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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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2
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Val P, Lyons NJ, Gasparini N, Willenbring JK, Albert JS. Landscape Evolution as a Diversification Driver in Freshwater Fishes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.788328] [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
The exceptional concentration of vertebrate diversity in continental freshwaters has been termed the “freshwater fish paradox,” with > 15,000 fish species representing more than 20% of all vertebrate species compressed into tiny fractions of the Earth’s land surface area (<0.5%) or total aquatic habitat volume (<0.001%). This study asks if the fish species richness of the world’s river basins is explainable in terms of river captures using topographic metrics as proxies. The River Capture Hypothesis posits that drainage-network rearrangements have accelerated biotic diversification through their combined effects on dispersal, speciation, and extinction. Yet rates of river capture are poorly constrained at the basin scale worldwide. Here we assess correlations between fish species density (data for 14,953 obligate freshwater fish species) and basin-wide metrics of landscape evolution (data for 3,119 river basins), including: topography (elevation, average relief, slope, drainage area) and climate (average rainfall and air temperature). We assess the results in the context of both static landscapes (e.g., species-area and habitat heterogeneity relationships) and transient landscapes (e.g., river capture, tectonic activity, landscape disequilibrium). We also relax assumptions of functional neutrality of basins (tropical vs. extratropical, tectonically stable vs. active terrains). We found a disproportionate number of freshwater species in large, lowland river basins of tropical South America, Africa, and Southeast Asia, under predictable conditions of large geographic area, tropical climate, low topographic relief, and high habitat volume (i.e., high rainfall rates). However, our results show that these conditions are only necessary, but not fully sufficient, to explain the basins with the highest diversity. Basins with highest diversity are all located on tectonically stable regions, places where river capture is predicted to be most conducive to the formation of high fish species richness over evolutionary timescales. Our results are consistent with predictions of several landscape evolution models, including the River Capture Hypothesis, Mega Capture Hypothesis, and Intermediate Capture Rate Hypothesis, and support conclusions of numerical modeling studies indicating landscape transience as a mechanistic driver of net diversification in riverine and riparian organisms with widespread continental distributions.
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3
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Arbour JH, Curtis AA, Santana SE. Sensory adaptations reshaped intrinsic factors underlying morphological diversification in bats. BMC Biol 2021; 19:88. [PMID: 33931060 PMCID: PMC8086122 DOI: 10.1186/s12915-021-01022-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
Background Morphological evolution may be impacted by both intrinsic (developmental, constructional, physiological) and extrinsic (ecological opportunity and release) factors, but can intrinsic factors be altered by adaptive evolution and, if so, do they constrain or facilitate the subsequent diversification of biological form? Bats underwent deep adaptive divergences in skull shape as they evolved different sensory modes; here we investigate the potential impact of this process on two intrinsic factors that underlie morphological variation across organisms, allometry, and modularity. Results We use comparative phylogenetic and morphometric approaches to examine patterns of evolutionary allometry and modularity across a 3D geometric morphometric dataset spanning all major bat clades. We show that allometric relationships diverge between echolocators and visually oriented non-echolocators and that the evolution of nasal echolocation reshaped the modularity of the bat cranium. Conclusions Shifts in allometry and modularity may have significant consequences on the diversification of anatomical structures, as observed in the bat skull.
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Affiliation(s)
- J H Arbour
- Present Address: Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA.,Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - A A Curtis
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA
| | - S E Santana
- Department of Biology, University of Washington, Seattle, Washington, 98195, USA. .,Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, 98195, USA.
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4
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Grundler M, Rabosky DL. Complex Ecological Phenotypes on Phylogenetic Trees: A Markov Process Model for Comparative Analysis of Multivariate Count Data. Syst Biol 2020; 69:1200-1211. [DOI: 10.1093/sysbio/syaa031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 12/26/2022] Open
Abstract
AbstractThe evolutionary dynamics of complex ecological traits—including multistate representations of diet, habitat, and behavior—remain poorly understood. Reconstructing the tempo, mode, and historical sequence of transitions involving such traits poses many challenges for comparative biologists, owing to their multidimensional nature. Continuous-time Markov chains are commonly used to model ecological niche evolution on phylogenetic trees but are limited by the assumption that taxa are monomorphic and that states are univariate categorical variables. A necessary first step in the analysis of many complex traits is therefore to categorize species into a predetermined number of univariate ecological states, but this procedure can lead to distortion and loss of information. This approach also confounds interpretation of state assignments with effects of sampling variation because it does not directly incorporate empirical observations for individual species into the statistical inference model. In this study, we develop a Dirichlet-multinomial framework to model resource use evolution on phylogenetic trees. Our approach is expressly designed to model ecological traits that are multidimensional and to account for uncertainty in state assignments of terminal taxa arising from effects of sampling variation. The method uses multivariate count data across a set of discrete resource categories sampled for individual species to simultaneously infer the number of ecological states, the proportional utilization of different resources by different states, and the phylogenetic distribution of ecological states among living species and their ancestors. The method is general and may be applied to any data expressible as a set of observational counts from different categories. [Comparative methods; Dirichlet multinomial; ecological niche evolution; macroevolution; Markov model.]
