1
|
Herrando-Moraira S, Roquet C, Calleja JA, Chen YS, Fujikawa K, Galbany-Casals M, Garcia-Jacas N, Liu JQ, López-Alvarado J, López-Pujol J, Mandel JR, Mehregan I, Sáez L, Sennikov AN, Susanna A, Vilatersana R, Xu LS. Impact of the climatic changes in the Pliocene-Pleistocene transition on Irano-Turanian species. The radiation of genus Jurinea (Compositae). Mol Phylogenet Evol 2023; 189:107928. [PMID: 37714444 DOI: 10.1016/j.ympev.2023.107928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/07/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
The Irano-Turanian region is one of the world's richest floristic regions and the centre of diversity for numerous xerophytic plant lineages. However, we still have limited knowledge on the timing of evolution and biogeographic history of its flora, and potential drivers of diversification remain underexplored. To fill this knowledge gap, we focus on the Eurasian genus Jurinea (ca. 200 species), one of the largest plant radiations that diversified in the region. We applied a macroevolutionary integrative approach to explicitly test diversification hypotheses and investigate the relative roles of geography vs. ecology and niche conservatism vs. niche lability in speciation processes. To do so, we gathered a sample comprising 77% of total genus richness and obtained data about (1) its phylogenetic history, recovering 502 nuclear loci sequences; (2) growth forms; (3) ecological niche, compiling data of 21 variables for more than 2500 occurrences; and (4) paleoclimatic conditions, to estimate climatic stability. Our results revealed that climate was a key factor in the evolutionary dynamics of Jurinea. The main diversification and biogeographic events that occurred during past climate changes, which led to colder and drier conditions, are the following: (1) the origin of the genus (10.7 Ma); (2) long-distance dispersals from the Iranian Plateau to adjacent regions (∼7-4 Ma); and (3) the diversification shift during Pliocene-Pleistocene Transition (ca. 3 Ma), when net diversification rate almost doubled. Our results supported the pre-adaptation hypothesis, i.e., the evolutionary success of Jurinea was linked to the retention of the ancestral niche adapted to aridity. Interestingly, the paleoclimatic analyses revealed that in the Iranian Plateau long-term climatic stability favoured old-lineage persistence, resulting in current high species richness of semi-arid and cold adapted clades; whereas moderate climate oscillations stimulated allopatric diversification in the lineages distributed in the Circumboreal region. In contrast, growth form lability and high niche disparity among closely related species in the Central Asian clade suggest adaptive radiation to mountain habitats. In sum, the radiation of Jurinea is the result of both adaptive and non-adaptive processes influenced by climatic, orogenic and ecological factors.
Collapse
Affiliation(s)
- Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Cristina Roquet
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Juan-Antonio Calleja
- Departament of Biology (Botany), Faculty of Sciences, Research Centre on Biodiversity and Global Change (CIBC-UAM), 28049 Madrid, Spain
| | - You-Sheng Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Kazumi Fujikawa
- Kochi Prefectural Makino Botanical Garden, 4200-6, Godaisan, Kochi 781-8125, Japan
| | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Jian-Quan Liu
- Key Laboratory for Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Javier López-Alvarado
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Jennifer R Mandel
- Department of Biological Sciences, Center for Biodiversity, University of Memphis, Memphis, TN 38152, USA
| | - Iraj Mehregan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Llorenç Sáez
- Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Alexander N Sennikov
- Botanical Museum, Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. del Migdia, s.n., 08038 Barcelona, Spain
| | - Lian-Sheng Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
2
|
Espeland M, Chazot N, Condamine FL, Lemmon AR, Lemmon EM, Pringle E, Heath A, Collins S, Tiren W, Mutiso M, Lees DC, Fisher S, Murphy R, Woodhall S, Tropek R, Ahlborn SS, Cockburn K, Dobson J, Bouyer T, Kaliszewska ZA, Baker CCM, Talavera G, Vila R, Gardiner AJ, Williams M, Martins DJ, Sáfián S, Edge DA, Pierce NE. Rapid radiation of ant parasitic butterflies during the Miocene aridification of Africa. Ecol Evol 2023; 13:e10046. [PMID: 37193112 PMCID: PMC10182571 DOI: 10.1002/ece3.10046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 04/14/2023] [Indexed: 05/18/2023] Open
Abstract
