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Pannetier T, Martinez C, Bunnefeld L, Etienne RS. Branching patterns in phylogenies cannot distinguish diversity-dependent diversification from time-dependent diversification. Evolution 2020; 75:25-38. [PMID: 33205832 PMCID: PMC7898657 DOI: 10.1111/evo.14124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 10/06/2020] [Accepted: 10/10/2020] [Indexed: 01/08/2023]
Abstract
One of the primary goals of macroevolutionary biology has been to explain general trends in long‐term diversity patterns, including whether such patterns correspond to an upscaling of processes occurring at lower scales. Reconstructed phylogenies often show decelerated lineage accumulation over time. This pattern has often been interpreted as the result of diversity‐dependent (DD) diversification, where the accumulation of species causes diversification to decrease through niche filling. However, other processes can also produce such a slowdown, including time dependence without diversity dependence. To test whether phylogenetic branching patterns can be used to distinguish these two mechanisms, we formulated a time‐dependent, but diversity‐independent model that matches the expected diversity through time of a DD model. We simulated phylogenies under each model and studied how well likelihood methods could recover the true diversification mode. Standard model selection criteria always recovered diversity dependence, even when it was not present. We correct for this bias by using a bootstrap method and find that neither model is decisively supported. This implies that the branching pattern of reconstructed trees contains insufficient information to detect the presence or absence of diversity dependence. We advocate that tests encompassing additional data, for example, traits or range distributions, are needed to evaluate how diversity drives macroevolutionary trends.
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Affiliation(s)
- Théo Pannetier
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands.,Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - César Martinez
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands
| | - Lynsey Bunnefeld
- Biological and Environmental Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9712 CP, The Netherlands
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2
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Li J, Huang JP, Sukumaran J, Knowles LL. Microevolutionary processes impact macroevolutionary patterns. BMC Evol Biol 2018; 18:123. [PMID: 30097006 PMCID: PMC6086068 DOI: 10.1186/s12862-018-1236-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 08/01/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Macroevolutionary modeling of species diversification plays important roles in inferring large-scale biodiversity patterns. It allows estimation of speciation and extinction rates and statistically testing their relationships with different ecological factors. However, macroevolutionary patterns are ultimately generated by microevolutionary processes acting at population levels, especially when speciation and extinction are considered protracted instead of point events. Neglecting the connection between micro- and macroevolution may hinder our ability to fully understand the underlying mechanisms that drive the observed patterns. RESULTS In this simulation study, we used the protracted speciation framework to demonstrate that distinct microevolutionary scenarios can generate very similar biodiversity patterns (e.g., latitudinal diversity gradient). We also showed that current macroevolutionary models may not be able to distinguish these different scenarios. CONCLUSIONS Given the compounded nature of speciation and extinction rates, one needs to be cautious when inferring causal relationships between ecological factors and macroevolutioanry rates. Future studies that incorporate microevolutionary processes into current modeling approaches are in need.
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Affiliation(s)
- Jingchun Li
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, USA. .,Museum of Natural History, University of Colorado Boulder, Boulder, USA. .,Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA.
| | - Jen-Pen Huang
- Integrative Research Center, The Field Museum, Chicago, USA.,Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
| | - Jeet Sukumaran
- Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
| | - L Lacey Knowles
- Museum of Zoology, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
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3
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Mishra C, Kumar S, Panigrahi M, Yathish HM, Chaudhary R, Chauhan A, Kumar A, Sonawane AA. Single Nucleotide Polymorphisms in 5' Upstream Region of Bovine TLR4 Gene Affecting Expression Profile and Transcription Factor Binding Sites. Anim Biotechnol 2017; 29:119-128. [PMID: 28594279 DOI: 10.1080/10495398.2017.1326929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The present study in the 5' upstream region of TLR4 gene revealed four Single Nucleotide Polymorphisms (SNPs) in Vrindavani and Tharparkar cattle. The polymorphic information content (PIC), heterozygosity and allelic diversity values were low to moderate for these SNPs. In Vrindavani cattle, one SNP was found to be in Hardy-Weinberg Equilibrium (HWE) and the remaining three were found to be in linkage disequilibrium (LD) as indicated statistically (P > 0.05). In Tharparkar cattle, two SNPs were found to be in HWE and were not in LD as indicated statistically (P > 0.05). These SNPs were used for construction of haplotypes. In-silico analysis of these SNPs predicted abolition of eight transcription factor binding sites and creation of eight new sites. The quantitative real time PCR analysis did not show any significant variation of gene expression among haplotypes. However, gene expression between breed was found to be significant (P < 0.05) which suggested that upstream region of bovine TLR4 gene has a crucial role in its expression. These findings in TLR4 gene offer essential evidence that can be useful in future research exploring its role in immunity. TLR4 can be used as a marker for selection for disease resistance in bovines.
