1
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The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar. Nat Commun 2023; 14:14. [PMID: 36627274 PMCID: PMC9832013 DOI: 10.1038/s41467-022-35215-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/22/2022] [Indexed: 01/12/2023] Open
Abstract
Many of Madagascar's unique species are threatened with extinction. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. Here, we compile a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimate natural rates of extinction, colonization, and speciation. We measure how long it would take to restore Madagascar's mammalian biodiversity under these rates, the "evolutionary return time" (ERT). At the time of human arrival there were approximately 250 species of mammals on Madagascar, resulting from 33 colonisation events (28 by bats), but at least 30 of these species have gone extinct since then. We show that the loss of currently threatened species would have a much deeper long-term impact than all the extinctions since human arrival. A return from current to pre-human diversity would take 1.6 million years (Myr) for bats, and 2.9 Myr for non-volant mammals. However, if species currently classified as threatened go extinct, the ERT rises to 2.9 Myr for bats and 23 Myr for non-volant mammals. Our results suggest that an extinction wave with deep evolutionary impact is imminent on Madagascar unless immediate conservation actions are taken.
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2
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Heimburger B, Maurer SS, Schardt L, Scheu S, Hartke TR. Historical and future climate change fosters expansion of Australian harvester termites, Drepanotermes. Evolution 2022; 76:2145-2161. [PMID: 35842838 DOI: 10.1111/evo.14573] [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: 02/10/2022] [Revised: 05/05/2022] [Accepted: 05/25/2022] [Indexed: 01/22/2023]
Abstract
Past evolutionary adaptations to Australia's aridification can help us to understand the potential responses of species in the face of global climate change. Here, we focus on the Australian-endemic genus Drepanotermes, also known as Australian harvester termites, which are mainly found in semiarid and arid regions of Australia. We used species delineation, phylogenetic inference, and ancestral state reconstruction to investigate the evolution of mound-building in Drepanotermes and in relation to reconstructed past climatic conditions. Our findings suggest that mound-building evolved several times independently in Drepanotermes, apparently facilitating expansions into tropical and mesic regions of Australia. The phylogenetic signal of bioclimatic variables, especially limiting environmental factors (e.g., precipitation of the warmest quarter), suggests that the climate exerts a strong selective pressure. Finally, we used environmental niche modeling to predict the present and future habitat suitability for eight Drepanotermes species. Abiotic factors such as annual temperature contributed disproportionately to calibrations, while the inclusion of biotic factors such as predators and vegetation cover improved ecological niche models in some species. A comparison between present and future habitat suitability under two different emission scenarios revealed continued suitability of current ranges as well as substantial habitat gains for most studied species. Human-mediated climate change occurs more quickly than these termites can disperse into newly suitable habitat; however, their role in stabilizing arid ecosystems may allow them to mitigate effects on some other organisms at a local level.
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Affiliation(s)
- Bastian Heimburger
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Santiago Soto Maurer
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Leonie Schardt
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
| | - Stefan Scheu
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany.,Centre of Biodiversity and Sustainable Land Use, Büsgenweg 1, 37077, Göttingen, Germany
| | - Tamara R Hartke
- Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Untere Karspüle 2, 37073, Göttingen, Germany
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3
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Janzen T, Bokma F, Etienne RS. Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation. Syst Biol 2022; 71:1244-1254. [PMID: 34672354 PMCID: PMC9366449 DOI: 10.1093/sysbio/syab085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 11/14/2022] Open
Abstract
Although molecular mechanisms associated with the generation of mutations are highly conserved across taxa, there is widespread variation in mutation rates between evolutionary lineages. When phylogenies are reconstructed based on nucleotide sequences, such variation is typically accounted for by the assumption of a relaxed molecular clock, which is a statistical distribution of mutation rates without much underlying biological mechanism. Here, we propose that variation in accumulated mutations may be partly explained by an elevated mutation rate during speciation. Using simulations, we show how shifting mutations from branches to speciation events impacts inference of branching times in phylogenetic reconstruction. Furthermore, the resulting nucleotide alignments are better described by a relaxed than by a strict molecular clock. Thus, elevated mutation rates during speciation potentially explain part of the variation in substitution rates that is observed across the tree of life. [Molecular clock; phylogenetic reconstruction; speciation; substitution rate variation.].
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Affiliation(s)
- Thijs Janzen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| | - Folmer Bokma
- Department of BioSciences, Center for Ecological and Evolutionary Synthesis (CEES), University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
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4
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Hay EM, McGee MD, Chown SL. Geographic range size and speciation in honeyeaters. BMC Ecol Evol 2022; 22:86. [PMID: 35768772 PMCID: PMC9245323 DOI: 10.1186/s12862-022-02041-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Darwin and others proposed that a species' geographic range size positively influences speciation likelihood, with the relationship potentially dependent on the mode of speciation and other contributing factors, including geographic setting and species traits. Several alternative proposals for the influence of range size on speciation rate have also been made (e.g. negative or a unimodal relationship with speciation). To examine Darwin's proposal, we use a range of phylogenetic comparative methods, focusing on a large Australasian bird clade, the honeyeaters (Aves: Meliphagidae). RESULTS We consider the influence of range size, shape, and position (latitudinal and longitudinal midpoints, island or continental species), and consider two traits known to influence range size: dispersal ability and body size. Applying several analytical approaches, including phylogenetic Bayesian path analysis, spatiophylogenetic models, and state-dependent speciation and extinction models, we find support for both the positive relationship between range size and speciation rate and the influence of mode of speciation. CONCLUSIONS Honeyeater speciation rate differs considerably between islands and the continental setting across the clade's distribution, with range size contributing positively in the continental setting, while dispersal ability influences speciation regardless of setting. These outcomes support Darwin's original proposal for a positive relationship between range size and speciation likelihood, while extending the evidence for the contribution of dispersal ability to speciation.
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Affiliation(s)
- Eleanor M Hay
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia.
