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Buser TJ, Larouche O, Aguilar A, Neves MP, Sandel MW, Sidlauskas BL, Summers AP, Evans KM. Freshwater Habitats Promote Rapid Rates of Phenotypic Evolution in Sculpin Fishes (Perciformes: Cottoidea). Am Nat 2024; 204:345-360. [PMID: 39326057 DOI: 10.1086/731784] [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] [Indexed: 09/28/2024]
Abstract
AbstractInvasions of freshwater habitats by marine fishes provide exceptional cases of habitat-driven biological diversification. Freshwater habitats make up less than 1% of aquatic habitats but contain ∼50% of fish species. However, while the dominant group of freshwater fishes (Otophysi) is older than that of most marine fishes (Percomorphaceae), it is less morphologically diverse. Classically, scientists have invoked differences in the tempo and/or mode of evolution to explain such cases of unequal morphological diversification. We tested for evidence of these phenomena in the superfamily Cottoidea (sculpins), which contains substantial radiations of marine and freshwater fishes. We find that the morphology of freshwater sculpins evolves faster but under higher constraint than that of marine sculpins, causing widespread convergence in freshwater sculpins and more morphological disparity in marine sculpins. The endemic freshwater sculpins of Lake Baikal, Siberia, are exceptions that demonstrate elevated novelty akin to that of marine sculpins. Several tantalizing factors may explain these findings, such as differences in habitat stability and/or habitat connectivity between marine and freshwater systems.
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Martinez CM, Corn KA, Williamson S, Satterfield D, Roberts-Hugghis AS, Barley A, Borstein SR, McGee MD, Wainwright PC. Replicated Functional Evolution in Cichlid Adaptive Radiations. Am Nat 2024; 204:242-257. [PMID: 39179237 DOI: 10.1086/731477] [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] [Indexed: 08/26/2024]
Abstract
AbstractAdaptive radiations highlight the mechanisms by which species and traits diversify and the extent to which these patterns are predictable. We used 1,110 high-speed videos of suction feeding to study functional and morphological diversification in 300 cichlid species from three African Great Lake radiations of varying ages (Victoria, Malawi, and Tanganyika) and an older, spatially dispersed continental radiation in the Neotropics. Among African radiations, standing diversity was reflective of time. Morphological and functional variance in Lake Victoria, the youngest radiation, was a subset of that within Lake Malawi, which itself was nested within the older Tanganyikan radiation. However, functional diversity in Neotropical cichlids was often lower than that in Lake Tanganyika, despite being much older. These two radiations broadly overlapped, but each diversified into novel trait spaces not found in the youngest lake radiations. Evolutionary rates across radiations were inversely related to age, suggesting extremely rapid trait evolution at early stages, particularly in lake radiations. Despite this support for early bursts, other patterns of trait diversity were inconsistent with expectations of adaptive radiations. This work suggests that cichlid functional evolution has played out in strikingly similar fashion in different radiations, with contingencies eventually resulting in lineage-specific novelties.
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Backenstose NJC, MacGuigan DJ, Osborne CA, Bernal MA, Thomas EK, Normandeau E, Yule DL, Stott W, Ackiss AS, Albert VA, Bernatchez L, Krabbenhoft TJ. Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum. Commun Biol 2024; 7:978. [PMID: 39134631 PMCID: PMC11319351 DOI: 10.1038/s42003-024-06503-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 06/25/2024] [Indexed: 08/15/2024] Open
Abstract
The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex ("ciscoes") radiated rapidly prior to the Last Glacial Maximum (80-90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr (Salvelinus namaycush), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deep water created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation.
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Affiliation(s)
| | - Daniel J MacGuigan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | | | - Moisés A Bernal
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | | | - Eric Normandeau
- Plateforme de bio-informatique de l'IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, G1V 0A6, Canada
| | - Daniel L Yule
- US Geological Survey, Lake Superior Biological Station, Great Lakes Science Center, Ashland, WI, USA
| | - Wendylee Stott
- Freshwater Institute, Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, MB, R3T 2N6, Canada
| | - Amanda S Ackiss
- US Geological Survey, Great Lakes Science Center, Ann Arbor, MI, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
| | - Trevor J Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
- RENEW Institute, University at Buffalo, Buffalo, NY, USA.
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Gobbin TP, Vanhove MP, Seehausen O, Maan ME, Pariselle A. Four new species of Cichlidogyrus (Platyhelminthes, Monopisthocotyla, Dactylogyridae) from Lake Victoria haplochromine cichlid fishes, with the redescription of C. bifurcatus and C. longipenis. Parasite 2024; 31:46. [PMID: 39109983 PMCID: PMC11305117 DOI: 10.1051/parasite/2024039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/18/2024] [Indexed: 08/10/2024] Open
Abstract
African cichlids are model systems for evolutionary studies and host-parasite interactions, because of their adaptive radiations and because they harbour many species of monogenean parasites with high host-specificity. Five locations were sampled in southern Lake Victoria: gill-infecting monogeneans were surveyed from 18 cichlid species belonging to this radiation superflock and two others representing two older and distantly related lineages. We found one species of Gyrodactylidae, Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011, and seven species of Dactylogyridae. Four are described herein: Cichlidogyrus pseudodossoui n. sp., Cichlidogyrus nyanza n. sp., Cichlidogyrus furu n. sp., and Cichlidogyrus vetusmolendarius n. sp. Another Cichlidogyrus species is reported but not formally described (low number of specimens, morphological similarity with C. furu n. sp.). Two other species are redescribed: C. bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Our results confirm that the monogenean fauna of Victorian littoral cichlids displays lower species richness and lower host-specificity than that of Lake Tanganyika littoral cichlids. In C. furu n. sp., hooks V are clearly longer than the others, highlighting the need to re-evaluate the current classification system that considers hook pairs III-VII as rather uniform. Some morphological features of C. bifurcatus, C. longipenis, and C. nyanza n. sp. suggest that these are closely related to congeners that infect other haplochromines. Morphological traits indicate that representatives of Cichlidogyrus colonised Lake Victoria haplochromines or their ancestors at least twice, which is in line with the Lake Victoria superflock being colonised by two cichlid tribes (Haplochromini and Oreochromini).
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Affiliation(s)
- Tiziana P. Gobbin
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern Baltzerstrasse 6 3012 Bern Switzerland
- Groningen Institute for Evolutionary Life Sciences, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology Seestrasse 79 6047 Kastanienbaum Switzerland
- Research Group Zoology: Biodiversity & Toxicology, Centre for Environmental Sciences, Hasselt University Agoralaan Gebouw D 3590 Diepenbeek Belgium
| | - Maarten P.M. Vanhove
- Research Group Zoology: Biodiversity & Toxicology, Centre for Environmental Sciences, Hasselt University Agoralaan Gebouw D 3590 Diepenbeek Belgium
- Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven Charles Deberiotstraat 32 3000 Leuven Belgium
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki P.O. Box 17 00014 Helsinki Finland
| | - Ole Seehausen
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern Baltzerstrasse 6 3012 Bern Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology Seestrasse 79 6047 Kastanienbaum Switzerland
| | - Martine E. Maan
- Groningen Institute for Evolutionary Life Sciences, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Antoine Pariselle
- ISEM, CNRS, Université de Montpellier, IRD place Eugène Bataillon 34090 Montpellier France
- Laboratory of Biodiversity, Ecology and Genome, Faculty of Sciences, Mohammed V University 4 avenue Ibn Battouta B.P. 1014 RP 10000 Rabat Morocco
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5
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Chaparro-Pedraza PC. Differential Stage-Specific Mortality as a Mechanism for Diversification. Am Nat 2024; 204:E28-E41. [PMID: 39008841 DOI: 10.1086/730446] [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] [Indexed: 07/17/2024]
Abstract
AbstractIndividual variability in mortality is widespread in nature. The general rule is that larger organisms have a greater chance of survival than smaller conspecifics. There is growing evidence that differential mortality between developmental stages has important consequences for the ecology and evolution of populations and communities. However, we know little about how it can influence diversification. Using an eco-evolutionary model of diversification that considers individual variability in mortality, I show that commonly observed differences in mortality between juveniles and adults can facilitate adaptive diversification. In particular, diversification is expected to be less restricted when mortality is more biased toward juveniles. Additionally, I find stage-specific differences in metabolic cost and foraging capacity to further facilitate diversification when adults are slightly superior competitors, due to either a lower metabolic cost or a higher foraging capacity, than juveniles. This is because by altering the population composition, differential stage-specific mortality and competitive ability can modulate the strength of intraspecific competition, which in turn determines the outcome of diversification. These results demonstrate the strong influence that ecological differences between developmental stages have on diversification and highlight the need for integrating developmental processes into diversification theory.
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6
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Grimwood RM, Waller SJ, Wierenga JR, Lim L, Dubrulle J, Holmes EC, Geoghegan JL. Viromes of Antarctic fish resemble the diversity found at lower latitudes. Virus Evol 2024; 10:veae050. [PMID: 39071139 PMCID: PMC11282168 DOI: 10.1093/ve/veae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/09/2024] [Accepted: 07/10/2024] [Indexed: 07/30/2024] Open
Abstract
Antarctica harbours some of the most isolated and extreme environments on Earth, concealing a largely unexplored and unique component of the global animal virosphere. To understand the diversity and evolutionary histories of viruses in these polar species, we determined the viromes of gill metatranscriptomes from 11 Antarctic fish species with 248 samples collected from the Ross Sea region spanning the Perciformes, Gadiformes, and Scorpaeniformes orders. The continent's shift southward and cooling temperatures >20 million years ago led to a reduction in biodiversity and subsequent radiation of some marine fauna, such as the notothenioid fishes. Despite decreased host species richness in polar regions, we revealed a surprisingly complex virome diversity in Ross Sea fish, with the types and numbers of viruses per host species and individuals sampled comparable to that of fish in warmer marine environments with higher host community diversity. We also observed a higher number of closely related viruses likely representing instances of recent and historic host-switching events among the Perciformes (all notothenioids) than in the Gadiformes, suggesting that rapid speciation events within this order generated closely related host species with few genetic barriers to cross-species transmission. Additionally, we identified novel genomic variation in an arenavirus with a split nucleoprotein sequence containing a stable helical structure, indicating potential adaptation of viral proteins to extreme temperatures. These findings enhance our understanding of virus evolution and virus-host interactions in response to environmental shifts, especially in less diverse ecosystems that are more vulnerable to the impacts of anthropogenic and climate changes.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Stephanie J Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Janelle R Wierenga
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Lauren Lim
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jérémy Dubrulle
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Institute of Environmental Science and Research, Wellington 5018, New Zealand
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Ciezarek AG, Mehta TK, Man A, Ford AGP, Kavembe GD, Kasozi N, Ngatunga BP, Shechonge AH, Tamatamah R, Nyingi DW, Cnaani A, Ndiwa TC, Di Palma F, Turner GF, Genner MJ, Haerty W. Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes. Mol Biol Evol 2024; 41:msae116. [PMID: 38865496 PMCID: PMC11221657 DOI: 10.1093/molbev/msae116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/14/2024] Open
Abstract
Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.