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Affiliation(s)
- Chinmoy Mishra
- a Department of Animal Genetics , Indian Veterinary Research Institute , Uttar Pradesh , India
| | - Subodh Kumar
- a Department of Animal Genetics , Indian Veterinary Research Institute , Uttar Pradesh , India
| | - Manjit Panigrahi
- a Department of Animal Genetics , Indian Veterinary Research Institute , Uttar Pradesh , India
| | - H M Yathish
- a Department of Animal Genetics , Indian Veterinary Research Institute , Uttar Pradesh , India
| | - Rajni Chaudhary
- a Department of Animal Genetics , Indian Veterinary Research Institute , Uttar Pradesh , India
| | - Anuj Chauhan
- a Department of Animal Genetics , Indian Veterinary Research Institute , Uttar Pradesh , India
| | - Amit Kumar
- a Department of Animal Genetics , Indian Veterinary Research Institute , Uttar Pradesh , India
| | - Arvind A Sonawane
- a Department of Animal Genetics , Indian Veterinary Research Institute , Uttar Pradesh , India
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4
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Verheye ML, Backeljau T, d'Udekem d'Acoz C. Locked in the icehouse: Evolution of an endemic Epimeria (Amphipoda, Crustacea) species flock on the Antarctic shelf. Mol Phylogenet Evol 2017; 114:14-33. [PMID: 28528744 DOI: 10.1016/j.ympev.2017.05.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/12/2017] [Accepted: 05/14/2017] [Indexed: 11/24/2022]
Abstract
The Antarctic shelf's marine biodiversity has been greatly influenced by the climatic and glacial history of the region. Extreme temperature changes led to the extinction of some lineages, while others adapted and flourished. The amphipod genus Epimeria is an example of the latter, being particularly diverse in the Antarctic region. By reconstructing a time-calibrated phylogeny based on mitochondrial (COI) and nuclear (28S and H3) markers and including Epimeria species from all oceans, this study provides a temporal and geographical framework for the evolution of Antarctic Epimeria. The monophyly of this genus is not supported by Bayesian Inference, as Antarctic and non-Antarctic Epimeria form two distinct well-supported clades, with Antarctic Epimeria being a sister clade to two stilipedid species. The monophyly of Antarctic Epimeria suggests that this clade evolved in isolation since its origin. While the precise timing of this origin remains unclear, it is inferred that the Antarctic lineage arose from a late Gondwanan ancestor and hence did not colonize the Antarctic region after the continent broke apart from the other fragments of Gondwanaland. The initial diversification of the clade occurred 38.04Ma (95% HPD [48.46Ma; 28.36Ma]) in a cooling environment. Adaptation to cold waters, along with the extinction of cold-intolerant taxa and resulting ecological opportunities, likely led to the successful diversification of Epimeria on the Antarctic shelf. However, there was neither evidence of a rapid lineage diversification early in the clade's history, nor of any shifts in diversification rates induced by glacial cycles. This suggests that a high turnover rate on the repeatedly scoured Antarctic shelf could have masked potential signals of diversification bursts.
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Affiliation(s)
- Marie L Verheye
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, rue Vautier 29, 1000 Brussels, Belgium; Catholic University of Louvain-la-Neuve, Department of Biology, Marine Biology Laboratory, Croix du Sud 3 bte L7.06.04, 1348 Louvain-la-Neuve, Belgium.