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Affiliation(s)
- Michael Grundler
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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5
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Felice RN, Tobias JA, Pigot AL, Goswami A. Dietary niche and the evolution of cranial morphology in birds. Proc Biol Sci 2020; 286:20182677. [PMID: 30963827 PMCID: PMC6408879 DOI: 10.1098/rspb.2018.2677] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cranial morphology in birds is thought to be shaped by adaptive evolution for foraging performance. This understanding of ecomorphological evolution is supported by observations of avian island radiations, such as Darwin's finches, which display rapid evolution of skull shape in response to food resource availability and a strong fit between cranial phenotype and trophic ecology. However, a recent analysis of larger clades has suggested that diet is not necessarily a primary driver of cranial shape and that phylogeny and allometry are more significant factors in skull evolution. We use phenome-scale morphometric data across the breadth of extant bird diversity to test the influence of diet and foraging behaviour in shaping cranial evolution. We demonstrate that these trophic characters are significant but very weak predictors of cranial form at this scale. However, dietary groups exhibit significantly different rates of morphological evolution across multiple cranial regions. Granivores and nectarivores exhibit the highest rates of evolution in the face and cranial vault, whereas terrestrial carnivores evolve the slowest. The basisphenoid, occipital, and jaw joint regions have less extreme differences among dietary groups. These patterns demonstrate that dietary niche shapes the tempo and mode of phenotypic evolution in deep time, despite a weaker than expected form–function relationship across large clades.
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Affiliation(s)
- Ryan N Felice
- 1 Department of Cell and Developmental Biology, University College London , London WC1E 6BT , UK.,3 Department of Life Sciences, The Natural History Museum , London SW7 5DB , UK
| | - Joseph A Tobias
- 4 Department of Life Sciences, Imperial College London , Ascot , UK
| | - Alex L Pigot
- 2 Centre for Biodiversity and Environment Research, Department of Genetics, Evolution, and Environment, University College London , London WC1E 6BT , UK
| | - Anjali Goswami
- 2 Centre for Biodiversity and Environment Research, Department of Genetics, Evolution, and Environment, University College London , London WC1E 6BT , UK.,3 Department of Life Sciences, The Natural History Museum , London SW7 5DB , UK
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6
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Arbour JH, Montaña CG, Winemiller KO, Pease AA, Soria-Barreto M, Cochran-Biederman JL, López-Fernández H. Macroevolutionary analyses indicate that repeated adaptive shifts towards predatory diets affect functional diversity in Neotropical cichlids. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Abstract
During adaptive radiation, diversification within clades is limited by adaptation to the available ecological niches, and this may drive patterns of both trait and species diversity. However, adaptation to disparate niches may result in varied impacts on the timing, pattern and rate of morphological evolution. In this study, we examined the relationship between feeding ecology and functional diversification across a diverse clade of freshwater fishes, the Neotropical cichlids. Species dietary niches were ordinated via multivariate analysis of stomach content data. We investigated changes in the rate and pattern of morphological diversification associated with feeding, including dietary niche and degree of dietary specialization. A major division in dietary niche space was observed between predators that consume fish and macroinvertebrates vs. other groups with diets dominated by small invertebrates, detritus or vegetation. These trophic niches were strongly associated with groupings defined by functional morphospace. Clades within the piscivore/macroinvertivore group rarely transitioned to other dietary niches. Comparatively, high dietary specialization enhanced functional diversification, driving the evolution of more extreme morphologies. Divergent patterns of trophic diversification among Neotropical cichlids appear to derive from different performance demands in regional abiotic and biotic environments associated with biogeographical history.
