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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.
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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.
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2
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Lizana P, Mutis A, Palma-Millanao R, González-González A, Ceballos R, Quiroz A, Bardehle L, Hidalgo A, Torres F, Romero-López A, Venthur H. Comparative transcriptomic analysis of chemoreceptors in two sympatric scarab beetles, Hylamorpha elegans and Brachysternus prasinus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 49:101174. [PMID: 38096641 DOI: 10.1016/j.cbd.2023.101174] [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: 07/05/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 02/15/2024]
Abstract
Chemoreception through odorant receptors (ORs), ionotropic receptors (IRs) and gustatory receptors (GRs) represents the functions of key proteins in the chemical ecology of insects. Recent studies have identified chemoreceptors in coleopterans, facilitating the evolutionary analysis of not only ORs but also IRs and GRs. Thus, Cerambycidae, Tenebrionidae and Curculionidae have received increased attention. However, knowledge of the chemoreceptors from Scarabaeidae is still limited, particularly for those that are sympatric. Considering the roles of chemoreceptors, this analysis could shed light on evolutionary processes in the context of sympatry. Therefore, the aim of this study was to identify and compare the repertoires of ORs, GRs and IRs between two sympatric scarab beetles, Hylamorpha elegans and Brachysternus prasinus. Here, construction of the antennal transcriptomes of both scarab beetle species and analyses of their phylogeny, molecular evolution and relative expression were performed. Thus, 119 new candidate chemoreceptors were identified for the first time, including 17 transcripts for B. prasinus (1 GR, 3 IRs and 13 ORs) and 102 for H. elegans (22 GRs, 14 IRs and 66 ORs). Orthologs between the two scarab beetle species were found, revealing specific expansions as well as absence in some clades. Purifying selection appears to have occurred on H. elegans and B. prasinus ORs. Further efforts will be focused on target identification to characterize kairomone and/or pheromone receptors.
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Affiliation(s)
- Paula Lizana
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile; Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile
| | - Ana Mutis
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile; Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Temuco, Chile
| | - Rubén Palma-Millanao
- Vicerrectoría de Investigación y Postgrado, Universidad de La Frontera, Temuco, Chile
| | - Angélica González-González
- Laboratorio de Interacciones Insecto-Planta, Instituto de Ciencias Biológicas, Universidad de Talca, Casilla 747, Talca, Chile
| | - Ricardo Ceballos
- Laboratorio de Ecología Química, Centro Tecnológico de Control Biológico, Instituto de Investigaciones Agropecuarias (INIA)-Quilamapu, Chillán, Chile
| | - Andrés Quiroz
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile; Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Temuco, Chile
| | - Leonardo Bardehle
- Departamento de Producción Agropecuaria, Facultad de Ciencias Agropecuarias y Forestales, Universidad de La Frontera, Temuco, Chile
| | - Alejandro Hidalgo
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Fernanda Torres
- Carrera de Química y Farmacia, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Angel Romero-López
- Laboratorio de Infoquímicos y Otros Productos Bióticos, Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Mexico
| | - Herbert Venthur
- Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Temuco, Chile; Centro de Investigación Biotecnológica Aplicada al Medio Ambiente (CIBAMA), Universidad de La Frontera, Temuco, Chile.
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3
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Mu W, Li K, Yang Y, Breiman A, Lou S, Yang J, Wu Y, Wu S, Liu J, Nevo E, Catalan P. Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei. Proc Natl Acad Sci U S A 2023; 120:e2304848120. [PMID: 37903254 PMCID: PMC10636366 DOI: 10.1073/pnas.2304848120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/27/2023] [Indexed: 11/01/2023] Open
Abstract
Ecological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains a captivating topic in evolutionary biology. However, the pattern of genetic divergence underlying this process across the genome may vary between species and mating systems. Here, we present evidence that Brachypodium stacei, an annual and highly selfing grass model species, has undergone sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses together with lab experiments mimicking the two opposite environmental conditions suggest that diploid B. stacei populations have diverged sympatrically in two slopes characterized by distinct biomes at Evolution Canyon I (ECI), Mount Carmel, Israel. Despite ongoing gene flow, primarily facilitated by seed dispersal, the level of gene flow has progressively decreased over time. This local adaptation involves the scattered divergence of many unlinked loci across the total genome that include both coding genes and noncoding regions. Additionally, we have identified significant differential expressions of genes related to the ABA signaling pathway and contrasting metabolome composition between the arid- vs. forest-adapted B. stacei populations in ECI. These results suggest that multiple small loci involved in environmental responses act additively to account for ecological adaptations by this selfing species in contrasting environments.
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Affiliation(s)
- Wenjie Mu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou730000, China
- Departamento de Agricultura y Medio Ambiente, Escuela Politecnica Superior de Huesca, Universidad de Zaragoza, Huesca22071, Spain
| | - Kexin Li
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Adina Breiman
- Department of Molecular Biology and Ecology of Plants, Faculty of Life Sciences, University of Tel-Aviv, Tel-Aviv6997801, Israel
| | - Shangling Lou
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jiao Yang
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Ying Wu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Shuang Wu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou730000, China
| | - Eviatar Nevo
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Mount Carmel, Haifa3498838, Israel
| | - Pilar Catalan
- Departamento de Agricultura y Medio Ambiente, Escuela Politecnica Superior de Huesca, Universidad de Zaragoza, Huesca22071, Spain
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Gayford JH, Whitehead DA. The biology and ecology of the Pacific sharpnose shark Rhizoprionodon longurio. Ecol Evol 2023; 13:e10600. [PMID: 37829178 PMCID: PMC10565905 DOI: 10.1002/ece3.10600] [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: 06/26/2023] [Revised: 09/04/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
Amidst global declines in elasmobranch populations resulting predominantly from overfishing, the need to gather data regarding shark ecology is greater than ever. Many species remain data deficient or at risk of going extinct before sufficient conservation measures can be applied. In this review, we summarise existing knowledge regarding the biology and ecology of the Pacific sharpnose shark Rhizoprionodon longurio (Jordan & Hilbert, 1882), a small-bodied carcharhinid shark found in coastal waters of the Eastern Tropical Pacific Ocean that is of both commercial and ecological importance. We compare ecological parameters of this species with its closest extant relatives and identify major knowledge gaps and avenues for future research. In particular, additional studies investigating the behavioural and sensory ecology, as well as potential migratory patterns of the species are needed. Such studies will not only improve our understanding of R. longurio, but provide insight into the extent to which the numerous studies performed on a close relative-Rhizoprionodon terraenovae-provide an accurate representation of the biology and ecology of Rhizoprionodon and carcharhinids more generally.
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Affiliation(s)
- Joel H. Gayford
- Department of Life SciencesSilwood Park Campus, Imperial College LondonLondonUK
- Shark MeasurementsLondonUK
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5
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Yamahira K, Kobayashi H, Kakioka R, Montenegro J, Masengi KWA, Okuda N, Nagano AJ, Tanaka R, Naruse K, Tatsumoto S, Go Y, Ansai S, Kusumi J. Ghost introgression in ricefishes of the genus Adrianichthys in an ancient Wallacean lake. J Evol Biol 2023; 36:1484-1493. [PMID: 37737547 DOI: 10.1111/jeb.14223] [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: 05/11/2023] [Revised: 07/06/2023] [Accepted: 08/01/2023] [Indexed: 09/23/2023]
Abstract
Because speciation might have been promoted by ancient introgression from an extinct lineage, it is important to detect the existence of 'ghost introgression' in focal taxa and examine its contribution to their diversification. In this study, we examined possible ghost introgression and its contributions to the diversification of ricefishes of the genus Adrianichthys in Lake Poso, an ancient lake on Sulawesi Island, in which some extinctions are known to have occurred. Population-genomic analysis revealed that two extant Adrianichthys species, A. oophorus and A. poptae are reproductively isolated from each other. Comparisons of demographic models demonstrated that introgression from a ghost population, which diverged from the common ancestor of A. oophorus and A. poptae, is essential for reconstructing the demographic history of Adrianichthys. The best model estimated that the divergence of the ghost population greatly predated the divergence between A. oophorus and A. poptae, and that the ghost population secondarily contacted the two extant species within Lake Poso more recently. Genome scans and simulations detected a greatly divergent locus, which cannot be explained without ghost introgression. This locus was also completely segregated between A. oophorus and A. poptae. These findings suggest that variants that came from a ghost population have contributed to the divergence between A. oophorus and A. poptae, but the large time-lag between their divergence and ghost introgression indicates that the contribution of introgression may be restricted.
