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Barreto E, Lim MCW, Rojas D, Dávalos LM, Wüest RO, Machac A, Graham CH. Morphology and niche evolution influence hummingbird speciation rates. Proc Biol Sci 2023; 290:20221793. [PMID: 37072043 PMCID: PMC10113027 DOI: 10.1098/rspb.2022.1793] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/21/2023] [Indexed: 04/20/2023] Open
Abstract
How traits affect speciation is a long-standing question in evolution. We investigate whether speciation rates are affected by the traits themselves or by the rates of their evolution, in hummingbirds, a clade with great variation in speciation rates, morphology and ecological niches. Further, we test two opposing hypotheses, postulating that speciation rates are promoted by trait conservatism or, alternatively, by trait divergence. To address these questions, we analyse morphological (body mass and bill length) and niche traits (temperature and precipitation position and breadth, and mid-elevation), using a variety of methods to estimate speciation rates and correlate them with traits and their evolutionary rates. When it comes to the traits, we find faster speciation in smaller hummingbirds with shorter bills, living at higher elevations and experiencing greater temperature ranges. As for the trait evolutionary rates, we find that speciation increases with rates of divergence in the niche traits, but not in the morphological traits. Together, these results reveal the interplay of mechanisms through which different traits and their evolutionary rates (conservatism or divergence) influence the origination of hummingbird diversity.
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Affiliation(s)
- Elisa Barreto
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Departamento de Ecologia, Universidade Federal de Goiás, Campus Samambaia, Goiânia, Goiás, Brazil
| | - Marisa C. W. Lim
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
| | - Danny Rojas
- Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cl. 18 #118-250, Cali, Valle del Cauca, Colombia
| | - Liliana M. Dávalos
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, 129 Dana Hall, Stony Brook, NY 11794, USA
| | - Rafael O. Wüest
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Antonin Machac
- Villum Center for Global Mountain Biodiversity and Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
- Center for Theoretical Study, Charles University and the Czech Academy of Science, Jilska 1, 11000 Prague, Czechia
- Department of Ecology, Charles University, Vinicna 7, 12844 Prague, Czechia
| | - Catherine H. Graham
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
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Moreira MO, Fonseca C, Rojas D. ES-sim-GLM, a Multiple Regression Trait-Dependent Diversification Approach. Evol Biol 2022. [DOI: 10.1007/s11692-021-09557-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Fuzessy L, Silveira FAO, Culot L, Jordano P, Verdú M. Phylogenetic congruence between Neotropical primates and plants is driven by frugivory. Ecol Lett 2021; 25:320-329. [PMID: 34775664 DOI: 10.1111/ele.13918] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/27/2022]
Abstract
Seed dispersal benefits plants and frugivores, and potentially drives co-evolution, with consequences to diversification evidenced for, e.g., primates. Evidence for macro-coevolutionary patterns in multi-specific, plant-animal mutualisms is scarce, and the mechanisms driving them remain unexplored. We tested for phylogenetic congruences in primate-plant interactions and showed strong co-phylogenetic signals across Neotropical forests, suggesting that both primates and plants share evolutionary history. Phylogenetic congruence between Platyrrhini and Angiosperms was driven by the most generalist primates, modulated by their functional traits, interacting with a wide-range of Angiosperms. Consistently similar eco-evolutionary dynamics seem to be operating irrespective of local assemblages, since co-phylogenetic signal emerged independently across three Neotropical regions. Our analysis supports the idea that macroevolutionary, coevolved patterns among interacting mutualistic partners are driven by super-generalist taxa. Trait convergence among multiple partners within multi-specific assemblages appears as a mechanism favouring these likely coevolved outcomes.
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Affiliation(s)
- Lisieux Fuzessy
- Department of Biodiversity, Universidade Estadual Paulista, UNESP campus Rio Claro, São Paulo, Brazil.,CREAF, Centre de Recerca Ecològica i Aplicacions Foresta, Universitat Autònoma de Barcelona, Catalunya, Spain.,Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain
| | - Fernando A O Silveira
- Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Laurence Culot
- Department of Biodiversity, Universidade Estadual Paulista, UNESP campus Rio Claro, São Paulo, Brazil
| | - Pedro Jordano
- Estación Biológica de Doñana, EBD-CSIC, Sevilla, Spain.,Facultad de Biología, Department Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Miguel Verdú
- Centro de Investigaciones sobre Desertificación, CSIC-UV-GV, Moncada, Valencia, Spain
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4
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Extinction risk in vascular plants and vertebrates is negatively correlated with family size. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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5
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Pie MR, Caron FS, Divieso R. The evolution of species abundances in terrestrial vertebrates. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marcio R. Pie
- Departamento de Zoologia Universidade Federal do Paraná Curitiba Brazil
| | - Fernanda S. Caron
- Departamento de Zoologia Universidade Federal do Paraná Curitiba Brazil
| | - Raquel Divieso
- Departamento de Zoologia Universidade Federal do Paraná Curitiba Brazil
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6
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Machine learning approaches identify male body size as the most accurate predictor of species richness. BMC Biol 2020; 18:105. [PMID: 32854698 PMCID: PMC7453550 DOI: 10.1186/s12915-020-00835-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness -the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera. RESULTS We test the predictive power of 22 variables from spiders' morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness. CONCLUSIONS We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly.