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Affiliation(s)
- Adam G Ciezarek
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- Centre of Environment, Fisheries and Aquaculture Science (Cefas), Scientific Advice for Fisheries Management Team (SAFM), Lowestoft NR33 0H5, UK
| | - Tarang K Mehta
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Angela Man
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Antonia G P Ford
- School of Life and Health Sciences, Whitelands College, University of Roehampton, London SW15 4NA, UK
| | | | - Nasser Kasozi
- National Agricultural Research Organisation, Buginyanya Zonal Agricultural Research and Development Institute, Mbale, Uganda
| | | | | | | | | | - Avner Cnaani
- Institute of Animal Science, Agricultural Research Organization, Rishon LeZion 7528809, Israel
| | - Titus C Ndiwa
- Department of Clinical Studies, University of Nairobi, Nairobi, Kenya
| | - Federica Di Palma
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - George F Turner
- School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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Pontarp M, Lundberg P, Ripa J. The succession of ecological divergence and reproductive isolation in adaptive radiations. J Theor Biol 2024; 587:111819. [PMID: 38589008 DOI: 10.1016/j.jtbi.2024.111819] [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: 08/27/2023] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
Adaptive radiation is a major source of biodiversity but the way in which known components of ecological opportunity, ecological differentiation, and reproductive isolation underpin such biodiversity patterns remains elusive. Much is known about the evolution of ecological differentiation and reproductive isolation during single speciation events, but exactly how those processes scale up to complete adaptive radiations is less understood. Do we expect complete reproductive barriers between newly formed species before the ecological differentiation continues, or does proper species formation occur much later, long after the ecological diversification? Our goal is to improve our mechanistic understanding of adaptive radiations by analyzing an individual-based model that includes a suite of mechanisms that are known to contribute to biodiversity. The model includes variable biogeographic settings, ecological opportunities, and types of mate choice, which makes several different scenarios of an adaptive radiation possible. We find that evolving clades tend to exploit ecological opportunities early whereas reproductive barriers evolve later, demonstrating a decoupling of ecological differentiation and species formation. In many cases, we also find a long-term trend where assortative mating associated with ecological traits is replaced by sexual selection of neutral display traits as the primary mechanism for reproductive isolation. Our results propose that reticulate phylogenies are likely common and stem from initially low reproductive barriers, rather than the previously suggested idea of repeated hybridization events between well-separated species.
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Affiliation(s)
- Mikael Pontarp
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden.
| | - Per Lundberg
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden
| | - Jörgen Ripa
- Department of Biology, Lund University, Sölvegatan 37, SE-223 62 Lund, Sweden
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9
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Lecocq de Pletincx N, Cerdà X, Kiran K, Karaman C, Taheri A, Aron S. Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants. iScience 2024; 27:109852. [PMID: 38779477 PMCID: PMC11109030 DOI: 10.1016/j.isci.2024.109852] [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: 11/30/2023] [Revised: 03/20/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Biological diversity often arises as organisms adapt to new ecological conditions (i.e., ecological opportunities) or colonize suitable areas (i.e., spatial opportunities). Cases of geographical expansion followed by local ecological divergence are well described; they result in clades comprising ecologically heterogeneous subclades. Here, we show that the desert ant genus Cataglyphis likely originated in open grassland habitats in the Middle East ∼18 million years ago and became a taxon of diverse species specializing in prey of different masses. The genus then colonized the Mediterranean Basin around 9 million years ago. The result was the rapid accumulation of species, and the appearance of local assemblages containing species from different lineages that still displayed ancestral foraging specialties. These findings highlight that, in Cataglyphis, ecological diversification preceded geographical expansion, resulting in a clade composed of ecologically homogeneous subclades.
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Affiliation(s)
- Nathan Lecocq de Pletincx
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
| | - Xim Cerdà
- Department of Ethology and Biodiversity Conservation, Estación Biológica de Doñana, CSIC, Sevilla, Spain
| | - Kadri Kiran
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Celal Karaman
- Department of Biology, Faculty of Sciences, Trakya University, Edirne 22030, Türkiye
| | - Ahmed Taheri
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences of El Jadida, University Chouaïb Doukkali, El Jadida, Morocco
| | - Serge Aron
- Evolutionary Biology and Ecology, Faculty of Sciences, Université Libre de Bruxelles, CP 160/12, av. FD Roosevelt, 1050 Brussels, Belgium
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Domínguez-Guerrero SF, Esquerré D, Burress ED, Maciel-Mata CA, Alencar LRV, Muñoz MM. Viviparity imparts a macroevolutionary signature of ecological opportunity in the body size of female Liolaemus lizards. Nat Commun 2024; 15:4966. [PMID: 38862522 PMCID: PMC11167029 DOI: 10.1038/s41467-024-49464-x] [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: 08/29/2023] [Accepted: 06/05/2024] [Indexed: 06/13/2024] Open
Abstract
Viviparity evolved ~115 times across squamate reptiles, facilitating the colonization of cold habitats, where oviparous species are scarce or absent. Whether the ecological opportunity furnished by such colonization reconfigures phenotypic diversity and accelerates evolution is unclear. We investigated the association between viviparity and patterns and rates of body size evolution in female Liolaemus lizards, the most species-rich tetrapod genus from temperate regions. Here, we discover that viviparous species evolve ~20% larger optimal body sizes than their oviparous relatives, but exhibit similar rates of body size evolution. Through a causal modeling approach, we find that viviparity indirectly influences body size evolution through shifts in thermal environment. Accordingly, the colonization of cold habitats favors larger body sizes in viviparous species, reconfiguring body size diversity in Liolaemus. The catalyzing influence of viviparity on phenotypic evolution arises because it unlocks access to otherwise inaccessible sources of ecological opportunity, an outcome potentially repeated across the tree of life.
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Affiliation(s)
| | - Damien Esquerré
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Edward D Burress
- Department of Ecology and Evolutionary Biology, Yale University, 06511, New Haven, CT, USA
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35487, USA
| | - Carlos A Maciel-Mata
- Predio Intensivo de Manejo de Vida Silvestre X-Plora Reptilia, 43350, Metztitlán, Hidalgo, México
| | - Laura R V Alencar
- Department of Ecology and Evolutionary Biology, Yale University, 06511, New Haven, CT, USA
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, 06511, New Haven, CT, USA
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11
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Choi N, Mathevon N, Hebets EA, Beauchaud M. Influence of ambient water coloration on habitat and conspecific choice in the female Lake Malawi cichlid, Metriaclima zebra. Curr Zool 2024; 70:214-224. [PMID: 38726246 PMCID: PMC11078059 DOI: 10.1093/cz/zoad015] [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: 02/01/2023] [Accepted: 04/19/2023] [Indexed: 05/12/2024] Open
Abstract
Female cichlid fish living in African great lakes are known to have sensory systems that are adapted to ambient light environments. These sensory system adaptations are hypothesized to have influenced the evolution of the diverse male nuptial coloration. In rock-dwelling Lake Malawi mbuna cichlids, however, the extent to which ambient light environments influence female sensory systems and potentially associated male nuptial coloration remains unknown. Yet, the ubiquitous blue flank coloration and UV reflection of male mbuna cichlids suggest the potential impacts of the blue-shifted ambient light environment on these cichlid's visual perception and male nuptial coloration in the shallow water depth in Lake Malawi. In the present study, we explored whether and how the sensory bias of females influences intersexual communication in the mbuna cichlid, Metriaclima zebra. A series of choice experiments in various light environments showed that M. zebra females 1) have a preference for the blue-shifted light environment, 2) prefer to interact with males in blue-shifted light environments, 3) do not show a preference between dominant and subordinate males in full-spectrum, long-wavelength filtered, and short-wavelength filtered light environments, and 4) show a "reversed" preference for subordinate males in the UV-filtered light environment. These results suggest that the visual perception of M. zebra females may be biased to the ambient light spectra in their natural habitat by local adaptation and that this sensory bias may influence the evolution of blue and UV reflective patterns in male nuptial coloration.
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Affiliation(s)
- Noori Choi
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
- ENES Bioacoustics Research Laboratory, CRNL, CNRS, Inserm, Université de Saint-Etienne, Saint-Etienne, France
- Max Planck Institute of Animal Behavior, Konstanz, Germany
| | - Nicolas Mathevon
- ENES Bioacoustics Research Laboratory, CRNL, CNRS, Inserm, Université de Saint-Etienne, Saint-Etienne, France
| | - Eileen A Hebets
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Marilyn Beauchaud
- ENES Bioacoustics Research Laboratory, CRNL, CNRS, Inserm, Université de Saint-Etienne, Saint-Etienne, France
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Zhao W, Gao J, Hall D, Andersson BA, Bruxaux J, Tomlinson KW, Drouzas AD, Suyama Y, Wang XR. Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow. THE NEW PHYTOLOGIST 2024. [PMID: 38515228 DOI: 10.1111/nph.19694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Evolutionary radiation, a pivotal aspect of macroevolution, offers valuable insights into evolutionary processes. The genus Pinus is the largest genus in conifers withc . $$ c. $$ 90% of the extant species emerged in the Miocene, which signifies a case of rapid diversification. Despite this remarkable history, our understanding of the mechanisms driving radiation within this expansive genus has remained limited. Using exome capture sequencing and a fossil-calibrated phylogeny, we investigated the divergence history, niche diversification, and introgression among 13 closely related Eurasian species spanning climate zones from the tropics to the boreal Arctic. We detected complex introgression among lineages in subsection Pinus at all stages of the phylogeny. Despite this widespread gene exchange, each species maintained its genetic identity and showed clear niche differentiation. Demographic analysis unveiled distinct population histories among these species, which further influenced the nucleotide diversity and efficacy of purifying and positive selection in each species. Our findings suggest that radiation in the Eurasian pines was likely fueled by interspecific recombination and further reinforced by their adaptation to distinct environments. Our study highlights the constraints and opportunities for evolutionary change, and the expectations of future adaptation in response to environmental changes in different lineages.
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Affiliation(s)
- Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - David Hall
- Forestry Research Institute of Sweden (Skogforsk), Sävar, SE-91833, Sweden
| | - Bea Angelica Andersson
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Jade Bruxaux
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
| | - Kyle W Tomlinson
- Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephant, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
| | - Andreas D Drouzas
- Laboratory of Systematic Botany and Phytogeography, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Miyagi, 989-6711, Japan
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Center, Umeå University, Umeå, SE-90187, Sweden
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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13
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Edgley DE, Carruthers M, Gabagambi NP, Saxon AD, Smith AM, Joyce DA, Vernaz G, Santos ME, Turner GF, Genner MJ. Lateral line system diversification during the early stages of ecological speciation in cichlid fish. BMC Ecol Evol 2024; 24:24. [PMID: 38378480 PMCID: PMC10877828 DOI: 10.1186/s12862-024-02214-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND The mechanosensory lateral line system is an important sensory modality in fishes, informing multiple behaviours related to survival including finding food and navigating in dark environments. Given its ecological importance, we may expect lateral line morphology to be under disruptive selection early in the ecological speciation process. Here we quantify the lateral line system morphology of two ecomorphs of the cichlid fish Astatotilapia calliptera in crater Lake Masoko that have diverged from common ancestry within the past 1,000 years. RESULTS Based on geometric morphometric analyses of CT scans, we show that the zooplanktivorous benthic ecomorph that dominates the deeper waters of the lake has large cranial lateral line canal pores, relative to those of the nearshore invertebrate-feeding littoral ecomorph found in the shallower waters. In contrast, fluorescence imaging revealed no evidence for divergence between ecomorphs in the number of either superficial or canal neuromasts. We illustrate the magnitude of the variation we observe in Lake Masoko A. calliptera in the context of the neighbouring Lake Malawi mega-radiation that comprises over 700 species. CONCLUSIONS These results provide the first evidence of divergence in this often-overlooked sensory modality in the early stages of ecological speciation, suggesting that it may have a role in the broader adaptive radiation process.