Africa has undergone a progressive aridification during the last 20 My that presumably impacted organisms and fostered the evolution of life history adaptations. We test the hypothesis that shift to living in ant nests and feeding on ant brood by larvae of phyto-predaceous Lepidochrysops butterflies was an adaptive response to the aridification of Africa that facilitated the subsequent radiation of butterflies in this genus. Using anchored hybrid enrichment we constructed a time-calibrated phylogeny for Lepidochrysops and its closest, non-parasitic relatives in the Euchrysops section (Poloyommatini). We estimated ancestral areas across the phylogeny with process-based biogeographical models and diversification rates relying on time-variable and clade-heterogeneous birth-death models. The Euchrysops section originated with the emerging Miombo woodlands about 22 million years ago (Mya) and spread to drier biomes as they became available in the late Miocene. The diversification of the non-parasitic lineages decreased as aridification intensified around 10 Mya, culminating in diversity decline. In contrast, the diversification of the phyto-predaceous Lepidochrysops lineage proceeded rapidly from about 6.5 Mya when this unusual life history likely first evolved. The Miombo woodlands were the cradle for diversification of the Euchrysops section, and our findings are consistent with the hypothesis that aridification during the Miocene selected for a phyto-predaceous life history in species of Lepidochrysops, with ant nests likely providing caterpillars a safe refuge from fire and a source of food when vegetation was scarce.
Collapse
Affiliation(s)
- Marianne Espeland
- Centre for Taxonomy and MorphologyLeibniz Institute for the Analysis of Evolutionary Change – Museum KoenigBonnGermany
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusettsUSA
| | - Nicolas Chazot
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | - Fabien L. Condamine
- CNRSUMR 5554 Institut des Sciences de l'Evolution de MontpellierMontpellierFrance
| | - Alan R. Lemmon
- Department of Scientific ComputingFlorida State UniversityTallahasseeFloridaUSA
| | | | | | - Alan Heath
- Lepidopterists' Society of AfricaKnysnaSouth Africa
| | | | | | | | - David C. Lees
- Department of Life SciencesNatural History MuseumLondonUK
| | | | | | | | - Robert Tropek
- Department of Ecology, Faculty of ScienceCharles UniversityPragueCzechia
- Institute of Entomology, Biology CentreCzech Academy of SciencesCeske BudejoviceCzechia
| | - Svenja S. Ahlborn
- Centre for Taxonomy and MorphologyLeibniz Institute for the Analysis of Evolutionary Change – Museum KoenigBonnGermany
| | | | | | | | - Zofia A. Kaliszewska
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusettsUSA
| | - Christopher C. M. Baker
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusettsUSA
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB, CSIC‐Ajuntament de Barcelona)BarcelonaSpain
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC‐UPF)BarcelonaSpain
| | | | | | - Dino J. Martins
- Turkana Basin InstituteStony Brook UniversityStony BrookNew YorkUSA
| | - Szabolcs Sáfián
- Institute of Silviculture and Forest ProtectionUniversity of SopronSopronHungary
| | | | - Naomi E. Pierce
- Department of Organismic and Evolutionary Biology and Museum of Comparative ZoologyHarvard UniversityCambridgeMassachusettsUSA
| |
Collapse
|
3
|
Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes. Proc Natl Acad Sci U S A 2022; 119:e2123544119. [PMID: 36252009 PMCID: PMC9618140 DOI: 10.1073/pnas.2123544119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, >65% of marine teleost fish species are restricted to the photic zone <200 m, which comprises less than 10% of the ocean's total volume. From a macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow water lineages have had more time to diversify than deep-sea lineages, 2) shallow water lineages have faster rates of speciation than deep-sea lineages, or 3) shallow-to-deep sea transition rates limit deep-sea richness. Here we use phylogenetic comparative methods to test among these three non-mutually exclusive hypotheses. While we found support for all hypotheses, the disparity in species richness is better described as the uneven outcome of alternating phases that favored shallow or deep diversification over the past 200 million y. Shallow marine teleosts became incredibly diverse 100 million y ago during a period of warm temperatures and high sea level, suggesting the importance of reefs and epicontinental settings. Conversely, deep-sea colonization and speciation was favored during brief episodes when cooling temperatures increased the efficiency of the ocean's carbon pump. Finally, time-variable ecological filters limited shallow-to-deep colonization for much of teleost history, which helped maintain higher shallow richness. A pelagic lifestyle and large jaws were associated with early deep-sea colonists, while a demersal lifestyle and a tapered body plan were typical of later colonists. Therefore, we also suggest that some hallmark characteristics of deep-sea fishes evolved prior to colonizing the deep sea.