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Modica MV, Gorson J, Fedosov AE, Malcolm G, Terryn Y, Puillandre N, Holford M. Macroevolutionary Analyses Suggest That Environmental Factors, Not Venom Apparatus, Play Key Role in Terebridae Marine Snail Diversification. Syst Biol 2020; 69:413-430. [PMID: 31504987 PMCID: PMC7164365 DOI: 10.1093/sysbio/syz059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
How species diversification occurs remains an unanswered question in predatory marine invertebrates, such as sea snails of the family Terebridae. However, the anatomical disparity found throughput the Terebridae provides a unique perspective for investigating diversification patterns in venomous predators. In this study, a new dated molecular phylogeny of the Terebridae is used as a framework for investigating diversification of the family through time, and for testing the putative role of intrinsic and extrinsic traits, such as shell size, larval ecology, bathymetric distribution, and anatomical features of the venom apparatus, as drivers of terebrid species diversification. Macroevolutionary analysis revealed that when diversification rates do not vary across Terebridae clades, the whole family has been increasing its global diversification rate since 25 Ma. We recovered evidence for a concurrent increase in diversification of depth ranges, while shell size appeared to have undergone a fast divergence early in terebrid evolutionary history. Our data also confirm that planktotrophy is the ancestral larval ecology in terebrids, and evolutionary modeling highlighted that shell size is linked to larval ecology of the Terebridae, with species with long-living pelagic larvae tending to be larger and have a broader size range than lecithotrophic species. Although we recovered patterns of size and depth trait diversification through time and across clades, the presence or absence of a venom gland (VG) did not appear to have impacted Terebridae diversification. Terebrids have lost their venom apparatus several times and we confirm that the loss of a VG happened in phylogenetically clustered terminal taxa and that reversal is extremely unlikely. Our findings suggest that environmental factors, and not venom, have had more influence on terebrid evolution.
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Affiliation(s)
- Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- UMR5247, Université de Montpellier CC 1703, Place Eugène Bataillon 34095 Montpellier, France
| | - Juliette Gorson
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
| | - Alexander E Fedosov
- Institute of Ecology and Evolution of Russian Academy of Sciences, Leninskiy Prospect, 33, Moscow 119071, Russia
| | - Gavin Malcolm
- Bird Hill, Barnes Lane, Milford on Sea, Hampshire, UK
| | - Yves Terryn
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antillles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Mandë Holford
- Department of Chemistry, Hunter College Belfer Research Center, 413 E. 69th Street, BRB 424, New York, NY 10021, USA
- Department of Biochemistry, Weill Cornell Medical College, Cornell University, New York, NY 10021, USA
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8
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Scott JE. Reevaluating cases of trait-dependent diversification in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:244-256. [DOI: 10.1002/ajpa.23621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/23/2018] [Accepted: 05/12/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Jeremiah E. Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific; Western University of Health Sciences; Pomona California 91766
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9
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Alhajeri BH, Steppan SJ. Ecological and Ecomorphological Specialization Are Not Associated with Diversification Rates in Muroid Rodents (Rodentia: Muroidea). Evol Biol 2018. [DOI: 10.1007/s11692-018-9449-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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Harvey MG, Rabosky DL. Continuous traits and speciation rates: Alternatives to state‐dependent diversification models. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12949] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Michael G. Harvey
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology University of Michigan Ann Arbor MI USA
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11
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Diversification dynamics of rhynchostomatian ciliates: the impact of seven intrinsic traits on speciation and extinction in a microbial group. Sci Rep 2017; 7:9918. [PMID: 28855561 PMCID: PMC5577237 DOI: 10.1038/s41598-017-09472-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/26/2017] [Indexed: 01/30/2023] Open
Abstract
Ciliates are a suitable microbial model to investigate trait-dependent diversification because of their comparatively complex morphology and high diversity. We examined the impact of seven intrinsic traits on speciation, extinction, and net-diversification of rhynchostomatians, a group of comparatively large, predatory ciliates with proboscis carrying a dorsal brush (sensoric structure) and toxicysts (organelles used to kill the prey). Bayesian estimates under the binary-state speciation and extinction model indicate that two types of extrusomes and two-rowed dorsal brush raise diversification through decreasing extinction. On the other hand, the higher number of contractile vacuoles and their dorsal location likely increase diversification via elevating speciation rate. Particular nuclear characteristics, however, do not significantly differ in their diversification rates and hence lineages with various macronuclear patterns and number of micronuclei have similar probabilities to generate new species. Likelihood-based quantitative state diversification analyses suggest that rhynchostomatians conform to Cope’s rule in that their diversity linearly grows with increasing body length and relative length of the proboscis. Comparison with other litostomatean ciliates indicates that rhynchostomatians are not among the cladogenically most successful lineages and their survival over several hundred million years could be associated with their comparatively large and complex bodies that reduce the risk of extinction.