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Affiliation(s)
- Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | | | - Noboru Okuda
- Research Center for Inland Seas, Kobe University, Kobe, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Japan
| | - Shoji Tatsumoto
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
| | - Yasuhiro Go
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
- Department of System Neuroscience, Division of Behavioral Development, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama, Japan
| | - Satoshi Ansai
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
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6
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Ruskie EL, Zakas C. Assortative mating and mate-choice contributes to the maintenance of a developmental dimorphism in Streblospio benedicti. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:424-430. [PMID: 37158462 PMCID: PMC10525012 DOI: 10.1002/jez.b.23196] [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: 03/31/2023] [Revised: 04/13/2023] [Accepted: 04/23/2023] [Indexed: 05/10/2023]
Abstract
Assortative mating, where individuals non-randomly mate with respect to phenotype or genotype, can occur when preferences between potential mates have evolved. When such mate preferences occur in a population it can drive evolutionary and phenotypic divergence. But the extent to which assortative mating, mate preference, and development are evolutionarily linked remains unclear. Here we use Streblospio benedicti, a marine annelid with a rare developmental dimorphism, to investigate if mate-choice could contribute to developmental evolution. For S. benedicti two types of ecologically and phenotypically similar adults persist in natural populations, but they give rise to distinctly different offspring with alternative life-histories. This dimorphism persists despite the absence of post-zygotic reproductive barriers, where crosses between the developmental types can produce phenotypically intermediate offspring. How this life-history strategy evolved remains unknown, but assortative mating is a typical first step in evolutionary divergence. Here we investigate if female mate-choice is occurring in this species. We find that mate preferences could be contributing to the maintenance of alternative developmental and life-history strategies.
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Affiliation(s)
- Erika L. Ruskie
- North Carolina State University, Department of Biological Sciences, Raleigh, North Carolina, 27607
| | - Christina Zakas
- North Carolina State University, Department of Biological Sciences, Raleigh, North Carolina, 27607
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Chang J, Nakamura K, Chao C, Luo M, Liao P. Ghost introgression facilitates genomic divergence of a sympatric cryptic lineage in Cycas revoluta. Ecol Evol 2023; 13:e10435. [PMID: 37600490 PMCID: PMC10439367 DOI: 10.1002/ece3.10435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023] Open
Abstract
A cryptic lineage is a genetically diverged but morphologically unrecognized variant of a known species. Clarifying cryptic lineage evolution is essential for quantifying species diversity. In sympatric cryptic lineage divergence compared with allopatric divergence, the forces of divergent selection and mating patterns override geographical isolation. Introgression, by supplying preadapted or neutral standing genetic variations, can promote sympatric cryptic lineage divergence via selection. However, most studies concentrated on extant species introgression, ignoring the genetic legacy of introgression from extinct or unsampled lineages ("ghost introgression"). Cycads are an ideal plant for studying the influence of ghost introgression because of their common interspecific gene flow and past high extinction rate. Here, we utilized reference-based ddRADseq to clarify the role of ghost introgression in the evolution of a previously identified sympatric cryptic lineage in Cycas revoluta. After re-evaluating the evolutionary independency of cryptic lineages, the group-wise diverged single-nucleotide polymorphisms among sympatric and allopatric lineages were compared and functionally annotated. Next, we employed an approximate Bayesian computation method for hypothesis testing to clarify the cryptic lineage evolution and ghost introgression effect. SNPs with the genomic signatures of ghost introgression were further annotated. Our results reconfirmed the evolutionary independency of cryptic lineage among C. revoluta and demonstrated that ghost introgression to the noncryptic lineage facilitated their divergence. Gene function related to heat stress and disease resistance implied ecological adaptation of the main extant populations of C. revoluta.
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Affiliation(s)
- Jui‐Tse Chang
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern BiosphereHokkaido UniversitySapporoJapan
| | - Chien‐Ti Chao
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Min‐Xin Luo
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
| | - Pei‐Chun Liao
- School of Life ScienceNational Taiwan Normal UniversityTaipeiTaiwan
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Mandagi IF, K A Sumarto B, Nuryadi H, Mokodongan DF, Lawelle SA, W A Masengi K, Nagano AJ, Kakioka R, Kitano J, Ansai S, Kusumi J, Yamahira K. Multiple colonizations and hybridization of a freshwater fish group on a satellite island of Sulawesi. Mol Phylogenet Evol 2023; 184:107804. [PMID: 37120113 DOI: 10.1016/j.ympev.2023.107804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/27/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Repeated colonizations and resultant hybridization may increase lineage diversity on an island if introgression occurs only in a portion of the indigenous island lineage. Therefore, to precisely understand how island biodiversity was shaped, it is essential to reconstruct the history of secondary colonization and resultant hybridization both in time and space. In this study, we reconstructed the history of multiple colonizations of the Oryzias woworae species group, a freshwater fish group of the family Adrianichthyidae, from Sulawesi Island to its southeast satellite island, Muna Island. Phylogenetic and species tree analyses using genome-wide single-nucleotide polymorphisms revealed that all local populations on Muna Island were monophyletic, but that there were several genetically distinct lineages within the island. Population structure and phylogenetic network analyses demonstrated that colonization of this island occurred more than once, and that secondary colonization and resultant introgressive hybridization occurred only in one local population on the island. The spatially heterogeneous introgression induced by the multiple colonizations were also supported by differential admixture analyses. In addition, the differential admixture analyses detected reverse colonization from Muna Island to the Sulawesi mainland. Coalescence-based demographic inference estimated that these mutual colonizations occurred during the middle to late Quaternary period, during which sea level repeatedly declined; this indicates that the colonizations occurred via land bridges. We conclude that these mutual colonizations between Muna Island and the Sulawesi mainland, and the resultant spatially heterogeneous introgression shaped the current biodiversity of this species group in this area.
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Affiliation(s)
- Ixchel F Mandagi
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado 95115, Indonesia.
| | - Bayu K A Sumarto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
| | - Handung Nuryadi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
| | - Daniel F Mokodongan
- Museum Zoologicum Bogoriense, Research Center for Biology, National Research and Innovation Agency, Cibinong 16911, Indonesia.
| | - Sjamsu A Lawelle
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia.
| | - Kawilarang W A Masengi
- Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado 95115, Indonesia.
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan.
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan.
| | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka 819-0395, Japan.
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan.
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9
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de Albuquerque NRM, Haag KL. Using average nucleotide identity (ANI) to evaluate microsporidia species boundaries based on their genetic relatedness. J Eukaryot Microbiol 2023; 70:e12944. [PMID: 36039868 DOI: 10.1111/jeu.12944] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/28/2022]
Abstract
Microsporidia are obligatory intracellular parasites related to fungi and since their discovery their classification and origin has been controversial due to their unique morphology. Early taxonomic studies of microsporidia were based on ultrastructural spore features, characteristics of their life cycle and transmission modes. However, taxonomy and phylogeny based solely on these characteristics can be misleading. SSU rRNA is a traditional marker used in taxonomical classifications, but the power of SSU rRNA to resolve phylogenetic relationships between microsporidia is considered weak at the species level, as it may not show enough variation to distinguish closely related species. Overall genome relatedness indices (OGRI), such as average nucleotide identity (ANI), allows fast and easy-to-implement comparative measurements between genomes to assess species boundaries in prokaryotes, with a 95% cutoff value for grouping genomes of the same species. Due to the increasing availability of complete genomes, metrics of genome relatedness have been applied for eukaryotic microbes taxonomy such as microsporidia. However, the distribution of ANI values and cutoff values for species delimitation have not yet been fully tested in microsporidia. In this study we examined the distribution of ANI values for 65 publicly available microsporidian genomes and tested whether the 95% cutoff value is a good estimation for circumscribing species based on their genetic relatedness.