Collapse
|
4
|
Gamboa S, Condamine FL, Cantalapiedra JL, Varela S, Pelegrín JS, Menéndez I, Blanco F, Hernández Fernández M. A phylogenetic study to assess the link between biome specialization and diversification in swallowtail butterflies. GLOBAL CHANGE BIOLOGY 2022; 28:5901-5913. [PMID: 35838418 PMCID: PMC9543414 DOI: 10.1111/gcb.16344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The resource-use hypothesis, proposed by E.S. Vrba, states that habitat fragmentation caused by climatic oscillations would affect particularly biome specialists (species inhabiting only one biome), which might show higher speciation and extinction rates than biome generalists. If true, lineages would accumulate biome-specialist species. This effect would be particularly exacerbated for biomes located at the periphery of the global climatic conditions, namely, biomes that have high/low precipitation and high/low temperature such as rainforest (warm-humid), desert (warm-dry), steppe (cold-dry) and tundra (cold-humid). Here, we test these hypotheses in swallowtail butterflies, a clade with more than 570 species, covering all the continents but Antarctica, and all climatic conditions. Swallowtail butterflies are among the most studied insects, and they are a model group for evolutionary biology and ecology studies. Continental macroecological rules are normally tested using vertebrates, this means that there are fewer examples exploring terrestrial invertebrate patterns at global scale. Here, we compiled a large Geographic Information System database on swallowtail butterflies' distribution maps and used the most complete time-calibrated phylogeny to quantify diversification rates (DRs). In this paper, we aim to answer the following questions: (1) Are there more biome-specialist swallowtail butterflies than biome generalists? (2) Is DR related to biome specialization? (3) If so, do swallowtail butterflies inhabiting extreme biomes show higher DRs? (4) What is the effect of species distribution area? Our results showed that swallowtail family presents a great number of biome specialists which showed substantially higher DRs compared to generalists. We also found that biome specialists are unevenly distributed across biomes. Overall, our results are consistent with the resource-use hypothesis, species climatic niche and biome fragmentation as key factors promoting isolation.
Collapse
Affiliation(s)
- Sara Gamboa
- Centro de Investigación Mariña (CIM)Universidade de Vigo, Grupo de Ecoloxía Animal (GEA), MAPAS LabVigoPontevedraSpain
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
- CNRSUMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier)MontpellierFrance
| | - Fabien L. Condamine
- CNRSUMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier)MontpellierFrance
| | - Juan L. Cantalapiedra
- Departamento de Ciencias de la Vida, Edificio de Ciencias Campus Científico‐TecnológicoUniversidad de AlcaláAlcalá de HenaresSpain
| | - Sara Varela
- Centro de Investigación Mariña (CIM)Universidade de Vigo, Grupo de Ecoloxía Animal (GEA), MAPAS LabVigoPontevedraSpain
| | - Jonathan S. Pelegrín
- Área de Biología y Ciencias Ambientales Facultades de Ciencias Básicas y EducaciónUniversidad Santiago de CaliSantiago de CaliValle del CaucaColombia
- Departamento de Biología, Facultad de Ciencias Naturales y ExactasUniversidad del Valle, Campus MeléndezSantiago de CaliValle del CaucaColombia
| | - Iris Menéndez
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
| | - Fernando Blanco
- Museum für Naturkunde, Leibniz‐Institut für Evolutions und BiodiversitätsforschungBerlinGermany
| | - Manuel Hernández Fernández
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias GeológicasUniversidad Complutense de MadridMadridSpain
- Departamento de Cambio MedioambientalInstituto de Geociencias (UCM, CSIC)MadridSpain
| |
Collapse
|
5
|
Cogni R, Quental TB, Guimarães PR. Ehrlich and Raven escape and radiate coevolution hypothesis at different levels of organization: Past and future perspectives. Evolution 2022; 76:1108-1123. [PMID: 35262199 DOI: 10.1111/evo.14456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 01/21/2023]
Abstract
The classic paper by Ehrlich and Raven on coevolution will soon be 60 years old. Although they were not the first to develop the idea of coevolution, their thought-provoking paper certainly popularized this idea and inspired several generations of scientists interested in coevolution. Here, we describe some of their main contributions, quantitatively measure the impact of their seminal paper on different fields of research, and discuss how ideas related to their original paper might push the study of coevolution forward. To guide our discussion, we explore their original hypothesis into three research fields that are associated with distinct scales/levels of organization: (1) the genetic mechanisms underlying coevolutionary interactions; (2) the potential association between coevolutionary diversification and the organization of ecological networks; and (3) the micro- and macroevolutionary mechanisms and expected patterns under their hypothesis. By doing so, we discuss potentially overlooked aspects and future directions for the study of coevolutionary dynamics and diversification.