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12
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Crawford FW, Suchard MA. Diversity, disparity, and evolutionary rate estimation for unresolved Yule trees. Syst Biol 2013; 62:439-55. [PMID: 23417679 PMCID: PMC3622899 DOI: 10.1093/sysbio/syt010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 09/05/2012] [Accepted: 02/08/2013] [Indexed: 01/23/2023] Open
Abstract
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes the evolutionary relationships of the organisms of interest. The probability of the observed trait data can be computed by assuming a model for trait evolution, such as Brownian motion, over the branches of this fixed tree. However, the phylogenetic tree itself contributes statistical uncertainty to estimates of rates of phenotypic evolution, and many comparative evolutionary biologists regard the tree as a nuisance parameter. In this article, we present a framework for analytically integrating over unknown phylogenetic trees in comparative evolutionary studies by assuming that the tree arises from a continuous-time Markov branching model called the Yule process. To do this, we derive a closed-form expression for the distribution of phylogenetic diversity (PD), which is the sum of branch lengths connecting the species in a clade. We then present a generalization of PD which is equivalent to the expected trait disparity in a set of taxa whose evolutionary relationships are generated by a Yule process and whose traits evolve by Brownian motion. We find expressions for the distribution of expected trait disparity under a Yule tree. Given one or more observations of trait disparity in a clade, we perform fast likelihood-based estimation of the Brownian variance for unresolved clades. Our method does not require simulation or a fixed phylogenetic tree. We conclude with a brief example illustrating Brownian rate estimation for 12 families in the mammalian order Carnivora, in which the phylogenetic tree for each family is unresolved.
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13
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García-Rangel S, Pettorelli N. Thinking spatially: The importance of geospatial techniques for carnivore conservation. ECOL INFORM 2013. [DOI: 10.1016/j.ecoinf.2012.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Fabre PH, Hautier L, Dimitrov D, Douzery EJP. A glimpse on the pattern of rodent diversification: a phylogenetic approach. BMC Evol Biol 2012; 12:88. [PMID: 22697210 PMCID: PMC3532383 DOI: 10.1186/1471-2148-12-88] [Citation(s) in RCA: 300] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 05/14/2012] [Indexed: 11/17/2022] Open
Abstract
Background Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia. Results Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation. Conclusions The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.
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Affiliation(s)
- Pierre-Henri Fabre
- Center for Macroecology, Evolution and Climate (CMEC, Department of Biology), Zoological Museum, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
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15
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Zimkus BM, Lawson L, Loader SP, Hanken J. Terrestrialization, miniaturization and rates of diversification in African puddle frogs (Anura: Phrynobatrachidae). PLoS One 2012; 7:e35118. [PMID: 22509392 PMCID: PMC3325629 DOI: 10.1371/journal.pone.0035118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 03/13/2012] [Indexed: 11/29/2022] Open
Abstract
Terrestrialization, the evolution of non-aquatic oviposition, and miniaturization, the evolution of tiny adult body size, are recurring trends in amphibian evolution, but the relationships among the traits that characterize these phenomena are not well understood. Furthermore, these traits have been identified as possible "key innovations" that are predicted to increase rates of speciation in those lineages in which they evolve. We examine terrestrialization and miniaturization in sub-Saharan puddle frogs (Phrynobatrachidae) in a phylogenetic context to investigate the relationship between adaptation and diversification through time. We use relative dating techniques to ascertain if character trait shifts are associated with increased diversification rates, and we evaluate the likelihood that a single temporal event can explain the evolution of those traits. Results indicate alternate reproductive modes evolved independently in Phrynobatrachus at least seven times, including terrestrial deposition of eggs and terrestrial, non-feeding larvae. These shifts towards alternate reproductive modes are not linked to a common temporal event. Contrary to the "key innovations" hypothesis, clades that exhibit alternate reproductive modes have lower diversification rates than those that deposit eggs aquatically. Adult habitat, pedal webbing and body size have no effect on diversification rates. Though these traits putatively identified as key innovations for Phrynobatrachus do not seem to be associated with increased speciation rates, they may still provide opportunities to extend into new niches, thus increasing overall diversity.
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Affiliation(s)
- Breda M Zimkus
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
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16
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Collen B, McRae L, Deinet S, De Palma A, Carranza T, Cooper N, Loh J, Baillie JEM. Predicting how populations decline to extinction. Philos Trans R Soc Lond B Biol Sci 2011; 366:2577-86. [PMID: 21807738 DOI: 10.1098/rstb.2011.0015] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Global species extinction typically represents the endpoint in a long sequence of population declines and local extinctions. In comparative studies of extinction risk of contemporary mammalian species, there appear to be some universal traits that may predispose taxa to an elevated risk of extinction. In local population-level studies, there are limited insights into the process of population decline and extinction. Moreover, there is still little appreciation of how local processes scale up to global patterns. Advancing the understanding of factors which predispose populations to rapid declines will benefit proactive conservation and may allow us to target at-risk populations as well as at-risk species. Here, we take mammalian population trend data from the largest repository of population abundance trends, and combine it with the PanTHERIA database on mammal traits to answer the question: what factors can be used to predict decline in mammalian abundance? We find in general that environmental variables are better determinants of cross-species population-level decline than intrinsic biological traits. For effective conservation, we must not only describe which species are at risk and why, but also prescribe ways to counteract this.
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Affiliation(s)
- Ben Collen
- Institute of Zoology, Zoological Society of London, Regent's Park, London, UK.