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, rue Vautier 29, 1000 Brussels, Belgium; University of Antwerp, Evolutionary Ecology Group, Universiteitsplein 1, 2160 Antwerp, Belgium
| | - Cédric d'Udekem d'Acoz
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, rue Vautier 29, 1000 Brussels, Belgium
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Cardoso GC, Cortesão M, García C. Ecological Marginalization Facilitated Diversification in Conifers. Evol Biol 2015. [DOI: 10.1007/s11692-015-9306-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Wahlberg N, Wheat CW, Peña C. Timing and patterns in the taxonomic diversification of Lepidoptera (butterflies and moths). PLoS One 2013; 8:e80875. [PMID: 24282557 PMCID: PMC3839996 DOI: 10.1371/journal.pone.0080875] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/07/2013] [Indexed: 11/18/2022] Open
Abstract
The macroevolutionary history of the megadiverse insect order Lepidoptera remains little-known, yet coevolutionary dynamics with their angiospermous host plants are thought to have influenced their diversification significantly. We estimate the divergence times of all higher-level lineages of Lepidoptera, including most extant families. We find that the diversification of major lineages in Lepidoptera are approximately equal in age to the crown group of angiosperms and that there appear to have been three significant increases in diversification rates among Lepidoptera over evolutionary time: 1) at the origin of the crown group of Ditrysia about 150 million years ago (mya), 2) at the origin of the stem group of Apoditrysia about 120 mya and finally 3) a spectacular increase at the origin of the stem group of the quadrifid noctuoids about 70 mya. In addition, there appears to be a significant increase in diversification rate in multiple lineages around 90 mya, which is concordant with the radiation of angiosperms. Almost all extant families appear to have begun diversifying soon after the Cretaceous/Paleogene event 65.51 mya.
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Affiliation(s)
| | | | - Carlos Peña
- Department of Biology, University of Turku, Turku, Finland
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Rabosky DL. Diversity-Dependence, Ecological Speciation, and the Role of Competition in Macroevolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135800] [Citation(s) in RCA: 183] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109;
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Systematics and evolutionary history of butterflies in the “Taygetis clade” (Nymphalidae: Satyrinae: Euptychiina): Towards a better understanding of Neotropical biogeography. Mol Phylogenet Evol 2013; 66:54-68. [DOI: 10.1016/j.ympev.2012.09.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 08/29/2012] [Accepted: 09/06/2012] [Indexed: 11/23/2022]
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9
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Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, Rabosky DL, Stadler T, Steiner C, Ryder OA, Janečka JE, Fisher CA, Murphy WJ. Macroevolutionary dynamics and historical biogeography of primate diversification inferred from a species supermatrix. PLoS One 2012; 7:e49521. [PMID: 23166696 PMCID: PMC3500307 DOI: 10.1371/journal.pone.0049521] [Citation(s) in RCA: 270] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 10/09/2012] [Indexed: 01/24/2023] Open
Abstract
Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ("Grande Coupure") at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.
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Affiliation(s)
- Mark S. Springer
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert W. Meredith
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology and Molecular Biology, Montclair State University, Montclair, New Jersey, United States of America
| | - John Gatesy
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Christopher A. Emerling
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Jong Park
- Department of Biology, University of California Riverside, Riverside, California, United States of America
- Department of Biology, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Rabosky
- Department of Integrative Biology, University of California, Berkeley, California, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tanja Stadler
- Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zurich, Zurich, Switzerland
| | - Cynthia Steiner
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Oliver A. Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, San Diego, California, United States of America
| | - Jan E. Janečka
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - Colleen A. Fisher
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
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10
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Shah P, Fitzpatrick BM, Fordyce JA. A PARAMETRIC METHOD FOR ASSESSING DIVERSIFICATION-RATE VARIATION IN PHYLOGENETIC TREES. Evolution 2012; 67:368-77. [DOI: 10.1111/j.1558-5646.2012.01791.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Rabosky DL, Adams DC. RATES OF MORPHOLOGICAL EVOLUTION ARE CORRELATED WITH SPECIES RICHNESS IN SALAMANDERS. Evolution 2012; 66:1807-18. [DOI: 10.1111/j.1558-5646.2011.01557.