Collapse
Affiliation(s)
- Rodrigo Cogni
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Tiago B Quental
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| | - Paulo R Guimarães
- Department of Ecology, University of São Paulo, São Paulo, SP, 05508-900, Brazil
| |
Collapse
|
6
|
Biogeographical and Diversification Analyses of Indian Pseudoscorpions Reveal the Western Ghats as Museums of Ancient Biodiversity. Mol Phylogenet Evol 2022; 175:107495. [DOI: 10.1016/j.ympev.2022.107495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022]
|
7
|
Upham NS, Esselstyn JA, Jetz W. Molecules and fossils tell distinct yet complementary stories of mammal diversification. Curr Biol 2021; 31:4195-4206.e3. [PMID: 34329589 DOI: 10.1016/j.cub.2021.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 07/07/2021] [Indexed: 11/25/2022]
Abstract
Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to "pull" speciation rates downward, but the temporal scale at which this bias matters is unclear. To investigate this problem, we compare mammalian diversification-rate signatures in a credible set of molecular timetrees (n = 5,911 species, ∼70% from DNA) to those in fossil genus durations (n = 5,320). We use fossil extinction rates to correct or "push" the timetree-based (pulled) speciation-rate estimates, finding a surge of speciation during the Paleocene (∼66-56 million years ago, Ma) between the Cretaceous-Paleogene (K-Pg) boundary and the Paleocene-Eocene Thermal Maximum (PETM). However, about two-thirds of the K-Pg-to-PETM originating taxa did not leave modern descendants, indicating that this rate signature is likely undetectable from extant lineages alone. For groups without substantial fossil records, thankfully all is not lost. Pushed and pulled speciation rates converge starting ∼10 Ma and are equal at the present day when recent evolutionary processes can be estimated without bias using species-specific "tip" rates of speciation. Clade-wide moments of tip rates also enable enriched inference, as the skewness of tip rates is shown to approximate a clade's extent of past diversification-rate shifts. Molecular timetrees need fossil-correction to address deep-time questions, but they are sufficient for shallower time questions where extinctions are fewer.
Collapse
Affiliation(s)
- Nathan S Upham
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Center for Biodiversity and Global Change, Yale University, New Haven, CT 06511, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Jacob A Esselstyn
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Walter Jetz
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT 06511, USA; Center for Biodiversity and Global Change, Yale University, New Haven, CT 06511, USA.
| |
Collapse
|
8
|
Helmstetter AJ, Glemin S, Käfer J, Zenil-Ferguson R, Sauquet H, de Boer H, Dagallier LPMJ, Mazet N, Reboud EL, Couvreur TLP, Condamine FL. Pulled Diversification Rates, Lineages-Through-Time Plots and Modern Macroevolutionary Modelling. Syst Biol 2021; 71:758-773. [PMID: 34613395 PMCID: PMC9016617 DOI: 10.1093/sysbio/syab083] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/29/2022] Open
Abstract
Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth–death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticized such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here, we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations, we illustrate the characteristics of newly proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modeling, but they in no way suggest we should abandon diversification modeling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community. [Birth–death models; extinction; phylogenetics; speciation.]