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
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5
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Torkkola JJ, Wilmer JW, Hutchinson MN, Couper PJ, Oliver PM. Die on this hill? A new monotypic, microendemic and montane vertebrate genus from the Australian Wet Tropics. ZOOL SCR 2022. [DOI: 10.1111/zsc.12550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Janne J. Torkkola
- Snake Out Brisbane Kenmore Queensland Australia
- Biodiversity and Geosciences Program Queensland Museum South Brisbane Queensland Australia
| | | | - Mark N. Hutchinson
- South Australian Museum, North Terrace Adelaide South Australia Australia
| | - Patrick J. Couper
- Biodiversity and Geosciences Program Queensland Museum South Brisbane Queensland Australia
| | - Paul M. Oliver
- Biodiversity and Geosciences Program Queensland Museum South Brisbane Queensland Australia
- Centre for Planetary Health and Food Security Griffith University Brisbane Queensland Australia
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6
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Salisbury SJ, Ruzzante DE. Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms. Annu Rev Anim Biosci 2021; 10:81-106. [PMID: 34758272 DOI: 10.1146/annurev-animal-051021-080709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- S J Salisbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
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7
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Neves DM, Kerkhoff AJ, Echeverría-Londoño S, Merow C, Morueta-Holme N, Peet RK, Sandel B, Svenning JC, Wiser SK, Enquist BJ. The adaptive challenge of extreme conditions shapes evolutionary diversity of plant assemblages at continental scales. Proc Natl Acad Sci U S A 2021; 118:e2021132118. [PMID: 34504011 PMCID: PMC8449343 DOI: 10.1073/pnas.2021132118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 11/26/2022] Open
Abstract
The tropical conservatism hypothesis (TCH) posits that the latitudinal gradient in biological diversity arises because most extant clades of animals and plants originated when tropical environments were more widespread and because the colonization of colder and more seasonal temperate environments is limited by the phylogenetically conserved environmental tolerances of these tropical clades. Recent studies have claimed support of the TCH, indicating that temperate plant diversity stems from a few more recently derived lineages that are nested within tropical clades, with the colonization of the temperate zone being associated with key adaptations to survive colder temperatures and regular freezing. Drought, however, is an additional physiological stress that could shape diversity gradients. Here, we evaluate patterns of evolutionary diversity in plant assemblages spanning the full extent of climatic gradients in North and South America. We find that in both hemispheres, extratropical dry biomes house the lowest evolutionary diversity, while tropical moist forests and many temperate mixed forests harbor the highest. Together, our results support a more nuanced view of the TCH, with environments that are radically different from the ancestral niche of angiosperms having limited, phylogenetically clustered diversity relative to environments that show lower levels of deviation from this niche. Thus, we argue that ongoing expansion of arid environments is likely to entail higher loss of evolutionary diversity not just in the wet tropics but in many extratropical moist regions as well.
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Affiliation(s)
- Danilo M Neves
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | | | - Susy Echeverría-Londoño
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, W2 1PG, United Kingdom
| | - Cory Merow
- Eversource Energy Center, Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06268
| | - Naia Morueta-Holme
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Robert K Peet
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Brody Sandel
- Department of Biology, Santa Clara University, Santa Clara, CA 95053
| | - Jens-Christian Svenning
- Center for Biodiversity Dynamics in a Changing World, Department of Biology, Aarhus University, Aarhus 8000, Denmark
| | - Susan K Wiser
- Ecosystems and Conservation Group, Manaaki Whenua - Landcare Research, Lincoln 7640, New Zealand
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
- The Santa Fe Institute, Santa Fe, NM 87501
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8
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Jennings WB. Evolutionary relationships among the snakelike pygopodid lizards: a review of phylogenetic studies of an enigmatic Australian adaptive radiation. PeerJ 2021; 9:e11502. [PMID: 34249485 PMCID: PMC8253114 DOI: 10.7717/peerj.11502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/03/2021] [Indexed: 12/03/2022] Open
Abstract
Here, I review phylogenetic studies of the lizard family Pygopodidae, a group of 47 extant species that diversified in Australia and New Guinea. The goal of this study was to examine published phylogenetic and phylogenomic hypotheses on pygopodids to identify the strengths and weaknesses in our understanding of their phylogeny. Many parts of the pygopodid family tree are well established by multiple independent tree inferences including: (1) all multispecies genera (i.e., Aprasia, Delma, Lialis, Pletholax, and Pygopus) are monophyletic groups; (2) the root of the pygopodid tree is located along the branch leading to the Delma clade, thus showing that Delma is the sister group to all other pygopodid genera; (3) the Aprasia repens group, Delma tincta group, and several other groups of closely related species are demonstrated to be monophyletic entities; and (4) the monotypic Paradelma orientalis is the sister lineage to the Pygopus clade. Based on accumulated phylogenetic evidence, two taxonomic recommendations are given: Paradelma merits generic status rather than being subsumed into Pygopus as some earlier studies had suggested, and the monotypic Aclys concinna should be recognized as a member of Delma (following current practice) until future studies clarify its placement inside or outside the Delma clade. One chronic problem with phylogenetic studies of pygopodids, which has limited the explanatory power of many tree hypotheses, concerns the undersampling of known species. Although the continual addition of newly described species, especially over the past two decades, has been a major reason for these taxon sampling gaps, deficits in species sampling for ingroups and/or outgroups in several studies of pygopodid species complexes has confounded the testing of some ingroup monophyly hypotheses. Ancient hybridization between non-sister lineages may also be confounding attempts to recover the relationships among pygopodids using molecular data. Indeed, such a phenomenon can explain at least five cases of mito-nuclear discordance and conflicts among trees based on nuclear DNA datasets. Another problem has been the lack of consensus on the relationships among most pygopodid genera, an issue that may stem from rapid diversification of these lineages early in the group's history. Despite current weaknesses in our understanding of pygopodid phylogeny, enough evidence exists to clarify many major and minor structural parts of their family tree. Accordingly, a composite tree for the Pygopodidae was able to be synthesized. This novel tree hypothesis contains all recognized pygopodid species and reveals that about half of the clades are corroborated by multiple independent tree hypotheses, while the remaining clades have less empirical support.
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Affiliation(s)
- W. Bryan Jennings
- Department of Evolution, Ecology, & Organismal Biology, University of California, Riverside, Riverside, California, United States of America
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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9
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Rix MG, Wilson JD, Huey JA, Hillyer MJ, Gruber K, Harvey MS. Diversification of the mygalomorph spider genus Aname (Araneae: Anamidae) across the Australian arid zone: Tracing the evolution and biogeography of a continent-wide radiation. Mol Phylogenet Evol 2021; 160:107127. [PMID: 33667632 DOI: 10.1016/j.ympev.2021.107127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/26/2021] [Accepted: 02/24/2021] [Indexed: 02/08/2023]
Abstract
The assembly of the Australian arid zone biota has long fascinated biogeographers. Covering over two-thirds of the continent, Australia's vast arid zone biome is home to a distinctive fauna and flora, including numerous lineages which have diversified since the Eocene. Tracing the origins and speciation history of these arid zone taxa has been an ongoing endeavour since the advent of molecular phylogenetics, and an increasing number of studies on invertebrate animals are beginning to complement a rich history of research on vertebrate and plant taxa. In this study, we apply continent-wide genetic sampling and one of the largest phylogenetic data matrices yet assembled for a genus of Australian spiders, to reconstruct the phylogeny and biogeographic history of the open-holed trapdoor spider genus Aname L. Koch, 1873. This highly diverse lineage of Australian mygalomorph spiders has a distribution covering the majority of Australia west of the Great Dividing Range, but apparently excluding the high rainfall zones of eastern Australia and Tasmania. Original and legacy sequences were obtained for three mtDNA and four nuDNA markers from 174 taxa in seven genera, including 150 Aname specimen terminals belonging to 102 species-level operational taxonomic units, sampled from 32 bioregions across Australia. Reconstruction of the phylogeny and biogeographic history of Aname revealed three radiations (Tropical, Temperate-Eastern and Continental), which could be further broken into eight major inclusive clades. Ancestral area reconstruction revealed the Pilbara, Monsoon Tropics and Mid-West to be important ancestral areas for the genus Aname and its closest relatives, with the origin of Aname itself inferred in the Pilbara bioregion. From these origins in the arid north-west of Australia, our study found evidence for a series of subsequent biome transitions in separate lineages, with at least eight tertiary incursions back into the arid zone from more mesic tropical, temperate or eastern biomes, and only two major clades which experienced widespread (primary) in situ diversification within the arid zone. Based on our phylogenetic results, and results from independent legacy divergence dating studies, we further reveal the importance of climate-driven biotic change in the Miocene and Pliocene in shaping the distribution and composition of the Australian arid zone biota, and the value of continent-wide studies in revealing potentially complex patterns of arid zone diversification in dispersal-limited invertebrate taxa.