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17
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Slater GJ, Harmon LJ, Wegmann D, Joyce P, Revell LJ, Alfaro ME. FITTING MODELS OF CONTINUOUS TRAIT EVOLUTION TO INCOMPLETELY SAMPLED COMPARATIVE DATA USING APPROXIMATE BAYESIAN COMPUTATION. Evolution 2011; 66:752-762. [DOI: 10.1111/j.1558-5646.2011.01474.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Goldie X, Lanfear R, Bromham L. Diversification and the rate of molecular evolution: no evidence of a link in mammals. BMC Evol Biol 2011; 11:286. [PMID: 21967038 PMCID: PMC3205075 DOI: 10.1186/1471-2148-11-286] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 10/04/2011] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Recent research has indicated a positive association between rates of molecular evolution and diversification in a number of taxa. However debate continues concerning the universality and cause of this relationship. Here, we present the first systematic investigation of this relationship within the mammals. We use phylogenetically independent sister-pair comparisons to test for a relationship between substitution rates and clade size at a number of taxonomic levels. Total, non-synonymous and synonymous substitution rates were estimated from mitochondrial and nuclear DNA sequences. RESULTS We found no evidence for an association between clade size and substitution rates in mammals, for either the nuclear or the mitochondrial sequences. We found significant associations between body size and substitution rates, as previously reported. CONCLUSIONS Our results present a contrast to previous research, which has reported significant positive associations between substitution rates and diversification for birds, angiosperms and reptiles. There are three possible reasons for the differences between the observed results in mammals versus other clades. First, there may be no link between substitution rates and diversification in mammals. Second, this link may exist, but may be much weaker in mammals than in other clades. Third, the link between substitution rates and diversification may exist in mammals, but may be confounded by other variables.
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Affiliation(s)
- Xavier Goldie
- Centre for Macroevolution and Macroecology, Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, A.C.T. 0200, Australia
| | - Robert Lanfear
- Centre for Macroevolution and Macroecology, Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, A.C.T. 0200, Australia
| | - Lindell Bromham
- Centre for Macroevolution and Macroecology, Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, A.C.T. 0200, Australia
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19
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Assessing the ecological basis of conservation priority lists for bird species in an island scenario. J Nat Conserv 2011. [DOI: 10.1016/j.jnc.2010.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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20
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Matthews LJ, Arnold C, Machanda Z, Nunn CL. Primate extinction risk and historical patterns of speciation and extinction in relation to body mass. Proc Biol Sci 2010; 278:1256-63. [PMID: 20943699 DOI: 10.1098/rspb.2010.1489] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Body mass is thought to influence diversification rates, but previous studies have produced ambiguous results. We investigated patterns of diversification across 100 trees obtained from a new Bayesian inference of primate phylogeny that sampled trees in proportion to their posterior probabilities. First, we used simulations to assess the validity of previous studies that used linear models to investigate the links between IUCN Red List status and body mass. These analyses support the use of linear models for ordinal ranked data on threat status, and phylogenetic generalized linear models revealed a significant positive correlation between current extinction risk and body mass across our tree block. We then investigated historical patterns of speciation and extinction rates using a recently developed maximum-likelihood method. Specifically, we predicted that body mass correlates positively with extinction rate because larger bodied organisms reproduce more slowly, and body mass correlates negatively with speciation rate because smaller bodied organisms are better able to partition niche space. We failed to find evidence that extinction rates covary with body mass across primate phylogeny. Similarly, the speciation rate was generally unrelated to body mass, except in some tests that indicated an increase in the speciation rate with increasing body mass. Importantly, we discovered that our data violated a key assumption of sample randomness with respect to body mass. After correcting for this bias, we found no association between diversification rates and mass.
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Affiliation(s)
- Luke J Matthews
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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Affiliation(s)
- Richard G. FitzJohn
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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Hardy NB, Cook LG. Gall-induction in insects: evolutionary dead-end or speciation driver? BMC Evol Biol 2010; 10:257. [PMID: 20735853 PMCID: PMC2939573 DOI: 10.1186/1471-2148-10-257] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 08/25/2010] [Indexed: 12/05/2022] Open
Abstract
Background The tree of life is significantly asymmetrical - a result of differential speciation and extinction - but general causes of such asymmetry are unclear. Differences in niche partitioning are thought to be one possible general explanation. Ecological specialization might lead to increases in diversification rate or, alternatively, specialization might limit the evolutionary potential of specialist lineages and increase their extinction risk. Here we compare the diversification rates of gall-inducing and non-galling insect lineages. Compared with other insect herbivores feeding on the same host plant, gall-inducing insects feed on plant tissue that is more nutritious and less defended, and they do so in a favorable microhabitat that may also provide some protection from natural enemies. We use sister-taxon comparisons to test whether gall-inducing lineages are more host-specific than non-galling lineages, and more or less diverse than non-gallers. We evaluate the significance of diversity bipartitions under Equal Rates Markov models, and use maximum likelihood model-fitting to test for shifts in diversification rates. Results We find that, although gall-inducing insect groups are more host-specific than their non-galling relatives, there is no general significant increase in diversification rate in gallers. However, gallers are found at both extremes - two gall-inducing lineages are exceptionally diverse (Euurina sawflies on Salicaceae and Apiomorpha scale insects on Eucalytpus), and one gall-inducing lineage is exceptionally species-poor (Maskellia armored scales on Eucalyptus). Conclusions The effect of ecological specialization on diversification rates is complex in the case of gall-inducing insects, but host range may be an important factor. When a gall-inducing lineage has a host range approximate to that of its non-galling sister, the gallers are more diverse. When the non-galler clade has a much wider host range than the galler, the non-galler is also much more diverse. There are also lineage-specific effects, with gallers on the same host group exhibiting very different diversities. No single general model explains the observed pattern.