Collapse
Affiliation(s)
- Andrew J Helmstetter
- Fondation pour la Recherche sur la Biodiversité - Centre for the Synthesis and Analysis of Biodiversity, 34000 Montpellier, France
| | - Sylvain Glemin
- CNRS, Ecosystmes Biodiversit Evolution (Universit de Rennes), 35000 Rennes, France
| | - Jos Käfer
- Universit de Lyon, Universit Lyon 1, CNRS, Laboratoire de Biomtrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | | | - Herv Sauquet
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, 2000, Australia.,Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Hugo de Boer
- Natural History Museum, University of Oslo, 0318 Oslo, Norway
| | | | - Nathan Mazet
- CNRS, Institut des Sciences de l'Evolution de Montpellier (Universit de Montpellier), Place Eugne Bataillon, 34095 Montpellier, France
| | - Eliette L Reboud
- CNRS, Institut des Sciences de l'Evolution de Montpellier (Universit de Montpellier), Place Eugne Bataillon, 34095 Montpellier, France
| | | | - Fabien L Condamine
- CNRS, Institut des Sciences de l'Evolution de Montpellier (Universit de Montpellier), Place Eugne Bataillon, 34095 Montpellier, France
| |
Collapse
|
9
|
Chazot N, Condamine FL, Dudas G, Peña C, Kodandaramaiah U, Matos-Maraví P, Aduse-Poku K, Elias M, Warren AD, Lohman DJ, Penz CM, DeVries P, Fric ZF, Nylin S, Müller C, Kawahara AY, Silva-Brandão KL, Lamas G, Kleckova I, Zubek A, Ortiz-Acevedo E, Vila R, Vane-Wright RI, Mullen SP, Jiggins CD, Wheat CW, Freitas AVL, Wahlberg N. Conserved ancestral tropical niche but different continental histories explain the latitudinal diversity gradient in brush-footed butterflies. Nat Commun 2021; 12:5717. [PMID: 34588433 PMCID: PMC8481491 DOI: 10.1038/s41467-021-25906-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
The global increase in species richness toward the tropics across continents and taxonomic groups, referred to as the latitudinal diversity gradient, stimulated the formulation of many hypotheses to explain the underlying mechanisms of this pattern. We evaluate several of these hypotheses to explain spatial diversity patterns in a butterfly family, the Nymphalidae, by assessing the contributions of speciation, extinction, and dispersal, and also the extent to which these processes differ among regions at the same latitude. We generate a time-calibrated phylogeny containing 2,866 nymphalid species (~45% of extant diversity). Neither speciation nor extinction rate variations consistently explain the latitudinal diversity gradient among regions because temporal diversification dynamics differ greatly across longitude. The Neotropical diversity results from low extinction rates, not high speciation rates, and biotic interchanges with other regions are rare. Southeast Asia is also characterized by a low speciation rate but, unlike the Neotropics, is the main source of dispersal events through time. Our results suggest that global climate change throughout the Cenozoic, combined with tropical niche conservatism, played a major role in generating the modern latitudinal diversity gradient of nymphalid butterflies.
Collapse
Affiliation(s)
- Nicolas Chazot
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 75651, Uppsala, Sweden.
- Systematic Biology Group, Department of Biology, Lund University, Lund, Sweden.