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Affiliation(s)
- Michael G Rix
- Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD 4101, Australia; Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia.
| | - Jeremy D Wilson
- Biodiversity and Geosciences Program, Queensland Museum, South Brisbane, QLD 4101, Australia; Division of Arachnology, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Av. Ángel Gallardo 470 (C1405DJR), Buenos Aires, Argentina
| | - Joel A Huey
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia; School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Mia J Hillyer
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia
| | - Karl Gruber
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia; School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Mark S Harvey
- Collections and Research Centre, Western Australian Museum, Welshpool, WA 6106, Australia; School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
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10
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Thorn KM, Hutchinson MN, Lee MSY, Brown NJ, Camens AB, Worthy TH. A new species of Proegernia from the Namba Formation in South Australia and the early evolution and environment of Australian egerniine skinks. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201686. [PMID: 33972861 PMCID: PMC8074667 DOI: 10.1098/rsos.201686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
The diverse living Australian lizard fauna contrasts greatly with their limited Oligo-Miocene fossil record. New Oligo-Miocene fossil vertebrates from the Namba Formation (south of Lake Frome, South Australia) were uncovered from multiple expeditions from 2007 to 2018. Abundant disarticulated material of small vertebrates was concentrated in shallow lenses along the palaeolake edges, now exposed on the western of Lake Pinpa also known from Billeroo Creek 2 km northeast. The fossiliferous lens within the Namba Formation hosting the abundant aquatic (such as fish, platypus Obdurodon and waterfowl) and diverse terrestrial (such as possums, dasyuromorphs and scincids) vertebrates and is hereafter recognized as the Fish Lens. The stratigraphic provenance of these deposits in relation to prior finds in the area is also established. A new egerniine scincid taxon Proegernia mikebulli sp. nov. described herein, is based on a near-complete reconstructed mandible, maxilla, premaxilla and pterygoid. Postcranial scincid elements were also recovered with this material, but could not yet be confidently associated with P. mikebulli. This new taxon is recovered as the sister species to P. palankarinnensis, in a tip-dated total-evidence phylogenetic analysis, where both are recovered as stem Australian egerniines. These taxa also help pinpoint the timing of the arrival of scincids to Australia, with egerniines the first radiation to reach the continent.
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Affiliation(s)
- K. M. Thorn
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
- South Australian Museum, North Terrace, Adelaide 5000, South Australia
| | - M. N. Hutchinson
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
- South Australian Museum, North Terrace, Adelaide 5000, South Australia
| | - M. S. Y. Lee
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
- South Australian Museum, North Terrace, Adelaide 5000, South Australia
| | - N. J. Brown
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
| | - A. B. Camens
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
| | - T. H. Worthy
- College of Science and Engineering, Flinders University, Bedford Park 5042, South Australia
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11
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Chang J, Rabosky DL, Alfaro ME. Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions. Syst Biol 2020; 69:602-611. [PMID: 31804691 DOI: 10.1093/sysbio/syz081] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/12/2019] [Accepted: 12/01/2019] [Indexed: 11/13/2022] Open
Abstract
Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on "sampling fractions" can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (Taxonomic Addition for Complete Trees [TACT]) that uses birth-death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling. [Birth-death process; diversification; incomplete sampling; phylogenetic uncertainty; rate heterogeneity; rate shifts; stochastic polytomy resolution.].
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Affiliation(s)
- Jonathan Chang
- School of Biological Sciences, Monash University, 25 Rainforest Walk, Melbourne, VIC 3800, Australia.,Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, USA.,Department of Ecology and Evolutionary Biology, University of California, 612 Charles E Young Dr S, Los Angeles, CA 90095, USA
| | - Daniel L Rabosky
- Department of Ecology and Evolutionary Biology & Museum of Zoology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E Young Dr S, Los Angeles, CA 90095, USA
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12
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Renner MAM, Foster CSP, Miller JT, Murphy DJ. Increased diversification rates are coupled with higher rates of climate space exploration in Australian Acacia (Caesalpinioideae). THE NEW PHYTOLOGIST 2020; 226:609-622. [PMID: 31792997 DOI: 10.1111/nph.16349] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/17/2019] [Indexed: 06/10/2023]
Abstract
Australia is an excellent setting to explore relationships between climate change and diversification dynamics. Aridification since the Eocene has resulted in spectacular radiations within one or more Australian biomes. Acacia is the largest plant genus on the Australian continent, with around 1000 species, and is present in all biomes. We investigated the macroevolutionary dynamics of Acacia within climate space. We analysed phylogenetic and climatic data for 503 Acacia species to estimate a time-calibrated phylogeny and central climatic tendencies for BioClim layers from 132 000 herbarium specimens. Diversification rate heterogeneity and rates of climate space exploration were tested. We inferred two diversification rate increases, both associated with significantly higher rates of climate space exploration. Observed spikes in climate disparity within the Pleistocene correspond with onset of Pleistocene glacial-interglacial cycling. Positive time dependency in environmental disparity applies in the basal grade of Acacia, though climate space exploration rates were lower. Incongruence between rates of climate space exploration and disparity suggests different Acacia lineages have experienced different macroevolutionary processes. The second diversification rate increase is associated with a south-east Australian mesic lineage, suggesting adaptations to progressively aridifying environments and ability to transition into mesic environments contributed to Acacia's dominance across Australia.