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Affiliation(s)
- Duncan E Edgley
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Madeleine Carruthers
- School of Biological Sciences, University of Bristol, Bristol, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Nestory P Gabagambi
- Tanzania Fisheries Research Institute, Kyela Centre, P.O. Box 98, Kyela, Mbeya, Tanzania
| | - Andrew D Saxon
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Alan M Smith
- School of Natural Sciences, University of Hull, Hull, UK
| | - Domino A Joyce
- School of Natural Sciences, University of Hull, Hull, UK
| | - Grégoire Vernaz
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK
- Wellcome/Cancer Research UK, Gurdon Institute, University of Cambridge, Cambridge, UK
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Martin J Genner
- School of Biological Sciences, University of Bristol, Bristol, UK.
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14
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Morita K, Saito T, Uechi T, Sawada N, Miura O. Out of the ancient lake: Multiple riverine colonizations and diversification of the freshwater snails in the genus Semisulcospira around Lake Biwa. Mol Phylogenet Evol 2024; 191:107987. [PMID: 38081401 DOI: 10.1016/j.ympev.2023.107987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023]
Abstract
Ancient lakes are a hotspot of biodiversity. Freshwater species often experience spectacular species radiation after colonizing lakes from riverine habitats. Therefore, the relationship between the fauna of the ancient lakes and the surrounding riverine system has a special significance in understanding their origin and evolutionary history. The study of ancient lake species often focused on the lake colonization of riverine species. In contrast, far less attention has been placed on the reverse direction: the riverine colonization of the lake species, despite its importance in disentangling their complex evolutionary history. The freshwater snails in the genus Semisulcospira involve endemic groups that radiated in the ancient Lake Biwa. Using genetics and fossil records, we inferred that the ancestors of these lake-endemic Semisulcospira snails historically colonized the riverine habitats at least three times during the Middle Pleistocene. Each colonization resulted in the formation of a new lineage that was genetically and morphologically distinct from other lineages. Further, one of these colonizations was followed by hybridization with a cosmopolitan riverine species, which potentially facilitated the population persistence of the colonizers in the new environment. Despite their complex histories, all these colonizers were currently grouped within a single species, Semisulcospira kurodai, suggesting cryptic diversity in this species. This study highlights the significance of the riverine colonizations of the lake species to fully understand the diversification history of freshwater fauna in and around the ancient lakes.
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Affiliation(s)
- Kohei Morita
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502 Japan
| | - Takumi Saito
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Takeru Uechi
- Major in Environmental Management, Graduate School of Agriculture, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Naoto Sawada
- Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo, Kyoto, Kyoto 606-8502 Japan
| | - Osamu Miura
- Faculty of Agriculture and Marine Science, Kochi University, 200 Monobe, Nankoku, Kochi 783-8502 Japan.
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15
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DeLorenzo L, Powder KE. Epigenetics and the evolution of form: Experimental manipulation of a chromatin modification causes species-specific changes to the craniofacial skeleton. Evol Dev 2024; 26:e12461. [PMID: 37850843 PMCID: PMC10842503 DOI: 10.1111/ede.12461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/18/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023]
Abstract
A central question in biology is the molecular origins of phenotypic diversity. While genetic changes are key to the genotype-phenotype relationship, alterations to chromatin structure and the physical packaging of histone proteins may also be important drivers of vertebrate divergence. We investigate the impact of such an epigenetic mechanism, histone acetylation, within a textbook example of an adaptive radiation. Cichlids of Lake Malawi have adapted diverse craniofacial structures, and here we investigate how histone acetylation influences morphological variation in these fishes. Specifically, we assessed the effect of inhibiting histone deacetylation using the drug trichostatin A (TSA) on developing facial structures. We examined this during three critical developmental windows in two cichlid species with alternate adult morphologies. Exposure to TSA during neural crest cell (NCC) migration and as postmigratory NCCs proliferate in the pharyngeal arches resulted in significant changes in lateral and ventral shape in Maylandia, but not in Tropheops. This included an overall shortening of the head, widening of the lower jaw, and steeper craniofacial profile, all of which are paedomorphic morphologies. In contrast, treatment with TSA during early chondrogenesis did not result in significant morphological changes in either species. Together, these data suggest a sensitivity to epigenetic alterations that are both time- and species-dependent. We find that morphologies are due to nonautonomous or potentially indirect effects on NCC development, including in part a global developmental delay. Our research bolsters the understanding that proper histone acetylation is essential for early craniofacial development and identifies a species-specific robustness to developmental change. Overall, this study demonstrates how epigenetic regulation may play an important role in both generating and buffering morphological variation.
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Affiliation(s)
- Leah DeLorenzo
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Kara E Powder
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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16
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Lapiedra O, Morales N, Yang LH, Fernández-Bellon D, Michaelides SN, Giery ST, Piovia-Scott J, Schoener TW, Kolbe JJ, Losos JB. Predator-driven behavioural shifts in a common lizard shape resource-flow from marine to terrestrial ecosystems. Ecol Lett 2024; 27:e14335. [PMID: 37972585 DOI: 10.1111/ele.14335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 11/19/2023]
Abstract
Foraging decisions shape the structure of food webs. Therefore, a behavioural shift in a single species can potentially modify resource-flow dynamics of entire ecosystems. To examine this, we conducted a field experiment to assess foraging niche dynamics of semi-arboreal brown anole lizards in the presence/absence of predatory ground-dwelling curly-tailed lizards in a replicated set of island ecosystems. One year after experimental translocation, brown anoles exposed to these predators had drastically increased perch height and reduced consumption of marine-derived food resources. This foraging niche shift altered marine-to-terrestrial resource-flow dynamics and persisted in the diets of the first-generation offspring. Furthermore, female lizards that displayed more risk-taking behaviours consumed more marine prey on islands with predators present. Our results show how predator-driven rapid behavioural shifts can alter food-web connectivity between oceanic and terrestrial ecosystems and underscore the importance of studying behaviour-mediated niche shifts to understand ecosystem functioning in rapidly changing environments.
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Affiliation(s)
- Oriol Lapiedra
- CREAF, Edifici C Campus de Bellaterra, Cerdanyola del Valles, Spain
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nina Morales
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Louie H Yang
- Department of Entomology and Nematology, University of California, Davis, California, USA
| | - Darío Fernández-Bellon
- School of Biological, Earth and Environmental Science (BEES), University College Cork, Cork, Ireland
| | | | - Sean T Giery
- Department of Biology, Ohio University, Athens, Ohio, USA
| | - Jonah Piovia-Scott
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Thomas W Schoener
- Department of Entomology, University of California, Davis, California, USA
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Jonathan B Losos
- Department of Biology, Washington University of St. Louis, St. Louis, Missouri, USA
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17
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Irazábal-González L, Wright DS, Maan ME. Developmental and environmental plasticity in opsin gene expression in Lake Victoria cichlid fish. Evol Dev 2024; 26:e12465. [PMID: 38041513 DOI: 10.1111/ede.12465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023]
Abstract
In many organisms, sensory abilities develop and evolve according to the changing demands of navigating, foraging, and communication across different environments and life stages. Teleost fish inhabit heterogeneous light environments and exhibit a large diversity in visual system properties among species. Cichlids are a classic example of this diversity; visual system variation is generated by different tuning mechanisms that involve both genetic factors and phenotypic plasticity. Here, we document the developmental progression of visual pigment gene expression in Lake Victoria cichlids and test if these patterns are influenced by variation in light conditions. We reared two sister species of Pundamilia to adulthood in two distinct visual conditions that resemble the light environments that they naturally inhabit in Lake Victoria. We also included interspecific first-generation hybrids. We focused on the four opsins that are expressed in Pundamilia adults (using real-time quantitative polymerase chain reaction (RT-qPCR)) (SWS2B, SWS2A, RH2A, and LWS) at 17 time points. We find that opsin expression profiles progress from shorter-wavelength sensitive opsins to longer-wavelength sensitive opsins with increasing age, in both species and their hybrids. The developmental trajectories of opsin expression also responded plastically to the visual conditions. Developmental and environmental plasticity in opsin expression may provide an important stepping stone in the evolution of cichlid visual system diversity.
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Affiliation(s)
- Lucia Irazábal-González
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Daniel S Wright
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Martine E Maan
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
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18
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Seeholzer GF, Brumfield RT. Speciation-by-Extinction. Syst Biol 2023; 72:1433-1442. [PMID: 37542735 DOI: 10.1093/sysbio/syad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023] Open
Abstract
Extinction is a dominant force shaping patterns of biodiversity through time; however its role as a catalyst of speciation through its interaction with intraspecific variation has been overlooked. Here, we synthesize ideas alluded to by Darwin and others into the model of "speciation-by-extinction" in which speciation results from the extinction of intermediate populations within a single geographically variable species. We explore the properties and distinguishing features of speciation-by-extinction with respect to other established speciation models. We demonstrate its plausibility by showing that the experimental extinction of populations within variable species can result in speciation. The prerequisites for speciation-by-extinction, geographically structured intraspecific variation and local extinction, are ubiquitous in nature. We propose that speciation-by-extinction may be a prevalent, but underappreciated, speciation mechanism.
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Affiliation(s)
- Glenn F Seeholzer
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY, 14850, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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19
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Cao X, Deng S, Liu Q, Wu L, Zhuang X, Ding S. Important Role of the Ihh Signaling Pathway in Initiating Early Cranial Remodeling and Morphological Specialization in Cromileptes altivelis. Animals (Basel) 2023; 13:3840. [PMID: 38136878 PMCID: PMC10740873 DOI: 10.3390/ani13243840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
In this study, we identified the important contribution of frontal bone remodeling in shaping the 'sunken head and humpback' appearance in C. altivelis. Our investigation identified a developmental milestone at a total length of 5-6 cm, making the onset of its morphologic specialization in this species. A comparative analysis with closely related species reveals heightened activity in the frontal osteoblasts of the humpback grouper, potentially providing a physiological basis for its remodeling. Furthermore, our findings highlight that a significant upregulation in the expression levels of Ihhb, Ptch1, and Gli2a genes was seen in C. altivelis within the specified developmental stage, indicating an important involvement of the Ihhb-Ptch1-Gli2a signaling pathway in initiating the morphological specialization. We hypothesized that Ihh signaling could be attributed to shifts in mechanical stress, resulting from muscle traction on the frontal bone due to changes in swimming patterns during development. This study not only offers significant insights into unraveling the molecular mechanisms that govern phenotypic specialization and ecological adaptations in the humpback grouper but also serves as a valuable reference for studies on fishes with a controversial morphology and molecular phylogeny.
