9869077 DOI: 10.1093/nsr/nwac280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/04/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). In an alternative view, species may also be delineated by a small set of 'speciation genes' without full RI, a view that has gained broad acceptance. A recent survey, however, suggested that the extensive literature on 'speciation with gene flow' is mostly (if not all) about exchanges in the early stages of speciation. There is no definitive evidence that the observed gene flow actually happened after speciation is completed. Here, we wish to know whether 'good species' (defined by the 'secondary sympatry' test) do continue to exchange genes and, importantly, under what conditions such exchanges can be observed. De novo whole-genome assembly and re-sequencing of individuals across the range of two closely related mangrove species (Rhizophora mucronata and R. stylosa) reveal the genomes to be well delineated in allopatry. They became sympatric in northeastern Australia but remain distinct species. Nevertheless, their genomes harbor ∼4000-10 000 introgression blocks averaging only about 3-4 Kb. These fine-grained introgressions indicate continual gene flow long after speciation as non-introgressable 'genomic islets,' ∼1.4 Kb in size, often harbor diverging genes of flower or gamete development. The fine-grained introgression in secondary sympatry may help settle the debate about sympatric vs. micro-allopatric speciation. In conclusion, true 'good species' may often continue to exchange genes but the opportunity for detection is highly constrained.
Collapse
Affiliation(s)
| | | | | | - Ming Yang
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA98195, USA
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Shao Shao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Sen Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou510275, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou571100, China
| | - Norman C Duke
- Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, QLD 4811, Australia
| | | |
Collapse
|
45
|
Anderson SAS, López-Fernández H, Weir JT. Ecology and the origin of non-ephemeral species. Am Nat 2022; 201:619-638. [PMID: 37130236 DOI: 10.1086/723763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractResearch over the past three decades has shown that ecology-based extrinsic reproductive barriers can rapidly arise to generate incipient species-but such barriers can also rapidly dissolve when environments change, resulting in incipient species collapse. Understanding the evolution of unconditional, "intrinsic" reproductive barriers is therefore important for understanding the longer-term buildup of biodiversity. In this article, we consider ecology's role in the evolution of intrinsic reproductive isolation. We suggest that this topic has fallen into a gap between disciplines: while evolutionary ecologists have traditionally focused on the rapid evolution of extrinsic isolation between co-occurring ecotypes, speciation geneticists studying intrinsic isolation in other taxa have devoted little attention to the ecological context in which it evolves. We argue that for evolutionary ecology to close this gap, the field will have to expand its focus beyond rapid adaptation and its traditional model systems. Synthesizing data from several subfields, we present circumstantial evidence for and against different forms of ecological adaptation as promoters of intrinsic isolation and discuss alternative forces that may be significant. We conclude by outlining complementary approaches that can better address the role of ecology in the evolution of nonephemeral reproductive barriers and, by extension, less ephemeral species.
Collapse
|
46
|
Harvati K, Reyes-Centeno H. Evolution of Homo in the Middle and Late Pleistocene. J Hum Evol 2022; 173:103279. [PMID: 36375244 PMCID: PMC9703123 DOI: 10.1016/j.jhevol.2022.103279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022]
Abstract
The Middle and Late Pleistocene is arguably the most interesting period in human evolution. This broad period witnessed the evolution of our own lineage, as well as that of our sister taxon, the Neanderthals, and related Denisovans. It is exceptionally rich in both fossil and archaeological remains, and uniquely benefits from insights gained through molecular approaches, such as paleogenetics and paleoproteomics, that are currently not widely applicable in earlier contexts. This wealth of information paints a highly complex picture, often described as 'the Muddle in the Middle,' defying the common adage that 'more evidence is needed' to resolve it. Here we review competing phylogenetic scenarios and the historical and theoretical developments that shaped our approaches to the fossil record, as well as some of the many remaining open questions associated with this period. We propose that advancing our understanding of this critical time requires more than the addition of data and will necessitate a major shift in our conceptual and theoretical framework.