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Affiliation(s)
- Nate B Hardy
- Queensland Primary Industries and Fisheries, Entomology, Brisbane, Queensland 4068, Australia.
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Durant SM, Craft ME, Foley C, Hampson K, Lobora AL, Msuha M, Eblate E, Bukombe J, McHetto J, Pettorelli N. Does size matter? An investigation of habitat use across a carnivore assemblage in the Serengeti, Tanzania. J Anim Ecol 2010; 79:1012-22. [PMID: 20646121 DOI: 10.1111/j.1365-2656.2010.01717.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1. This study utilizes a unique data set covering over 19 000 georeferenced records of species presence collected between 1993 and 2008, to explore the distribution and habitat selectivity of an assemblage of 26 carnivore species in the Serengeti-Ngorongoro landscape in northern Tanzania. 2. Two species, the large-spotted genet and the bushy-tailed mongoose, were documented for the first time within this landscape. Ecological Niche Factor Analysis (ENFA) was used to examine habitat selectivity for 18 of the 26 carnivore species for which there is sufficient data. Eleven ecogeographical variables (EGVs), such as altitude and habitat type, were used for these analyses. 3. The ENFA demonstrated that species differed in their habitat selectivity, and supported the limited ecological information already available for these species, such as the golden jackals' preference for grassland and the leopards' preference for river valleys. 4. Two aggregate scores, marginality and tolerance, are generated by the ENFA, and describe each species' habitat selectivity in relation to the suite of EGVs. These scores were used to test the hypothesis that smaller species are expected to be more selective than larger species [Science, 1989, 243, 1145]. Two predictions were tested: Marginality should decrease with body mass; and tolerance should increase with body mass. Our study provided no evidence for either prediction. 5. Our results not only support previous analyses of carnivore diet breadth, but also represent a novel approach to the investigation of habitat selection across species assemblages. Our method provides a powerful tool to explore similar questions in other systems and for other taxa.
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Affiliation(s)
- Sarah M Durant
- The Zoological Society of London (ZSL), Institute of Zoology, Regent's Park, London NW1 4RY, UK.
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Fabre PH, Rodrigues A, Douzery EJP. Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA. Mol Phylogenet Evol 2009; 53:808-25. [PMID: 19682589 DOI: 10.1016/j.ympev.2009.08.004] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 07/08/2009] [Accepted: 08/03/2009] [Indexed: 11/18/2022]
Abstract
Here, we present a new primate phylogeny inferred from molecular supermatrix analyses of size 42 kb containing 70% of missing data, and representing 75% of primate species diversity. The supermatrix was analysed using a gene-partitioned maximum likelihood approach to obtain an exhaustive molecular phylogenetic framework. All clades recovered from recent molecular works were upheld in our analyses demonstrating that the presence of missing data did not bias our supermatrix inference. The resulting phylogenetic tree was subsequently dated with a molecular dating method to provide a timescale for speciation events. Results obtained from our relaxed molecular clock analyses concurred with previous works based on the same fossil constraints. The resulting dated tree allowed to infer of macroevolutionary processes among the primates. Shifts in diversification rate and speciation rates were determined using the SymmeTREE method and a birthdeath process. No significant asymmetry was detected for the primate clade, but significant shifts in diversification rate were identified for seven clades: Anthropoidea, Lemuriformes, Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian Macaca. Comparisons with previous primate supertree results reveal that (i) there was a diversification event at the root of the Lemuriformes, (ii) a higher diversification rate is detected for Cercopithecidae and Anthropoidea and (iii) a shift in diversification is always recovered for Macaca genus. Macroevolutionary inferences and primate divergence dates show that major primate diversification events occurred after the Paleogene, suggesting the extinction of ancient primate lineages.
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Affiliation(s)
- P-H Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, Place E. Bataillon, CC 064, 34095 Montpellier Cedex 5, France.
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Abstract
Sexual selection as a promoter of speciation has received much attention in recent years, but has produced highly equivocal evidence. Here, I test whether sexual conflict is related to species richness among genera in accipitrid birds of prey using phylogenetically controlled comparative analyses. Increased species richness was associated with both 'male-win' as well as 'female-win' situations, i.e. males being able to promote gene flow through mating or females being able to restrict gene flow through female choice. Species richness was higher when plumage differed between males and females and in polygynous breeding systems compared with monogamous ones. To assess the relative importance of sexual conflict and natural selection as correlates of species richness simultaneously, I also performed a multivariate analysis of correlates of species richness. Population density, plumage polymorphism, geographic range size and breeding latitude were predictors of species richness for birds of prey. These results stress the importance of both sexual and natural selection in determining species richness but with a clear overall emphasis on natural selection in birds of prey.
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Affiliation(s)
- O Krüger
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.
