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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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2
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Ascensao JA, Denk J, Lok K, Yu Q, Wetmore KM, Hallatschek O. Rediversification following ecotype isolation reveals hidden adaptive potential. Curr Biol 2024; 34:855-867.e6. [PMID: 38325377 PMCID: PMC10911448 DOI: 10.1016/j.cub.2024.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/09/2023] [Accepted: 01/10/2024] [Indexed: 02/09/2024]
Abstract
Microbial communities play a critical role in ecological processes, and their diversity is key to their functioning. However, little is known about whether communities can regenerate ecological diversity following ecotype removal or extinction and how the rediversified communities would compare to the original ones. Here, we show that simple two-ecotype communities from the E. coli long-term evolution experiment (LTEE) consistently rediversified into two ecotypes following the isolation of one of the ecotypes, coexisting via negative frequency-dependent selection. Communities separated by more than 30,000 generations of evolutionary time rediversify in similar ways. The rediversified ecotype appears to share a number of growth traits with the ecotype it replaces. However, the rediversified community is also different from the original community in ways relevant to the mechanism of ecotype coexistence-for example, in stationary phase response and survival. We found substantial variation in the transcriptional states between the two original ecotypes, whereas the differences within the rediversified community were comparatively smaller, although the rediversified community showed unique patterns of differential expression. Our results suggest that evolution may leave room for alternative diversification processes even in a maximally reduced community of only two strains. We hypothesize that the presence of alternative evolutionary pathways may be even more pronounced in communities of many species where there are even more potential niches, highlighting an important role for perturbations, such as species removal, in evolving ecological communities.
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Affiliation(s)
- Joao A Ascensao
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Jonas Denk
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Kristen Lok
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
- Present affiliation: Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - QinQin Yu
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Present affiliation: Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Kelly M Wetmore
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Oskar Hallatschek
- Department of Physics, University of California Berkeley Berkeley, CA, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Peter Debye Institute for Soft Matter Physics, Leipzig University, 04103 Leipzig, Germany
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3
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Beavan A, Domingo-Sananes MR, McInerney JO. Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome. Proc Natl Acad Sci U S A 2024; 121:e2304934120. [PMID: 38147560 PMCID: PMC10769857 DOI: 10.1073/pnas.2304934120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/05/2023] [Indexed: 12/28/2023] Open
Abstract
Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of the presence or absence of other accessory genes within a genome. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. We find that the presence or absence of a substantial set of genes is highly predictable from other genes alone, indicating that selection potentiates and maintains gene-gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution and is robust to differences in host evolutionary history. We propose that at least part of the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem's set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene-gene relationships across the pangenome.
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Affiliation(s)
- Alan Beavan
- School of Life Sciences, The University of Nottingham, NottinghamNG7 2UH, United Kingdom
| | - Maria Rosa Domingo-Sananes
- School of Life Sciences, The University of Nottingham, NottinghamNG7 2UH, United Kingdom
- School of Science and Technology, Nottingham Trent University, NottinghamNG1 4FQ, United Kingdom
| | - James O. McInerney
- School of Life Sciences, The University of Nottingham, NottinghamNG7 2UH, United Kingdom
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4
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Payne ARD, Mannion PD, Lloyd GT, Davis KE. Decoupling speciation and extinction reveals both abiotic and biotic drivers shaped 250 million years of diversity in crocodile-line archosaurs. Nat Ecol Evol 2024; 8:121-132. [PMID: 38049481 PMCID: PMC10781641 DOI: 10.1038/s41559-023-02244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/26/2023] [Indexed: 12/06/2023]
Abstract
Whereas living representatives of Pseudosuchia, crocodylians, number fewer than 30 species, more than 700 pseudosuchian species are known from their 250-million-year fossil record, displaying far greater ecomorphological diversity than their extant counterparts. With a new time-calibrated tree of >500 species, we use a phylogenetic framework to reveal that pseudosuchian evolutionary history and diversification dynamics were directly shaped by the interplay of abiotic and biotic processes over hundreds of millions of years, supported by information theory analyses. Speciation, but not extinction, is correlated with higher temperatures in terrestrial and marine lineages, with high sea level associated with heightened extinction in non-marine taxa. Low lineage diversity and increased speciation in non-marine species is consistent with opportunities for niche-filling, whereas increased competition may have led to elevated extinction rates. In marine lineages, competition via increased lineage diversity appears to have driven both speciation and extinction. Decoupling speciation and extinction, in combination with ecological partitioning, reveals a more complex picture of pseudosuchian evolution than previously understood. As the number of species threatened with extinction by anthropogenic climate change continues to rise, the fossil record provides a unique window into the drivers that led to clade success and those that may ultimately lead to extinction.
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Affiliation(s)
- Alexander R D Payne
- Department of Biology, University of York, York, UK
- Leverhulme Centre for Anthropocene Biodiversity, University of York, York, UK
| | - Philip D Mannion
- Department of Earth Sciences, University College London, London, UK
| | | | - Katie E Davis
- Department of Biology, University of York, York, UK.
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5
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Olivares I, Tusso S, José Sanín M, de La Harpe M, Loiseau O, Rolland J, Salamin N, Kessler M, Shimizu KK, Paris M. Hyper-Cryptic radiation of a tropical montane plant lineage. Mol Phylogenet Evol 2024; 190:107954. [PMID: 37898295 DOI: 10.1016/j.ympev.2023.107954] [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: 05/01/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Species are seen as the fundamental unit of biotic diversity, and thus their delimitation is crucial for defining measures for diversity assessments and studying evolution. Differences between species have traditionally been associated with variation in morphology. And yet, the discovery of cryptic diversity suggests that the evolution of distinct lineages does not necessarily involve morphological differences. Here, we analyze 1,684,987 variant sites and over 4,000 genes for more than 400 samples to show how a tropical montane plant lineage (Geonoma undata species complex) is composed of numerous unrecognized genetic groups that are not morphologically distinct. We find that 11 to 14 clades do not correspond to the three currently recognized species. Most clades are genetically different and geographic distance and topography are the most important factors determining this genetic divergence. The genetic structure of this lineage does not match its morphological variation. Instead, this species complex constitutes the first example of a hyper-cryptic plant radiation in tropical mountains.
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Affiliation(s)
- Ingrid Olivares
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland.
| | - Sergio Tusso
- Department of Genetics, Faculty of Biology, Ludwig Maximilian Universität München, Germany
| | - María José Sanín
- School of Mathematical and Natural Sciences, Arizona State University. United States; Facultad de Ciencias y Biotecnología, Universidad CES, Colombia
| | - Marylaure de La Harpe
- Office for Nature Conservation and Environment of the Canton of Graubünden, Switzerland
| | - Oriane Loiseau
- School of Geosciences, University of Edinburgh, United Kingdom
| | - Jonathan Rolland
- CNRS, Laboratoire Evolution et Diversité Biologique, Université Toulouse, France
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Switzerland
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland; Kihara Institute of Biological Research, Yokohama City University, Japan
| | - Margot Paris
- Department of Biology. University of Fribourg, Switzerland
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6
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Sato H. The evolution of ectomycorrhizal symbiosis in the Late Cretaceous is a key driver of explosive diversification in Agaricomycetes. THE NEW PHYTOLOGIST 2024; 241:444-460. [PMID: 37292019 DOI: 10.1111/nph.19055] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
Ectomycorrhizal (EcM) symbiosis, a ubiquitous plant-fungus interaction in forests, evolved in parallel in fungi. Why the evolution of EcM fungi did not necessarily increase ecological opportunities for explosive diversification remains unclear. This study aimed to reveal the driving mechanism of the evolutionary diversification in the fungal class Agaricomycetes, specifically by testing whether the evolution of EcM symbiosis in the Late Cretaceous increased ecological opportunities. The historical character transitions of trophic state and fruitbody form were estimated based on phylogenies inferred from fragments of 89 single-copy genes. Moreover, five analyses were used to estimate the net diversification rates (speciation rate minus extinction rate). The results indicate that the unidirectional evolution of EcM symbiosis occurred 27 times, ranging in date from the Early Triassic to the Early Paleogene. The increased diversification rates appeared to occur intensively at the stem of EcM fungal clades diverging in the Late Cretaceous, coinciding with the rapid diversification of EcM angiosperms. By contrast, the evolution of fruitbody form was not strongly linked with the increased diversification rates. These findings suggest that the evolution of EcM symbiosis in the Late Cretaceous, supposedly with coevolving EcM angiosperms, was the key drive of the explosive diversification in Agaricomycetes.
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Affiliation(s)
- Hirotoshi Sato
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo, Kyoto, 606-8501, Japan
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7
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Oto Y, Kuroki M, Iida M, Ito R, Nomura S, Watanabe K. A key evolutionary step determining osmoregulatory ability for freshwater colonisation in early life stages of fish. J Exp Biol 2023; 226:jeb246110. [PMID: 37767765 DOI: 10.1242/jeb.246110] [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: 05/15/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023]
Abstract
Colonisation of freshwater habitats by marine animals is a remarkable evolutionary event that has enriched biodiversity in freshwater ecosystems. The acquisition of tolerance to hypotonic stress during early life stages is presumed to be essential for their successful freshwater colonisation, but very little empirical evidence has been obtained to support this idea. This study aimed to comprehend the evolutionary changes in osmoregulatory mechanisms that enhance larval freshwater tolerance in amphidromous fishes, which typically spend their larval period in marine (ancestral) habitats and the rest of their life history stages in freshwater (derived) habitats. We compared the life history patterns and changes in larval survivorship and gene expression depending on salinity among three congeneric marine-originated amphidromous goby species (Gymnogobius), which had been suggested to differ in their larval dependence on freshwater habitats. An otolith microchemical analysis and laboratory-rearing experiment confirmed the presence of freshwater residents only in G. urotaenia and higher larval survivorship of this species in the freshwater condition than in the obligate amphidromous G. petschiliensis and G. opperiens. Larval whole-body transcriptome analysis revealed that G. urotaenia from both amphidromous and freshwater-resident populations exhibited the greatest differences in expression levels of several osmoregulatory genes, including aqp3, which is critical for water discharge from their body during early fish development. The present results consistently support the importance of enhanced freshwater tolerance and osmoregulatory plasticity in larval fish to establish freshwater forms, and further identified key candidate genes for larval freshwater adaptation and colonisation in the goby group.