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Affiliation(s)
- Matt A M Renner
- Royal Botanic Garden and Domain Trust, Sydney, NSW, 2000, Australia
| | - Charles S P Foster
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Joseph T Miller
- Global Biodiversity Information Facility, DK-2100, Copenhagen, Denmark
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, 3004, VIC, Australia
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13
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Roycroft EJ, Nations JA, Rowe KC. Environment predicts repeated body size shifts in a recent radiation of Australian mammals. Evolution 2019; 74:671-680. [PMID: 31595503 DOI: 10.1111/evo.13859] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022]
Abstract
Closely related species that occur across steep environmental gradients often display clear body size differences, and examining this pattern is crucial to understanding how environmental variation shapes diversity. Australian endemic rodents in the Pseudomys Division (Muridae: Murinae) have repeatedly colonized the arid, monsoon, and mesic biomes over the last 5 million years. Using occurrence records, body mass data, and Bayesian phylogenetic models, we test whether body mass of 31 species in the Pseudomys Division can be predicted by their biome association. We also model the effect of eight environmental variables on body mass. Despite high phylogenetic signal in body mass evolution across the phylogeny, we find that mass predictably increases in the mesic biome and decreases in arid and monsoon biomes. As per Bergmann's rule, temperature is strongly correlated with body mass, as well as several other variables. Our results highlight two important findings. First, body size in Australian rodents has tracked with climate through the Pleistocene, likely due to several environmental variables rather than a single factor. Second, support for both Brownian motion and predictable change at different taxonomic levels in the Pseudomys Division phylogeny demonstrates how the level at which we test hypotheses can alter interpretation of evolutionary processes.
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Affiliation(s)
- Emily J Roycroft
- School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.,Sciences Department, Museums Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
| | - Jonathan A Nations
- Museum of Natural Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Kevin C Rowe
- School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.,Sciences Department, Museums Victoria, GPO Box 666, Melbourne, Victoria, 3001, Australia
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14
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Simon C, Gordon ERL, Moulds MS, Cole JA, Haji D, Lemmon AR, Lemmon EM, Kortyna M, Nazario K, Wade EJ, Meister RC, Goemans G, Chiswell SM, Pessacq P, Veloso C, McCutcheon JP, Łukasik P. Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Phylogenetic asymmetry is common throughout the tree of life and results from contrasting patterns of speciation and extinction in the paired descendant lineages of ancestral nodes. On the depauperate side of a node, we find extant ‘relict’ taxa that sit atop long, unbranched lineages. Here, we show that a tiny, pale green, inconspicuous and poorly known cicada in the genus Derotettix, endemic to degraded salt-plain habitats in arid regions of central Argentina, is a relict lineage that is sister to all other modern cicadas. Nuclear and mitochondrial phylogenies of cicadas inferred from probe-based genomic hybrid capture data of both target and non-target loci and a morphological cladogram support this hypothesis. We strengthen this conclusion with genomic data from one of the cicada nutritional bacterial endosymbionts, Sulcia, an ancient and obligate endosymbiont of the larger plant-sucking bugs (Auchenorrhyncha) and an important source of maternally inherited phylogenetic data. We establish Derotettiginae subfam. nov. as a new, monogeneric, fifth cicada subfamily, and compile existing and new data on the distribution, ecology and diet of Derotettix. Our consideration of the palaeoenvironmental literature and host-plant phylogenetics allows us to predict what might have led to the relict status of Derotettix over 100 Myr of habitat change in South America.
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Affiliation(s)
- Chris Simon
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Eric R L Gordon
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - M S Moulds
- Australian Museum Research Institute, Sydney, NSW, Australia
| | - Jeffrey A Cole
- Natural Sciences Division, Pasadena City College, Pasadena, CA, USA
| | - Diler Haji
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, USA
| | | | - Michelle Kortyna
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Katherine Nazario
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Elizabeth J Wade
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Department of Natural Sciences and Mathematics, Curry College, Milton, MA, USA
| | - Russell C Meister
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Geert Goemans
- Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | | | - Pablo Pessacq
- Centro de Investigaciones Esquel de Montaña y Estepa Patagónicas, Esquel, Chubut, Argentina
| | - Claudio Veloso
- Department of Ecological Sciences, Science Faculty, University of Chile, Santiago, Chile
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Piotr Łukasik
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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15
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Louca S, Pennell MW. A General and Efficient Algorithm for the Likelihood of Diversification and Discrete-Trait Evolutionary Models. Syst Biol 2019; 69:545-556. [DOI: 10.1093/sysbio/syz055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
As the size of phylogenetic trees and comparative data continue to grow and more complex models are developed to investigate the processes that gave rise to them, macroevolutionary analyses are becoming increasingly limited by computational requirements. Here, we introduce a novel algorithm, based on the “flow” of the differential equations that describe likelihoods along tree edges in backward time, to reduce redundancy in calculations and efficiently compute the likelihood of various macroevolutionary models. Our algorithm applies to several diversification models, including birth–death models and models that account for state- or time-dependent rates, as well as many commonly used models of discrete-trait evolution, and provides an alternative way to describe macroevolutionary model likelihoods. As a demonstration of our algorithm’s utility, we implemented it for a popular class of state-dependent diversification models—BiSSE, MuSSE, and their extensions to hidden-states. Our implementation is available through the R package $\texttt{castor}$. We show that, for these models, our algorithm is one or more orders of magnitude faster than existing implementations when applied to large phylogenies. Our algorithm thus enables the fitting of state-dependent diversification models to modern massive phylogenies with millions of tips and may lead to potentially similar computational improvements for many other macroevolutionary models.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, 1210 University of Oregon, Eugene, OR 97403, USA
- Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403, USA
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, V6T1Z4 British Columbia, Canada
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, V6T1Z4 British Columbia, Canada
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16
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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17
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Sanchez JL, Bracken-Grissom HD, Trexler JC. Freshwater-to-marine transitions may explain the evolution of herbivory in the subgenus Mollienesia (genus Poecilia, mollies and guppies). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The ability of organisms to cross ecosystem boundaries is an important catalyst of evolutionary diversification. The genus Poecilia (mollies and guppies) is an excellent system for studying ecosystem transitions because species display a range of salinity and dietary preferences, with herbivory concentrated in the subgenus Mollienesia. We reconstructed ancestral habitats and diets across a phylogeny of the genus Poecilia, evaluated diversification rates and used phylogenetically independent contrasts to determine whether diet evolved in response to habitat transition in this group. The results suggest that ancestors of subgenus Mollienesia were exclusively herbivorous, whereas ancestral diets of other Poecilia included animals. We found that transitions across euryhaline boundaries occurred at least once in this group, probably after the divergence of the subgenus Mollienesia. Furthermore, increased salinity affiliation explained 24% of the decrease in animals in the gut, and jaw morphology was associated with the percentage of animals in the gut, but not with the percentage of species occupying saline habitats. These findings suggest that in the genus Poecilia, herbivory evolved in association with transitions from fresh to euryhaline habitats, and jaw morphology evolved in response to the appearance of herbivory. These results provide a rare example of increased diet diversification associated with the transition from freshwater to euryhaline habitats.