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Affiliation(s)
- Xiaoying Cao
- State Key Laboratory of Marine Environment Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Shunyun Deng
- State Key Laboratory of Marine Environment Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Quanyin Liu
- State Key Laboratory of Marine Environment Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Lisheng Wu
- State Key Laboratory of Marine Environment Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Xuan Zhuang
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Shaoxiong Ding
- State Key Laboratory of Marine Environment Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
- Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
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20
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Muschick M, Jemmi E, Lengacher N, Hänsch S, Wales N, Kishe MA, Mwaiko S, Dieleman J, Lever MA, Salzburger W, Verschuren D, Seehausen O. Ancient DNA is preserved in fish fossils from tropical lake sediments. Mol Ecol 2023; 32:5913-5931. [PMID: 37830773 DOI: 10.1111/mec.17159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/30/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
Tropical freshwater lakes are well known for their high biodiversity, and particularly the East African Great Lakes are renowned for their adaptive radiation of cichlid fishes. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, little is known about evolutionary trajectories within lineages, the impacts of environmental drivers, or the scope and nature of now-extinct diversity. Time-structured palaeodata from geologically young fossil records, such as fossil counts and particularly ancient DNA (aDNA) data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous aDNA. Despite generally low endogenous content and high sample dropout, the application of high-throughput sequencing and, in some cases, sequence capture allowed taxonomic assignment and phylogenetic placement of 17% of analysed fish fossils to family or tribe level, including remains which are up to 2700 years old or weigh less than 1 mg. The relationship between aDNA degradation and the thermal age of samples is similar to that described for terrestrial samples from cold environments when adjusted for elevated temperature. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in bottom water oxygenation. Our study demonstrates that the sediment records of tropical lakes can preserve genetic information on rapidly diversifying fish taxa over time scales of millennia.
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Affiliation(s)
- Moritz Muschick
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Eliane Jemmi
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Nicholas Lengacher
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Stephanie Hänsch
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Nathan Wales
- Department of Archaeology, University of York, York, UK
| | - Mary A Kishe
- Tanzania Fisheries Research Institute, Dar es Salaam, Tanzania
| | - Salome Mwaiko
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Jorunn Dieleman
- Limnology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Mark Alexander Lever
- Institute of Biogeochemistry and Pollutant Dynamics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
- Marine Science Institute, University of Texas at Austin, Port Aransas, Texas, USA
| | | | - Dirk Verschuren
- Limnology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
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21
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Zhang C, Meng R, Meng Y, Guo BL, Liu QR, Nie ZL. Parallel evolution, atavism, and extensive introgression explain the radiation of Epimedium sect. Diphyllon (Berberidaceae) in southern East Asia. FRONTIERS IN PLANT SCIENCE 2023; 14:1234148. [PMID: 37915504 PMCID: PMC10616310 DOI: 10.3389/fpls.2023.1234148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
East Asia is the richest region of plant biodiversity in the northern temperate zone, and its radiation provides key insights for understanding rapid speciation, including evolutionary patterns and processes. However, it is challenging to investigate the recent evolutionary radiation among plants because of the lack of genetic divergence, phenotypic convergence, and interspecific gene flow. Epimedium sect. Diphyllon is a rarely studied plant lineage endemic to East Asia, especially highly diversified in its southern part. In this study, we report a robust phylogenomic analysis based on genotyping-by-sequencing data of this lineage. The results revealed a clear biogeographic pattern for Epimedium sect. Diphyllon with recognition into two major clades corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms of East Asian Flora and rapid diversification of the extant species dated to the Pleistocene. Evolutionary radiation of Epimedium sect. Diphyllon is characterized by recent and predominant parallel evolution and atavism between the two subkingdom regions, with extensive reticulating hybridization within each region during the course of diversification in southern East Asia. A parallel-atavism-introgression hypothesis is referred to in explaining the radiation of plant diversity in southern East Asia, which represents a potential model for the rapid diversification of plants under global climate cooling in the late Tertiary. Our study advances our understanding of the evolutionary processes of plant radiation in East Asia as well as in other biodiversity hotspot regions.
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Affiliation(s)
- Cheng Zhang
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ran Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Ying Meng
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
| | - Bao-Lin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Quan-Ru Liu
- Key Laboratory of Biodiversity Science and Ecological Engineering of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ze-Long Nie
- College of Biological Resources and Environmental Sciences, Jishou University, Jishou, Hunan, China
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22
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Ngoepe N, Muschick M, Kishe MA, Mwaiko S, Temoltzin-Loranca Y, King L, Courtney Mustaphi C, Heiri O, Wienhues G, Vogel H, Cuenca-Cambronero M, Tinner W, Grosjean M, Matthews B, Seehausen O. A continuous fish fossil record reveals key insights into adaptive radiation. Nature 2023; 622:315-320. [PMID: 37794187 PMCID: PMC10567567 DOI: 10.1038/s41586-023-06603-6] [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: 03/14/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Adaptive radiations have been instrumental in generating a considerable amount of life's diversity. Ecological opportunity is thought to be a prerequisite for adaptive radiation1, but little is known about the relative importance of species' ecological versatility versus effects of arrival order in determining which lineage radiates2. Palaeontological records that could help answer this are scarce. In Lake Victoria, a large adaptive radiation of cichlid fishes evolved in an exceptionally short and recent time interval3. We present a rich continuous fossil record extracted from a series of long sediment cores along an onshore-offshore gradient. We reconstruct the temporal sequence of events in the assembly of the fish community from thousands of tooth fossils. We reveal arrival order, relative abundance and habitat occupation of all major fish lineages in the system. We show that all major taxa arrived simultaneously as soon as the modern lake began to form. There is no evidence of the radiating haplochromine cichlid lineage arriving before others, nor of their numerical dominance upon colonization; therefore, there is no support for ecological priority effects. However, although many taxa colonized the lake early and several became abundant, only cichlids persisted in the new deep and open-water habitats once these emerged. Because these habitat gradients are also known to have played a major role in speciation, our findings are consistent with the hypothesis that ecological versatility was key to adaptive radiation, not priority by arrival order nor initial numerical dominance.
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Affiliation(s)
- Nare Ngoepe
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland.
| | - Moritz Muschick
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Mary A Kishe
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Salome Mwaiko
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | | | - Leighton King
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Colin Courtney Mustaphi
- Geoecology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Center for Water Infrastructure and Sustainable Energy (WISE) Futures, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Oliver Heiri
- Geoecology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Giulia Wienhues
- Institute of Geography & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Maria Cuenca-Cambronero
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
- Aquatic Ecology, University of Vic - Central University of Catalonia, Vic, Spain
| | - Willy Tinner
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Martin Grosjean
- Institute of Geography & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Blake Matthews
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
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23
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Meier JI, McGee MD, Marques DA, Mwaiko S, Kishe M, Wandera S, Neumann D, Mrosso H, Chapman LJ, Chapman CA, Kaufman L, Taabu-Munyaho A, Wagner CE, Bruggmann R, Excoffier L, Seehausen O. Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science 2023; 381:eade2833. [PMID: 37769075 DOI: 10.1126/science.ade2833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/21/2023] [Indexed: 09/30/2023]
Abstract
Although some lineages of animals and plants have made impressive adaptive radiations when provided with ecological opportunity, the propensities to radiate vary profoundly among lineages for unknown reasons. In Africa's Lake Victoria region, one cichlid lineage radiated in every lake, with the largest radiation taking place in a lake less than 16,000 years old. We show that all of its ecological guilds evolved in situ. Cycles of lineage fusion through admixture and lineage fission through speciation characterize the history of the radiation. It was jump-started when several swamp-dwelling refugial populations, each of which were of older hybrid descent, met in the newly forming lake, where they fused into a single population, resuspending old admixture variation. Each population contributed a different set of ancient alleles from which a new adaptive radiation assembled in record time, involving additional fusion-fission cycles. We argue that repeated fusion-fission cycles in the history of a lineage make adaptive radiation fast and predictable.
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Affiliation(s)
- Joana I Meier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D McGee
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Natural History Museum Basel, Basel, Switzerland
| | - Salome Mwaiko
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Mary Kishe
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Sylvester Wandera
- National Fisheries Resources Research Institute (NAFIRRI), Jinja, Uganda
| | - Dirk Neumann
- Leipniz Institute for Biodiversity Change, Hamburg, Germany
| | - Hilary Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Colin A Chapman
- Wilson Center, Washington, DC, USA
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Les Kaufman
- Boston University Marine Program, Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
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24
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Haberthür D, Law M, Ford K, Häsler M, Seehausen O, Hlushchuk R. Microtomographic investigation of a large corpus of cichlids. PLoS One 2023; 18:e0291003. [PMID: 37756267 PMCID: PMC10529598 DOI: 10.1371/journal.pone.0291003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
A large collection of cichlids (N = 133) from Lake Victoria in Africa, with total lengths ranging from 6 to 18 cm was nondestructively imaged using micro-computed tomography. We present a method to efficiently obtain three-dimensional tomographic datasets of the oral and pharyngeal jaws and the whole skull of these fishes to accurately describe their morphology. The tomographic data we acquired (9.8 TB of projection images) yielded 1.5 TB of three-dimensional image stacks used for extracting the relevant features of interest. Herein we present our method and outlooks on analyzing the acquired data; a morphological description of the oral and pharyngeal jaws, a three-dimensional geometric morphometrics analysis of landmarked skull features, and a robust method to automatically extract otoliths from the tomographic data.
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Affiliation(s)
| | - Mikki Law
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Kassandra Ford
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
- Department of Biological Sciences, George Washington University, Washington, DC, United States of America
| | - Marcel Häsler
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute for Aquatic Science and Technology, Kastanienbaum, Switzerland
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25
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Roberts-Hugghis AS, Burress ED, Lam B, Wainwright PC. The cichlid pharyngeal jaw novelty enhances evolutionary integration in the feeding apparatus. Evolution 2023; 77:1917-1929. [PMID: 37326103 DOI: 10.1093/evolut/qpad109] [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: 05/29/2023] [Accepted: 06/14/2023] [Indexed: 06/17/2023]
Abstract
The modified pharyngeal jaw system of cichlid fishes is widely viewed as a key innovation that substantially facilitated the evolutionary exuberance of this iconic evolutionary radiation. We conduct comparative phylogenetic analyses of integration, disparity, and rate of evolution among feeding-related, skeletal structures in Neotropical cichlids and North American centrarchids, which lack the specialized pharyngeal jaw. Contrasting evolutionary patterns in these two continental radiations, we test a classic decoupling hypothesis. Specifically, we ask whether the modified pharyngeal jaw in cichlids resulted in enhanced evolutionary independence of the oral and pharyngeal jaws, leading to increased diversity of trophic structures. Contrary to this prediction, we find significantly stronger evolutionary integration between the oral and pharyngeal jaws in cichlids compared to centrarchids, although the two groups do not differ in patterns of integration within each jaw system. Further, though we find no significant differences in disparity, centrarchids show faster rates of morphological evolution. Our results suggest that the modified pharyngeal jaw resulted in less evolutionary independence and slower rates of evolution within the feeding system. Thus, we raise the possibility that the cichlid novelty enhances feeding performance, but does not prompt increased morphological diversification within the feeding apparatus, as has long been thought.