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Affiliation(s)
- Yumeki Oto
- Division of Biological Sciences, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto City, Kyoto Prefecture 606-8502, Japan
| | - Mari Kuroki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo Metropolitan 113-8657, Japan
| | - Midori Iida
- Marine Biological Station, Sado Island Center for Ecological Sustainability, Niigata University, 87 Tassha, Sado City, Niigata Prefecture 952-2135, Japan
| | - Ryosuke Ito
- Division of Biological Sciences, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto City, Kyoto Prefecture 606-8502, Japan
| | - Shota Nomura
- Division of Biological Sciences, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto City, Kyoto Prefecture 606-8502, Japan
| | - Katsutoshi Watanabe
- Division of Biological Sciences, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto City, Kyoto Prefecture 606-8502, Japan
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8
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Grismer LL, Anuar MSS, Muin MA, Ahmad N, Quah ESH. Genetic and morphological concordance and discordance within the Cyrtodactylus brevipalmatus group (Squamata: Gekkonidae). Zootaxa 2023; 5353:265-275. [PMID: 38220685 DOI: 10.11646/zootaxa.5353.3.4] [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: 10/09/2023] [Indexed: 01/16/2024]
Abstract
We use data sets from the Cyrtodactylus brevipalmatus group with limited genetic and morphological sampling to demonstrate that not accounting for sampling error may adversely influence decisions regarding species delimitation and diagnosis. Lack of geographic sampling between the endpoints of a species range may recover notable interpopulational genetic differentiation consistent with species-level differentiation. Additionally, small population sample sizes may fail recover statistically different diagnostic morphological differences. Combined, these types of sampling error can produce results seemingly consistent with the recognition of cryptic speciesgenetically delimited populations lacking diagnostic morphological characters. This is the current situation within some lineages of the C. brevipalmatus group whereas in others, sampling error is less problematic and does not jeopardize their taxonomy. We note the potential negative effects for comparative biology as a whole if sampling error is not taken into consideration prior to constructing taxonomies.
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Affiliation(s)
- L Lee Grismer
- Herpetology Laboratory; Department of Biology; La Sierra University; 4500 Riverwalk Parkway; Riverside; California 92505; USA.; Department of Herpetology; San Diego Natural History Museum; PO Box 121390; San Diego; California; 92112; USA; Institute for Tropical Biology and Conservation; Universiti Malaysia Sabah; Jalan UMS; 88400; Kota Kinabalu; Sabah; Malaysia.
| | - M S Shahrul Anuar
- School of Biological Sciences; Universiti Sains Malaysia; 11800 Minden; Penang; Malaysia; Center for Marine and Coastal Studies; Universiti Sains Malaysia; 11800 USM; Pulau Pinang; Malaysia..
| | - M A Muin
- Centre for Global Sustainability Studies (CGSS); Level 5; Hamzah Sendut Library; Universiti Sains Malaysia; 11800 USM; Penang.
| | - N Ahmad
- Institute for Environment and Development; (LESTARI); Universiti Kebangsaan Malaysia; 43600 Bangi; Selangor Darul Eshan; Malaysia.
| | - Evan S H Quah
- Institute for Tropical Biology and Conservation; Universiti Malaysia Sabah; Jalan UMS; 88400; Kota Kinabalu; Sabah; Malaysia.; Lee Kong Chian Natural History Museum; National University of Singapore; 2 Conservatory Drive; 117377; Singapore.
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9
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Spanke T, Gabelaia M, Flury JM, Hilgers L, Wantania LL, Misof B, Wipfler B, Wowor D, Mokodongan DF, Herder F, Schwarzer J. A landmark-free analysis of the pelvic girdle in Sulawesi ricefishes (Adrianichthyidae): How 2D and 3D geometric morphometrics can complement each other in the analysis of a complex structure. Ecol Evol 2023; 13:e10613. [PMID: 37859830 PMCID: PMC10582673 DOI: 10.1002/ece3.10613] [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: 05/19/2023] [Revised: 08/29/2023] [Accepted: 09/27/2023] [Indexed: 10/21/2023] Open
Abstract
Geometric morphometrics (GM) enable the quantification of morphological variation on various scales. Recent technical advances allow analyzing complex three-dimensional shapes also in cases where landmark-based approaches are not appropriate. Pelvic girdle bones (basipterygia) of Sulawesi ricefishes are 3D structures that challenge traditional morphometrics. We hypothesize that the pelvic girdle of ricefishes experienced sex-biased selection pressures in species where females provide brood care by carrying fertilized eggs supported by elongated pelvic fins ("pelvic brooding"). We test this by comparing pelvic bone shapes of both sexes in species exhibiting pelvic brooding and the more common reproductive strategy "transfer brooding," by using landmark-free 2D and 3D GM, as well as qualitative shape descriptions. Both landmark-free approaches revealed significant interspecific pelvic bone variation in the lateral process, medial facing side of the pelvic bone, and overall external and internal wing shape. Within pelvic brooders, the three analyzed species are clearly distinct, while pelvic bones of the genus Adrianichthys are more similar to transfer brooding Oryzias. Female pelvic brooding Oryzias exhibit prominent, medially pointing tips extending from the internal wing and basipterygial plate that are reduced or absent in conspecific males, Adrianichthys and transfer brooding Oryzias, supporting our hypothesis that selection pressures affecting pelvic girdle shape are sex-biased in Sulawesi ricefishes. Furthermore, both sexes of pelvic brooding Oryzias have overall larger pelvic bones than other investigated ricefishes. Based on these differences, we characterized two reproductive strategy- and sex-dependent pelvic girdle types for Sulawesi ricefishes. Morphological differences between the investigated pelvic brooding genera Adrianichthys and Oryzias provide additional evidence for two independent origins of pelvic brooding. Overall, our findings add to a better understanding on traits related to pelvic brooding in ricefishes and provide a basis for upcoming studies on pelvic girdle function and morphology.
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Affiliation(s)
- Tobias Spanke
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum Koenig BonnBonnGermany
| | - Mariam Gabelaia
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum Koenig BonnBonnGermany
| | - Jana M. Flury
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum Koenig BonnBonnGermany
- Department of Environmental SciencesUniversity of BaselBaselSwitzerland
| | - Leon Hilgers
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum Koenig BonnBonnGermany
- LOEWE‐Zentrum für Translationale BiodiversitätsgenomikFrankfurtGermany
| | - Letha Louisiana Wantania
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum Koenig BonnBonnGermany
- Faculty of Fisheries and Marine ScienceSam Ratulangi UniversityManadoIndonesia
| | - Bernhard Misof
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum Koenig BonnBonnGermany
| | - Benjamin Wipfler
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum Koenig BonnBonnGermany
| | - Daisy Wowor
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and EvolutionNational Research and Innovation Agency (BRIN)CibinongIndonesia
| | - Daniel F. Mokodongan
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and EvolutionNational Research and Innovation Agency (BRIN)CibinongIndonesia
| | - Fabian Herder
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum Koenig BonnBonnGermany
| | - Julia Schwarzer
- Leibniz Institute for the Analysis of Biodiversity Change (LIB)Museum Koenig BonnBonnGermany
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10
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Teng W, Fu H, Li Z, Zhang Q, Xu C, Yu H, Kong L, Liu S, Li Q. Parallel evolution in Crassostrea oysters along the latitudinal gradient is associated with variation in multiple genes involved in adipogenesis. Mol Ecol 2023; 32:5276-5287. [PMID: 37606178 DOI: 10.1111/mec.17108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/05/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023]
Abstract
Parallel diversification provides a proper framework for studying the role of natural selection in evolution. Yet, empirical studies from ecological 'non-model' species of invertebrates are limited at the whole genome level. Here, we presented a chromosome-scale genome assembly for Crassostrea angulata and investigated the parallel genomic evolution in oysters. Specifically, we used population genomics approaches to compare two southern-northern oyster species pairs (C. angulata-C. gigas and southern-northern C. ariakensis) along the coast of China. The estimated divergence time of C. angulata and C. gigas is earlier than that of southern and northern C. ariakensis, which aligns with the overall elevated genome-wide divergence. However, the southern-northern C. ariakensis FST profile represented more extremely divergent "islands". Combined with recent reciprocal hybridization studies, we proposed that they are currently at an early stage of speciation. These two southern-northern oyster species pairs exhibited significant repeatability in patterns of genome-wide differentiation, especially in genomic regions with extremely high and low divergence. This suggested that divergent and purifying selection has contributed to the genomic parallelism between southern and northern latitudes. Top differentiated genomic regions shared in these two oyster species pairs contained candidate genes enriched for functions in energy metabolism, especially adipogenesis, which are closely related to reproductive behaviours. These genes might be good candidates for further investigation in vivo. In conclusion, our results suggest that similar divergent selection and shared genomic features could predictably transform standing genetic variation within one species pair into differences in another.
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Affiliation(s)
- Wen Teng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Huiru Fu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Zhuanzhuan Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Qian Zhang
- Public Technology Service Center, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Chengxun Xu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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11
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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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12
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Cerezer FO, Dambros CS, Coelho MTP, Cassemiro FAS, Barreto E, Albert JS, Wüest RO, Graham CH. Accelerated body size evolution in upland environments is correlated with recent speciation in South American freshwater fishes. Nat Commun 2023; 14:6070. [PMID: 37770447 PMCID: PMC10539357 DOI: 10.1038/s41467-023-41812-7] [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: 02/01/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Speciation rates vary greatly among taxa and regions and are shaped by both biotic and abiotic factors. However, the relative importance and interactions of these factors are not well understood. Here we investigate the potential drivers of speciation rates in South American freshwater fishes, the most diverse continental vertebrate fauna, by examining the roles of multiple biotic and abiotic factors. We integrate a dataset on species geographic distribution, phylogenetic, morphological, climatic, and habitat data. We find that Late Neogene-Quaternary speciation events are strongly associated with body-size evolution, particularly in lineages with small body sizes that inhabit higher elevations near the continental periphery. Conversely, the effects of temperature, area, and diversity-dependence, often thought to facilitate speciation, are negligible. By evaluating multiple factors simultaneously, we demonstrate that habitat characteristics associated with elevation, as well as body size evolution, correlate with rapid speciation in South American freshwater fishes. Our study emphasizes the importance of integrative approaches that consider the interplay of biotic and abiotic factors in generating macroecological patterns of species diversity.
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Affiliation(s)
- Felipe O Cerezer
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland.