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Hardman M, Hardman LM. The Relative Importance of Body Size and Paleoclimatic Change as Explanatory Variables Influencing Lineage Diversification Rate: An Evolutionary Analysis of Bullhead Catfishes (Siluriformes: Ictaluridae). Syst Biol 2008; 57:116-30. [DOI: 10.1080/10635150801902193] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Michael Hardman
- Laboratory of Molecular Systematics, Finnish Forest Research Institute Jokiniemenkuja 1, 01301, Vantaa, Finland; E-mail: (M.H.)
| | - Lotta M. Hardman
- Laboratory of Molecular Systematics, Finnish Forest Research Institute Jokiniemenkuja 1, 01301, Vantaa, Finland; E-mail: (M.H.)
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Maddison WP, Midford PE, Otto SP. Estimating a Binary Character's Effect on Speciation and Extinction. Syst Biol 2007; 56:701-10. [PMID: 17849325 DOI: 10.1080/10635150701607033] [Citation(s) in RCA: 691] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Determining whether speciation and extinction rates depend on the state of a particular character has been of long-standing interest to evolutionary biologists. To assess the effect of a character on diversification rates using likelihood methods requires that we be able to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect. Here we describe how to calculate this probability for a phylogenetic tree and a two-state (binary) character under a simple model of evolution (the "BiSSE" model, binary-state speciation and extinction). The model involves six parameters, specifying two speciation rates (rate when the lineage is in state 0; rate when in state 1), two extinction rates (when in state 0; when in state 1), and two rates of character state change (from 0 to 1, and from 1 to 0). Using these probability calculations, we can do maximum likelihood inference to estimate the model's parameters and perform hypothesis tests (e.g., is the rate of speciation elevated for one character state over the other?). We demonstrate the application of the method using simulated data with known parameter values.
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Affiliation(s)
- Wayne P Maddison
- Department of Zoology, University of British Columbia, Vancouver, Canada.
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McPeek MA, Brown JM. Clade age and not diversification rate explains species richness among animal taxa. Am Nat 2007; 169:E97-106. [PMID: 17427118 DOI: 10.1086/512135] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Accepted: 12/14/2006] [Indexed: 11/03/2022]
Abstract
Animal taxa show remarkable variability in species richness across phylogenetic groups. Most explanations for this disparity postulate that taxa with more species have phenotypes or ecologies that cause higher diversification rates (i.e., higher speciation rates or lower extinction rates). Here we show that clade longevity, and not diversification rate, has primarily shaped patterns of species richness across major animal clades: more diverse taxa are older and thus have had more time to accumulate species. Diversification rates calculated from 163 species-level molecular phylogenies were highly consistent within and among three major animal phyla (Arthropoda, Chordata, Mollusca) and did not correlate with species richness. Clades with higher estimated diversification rates were younger, but species numbers increased with increasing clade age. A fossil-based data set also revealed a strong, positive relationship between total extant species richness and crown group age across the orders of insects and vertebrates. These findings do not negate the importance of ecology or phenotype in influencing diversification rates, but they do show that clade longevity is the dominant signal in major animal biodiversity patterns. Thus, some key innovations may have acted through fostering clade longevity and not by heightening diversification rate.
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Affiliation(s)
- Mark A McPeek
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA.
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Nunn CL, Altizer S, Sechrest W, Jones KE, Barton RA, Gittleman JL. Parasites and the evolutionary diversification of primate clades. Am Nat 2007; 164 Suppl 5:S90-103. [PMID: 15540145 DOI: 10.1086/424608] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Coevolutionary interactions such as those between hosts and parasites have been regarded as an underlying cause of evolutionary diversification, but evidence from natural populations is limited. Among primates and other mammalian groups, measures of host diversification rates vary widely among lineages, but comparative studies have not yet identified a reliable explanation for this variation. In this study, we used a comprehensive data set of disease-causing organisms from free-living primates to illustrate how phylogenetic comparative methods can be used to examine mammalian lineage diversity in relation to parasite species richness. Our results provide evidence that the phylogenetic diversity of primate clades is correlated positively with the number of parasite species harbored by each host and that this pattern is largely independent of other host traits that have been shown to influence diversification rates and parasite species richness in primates. We investigated two possible mechanisms that could explain this association, namely that parasites themselves drive host evolutionary diversification through processes linked with sexual selection and that host shifts or host sharing increases parasite species richness among diverse primate clades. Neither parasite species richness nor host diversification is related to measures of sexual selection in primates. Further, we found only partial evidence that more rapidly diversifying host lineages produced increased opportunities for host sharing or host shifting by parasites through mechanisms involving species' geographic range overlap. Thus, our analyses provide evidence for an important link between the evolutionary diversification of primates and the richness of their parasite communities, but other mechanisms, particularly those related to reciprocal selection or coextinction of hosts and parasites, require further investigation.
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Affiliation(s)
- Charles L Nunn
- Section of Evolution and Ecology, University of California, Davis, California 95616, USA.