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Affiliation(s)
| | - Edward D Burress
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Brian Lam
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, United States
| | - Peter C Wainwright
- Department of Evolution and Ecology, University of California-Davis, Davis, CA, United States
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26
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Moons T, Kmentová N, Pariselle A, Artois T, Bert W, Vanhove MP, Cruz-Laufer AJ. All quiet on the western front? The evolutionary history of monogeneans (Dactylogyridae: Cichlidogyrus, Onchobdella) infecting a West and Central African tribe of cichlid fishes (Chromidotilapiini). Parasite 2023; 30:25. [PMID: 37404116 PMCID: PMC10321234 DOI: 10.1051/parasite/2023023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/21/2023] [Indexed: 07/06/2023] Open
Abstract
Owing to the largely unexplored diversity of metazoan parasites, their speciation mechanisms and the circumstances under which such speciation occurs - in allopatry or sympatry - remain vastly understudied. Cichlids and their monogenean flatworm parasites have previously served as a study system for macroevolutionary processes, e.g., for the role of East African host radiations on parasite communities. Here, we investigate the diversity and evolution of the poorly explored monogeneans infecting a West and Central African lineage of cichlid fishes: Chromidotilapiini, which is the most species-rich tribe of cichlids in this region. We screened gills of 149 host specimens (27 species) from natural history collections and measured systematically informative characters of the sclerotised attachment and reproductive organs of the parasites. Ten monogenean species (Dactylogyridae: Cichlidogyrus and Onchobdella) were found, eight of which are newly described and one redescribed herein. The phylogenetic positions of chromidotilapiines-infecting species of Cichlidogyrus were inferred through a parsimony analysis of the morphological characters. Furthermore, we employed machine learning algorithms to detect morphological features associated with the main lineages of Cichlidogyrus. Although the results of these experimental algorithms remain inconclusive, the parsimony analysis indicates that West and Central African lineages of Cichlidogyrus and Onchobdella are monophyletic, unlike the paraphyletic host lineages. Several instances of host sharing suggest occurrences of intra-host speciation (sympatry) and host switching (allopatry). Some morphological variation was recorded that may also indicate the presence of species complexes. We conclude that collection material can provide important insights on parasite evolution despite the lack of well-preserved DNA material.
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Affiliation(s)
- Tanisha Moons
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
- Nematology Research Unit, Department of Biology, Ghent University K.L. Ledeganckstraat 35 9000 Ghent Belgium
- Department of Parasitology, Faculty of Science, University of South Bohemia České Budějovice 37005 Czech Republic
| | - Nikol Kmentová
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
| | - Antoine Pariselle
- ISEM, Université de Montpellier, CNRS, IRD 34095 Montpellier France
- Faculty of Sciences, Laboratory “Biodiversity, Ecology and Genome”, Research Centre “Plant and Microbial Biotechnology, Biodiversity and Environment”, Mohammed V University 10000 Rabat Morocco
| | - Tom Artois
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
| | - Wim Bert
- Nematology Research Unit, Department of Biology, Ghent University K.L. Ledeganckstraat 35 9000 Ghent Belgium
| | - Maarten P.M. Vanhove
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
| | - Armando J. Cruz-Laufer
- UHasselt – Hasselt University, Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Agoralaan Gebouw D 3590 Diepenbeek Belgium
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27
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Tetrault E, Swenson J, Aaronson B, Marcho C, Albertson RC. The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments. Mol Ecol 2023; 32:3922-3941. [PMID: 37160741 PMCID: PMC10524807 DOI: 10.1111/mec.16975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Adaptive phenotypes are shaped by a combination of genetic and environmental forces, but how they interact remains poorly understood. Here, we utilize the cichlid oral jaw apparatus to better understand these gene-by-environment effects. First, we employed RNA-seq in bony and ligamentous tissues important for jaw opening to identify differentially expressed genes between species and across foraging environments. We used two Lake Malawi species adapted to different foraging habitats along the pelagic-benthic ecomorphological axis. Our foraging treatments were designed to force animals to employ either suction or biting/scraping, which broadly mimic pelagic or benthic modes of feeding. We found a large number of differentially expressed genes between species, and while we identified relatively few differences between environments, species differences were far more pronounced when they were challenged with a pelagic versus benthic foraging mode. Expression data carried the signature of genetic assimilation, and implicated cell cycle regulation in shaping the jaw across species and environments. Next, we repeated the foraging experiment and performed ATAC-seq procedures on nuclei harvested from the same tissues. Cross-referencing results from both analyses revealed subsets of genes that were both differentially expressed and differentially accessible. This reduced dataset implicated notable candidate genes including the Hedgehog effector, KIAA0586 and the ETS transcription factor, etv4, which connects environmental stress and craniofacial morphogenesis. Taken together, these data provide novel insights into the epigenetic, genetic and cellular bases of species- and environment-specific bone shapes.
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Affiliation(s)
- Emily Tetrault
- Graduate Program in Molecular and Cell Biology, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - John Swenson
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - Ben Aaronson
- Biology Department, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - Chelsea Marcho
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst MA, 01003, U.S.A
| | - R. Craig Albertson
- Biology Department, University of Massachusetts, Amherst MA, 01003, U.S.A
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28
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Álvarez-Ocaña R, Shahandeh MP, Ray V, Auer TO, Gompel N, Benton R. Odor-regulated oviposition behavior in an ecological specialist. Nat Commun 2023; 14:3041. [PMID: 37236992 DOI: 10.1038/s41467-023-38722-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Colonization of a novel ecological niche can require, or be driven by, evolution of an animal's behaviors promoting their reproductive success. We investigated the evolution and sensory basis of oviposition in Drosophila sechellia, a close relative of Drosophila melanogaster that exhibits extreme specialism for Morinda citrifolia noni fruit. D. sechellia produces fewer eggs than other drosophilids and lays these almost exclusively on noni substrates. We show that visual, textural and social cues do not explain this species-specific preference. By contrast, we find that loss of olfactory input in D. sechellia, but not D. melanogaster, essentially abolishes egg-laying, suggesting that olfaction gates gustatory-driven noni preference. Noni odors are detected by redundant olfactory pathways, but we discover a role for hexanoic acid and the cognate Ionotropic receptor 75b (Ir75b) in odor-evoked oviposition. Through receptor exchange in D. melanogaster, we provide evidence for a causal contribution of odor-tuning changes in Ir75b to the evolution of D. sechellia's oviposition behavior.
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Affiliation(s)
- Raquel Álvarez-Ocaña
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Michael P Shahandeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Vijayaditya Ray
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Thomas O Auer
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Nicolas Gompel
- Evolutionary Ecology, Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015, Lausanne, Switzerland.
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29
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Sil M, Roy A, Bhat HNP, Palden T, Karanth KP, Aravind NA. Role of paleoclimatic and paleohydrological processes in lineage divergence in freshwater organisms: A snippet from lentic genus Pila. Mol Phylogenet Evol 2023; 181:107723. [PMID: 36720420 DOI: 10.1016/j.ympev.2023.107723] [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: 11/18/2021] [Revised: 11/09/2022] [Accepted: 01/24/2023] [Indexed: 01/31/2023]
Abstract
The Indian subcontinent is extremely diverse in terms of its flora and fauna. However, only a handful of studies have aimed to understand the diversity of freshwater invertebrates using multiple lines of evidence in recent times. Here we aimed to estimate the cryptic diversity of two widespread freshwater snail species within the genus Pila (Röding, 1798) and uncover the processes behind lineage diversification in these species. We sequenced mitochondrial and nuclear markers from a comprehensive sampling of specimens from different river basins in India. We implemented an integrative taxonomy approach to delimit the lineages in these groups, employing phylogenetic, geometric morphometric and niche modelling-based methods. Then, we investigated the drivers of lineage divergence in these species using population genetic tools in conjunction with divergence time estimation. We found that both species consist of several genetically and ecologically distinct lineages. The genetic data showed that several of these lineages are restricted to a single or a few river basins. The divergence time estimation analyses indicated that the time frame of divergence within the species coincided with paleohydrological and paleoclimatic events in the Miocene. The diversification was primarily driven by allopatric isolation into different river basins. To conclude, the study sheds light on the complex interaction between the habitat preference of the species and the environment in shaping the diversification patterns in this group.
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Affiliation(s)
- Maitreya Sil
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, India; National Institute for Science Education and Research, Bhubaneswar 752050, India.
| | - Abhisikta Roy
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, India
| | - H N Poorna Bhat
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, India
| | - Tenzin Palden
- Centre for Ecological Sciences, Indian Institute of Science, Malleshwaram, Bangalore 560012, India
| | - K Praveen Karanth
- Centre for Ecological Sciences, Indian Institute of Science, Malleshwaram, Bangalore 560012, India
| | - N A Aravind
- Suri Sehgal Centre for Biodiversity and Conservation, Ashoka Trust for Research in Ecology and the Environment (ATREE), Royal Enclave, Srirampura, Jakkur PO, Bangalore 560064, India; Yenepoya Research Centre, Yenepoya University, Derlakatte, Mangalore, India.
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30
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Mancini AN, Chandrashekar A, Lahitsara JP, Ogbeta DG, Rajaonarivelo JA, Ranaivorazo NR, Rasoazanakolona J, Safwat M, Solo J, Razafindraibe JG, Razafindrakoto G, Baden AL. Terrain Ruggedness and Canopy Height Predict Short-Range Dispersal in the Critically Endangered Black-and-White Ruffed Lemur. Genes (Basel) 2023; 14:746. [PMID: 36981017 PMCID: PMC10048730 DOI: 10.3390/genes14030746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
Dispersal is a fundamental aspect of primates' lives and influences both population and community structuring, as well as species evolution. Primates disperse within an environmental context, where both local and intervening environmental factors affect all phases of dispersal. To date, research has primarily focused on how the intervening landscape influences primate dispersal, with few assessing the effects of local habitat characteristics. Here, we use a landscape genetics approach to examine between- and within-site environmental drivers of short-range black-and-white ruffed lemur (Varecia variegata) dispersal in the Ranomafana region of southeastern Madagascar. We identified the most influential drivers of short-range ruffed lemur dispersal as being between-site terrain ruggedness and canopy height, more so than any within-site habitat characteristic evaluated. Our results suggest that ruffed lemurs disperse through the least rugged terrain that enables them to remain within their preferred tall-canopied forest habitat. Furthermore, we noted a scale-dependent environmental effect when comparing our results to earlier landscape characteristics identified as driving long-range ruffed lemur dispersal. We found that forest structure drives short-range dispersal events, whereas forest presence facilitates long-range dispersal and multigenerational gene flow. Together, our findings highlight the importance of retaining high-quality forests and forest continuity to facilitate dispersal and maintain functional connectivity in ruffed lemurs.