- Programa de Pós-Graduação em Biodiversidade Animal, Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, Brazil.
| | - Cristian S Dambros
- Programa de Pós-Graduação em Biodiversidade Animal, Departamento de Ecologia e Evolução, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Marco T P Coelho
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
| | - Fernanda A S Cassemiro
- Programa de Pós-Graduação em Ecologia e Evolução, Universidade Federal de Goiás, Goiânia, Brazil
| | - Elisa Barreto
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
| | - James S Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Rafael O Wüest
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
| | - Catherine H Graham
- Swiss Federal Research Institute for Forest, Snow, and Landscape (WSL), Birmensdorf, Switzerland
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13
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Riedel J, Klemm M, Higham T, Grismer LL, Ziegler T, Russell A, Rödder D, Reinhold K. Variation in claw morphology among the digits of Bent-toed geckos (Cyrtodactylus: Gekkota: Gekkonidae). BMC ZOOL 2023; 8:19. [PMID: 37684659 PMCID: PMC10492352 DOI: 10.1186/s40850-023-00180-x] [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: 01/23/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Ecomorphological studies of lizards have increasingly employed comparison of claw morphology among species in relation to spatial niche use. Typically, such studies focus on digit IV of the autopodia, especially the pes. Uniformity of claw morphology among digits is more often implicitly assumed than tested. RESULTS Using four species of Cyrtodactylus, comprising two generalist and two scansorial taxa that use different substrates, we examined whether claw morphology is uniform among digits and among species. We found that, within each species, ventral claw curvature is uniform across all digits whereas there are small but insignificant differences in ventral claw length and claw depth. The claws of the pes of each species are longer and deeper than those of the corresponding digits of the manus. The claw of digit I of each species is significantly shorter and shallower on both autopodia compared to those on digits IV and V (digit I, including its claw, is idiosyncratically variable among lizards in general). CONCLUSIONS We conclude that digit IV is an adequate representative of claw form in each species and exhibits variation among species, thereby serving as an exemplar for use in studies of potential discrimination between ecomorphological types in studies of Cyrtodactylus.
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Affiliation(s)
- Jendrian Riedel
- Section Herpetology, Leibniz Institute for the Analysis of Biodiversity Change - Museum Koenig, Bonn, Germany.
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany.
| | - Melinda Klemm
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
| | - Timothy Higham
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - L Lee Grismer
- Department of Biology, La Sierra University, Riverside, CA, USA
- Department of Herpetology, San Diego Natural History Museum, San Diego, CA, USA
| | - Thomas Ziegler
- Cologne Zoo, Cologne, Germany
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Anthony Russell
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Dennis Rödder
- Section Herpetology, Leibniz Institute for the Analysis of Biodiversity Change - Museum Koenig, Bonn, Germany
| | - Klaus Reinhold
- Department of Evolutionary Biology, Bielefeld University, Bielefeld, Germany
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14
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Cerca J, Cotoras DD, Santander CG, Bieker VC, Hutchins L, Morin-Lagos J, Prada CF, Kennedy S, Krehenwinkel H, Rominger AJ, Meier J, Dimitrov D, Struck TH, Gillespie RG. Multiple paths toward repeated phenotypic evolution in the spiny-leg adaptive radiation (Tetragnatha; Hawai'i). Mol Ecol 2023; 32:4971-4985. [PMID: 37515430 DOI: 10.1111/mec.17082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
The repeated evolution of phenotypes provides clear evidence for the role of natural selection in driving evolutionary change. However, the evolutionary origin of repeated phenotypes can be difficult to disentangle as it can arise from a combination of factors such as gene flow, shared ancestral polymorphisms or mutation. Here, we investigate the presence of these evolutionary processes in the Hawaiian spiny-leg Tetragnatha adaptive radiation, which includes four microhabitat-specialists or ecomorphs, with different body pigmentation and size (Green, Large Brown, Maroon, and Small Brown). We investigated the evolutionary history of this radiation using 76 newly generated low-coverage, whole-genome resequenced samples, along with phylogenetic and population genomic tools. Considering the Green ecomorph as the ancestral state, our results suggest that the Green ecomorph likely re-evolved once, the Large Brown and Maroon ecomorphs evolved twice and the Small Brown evolved three times. We found that the evolution of the Maroon and Small Brown ecomorphs likely involved ancestral hybridization events, while the Green and Large Brown ecomorphs likely evolved through novel mutations, despite a high rate of incomplete lineage sorting in the dataset. Our findings demonstrate that the repeated evolution of ecomorphs in the Hawaiian spiny-leg Tetragnatha is influenced by multiple evolutionary processes.
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Affiliation(s)
- José Cerca
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Oslo, Norway
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Darko D Cotoras
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany
- Department of Entomology, California Academy of Sciences, San Francisco, California, USA
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Leke Hutchins
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
| | - Jaime Morin-Lagos
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos, Facultad de Ciencias, Universidad del Tolima, Tolima, Colombia
| | - Susan Kennedy
- Department of Biogeography, Trier University, Trier, Germany
| | | | - Andrew J Rominger
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Joana Meier
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Sanger Institute, Hinxton, UK
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, Bergen, Norway
| | - Torsten H Struck
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Rosemary G Gillespie
- Berkeley Evolab, Department of Environmental Science, Policy, and Management, UC Berkeley, Berkeley, California, USA
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15
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Hunt ESE, Felice RN, Tobias JA, Goswami A. Ecological and life-history drivers of avian skull evolution. Evolution 2023; 77:1720-1729. [PMID: 37105944 DOI: 10.1093/evolut/qpad079] [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: 02/03/2023] [Revised: 04/04/2023] [Accepted: 04/26/2023] [Indexed: 04/29/2023]
Abstract
One of the most famous examples of adaptive radiation is that of the Galápagos finches, where skull morphology, particularly the beak, varies with feeding ecology. Yet increasingly studies are questioning the strength of this correlation between feeding ecology and morphology in relation to the entire neornithine radiation, suggesting that other factors also significantly affect skull evolution. Here, we broaden this debate to assess the influence of a range of ecological and life-history factors, specifically habitat density, migration, and developmental mode, in shaping avian skull evolution. Using 3D geometric morphometric data to robustly quantify skull shape for 354 extant species spanning avian diversity, we fitted flexible phylogenetic regressions and estimated evolutionary rates for each of these factors across the full data set. The results support a highly significant relationship between skull shape and both habitat density and migration, but not developmental mode. We further found heterogenous rates of evolution between different character states within habitat density, migration, and developmental mode, with rapid skull evolution in species that occupy dense habitats, are migratory, or are precocial. These patterns demonstrate that diverse factors affect the tempo and mode of avian phenotypic evolution and that skull evolution in birds is not simply a reflection of feeding ecology.
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Affiliation(s)
- Eloise S E Hunt
- Department of Life Sciences and Grantham Institute, Imperial College London, London, United Kingdom
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Ryan N Felice
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Anjali Goswami
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- Department of Genetics, Evolution, and Environment, University College London, London, United Kingdom
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16
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Tiburtini M, Bacchetta G, Sarigu M, Cambria S, Caputo P, De Luca D, Domina G, Turini A, Peruzzi L. Integrative Taxonomy of Armeria Taxa (Plumbaginaceae) Endemic to Sardinia and Corsica. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112229. [PMID: 37299208 DOI: 10.3390/plants12112229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Sardinia and Corsica are two Mediterranean islands where the genus Armeria is represented by 11 taxa, 10 out of which are endemic. An integrative approach, using molecular phylogeny, karyology, and seed and plant morphometry was used to resolve the complex taxonomy and systematics in this group. We found that several taxa are no longer supported by newly produced data. Accordingly, we describe a new taxonomic hypothesis that only considers five species: Armeria leucocephala and A. soleirolii, endemic to Corsica, and A. morisii, A. sardoa, and A. sulcitana, endemic to Sardinia.
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Affiliation(s)
- Manuel Tiburtini
- PLANTSEED Lab, Department of Biology, University of Pisa, Via Derna 1, 56126 Pisa, Italy
| | - Gianluigi Bacchetta
- Centre for Conservation of Biodiversity (CCB), Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123 Cagliari, Italy
| | - Marco Sarigu
- Centre for Conservation of Biodiversity (CCB), Department of Life and Environmental Sciences, University of Cagliari, V.le S. Ignazio da Laconi 13, 09123 Cagliari, Italy
| | - Salvatore Cambria
- Department of Biological, Geological and Environmental Sciences, University of Catania, Via Antonino Longo 19, 95125 Catania, Italy
| | - Paolo Caputo
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80100 Naples, Italy
| | - Daniele De Luca
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80100 Naples, Italy
| | - Gianniantonio Domina
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze 4, 90128 Palermo, Italy
| | - Alessia Turini
- PLANTSEED Lab, Department of Biology, University of Pisa, Via Derna 1, 56126 Pisa, Italy
| | - Lorenzo Peruzzi
- PLANTSEED Lab, Department of Biology, University of Pisa, Via Derna 1, 56126 Pisa, Italy
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17
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López-Romero FA, Stumpf S, Kamminga P, Böhmer C, Pradel A, Brazeau MD, Kriwet J. Shark mandible evolution reveals patterns of trophic and habitat-mediated diversification. Commun Biol 2023; 6:496. [PMID: 37156994 PMCID: PMC10167336 DOI: 10.1038/s42003-023-04882-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 04/27/2023] [Indexed: 05/10/2023] Open
Abstract
Environmental controls of species diversity represent a central research focus in evolutionary biology. In the marine realm, sharks are widely distributed, occupying mainly higher trophic levels and varied dietary preferences, mirrored by several morphological traits and behaviours. Recent comparative phylogenetic studies revealed that sharks present a fairly uneven diversification across habitats, from reefs to deep-water. We show preliminary evidence that morphological diversification (disparity) in the feeding system (mandibles) follows these patterns, and we tested hypotheses linking these patterns to morphological specialisation. We conducted a 3D geometric morphometric analysis and phylogenetic comparative methods on 145 specimens representing 90 extant shark species using computed tomography models. We explored how rates of morphological evolution in the jaw correlate with habitat, size, diet, trophic level, and taxonomic order. Our findings show a relationship between disparity and environment, with higher rates of morphological evolution in reef and deep-water habitats. Deep-water species display highly divergent morphologies compared to other sharks. Strikingly, evolutionary rates of jaw disparity are associated with diversification in deep water, but not in reefs. The environmental heterogeneity of the offshore water column exposes the importance of this parameter as a driver of diversification at least in the early part of clade history.
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Affiliation(s)
- Faviel A López-Romero
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Palaeontology, Evolutionary Morphology Research Group, Josef-Holaubek-Platz 2, 1190, Vienna, Austria.