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Affiliation(s)
- Jessica H Arbour
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Carmen G Montaña
- Department of Biology, Stephen F. Austin State University, Nacogdoches, TX, USA
| | - Kirk O Winemiller
- Department of Wildlife and Fisheries Sciences, Texas A&M University, TAMU, College Station, TX, USA
| | - Allison A Pease
- Department of Natural Resources Management, Texas Tech University, Lubbock, TX, USA
| | - Miriam Soria-Barreto
- Departamento de Conservación de la Biodiversidad, CONACYT - El Colegio de la Frontera Sur (ECOSUR), San Cristóbal de Las Casas, Chiapas, Mexico
- Centro de Investigación de Ciencias Ambientales, Universidad Autónoma del Carmen, Ciudad del Carmen, Campeche, Mexico
| | | | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
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7
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Ebner BC, Donaldson JA, Starrs D. Barred grunters shift objects to access benthic invertebrates in a crater lake. FOOD WEBS 2019. [DOI: 10.1016/j.fooweb.2019.e00119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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8
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Moody EK, Lujan NK, Roach KA, Winemiller KO. Threshold elemental ratios and the temperature dependence of herbivory in fishes. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13301] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Eric K. Moody
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames Iowa
| | - Nathan K. Lujan
- Department of Biological Sciences University of Toronto Scarborough Toronto Ontario Canada
| | - Katherine A. Roach
- Department of Wildlife and Fisheries Sciences Program of Ecology and Evolutionary Biology Texas A&M University College Station Texas
| | - Kirk O. Winemiller
- Department of Wildlife and Fisheries Sciences Program of Ecology and Evolutionary Biology Texas A&M University College Station Texas
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9
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Gidmark NJ, Pos K, Matheson B, Ponce E, Westneat MW. Functional Morphology and Biomechanics of Feeding in Fishes. FEEDING IN VERTEBRATES 2019. [DOI: 10.1007/978-3-030-13739-7_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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10
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Specialization boosts reef fish functional diversity. Nat Ecol Evol 2018; 3:153-154. [PMID: 30510180 DOI: 10.1038/s41559-018-0760-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Reef fish functional traits evolve fastest at trophic extremes. Nat Ecol Evol 2018; 3:191-199. [DOI: 10.1038/s41559-018-0725-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 10/21/2018] [Indexed: 12/11/2022]
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12
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Cryptic biodiversity in the freshwater fishes of the Kimberley endemism hotspot, northwestern Australia. Mol Phylogenet Evol 2018; 127:843-858. [DOI: 10.1016/j.ympev.2018.06.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 06/09/2018] [Accepted: 06/19/2018] [Indexed: 11/19/2022]
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13
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Herrera-Alsina L, van Els P, Etienne RS. Detecting the Dependence of Diversification on Multiple Traits from Phylogenetic Trees and Trait Data. Syst Biol 2018; 68:317-328. [DOI: 10.1093/sysbio/syy057] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 09/08/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Leonel Herrera-Alsina
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, Groningen 9700 CC, The Netherlands
| | - Paul van Els
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, Groningen 9700 CC, The Netherlands
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, Groningen 9700 CC, The Netherlands
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14
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Hundt PJ, Simons AM. Extreme dentition does not prevent diet and tooth diversification within combtooth blennies (Ovalentaria: Blenniidae). Evolution 2018; 72:930-943. [PMID: 29457222 DOI: 10.1111/evo.13453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 01/10/2018] [Accepted: 01/30/2018] [Indexed: 11/28/2022]
Abstract
The dentition of fishes can be quite striking and is often correlated with a specific diet. Combtooth blennies have long incisiform oral teeth, unlike most actinopterygians. It has been suggested that the long tooth morphology is an adaptation for detritivory, but given the diversity of diets (detritus, coral polyps, polychaetes, and pieces of other fishes), are blenny teeth indeed monomorphic? Or does tooth variation associated with diet still exist at this extreme? To explore tooth and diet diversification, we used a new phylogenetic hypothesis of Blenniidae, measured tooth shape, number, and mode of attachment, and quantified blenniid diet. The ancestral diet of blennies contained detritus and diversified into many different diets, including almost exclusively detritivory. Our results reveal a dental cline that may be constrained by tooth shape, but has not prevented diet diversification. Ancestral state reconstruction of tooth morphologies suggests that the ancestor of blennies had many unattached teeth and featured transitions to fewer attached teeth, with several transitions back to attached or unattached teeth. The dentition of blenniids is not monotypic; rather it is diverse and small changes in tooth shape are accompanied by changes in size, number, attachment, and often diet.