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Affiliation(s)
- Amanda N. Mancini
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
| | - Aparna Chandrashekar
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
| | | | - Daisy Gold Ogbeta
- Department of Nursing, Helene Fuld College of Nursing, New York, NY 10035, USA
- Department of Chemistry, Hunter College, New York, NY 10065, USA
| | - Jeanne Arline Rajaonarivelo
- UMI 233 TransVIHMI, Institut de Recherche pour le Développement (IRD), University of Montpellier, Inserm U 1175, 34000 Montpellier, France
| | | | - Joseane Rasoazanakolona
- Department of Zoology and Animal Biodiversity, Faculty of Science, University of Antananarivo, Antananarivo 101, Madagascar
| | - Mayar Safwat
- Department of Chemistry, Hunter College, New York, NY 10065, USA
| | - Justin Solo
- Centre ValBio Research Center, Ranomafana, Ifanadiana 312, Madagascar (J.G.R.)
| | | | | | - Andrea L. Baden
- Department of Anthropology, The Graduate Center, City University of New York, New York, NY 10016, USA
- The New York Consortium in Evolutionary Primatology (NYCEP), New York, NY 10065, USA
- Department of Anthropology, Hunter College, New York, NY 10065, USA
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31
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Calvo R, Hofmann MH, Schluessel V. Brain areas activated during visual learning in the cichlid fish Pseudotropheus zebra. Brain Struct Funct 2023; 228:859-873. [PMID: 36920630 PMCID: PMC10147796 DOI: 10.1007/s00429-023-02627-w] [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: 12/25/2022] [Accepted: 03/05/2023] [Indexed: 03/16/2023]
Abstract
The neural correlates of most cognitive functions in fish are unknown. This project aimed to identify brain regions involved in visual learning in the cichlid fish Pseudotropheus zebra. The expression of the protein pS6 was measured in 19 brain areas and compared between groups of individuals subjected to four different behavioral contexts (control, avoidance, trained, and novelty groups). Control group individuals were sacrificed with minimal interactions. Fish in the avoidance group were chased with a net for an hour, after which they were sacrificed. Individuals in the trained group received daily training sessions to associate a visual object with a food reward. They were sacrificed the day they reached learning criterion. Fish in the novelty group were habituated to one set of visual stimuli, then faced a change in stimulus type (novelty stimulus) before they were sacrificed. Fish in the three treatment groups showed the largest activation of pS6 in the inferior lobes and the tectum opticum compared to the control group. The avoidance group showed additional activation in the preoptic area, several telencephalic regions, the torus semicircularis, and the reticular formation. The trained group that received a food reward, showed additional activation of the torus lateralis, a tertiary gustatory center. The only area that showed strong activation in all three treatment groups was the nucleus diffusus situated within the inferior lobe. The inferior lobe receives prominent visual input from the tectum via the nucleus glomerulosus but so far, nothing is known about the functional details of this pathway. Our study showed for the first time that the inferior lobes play an important role in visual learning and object recognition.
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Affiliation(s)
- R Calvo
- Institute of Zoology, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, Meckenheimer Allee 169, 53115, Bonn, Germany.
| | - M H Hofmann
- Institute of Zoology, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, Meckenheimer Allee 169, 53115, Bonn, Germany
| | - V Schluessel
- Institute of Zoology, Rheinische Friedrich-Wilhelms-Universität Bonn, Poppelsdorfer Schloss, Meckenheimer Allee 169, 53115, Bonn, Germany
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32
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Fiteha YG, Rashed MA, Ali RAM, Magdy M. Characterization and phylogenetic analysis of the complete mitochondrial genome of Mango tilapia (Sarotherodon galilaeus: Cichlidae). Mol Biol Rep 2023; 50:3945-3950. [PMID: 36781609 PMCID: PMC10042889 DOI: 10.1007/s11033-023-08288-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/17/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND Sarotherodon galilaeus (Linné, 1758) is a member of the family Cichlidae, which is considered the most important aquaculture freshwater species endemic to Africa and the Middle East. The genetics and molecular biology of this species are rare. This requires more comprehensive mitochondrial genomes-based phylogenetics to enhance understanding of the relationship and delineate this species. METHODS AND RESULTS Here, we assembled the complete mitogenome of S. galilaeus using Illumina high-throughput sequencing technology. The mango tilapia mitogenome was 16,631 bp in length with an AT composition of 53.4% and 46.4% GC content. It encodes 37 genes comprising two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 13 protein-coding genes (PCGs) as well as the D-loop known as the control region. The phylogenetic tree was conducted to provide a relationship within the haplotilapiine lineage based on the maximum likelihood method, and the newly sequenced S. galilaeus was clustered with other Sarotherodon species. CONCLUSION Our results provide a new perception of the genetic basis of S. galilaeus species for further research on systematics, evolution, population genetics, and molecular ecology.
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Affiliation(s)
- Yosur G Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
- Zoology Department, Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | - M A Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - R A M Ali
- Zoology Department, Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo, Egypt
| | - M Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt.
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33
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Anderson CB, Ospina O, Beerli P, Lemmon AR, Banker SE, Hassinger AB, Dye M, Kortyna ML, Lemmon EM. The population genetics of speciation by cascade reinforcement. Ecol Evol 2023; 13:e9773. [PMID: 36789346 PMCID: PMC9905665 DOI: 10.1002/ece3.9773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/22/2022] [Accepted: 01/09/2023] [Indexed: 02/10/2023] Open
Abstract
Species interactions drive diverse evolutionary outcomes. Speciation by cascade reinforcement represents one example of how species interactions can contribute to the proliferation of species. This process occurs when the divergence of mating traits in response to selection against interspecific hybridization incidentally leads to reproductive isolation among populations of the same species. Here, we investigated the population genetic outcomes of cascade reinforcement in North American chorus frogs (Hylidae: Pseudacris). Specifically, we estimated the frequency of hybridization among three taxa, assessed genetic structure within the focal species, P. feriarum, and ascertained the directionality of gene flow within P. feriarum across replicated contact zones via coalescent modeling. Through field observations and preliminary experimental crosses, we assessed whether hybridization is possible under natural and laboratory conditions. We found that hybridization occurs among P. feriarum and two conspecifics at a low rate in multiple contact zones, and that gene flow within the former species is unidirectional from allopatry into sympatry with these other species in three of four contact zones studied. We found evidence of substantial genetic structuring within P. feriarum including a divergent western allopatric cluster, a behaviorally-distinct sympatric South Carolina cluster, and several genetically-overlapping clusters from the remainder of the distribution. Furthermore, we found sub-structuring between reinforced and nonreinforced populations in the two most intensely-sampled contact zones. Our literature review indicated that P. feriarum hybridizes with at least five heterospecifics at the periphery of its range providing a mechanism for further intraspecific diversification. This work strengthens the evidence for cascade reinforcement in this clade, revealing the geographic and genetic landscape upon which this process can contribute to the proliferation of species.
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Affiliation(s)
- Carlie B Anderson
- Department of Biological Science Florida State University Tallahassee Florida USA
| | - Oscar Ospina
- Department of Biostatistics and Bioinformatics Moffitt Cancer Center Tampa Florida USA
| | - Peter Beerli
- Department of Scientific Computing Florida State University Tallahassee Florida USA
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee Florida USA
| | - Sarah E Banker
- Department of Biological Science Florida State University Tallahassee Florida USA
- Pfizer Clinical Pharmacogenomics Group Groton Connecticut USA
| | - Alyssa Bigelow Hassinger
- Department of Biological Science Florida State University Tallahassee Florida USA
- Varigen Biosciences Middleton Wisconsin USA
| | - Mysia Dye
- Department of Biological Science Florida State University Tallahassee Florida USA
| | - Michelle L Kortyna
- Department of Biological Science Florida State University Tallahassee Florida USA
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34
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Cavallino L, Rincón L, Scaia MF. Social behaviors as welfare indicators in teleost fish. Front Vet Sci 2023; 10:1050510. [PMID: 37168096 PMCID: PMC10164990 DOI: 10.3389/fvets.2023.1050510] [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: 09/21/2022] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
Animal welfare is a key issue not only for aquaculture industry and food production, but also for daily husbandry practices in research topics related to physiology in wild and farmed animals. In this context, teleost fish constitute interesting models to assess alternative welfare indicators because of their wide diversity in reproductive and social structures. Any framework for assessing teleost fish welfare needs to account for the physiological mechanisms involved in each species as a first step. A comprehensive approach should also take into account how these physiological and behavioral parameters can be altered by environmental enrichment considering the specific requirements in each case and identifying intrinsic biological characteristics of individual species. This review will show how cortisol and sex steroids regulate social behavior in teleost fish, and how different aspects of social behavior can be employed as welfare indicators according to specific characteristics in each case. This article will consider evidence in teleost fish, including cichlids, characids and cyprinids with different reproductive strategies and social structures (e.g., territorial social hierarchies or shoaling behavior). Neotropical species will be particularly emphasized. The main laboratory-based animal welfare indicators are cortisol, a classical stress hormone, together with sex steroids. Considering that the endocrine landscape is intrinsically related to social behavior, reproductive and agonistic behavioral traits such as aggression, anxiety and courtship are key elements to assess welfare under housing and culture conditions. This review highlights the importance of assessing physiological mechanisms and identifying behavioral characteristics in teleost fish, especially in Neotropical species, as a baseline to understand which environmental enrichment can improve animal welfare in each individual species.
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Affiliation(s)
- Luciano Cavallino
- Instituto de Biodiversidad y Biología Experimental y Aplicada – CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Neuroendocrinología y Comportamiento, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Laura Rincón
- Instituto de Biodiversidad y Biología Experimental y Aplicada – CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Neuroendocrinología y Comportamiento, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Florencia Scaia
- Instituto de Biodiversidad y Biología Experimental y Aplicada – CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Neuroendocrinología y Comportamiento, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- *Correspondence: María Florencia Scaia,
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35
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MacGuigan DJ, Orr OD, Near TJ. Phylogeography, hybridization, and species discovery in the Etheostoma nigrum complex (Percidae: Etheostoma: Boleosoma). Mol Phylogenet Evol 2023; 178:107645. [PMID: 36252933 DOI: 10.1016/j.ympev.2022.107645] [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: 03/09/2022] [Revised: 07/29/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Abstract
The history of riverine fish diversification is largely a product of geographic isolation. Physical barriers that reduce or eliminate gene flow between populations facilitate divergence via genetic drift and natural selection, eventually leading to speciation. For freshwater organisms, diversification is often the product of drainage basin rearrangements. In young clades where the history of isolation is the most recent, evolutionary relationships can resemble a tangled web. One especially recalcitrant group of freshwater fishes is the Johnny Darter (Etheostoma nigrum) species complex, where traditional taxonomy and molecular phylogenetics indicate a history of gene flow and conflicting inferences of species diversity. Here we assemble a genomic dataset using double digest restriction site associated DNA (ddRAD) sequencing and use phylogenomic and population genetic approaches to investigate the evolutionary history of the complex of species that includes E. nigrum, E. olmstedi, E. perlongum, and E. susanae. We reveal and validate several evolutionary lineages that we delimit as species, highlighting the need for additional work to formally describe the diversity of the Etheostoma nigrum complex. Our analyses also identify gene flow among recently diverged lineages, including one instance involving E. susanae, a localized and endangered species. Phylogeographic structure within the Etheostoma nigrum species complex coincides with major geologic events, such as parallel divergence in river basins during Pliocene inundation of the Atlantic coastal plain and multiple northward post-glacial colonization routes tracking river basin rearrangements. Our study serves as a nuanced example of how low dispersal rates coupled with geographic isolation among disconnected river systems in eastern North America has produced one of the world's freshwater biodiversity hotspots.