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Affiliation(s)
- Nathalia R M de Albuquerque
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Karen L Haag
- Department of Genetics and Post-Graduation Program of Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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Briševac D, Peralta CM, Kaiser TS. An oligogenic architecture underlying ecological and reproductive divergence in sympatric populations. eLife 2023; 12:82825. [PMID: 36852479 PMCID: PMC9977317 DOI: 10.7554/elife.82825] [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: 08/18/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
The evolutionary trajectories and genetic architectures underlying ecological divergence with gene flow are poorly understood. Sympatric timing types of the intertidal insect Clunio marinus (Diptera) from Roscoff (France) differ in lunar reproductive timing. One type reproduces at full moon, the other at new moon, controlled by a circalunar clock of yet unknown molecular nature. Lunar reproductive timing is a magic trait for a sympatric speciation process, as it is both ecologically relevant and entails assortative mating. Here, we show that the difference in reproductive timing is controlled by at least four quantitative trait loci (QTL) on three different chromosomes. They are partly associated with complex inversions, but differentiation of the inversion haplotypes cannot explain the different phenotypes. The most differentiated locus in the entire genome, with QTL support, is the period locus, implying that this gene could not only be involved in circadian timing but also in lunar timing. Our data indicate that magic traits can be based on an oligogenic architecture and can be maintained by selection on several unlinked loci.
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Affiliation(s)
- Dušica Briševac
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary BiologyPloenGermany
| | - Carolina M Peralta
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary BiologyPloenGermany
| | - Tobias S Kaiser
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary BiologyPloenGermany
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11
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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
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12
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Estivals G, Duponchelle F, García-Dávila C, Römer U, Mariac C, Renno JF. Exceptional Genetic Differentiation at a Micro-geographic Scale in Apistogramma agassizii (Steindachner, 1875) from the Peruvian Amazon: Sympatric Speciation? Evol Biol 2022. [DOI: 10.1007/s11692-022-09587-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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13
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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
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14
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Galvez JR, St John ME, McLean K, Touokong CD, Gonwouo LN, Martin CH. Trophic specialization on unique resources despite limited niche divergence in a celebrated example of sympatric speciation. ECOLOGY OF FRESHWATER FISH 2022; 31:675-692. [PMID: 36211622 PMCID: PMC9542214 DOI: 10.1111/eff.12661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 04/02/2022] [Indexed: 06/16/2023]
Abstract
Trophic niche partitioning is observed in many adaptive radiations and is hypothesized to be a central process underlying species divergence. However, patterns of dietary niche partitioning are inconsistent across radiations and there are few studies of niche partitioning in putative examples of sympatric speciation. Here, we conducted the first quantitative study of dietary niche partitioning using stomach contents and stable isotope analyses in one of the most celebrated examples of sympatric speciation: the cichlid radiation from crater lake Barombi Mbo, Cameroon. We found little evidence for trophic niche partitioning among cichlids, including the nine species coexisting in the narrow littoral zone. Stable isotope analyses supported these conclusions of substantial dietary overlap. Our data, however, did reveal that five of eleven species consume rare dietary items, including freshwater sponge, terrestrial ants, and nocturnal foraging on shrimp. Stomach contents of the spongivore (Pungu maclareni) were 20% freshwater sponge, notable considering that only 0.04% of all fishes consume sponges. Overall, we conclude that cichlid species in lake Barombi Mbo overlap considerably in broad dietary niches-in part due to the large proportion of detritus in the stomach contents of all species-but there is evidence for divergence among species in their diet specializations on unique resources. We speculate that these species may utilize these additional specialized resources during periods of low resource abundance in support of Liem's paradox.
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Affiliation(s)
- Jacquelyn R Galvez
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Michelle E St John
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
| | - Keara McLean
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Legrand Nono Gonwouo
- Laboratory of Zoology, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | - Christopher H Martin
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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15
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Moyle LC. Forty-two, and other precise answers to difficult questions: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1183-1187. [PMID: 36063157 DOI: 10.1111/jeb.14037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 01/04/2023]
Affiliation(s)
- Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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16
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Wang Z, Cai X, Jiang X, Xia Q, Li L, Lu B. Sympatric genetic divergence between early- and late-season weedy rice populations. THE NEW PHYTOLOGIST 2022; 235:2066-2080. [PMID: 35637631 PMCID: PMC9544748 DOI: 10.1111/nph.18288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Sympatric genetic divergence is the most appealing and controversial pattern in the theory of ecological speciation. Examples that support sympatric genetic divergence in plant species are extremely rare. Solid evidence of sympatric genetic divergence will provide deep insights for revealing the underlying mechanisms of ecological speciation. We analysed the total genomic DNA sequences of 120 weedy rice (WR; Oryza sativa f. spontanea) plants, representing three WR population pairs separately from three early- and late-season rice fields, in comparison with those of the co-occurring rice cultivars and other rice materials. We detected substantial genetic divergence within the pairs of the sympatric early- and late-season WR populations, although genetic divergence was unevenly distributed across the genomes. Restricted gene flow was determined between the sympatric WR populations, resulting in their distinct genetic structures. We also detected relatively low genetic diversity that was likely to be associated with stronger selection in early-season WR populations. Our findings provide strong evidence for sympatric genetic divergence between the WR populations in the same fields but in different seasons. We conclude that temporal isolation plays an important role in creating genetic divergence between sympatric populations/species in plants.
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Affiliation(s)
- Zhi Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Xingxing Cai
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Xiao‐Qi Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Qi‐Yu Xia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction RegionsInstitute of Tropical Bioscience and Biotechnology, CATASHaikou571101China
| | - Lin‐Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
| | - Bao‐Rong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary BiologyFudan UniversitySonghu Road 2005Shanghai200438China
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17
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Bereczki J, Sielezniew M, Verovnik R, Beshkov S, Kuznetsov G, Bonelli S, Tóth JP. Phylogeography reveals the origin of the two phenological forms of large blue, Phengaris arion (Lepidoptera: Lycaenidae). Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Our main goal was to investigate the phylogeography of the butterfly Phengaris arion to reveal the evolutionary origin of its ‘spring’ and ‘summer’ forms. Molecular analyses based on highly variable microsatellites, together with Wolbachia screening, were carried out on 34 populations in Europe. We found three well-defined genetic lineages of different origins: the Apennine, the central and the eastern. The highly distinct Apennine lineage is limited by the Alps and evaluated as an Evolutionary Significant Unit (ESU). Therefore, the taxon name ligurica, described from the Ligurian coast (Italy), should not be applied to denote the ‘summer form’ of the Pannonian region. The central lineage is limited by the Carpathians and the most eastern ranges of the Alps, and lacks major range fluctuations related to glaciations, although there is evidence for extra-Mediterranean refugia in the Carpathian Basin. The eastern clade could have had refugia in central Asia. Our results exclude the potential allopatric origin of the ‘spring’ and ‘summer’ arion, and support the hypothesis that the existence of the two forms could be a result of local adaptation to the distinctive phenology of host plant flowering which is manifested in the genetic differences between them. Wolbachia infection has been ruled out as a driver of sympatric speciation in P. arion.
