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Platania L, Gómez-Zurita J. Analysis of intrinsic evolutionary factors leading to microendemic distributions in New Caledonian leaf beetles. Sci Rep 2023; 13:6909. [PMID: 37106022 PMCID: PMC10140066 DOI: 10.1038/s41598-023-34104-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/24/2023] [Indexed: 04/29/2023] Open
Abstract
Microendemicity, or the condition of some species having local ranges, is a relatively common pattern in nature. However, the factors that lead to this pattern are still largely unknown. Most studies addressing this issue tend to focus on extrinsic factors associated with microendemic distributions, such as environmental conditions, hypothesising a posteriori about underlying potential speciation mechanisms, linked or not to these conditions. Here, we use a multi-faceted approach mostly focusing on intrinsic factors instead, namely diversification dynamics and speciation modes in two endemic sibling genera of leaf beetles with microendemic distributions, Taophila and Tricholapita, in a microendemicity hotspot, New Caledonia. Results suggest that the diversification rate in this lineage slowed down through most of the Neogene and consistently with a protracted speciation model possibly combined with several ecological and environmental factors potentially adding rate-slowing effects through time. In turn, species accumulated following successive allopatric speciation cycles, possibly powered by marked geological and climatic changes in the region in the last 25 million years, with daughter species ranges uncorrelated with the time of speciation. In this case, microendemicity seems to reflect a mature state for the system, rather than a temporary condition for recent species, as suggested for many microendemic organisms.
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Affiliation(s)
- Leonardo Platania
- Botanical Institute of Barcelona (CSIC-Ajuntament Barcelona), Pg. del Migdia S/N, 08038, Barcelona, Spain
- Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Jesús Gómez-Zurita
- Botanical Institute of Barcelona (CSIC-Ajuntament Barcelona), Pg. del Migdia S/N, 08038, Barcelona, Spain.
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2
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Belluardo F, Jesus Muñoz-Pajares A, Miralles A, Silvestro D, Cocca W, Mihaja Ratsoavina F, Villa A, Roberts SH, Mezzasalma M, Zizka A, Antonelli A, Crottini A. Slow and steady wins the race: Diversification rate is independent from body size and lifestyle in Malagasy skinks (Squamata: Scincidae: Scincinae). Mol Phylogenet Evol 2023; 178:107635. [PMID: 36208694 DOI: 10.1016/j.ympev.2022.107635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/18/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many ecomorphological adaptations to a fossorial (burrowing) lifestyle. Here we propose a new phylogenetic hypothesis for their diversification based on the largest taxon sampling so far compiled for this group. We estimated divergence times and investigated several aspects of their diversification (diversification rate, body size and fossorial lifestyle evolution, and biogeography). We found that diversification rate was constant throughout most of the evolutionary history of the group, but decreased over the last 6-4 million years and independently from body size and fossorial lifestyle evolution. Fossoriality has evolved from fully quadrupedal ancestors at least five times independently, which demonstrates that even complex morphological syndromes - in this case involving traits such as limb regression, body elongation, modification of cephalic scalation, depigmentation, and eyes and ear-opening regression - can evolve repeatedly and independently given enough time and eco-evolutionary advantages. Initial diversification of the group likely occurred in forests, and the divergence of sand-swimmer genera around 20 Ma appears linked to a period of aridification. Our results show that the large phenotypic variability of Malagasy Scincinae has not influenced diversification rate and that their rich species diversity results from a constant accumulation of lineages through time. By compiling large geographic and trait-related datasets together with the computation of a new time tree for the group, our study contributes important insights on the diversification of Malagasy vertebrates.