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier|CNRS|IRD|EPHE), Place Eugene Bataillon, 34095, Montpellier, France
| | - Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Carlos Peña
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, India
| | - Pável Matos-Maraví
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Kwaku Aduse-Poku
- Department of Life and Earth Sciences, Perimeter College, Georgia State University, 33 Gilmer Street, Atlanta, GA, 30303, USA
| | - Marianne Elias
- ISYEB, CNRS, MNHN, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, Paris, 75005, France
| | - Andrew D Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - David J Lohman
- City College of New York and Graduate Center, CUNY, New York, NY, USA
- National Museum of Natural History, Manila, Philippines
| | - Carla M Penz
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
| | - Phil DeVries
- Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
| | - Zdenek F Fric
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Soren Nylin
- Department of Zoology, Stockholm University, 10691, Stockholm, Sweden
| | - Chris Müller
- Australian Museum, 6 College Street, Sydney, NSW, 2010, Australia
| | - Akito Y Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Karina L Silva-Brandão
- Universidade Estadual de Campinas, Centro de Biologia Molecular e Engenharia Genética, Av. Candido Rondom, 400, 13083-875, Campinas, SP, Brazil
| | - Gerardo Lamas
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Irena Kleckova
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - Anna Zubek
- Nature Education Centre, Jagiellonian University, ul. Gronostajowa 5, 30-387, Kraków, Poland
| | - Elena Ortiz-Acevedo
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Departamento de Química y Biología, Universidad del Norte, Barranquilla, Colombia
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Richard I Vane-Wright
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- Durrell Institute of Conservation and Ecology (DICE), University of Kent, Canterbury, CT2 7NR, UK
| | - Sean P Mullen
- 5 Cummington Street, Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing St., Cambridge, CB2 3EJ, UK
- Smithsonian Tropical Research Institute, Gamboa, Panama
| | | | - Andre V L Freitas
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), 13083-862, Campinas, SP, Brazil
| | - Niklas Wahlberg
- Systematic Biology Group, Department of Biology, Lund University, Lund, Sweden
| |
Collapse
|
10
|
Burin G, Guimarães PR, Quental TB. Macroevolutionary stability predicts interaction patterns of species in seed dispersal networks. Science 2021; 372:733-737. [DOI: 10.1126/science.abf0556] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/24/2021] [Indexed: 12/26/2022]
Abstract
Assessing deep-time mechanisms affecting the assembly of ecological networks is key to understanding biodiversity changes on broader time scales. We combined analyses of diversification rates with interaction network descriptors from 468 bird species belonging to 29 seed dispersal networks to show that bird species that contribute most to the network structure of plant–frugivore interactions belong to lineages that show higher macroevolutionary stability. This association is stronger in warmer, wetter, less seasonal environments. We infer that the macroevolutionary sorting mechanism acts through the regional pool of species by sorting species on the basis of the available relative differences in diversification rates, rather than absolute rates. Our results illustrate how the interplay between interaction patterns and diversification dynamics may shape the organization and long-term dynamics of ecological networks.
Collapse
Affiliation(s)
- Gustavo Burin
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, Brazil
| | - Paulo R. Guimarães
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, Brazil
| | - Tiago B. Quental
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Sao Paulo, Brazil
| |
Collapse
|
11
|
Pouchon C, Lavergne S, Fernández Á, Alberti A, Aubert S, Mavárez J. Phylogenetic signatures of ecological divergence and leapfrog adaptive radiation in Espeletia. AMERICAN JOURNAL OF BOTANY 2021; 108:113-128. [PMID: 33426651 DOI: 10.1002/ajb2.1591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/21/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Events of accelerated species diversification represent one of Earth's most celebrated evolutionary outcomes. Northern Andean high-elevation ecosystems, or páramos, host some plant lineages that have experienced the fastest diversification rates, likely triggered by ecological opportunities created by mountain uplifts, local climate shifts, and key trait innovations. However, the mechanisms behind rapid speciation into the new adaptive zone provided by these opportunities have long remained unclear. METHODS We address this issue by studying the Venezuelan clade of Espeletia, a species-rich group of páramo-endemics showing a dazzling ecological and morphological diversity. We performed several comparative analyses to study both lineage and trait diversification, using an updated molecular phylogeny of this plant group. RESULTS We showed that sets of either vegetative or reproductive traits have conjointly diversified in Espeletia along different vegetation belts, leading to adaptive syndromes. Diversification in vegetative traits occurred earlier than in reproductive ones. The rate of species and morphological diversification showed a tendency to slow down over time, probably due to diversity dependence. We also found that closely related species exhibit significantly more overlap in their geographic distributions than distantly related taxa, suggesting that most events of ecological divergence occurred at close geographic proximity within páramos. CONCLUSIONS These results provide compelling support for a scenario of small-scale ecological divergence along multiple ecological niche dimensions, possibly driven by competitive interactions between species, and acting sequentially over time in a leapfrog pattern.