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Affiliation(s)
- Judit Bereczki
- Molecular Taxonomy Laboratory, Hungarian Natural History Museum , Budapest , Hungary
| | - Marcin Sielezniew
- Laboratory of Insect Evolutionary Biology and Ecology, Institute of Biology, University of Bialystok , Białystok , Poland
| | - Rudi Verovnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana , Ljubljana , Slovenia
| | - Stoyan Beshkov
- National Museum of Natural History, Bulgarian Academy of Sciences , Sofia , Bulgaria
| | - Gennadij Kuznetsov
- Independent researcher , Volgograd , Russia , http://babochki-kavkaza.ru
| | - Simona Bonelli
- Department of Life Sciences and Systems Biology, University of Turin , Turin , Italy
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18
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Nofrianto AB, Lawelle SA, Mokodongan DF, Masengi KWA, Inomata N, Hashiguchi Y, Kitano J, Sumarto BKA, Kakioka R, Yamahira K. Ancient Admixture in Freshwater Halfbeaks of the Genus Nomorhamphus in Southeast Sulawesi. Zoolog Sci 2022; 39:453-458. [DOI: 10.2108/zs220023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022]
Affiliation(s)
- Andy B. Nofrianto
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia
| | - Sjamsu A. Lawelle
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia
| | - Daniel F. Mokodongan
- Faculty of Fisheries and Marine Science, Halu Oleo University, Kendari 93232, Indonesia
| | | | - Nobuyuki Inomata
- Department of Environmental Science, Fukuoka Women's University, Fukuoka 813-8529, Japan
| | - Yasuyuki Hashiguchi
- Department of Biology, Osaka Medical and Pharmaceutical University, Osaka 569-8686, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Bayu K. A. Sumarto
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
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19
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Maltseva AL, Lobov AA, Pavlova PA, Panova M, Gafarova ER, Marques JP, Danilov LG, Granovitch AI. Orphan gene in Littorina: An unexpected role of symbionts in the host evolution. Gene 2022; 824:146389. [PMID: 35257790 DOI: 10.1016/j.gene.2022.146389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/29/2022] [Accepted: 02/28/2022] [Indexed: 11/16/2022]
Abstract
Mechanisms of reproductive isolation between closely related sympatric species are of high evolutionary significance as they may function as initial drivers of speciation and protect species integrity afterwards. Proteins involved in the establishment of reproductive barriers often evolve fast and may be key players in cessation of gene flow between the incipient species. The five Atlantic Littorina (Neritrema) species represent a notable example of recent radiation. The geographic ranges of these young species largely overlap and the mechanisms of reproductive isolation are poorly understood. In this study, we performed a detailed analysis of the reproductive protein LOSP, previously identified in Littorina. We showed that this protein is evolutionary young and taxonomically restricted to the genus Littorina. It has high sequence variation both within and between Littorina species, which is compatible with its presumable role in the reproductive isolation. The strongest differences in the LOSP structure were detected between Littorina subgenera with distinctive repetitive motifs present exclusively in the Neritrema species, but not in L. littorea. Moreover, the sequence of these repetitive structural elements demonstrates a high homology with genetic elements of bacteria, identified as components of Littorina associated microbiomes. We suggest that these elements were acquired from a symbiotic bacterial donor via horizontal genetic transfer (HGT), which is indirectly confirmed by the presence of multiple transposable elements in the LOSP flanking and intronic regions. Furthermore, we hypothesize that this HGT-driven evolutionary innovation promoted LOSP function in reproductive isolation, which might be one of the factors determining the intensive cladogenesis in the Littorina (Neritrema) lineage in contrast to the anagenesis in the L. littorea clade.
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Affiliation(s)
- A L Maltseva
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.
| | - A A Lobov
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St Petersburg, Russia
| | - P A Pavlova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - M Panova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia; Department of Marine Sciences - Tjärnö, University of Gothenburg, Sweden
| | - E R Gafarova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - J P Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências do Porto, 4169-007 Porto, Portugal; ISEM, Univ Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
| | - L G Danilov
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia
| | - A I Granovitch
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
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20
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Fernández-Meirama M, Rolán-Alvarez E, Carvajal-Rodríguez A. A Simulation Study of the Ecological Speciation Conditions in the Galician Marine Snail Littorina saxatilis. Front Genet 2022; 13:680792. [PMID: 35480312 PMCID: PMC9037070 DOI: 10.3389/fgene.2022.680792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
In the last years, the interest in evolutionary divergence at small spatial scales has increased and so did the study of speciation caused by ecologically based divergent natural selection. The evolutionary interplay between gene flow and local adaptation can lead to low-dispersal locally adapted specialists. When this occurs, the evolutionary interplay between gene flow and local adaptation could eventually lead to speciation. The L. saxatilis system consists of two ecotypes displaying a microhabitat-associated intraspecific dimorphism along the wave-exposed rocky shores of Galicia. Despite being a well-known system, the dynamics of the ecotype formation remain unclear and cannot be studied from empirical evidence alone. In this study, individual-based simulations were used to incorporate relevant ecological, spatial, and genetic information, to check different evolutionary scenarios that could evolve non-random mating preferences and finally may facilitate speciation. As main results, we observed the evolution of intermediate values of choice which matches the estimates from empirical data of L. saxatilis in Galician shores and coincides with previous theoretical outcomes. Also, the use of the mating correlation as a proxy for assortative mating led to spuriously inferring greater reproductive isolation in the middle habitat than in the others, which does not happen when directly considering the choice values from the simulations. We also corroborate the well-known fact that the occurrence of speciation is influenced by the strength of selection. Taken together, this means, also according to other L. saxatilis systems, that speciation is not an immediate consequence of local divergent selection and mating preferences, but a fine tuning among several factors including the ecological conditions in the shore levels, the selection strength, the mate choice stringency, and cost to choosiness. The L. saxatilis system could correspond to a case of incomplete reproductive isolation, where the choice intensity is intermediate and local adaptation within the habitat is strong. These results support previous interpretations of the L. saxatilis model system and indicate that further empirical studies would be interesting to test whether the mate choice mechanism functions as a similarity-like mechanism as has been shown in other littorinids.
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Affiliation(s)
- M Fernández-Meirama
- Departamento de Bioquímica, Genética e Inmunología and Centro de Investigación Mariña (CIM), Universidade de Vigo, Vigo, Spain
| | - E Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología and Centro de Investigación Mariña (CIM), Universidade de Vigo, Vigo, Spain
| | - A Carvajal-Rodríguez
- Departamento de Bioquímica, Genética e Inmunología and Centro de Investigación Mariña (CIM), Universidade de Vigo, Vigo, Spain
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21
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David JR, Ferreira EA, Jabaud L, Ogereau D, Bastide H, Yassin A. Evolution of assortative mating following selective introgression of pigmentation genes between two
Drosophila
species. Ecol Evol 2022; 12:e8821. [PMID: 35432924 PMCID: PMC9006235 DOI: 10.1002/ece3.8821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/03/2022] Open
Abstract
Adaptive introgression is ubiquitous in animals, but experimental support for its role in driving speciation remains scarce. In the absence of conscious selection, admixed laboratory strains of Drosophila asymmetrically and progressively lose alleles from one parental species and reproductive isolation against the predominant parent ceases after 10 generations. Here, we selectively introgressed during 1 year light pigmentation genes of D. santomea into the genome of its dark sibling D. yakuba, and vice versa. We found that the pace of phenotypic change differed between the species and the sexes and identified through genome sequencing common as well as distinct introgressed loci in each species. Mating assays showed that assortative mating between introgressed flies and both parental species persisted even after 4 years (~60 generations) from the end of the selection. Those results indicate that selective introgression of as low as 0.5% of the genome can beget morphologically distinct and reproductively isolated strains, two prerequisites for the delimitation of new species. Our findings hence represent a significant step toward understanding the genome‐wide dynamics of speciation‐through‐introgression.
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Affiliation(s)
- Jean R. David
- Laboratoire Évolution, Génomes, Comportement et Écologie CNRS IRD Université Paris‐Saclay – Institut Diversité Ecologie et Evolution du Vivant (IDEEV) Gif‐sur‐Yvette France
| | - Erina A. Ferreira
- Laboratoire Évolution, Génomes, Comportement et Écologie CNRS IRD Université Paris‐Saclay – Institut Diversité Ecologie et Evolution du Vivant (IDEEV) Gif‐sur‐Yvette France
| | - Laure Jabaud
- Laboratoire Évolution, Génomes, Comportement et Écologie CNRS IRD Université Paris‐Saclay – Institut Diversité Ecologie et Evolution du Vivant (IDEEV) Gif‐sur‐Yvette France
| | - David Ogereau
- Laboratoire Évolution, Génomes, Comportement et Écologie CNRS IRD Université Paris‐Saclay – Institut Diversité Ecologie et Evolution du Vivant (IDEEV) Gif‐sur‐Yvette France
| | - Héloïse Bastide
- Laboratoire Évolution, Génomes, Comportement et Écologie CNRS IRD Université Paris‐Saclay – Institut Diversité Ecologie et Evolution du Vivant (IDEEV) Gif‐sur‐Yvette France
| | - Amir Yassin
- Laboratoire Évolution, Génomes, Comportement et Écologie CNRS IRD Université Paris‐Saclay – Institut Diversité Ecologie et Evolution du Vivant (IDEEV) Gif‐sur‐Yvette France
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22
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Mandagi IF, Kakioka R, Montenegro J, Kobayashi H, Masengi KWA, Inomata N, Nagano AJ, Toyoda A, Ansai S, Matsunami M, Kimura R, Kitano J, Kusumi J, Yamahira K. Species divergence and repeated ancient hybridization in a Sulawesian lake system. J Evol Biol 2021; 34:1767-1780. [PMID: 34532915 DOI: 10.1111/jeb.13932] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 09/09/2021] [Indexed: 01/02/2023]
Abstract
An increasing volume of empirical studies demonstrated that hybridization between distant lineages may have promoted speciation in various taxa. However, the timing, extent and direction of introgressive hybridization remain unknown in many cases. Here, we report a possible case in which repeated hybridization promoted divergence of Oryzias ricefishes (Adrianichthyidae) on Sulawesi, an island of Wallacea. Four Oryzias species are endemic to the Malili Lake system in central Sulawesi, which is composed of five tectonic lakes; of these, one lake is inhabited by two species. Morphological and population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that these two sympatric species are phylogenetically sister to but substantially reproductively isolated from each other. Analyses of admixture and comparison of demographic models revealed that the two sympatric species experienced several substantial introgressions from outgroup populations that probably occurred soon after they had secondary contact with each other in the lake. However, the ratio of migrants from the outgroups was estimated to be different between the two species, which is consistent with the hypothesis that these introgressions aided their divergence or prevented them from forming a hybrid swarm. Repeated lake fragmentations and fusions may have promoted diversification of this freshwater fish species complex that is endemic to this ancient lake system.