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Affiliation(s)
| | | | - Joel C Trexler
- Department of Biological Sciences, Florida International University, Miami, FL, USA
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18
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Smissen PJ, Rowe KC. Repeated biome transitions in the evolution of Australian rodents. Mol Phylogenet Evol 2018; 128:182-191. [DOI: 10.1016/j.ympev.2018.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/26/2018] [Accepted: 07/16/2018] [Indexed: 12/31/2022]
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19
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Remeš V, Harmáčková L. Disentangling direct and indirect effects of water availability, vegetation, and topography on avian diversity. Sci Rep 2018; 8:15475. [PMID: 30341321 PMCID: PMC6195560 DOI: 10.1038/s41598-018-33671-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/21/2018] [Indexed: 12/24/2022] Open
Abstract
Climate is a major driver of species diversity. However, its effect can be either direct due to species physiological tolerances or indirect, whereby wetter climates facilitate more complex vegetation and consequently higher diversity due to greater resource availability. Yet, studies quantifying both direct and indirect effects of climate on multiple dimensions of diversity are rare. We used extensive data on species distributions, morphological and ecological traits, and vegetation across Australia to quantify both direct (water availability) and indirect (habitat diversity and canopy height) effects of climate on the species richness (SR), phylogenetic diversity (PD), and functional diversity (FD) of 536 species of birds. Path analyses revealed that SR increased with wetter climates through both direct and indirect effects, lending support for the influence of both physiological tolerance and vegetation complexity. However, residual PD and residual FD (adjusted for SR by null models) were poorly predicted by environmental conditions. Thus, the FD and PD of Australian birds mostly evolved in concert with SR, with the possible exception of the higher-than-expected accumulation of avian lineages in wetter and more productive areas in northern and eastern Australia (with high residual PD), permitted probably by older biome age.
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Affiliation(s)
- Vladimír Remeš
- Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacky University, 17. listopadu 50, 77146, Olomouc, Czech Republic.
| | - Lenka Harmáčková
- Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacky University, 17. listopadu 50, 77146, Olomouc, Czech Republic.
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20
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Brennan IG, Keogh JS. Miocene biome turnover drove conservative body size evolution across Australian vertebrates. Proc Biol Sci 2018; 285:rspb.2018.1474. [PMID: 30333208 DOI: 10.1098/rspb.2018.1474] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/26/2018] [Indexed: 11/12/2022] Open
Abstract
On deep time scales, changing climatic trends can have a predictable influence on macroevolution. From evidence of mass extinctions, we know that rapid climatic oscillations can indirectly open niche space and precipitate adaptive radiation, changing the course of ecological diversification. These dramatic shifts in the global climate, however, are rare events relative to extended periods of protracted climate change and biome turnover. It remains unclear whether during gradually changing periods, shifting habitats may instead promote non-adaptive speciation by facilitating allopatry and phenotypic conservatism. Using fossil-calibrated, species-level phylogenies for five Australian radiations comprising more than 800 species, we investigated temporal trends in biogeography and body size evolution. Here, we demonstrate that gradual Miocene cooling and aridification correlates with the restricted phenotypic diversification of multiple ecologically diverse vertebrate groups. This probably occurred as species ranges became fractured and isolated during continental biome restructuring, encouraging a shift towards conservatism in body size evolution. Our results provide further evidence that abiotic changes, not only biotic interactions, may act as selective forces influencing phenotypic macroevolution.
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Affiliation(s)
- Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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21
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Singhal S, Huang H, Grundler MR, Marchán-Rivadeneira MR, Holmes I, Title PO, Donnellan SC, Rabosky DL. Does Population Structure Predict the Rate of Speciation? A Comparative Test across Australia’s Most Diverse Vertebrate Radiation. Am Nat 2018; 192:432-447. [DOI: 10.1086/699515] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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22
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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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23
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García-Navas V, Westerman M. Niche conservatism and phylogenetic clustering in a tribe of arid-adapted marsupial mice, the Sminthopsini. J Evol Biol 2018; 31:1204-1215. [PMID: 29808505 DOI: 10.1111/jeb.13297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 11/27/2022]
Abstract
The progressive expansion of the Australian arid zone during the last 20 Ma appears to have spurred the diversification of several families of plants, vertebrates and invertebrates, yet such taxonomic groups appear to show limited niche radiation. Here, we test whether speciation is associated with niche conservatism (constraints on ecological divergence) or niche divergence in a tribe of marsupial mice (Sminthopsini; 23 taxa) that includes the most speciose genus of living dasyurids, the sminthopsins. To that end, we integrated phylogenetic data with ecological niche modelling, to enable us to reconstruct the evolution of climatic suitability within Sminthopsini. Niche overlap among species was low-moderate (but generally higher than expected given environmental background similarity), and the degree of phylogenetic clustering increased with aridity. Climatic niche reconstruction illustrates that there has been little apparent evolution of climatic tolerance within clades. Accordingly, climatic disparity tends to be accumulated among clades, suggesting considerable niche conservatism. Our results also indicate that evolution of climatic tolerances has been heterogeneous across different dimensions of climate (temperature vs. precipitation) and across phylogenetic clusters (Sminthopsis murina group vs. other groups). Although some results point to the existence of shifts in climatic niches during the speciation of sminthopsins, our study provides evidence for substantial phylogenetic niche conservatism in the group. We conclude that niche diversification had a low impact on the speciation of this tribe of small, but highly mobile marsupials.
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Affiliation(s)
- Vicente García-Navas
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Michael Westerman
- Department of Ecology, Environment and Evolution, LaTrobe University, Melbourne, Vic., Australia
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24
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Simpson AG, Wagner PJ, Wing SL, Fenster CB. Binary-state speciation and extinction method is conditionally robust to realistic violations of its assumptions. BMC Evol Biol 2018; 18:69. [PMID: 29739313 PMCID: PMC5941815 DOI: 10.1186/s12862-018-1174-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/10/2018] [Indexed: 11/26/2022] Open
Abstract
Background Phylogenetic comparative methods allow us to test evolutionary hypotheses without the benefit of an extensive fossil record. These methods, however, make simplifying assumptions, among them that clades are always increasing or stable in diversity, an assumption we know to be false. This study simulates hypothetical clades to test whether the Binary State Speciation and Extinction (BiSSE) method can be used to correctly detect relative differences in diversification rate between ancestral and derived character states even as net diversification rates are declining overall. We simulate clades with declining but positive diversification rates, as well those in which speciation rates decline below extinction rates so that they are losing richness for part of their history. We run these analyses both with simulated symmetric and asymmetric speciation rates to test whether BiSSE can be used to detect them correctly. Results For simulations with a neutral character, the fit for a BiSSE model with a neutral character is better than alternative models so long as net diversification rates remain positive. Once net diversification rates become negative, the BiSSE model with the greatest likelihood often has a non-neutral character, even though there is no such character in the simulation. BiSSE’s usefulness in detecting real asymmetry in speciation rates improves with clade age, even well after net diversification rates have become negative. Conclusions BiSSE is most useful in analyzing clades of intermediate age, before they have reached peak diversity and gone into decline. After this point, users of BiSSE risk incorrectly inferring differential evolutionary rates when none exist. Fortunately, most studies using BiSSE and similar models focus on rapid, recent diversifications, and are less likely to encounter the biases BiSSE models are subject to for older clades. For extant groups that were once more diverse than now, however, caution should be taken in inferring past diversification patterns without fossil data. Electronic supplementary material The online version of this article (10.1186/s12862-018-1174-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew G Simpson
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington D.C., USA. .,Program in Behavior, Ecology, Evolution, and Systematics, University of Maryland, College Park, USA.