- University of Vienna, Vienna Doctoral School of Ecology and Evolution (VDSEE), Djerassiplatz 1, 1030, Vienna, Austria.
| | - Sebastian Stumpf
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Palaeontology, Evolutionary Morphology Research Group, Josef-Holaubek-Platz 2, 1190, Vienna, Austria
| | - Pepijn Kamminga
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Christine Böhmer
- MECADEV UMR 7179 CNRS/MNHN, Département Adaptations du Vivant, Muséum National d'Histoire Naturelle, CP 55, 57 rue Cuvier, 75231, Paris, France
- Department für Geo- und Umweltwissenschaften und GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Straße 10, 80333, München, Germany
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Alan Pradel
- CR2P, Centre de Recherche en Paléontologie - Paris, Muséum National d'Histoire Naturelle-Sorbonne Université-CNRS, CP 38, 57 rue Cuvier, F75231, Paris, Cedex 05, France
| | - Martin D Brazeau
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY, London, UK
- The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Jürgen Kriwet
- University of Vienna, Faculty of Earth Sciences, Geography and Astronomy, Department of Palaeontology, Evolutionary Morphology Research Group, Josef-Holaubek-Platz 2, 1190, Vienna, Austria
- University of Vienna, Vienna Doctoral School of Ecology and Evolution (VDSEE), Djerassiplatz 1, 1030, Vienna, Austria
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18
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Olvera-Ríos YN, González-Díaz AA, Soria-Barreto M, Castillo-Uscanga MM, Cazzanelli M. Comparative analysis of cranial morphology in Middle-American heroine cichlids (Actinopterygii: Cichliformes). J Morphol 2023; 284:e21571. [PMID: 36802087 DOI: 10.1002/jmor.21571] [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: 10/30/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/21/2023]
Abstract
Heroine cichlids are characterized by high morphological diversity, mainly in structures related to the capture and processing of food. The existence of ecomorphological groups has been proposed based on feeding behavior, where it is common for some phylogenetically unrelated species to show evolutionary convergence. Using geometric morphometrics and comparative phylogenetic methods, the variation in cranial morphology was evaluated for 17 species of heroine cichlids representing 5 ecomorphs. Cranial ecomorphs were recovered and significant differences were determined. Morphological variation of the ecomorphs was mainly explained by two axes: (1) the position of the mouth determined by the shape of the bones of the oral jaw and (2) the height of the head, defined by the size and position of the supraoccipital crest and the distance to the interopercle-subopercle junction. Cranial variation among species was related to phylogeny. To better understand the evolution of cranial morphology, it is necessary to evaluate the morphofunctional relationship of other anatomical structures related to feeding, as well as to increase the number of study species in each ecomorph by including other lineages.
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Affiliation(s)
- Yuriria Noemy Olvera-Ríos
- Maestría en Ciencias en Recursos Naturales y Desarrollo Rural, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, México
| | - Alfonso A González-Díaz
- Departamento Conservación de la Biodiversidad, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, México
| | - Miriam Soria-Barreto
- Departamento Conservación de la Biodiversidad, El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, México
| | | | - Matteo Cazzanelli
- Departamento de Conservación de la Biodiversidad, CONACYT-El Colegio de la Frontera Sur, San Cristóbal de Las Casas, Chiapas, México
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19
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Cerca J, Cotoras DD, Bieker VC, De-Kayne R, Vargas P, Fernández-Mazuecos M, López-Delgado J, White O, Stervander M, Geneva AJ, Guevara Andino JE, Meier JI, Roeble L, Brée B, Patiño J, Guayasamin JM, Torres MDL, Valdebenito H, Castañeda MDR, Chaves JA, Díaz PJ, Valente L, Knope ML, Price JP, Rieseberg LH, Baldwin BG, Emerson BC, Rivas-Torres G, Gillespie R, Martin MD. Evolutionary genomics of oceanic island radiations. Trends Ecol Evol 2023:S0169-5347(23)00032-0. [PMID: 36870806 DOI: 10.1016/j.tree.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.
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Affiliation(s)
- José Cerca
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Darko D Cotoras
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Pablo Vargas
- Biodiversity and Conservation, Real Jardín Botánico, 28014 Madrid, Spain
| | - Mario Fernández-Mazuecos
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Calle Darwin 2, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid (CIBC-UAM), Calle Darwin 2, 28049 Madrid, Spain
| | - Julia López-Delgado
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Oliver White
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Martin Stervander
- Bird Group, Natural History Museum, Akeman Street, Tring, Hertfordshire HP23 6AP, UK
| | - Anthony J Geneva
- Department of Biology and Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - Juan Ernesto Guevara Andino
- Grupo de Investigación en Biodiversidad Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
| | - Joana Isabel Meier
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Lizzie Roeble
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Baptiste Brée
- Université de Pau et des Pays de l'Adour (UPPA), Energy Environment Solutions (E2S), Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), 64000 Pau, France
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Calle Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Juan M Guayasamin
- Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - María de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - Hugo Valdebenito
- Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador; Herbarium of Economic Botany of Ecuador (Herabario QUSF), Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador
| | | | - Jaime A Chaves
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA; Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador
| | - Patricia Jaramillo Díaz
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Department of Botany and Plant Physiology, University of Málaga, Málaga, Spain
| | - Luis Valente
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Matthew L Knope
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Jonathan P Price
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Bruce G Baldwin
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building 2465, University of California, Berkeley, CA 94720-2465, USA
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Spain
| | - Gonzalo Rivas-Torres
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Rosemary Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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20
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Friedman ST, Muñoz MM. A latitudinal gradient of deep-sea invasions for marine fishes. Nat Commun 2023; 14:773. [PMID: 36774385 PMCID: PMC9922314 DOI: 10.1038/s41467-023-36501-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/03/2023] [Indexed: 02/13/2023] Open
Abstract
Although the tropics harbor the greatest species richness globally, recent work has demonstrated that, for many taxa, speciation rates are faster at higher latitudes. Here, we explore lability in oceanic depth as a potential mechanism for this pattern in the most biodiverse vertebrates - fishes. We demonstrate that clades with the highest speciation rates also diversify more rapidly along the depth gradient, drawing a fundamental link between evolutionary and ecological processes on a global scale. Crucially, these same clades also inhabit higher latitudes, creating a prevailing latitudinal gradient of deep-sea invasions concentrated in poleward regions. We interpret these findings in the light of classic ecological theory, unifying the latitudinal variation of oceanic features and the physiological tolerances of the species living there. This work advances the understanding of how niche lability sculpts global patterns of species distributions and underscores the vulnerability of polar ecosystems to changing environmental conditions.
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Affiliation(s)
- Sarah T Friedman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA. .,Yale Institute for Biospheric Studies, Yale University, New Haven, CT, 06511, USA.
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
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21
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Button DJ, Porro LB, Lautenschlager S, Jones MEH, Barrett PM. Multiple pathways to herbivory underpinned deep divergences in ornithischian evolution. Curr Biol 2023; 33:557-565.e7. [PMID: 36603586 DOI: 10.1016/j.cub.2022.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023]
Abstract
The extent to which evolution is deterministic is a key question in biology,1,2,3,4,5,6,7,8,9 with intensive debate on how adaptation6,10,11,12,13 and constraints14,15,16 might canalize solutions to ecological challenges.4,5,6 Alternatively, unique adaptations1,9,17 and phylogenetic contingency1,3,18 may render evolution fundamentally unpredictable.3 Information from the fossil record is critical to this debate,1,2,11 but performance data for extinct taxa are limited.7 This knowledge gap is significant, as general morphology may be a poor predictor of biomechanical performance.17,19,20 High-fiber herbivory originated multiple times within ornithischian dinosaurs,21 making them an ideal clade for investigating evolutionary responses to similar ecological pressures.22 However, previous biomechanical modeling studies on ornithischian crania17,23,24,25 have not compared early-diverging taxa spanning independent acquisitions of herbivory. Here, we perform finite-element analysis on the skull of five early-diverging members of the major ornithischian clades to characterize morphofunctional pathways to herbivory. Results reveal limited functional convergence among ornithischian clades, with each instead achieving comparable performance, in terms of reconstructed patterns and magnitudes of functionally induced stress, through different adaptations of the feeding apparatus. Thyreophorans compensated for plesiomorphic low performance through increased absolute size, heterodontosaurids expanded jaw adductor muscle volume, ornithopods increased jaw system efficiency, and ceratopsians combined these approaches. These distinct solutions to the challenges of herbivory within Ornithischia underpinned the success of this diverse clade. Furthermore, the resolution of multiple solutions to equivalent problems within a single clade through macroevolutionary time demonstrates that phenotypic evolution is not necessarily predictable, instead arising from the interplay of adaptation, innovation, contingency, and constraints.1,2,3,7,8,9,18.
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Affiliation(s)
- David J Button
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
| | - Laura B Porro
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6DE, UK
| | - Stephan Lautenschlager
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Marc E H Jones
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Paul M Barrett
- Science Group, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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22
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Miller AH, Stroud JT, Losos JB. The ecology and evolution of key innovations. Trends Ecol Evol 2023; 38:122-131. [PMID: 36220711 DOI: 10.1016/j.tree.2022.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/05/2022]
Abstract
The idea of 'key innovations' has long been influential in theoretical and empirical approaches to understanding adaptive diversification. Despite originally revolving around traits inducing major ecological shifts, the key innovation concept itself has evolved, conflating lineage diversification with trait-dependent ecological shifts. In this opinion article we synthesize the history of the term, clarify the relationship between key innovations and adaptive radiation, and propose a return to the original concept of key innovations: the evolution of organismal features which permit a species to occupy a previously inaccessible ecological state. Ultimately, we suggest an integrative approach to studying key innovations, necessitating experimental approaches of form and function, natural history studies of resource use, and phylogenetic comparative perspectives.
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Affiliation(s)
- Aryeh H Miller
- Department of Biology, Washington University, St Louis, MO, USA.
| | - James T Stroud
- Department of Biology, Washington University, St Louis, MO, USA.
| | - Jonathan B Losos
- Department of Biology, Washington University, St Louis, MO, USA.