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Affiliation(s)
- Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
| | - A Jesus Muñoz-Pajares
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Genética, Universidad de Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
| | - Aurélien Miralles
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Ch. du Musée 10, 1700 Fribourg, Switzerland; Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden
| | - Walter Cocca
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
| | - Fanomezana Mihaja Ratsoavina
- Mention Zoologie et Biodiversité Animale, Domaine Sciences et Technologies, Université d'Antananarivo, B.P. 906, 101 Antananarivo, Madagascar
| | - Andrea Villa
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, 08193 Cerdanyola del Vallès, Spain
| | - Sam Hyde Roberts
- SEED Madagascar, Unit 7, Beethoven Street 1A, W10 4LG London, UK; Oxford Brookes University, Headington Campus, 0X3 0BP Oxford, UK; Operation Wallacea, Wallace House, Old Bolingbroke, PE23 4EX Spilsby, UK
| | - Marcello Mezzasalma
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Department of Biology, Ecology and Earth Sciences, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden; Gothenburg Global Biodiversity Centre, Box 461, 405 30 Göteborg, Sweden; Royal Botanic Gardens, Kew, TW9 3AE Richmond, UK; Department of Biology, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Praça Gomes Teixeira, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
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3
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Esquerré D, Brennan IG, Donnellan S, Keogh JS. Evolutionary models demonstrate rapid and adaptive diversification of Australo-Papuan pythons. Biol Lett 2022; 18:20220360. [PMID: 36541096 PMCID: PMC9768648 DOI: 10.1098/rsbl.2022.0360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Lineages may diversify when they encounter available ecological niches. Adaptive divergence by ecological opportunity often appears to follow the invasion of a new environment with open ecological space. This evolutionary process is hypothesized to explain the explosive diversification of numerous Australian vertebrate groups following the collision of the Eurasian and Australian plates 25 Mya. One of these groups is the pythons, which demonstrate their greatest phenotypic and ecological diversity in Australo-Papua (Australia and New Guinea). Here, using an updated and near complete time-calibrated phylogenomic hypothesis of the group, we show that following invasion of this region, pythons experienced a sudden burst of speciation rates coupled with multiple instances of accelerated phenotypic evolution in head and body shape and body size. These results are consistent with adaptive radiation theory with an initial rapid niche-filling phase and later slow-down approaching niche saturation. We discuss these findings in the context of other Australo-Papuan adaptive radiations and the importance of incorporating adaptive diversification systems that are not extraordinarily species-rich but ecomorphologically diverse to understand how biodiversity is generated.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Ian G. Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
| | - J. Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University 0200, Canberra, ACT, Australia
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4
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Crouch NMA, Jablonski D. Is species richness mediated by functional and genetic divergence? A global analysis in birds. Funct Ecol 2022; 37:125-138. [PMID: 37064506 PMCID: PMC10086807 DOI: 10.1111/1365-2435.14153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 06/10/2022] [Indexed: 11/28/2022]
Abstract
Unravelling why species richness shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness (e.g. with latitude) requires a compensatory trade-off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes.Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank.We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that points sampled in the tropics have comparatively greater packing than temperate ones relative to their species richness. We find limited evidence that geographical co-occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis.Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness. Read the free Plain Language Summary for this article on the Journal blog.
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Affiliation(s)
- Nicholas M. A. Crouch
- Dept. of the Geophysical Sciences The University of Chicago s Chicago Illinois U.S.A
| | - David Jablonski
- Dept. of the Geophysical Sciences The University of Chicago s Chicago Illinois U.S.A
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5
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Takashina N, Plank MJ, Jenkins CN, Economo EP. Species-range-size distributions: Integrating the effects of speciation, transformation, and extinction. Ecol Evol 2022; 12:e8341. [PMID: 35127000 PMCID: PMC8796946 DOI: 10.1002/ece3.8341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/23/2021] [Accepted: 10/25/2021] [Indexed: 12/02/2022] Open
Abstract
The species-range size distribution is a product of speciation, transformation of range-sizes, and extinction. Previous empirical studies showed that it has a left-skewed lognormal-like distribution. We developed a new mathematical framework to study species-range-size distributions, one in which allopatric speciation, transformation of range size, and the extinction process are explicitly integrated. The approach, which we call the gain-loss-allopatric speciation model, allows us to explore the effects of various speciation scenarios. Our model captures key dynamics thought to lead to known range-size distributions. We also fitted the model to empirical range-size distributions of birds, mammals, and beetles. Since geographic range dynamics are linked to speciation and extinction, our model provides predictions for the dynamics of species richness. When a species-range-size distribution initially evolves away from the range sizes at which the likelihood of speciation is low, it tends to cause diversification slowdown even in the absence of (bio)diversity dependence in speciation rate. Using the mathematical model developed here, we give a potential explanation for how observed range-size distributions emerge from range-size dynamics. Although the framework presented is minimalistic, it provides a starting point for examining hypotheses based on more complex mechanisms.