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Affiliation(s)
- Ixchel F Mandagi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.,Faculty of Fisheries and Marine Science, Sam Ratulangi University, Manado, Indonesia
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Javier Montenegro
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | | | - Nobuyuki Inomata
- Department of Environmental Science, Fukuoka Women's University, Fukuoka, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Junko Kusumi
- Faculty of Social and Cultural Studies, Kyushu University, Fukuoka, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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23
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Choi JY, Dai X, Alam O, Peng JZ, Rughani P, Hickey S, Harrington E, Juul S, Ayroles JF, Purugganan MD, Stacy EA. Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands. Proc Natl Acad Sci U S A 2021; 118:e2023801118. [PMID: 34497122 PMCID: PMC8449318 DOI: 10.1073/pnas.2023801118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2021] [Indexed: 01/05/2023] Open
Abstract
Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for Metrosideros polymorpha var. incana and analyzed whole-genome sequences of 131 individuals from 11 taxa sampled across the islands. Demographic modeling and population genomics analyses suggested that Hawaiian Metrosideros originated from a single colonization event and subsequently spread across the archipelago following the formation of new islands. The evolutionary history of Hawaiian Metrosideros shows evidence of extensive reticulation associated with significant sharing of ancestral variation between taxa and secondarily with admixture. Taking advantage of the highly contiguous genome assembly, we investigated the genomic architecture underlying the adaptive radiation and discovered that divergent selection drove the formation of differentiation outliers in paired taxa representing early stages of speciation/divergence. Analysis of the evolutionary origins of the outlier single nucleotide polymorphisms (SNPs) showed enrichment for ancestral variations under divergent selection. Our findings suggest that Hawaiian Metrosideros possesses an unexpectedly rich pool of ancestral genetic variation, and the reassortment of these variations has fueled the island adaptive radiation.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003;
| | - Xiaoguang Dai
- Oxford Nanopore Technologies Inc., New York, NY 10013
| | - Ornob Alam
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Julie Z Peng
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | | | - Scott Hickey
- Oxford Nanopore Technologies Inc., San Francisco, CA 94501
| | | | - Sissel Juul
- Oxford Nanopore Technologies Inc., New York, NY 10013
| | - Julien F Ayroles
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003
| | - Elizabeth A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89119;
- College of Agriculture, Forestry, and Natural Resource Management, University of Hawaii Hilo, Hilo, HI 96720
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24
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Levin B, Simonov E, Franchini P, Mugue N, Golubtsov A, Meyer A. Rapid adaptive radiation in a hillstream cyprinid fish in the East African White Nile River basin. Mol Ecol 2021; 30:5530-5550. [PMID: 34409661 DOI: 10.1111/mec.16130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022]
Abstract
Adaptive radiation of freshwater fishes was long thought to be possible only in lacustrine environments. Recently, several studies have shown that riverine and stream environments also provide the ecological opportunity for adaptive radiation. In this study, we report on a riverine adaptive radiation of six ecomorphs of cyprinid hillstream fishes of the genus Garra in a river located in the Ethiopian Highlands in East Africa. Garra are predominantly highly specialized algae-scrapers with a wide distribution ranging from Southeast Asia to West Africa. However, adaptive phenotypic diversification in mouth type, sucking disc morphology, gut length and body shape have probably been found among these ecomorphs in a single Ethiopian river. Moreover, we found two novel phenotypes of Garra ("thick-lipped" and "predatory") that had not been discovered before in this species-rich genus (>160 species). Mitochondrial and genome-wide data suggest monophyletic, intrabasin evolution of Garra phenotypic diversity with signatures of gene flow from other local populations. Although sympatric ecomorphs are genetically distinct and can be considered to being young species as suggested by genome-wide single nucleotide polymorphism data, mitochondrial DNA was unable to identify any genetic structure suggesting recent and rapid speciation events. Some data suggest a hybrid origin of the novel "thick-lipped" ecomorph. Here we highlight how, driven by ecological opportunity, an ancestral trophically highly specialized lineage is likely to have rapidly radiated in a riverine environment promoted by the evolution of novel feeding strategies.
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Affiliation(s)
- Boris Levin
- Papanin Institute of Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia.,Zoological Institute of Russian Academy of Sciences, Cherepovets State University, St. Petersburg, Russia
| | - Evgeniy Simonov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, Russia
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nikolai Mugue
- Koltzov Institute for Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Golubtsov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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25
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Maltseva AL, Varfolomeeva MA, Ayanka RV, Gafarova ER, Repkin EA, Pavlova PA, Shavarda AL, Mikhailova NA, Granovitch AI. Linking ecology, morphology, and metabolism: Niche differentiation in sympatric populations of closely related species of the genus Littorina ( Neritrema). Ecol Evol 2021; 11:11134-11154. [PMID: 34429908 PMCID: PMC8366845 DOI: 10.1002/ece3.7901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 05/08/2021] [Accepted: 06/22/2021] [Indexed: 12/03/2022] Open
Abstract
Divergence of ecological niches in phylogenetically closely related species indicates the importance of ecology in speciation, especially for sympatric species are considered. Such ecological diversification provides an advantage of alleviating interspecies competition and promotes more efficient exploitation of environmental resources, thus being a basis for ecological speciation. We analyzed a group of closely related species from the subgenus Neritrema (genus Littorina, Caenogastropoda) from the gravel-bouldery shores. In two distant sites at the Barents and Norwegian Sea, we examined the patterns of snail distribution during low tide (quantitative sampling stratified by intertidal level, presence of macrophytes, macrophyte species, and position on them), shell shape and its variability (geometric morphometrics), and metabolic characteristics (metabolomic profiling). The studied species diversified microbiotopes, which imply an important role of ecological specification in the recent evolution of this group. The only exception to this trend was the species pair L. arcana / L. saxatilis, which is specifically discussed. The ecological divergence was accompanied by differences in shell shape and metabolomic characteristics. Significant differences were found between L. obtusata versus L. fabalis and L. saxatilis / L. arcana versus L. compressa both in shell morphology and in metabolomes. L. saxatilis demonstrated a clear variability depending on intertidal level which corresponds to a shift in conditions within the occupied microhabitat. Interestingly, the differences between L. arcana (inhabiting the upper intertidal level) and L. compressa (inhabiting the lower one) were analogous to those between the upper and lower fractions of L. saxatilis. No significant level-dependent changes were found between the upper and lower fractions of L. obtusata, most probably due to habitat amelioration by fucoid macroalgae. All these results are discussed in the contexts of the role of ecology in speciation, ecological niche dynamics and conservatism, and evolutionary history of the Neritrema species.