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23
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The Dynamic Ontogenetic Shape Patterns of Adaptive Divergence and Sexual Dimorphism. Evol Biol 2023. [DOI: 10.1007/s11692-022-09592-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
AbstractThe interplay between ecological diversification and sexual dimorphism has been largely overlooked in the literature. Sexually dimorphic species which are also undergoing adaptive radiations are ideal for filling this knowledge gap. The Arctic charr in lake Thingvallavatn is one such system: it is a sexually dimorphic species which has recently diverged along the benthic-limnetic ecological axis. In a long-running common-garden experiment we studied the shape variation throughout ontogeny of intra- and inter- morph crosses of benthic and limnetic charr from the lake. We found that shape differences between ecomorphs and sexes had a genetic component. Prior to the onset of sexual maturation, shape differences were attributable to cross type and were related to adaptations to benthic and limnetic niches, i.e., shorter lower jaws and rounder snouts in the benthic and evenly protruding snouts and pointier snouts in the limnetic. Reciprocal hybrids showed intermediate, transgressive and/or maternal morphologies. However, after the onset of sexual maturation larger morphological differences occurred between sexes than among cross types. Taken together, our results demonstrate that the interplay between ecological diversification and sexual dimorphism is complex and dynamic throughout ontogeny, and that long-term common garden experiments are immensely valuable for studying shape dynamics in different evolutionary scenarios.
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24
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Environmental signal in the evolutionary diversification of bird skeletons. Nature 2022; 611:306-311. [DOI: 10.1038/s41586-022-05372-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 09/21/2022] [Indexed: 11/08/2022]
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25
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Frishkoff LO, Lertzman-Lepofsky G, Mahler DL. Evolutionary opportunity and the limits of community similarity in replicate radiations of island lizards. Ecol Lett 2022; 25:2384-2396. [PMID: 36192673 DOI: 10.1111/ele.14098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022]
Abstract
Ecological community structure ultimately depends on the production of community members by speciation. To understand how macroevolution shapes communities, we surveyed Anolis lizard assemblages across elevations on Jamaica and Hispaniola, neighbouring Caribbean islands similar in environment, but contrasting in the richness of their endemic evolutionary radiations. The impact of diversification on local communities depends on available spatial opportunities for speciation within or between ecologically distinct sub-regions. In the spatially expansive lowlands of both islands, communities converge in species richness and average morphology. But communities diverge in the highlands. On Jamaica, where limited highland area restricted diversification, communities remain depauperate and consist largely of elevational generalists. In contrast, a unique fauna of high-elevation specialists evolved in the vast Hispaniolan highlands, augmenting highland richness and driving islandwide turnover in community composition. Accounting for disparate evolutionary opportunities may illuminate when regional diversity will enhance local diversity and help predict when communities should converge in structure.
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26
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Jamy M, Biwer C, Vaulot D, Obiol A, Jing H, Peura S, Massana R, Burki F. Global patterns and rates of habitat transitions across the eukaryotic tree of life. Nat Ecol Evol 2022; 6:1458-1470. [PMID: 35927316 PMCID: PMC9525238 DOI: 10.1038/s41559-022-01838-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/23/2022] [Indexed: 12/30/2022]
Abstract
The successful colonization of new habitats has played a fundamental role during the evolution of life. Salinity is one of the strongest barriers for organisms to cross, which has resulted in the evolution of distinct marine and non-marine (including both freshwater and soil) communities. Although microbes represent by far the vast majority of eukaryote diversity, the role of the salt barrier in shaping the diversity across the eukaryotic tree is poorly known. Traditional views suggest rare and ancient marine/non-marine transitions but this view is being challenged by the discovery of several recently transitioned lineages. Here, we investigate habitat evolution across the tree of eukaryotes using a unique set of taxon-rich phylogenies inferred from a combination of long-read and short-read environmental metabarcoding data spanning the ribosomal DNA operon. Our results show that, overall, marine and non-marine microbial communities are phylogenetically distinct but transitions have occurred in both directions in almost all major eukaryotic lineages, with hundreds of transition events detected. Some groups have experienced relatively high rates of transitions, most notably fungi for which crossing the salt barrier has probably been an important aspect of their successful diversification. At the deepest phylogenetic levels, ancestral habitat reconstruction analyses suggest that eukaryotes may have first evolved in non-marine habitats and that the two largest known eukaryotic assemblages (TSAR and Amorphea) arose in different habitats. Overall, our findings indicate that the salt barrier has played an important role during eukaryote evolution and provide a global perspective on habitat transitions in this domain of life.
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Affiliation(s)
- Mahwash Jamy
- Department of Organismal Biology (Systematic Biology), Uppsala University, Uppsala, Sweden
| | - Charlie Biwer
- Department of Organismal Biology (Systematic Biology), Uppsala University, Uppsala, Sweden
| | - Daniel Vaulot
- CNRS, UMR7144, Team ECOMAP, Station Biologique, Sorbonne Université, Roscoff, France
| | - Aleix Obiol
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Hongmei Jing
- CAS Key Lab for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Sari Peura
- Department of Ecology and Genetics (Limnology), Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ramon Massana
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Uppsala, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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27
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Sansalone G, Paolo C, Riccardo C, Stephen W, Silvia C, Pasquale R. Trapped in the morphospace: The relationship between morphological integration and functional performance. Evolution 2022; 76:2020-2031. [PMID: 35864587 PMCID: PMC9542761 DOI: 10.1111/evo.14575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 01/22/2023]
Abstract
The evolution of complex morphological structures can be characterized by the interplay between different anatomical regions evolving under functional integration in response to shared selective pressures. Using the highly derived humeral morphology of talpid moles as a model, here we test whether functional performance is linked to increased levels of evolutionary integration between humerus subunits and, if so, what the strength is of the relationship. Combining two-dimensional geometric morphometrics, phylogenetic comparative methods, and functional landscape modeling, we demonstrate that the high biomechanical performance of subterranean moles' humeri is coupled with elevated levels of integration, whereas taxa with low-performance values show intermediate or low integration. Theoretical morphs occurring in high-performance areas of the functional landscape are not occupied by any species, and show a marked drop in covariation levels, suggesting the existence of a strong relationship between integration and performance in the evolution of talpid moles' humeri. We argue that the relative temporal invariance of the subterranean environment may have contributed to stabilize humeral morphology, trapping subterranean moles in a narrow region of the landscape and impeding any attempt to reposition on a new ascending slope.
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Affiliation(s)
- Gabriele Sansalone
- Function, Evolution and Anatomy Research Lab, Zoology Division, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia,Institute for Marine Biological Resources and Biotechnology (IRBIM)National Research CouncilMessina98122Italy
| | - Colangelo Paolo
- Research Institute on Terrestrial EcosystemsNational Research CouncilMontelibretti00015Italy
| | - Castiglia Riccardo
- Department of Biology and Biotechnology “Charles Darwin,”“La Sapienza” University of RomeRoma00161Italy
| | - Wroe Stephen
- Function, Evolution and Anatomy Research Lab, Zoology Division, School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2351Australia
| | - Castiglione Silvia
- Department of Earth Sciences, Environment and ResourcesUniversità degli Studi di Napoli Federico IINaples80138Italy
| | - Raia Pasquale
- Department of Earth Sciences, Environment and ResourcesUniversità degli Studi di Napoli Federico IINaples80138Italy
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28
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Crouch NMA, Jablonski D. Is species richness mediated by functional and genetic divergence? A global analysis in birds. Funct Ecol 2022; 37:125-138. [PMID: 37064506 PMCID: PMC10086807 DOI: 10.1111/1365-2435.14153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
Unravelling why species richness shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness (e.g. with latitude) requires a compensatory trade-off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes.Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank.We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that points sampled in the tropics have comparatively greater packing than temperate ones relative to their species richness. We find limited evidence that geographical co-occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis.Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness. Read the free Plain Language Summary for this article on the Journal blog.
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Affiliation(s)
- Nicholas M. A. Crouch
- Dept. of the Geophysical Sciences The University of Chicago s Chicago Illinois U.S.A
| | - David Jablonski
- Dept. of the Geophysical Sciences The University of Chicago s Chicago Illinois U.S.A
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29
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Wainwright JB, Montgomery SH. Neuroanatomical shifts mirror patterns of ecological divergence in three diverse clades of mimetic butterflies. Evolution 2022; 76:1806-1820. [PMID: 35767896 PMCID: PMC9540801 DOI: 10.1111/evo.14547] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 01/22/2023]
Abstract
Microhabitat partitioning in heterogenous environments can support more diverse communities but may expose partitioned species to distinct perceptual challenges. Divergence across microhabitats could therefore lead to local adaptation to contrasting sensory conditions across small spatial scales, but this aspect of community structuring is rarely explored. Diverse communities of ithomiine butterflies provide an example where closely related species partition tropical forests, where shifts in mimetic coloration are tightly associated with shifts in habitat preference. We test the hypothesis that these mimetic and ecological shifts are associated with distinct patterns of sensory neural investment by comparing brain structure across 164 individuals of 16 species from three ithomiine clades. We find distinct brain morphologies between Oleriina and Hypothyris, which are mimetically homogenous and occupy a single microhabitat. Oleriina, which occurs in low-light microhabitats, invests less in visual brain regions than Hypothyris, with one notable exception, Hyposcada anchiala, the only Oleriina sampled to have converged on mimicry rings found in Hypothyris. We also find that Napeogenes, which has diversified into a range of mimicry rings, shows intermediate patterns of sensory investment. We identify flight height as a critical factor shaping neuroanatomical diversity, with species that fly higher in the canopy investing more in visual structures. Our work suggests that the sensory ecology of species may be impacted by, and interact with, the ways in which communities of closely related organisms are adaptively assembled.