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Affiliation(s)
- Peter J Hundt
- Conservation Sciences Graduate Program, University of Minnesota, St. Paul, Minnesota, 55108.,Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota, 55108.,Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, Minnesota, 55108
| | - Andrew M Simons
- Bell Museum of Natural History, University of Minnesota, St. Paul, Minnesota, 55108.,Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, St. Paul, Minnesota, 55108
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15
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Davis AM, Betancur-R R. Widespread ecomorphological convergence in multiple fish families spanning the marine-freshwater interface. Proc Biol Sci 2018; 284:rspb.2017.0565. [PMID: 28515206 DOI: 10.1098/rspb.2017.0565] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/19/2017] [Indexed: 11/12/2022] Open
Abstract
The theoretical definition and quantification of convergence is an increasingly topical focus in evolutionary research, with particular growing interest on study scales spanning deep phylogenetic divergences and broad geographical areas. While much progress has recently been made in understanding the role of convergence in driving terrestrial (e.g. anole lizards) and aquatic (e.g. cichlids) radiations, little is known about its macroevolutionary effects across environmental gradients. This study uses a suite of recently developed comparative approaches integrating diverse aspects of morphology, dietary data, habitat affiliation and phylogeny to assess convergence across several well-known tropical-temperate fish families in the percomorph suborder Terapontoidei, a clade with considerable phenotypic and ecological diversity radiating in both marine and freshwater environments. We demonstrate significant widespread convergence across many lineages occupying equivalent trophic niches, particularly feeding habits such as herbivory and biting of attached prey off hard substrates. These include several examples of convergent morphotypes evolving independently in marine and freshwater clades, separated by deep evolutionary divergences (tens of millions of years). The Terapontoidei present a new example of the macroevolutionary dynamics of morphological and ecological coevolution in relation to habitat and trophic preferences, at a greater phylogenetic and habitat scale than most well-studied adaptive radiations.
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Affiliation(s)
- Aaron M Davis
- Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER), and School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia .,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 159, Washington, DC 20013-7012, USA
| | - Ricardo Betancur-R
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 159, Washington, DC 20013-7012, USA.,Department of Biology, University of Puerto Rico, Río Piedras, PO Box 23360, San Juan, Puerto Rico 00931, USA
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16
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Meyer ALS, Wiens JJ. Estimating diversification rates for higher taxa: BAMM can give problematic estimates of rates and rate shifts. Evolution 2017; 72:39-53. [DOI: 10.1111/evo.13378] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Andreas L. S. Meyer
- Graduate Program in Zoology Universidade Federal do Paraná Curitiba Paraná 81531 Brazil
- Department of Ecology and Evolution University of Arizona Tucson Arizona 85721
| | - John J. Wiens
- Department of Ecology and Evolution University of Arizona Tucson Arizona 85721
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17
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Betancur-R R, Wiley EO, Arratia G, Acero A, Bailly N, Miya M, Lecointre G, Ortí G. Phylogenetic classification of bony fishes. BMC Evol Biol 2017; 17:162. [PMID: 28683774 PMCID: PMC5501477 DOI: 10.1186/s12862-017-0958-3] [Citation(s) in RCA: 410] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/26/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. RESULTS The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. CONCLUSIONS This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.
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Affiliation(s)
- Ricardo Betancur-R
- Department of Biology, University of Puerto Rico, Río Piedras, P.O. Box 23360, San Juan, PR 00931 USA
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
| | - Edward O. Wiley
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS USA
- Sam Houston State Natural History Collections, Sam Houston State University, Huntsville, Texas USA
| | - Gloria Arratia
- Biodiversity Institute and Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS USA
| | - Arturo Acero
- Universidad Nacional de Colombia sede Caribe, Cecimar, El Rodadero, Santa Marta, Magdalena Colombia
| | - Nicolas Bailly
- FishBase Information and Research Group, Los Baños, Philippines
| | - Masaki Miya
- Department Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
| | - Guillaume Lecointre
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Guillermo Ortí
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC USA
- Department of Biology, The George Washington University, Washington, DC USA
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18
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Affiliation(s)
- G McGregor Reid
- Natural History Museum, London, SW7 5BD, U.K
- National Zoonoses Research Centre, Veterinary School, University of Liverpool, Neston, CH64 7TE, U.K
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Sidlauskas BL, Ferraris C, Funk V, Parenti LR, de Pinna M, Reid GM. In Memoriam: Richard Peter Vari (August 24, 1949–January 15, 2016). COPEIA 2017. [DOI: 10.1643/ci-16-550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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