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Davis RB, Nicholson DB, Saunders ELR, Mayhew PJ. Fossil gaps inferred from phylogenies alter the apparent nature of diversification in dragonflies and their relatives. BMC Evol Biol 2011; 11:252. [PMID: 21917167 PMCID: PMC3179963 DOI: 10.1186/1471-2148-11-252] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 09/14/2011] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The fossil record has suggested that clade growth may differ in marine and terrestrial taxa, supporting equilibrial models in the former and expansionist models in the latter. However, incomplete sampling may bias findings based on fossil data alone. To attempt to correct for such bias, we assemble phylogenetic supertrees on one of the oldest clades of insects, the Odonatoidea (dragonflies, damselflies and their extinct relatives), using MRP and MRC. We use the trees to determine when, and in what clades, changes in taxonomic richness have occurred. We then test whether equilibrial or expansionist models are supported by fossil data alone, and whether findings differ when phylogenetic information is used to infer gaps in the fossil record. RESULTS There is broad agreement in family-level relationships between both supertrees, though with some uncertainty along the backbone of the tree regarding dragonflies (Anisoptera). "Anisozygoptera" are shown to be paraphyletic when fossil information is taken into account. In both trees, decreases in net diversification are associated with species-poor extant families (Neopetaliidae, Hemiphlebiidae), and an upshift is associated with Calopterygidae + Polythoridae. When ghost ranges are inferred from the fossil record, many families are shown to have much earlier origination dates. In a phylogenetic context, the number of family-level lineages is shown to be up to twice as high as the fossil record alone suggests through the Cretaceous and Cenozoic, and a logistic increase in richness is detected in contrast to an exponential increase indicated by fossils alone. CONCLUSIONS Our analysis supports the notion that taxa, which appear to have diversified exponentially using fossil data, may in fact have diversified more logistically. This in turn suggests that one of the major apparent differences between the marine and terrestrial fossil record may simply be an artifact of incomplete sampling. Our results also support previous notions that adult colouration plays an important role in odonate radiation, and that Anisozygoptera should be grouped in a single inclusive taxon with Anisoptera, separate from Zygoptera.
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Affiliation(s)
- Robert B Davis
- Department of Biology, University of York, York, YO10 5YW, UK
- Department of Zoology, University of Tartu, Vanemuise 46, EE-51014 Tartu, Estonia
| | - David B Nicholson
- Department of Biology, University of York, York, YO10 5YW, UK
- Department of Palaeontology, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- National Museums of Scotland, Department of Natural Sciences, Edinburgh, Midlothian, EH1 1JF, UK
| | | | - Peter J Mayhew
- Department of Biology, University of York, York, YO10 5YW, UK
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Fritz SA, Jønsson KA, Fjeldså J, Rahbek C. Diversification and biogeographic patterns in four island radiations of passerine birds. Evolution 2011; 66:179-90. [PMID: 22220873 DOI: 10.1111/j.1558-5646.2011.01430.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Declining diversification rates over time are a well-established evolutionary pattern, often interpreted as indicating initial rapid radiation with filling of ecological niche space. Here, we test the hypothesis that island radiations may show constant net diversification rates over time, due to continued expansion into new niche space in highly dispersive taxa. We investigate diversification patterns of four passerine bird families originating from the Indo-Pacific archipelagos, and link these to biogeographic patterns to provide independent indications of niche filling. We find a declining diversification rate for only one family, the Paradisaeidae (41 species). These are almost completely restricted to New Guinea, and have on average smaller species ranges and higher levels of species richness within grid cells than the other three families. In contrast, we cannot reject constant diversification rates for Campephagidae (93 species), Oriolidae (35 species), and Pachycephalidae (53 species), groups that have independently colonized neighboring archipelagos and continents. We propose that Paradisaeidae have reached the diversity limit imposed by their restricted distribution, whereas high dispersal and colonization success across the geologically dynamic Indo-Pacific archipelagos may have sustained high speciation rates for the other three families. Alternatively, increasing extinction rates may have obscured declining speciation rates in those three phylogenies.
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Affiliation(s)
- Susanne A Fritz
- Center for Macroecology, Evolution and Climate, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark.
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McInnes L, Baker WJ, Barraclough TG, Dasmahapatra KK, Goswami A, Harmon LJ, Morlon H, Purvis A, Rosindell J, Thomas GH, Turvey ST, Phillimore AB. Integrating ecology into macroevolutionary research. Biol Lett 2011; 7:644-6. [PMID: 21527505 DOI: 10.1098/rsbl.2011.0358] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
On 9 March, over 150 biologists gathered in London for the Centre for Ecology and Evolution spring symposium, 'Integrating Ecology into Macroevolutionary Research'. The event brought together researchers from London-based institutions alongside others from across the UK, Europe and North America for a day of talks. The meeting highlighted methodological advances and recent analyses of exemplar datasets focusing on the exploration of the role of ecological processes in shaping macroevolutionary patterns.
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Affiliation(s)
- Lynsey McInnes
- Division of Biology, Imperial College London, Silwood Park, Ascot, Berkshire SL5 7PY, UK.
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