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30
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Donoghue MJ, Eaton DAR, Maya-Lastra CA, Landis MJ, Sweeney PW, Olson ME, Cacho NI, Moeglein MK, Gardner JR, Heaphy NM, Castorena M, Rivas AS, Clement WL, Edwards EJ. Replicated radiation of a plant clade along a cloud forest archipelago. Nat Ecol Evol 2022; 6:1318-1329. [DOI: 10.1038/s41559-022-01823-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 06/08/2022] [Indexed: 11/09/2022]
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31
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Decoupling in Diversification and Body Size Rates During the Radiation of Phyllodactylus: Evidence Suggests Minor Role of Ecology in Shaping Phenotypes. Evol Biol 2022. [DOI: 10.1007/s11692-022-09575-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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32
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Mittan CS, Zamudio KR, Thomé MTC, Camurugi F, Colli GR, Garda AA, Haddad CFB, Prado CPA. Temporal and spatial diversification along the Amazonia-Cerrado transition in Neotropical treefrogs of the Boana albopunctata species group. Mol Phylogenet Evol 2022; 175:107579. [PMID: 35835425 DOI: 10.1016/j.ympev.2022.107579] [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: 10/22/2021] [Revised: 06/23/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
Abstract
Despite extensive research on biodiversity in Neotropical forests, biodiversity in seasonally dry, open biomes in South America has been underestimated until recently. We leverage a widespread group, Boana albopunctata, to uncover cryptic lineages and investigate the timing of diversification in Neotropical anurans with a focus on dry diagonal biomes (Cerrado, Caatinga and Chaco) and the ecotone between Amazonia and the Cerrado. We inferred a multilocus phylogeny of the B. albopunctata species group that includes 15 of 18 described species, recovered two cryptic species, and reconstructed the timing of diversification among species distributed across multiple South American biomes. One new potential species (B. aff. steinbachi), sampled in the Amazonian state of Acre, clustered within the B. calcara-fasciata species complex and is close to B. steinbachi. A second putative new species (B. aff. multifasciata), sampled in the Amazonia-Cerrado ecotone, is closely related to B. multifasciata. Lastly, we place a recently identified Cerrado lineage (B. aff. albopuncata) into the B. albopunctata species group phylogeny for the first time. Our ancestral range reconstruction showed that species in the B. albopuctata group likely dispersed from Amazonia-Cerrado into the dry-diagonal and Atlantic Forest. Intraspecies demography showed, for both B. raniceps and B. albopunctata, signs of rapid expansion across the dry diagonal. Similarly, for one clade of B. multifasciata, our analyses support an invasion of the Cerrado from Amazonia, followed by a rapid expansion across the open diagonal biomes. Thus, our study recovers several recent divergences along the Amazonia-Cerrado ecotone in northern Brazil. Tectonic uplift and erosion in the late Miocene and climate oscillations in the Pleistocene corresponded with estimated divergence times in the dry diagonal and Amazonia-Cerrado ecotone. Our study highlights the importance of these threatened open formations in the generation of biodiversity in the Neotropics.
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Affiliation(s)
- Cinnamon S Mittan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - M Tereza C Thomé
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, São Paulo State University (Unesp), Rio Claro, São Paulo, Brazil
| | - Felipe Camurugi
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Cidade Universitária, Campo Grande, Brazil; Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, Brasília, DF, Brazil
| | - Adrian A Garda
- Laboratório de Anfíbios e Répteis, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Célio F B Haddad
- Departamento de Biodiversidade e Centro de Aquicultura, Instituto de Biociências, São Paulo State University (Unesp), Rio Claro, São Paulo, Brazil
| | - Cynthia P A Prado
- Departamento de Morfologia e Fisiologia Animal, Faculdade de Ciências Agrárias e Veterinárias, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
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33
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Manrubia S. The simple emergence of complex molecular function. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200422. [PMID: 35599566 DOI: 10.1098/rsta.2020.0422] [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] [Indexed: 05/07/2023]
Abstract
At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge de novo with relative ease. At early times of molecular evolution, random polymers could have sufficed for the appearance of incipient chemical activity, while the cellular environment harbours a myriad of proto-functional molecules. The emergence of function is facilitated by several mechanisms intrinsic to molecular organization, such as redundant mapping of sequences into structures, phenotypic plasticity, modularity or cooperative associations between genomic sequences. It is the availability of niches in the molecular ecology that filters new potentially functional proposals. New phenotypes and subsequent levels of molecular complexity could be attained through combinatorial explorations of currently available molecular variants. Natural selection does the rest. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Susanna Manrubia
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Systems Biology Department, National Biotechnology Centre (CSIC), c/Darwin 3, 28049 Madrid, Spain
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Abstract
AbstractEvolvability is best addressed from a multi-level, macroevolutionary perspective through a comparative approach that tests for among-clade differences in phenotypic diversification in response to an opportunity, such as encountered after a mass extinction, entering a new adaptive zone, or entering a new geographic area. Analyzing the dynamics of clades under similar environmental conditions can (partially) factor out shared external drivers to recognize intrinsic differences in evolvability, aiming for a macroevolutionary analog of a common-garden experiment. Analyses will be most powerful when integrating neontological and paleontological data: determining differences among extant populations that can be hypothesized to generate large-scale, long-term contrasts in evolvability among clades; or observing large-scale differences among clade histories that can by hypothesized to reflect contrasts in genetics and development observed directly in extant populations. However, many comparative analyses can be informative on their own, as explored in this overview. Differences in clade-level evolvability can be visualized in diversity-disparity plots, which can quantify positive and negative departures of phenotypic productivity from stochastic expectations scaled to taxonomic diversification. Factors that evidently can promote evolvability include modularity—when selection aligns with modular structure or with morphological integration patterns; pronounced ontogenetic changes in morphology, as in allometry or multiphase life cycles; genome size; and a variety of evolutionary novelties, which can also be evaluated using macroevolutionary lags between the acquisition of a trait and phenotypic diversification, and dead-clade-walking patterns that may signal a loss of evolvability when extrinsic factors can be excluded. High speciation rates may indirectly foster phenotypic evolvability, and vice versa. Mechanisms are controversial, but clade evolvability may be higher in the Cambrian, and possibly early in the history of clades at other times; in the tropics; and, for marine organisms, in shallow-water disturbed habitats.
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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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36
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de Brito V, Betancur-R R, Burns MD, Buser TJ, Conway KW, Fontenelle JP, Kolmann MA, McCraney WT, Thacker CE, Bloom DD. Patterns of Phenotypic Evolution Associated with Marine/Freshwater Transitions in Fishes. Integr Comp Biol 2022; 62:406-423. [PMID: 35675320 DOI: 10.1093/icb/icac085] [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: 03/31/2022] [Revised: 06/01/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
Evolutionary transitions between marine and freshwater ecosystems have occurred repeatedly throughout the phylogenetic history of fishes. The theory of ecological opportunity predicts that lineages that colonize species-poor regions will have greater potential for phenotypic diversification than lineages invading species-rich regions. Thus, transitions between marine and freshwaters may promote phenotypic diversification in trans-marine/freshwater fish clades. We used phylogenetic comparative methods to analyze body size data in nine major fish clades that have crossed the marine/freshwater boundary. We explored how habitat transitions, ecological opportunity, and community interactions influenced patterns of phenotypic diversity. Our analyses indicated that transitions between marine and freshwater habitats did not drive body size evolution, and there are few differences in body size between marine and freshwater lineages. We found that body size disparity in freshwater lineages is not correlated with the number of independent transitions to freshwaters. We found a positive correlation between body size disparity and overall species richness of a given area, and a negative correlation between body size disparity and diversity of closely related species. Our results indicate that the diversity of incumbent freshwater species does not restrict phenotypic diversification, but the diversity of closely related taxa can limit body size diversification. Ecological opportunity arising from colonization of novel habitats does not seem to have a major effect in the trajectory of body size evolution in trans-marine/freshwater clades. Moreover, competition with closely related taxa in freshwaters has a greater effect than competition with distantly related incumbent species.
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Affiliation(s)
- Victor de Brito
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5410, USA
| | - Ricardo Betancur-R
- Department of Biology, University of Oklahoma, 730 Van Vleet Oval, Room 314, Norman, OK 73019, USA
| | - Michael D Burns
- Cornell Lab of Ornithology, Cornell Museum of Vertebrates, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850-1923, USA
| | - Thaddaeus J Buser
- Department of BioSciences, Rice University, W100 George R. Brown Hall, 6100 Main Street, Houston, TX 77005, USA
| | - Kevin W Conway
- Department of Ecology and Conservation Biology and Biodiversity Research and Teaching Collections, Texas A&M University, College Station, TX 77843, USA
| | - João Pedro Fontenelle
- Institute of Forestry and Conservation, University of Toronto, 33 Willcocks St., Toronto, ON M5S 3E8, Canada
| | - Matthew A Kolmann
- Museum of Paleontology, Biological Sciences Building, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109-1085, USA
| | - W Tyler McCraney
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Drive South, Los Angeles, CA 90095-7246, USA
| | - Christine E Thacker
- Research and Collections, Section of Ichthyology, Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA 90007, USA.,Vertebrate Zoology, Santa Barbara Museum of Natural History, 2559 Puesta del Sol, Santa Barbara, CA 93105, USA
| | - Devin D Bloom
- Department of Biological Sciences, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5410, USA.,Institute of the Environment and Sustainability, Western Michigan University, 1903 W Michigan Ave, Kalamazoo, MI 49008-5419, USA
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37
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Ocampo M, Pincheira-Donoso D, Sayol F, Rios RS. Evolutionary transitions in diet influence the exceptional diversification of a lizard adaptive radiation. BMC Ecol Evol 2022; 22:74. [PMID: 35672668 PMCID: PMC9175459 DOI: 10.1186/s12862-022-02028-3] [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: 11/06/2021] [Accepted: 05/24/2022] [Indexed: 11/11/2022] Open
Abstract
Background Diet is a key component of a species ecological niche and plays critical roles in guiding the trajectories of evolutionary change. Previous studies suggest that dietary evolution can influence the rates and patterns of species diversification, with omnivorous (animal and plant, ‘generalist’) diets slowing down diversification compared to more restricted (‘specialist’) herbivorous and carnivorous diets. This hypothesis, here termed the “dietary macroevolutionary sink” hypothesis (DMS), predicts that transitions to omnivorous diets occur at higher rates than into any specialist diet, and omnivores are expected to have the lowest diversification rates, causing an evolutionary sink into a single type of diet. However, evidence for the DMS hypothesis remains conflicting. Here, we present the first test of the DMS hypothesis in a lineage of ectothermic tetrapods—the prolific Liolaemidae lizard radiation from South America. Results Ancestral reconstructions suggest that the stem ancestor was probably insectivorous. The best supported trait model is a diet-dependent speciation rate, with independent extinction rates. Herbivory has the highest net diversification rate, omnivory ranks second, and insectivory has the lowest. The extinction rate is the same for all three diet types and is much lower than the speciation rates. The highest transition rate was from omnivory to insectivory, and the lowest transition rates were between insectivory and herbivory. Conclusions Our findings challenge the core prediction of the DMS hypothesis that generalist diets represent an ‘evolutionary sink’. Interestingly, liolaemid lizards have rapidly and successfully proliferated across some of the world’s coldest climates (at high elevations and latitudes), where species have evolved mixed arthropod-plant (omnivore) or predominantly herbivore diets. This longstanding observation is consistent with the higher net diversification rates found in both herbivory and omnivory. Collectively, just like the evolution of viviparity has been regarded as a ‘key adaptation’ during the liolaemid radiation across cold climates, our findings suggest that transitions from insectivory to herbivory (bridged by omnivory) are likely to have played a role as an additional key adaptation underlying the exceptional diversification of these reptiles across extreme climates. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02028-3.