Collapse
Affiliation(s)
- Charles Pouchon
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
| | - Ángel Fernández
- Herbario IVIC. Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas, 1020-A, Venezuela
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Serge Aubert
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
- Université Grenoble Alpes, CNRS, Université Savoie Mont Blanc, SAJF, Station Alpine Joseph Fourier, 38000, Grenoble, France
| | - Jesús Mavárez
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
| |
Collapse
|
12
|
Bisconti M, Damarco P, Pavia M, Sorce B, Carnevale G. Marzanoptera tersillae, a new balaenopterid genus and species from the Pliocene of Piedmont, north-west Italy. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Marzanoptera tersillae gen. & sp. nov., a new balaenopterid from the Pliocene of the Piedmont in north-west Italy, is described based on a partial skeleton and compared with other living and fossil baleen whales. Marzanoptera tersillae shares characters, such as the shape of the supraoccipital, glenoid fossa of the squamosal and zygomatic process of the squamosal, with ‘Balaenoptera’ bertae. We used a computed tomography scan to view parts of the skull that were otherwise impossible to observe, such as the periotic. A phylogenetic analysis based on 355 character states scored from 87 taxa revealed a well-resolved hypothesis of relationships for Balaenopteridae and a general phylogenetic hypothesis for chaeomysticetes. The monophyly of all superfamily- and family-rank clades and of crown balaenopterid species was confirmed. In addition, a monophyletic group including most basal thalassotherian taxa was recovered. The mollusc fauna associated with the specimen was autochtonous and constituted a residual fossil assemblage indicative of an environmental context located below the base of the storm wave, characterized by a low-energy hydrodynamic regimen. Many shark teeth have been found in close association or embedded within the bones, suggesting a possible scavenging action by two shark species on the whale carcass.
Collapse
Affiliation(s)
- Michelangelo Bisconti
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, via Valperga Caluso 35, 10135 Torino, Italia
- San Diego Natural History Museum, El Prado 1788, San Diego, CA, USA
| | - Piero Damarco
- Ente di Gestione del Parco Paleontologico Astigiano, Museo Paleontologico Territoriale dell’Astigiano, Corso Vittorio Alfieri 381, 14100, Asti, Italia
| | - Marco Pavia
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, via Valperga Caluso 35, 10135 Torino, Italia
| | - Barbara Sorce
- Unitre Cecina-Livorno, via Cecchini 3, Cecina, Italia
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, via Valperga Caluso 35, 10135 Torino, Italia
| |
Collapse
|
13
|
S Meseguer A, Condamine FL. Ancient tropical extinctions at high latitudes contributed to the latitudinal diversity gradient. Evolution 2020; 74:1966-1987. [PMID: 32246727 DOI: 10.1111/evo.13967] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 03/04/2020] [Accepted: 03/21/2020] [Indexed: 01/15/2023]
Abstract
Global biodiversity currently peaks at the equator and decreases toward the poles. Growing fossil evidence suggest this hump-shaped latitudinal diversity gradient (LDG) has not been persistent through time, with similar diversity across latitudes flattening out the LDG during past greenhouse periods. However, when and how diversity declined at high latitudes to generate the modern LDG remains an open question. Although diversity-loss scenarios have been proposed, they remain mostly undemonstrated. We outline the "asymmetric gradient of extinction and dispersal" framework that contextualizes previous ideas behind the LDG under a time-variable scenario. Using phylogenies and fossils of Testudines, Crocodilia, and Lepidosauria, we find that the hump-shaped LDG could be explained by (1) disproportionate extinctions of high-latitude tropical-adapted clades when climate transitioned from greenhouse to icehouse, and (2) equator-ward biotic dispersals tracking their climatic preferences when tropical biomes became restricted to the equator. Conversely, equivalent diversification rates across latitudes can account for the formation of an ancient flat LDG. The inclusion of fossils in macroevolutionary studies allows revealing time-dependent extinction rates hardly detectable from phylogenies only. This study underscores that the prevailing evolutionary processes generating the LDG during greenhouses differed from those operating during icehouses.
Collapse
Affiliation(s)
- Andrea S Meseguer
- INRA, UMR 1062 Centre de Biologie pour la Gestion des Populations (INRA | IRD | CIRAD | Montpellier SupAgro), Montferrier-sur-Lez, France
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Montpellier, France
- Real Jardín Botánico de Madrid (RJB-CSIC), Madrid, Spain
| | - Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier | CNRS | IRD | EPHE), Montpellier, France
| |
Collapse
|
14
|
Sun M, Folk RA, Gitzendanner MA, Soltis PS, Chen Z, Soltis DE, Guralnick RP. Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids. AMERICAN JOURNAL OF BOTANY 2020; 107:895-909. [PMID: 32519354 PMCID: PMC7384126 DOI: 10.1002/ajb2.1479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/03/2020] [Indexed: 05/03/2023]
Abstract
PREMISE Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. METHODS We used a supermatrix for rosids and one well-sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). RESULTS We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. CONCLUSIONS We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.