| | - Peter J Wagner
- Department of Earth & Atmospheric Sciences and School of Biological Sciences, University of Nebraska, Lincoln, USA
| | - Scott L Wing
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington D.C., USA.,Program in Behavior, Ecology, Evolution, and Systematics, University of Maryland, College Park, USA
| | - Charles B Fenster
- Department of Biology and Microbiology, South Dakota State University, Brookings, USA
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25
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Rajeh A, Lv J, Lin Z. Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota. BMC Genomics 2018; 19:282. [PMID: 29690866 PMCID: PMC5937819 DOI: 10.1186/s12864-018-4683-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/16/2018] [Indexed: 01/06/2023] Open
Abstract
Background Chromosomal rearrangements have been shown to facilitate speciation through creating a barrier of gene flow. However, it is not known whether heterogeneous rates of chromosomal rearrangement at the genome scale contributed to the huge disparity of species richness among different groups of organisms, which is one of the most remarkable and pervasive patterns on Earth. The largest fungal phylum Ascomycota is an ideal study system to address this question because it comprises three subphyla (Saccharomycotina, Taphrinomycotina, and Pezizomycotina) whose species numbers differ by two orders of magnitude (59,000, 1000, and 150 respectively). Results We quantified rates of genome rearrangement for 71 Ascomycota species that have well-assembled genomes. The rates of inter-species genome rearrangement, which were inferred based on the divergence rates of gene order, are positively correlated with species richness at both ranks of subphylum and class in Ascomycota. This finding is further supported by our quantification of intra-species rearrangement rates based on paired-end genome sequencing data of 216 strains from three representative species, suggesting a difference of intrinsic genome instability among Ascomycota lineages. Our data also show that different rates of imbalanced rearrangements, such as deletions, are a major contributor to the heterogenous rearrangement rates. Conclusions Various lines of evidence in this study support that a higher rate of rearrangement at the genome scale might have accelerated the speciation process and increased species richness during the evolution of Ascomycota species. Our findings provide a plausible explanation for the species disparity among Ascomycota lineages, which will be valuable to unravel the underlying causes for the huge disparity of species richness in various taxonomic groups. Electronic supplementary material The online version of this article (10.1186/s12864-018-4683-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ahmad Rajeh
- Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA.,Department of Computer Science, Saint Louis University, St. Louis, MO, 63103, USA
| | - Jie Lv
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO, 63103, USA.
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26
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García-Navas V, Rodríguez-Rey M. The Evolution of Climatic Niches and its Role in Shaping Diversity Patterns in Diprotodontid Marsupials. J MAMM EVOL 2018. [DOI: 10.1007/s10914-018-9435-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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27
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García-Navas V, Rodríguez-Rey M, Westerman M. Bursts of morphological and lineage diversification in modern dasyurids, a ‘classic’ adaptive radiation. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Vicente García-Navas
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Michael Westerman
- Department of Ecology, Environment and Evolution, LaTrobe University, Melbourne, Victoria, Australia
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28
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Bragg JG, Potter S, Afonso Silva AC, Hoskin CJ, Bai BYH, Moritz C. Phylogenomics of a rapid radiation: the Australian rainbow skinks. BMC Evol Biol 2018; 18:15. [PMID: 29402211 PMCID: PMC5800007 DOI: 10.1186/s12862-018-1130-4] [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: 06/28/2017] [Accepted: 01/25/2018] [Indexed: 12/13/2022] Open
Abstract
Background The application of target capture with next-generation sequencing now enables phylogenomic analyses of rapidly radiating clades of species. But such analyses are complicated by extensive incomplete lineage sorting, demanding the use of methods that consider this process explicitly, such as the multispecies coalescent (MSC) model. However, the MSC makes strong assumptions about divergence history and population structure, and when using the full Bayesian implementation, current computational limits mean that relatively few loci and samples can be analysed for even modest sized radiations. We explore these issues through analyses of an extensive (> 1000 loci) dataset for the Australian rainbow skinks. This group consists of 3 genera and 41 described species, which likely diversified rapidly in Australia during the mid-late Miocene to occupy rainforest, woodland, and rocky habitats with corresponding diversity of morphology and breeding colouration. Previous phylogenetic analyses of this group have revealed short inter-nodes and high discordance among loci, limiting the resolution of inferred trees. A further complication is that many species have deep phylogeographic structure – this poses the question of how to sample individuals within species for analyses using the MSC. Results Phylogenies obtained using concatenation and summary coalescent species tree approaches to the full dataset are well resolved with generally consistent topology, including for previously intractable relationships near the base of the clade. As expected, branch lengths at the tips are substantially overestimated using concatenation. Comparisons of different strategies for sampling haplotypes for full Bayesian MSC analyses (for one clade and using smaller sets of loci) revealed, unexpectedly, that combining haplotypes across divergent phylogeographic lineages yielded consistent species trees. Conclusions This study of more than 1000 loci provides a strongly-supported estimate of the phylogeny of the Australian rainbow skinks, which will inform future research on the evolution and taxonomy of this group. Our analyses suggest that species tree estimation with the MSC can be quite robust to violation of the assumption that the individuals representing a taxon are sampled from a panmictic population. Electronic supplementary material The online version of this article (10.1186/s12862-018-1130-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jason G Bragg
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia. .,Herbarium of NSW, Royal Botanic Gardens & Domain Trust, Sydney, Australia.
| | - Sally Potter
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia
| | - Ana C Afonso Silva
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Conrad J Hoskin
- College of Science & Engineering, James Cook University, Qld, Townsville, 4811, Australia
| | - Benjamin Y H Bai
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia.,Present address: Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Craig Moritz
- Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Canberra, Australia
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Stadler T, Smrckova J. Estimating shifts in diversification rates based on higher-level phylogenies. Biol Lett 2017; 12:rsbl.2016.0273. [PMID: 27703054 PMCID: PMC5095187 DOI: 10.1098/rsbl.2016.0273] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 09/09/2016] [Indexed: 11/27/2022] Open
Abstract
Macroevolutionary studies recently shifted from only reconstructing the past state, i.e. the species phylogeny, to also infer the past speciation and extinction dynamics that gave rise to the phylogeny. Methods for estimating diversification dynamics are sensitive towards incomplete species sampling. We introduce a method to estimate time-dependent diversification rates from phylogenies where clades of a particular age are represented by only one sampled species. A popular example of this type of data is phylogenies on the genus- or family-level, i.e. phylogenies where one species per genus or family is included. We conduct a simulation study to validate our method in a maximum-likelihood framework. Further, this method has already been introduced into the Bayesian package MrBayes, which led to new insights into the evolution of Hymenoptera.