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Affiliation(s)
- Arina L Maltseva
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Marina A Varfolomeeva
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Roman V Ayanka
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Elizaveta R Gafarova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Egor A Repkin
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Polina A Pavlova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
| | - Alexei L Shavarda
- Department of Analytical Phytochemistry Komarov Botanical Institute St. Petersburg Russia
- Research Park Centre for Molecular and Cell Technologies St. Petersburg State University St. Petersburg Russia
| | - Natalia A Mikhailova
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
- Centre of Cell Technologies Institute of Cytology Russian Academy of Sciences St. Petersburg Russia
| | - Andrei I Granovitch
- Department of Invertebrate Zoology St. Petersburg State University St. Petersburg Russia
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26
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Kakioka R, Sutra N, Kobayashi H, Ansai S, Masengi KWA, Nagano AJ, Okuda N, Tanaka R, Sato M, Yamahira K. Resource partitioning is not coupled with assortative mating in sympatrically divergent ricefish in a Wallacean ancient lake. J Evol Biol 2021; 34:1133-1143. [PMID: 34077583 DOI: 10.1111/jeb.13874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/07/2021] [Accepted: 05/25/2021] [Indexed: 11/30/2022]
Abstract
Sympatric speciation is considered to be difficult without the coupling between ecological traits that allow resource partitioning and reproductive traits that allow assortative mating. Such "magic traits" are known to be involved in most of the compelling examples of sympatric speciation. In this study, we report a possible case of sympatric speciation without magic traits. Three species of ricefish (genus Oryzias) are suggested to have diverged sympatrically within Lake Poso, an ancient lake in Sulawesi. An analysis of genome-wide single-nucleotide polymorphisms showed that these three species are reproductively isolated from each other throughout the lake. Stable isotope analyses revealed that the three species use different food resources, which reflect differences in their feeding morphologies (gill rakers and digestive tracts) and feeding sites. Field and laboratory observations showed that O. nebulosus and O. orthognathus share a mating habitat of cobbles, where they scatter fertilized eggs, whereas this site is never used by O. nigrimas, indicating that assortative mating is partly achieved by spatial isolation. The small, less-adhesive eggs of O. nebulosus and O. orthognathus probably reflect their adaptation to spawning on cobble beaches. Laboratory mating experiments showed strong prezygotic isolation between O. nebulosus and O. orthognathus, which is achieved by strong species recognition presumably by both sexes based on species-specific mating dances and nuptial coloration. In summary, the assortative mating of O. nebulosus and O. orthognathus is probably not coupled to resource partitioning. We discussed how sympatric speciation among these species might have been achieved even without magic traits.
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Affiliation(s)
- Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Nobu Sutra
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Satoshi Ansai
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | | | | | - Noboru Okuda
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Rieko Tanaka
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Masahiro Sato
- World Medaka Aquarium, Nagoya Higashiyama Zoo and Botanical Gardens, Nagoya, Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
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27
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Richards EJ, McGirr JA, Wang JR, St John ME, Poelstra JW, Solano MJ, O'Connell DC, Turner BJ, Martin CH. A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape. Proc Natl Acad Sci U S A 2021; 118:e2011811118. [PMID: 33990463 PMCID: PMC8157919 DOI: 10.1073/pnas.2011811118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior (prlh, cfap20, and rmi1) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development (itga5, ext1, cyp26b1, and galr2) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene (twist1) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation.
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Affiliation(s)
- Emilie J Richards
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Joseph A McGirr
- Department of Environmental Toxicology, University of California, Davis, CA 95616
| | - Jeremy R Wang
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514
| | - Michelle E St John
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Jelmer W Poelstra
- Molecular and Cellular Imaging Center, Ohio State University, Columbus, OH 43210
| | - Maria J Solano
- Department of Biology, University of North Carolina, Chapell Hill, NC 27514
| | | | - Bruce J Turner
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601
| | - Christopher H Martin
- Department of Integrative Biology, University of California, Berkeley, CA 94720;
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
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28
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Maltseva AL, Varfolomeeva MA, Lobov AA, Tikanova PO, Repkin EA, Babkina IY, Panova M, Mikhailova NA, Granovitch AI. Premating barriers in young sympatric snail species. Sci Rep 2021; 11:5720. [PMID: 33707514 PMCID: PMC7952697 DOI: 10.1038/s41598-021-84407-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/15/2021] [Indexed: 01/04/2023] Open
Abstract
Sympatric coexistence of recently diverged species raises the question of barriers restricting the gene flow between them. Reproductive isolation may be implemented at several levels, and the weakening of some, e.g. premating, barriers may require the strengthening of the others, e.g. postcopulatory ones. We analysed mating patterns and shell size of mates in recently diverged closely related species of the subgenus Littorina Neritrema (Littorinidae, Caenogastropoda) in order to assess the role of premating reproductive barriers between them. We compared mating frequencies observed in the wild with those expected based on relative densities using partial canonical correspondence analysis. We introduced the fidelity index (FI) to estimate the relative accuracy of mating with conspecific females and precopulatory isolation index (IPC) to characterize the strength of premating barriers. The species under study, with the exception of L. arcana, clearly demonstrated preferential mating with conspecifics. According to FI and IPC, L. fabalis and L. compressa appeared reliably isolated from their closest relatives within Neritrema. Individuals of these two species tend to be smaller than those of the others, highlighting the importance of shell size changes in gastropod species divergence. L. arcana males were often found in pairs with L. saxatilis females, and no interspecific size differences were revealed in this sibling species pair. We discuss the lack of discriminative mate choice in the sympatric populations of L. arcana and L. saxatilis, and possible additional mechanisms restricting gene flow between them.
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Affiliation(s)
- Arina L Maltseva
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.
| | - Marina A Varfolomeeva
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - Arseniy A Lobov
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.,Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St Petersburg, Russia
| | - Polina O Tikanova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria
| | - Egor A Repkin
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - Irina Y Babkina
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
| | - Marina Panova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.,Department of Marine Sciences - Tjärnö, University of Gothenburg, Gothenburg, Sweden
| | - Natalia A Mikhailova
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia.,Centre of Cell Technologies, Institute of Cytology Russian Academy of Sciences, St Petersburg, Russia
| | - Andrei I Granovitch
- Department of Invertebrate Zoology, St Petersburg State University, St Petersburg, Russia
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29
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Dean LL, Dunstan HR, Reddish A, MacColl ADC. Courtship behavior, nesting microhabitat, and assortative mating in sympatric stickleback species pairs. Ecol Evol 2021; 11:1741-1755. [PMID: 33614001 PMCID: PMC7882950 DOI: 10.1002/ece3.7164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/26/2020] [Accepted: 12/14/2020] [Indexed: 12/28/2022] Open
Abstract
The maintenance of reproductive isolation in the face of gene flow is a particularly contentious topic, but differences in reproductive behavior may provide the key to explaining this phenomenon. However, we do not yet fully understand how behavior contributes to maintaining species boundaries. How important are behavioral differences during reproduction? To what extent does assortative mating maintain reproductive isolation in recently diverged populations and how important are "magic traits"? Assortative mating can arise as a by-product of accumulated differences between divergent populations as well as an adaptive response to contact between those populations, but this is often overlooked. Here we address these questions using recently described species pairs of three-spined stickleback (Gasterosteus aculeatus), from two separate locations and a phenotypically intermediate allopatric population on the island of North Uist, Scottish Western Isles. We identified stark differences in the preferred nesting substrate and courtship behavior of species pair males. We showed that all males selectively court females of their own ecotype and all females prefer males of the same ecotype, regardless of whether they are from species pairs or allopatric populations. We also showed that mate choice does not appear to be driven by body size differences (a potential "magic trait"). By explicitly comparing the strength of these mating preferences between species pairs and single-ecotype locations, we were able to show that present levels of assortative mating due to direct mate choice are likely a by-product of other adaptations between ecotypes, and not subject to obvious selection in species pairs. Our results suggest that ecological divergence in mating characteristics, particularly nesting microhabitat may be more important than direct mate choice in maintaining reproductive isolation in stickleback species pairs.