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Affiliation(s)
- Daniel J MacGuigan
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo, Buffalo, NY 14260, USA.
| | - Oliver D Orr
- Department of Ecology and Evolutionary Biology, 165 Prospect Street, Yale University, New Haven, CT 06520, USA; Yale Peabody Museum of Natural History, 170 Whitney Ave, New Haven, CT 06520, USA
| | - Thomas J Near
- Department of Ecology and Evolutionary Biology, 165 Prospect Street, Yale University, New Haven, CT 06520, USA; Yale Peabody Museum of Natural History, 170 Whitney Ave, New Haven, CT 06520, USA
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36
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Fiteha YG, Rashed MA, Ali RA, Abd El-Moneim D, Alshanbari FA, Magdy M. Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae). BIOLOGY 2022; 12:biology12010040. [PMID: 36671733 PMCID: PMC9855864 DOI: 10.3390/biology12010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnSGCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.
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Affiliation(s)
- Yosur G. Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A. Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ramadan A. Ali
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Fahad A. Alshanbari
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52266, Saudi Arabia
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Correspondence:
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37
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Tyler J, Younger JL. Diving into a dead-end: asymmetric evolution of diving drives diversity and disparity shifts in waterbirds. Proc Biol Sci 2022; 289:20222056. [PMID: 36515120 PMCID: PMC9748772 DOI: 10.1098/rspb.2022.2056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Diving is a relatively uncommon and highly specialized foraging strategy in birds, mostly observed within the Aequorlitornithes (waterbirds) by groups such as penguins, cormorants and alcids. Three key diving techniques are employed within waterbirds: wing-propelled pursuit diving (e.g. penguins), foot-propelled pursuit diving (e.g. cormorants) and plunge diving (e.g. gannets). How many times diving evolved within waterbirds, whether plunge diving is an intermediate state between aerial foraging and submarine diving, and whether the transition to a diving niche is reversible are not known. Here, we elucidate the evolutionary history of diving in waterbirds. We show that diving has been acquired independently at least 14 times within waterbirds, and this acquisition is apparently irreversible, in a striking example of asymmetric evolution. All three modes of diving have evolved independently, with no evidence for plunge diving as an intermediate evolutionary state. Net diversification rates differ significantly between diving versus non-diving lineages, with some diving clades apparently prone to extinction. We find that body mass is evolving under multiple macroevolutionary regimes, with unique optima for each diving type with varying degrees of constraint. Our findings highlight the vulnerability of highly specialized lineages during the ongoing sixth mass extinction.
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Affiliation(s)
- Joshua Tyler
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Jane L. Younger
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK,Institute for Marine and Antarctic Studies, University of Tasmania, Battery Point, Hobart, Tasmania 7004, Australia
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38
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Esquerré D, Brennan IG, Donnellan S, Keogh JS. Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons. Biol Lett 2022; 18:20220360. [PMID: 36541096 PMCID: PMC9768648 DOI: 10.1098/rsbl.2022.0360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
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39
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Rabosky DL. Evolutionary time and species diversity in aquatic ecosystems worldwide. Biol Rev Camb Philos Soc 2022; 97:2090-2105. [PMID: 35899476 PMCID: PMC9796449 DOI: 10.1111/brv.12884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023]
Abstract
The latitudinal diversity gradient (LDG) is frequently described as the most dramatic biodiversity pattern on Earth, yet ecologists and biogeographers have failed to reach consensus on its primary cause. A key problem in explaining the LDG involves collinearity between multiple factors that are predicted to affect species richness in the same direction. In terrestrial systems, energy input, geographic area, and evolutionary time for species accumulation tend to covary positively with species richness at the largest spatial scales, such that their individual contributions to the LDG are confounded in global analyses. I review three diversity patterns from marine and freshwater systems that break this collinearity and which may thus provide stronger tests of the influence of time on global richness gradients. Specifically, I contrast biodiversity patterns along oceanic depth gradients, in geologically young versus ancient lakes, and in the north versus south polar marine biomes. I focus primarily on fishes due to greater data availability but synthesize patterns for invertebrates where possible. I find that regional-to-global species richness generally declines with depth in the oceans, despite the great age and stability of the deep-sea biome. Geologically ancient lakes generally do not contain more species than young lakes, and the Antarctic marine biome is not appreciably more species rich than the much younger Arctic marine biome. However, endemism is consistently higher in older systems. Patterns for invertebrate groups are less clear than for fishes and reflect a critical need for primary biodiversity data. In summary, the available data suggest that species richness is either decoupled from or only weakly related to the amount of time for diversification. These results suggest that energy, productivity, or geographic area are the primary drivers of large-scale diversity gradients. To the extent that marine and terrestrial diversity gradients result from similar processes, these examples provide evidence against a primary role for evolutionary time as the cause of the LDG.
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Affiliation(s)
- Daniel L. Rabosky
- Museum of Zoology & Department of Ecology and Evolutionary BiologyUniversity of Michigan2032 Biological Sciences BuildingAnn ArborMI48109USA
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40
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Carruthers M, Edgley DE, Saxon AD, Gabagambi NP, Shechonge A, Miska EA, Durbin R, Bridle JR, Turner GF, Genner MJ. Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes. Mol Biol Evol 2022; 39:msac251. [PMID: 36376993 PMCID: PMC10101686 DOI: 10.1093/molbev/msac251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.
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Affiliation(s)
- Madeleine Carruthers
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Duncan E Edgley
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Andrew D Saxon
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - Nestory P Gabagambi
- Tanzanian Fisheries Research Institute, Kyela Research
Centre, P.O. Box 98, Kyela, Mbeya, Tanzania
| | - Asilatu Shechonge
- Tanzanian Fisheries Research Institute, Dar es Salaam Research
Centre, P.O. Box 9750, Dar es Salaam, Tanzania
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge,
Cambridge CB2 1QN, United
Kingdom
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Richard Durbin
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, United
Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus,
Cambridge CB10 1SA, United Kingdom
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
| | - George F Turner
- School of Natural Sciences, Bangor University,
Bangor, Wales LL57 2UW, United
Kingdom
| | - Martin J Genner
- School of Biological Sciences, University of Bristol,
Bristol BS8 1TQ, United
Kingdom
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41
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Imfeld TS, Barker FK. Songbirds of the Americas show uniform morphological evolution despite heterogeneous diversification. J Evol Biol 2022; 35:1335-1351. [PMID: 36057939 DOI: 10.1111/jeb.14084] [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: 09/13/2021] [Revised: 06/17/2022] [Accepted: 07/19/2022] [Indexed: 11/30/2022]
Abstract
Studying the relationship between diversification and functional trait evolution among broadly co-occurring clades can shed light on interactions between ecology and evolutionary history. However, evidence from many studies is compromised because of their focus on overly broad geographic or narrow phylogenetic scales. We addressed these limitations by studying 46 independent, biogeographically delimited clades of songbirds that dispersed from the Eastern Hemisphere into the Americas and assessed (1) whether diversification has varied through time and/or among clades within this assemblage, (2) the extent of heterogeneity in clade-specific morphological trait disparity and (3) whether morphological disparity among these clades is consistent with a uniform diversification model. We found equivalent support for constant rates birth-death and density-dependent speciation processes, with notable outliers having significantly fewer or more species than expected given their age. We also found substantial variation in morphological disparity among these clades, but that variation was broadly consistent with uniform evolutionary rates, despite the existence of diversification outliers. These findings indicate relatively continuous, ongoing morphological diversification, arguing against conceptual models of adaptive radiation in these continental clades. Additionally, they suggest surprisingly consistent diversification among the majority of these clades, despite tremendous variance in colonization history, habitat valences and trophic specializations that exist among continental clades of birds.
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Affiliation(s)
- Tyler S Imfeld
- Department of Biology, Regis University, Denver, Colorado, USA
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, USA.,Bell Museum, University of Minnesota, St. Paul, Minnesota, USA
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42
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Stuckert AMM, Matute DR. Using neutral loci to quantify reproductive isolation and speciation: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1169-1174. [PMID: 36063155 DOI: 10.1111/jeb.14057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 01/23/2023]
Affiliation(s)
- Adam M M Stuckert
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, USA
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43
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Hayden B, Harrod C, Thomas S, Kahilainen KK. Winter ecology of specialist and generalist morphs of European whitefish, Coregonus lavaretus, in subarctic northern Europe. JOURNAL OF FISH BIOLOGY 2022; 101:389-399. [PMID: 35142375 DOI: 10.1111/jfb.14999] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
European whitefish is a model species for adaptive radiation of fishes in temperate and subarctic lakes. In northern Europe the most commonly observed morphotypes are a generalist (LSR) morph and a pelagic specialist (DR) morph. The evolution of a pelagic specialist morph is something of an enigma, however, as this region is characterized by long, dark winters with pelagic primary production limited to a brief window in late summer. We conducted the first winter-based study of polymorphic whitefish populations to determine the winter ecology of both morphs, and we combined seasonal diet and stable isotope analysis with several proxies of condition in three polymorphic whitefish populations. The generalist LSR morph fed on benthic and pelagic prey in summer but was solely reliant on benthic prey in winter. This was associated with a noticeable but moderate reduction in condition, lipid content and stomach fullness in winter relative to summer. In contrast, the DR whitefish occupied a strict pelagic niche in both seasons. A significant reduction in pelagic prey during winter resulted in severe decrease in condition, lipid content and stomach fullness in DR whitefish in winter relative to summer, with the pelagic morph apparently approaching starvation in winter. We suggest that this divergent approach to seasonal foraging is associated with the divergent life-history traits of both morphs.
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Affiliation(s)
- Brian Hayden
- Canadian Rivers Institute, Biology Department, University of New Brunswick, Fredericton, Canada
- Kilpisjärvi Biological Station, University of Helsinki, Helsinki, Finland
| | - Chris Harrod
- Instituto de Ciencias Naturales Alexander Von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
- Millennium Nucleus of Austral Invasive Salmonids, Concepción, Chile
| | | | - Kimmo K Kahilainen
- Kilpisjärvi Biological Station, University of Helsinki, Helsinki, Finland
- Lammi Biological Station, University of Helsinki, Helsinki, Finland
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44
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Astudillo-Clavijo V, Stiassny MLJ, Ilves KL, Musilova Z, Salzburger W, López-Fernández H. Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations. Syst Biol 2022; 72:134-149. [PMID: 35880863 DOI: 10.1093/sysbio/syac051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.