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Affiliation(s)
- Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Jana Smrckova
- Department of Zoology, Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
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30
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Laver RJ, Nielsen SV, Rosauer DF, Oliver PM. Trans-biome diversity in Australian grass-specialist lizards (Diplodactylidae: Strophurus). Mol Phylogenet Evol 2017; 115:62-70. [DOI: 10.1016/j.ympev.2017.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 05/30/2017] [Accepted: 07/13/2017] [Indexed: 11/27/2022]
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31
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Pimentel M, Escudero M, Sahuquillo E, Minaya MÁ, Catalán P. Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene? PeerJ 2017; 5:e3815. [PMID: 28951814 PMCID: PMC5611942 DOI: 10.7717/peerj.3815] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/26/2017] [Indexed: 11/24/2022] Open
Abstract
The Pooideae are a highly diverse C3 grass subfamily that includes some of the most economically important crops, nested within the highly speciose core-pooid clade. Here, we build and explore the phylogeny of the Pooideae within a temporal framework, assessing its patterns of diversification and its chromosomal evolutionary changes in the light of past environmental transformations. We sequenced five plastid DNA loci, two coding (ndhF, matk) and three non-coding (trnH-psbA, trnT-L and trnL-F), in 163 Poaceae taxa, including representatives for all subfamilies of the grasses and all but four ingroup Pooideae tribes. Parsimony and Bayesian phylogenetic analyses were conducted and divergence times were inferred in BEAST using a relaxed molecular clock. Diversification rates were assessed using the MEDUSA approach, and chromosome evolution was analyzed using the chromEvol software. Diversification of the Pooideae started in the Late-Eocene and was especially intense during the Oligocene-Miocene. The background diversification rate increased significantly at the time of the origin of the Poodae + Triticodae clade. This shift in diversification occurred in a context of falling temperatures that potentially increased ecological opportunities for grasses adapted to open areas around the world. The base haploid chromosome number n = 7 has remained stable throughout the phylogenetic history of the core pooids and we found no link between chromosome transitions and major diversification events in the Pooideae.
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Affiliation(s)
- Manuel Pimentel
- Evolutionary Biology Research Group (GIBE), Department of Biology, University of A Coruña, A Coruña, Galicia, Spain
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Sevilla, Sevilla, Andalucía, Spain
| | - Elvira Sahuquillo
- Evolutionary Biology Research Group (GIBE), Department of Biology, University of A Coruña, A Coruña, Galicia, Spain
| | - Miguel Ángel Minaya
- Department of Molecular Microbiology and Immunology, St. Louis University, Saint Louis, MO, United States of America
| | - Pilar Catalán
- High Polytechnic School of Huesca, University of Zaragoza, Huesca, Aragón, Spain.,Department of Botany, Institute of Biology, Tomsk State University, Tomsk, Russia
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32
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Owen CL, Marshall DC, Hill KBR, Simon C. How the Aridification of Australia Structured the Biogeography and Influenced the Diversification of a Large Lineage of Australian Cicadas. Syst Biol 2017; 66:569-589. [PMID: 28123112 DOI: 10.1093/sysbio/syw078] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 08/24/2016] [Indexed: 11/14/2022] Open
Abstract
Over the last 30 million years, Australia's landscape has undergone dramatic cooling and drying due to the establishment of the Antarctic Circumpolar Current and change in global CO$_{2}$ levels. Studies have shown that many Australian organisms went extinct during these major cooling events, while others experienced adaptive radiations and increases in diversification rates as a result of exploiting new niches in the arid zone. Despite the many studies on diversification and biogeography in Australia, few have been continent-wide and none have focused on a group of organisms adapted to feeding on plants. We studied 162 species of cicadas in the Australian Pauropsalta complex, a large generic lineage within the tribe Cicadettini. We asked whether there were changes in the diversification rate of Pauropsalta over time and if so: 1) which clades were associated with the rate change? 2) did timing of rate shifts correspond to known periods of dramatic historical climate change, 3) did increases in diversification rate along select lineages correspond to adaptive radiations with movement into the arid zone? To address these questions, we estimated a molecular phylogeny of the Pauropsalta complex using ${\sim}$5300 bp of nucleotide sequence data distributed among five loci (one mtDNA locus and four nDNA loci). We found that this large group of cicadas did not diversify at a constant rate as they spread through Australia; instead the signature of decreasing diversification rate changed roughly around the time of the expansion of the east Antarctic ice sheets ${\sim}$16 Ma and the glaciation of the northern hemisphere ${\sim}$3 Ma. Unlike other Australian taxa, the Pauropsalta complex did not explosively radiate in response to an early invasion of the arid zone. Instead multiple groups invaded the arid zone and experienced rates of diversification similar to mesic-distributed taxa. We found evidence for relictual groups, located in pre-Mesozoic habitat, that have not diversified and continue to reside on mesic hosts in isolated "habitat islands". Future work should focus on groups of similar ages with similar distribution patterns to determine whether this tempo and pattern of diversification and biogeography is consistent with evidence from other phytophagous insects.
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Affiliation(s)
- Christopher L Owen
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA.,Computational Biology Institute, George Washington University, Innovation Hall, Suite 305, 45085 University Drive, Ashburn, VA 20147-2766, USA
| | - David C Marshall
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
| | - Kathy B R Hill
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, CT 06269-3043, USA
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33
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Rix MG, Cooper SJ, Meusemann K, Klopfstein S, Harrison SE, Harvey MS, Austin AD. Post-Eocene climate change across continental Australia and the diversification of Australasian spiny trapdoor spiders (Idiopidae: Arbanitinae). Mol Phylogenet Evol 2017; 109:302-320. [DOI: 10.1016/j.ympev.2017.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/16/2016] [Accepted: 01/16/2017] [Indexed: 01/08/2023]
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34
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Brennan IG, Oliver PM. Mass turnover and recovery dynamics of a diverse Australian continental radiation. Evolution 2017; 71:1352-1365. [PMID: 28213971 DOI: 10.1111/evo.13207] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 11/29/2022]
Abstract
Trends in global and local climate history have been linked to observed macroevolutionary patterns across a variety of organisms. These climatic pressures may unilaterally or asymmetrically influence the evolutionary trajectory of clades. To test and compare signatures of changing global (Eocene-Oligocene boundary cooling) and continental (Miocene aridification) environments on a continental fauna, we investigated the macroevolutionary dynamics of one of Australia's most diverse endemic radiations, pygopodoid geckos. We generated a time-calibrated phylogeny (>90% taxon coverage) to test whether (i) asymmetrical pygopodoid tree shape may be the result of mass turnover deep in the group's history, and (ii) how Miocene aridification shaped trends in biome assemblages. We find evidence of mass turnover in pygopodoids following the isolation of the Australian continental plate ∼30 million years ago, and in contrast, gradual aridification is linked to elevated speciation rates in the young arid zone. Surprisingly, our results suggest that invasion of arid habitats was not an evolutionary end point. Instead, arid Australia has acted as a source for diversity, with repeated outward dispersals having facilitated diversification of this group. This pattern contrasts trends in richness and distribution of other Australian vertebrates, illustrating the profound effects historical biome changes have on macroevolutionary patterns.