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Affiliation(s)
- Laura L. Dean
- School of Life SciencesUniversity of NottinghamNottinghamUK
| | | | - Amelia Reddish
- School of Life SciencesUniversity of NottinghamNottinghamUK
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30
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Kaiser TS, von Haeseler A, Tessmar-Raible K, Heckel DG. Timing strains of the marine insect Clunio marinus diverged and persist with gene flow. Mol Ecol 2021; 30:1264-1280. [PMID: 33410230 DOI: 10.1111/mec.15791] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Genetic divergence of populations in the presence of gene flow is a central theme in speciation research. Theory predicts that divergence can happen with full range overlap - in sympatry - driven by ecological factors, but there are few empirical examples of how ecologically divergent selection can overcome gene flow and lead to reproductive isolation. In the marine midge Clunio marinus (Diptera: Chironomidae) reproduction is ecologically restricted to the time of the lowest tides, which is ensured through accurate control of development and adult emergence by circalunar and circadian clocks. As tidal regimes differ along the coastline, locally adapted timing strains of C. marinus are found in different sites across Europe. At the same time, ecologically suitable low tides occur at both full and new moon and twice a day, providing C. marinus with four nonoverlapping temporal niches at every geographic location. Along the coast of Brittany, which is characterized by a steep gradient in timing of the tides, we found an unusually large number of differentially adapted timing strains, and the first known instances of sympatric C. marinus strains occupying divergent temporal niches. Analysis of mitochondrial genotypes suggests that these timing strains originated from a single recent colonization event. Nuclear genotypes show strong gene flow, sympatric timing strains being the least differentiated. Even when sympatric strains exist in nonoverlapping temporal niches, timing adaptations do not result in genome-wide genetic divergence, suggesting timing adaptations are maintained by permanent ecological selection. This constitutes a model case for incipient ecological divergence with gene flow.
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Affiliation(s)
- Tobias S Kaiser
- Max Planck Research Group Biological Clocks, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.,Max Perutz Laboratories, University of Vienna, Vienna, Austria.,Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | | | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
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31
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On the Origin of Coexisting Species. Trends Ecol Evol 2020; 36:284-293. [PMID: 33353727 DOI: 10.1016/j.tree.2020.11.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/07/2020] [Accepted: 11/13/2020] [Indexed: 11/22/2022]
Abstract
Speciation is frequently initiated but rarely completed, a phenomenon hypothesized to arise due to the failure of nascent lineages to persist. Although a failure to persist often has ecological causes, key gaps exist between ecological and evolutionary theories that, if filled, would clarify when and why speciation succeeds or fails. Here, we apply ecological coexistence theory to show how the alignment between different forms of niche opportunity and niche use shape the initiation, progression, and completion of speciation. Niche evolution may drive coexistence or competitive exclusion, and an ability to coexist ecologically may help or hinder speciation. Our perspective allows progress towards unifying the origin and maintenance of species diversity across the tree of life.
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32
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Kautt AF, Kratochwil CF, Nater A, Machado-Schiaffino G, Olave M, Henning F, Torres-Dowdall J, Härer A, Hulsey CD, Franchini P, Pippel M, Myers EW, Meyer A. Contrasting signatures of genomic divergence during sympatric speciation. Nature 2020; 588:106-111. [PMID: 33116308 PMCID: PMC7759464 DOI: 10.1038/s41586-020-2845-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/23/2020] [Indexed: 01/25/2023]
Abstract
The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin1,2. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process3. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs4, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories5. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.
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Affiliation(s)
- Andreas F Kautt
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Alexander Nater
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Gonzalo Machado-Schiaffino
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Functional Biology, Area of Genetics, University of Oviedo, Oviedo, Spain
| | - Melisa Olave
- Department of Biology, University of Konstanz, Konstanz, Germany
- Argentine Dryland Research Institute of the National Council for Scientific Research (IADIZA-CONICET), Mendoza, Argentina
| | - Frederico Henning
- Department of Biology, University of Konstanz, Konstanz, Germany
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Andreas Härer
- Department of Biology, University of Konstanz, Konstanz, Germany
- Division of Biological Sciences, Section of Ecology, Behavior & Evolution, University of California San Diego, La Jolla, CA, USA
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
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33
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Choi JY, Purugganan M, Stacy EA. Divergent Selection and Primary Gene Flow Shape Incipient Speciation of a Riparian Tree on Hawaii Island. Mol Biol Evol 2020; 37:695-710. [PMID: 31693149 PMCID: PMC7038655 DOI: 10.1093/molbev/msz259] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A long-standing goal of evolutionary biology is to understand the mechanisms underlying the formation of species. Of particular interest is whether or not speciation can occur in the presence of gene flow and without a period of physical isolation. Here, we investigated this process within Hawaiian Metrosideros, a hypervariable and highly dispersible woody species complex that dominates the Hawaiian Islands in continuous stands. Specifically, we investigated the origin of Metrosideros polymorpha var. newellii (newellii), a riparian ecotype endemic to Hawaii Island that is purportedly derived from the archipelago-wide M. polymorpha var. glaberrima (glaberrima). Disruptive selection across a sharp forest-riparian ecotone contributes to the isolation of these varieties and is a likely driver of newellii's origin. We examined genome-wide variation of 42 trees from Hawaii Island and older islands. Results revealed a split between glaberrima and newellii within the past 0.3-1.2 My. Admixture was extensive between lineages within Hawaii Island and between islands, but introgression from populations on older islands (i.e., secondary gene flow) did not appear to contribute to the emergence of newellii. In contrast, recurrent gene flow (i.e., primary gene flow) between glaberrima and newellii contributed to the formation of genomic islands of elevated absolute and relative divergence. These regions were enriched for genes with regulatory functions as well as for signals of positive selection, especially in newellii, consistent with divergent selection underlying their formation. In sum, our results support riparian newellii as a rare case of incipient ecological speciation with primary gene flow in trees.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY
| | - Michael Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Elizabeth A Stacy
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV
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34
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Li K, Ren X, Song X, Li X, Zhou Y, Harlev E, Sun D, Nevo E. Incipient sympatric speciation in wild barley caused by geological-edaphic divergence. Life Sci Alliance 2020; 3:3/12/e202000827. [PMID: 33082129 PMCID: PMC7652381 DOI: 10.26508/lsa.202000827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 12/26/2022] Open
Abstract
Sympatric speciation is still contentious but here based on genome-wide analysis; we show incipient sympatric speciation of an emerging new wild barley species from Hordeum spontaneum, the progenitor of all cultivated barleys at “Evolution Plateau” (EP), Upper Galilee, Israel. Sympatric speciation (SS) has been contentious since the idea was suggested by Darwin. Here, we show in wild barley SS due to geologic and edaphic divergence in “Evolution Plateau,” Upper Galilee, Israel. Our whole genome resequencing data showed SS separating between the progenitor old Senonian chalk and abutting derivative young Pleistocene basalt wild barley populations. The basalt wild barley species unfolds larger effective population size, lower recombination rates, and larger genetic diversity. Both species populations show similar descending trend ∼200,000 yr ago associated with the last glacial maximum. Coalescent demography analysis indicates that SS was local, primary, in situ, and not due to a secondary contact from ex situ allopatric population. Adaptive divergent putatively selected genes were identified in both populations. Remarkably, disease resistant genes were selected in the wet basalt population, and genes related to flowering time, leading to temporal reproductive isolation, were selected in the chalk population. The evidence substantiates adaptive ecological SS in wild barley, highlighting the genome landscape during SS with gene flow, due to geologic-edaphic divergence.
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Affiliation(s)
- Kexin Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China.,Institute of Evolution, University of Haifa, Haifa, Israel
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoying Song
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Xiujuan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yu Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Eli Harlev
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
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35
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Liu X, Glémin S, Karrenberg S. Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene). Mol Ecol 2020; 29:3511-3525. [PMID: 32740990 PMCID: PMC7540528 DOI: 10.1111/mec.15571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 12/22/2022]
Abstract
Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions Silene dioica (L.) Clairv. and S. latifolia Poiret. Demographic modelling indicated that the two species diverged with gene flow. The best‐supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (FST) and sequence divergence (dXY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between‐species population pairs, isolation by distance was stronger for genomic regions with low between‐species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated, suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two Silene species, consistent with predictions for speciation in the face of gene flow.