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Affiliation(s)
- Mauricio Ocampo
- Departamento de Biología, Doctorado en Ciencias Biológicas, Ecología de Zonas Áridas (EZA), Universidad de la Serena, Casilla 554, La Serena, Chile. .,Red de Investigadores en Herpetología-Bolivia, Los Pinos Zona Sur, Av. José Aguirre 260, La Paz, Bolivia. .,Unidad de Zoología, Instituto de Ecología, Universidad Mayor de San Andrés, Casilla 10077-Correo Central, La Paz, Bolivia.
| | - Daniel Pincheira-Donoso
- MacroBiodiversity Lab, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Ferran Sayol
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Rodrigo S Rios
- Departamento de Biología, Doctorado en Ciencias Biológicas, Ecología de Zonas Áridas (EZA), Universidad de la Serena, Casilla 554, La Serena, Chile.,Instituto de Investigación Multidisciplinario en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
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38
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Davis KE, De Grave S, Delmer C, Payne ARD, Mitchell S, Wills MA. Ecological Transitions and the Shape of the Decapod Tree of Life. Integr Comp Biol 2022; 62:332-344. [PMID: 35612997 DOI: 10.1093/icb/icac052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 11/14/2022] Open
Abstract
Understanding the processes that shaped the distribution of species richness across the Tree of Life is a central macroevolutionary research agenda. Major ecological innovations, including transitions between habitats, may help to explain the striking asymmetries of diversity that are often observed between sister clades. Here, we test the impact of such transitions on speciation rates across decapod crustaceans, modelling diversification dynamics within a phylogenetic framework. Our results show that, while terrestrial lineages have higher speciation rates than either marine or freshwater lineages, there is no difference between mean speciation rates in marine and freshwater lineages across Decapoda. Partitioning our data by infraorder reveals that those clades with habitat heterogeneity have higher speciation rates in freshwater and terrestrial lineages, with freshwater rates up to 1.5 times faster than marine rates, and terrestrial rates approximately four times faster. This averaging out of marine and freshwater speciation rates results from the varying contributions of different clades to average speciation rates. However, with the exception of Caridea, we find no evidence for any causal relationship between habitat and speciation rate. Our results demonstrate that while statistical generalisations about ecological traits and evolutionary rates are valuable, there are many exceptions. Hence, while freshwater and terrestrial lineages typically speciate faster than their marine relatives, there are many atypically slow freshwater lineages and fast marine lineages across Decapoda. Future work on diversification patterns will benefit from the inclusion of fossil data, as well as additional ecological factors.
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Affiliation(s)
- Katie E Davis
- University of York, Department of Biology York, North Yorkshire, UK
| | - Sammy De Grave
- Oxford University Museum of Natural History, Oxford, Oxfordshire, UK
| | - Cyrille Delmer
- University of Bath, Department of Biology & Biochemistry, Bath, Bath and North East Somerset, UK
| | - Alexander R D Payne
- University of York, Leverhulme Centre for Anthropocene Biodiversity, York, North Yorkshire, UK
| | - Steve Mitchell
- University of Bath, Department of Biology & Biochemistry, Bath, Bath and North East Somerset, UK
| | - Matthew A Wills
- University of Bath, Department of Biology & Biochemistry, Bath, Bath and North East Somerset, UK
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39
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Feng S, Bai M, Rivas-González I, Li C, Liu S, Tong Y, Yang H, Chen G, Xie D, Sears KE, Franco LM, Gaitan-Espitia JD, Nespolo RF, Johnson WE, Yang H, Brandies PA, Hogg CJ, Belov K, Renfree MB, Helgen KM, Boomsma JJ, Schierup MH, Zhang G. Incomplete lineage sorting and phenotypic evolution in marsupials. Cell 2022; 185:1646-1660.e18. [PMID: 35447073 PMCID: PMC9200472 DOI: 10.1016/j.cell.2022.03.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/22/2021] [Accepted: 03/21/2022] [Indexed: 12/19/2022]
Abstract
Incomplete lineage sorting (ILS) makes ancestral genetic polymorphisms persist during rapid speciation events, inducing incongruences between gene trees and species trees. ILS has complicated phylogenetic inference in many lineages, including hominids. However, we lack empirical evidence that ILS leads to incongruent phenotypic variation. Here, we performed phylogenomic analyses to show that the South American monito del monte is the sister lineage of all Australian marsupials, although over 31% of its genome is closer to the Diprotodontia than to other Australian groups due to ILS during ancient radiation. Pervasive conflicting phylogenetic signals across the whole genome are consistent with some of the morphological variation among extant marsupials. We detected hundreds of genes that experienced stochastic fixation during ILS, encoding the same amino acids in non-sister species. Using functional experiments, we confirm how ILS may have directly contributed to hemiplasy in morphological traits that were established during rapid marsupial speciation ca. 60 mya.
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Affiliation(s)
- Shaohong Feng
- BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; School of Agriculture, Ningxia University, Yinchuan 750021, China; College of Plant Protection, Hebei Agricultural University, Baoding 071001, China
| | | | - Cai Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | - Yijie Tong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei 071001, China; Hainan Yazhou Bay Seed Lab, Building 1, No. 7 Yiju Road, Yazhou District, Sanya, Hainan 572024, China
| | - Haidong Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Guangji Chen
- BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duo Xie
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Lida M Franco
- Facultad de Ciencias Naturales y Matemáticas, Universidad de Ibagué, Carrera 22 Calle 67, Ibagué, Colombia
| | - Juan Diego Gaitan-Espitia
- The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Campus Isla Teja, Valdivia 5090000, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 6513677, Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile; Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remont Road, Front Royal, VA 22630, USA; The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, 4210 Silver Hill Rd., Suitland, MD 20746-2863, USA; Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Parice A Brandies
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, NSW 2010, Australia; Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacobus J Boomsma
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Guojie Zhang
- BGI-Shenzhen, Shenzhen 518083, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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40
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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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Genetic and Epigenetic Signatures Associated with the Divergence of Aquilegia Species. Genes (Basel) 2022; 13:genes13050793. [PMID: 35627179 PMCID: PMC9141525 DOI: 10.3390/genes13050793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Widely grown in the Northern Hemisphere, the genus Aquilegia (columbine) is a model system in adaptive radiation research. While morphological variations between species have been associated with environmental factors, such as pollinators, how genetic and epigenetic factors are involved in the rapid divergence in this genus remains under investigated. In this study, we surveyed the genomes and DNA methylomes of ten Aquilegia species, representative of the Asian, European and North American lineages. Our analyses of the phylogeny and population structure revealed high genetic and DNA methylomic divergence across these three lineages. By multi-level genome-wide scanning, we identified candidate genes exhibiting lineage-specific genetic or epigenetic variation patterns that were signatures of inter-specific divergence. We demonstrated that these species-specific genetic variations and epigenetic variabilities are partially independent and are both functionally related to various biological processes vital to adaptation, including stress tolerance, cell reproduction and DNA repair. Our study provides an exploratory overview of how genetic and epigenetic signatures are associated with the diversification of the Aquilegia species.
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42
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Ten Brink H, Seehausen O. Competition among small individuals hinders adaptive radiation despite ecological opportunity. Proc Biol Sci 2022; 289:20212655. [PMID: 35317672 PMCID: PMC8941390 DOI: 10.1098/rspb.2021.2655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Ontogenetic diet shifts, where individuals change their resource use during development, are the rule rather than the exception in the animal world. Here, we aim to understand how such changes in diet during development affect the conditions for an adaptive radiation in the presence of ecological opportunity. We use a size-structured consumer–resource model and the adaptive dynamics approach to study the ecological conditions for speciation. We assume that small individuals all feed on a shared resource. Large individuals, on the other hand, have access to multiple food sources on which they can specialize. We find that competition among small individuals can hinder an adaptive radiation to unfold, despite plenty of ecological opportunity for large individuals. When small individuals experience strong competition for food, they grow slowly and only a few individuals are recruited to the larger size classes. Hence, competition for food among large individuals is weak and there is therefore no disruptive selection. In addition, initial conditions determine if an adaptive radiation occurs or not. A consumer population initially dominated by small individuals will not radiate. On the other hand, a population initially dominated by large individuals may undergo adaptive radiation and diversify into multiple species.
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Affiliation(s)
- Hanna Ten Brink
- Eawag Swiss Federal Institute of Aquatic Science and Technology, Department of Fish Ecology and Evolution, Center of Ecology, Evolution, and Biogeochemistry, Kastanienbaum, Switzerland
| | - Ole Seehausen
- Eawag Swiss Federal Institute of Aquatic Science and Technology, Department of Fish Ecology and Evolution, Center of Ecology, Evolution, and Biogeochemistry, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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43
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González-Miguéns R, Soler-Zamora C, Useros F, Nogal-Prata S, Berney C, Blanco-Rotea A, Carrasco-Braganza MI, de Salvador-Velasco D, Guillén-Oterino A, Tenorio-Rodríguez D, Velázquez D, Heger TJ, Sanmartín I, Lara E. Cyphoderia ampulla (Cyphoderiidae: Rhizaria), a tale of freshwater sailors. The causes and consequences of ecological transitions through the salinity barrier in a family of benthic protists. Mol Ecol 2022; 31:2644-2663. [PMID: 35262986 PMCID: PMC9311665 DOI: 10.1111/mec.16424] [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] [Received: 12/01/2021] [Revised: 02/17/2022] [Accepted: 03/02/2022] [Indexed: 11/29/2022]
Abstract
The salinity barrier that separates marine and freshwater biomes is probably the most important division in biodiversity on Earth. Those organisms that successfully performed this transition had access to new ecosystems while undergoing changes in selective pressure, which often led to major shifts in diversification rates. While these transitions have been extensively investigated in animals, the tempo, mode, and outcome of crossing the salinity barrier have been scarcely studied in other eukaryotes. Here, we reconstructed the evolutionary history of the species complex Cyphoderia ampulla (Euglyphida: Cercozoa: Rhizaria) based on DNA sequences from the nuclear SSU rRNA gene and the mitochondrial cytochrome oxidase subunit I gene, obtained from publicly available environmental DNA data (GeneBank, EukBank) and isolated organisms. A tree calibrated with euglyphid fossils showed that four independent transitions towards freshwater systems occurred from the Mid Miocene onwards, coincident with important fluctuations in sea level. Ancestral trait reconstructions indicated that the whole family Cyphoderiidae had a marine origin and suggest that ancestors of the freshwater forms were euryhaline and lived in environments with fluctuating salinity. Diversification rates did not show any obvious increase concomitant with ecological transitions, but morphometric analyses indicated that species increased in size and homogenized their morphology after colonizing the new environments. This suggests adaptation to changes in selective pressure exerted by life in freshwater sediments.