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Clubb R, Mason GJ. Natural behavioural biology as a risk factor in carnivore welfare: How analysing species differences could help zoos improve enclosures. Appl Anim Behav Sci 2007. [DOI: 10.1016/j.applanim.2006.05.033] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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BININDA-EMONDS OLAFRP, GITTLEMAN JOHNL, PURVIS ANDY. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biol Rev Camb Philos Soc 2007. [DOI: 10.1111/j.1469-185x.1999.tb00184.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lehman SM, Rajaonson A, Day S. Edge effects and their influence on lemur density and distribution in Southeast Madagascar. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 129:232-41. [PMID: 16323178 DOI: 10.1002/ajpa.20241] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Edge effects are caused by the penetration of abiotic and biotic conditions from the matrix into forest interiors. Although edge effects influence the biogeography of many tropical organisms, they have not been studied directly in primates. Edge effects are particularly relevant to lemurs due to the loss of 80-90% of forests in Madagascar. In this study, data are presented on how biotic edge effects influenced the distribution and density of lemurs in the Vohibola III Classified Forest in southeastern Madagascar. In total, 415 lemur surveys were conducted during June-October 2003 and May-September 2004 along six 1,250-m transects that ran perpendicular to the forest edge. Data were also collected on lemur food trees along the six transects (density, height, diameter at breast height, area, volume, and distance to forest edge). Four nocturnal species (Avahi laniger, Cheirogaleus major, Lepilemur microdon, and Microcebus rufus) and four diurnal species (Eulemur rubriventer, Eulemur fulvus rufus, Hapalemur grisesus griseus, and Propithecus diadema edwardsi) were sighted during surveys. Regression analyses of lemur densities as a function of distance to forest edge provided edge tolerances for A. laniger (edge-tolerant), M. rufus (edge-tolerant), E. rubriventer (edge-tolerant or omnipresent), and H. g. griseus (omnipresent). The density and distribution of M. rufus and their foods trees were correlated. Edge-related variations in food quality and predation pressures may also be influencing lemurs in Vohibola III. Tolerance for edge effects may explain, in part, how lemurs have survived extreme habitat loss and forest fragmentation in southeastern Madagascar.
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Affiliation(s)
- Shawn M Lehman
- Department of Anthropology, University of Toronto, Toronto, Ontario M5S 3G3, Canada.
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Intra-specific variation and taxa- sampling affects the home range — body mass relationship. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/bf03192674] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Finarelli JA, Flynn JJ. Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record. Syst Biol 2006; 55:301-13. [PMID: 16611601 DOI: 10.1080/10635150500541698] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
A recent molecular phylogeny of the mammalian order Carnivora implied large body size as the ancestral condition for the caniform subclade Arctoidea using the distribution of species mean body sizes among living taxa. "Extant taxa-only" approaches such as these discount character state observations for fossil members of living clades and completely ignore data from extinct lineages. To more rigorously reconstruct body sizes of ancestral forms within the Caniformia, body size and first appearance data were collected for 149 extant and 367 extinct taxa. Body sizes were reconstructed for four ancestral nodes using weighted squared-change parsimony on log-transformed body mass data. Reconstructions based on extant taxa alone favored large body sizes (on the order of 10 to 50 kg) for the last common ancestors of both the Caniformia and Arctoidea. In contrast, reconstructions incorporating fossil data support small body sizes (< 5 kg) for the ancestors of those clades. When the temporal information associated with fossil data was discarded, body size reconstructions became ambiguous, demonstrating that incorporating both character state and temporal information from fossil taxa unambiguously supports a small ancestral body size, thereby falsifying hypotheses derived from extant taxa alone. Body size reconstructions for Caniformia, Arctoidea, and Musteloidea were not sensitive to potential errors introduced by uncertainty in the position of extinct lineages relative to the molecular topology, or to missing body size data for extinct members of an entire major clade (the aquatic Pinnipedia). Incorporating character state observations and temporal information from the fossil record into hypothesis testing has a significant impact on the ability to reconstruct ancestral characters and constrains the range of potential hypotheses of character evolution. Fossil data here provide the evidence to reliably document trends of both increasing and decreasing body size in several caniform clades. More generally, including fossils in such analyses incorporates evidence of directional trends, thereby yielding more reliable ancestral character state reconstructions.
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Affiliation(s)
- John A Finarelli
- Committee on Evolutionary Biology, University of Chicago, Illinois 60637, USA.
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Phillimore AB, Freckleton RP, Orme CDL, Owens IPF. Ecology predicts large-scale patterns of phylogenetic diversification in birds. Am Nat 2006; 168:220-9. [PMID: 16874631 DOI: 10.1086/505763] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Accepted: 04/26/2006] [Indexed: 11/03/2022]
Abstract
One of the most striking patterns in evolutionary biology is that clades may differ greatly in the number of species they contain. Numerous hypotheses have been put forward to explain this phenomenon, and several have been tested using phylogenetic methods. Remarkably, however, all such tests performed to date have been characterized by modest explanatory power, which has generated an interest in explanations stressing the importance of random processes. Here we make use of phylogenetic methods to test whether ecological variables, typically ignored in previous models, may explain phylogenetic tree imbalance in birds. We show that diversification rate possesses an intermediate phylogenetic signal across families. Using phylogenetic comparative methods, we then build a multipredictor model that explains more than 50% of the variation in diversification rate among clades. High annual dispersal is identified as the strongest predictor of high rates of diversification. In addition, high diversification rate is strongly associated with feeding generalization. In all but one instance, these key findings remain qualitatively unchanged when we use an alternative phylogeny and methodology and when small clades, containing five species or less, are excluded. Taken together, these results suggest that large-scale patterns in avian diversification can be explained by variation in intrinsic biology.
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Affiliation(s)
- Albert B Phillimore
- Division of Biology and Natural Environment Research Council Centre for Population Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, United Kingdom.