Collapse
Affiliation(s)
- Katerina Harvati
- Paleoanthropology, Institute for Archaeological Sciences and Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Rümelinstrasse 19-23, Tübingen 72070, Germany; DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past', Rümelinstrasse 19-23, Tübingen 72070, Germany.
| | - Hugo Reyes-Centeno
- Department of Anthropology, University of Kentucky, 211 Lafferty Hall, Lexington, KY 40506, USA; William S. Webb Museum of Anthropology, University of Kentucky, 1020 Export St, Lexington, KY 40504, USA
| |
Collapse
|
47
|
Johnson NA. Speciation: genomic sequence data and the biogeography of speciation. Natl Sci Rev 2022; 9:nwac294. [PMID: 36751303 PMCID: PMC9893999 DOI: 10.1093/nsr/nwac294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
|
48
|
Mallet J, Mullen SP. Reproductive isolation is a heuristic, not a measure: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1175-1182. [PMID: 36063161 DOI: 10.1111/jeb.14052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/17/2022]
Abstract
Reproductive isolation is the heuristic basis of the biological species concept, but what is it? Westram et al. (this issue) propose that it is a measurable quantity, "barrier strength," that prevents gene flow among populations. However, their attempt to make the concept of reproductive isolation more scientific is unlikely to satisfy the diverse opinions of all evolutionary biologists. There are many different opinions about the nature of species, even under the biological species concept. Complete reproductive isolation, where gene flow is effectively zero, is regarded by some biologists as an important end point of speciation. Others, including Westram et al., argue for a more nuanced approach, and they also suggest that reproductive isolation may differ in different parts of the genome due to variation in genetic linkage to divergently selected loci. In contrast to both these approaches, we favour as a key criterion of speciation the stable coexistence of divergent populations in sympatry. Obviously, such populations must be reproductively isolated in some sense, but neither the fraction of the genome that is exchanged, nor measures of overall barrier strength acting on neutral variation will yield very precise predictions as to species status. Although an overall measure of reproductive isolation is virtually unattainable for these reasons, its early generation components, such as assortative mating, divergent selection, or hybrid inviability and sterility are readily measurable and remain informative. For example, we can make the prediction that to remain divergent in sympatry, almost all sexual species will require strong assortative mating, as well as some sort of ecological or intrinsic selection against hybrids and introgressed variants.
Collapse
Affiliation(s)
- James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sean P Mullen
- Department of Biology, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
49
|
Genomic architecture of adaptive radiation and hybridization in Alpine whitefish. Nat Commun 2022; 13:4479. [PMID: 35918341 PMCID: PMC9345977 DOI: 10.1038/s41467-022-32181-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Adaptive radiations represent some of the most remarkable explosions of diversification across the tree of life. However, the constraints to rapid diversification and how they are sometimes overcome, particularly the relative roles of genetic architecture and hybridization, remain unclear. Here, we address these questions in the Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals of each of the 22 species belonging to six ecologically distinct ecomorph classes across several lake-systems. We reveal that repeated ecological and morphological diversification along a common environmental axis is associated with both genome-wide allele frequency shifts and a specific, larger effect, locus, associated with the gene edar. Additionally, we highlight the possible role of introgression between species from different lake-systems in facilitating the evolution and persistence of species with unique trait combinations and ecology. These results highlight the importance of both genome architecture and secondary contact with hybridization in fuelling adaptive radiation. In this genomic study on Alpine whitefish radiations, the authors reveal details on the genetic architecture underlying the repeated eco-morphological diversification and the role of hybridization in the evolution of endemic whitefish species.
Collapse
|
50
|
Boza Espinoza TE, Kessler M. A monograph of the genus Polylepis (Rosaceae). PHYTOKEYS 2022; 203:1-274. [PMID: 36761034 PMCID: PMC9849045 DOI: 10.3897/phytokeys.203.83529] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
We present a monograph of the high Andean tree genus Polylepis (Rosaceae), based on a species concept considering morphological, climatic and biogeographic distinctness as indicators of evolutionary independence. In total, we recognize 45 species of Polylepis, grouped in five sections. Polylepissect.Sericeae is represented by 15 species in four subsections, P.sect.Reticulatae by seven species, P.sect.Subsericantes by three species, P.sect.Australes by two species and P.sect.Incanaee by three subsections with 18 species. We describe seven new species, one from Colombia (P.frontinensis), one from Ecuador (P.simpsoniae) and five from Peru (P.acomayensis, P.fjeldsaoi, P.occidentalis, P.pilosissima and P.sacra). Three species from Peru (P.albicans, P.pallidistigma and P.serrata) are re-instated as valid species. Two taxa from Bolivia (P.incanoides and P.nana) are elevated from subspecies to species rank. The morphology, habitat, distribution, ecology and conservation status of each species are documented. We also provide an identification key to the species of the genus and general introductions on taxonomic history, morphology, evolution, ecology and conservation.
Collapse
Affiliation(s)
- Tatiana Erika Boza Espinoza
- Institute for Nature, Earth and Energy (INTE), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, Lima 15088, PeruPontificia Universidad Católica del Perú (PUCP)LimaPeru
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, SwitzerlandUniversity of ZurichZürichSwitzerland
| |
Collapse
|