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Affiliation(s)
- Viviana Astudillo-Clavijo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, 10024-5102, USA
| | - Katriina L Ilves
- Research & Collections, Zoology, Canadian Museum of Nature, Ottawa, K1P 6P4, Canada
| | - Zuzana Musilova
- Department of Zoology, Charles University in Prague, Vinicna 7, Prague, CZ-128 44, Czech Republic
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
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45
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Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients. Proc Natl Acad Sci U S A 2022; 119:e2121388119. [PMID: 35759654 PMCID: PMC9282390 DOI: 10.1073/pnas.2121388119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although biodiversity in East Africa is overall extremely high, species richness is not geographically uniform for fishes and mammals. We investigated the biogeographic relevance of past river activity in the Kenya Rift. We show that during a humid period 12,000 to 8,000 years ago, a river system connected currently isolated rift lakes and was partly connected to the Nile. While this river system formed pathways for the dispersal of fishes between lakes, it also acted as a barrier to the range expansion of forest mammals. This fairly recent hydrological connectivity between lakes has been a key driver of modern biodiversity patterns in East Africa. Climate-driven changes in drainage networks on multimillennial timescales are an important hypothesis in biodiversity research. East Africa is a global biodiversity hotspot and exhibits distinct longitudinal diversity gradients from west to east in freshwater fishes and forest mammals. The assembly of this exceptional biodiversity and the drivers behind diversity gradients remain poorly understood, with diversification often studied at local scales and less attention paid to biotic exchange between Afrotropical regions. Here, we reconstruct a river system that existed for several millennia along the now semiarid Kenya Rift Valley during the humid early Holocene and show how this river system influenced postglacial dispersal of fishes and mammals due to its dual role as a dispersal corridor and barrier. Using geomorphological, geochronological, isotopic, and fossil analyses and a synthesis of radiocarbon dates, we find that the overflow of Kenyan rift lakes between 12 and 8 ka before present formed a bidirectional river system consisting of a “Northern River” connected to the Nile Basin and a “Southern River,” a closed basin. The drainage divide between these rivers represented the only viable terrestrial dispersal corridor across the rift. The degree and duration of past hydrological connectivity between adjacent river basins determined spatial diversity gradients for East African fishes. Our reconstruction explains the isolated distribution of Nilotic fish species in modern Kenyan rift lakes, Guineo-Congolian mammal species in forests east of the Kenya Rift, and recent incipient vertebrate speciation and local endemism in this region. Climate-driven rearrangements of drainage networks unrelated to tectonic activity contributed significantly to the assembly of species diversity and modern faunas in the East African biodiversity hotspot.
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46
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Seidlová L, Benovics M, Šimková A. Gill monogeneans of neotropical cichlid fish: diversity, phylogenetic relationships, and host-parasite cophylogenetic associations. Int J Parasitol 2022; 52:603-615. [PMID: 35760375 DOI: 10.1016/j.ijpara.2022.05.001] [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: 01/24/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/05/2022]
Abstract
Host-parasite coevolution is one of the main topics of the evolutionary biology of host-parasite associations. The majority of monogeneans parasitizing fish exhibit a high degree of host specificity. As a result, their evolutionary history might be intertwined with that of their fish hosts. The Cichlidae represent a diverse group of secondary freshwater fish with disjunctive distribution. Host-specific dactylogyrid monogeneans commonly parasitize cichlid fish. Their high diversity is associated with the main areas of cichlid distribution, i.e., Neotropical America and Africa. Nevertheless, the parasite fauna of cichlids from Neotropical America is still underexplored. A total of 31 cichlid species were examined for the presence of monogeneans, with 20 of them being parasitized. On these cichlids, 30 monogeneans belonging to the genera Gussevia, Trinidactylus, and Scadicleithrum were identified, 17 of them potentially representing new species for science. Phylogenetic analyses revealed three monophyletic groups of Neotropic cichlid monogeneans. Genus Gussevia was monophyletic, while Sciadicleithrum resulted polyphyletic. Sciedicleithrum from South America and Sciadicleithrum from Mexico represented two divergent lineages. The plesiomorphic Neotropical cichlid host group for dactylogyrid monogeneans was Cichlini, from which the representatives of other Neotropical cichlid tribes were colonized. Cophylogenetic analyses revealed a statistically significant cophylogenetic signal in the investigated host-parasite system, with host switch and duplication representing the main coevolutionary events for monogeneans parasitizing Neotropical cichlids. This scenario is in accordance with previous studies focussed on dactylogyridean monogeneans parasitizing freshwater fish in Europe and Africa.
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Affiliation(s)
- Lucie Seidlová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic.
| | - Michal Benovics
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Andrea Šimková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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47
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Cruz-Laufer AJ, Artois T, Koblmüller S, Pariselle A, Smeets K, Van Steenberge M, Vanhove MPM. Explosive networking: The role of adaptive host radiations and ecological opportunity in a species-rich host-parasite assembly. Ecol Lett 2022; 25:1795-1812. [PMID: 35726545 DOI: 10.1111/ele.14059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/22/2022] [Accepted: 05/13/2022] [Indexed: 01/09/2023]
Abstract
Many species-rich ecological communities emerge from adaptive radiation events. Yet the effects of adaptive radiation on community assembly remain poorly understood. Here, we explore the well-documented radiations of African cichlid fishes and their interactions with the flatworm gill parasites Cichlidogyrus spp., including 10,529 reported infections and 477 different host-parasite combinations collected through a survey of peer-reviewed literature. We assess how evolutionary, ecological, and morphological parameters determine host-parasite meta-communities affected by adaptive radiation events through network metrics, host repertoire measures, and network link prediction. The hosts' evolutionary history mostly determined host repertoires of the parasites. Ecological and evolutionary parameters predicted host-parasite interactions. Generally, ecological opportunity and fitting have shaped cichlid-Cichlidogyrus meta-communities suggesting an invasive potential for hosts used in aquaculture. Meta-communities affected by adaptive radiations are increasingly specialised with higher environmental stability. These trends should be verified across other systems to infer generalities in the evolution of species-rich host-parasite networks.
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Affiliation(s)
- Armando J Cruz-Laufer
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Diepenbeek, Belgium
| | - Tom Artois
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Diepenbeek, Belgium
| | | | - Antoine Pariselle
- ISEM, CNRS, IRD, Université de Montpellier, Montpellier, France.,Faculty of Sciences, Laboratory "Biodiversity, Ecology and Genome", Research Centre "Plant and Microbial Biotechnology, Biodiversity and Environment", Mohammed V University, Rabat, Morocco
| | - Karen Smeets
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Diepenbeek, Belgium
| | - Maarten Van Steenberge
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Diepenbeek, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Maarten P M Vanhove
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Diepenbeek, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
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48
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Evolutionary Divergence and Radula Diversification in Two Ecomorphs from an Adaptive Radiation of Freshwater Snails. Genes (Basel) 2022; 13:genes13061029. [PMID: 35741791 PMCID: PMC9222583 DOI: 10.3390/genes13061029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 05/27/2022] [Accepted: 05/31/2022] [Indexed: 12/13/2022] Open
Abstract
(1) Background: Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. (2) Methods: To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. (3) Results: We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin’s finches. (4) Conclusions: Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.
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49
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Kunerth HD, Bogdanowicz SM, Searle JB, Harrison RG, Coates BS, Kozak GM, Dopman EB. Consequences of coupled barriers to gene flow for the build-up of genomic differentiation. Evolution 2022; 76:985-1002. [PMID: 35304922 DOI: 10.1111/evo.14466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/09/2021] [Accepted: 12/29/2021] [Indexed: 01/21/2023]
Abstract
Theory predicts that when different barriers to gene flow become coincident, their joint effects enhance reproductive isolation and genomic divergence beyond their individual effects, but empirical tests of this "coupling" hypothesis are rare. Here, we analyze patterns of gene exchange among populations of European corn borer moths that vary in the number of acting barriers, allowing for comparisons of genomic variation when barrier traits or loci are in coincident or independent states. We find that divergence is mainly restricted to barrier loci when populations differ by a single barrier, whereas the coincidence of temporal and behavioral barriers is associated with divergence of two chromosomes harboring barrier loci. Furthermore, differentiation at temporal barrier loci increases in the presence of behavioral divergence and differentiation at behavioral barrier loci increases in the presence of temporal divergence. Our results demonstrate how the joint action of coincident barrier effects leads to levels of genomic differentiation that far exceed those of single barriers acting alone, consistent with theory arguing that coupling allows indirect selection to combine with direct selection and thereby lead to a stronger overall barrier to gene flow. Thus, the state of barriers-independent or coupled-strongly influences the accumulation of genomic differentiation.
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Affiliation(s)
- Henry D Kunerth
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Steven M Bogdanowicz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Richard G Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Brad S Coates
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, Iowa, 50011
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, 02747, USA.,Department of Biology, Tufts University, Medford, Massachusetts, 02155
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts, 02155
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50
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Cruz-Laufer AJ, Pariselle A, Jorissen MWP, Muterezi Bukinga F, Al Assadi A, Van Steenberge M, Koblmüller S, Sturmbauer C, Smeets K, Huyse T, Artois T, Vanhove MPM. Somewhere I belong: phylogeny and morphological evolution in a species-rich lineage of ectoparasitic flatworms infecting cichlid fishes. Cladistics 2022; 38:465-512. [PMID: 35488795 DOI: 10.1111/cla.12506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
A substantial portion of biodiversity has evolved through adaptive radiation. However, the effects of explosive speciation on species interactions remain poorly understood. Metazoan parasites infecting radiating host lineages could improve our knowledge because of their intimate host relationships. Yet limited molecular, phenotypic and ecological data discourage multivariate analyses of evolutionary patterns and encourage the use of discrete characters. Here, we assemble new molecular, morphological and host range data widely inferred from a species-rich lineage of parasites (Cichlidogyrus, Platyhelminthes: Monogenea) infecting cichlid fishes to address data scarcity. We infer a multimarker (28S/18S rDNA, ITS1, COI mtDNA) phylogeny of 58 of 137 species and characterize major lineages through synapomorphies inferred from mapping morphological characters. We predict the phylogenetic position of species without DNA data through shared character states, a morphological phylogenetic analysis, and a classification analysis with support vector machines. Based on these predictions and a cluster analysis, we assess the systematic informativeness of continuous characters, search for continuous equivalents for discrete characters, and suggest new characters for morphological traits not analysed to date. We also model the attachment/reproductive organ and host range evolution using the data for 136 of 137 described species and multivariate phylogenetic comparative methods (PCMs). We show that discrete characters not only can mask phylogenetic signals, but also are key for characterizing species groups. Regarding the attachment organ morphology, a divergent evolutionary regime for at least one lineage was detected and a limited morphological variation indicates host and environmental parameters affecting its evolution. However, moderate success in predicting phylogenetic positions, and a low systematic informativeness and high multicollinearity of morphological characters call for a revaluation of characters included in species characterizations.
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Affiliation(s)
- Armando J Cruz-Laufer
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium
| | - Antoine Pariselle
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France.,Faculty of Sciences, Laboratory "Biodiversity, Ecology and Genome", Research Centre "Plant and Microbial Biotechnology, Biodiversity and Environment", Mohammed V University, Rabat, Morocco
| | - Michiel W P Jorissen
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium.,Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Fidel Muterezi Bukinga
- Section de Parasitologie, Département de Biologie, Centre de Recherche en Hydrobiologie, Uvira, Democratic Republic of the Congo
| | - Anwar Al Assadi
- Fraunhofer Institute for Manufacturing Engineering and Automation IPA, Nobelstraße 12, Stuttgart, 70569, Germany
| | - Maarten Van Steenberge
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium.,Operational Directorate Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, Brussels, B-1000, Belgium
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, Graz, 8010, Austria
| | - Karen Smeets
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium
| | - Tine Huyse
- Section de Parasitologie, Département de Biologie, Centre de Recherche en Hydrobiologie, Uvira, Democratic Republic of the Congo.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
| | - Tom Artois
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium
| | - Maarten P M Vanhove
- Faculty of Sciences, Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, UHasselt - Hasselt University, Agoralaan Gebouw D, Diepenbeek, 3590, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Charles Deberiotstraat 32, Leuven, B-3000, Belgium
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