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Ulrich W. Regional species richness of families and the distribution of abundance and rarity in a local community of forest Hymenoptera. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2005. [DOI: 10.1016/j.actao.2004.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Taxonomic and phylogenetic distinctiveness in regional conservation assessments: a case study based on extant South African Chiroptera and Carnivora. Anim Conserv 2005. [DOI: 10.1017/s1367943005002192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Isaac NJB, Jones KE, Gittleman JL, Purvis A. Correlates of Species Richness in Mammals: Body Size, Life History, and Ecology. Am Nat 2005; 165:600-7. [PMID: 15795856 DOI: 10.1086/429148] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Accepted: 11/24/2004] [Indexed: 11/04/2022]
Abstract
We present the most extensive examination to date of proposed correlates of species richness. We use rigorous phylogenetic comparative techniques, data for 1,692 mammal species in four clades, and multivariate statistics to test four hypotheses about species richness and compare the evidence for each. Overall, we find strong support for the life-history model of diversification. Species richness is significantly correlated with shorter gestation period in the carnivores and large litter size in marsupials. These traits and short interbirth intervals are also associated with species richness in a pooled analysis of all four clades. Additionally, we find some support for the abundance hypotheses in different clades of mammals: abundance correlates positively with species richness in primates but negatively in microchiropterans. Our analyses provide no evidence that mammalian species richness is associated with body size or degree of sexual dimorphism.
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Affiliation(s)
- Nick J B Isaac
- Division of Biology, Imperial College, Silwood Park, Ascot, Berkshire SL5 7PY, United Kingdom.
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Abstract
There are more small-bodied bird species than there are large-bodied, even on a logarithmic scale. In birds this pattern, which is also found in other higher taxa, appears not to be due to neutral evolution. It has often been suggested that the skew of body size frequency distributions is the result of a relationship between body size and the net rate of speciation, but phylogenetic analyses so far have rejected the hypothesis that small-bodied species are subject to higher net rates of speciation. On the contrary, we show that there exists a relationship between body size and its own evolutionary variability: avian families of small body size show less interspecific variation in body size than large-bodied families of similar age and species richness.
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Affiliation(s)
- F Bokma
- Department of Biology, University of Oulu, Oulu, Finland.
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Pacing polar bears and stoical sheep: testing ecological and evolutionary hypotheses about animal welfare. Anim Welf 2004. [DOI: 10.1017/s0962728600014354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
AbstractResponses to potential threats to welfare vary greatly between species. Even closely related animals often differ in their fear of humans and/or novelty; their behavioural responses to pain; and when captive, their overall welfare and the form and frequency of their stereotypies. Such species differences stimulate hypotheses about I) the way that responses to challenge co-vary with other biological traits; 2) the adaptive value of particular responses; and 3) the factors predicting responses to evolutionarily new scenarios, such as captivity. We illustrate how these ideas can be statistically tested with multi-species comparisons, and show how techniques such as the Comparative Analysis of Independent Contrasts can be used to control for any non-independence of data points caused by species’ relatedness. For each of the three types of hypothesis, we then provide several welfare-relevant examples including one that has been fully tested (respectively, the relationships between sociality and anti-predator behaviour in antelopes; predation pressure, foraging niche and neophobia in parrots; and home range size and stereotypy in carnivores). Ultimate explanations such as these, based on species’ ecology and evolutionary history, have great explanatory appeal. Species comparisons can also have great practical value, allowing the test of hypotheses that would be almost impossible to investigate experimentally, and generating principles that allow predictions about the welfare of similar unstudied species. Multi-species data, for example from the many taxa held in zoos, thus hold enormous potential for increasing the fundamental understanding of animal welfare.
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Using Supertrees to Investigate Species Richness in Grasses and Flowering Plants. COMPUTATIONAL BIOLOGY 2004. [DOI: 10.1007/978-1-4020-2330-9_22] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Etienne RS, Olff H. How Dispersal Limitation Shapes Species–Body Size Distributions in Local Communities. Am Nat 2004; 163:69-83. [PMID: 14767837 DOI: 10.1086/380582] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2002] [Accepted: 06/17/2003] [Indexed: 11/03/2022]
Abstract
A critical but poorly understood pattern in macroecology is the often unimodal species-body size distribution (also known as body size-diversity relationship) in a local community (embedded in a much larger regional species pool). Purely neutral community models that assume functional equivalence among species are incapable of explaining this pattern because body size is the key determinant of functional differences between species. Several niche-based explanations have been offered, but none of them is completely satisfactory. Here we develop a simple model that unites a neutral community model with niche-based theory to explain the relationship. In the model, species of similar size are assumed to belong to the same size guild. Within a size guild, all individuals are equivalent in their competition for resources, sensu Hubbell's neutral community model; they have the same speciation rate and dispersal capacities. Between size guilds, however, the total number of individuals, the speciation rate, and the dispersal capacities differ, but using known allometric scaling laws for these properties, we can describe the differences between size guilds. Our model predicts that species richness reaches an optimum at an intermediate body size, in agreement with observations. The optimum at intermediate body size is basically the result of a trade-off between, on the one hand, allometric scaling laws for the number of individuals and the speciation rate that decrease with body size and, on the other hand, the scaling law for active dispersal that increases with body size.
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Affiliation(s)
- Rampal S Etienne
- Community and Conservation Ecology Group, University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands.
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