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Affiliation(s)
| | - Carmen Soler-Zamora
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
| | - Fernando Useros
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
| | - Sandra Nogal-Prata
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
| | - Cédric Berney
- Université de la Sorbonne CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680, Roscoff, France.,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 10, Paris, France
| | - Andrés Blanco-Rotea
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - María Isabel Carrasco-Braganza
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - David de Salvador-Velasco
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - Antonio Guillén-Oterino
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - Daniel Tenorio-Rodríguez
- Estación Biológica Internacional Duero-Douro, (EUROPARQUES-EBI), Buque hidrográfico Helios-Cousteau en el Lago de Sanabria, 49632, Ribadelago, Castilla y León, Spain
| | - David Velázquez
- Dpt. of Biology, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Thierry J Heger
- Soil Science and Environment Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Route de Duillier 50, 1260, Nyon, Switzerland
| | - Isabel Sanmartín
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
| | - Enrique Lara
- Real Jardín Botánico de Madrid (RJB-CSIC), Plaza Murillo 2, 28014, Madrid, Spain
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44
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Toji T, Hirota SK, Ishimoto N, Suyama Y, Itino T. Intraspecific independent evolution of floral spur length in response to local flower visitor size in Japanese
Aquilegia
in different mountain regions. Ecol Evol 2022; 12:e8668. [PMID: 35261751 PMCID: PMC8888250 DOI: 10.1002/ece3.8668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Tsubasa Toji
- Graduate School of Medicine, Science and Technology Shinshu University Matsumoto Japan
| | - Shun K. Hirota
- Field Science Center, Graduate School of Agricultural Science Tohoku University Osaki Japan
| | | | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science Tohoku University Osaki Japan
| | - Takao Itino
- Faculty of Science Shinshu University Matsumoto Japan
- Department of Biology and Institute of Mountain Science Shinshu University Matsumoto Japan
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45
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Crouch NMA, Tobias JA. The causes and ecological context of rapid morphological evolution in birds. Ecol Lett 2022; 25:611-623. [PMID: 35199918 DOI: 10.1111/ele.13962] [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: 08/11/2021] [Revised: 09/29/2021] [Accepted: 12/20/2021] [Indexed: 12/14/2022]
Abstract
Episodic pulses in morphological diversification are a prominent feature of evolutionary history, driven by factors that remain widely disputed. Resolving this question has proved challenging because comprehensive species-level data are generally unavailable at sufficient scale. Combining global phylogenetic and morphological data for birds, we show that pulses of diversification in lineages and traits tend to occur independently and in different contexts. Speciation pulses are preceded by greater differentiation in overall morphology and habitat niche, then followed by increased rates of beak evolution. Contrary to standard hypotheses, pulses of morphological diversification tend to be associated with habitat niche stability rather than adaptation to different diets and habitat types. These patterns suggest that the timing of diversification varies across traits according to their ecological function, and that pulses of morphological evolution may occur when successful lineages subdivide niche space within particular habitat types. Our results highlight the growing potential of functional trait data sets to refine macroevolutionary models.
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Affiliation(s)
- Nicholas M A Crouch
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK
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46
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Morphological volatility precedes ecological innovation in early echinoderms. Nat Ecol Evol 2022; 6:263-272. [PMID: 35145267 DOI: 10.1038/s41559-021-01656-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/20/2021] [Indexed: 11/08/2022]
Abstract
Origins of higher taxonomic groups entail dramatic and nearly simultaneous changes in morphology and ecological function, limiting our ability to disentangle the drivers of evolutionary diversification. Here we phylogenetically compare the anatomy and life habits of Cambrian-Ordovician echinoderms to test which facet better facilitates future success. Rates of morphological evolution are faster and involve more volatile trait changes, allowing morphological disparity to accrue faster and earlier in the Cambrian. However, persistent life-habit evolution throughout the early Palaeozoic, combined with iterative functional convergence within adaptive strategies, results in major expansion of ecospace and functional diversity. The interactions between tempo, divergence and convergence demonstrate not only that anatomical novelty precedes ecological success, but also that ecological innovation is constrained, even during a phylum's origin.
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47
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Acosta MM, Zaman L. Ecological Opportunity and Necessity: Biotic and Abiotic Drivers Interact During Diversification of Digital Host-Parasite Communities. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.750772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most of Earth’s diversity has been produced in rounds of adaptive radiation, but the ecological drivers of diversification, such as abiotic complexity (i.e., ecological opportunity) or predation and parasitism (i.e., ecological necessity), are hard to disentangle. However, most of these radiations occurred hundreds of thousands if not millions of years ago, and the mechanisms promoting contemporary coexistence are not necessarily the same mechanisms that drove diversification in the first place. Experimental evolution has been one fruitful approach used to understand how different ecological mechanisms promote diversification in simple microbial microcosms, but these microbial systems come with their own limitations. To test how ecological necessity and opportunity interact, we use an unusual system of self-replicating computer programs that diversify to fill niches in a virtual environment. These organisms are subject to ecological pressures just like their natural counterparts. They experience biotic interactions from digital parasites, which steal host resources to replicate their own code and spread in the population. With the control afforded by experimenting with computational ecologies, we begin to unweave the complex interplay between ecological drivers of diversification. In particular, we find that the complexity of the abiotic environment and the size of the phenotypic space in which organisms are able to interact play different roles depending on the ecological driver of diversification. We find that in some situations, both ecological opportunity and necessity drive similar levels of diversity. However, the phenotypes that hosts uncover while coevolving with parasites are dramatically more complex than hosts evolving alone.
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48
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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49
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Tejero-Cicuéndez H, Simó-Riudalbas M, Menéndez I, Carranza S. Ecological specialization, rather than the island effect, explains morphological diversification in an ancient radiation of geckos. Proc Biol Sci 2021; 288:20211821. [PMID: 34933601 PMCID: PMC8692960 DOI: 10.1098/rspb.2021.1821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/26/2021] [Indexed: 12/24/2022] Open
Abstract
Island colonists are often assumed to experience higher levels of phenotypic diversification than continental taxa. However, empirical evidence has uncovered exceptions to this 'island effect'. Here, we tested this pattern using the geckos of the genus Pristurus from continental Arabia and Africa and the Socotra Archipelago. Using a recently published phylogeny and an extensive morphological dataset, we explore the differences in phenotypic evolution between Socotran and continental taxa. Moreover, we reconstructed ancestral habitat occupancy to examine if ecological specialization is correlated with morphological change, comparing phenotypic disparity and trait evolution between habitats. We found a heterogeneous outcome of island colonization. Namely, only one of the three colonization events resulted in a body size increase. However, in general, Socotran species do not present higher levels or rates of morphological diversification than continental groups. Instead, habitat specialization explains better the body size and shape evolution in Pristurus. Particularly, the colonization of ground habitats appears as the main driver of morphological change, producing the highest disparity and evolutionary rates. Additionally, arboreal species show very similar body size and head proportions. These results reveal a determinant role of ecological mechanisms in morphological evolution and corroborate the complexity of ecomorphological dynamics in continent-island systems.
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Affiliation(s)
- Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona 08003, Spain
| | - Marc Simó-Riudalbas
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona 08003, Spain
| | - Iris Menéndez
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, C/José Antonio Novais 12, Madrid 28040, Spain
- Departamento de Cambio Medioambiental, Instituto de Geociencias (UCM, CSIC), C/Severo Ochoa 7, Madrid 28040, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, Barcelona 08003, Spain
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50
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Linan AG, Myers JA, Edwards CE, Zanne AE, Smith SA, Arellano G, Cayola L, Farfan-Ríos W, Fuentes AF, García-Cabrera K, González-Caro S, Loza MI, Macía MJ, Malhi Y, Nieto-Ariza B, Salinas N, Silman M, Tello JS. The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades? THE NEW PHYTOLOGIST 2021; 232:2506-2519. [PMID: 34379801 DOI: 10.1111/nph.17674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Recent studies have demonstrated that ecological processes that shape community structure and dynamics change along environmental gradients. However, much less is known about how the emergence of the gradients themselves shape the evolution of species that underlie community assembly. In this study, we address how the creation of novel environments leads to community assembly via two nonmutually exclusive processes: immigration and ecological sorting of pre-adapted clades (ISPC), and recent adaptive diversification (RAD). We study these processes in the context of the elevational gradient created by the uplift of the Central Andes. We develop a novel approach and method based on the decomposition of species turnover into within- and among-clade components, where clades correspond to lineages that originated before mountain uplift. Effects of ISPC and RAD can be inferred from how components of turnover change with elevation. We test our approach using data from over 500 Andean forest plots. We found that species turnover between communities at different elevations is dominated by the replacement of clades that originated before the uplift of the Central Andes. Our results suggest that immigration and sorting of clades pre-adapted to montane habitats is the primary mechanism shaping tree communities across elevations.
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Affiliation(s)
- Alexander G Linan
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
| | - Jonathan A Myers
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Christine E Edwards
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
| | - Amy E Zanne
- Department of Biological Sciences, The George Washington University, Washington, DC, 20052, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gabriel Arellano
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Leslie Cayola
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - William Farfan-Ríos
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Alfredo F Fuentes
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Karina García-Cabrera
- Escuela Profesional de Biología, Universidad Nacional de San Antonio Abad del Cusco, Cusco, Peru
| | - Sebastián González-Caro
- Departamento de Ciencias Forestales, Universidad Nacional de Colombia Sede Medellín, Universidad Nacional de Colombia, Medellín, Colombia
| | - M Isabel Loza
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
- Department of Biology, University of Missouri-St Louis, St Louis, MO, 63121, USA
| | - Manuel J Macía
- Departamento de Biología, Área de Botánica, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | | | - Norma Salinas
- Institute for Nature Earth and Energy, Pontificia Universidad Catolica del Peru, Lima, Peru
| | - Miles Silman
- Center for Energy, Environment and Sustainability, Winston-Salem, NC, 27109, USA
| | - J Sebastián Tello
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
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