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Affiliation(s)
- Nao Takashina
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
- Department of International StudiesThe University of TokyoKashiwaJapan
| | - Michael J. Plank
- School of Mathematics and Statistics and Te Pūnaha MatatiniUniversity of CanterburyChristchurchNew Zealand
| | - Clinton N. Jenkins
- Department of Earth and EnvironmentKimberly Green Latin American and Caribbean CenterFlorida International UniversityMiamiFloridaUSA
| | - Evan P. Economo
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
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6
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Harmon LJ, Pennell MW, Henao-Diaz LF, Rolland J, Sipley BN, Uyeda JC. Causes and Consequences of Apparent Timescaling Across All Estimated Evolutionary Rates. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-011921-023644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolutionary rates play a central role in connecting micro- and macroevolution. All evolutionary rate estimates, including rates of molecular evolution, trait evolution, and lineage diversification, share a similar scaling pattern with time: The highest rates are those measured over the shortest time interval. This creates a disconnect between micro- and macroevolution, although the pattern is the opposite of what some might expect: Patterns of change over short timescales predict that evolution has tremendous potential to create variation and that potential is barely tapped by macroevolution. In this review, we discuss this shared scaling pattern across evolutionary rates. We break down possible explanations for scaling into two categories, estimation error and model misspecification, and discuss how both apply to each type of rate. We also discuss the consequences of this ubiquitous pattern, which can lead to unexpected results when comparing ratesover different timescales. Finally, after addressing purely statistical concerns, we explore a few possibilities for a shared unifying explanation across the three types of rates that results from a failure to fully understand and account for how biological processes scale over time.
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Affiliation(s)
- Luke J. Harmon
- Institute for Bioinformatics and Evolutionary Studies (IBEST) and Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA
| | - Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - L. Francisco Henao-Diaz
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jonathan Rolland
- Laboratoire Evolution et Diversité Biologique, CNRS, UMR5174, Université Toulouse III–Paul Sabatier, 31062 Toulouse, France
| | - Breanna N. Sipley
- Program for Bioinformatics and Computational Biology, University of Idaho, Moscow, Idaho 83844, USA
| | - Josef C. Uyeda
- Department of Biological Sciences, Virginia Tech University, Blacksburg, Virginia 24061, USA
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7
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Louca S, Pennell MW. Why extinction estimates from extant phylogenies are so often zero. Curr Biol 2021; 31:3168-3173.e4. [PMID: 34019824 DOI: 10.1016/j.cub.2021.04.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/11/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022]
Abstract
Time-calibrated phylogenies of extant species ("extant timetrees") are widely used to estimate historical speciation and extinction rates by fitting stochastic birth-death models.1 These approaches have long been controversial, as many phylogenetic studies report zero extinction in many taxa, contradicting the high extinction rates seen in the fossil record and the fact that the majority of species ever to have existed are now extinct.2-9 To date, the causes of this discrepancy remain unresolved. Here, we provide a novel and simple explanation for these "zero-inflated" extinction estimates, based on the recent discovery that there exist many alternative "congruent" diversification scenarios that cannot be distinguished based solely on extant timetrees.10 Due to such congruencies, estimation methods tend to converge to some scenario congruent to (i.e., statistically indistinguishable from) the true diversification scenario, but not necessarily to the true diversification scenario itself. This congruent scenario may exhibit negative extinction rates, a biologically meaningless but mathematically feasible situation, in which case estimators will tend to stick to the boundary of zero extinction. Based on this explanation, we make multiple testable predictions, which we confirm using analyses of simulated trees and 121 empirical trees. In contrast to other proposed mechanisms for erroneous extinction rate estimates,5,11-14 our proposed mechanism specifically explains the zero inflation of previous extinction rate estimates in the absence of detectable model violations, even for large trees. Not only do our results likely resolve a long-standing mystery in phylogenetics, they demonstrate that model congruencies can have severe consequences in practice.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, 1210 University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, 5289 University of Oregon, Eugene, OR 97403, USA.
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC V6T1Z4, Canada; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T1Z4, Canada.
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8
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Černý D, Madzia D, Slater GJ. Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades. Syst Biol 2021; 71:153-171. [PMID: 34110409 DOI: 10.1093/sysbio/syab045] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 02/01/2023] Open
Abstract
Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs, and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with a steep diversification drop (PyRate) or without one (BAMM), and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic datasets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to yield potentially unreliable inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations, and suggest how the latter may be mitigated.
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Affiliation(s)
- David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA
| | - Daniel Madzia
- Institute of Paleobiology, Polish Academy of Sciences, Warsaw 00-818, Poland
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA
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