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Affiliation(s)
- Xiaodong Liu
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,UMR CNRS 6553 ECOBIO, Université de Rennes I, Rennes Cedex, France
| | - Sophie Karrenberg
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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St John ME, Holzman R, Martin CH. Rapid adaptive evolution of scale-eating kinematics to a novel ecological niche. J Exp Biol 2020; 223:jeb217570. [PMID: 32029459 PMCID: PMC7097200 DOI: 10.1242/jeb.217570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/29/2020] [Indexed: 01/08/2023]
Abstract
The origins of novel trophic specialization, in which organisms begin to exploit resources for the first time, may be explained by shifts in behavior such as foraging preferences or feeding kinematics. One way to investigate behavioral mechanisms underlying ecological novelty is by comparing prey capture kinematics among species. We investigated the contribution of kinematics to the origins of a novel ecological niche for scale-eating within a microendemic adaptive radiation of pupfishes on San Salvador Island, Bahamas. We compared prey capture kinematics across three species of pupfish while they consumed shrimp and scales in the lab, and found that scale-eating pupfish exhibited peak gape sizes twice as large as in other species, but also attacked prey with a more obtuse angle between their lower jaw and suspensorium. We then investigated how this variation in feeding kinematics could explain scale-biting performance by measuring bite size (surface area removed) from standardized gelatin cubes. We found that a combination of larger peak gape and more obtuse lower jaw and suspensorium angles resulted in approximately 40% more surface area removed per strike, indicating that scale-eaters may reside on a performance optimum for scale biting. To test whether feeding performance could contribute to reproductive isolation between species, we also measured F1 hybrids and found that their kinematics and performance more closely resembled generalists, suggesting that F1 hybrids may have low fitness in the scale-eating niche. Ultimately, our results suggest that the evolution of strike kinematics in this radiation is an adaptation to the novel niche of scale eating.
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Affiliation(s)
- Michelle E St John
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roi Holzman
- School of Zoology, Tel Aviv University, Eilat 6997801, Israel
- Inter-University Institute for Marine Sciences, Eilat 8810302, Israel
| | - Christopher H Martin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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37
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Gillespie RG, Bennett GM, De Meester L, Feder JL, Fleischer RC, Harmon LJ, Hendry AP, Knope ML, Mallet J, Martin C, Parent CE, Patton AH, Pfennig KS, Rubinoff D, Schluter D, Seehausen O, Shaw KL, Stacy E, Stervander M, Stroud JT, Wagner C, Wogan GOU. Comparing Adaptive Radiations Across Space, Time, and Taxa. J Hered 2020; 111:1-20. [PMID: 31958131 PMCID: PMC7931853 DOI: 10.1093/jhered/esz064] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023] Open
Abstract
Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on (1) whether the primary drivers of ecological shifts are (a) external to the membership of the radiation itself (mostly divergent or disruptive ecological selection) or (b) due to competition within the radiation membership (interactions among members) subsequent to reproductive isolation in similar environments, and (2) the extent and timing of admixture. These differences translate into different patterns of species accumulation and subsequent patterns of diversity across an adaptive radiation. Adaptive radiations occur in an extraordinary diversity of different ways, and continue to provide rich data for a better understanding of the diversification of life.
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Affiliation(s)
- Rosemary G Gillespie
- University of California, Berkeley, Essig Museum of Entomology & Department of Environmental Science, Policy, and Management, Berkeley, CA
| | - Gordon M Bennett
- University of California Merced, Life and Environmental Sciences Unit, Merced, CA
| | - Luc De Meester
- University of Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belguim
| | - Jeffrey L Feder
- University of Notre Dame, Dept. of Biological Sciences, Notre Dame, IN
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
| | - Luke J Harmon
- University of Idaho, Dept. of Biological Sciences, Moscow, ID
| | | | | | | | - Christopher Martin
- University of California Berkeley, Integrative Biology and Museum of Vertebrate Zoology, Berkeley, CA
| | | | - Austin H Patton
- Washington State University, School of Biological Sciences, Pullman, WA
| | - Karin S Pfennig
- University of North Carolina at Chapel Hill, Department of Biology, Chapel Hill, NC
| | - Daniel Rubinoff
- University of Hawaiʻi at Manoa, Department of Plant and Environmental Protection Sciences, Honolulu, HI
| | | | - Ole Seehausen
- Institute of Ecology & Evolution, University of Bern, Bern, BE, Switzerland
- Center for Ecology, Evolution & Biogeochemistry, Eawag, Kastanienbaum, LU, Switzerland
| | - Kerry L Shaw
- Cornell University, Neurobiology and Behavior, Tower Road,, Ithaca, NY
| | - Elizabeth Stacy
- University of Nevada Las Vegas, School of Life Sciences, Las Vegas, NV
| | - Martin Stervander
- University of Oregon, Institute of Ecology and Evolution, Eugene, OR
| | - James T Stroud
- Washington University in Saint Louis, Biology, Saint Louis, MO
| | | | - Guinevere O U Wogan
- University of California Berkeley, Environmental Science Policy, and Management, Berkeley, CA
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Raffini F, Schneider RF, Franchini P, Kautt AF, Meyer A. Diving into divergence: Differentiation in swimming performances, physiology and gene expression between locally‐adapted sympatric cichlid fishes. Mol Ecol 2019; 29:1219-1234. [DOI: 10.1111/mec.15304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/24/2019] [Accepted: 11/08/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Francesca Raffini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
- Max Planck Institute for Ornithology Radolfzell Germany
| | - Ralf F. Schneider
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
| | - Paolo Franchini
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
| | - Andreas F. Kautt
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
| | - Axel Meyer
- Lehrstuhl für Zoologie und Evolutionsbiologie Department of Biology University of Konstanz Konstanz Germany
- International Max Planck Research School (IMPRS) for Organismal Biology Max‐Planck‐Institut für Ornithologie Radolfzell Germany
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Sutra N, Kusumi J, Montenegro J, Kobayashi H, Fujimoto S, Masengi KWA, Nagano AJ, Toyoda A, Matsunami M, Kimura R, Yamahira K. Evidence for sympatric speciation in a Wallacean ancient lake. Evolution 2019; 73:1898-1915. [DOI: 10.1111/evo.13821] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/03/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Nobu Sutra
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Junko Kusumi
- Faculty of Social and Cultural StudiesKyushu University Fukuoka 819‐0395 Japan
| | - Javier Montenegro
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Hirozumi Kobayashi
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
| | - Shingo Fujimoto
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | | | | | - Atsushi Toyoda
- Comparative Genomics LaboratoryNational Institute of Genetics Mishima 411‐8540 Japan
| | | | - Ryosuke Kimura
- Graduate School of MedicineUniversity of the Ryukyus Okinawa 903‐0125 Japan
| | - Kazunori Yamahira
- Tropical Biosphere Research CenterUniversity of the Ryukyus Okinawa 903‐0213 Japan
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Martin CH, McGirr JA, Richards EJ, St. John ME. How to Investigate the Origins of Novelty: Insights Gained from Genetic, Behavioral, and Fitness Perspectives. Integr Org Biol 2019; 1:obz018. [PMID: 33791533 PMCID: PMC7671130 DOI: 10.1093/iob/obz018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Biologists are drawn to the most extraordinary adaptations in the natural world, often referred to as evolutionary novelties, yet rarely do we understand the microevolutionary context underlying the origins of novel traits, behaviors, or ecological niches. Here we discuss insights gained into the origins of novelty from a research program spanning biological levels of organization from genotype to fitness in Caribbean pupfishes. We focus on a case study of the origins of novel trophic specialists on San Salvador Island, Bahamas and place this radiation in the context of other rapid radiations. We highlight questions that can be addressed about the origins of novelty at different biological levels, such as measuring the isolation of novel phenotypes on the fitness landscape, locating the spatial and temporal origins of adaptive variation contributing to novelty, detecting dysfunctional gene regulation due to adaptive divergence, and connecting behaviors with novel traits. Evolutionary novelties are rare, almost by definition, and we conclude that integrative case studies can provide insights into this rarity relative to the dynamics of adaptation to more common ecological niches and repeated parallel speciation, such as the relative isolation of novel phenotypes on fitness landscapes and the transient availability of ecological, genetic, and behavioral opportunities.
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Affiliation(s)
- C H Martin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - J A McGirr
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - E J Richards
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - M E St. John
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
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