Collapse
Affiliation(s)
- Miao Sun
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- Department of BioscienceAarhus UniversityAarhus8000Denmark
| | - Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippi39762USA
| | - Matthew A. Gitzendanner
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32608USA
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32608USA
| | - Robert P. Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
| |
Collapse
|
15
|
Diversification rates, clade ages, and macroevolutionary methods. Proc Natl Acad Sci U S A 2019; 116:24400. [PMID: 31719201 DOI: 10.1073/pnas.1915908116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
16
|
Costa CLN, Lemos-Costa P, Marquitti FMD, Fernandes LD, Ramos MF, Schneider DM, Martins AB, de Aguiar MAM. Signatures of Microevolutionary Processes in Phylogenetic Patterns. Syst Biol 2018; 68:131-144. [PMID: 29939352 DOI: 10.1093/sysbio/syy049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/13/2018] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic trees are representations of evolutionary relationships among species and contain signatures of the processes responsible for the speciation events they display. Inferring processes from tree properties, however, is challenging. To address this problem, we analyzed a spatially-explicit model of speciation where genome size and mating range can be controlled. We simulated parapatric and sympatric (narrow and wide mating range, respectively) radiations and constructed their phylogenetic trees, computing structural properties such as tree balance and speed of diversification. We showed that parapatric and sympatric speciation are well separated by these structural tree properties. Balanced trees with constant rates of diversification only originate in sympatry and genome size affected both the balance and the speed of diversification of the simulated trees. Comparison with empirical data showed that most of the evolutionary radiations considered to have developed in parapatry or sympatry are in good agreement with model predictions. Even though additional forces other than spatial restriction of gene flow, genome size, and genetic incompatibilities, do play a role in the evolution of species formation, the microevolutionary processes modeled here capture signatures of the diversification pattern of evolutionary radiations, regarding the symmetry and speed of diversification of lineages.
Collapse
Affiliation(s)
- Carolina L N Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Paula Lemos-Costa
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Flavia M D Marquitti
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Lucas D Fernandes
- Departamento de Entomologia e Acarologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13418-900 Piracicaba, SP, Brazil
| | - Marlon F Ramos
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - David M Schneider
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| | - Ayana B Martins
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil.,Department of Fish Ecology & Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Unicamp, 13083-970 Campinas, SP, Brazil
| |
Collapse
|
17
|
Kodandaramaiah U, Murali G. What affects power to estimate speciation rate shifts? PeerJ 2018; 6:e5495. [PMID: 30155369 PMCID: PMC6108317 DOI: 10.7717/peerj.5495] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 07/30/2018] [Indexed: 02/04/2023] Open
Abstract
The development of methods to estimate rates of speciation and extinction from time-calibrated phylogenies has revolutionized evolutionary biology by allowing researchers to correlate diversification rate shifts with causal factors. A growing number of researchers are interested in testing whether the evolution of a trait or a trait variant has influenced speciation rate, and three modelling methods-BiSSE, MEDUSA and BAMM-have been widely used in such studies. We simulated phylogenies with a single speciation rate shift each, and evaluated the power of the three methods to detect these shifts. We varied the degree of increase in speciation rate (speciation rate asymmetry), the number of tips, the tip-ratio bias (ratio of number of tips with each character state) and the relative age in relation to overall tree age when the rate shift occurred. All methods had good power to detect rate shifts when the rate asymmetry was strong and the sizes of the two lineages with the distinct speciation rates were large. Even when lineage size was small, power was good when rate asymmetry was high. In our simulated scenarios, small lineage sizes appear to affect BAMM most strongly. Tip-ratio influenced the accuracy of speciation rate estimation but did not have a strong effect on power to detect rate shifts. Based on our results, we provide suggestions to users of these methods.
Collapse
Affiliation(s)
- Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, India
| | - Gopal Murali
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE), School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, India
| |
Collapse
|