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Affiliation(s)
- Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Paul M Oliver
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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35
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Nagy LG, Házi J, Vágvölgyi C, Papp T. Phylogeny and species delimitation in the genusCoprinelluswith special emphasis on the haired species. Mycologia 2017; 104:254-75. [DOI: 10.3852/11-149] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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36
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Harrington S, Reeder TW. Rate heterogeneity across Squamata, misleading ancestral state reconstruction and the importance of proper null model specification. J Evol Biol 2016; 30:313-325. [DOI: 10.1111/jeb.13004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/24/2016] [Accepted: 10/24/2016] [Indexed: 11/29/2022]
Affiliation(s)
- S. Harrington
- Department of Biology; San Diego State University; San Diego CA USA
- Department of Biology; University of California; Riverside CA USA
| | - T. W. Reeder
- Department of Biology; San Diego State University; San Diego CA USA
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37
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Sánchez-García M, Matheny PB. Is the switch to an ectomycorrhizal state an evolutionary key innovation in mushroom-forming fungi? A case study in the Tricholomatineae (Agaricales). Evolution 2016; 71:51-65. [PMID: 27767208 DOI: 10.1111/evo.13099] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 10/05/2016] [Accepted: 10/10/2016] [Indexed: 01/31/2023]
Abstract
Although fungi are one of the most diverse groups of organisms, little is known about the processes that shape their high taxonomic diversity. This study focuses on evolution of ectomycorrhizal (ECM) mushroom-forming fungi, symbiotic associates of many trees and shrubs, in the suborder Tricholomatineae of the Agaricales. We used the BiSSE model and BAMM to test the hypothesis that the ECM habit represents an evolutionary key innovation that allowed the colonization of new niches followed by an increase in diversification rate. Ancestral state reconstruction (ASR) supports the ancestor of the Tricholomatineae as non-ECM. We detected two diversification rate increases in the genus Tricholoma and the Rhodopolioid clade of the genus Entoloma. However, no increases in diversification were detected in the four other ECM clades of Tricholomatineae. We suggest that diversification of Tricholoma was not only due to the evolution of the ECM lifestyle, but also to the expansion and dominance of its main hosts and ability to associate with a variety of hosts. Diversification in the Rhodopolioid clade could be due to the unique combination of spore morphology and ECM habit. The spore morphology may represent an exaptation that aided spore dispersal and colonization. This is the first study to investigate rate shifts across a phylogeny that contains both non-ECM and ECM lineages.
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Affiliation(s)
- Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee, 37996-1610.,Current Address: Biology Department, Clark University, Worcester, Massachusetts, 01610
| | - Patrick Brandon Matheny
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, Tennessee, 37996-1610
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38
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Oliver PM, McDonald PJ. Young relicts and old relicts: a novel palaeoendemic vertebrate from the Australian Central Uplands. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160018. [PMID: 27853534 PMCID: PMC5098959 DOI: 10.1098/rsos.160018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
Climatic change, and in particular aridification, has played a dominant role in shaping Southern Hemisphere biotas since the mid-Neogene. In Australia, ancient and geologically stable ranges within the vast arid zone have functioned as refugia for populations of mesic taxa extirpated from surrounding areas, yet the extent to which relicts may be linked to major aridification events before or after the Pliocene has not been examined in detail. Here we use molecular phylogenetic and morphological data to show that isolated populations of saxicoline geckos in the genus Oedura from the Australian Central Uplands, formerly confounded as a single taxon, actually comprise two divergent species with contrasting histories of isolation. The recently resurrected Oedura cincta has close relatives occurring elsewhere in the Australian arid biomes with estimated divergence dates concentrated in the early Pliocene. A new taxon (described herein) diverged from all extant Oedura much earlier, well before the end of the Miocene. A review of data for Central Uplands endemic vertebrates shows that for most (including Oedura cincta), gene flow with other parts of Australia probably occurred until at least the very late Miocene or Pliocene. There are, however, a small number of palaeoendemic taxa-often ecologically specialized forms-that show evidence of having persisted since earlier intensification of aridity in the late Miocene.
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Affiliation(s)
- Paul M. Oliver
- Division of Evolution, Ecology and Genetics, Research School of Biology and Centre for Biodiversity Analysis, The Australian National University, Building 116, Daley Road, Acton, Australian Capital Territory 2601, Australia
| | - Peter J. McDonald
- Flora and Fauna Division, Department of Land Resource Management, Alice Springs, Northern Territory 0870, Australia
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39
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Frenzke L, Goetghebeur P, Neinhuis C, Samain MS, Wanke S. Evolution of Epiphytism and Fruit Traits Act Unevenly on the Diversification of the Species-Rich Genus Peperomia (Piperaceae). FRONTIERS IN PLANT SCIENCE 2016; 7:1145. [PMID: 27555851 PMCID: PMC4977276 DOI: 10.3389/fpls.2016.01145] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 07/18/2016] [Indexed: 05/23/2023]
Abstract
The species-rich genus Peperomia (Black Pepper relatives) is the only genus among early diverging angiosperms where epiphytism evolved. The majority of fruits of Peperomia release sticky secretions or exhibit hook-shaped appendages indicative of epizoochorous dispersal, which is in contrast to other flowering plants, where epiphytes are generally characterized by fruit morphological adaptations for anemochory or endozoochory. We investigate fruit characters using Cryo-SEM. Comparative phylogenetic analyses are applied for the first time to include life form and fruit character information to study diversification in Peperomia. Likelihood ratio tests uncover correlated character evolution. We demonstrate that diversification within Peperomia is not homogenous across its phylogeny, and that net diversification rates increase by twofold within the most species-rich subgenus. In contrast to former land plant studies that provide general evidence for increased diversification in epiphytic lineages, we demonstrate that the evolution of epiphytism within Peperomia predates the diversification shift. An epiphytic-dependent diversification is only observed for the background phylogeny. An elevated frequency of life form transitions between epiphytes and terrestrials and thus evolutionary flexibility of life forms is uncovered to coincide with the diversification shift. The evolution of fruits showing dispersal related structures is key to diversification in the foreground region of the phylogeny and postdates the evolution of epiphytism. We conclude that the success of Peperomia, measured in species numbers, is likely the result of enhanced vertical and horizontal dispersal ability and life form flexibility but not the evolution of epiphytism itself.
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Affiliation(s)
- Lena Frenzke
- Department of Biology, Institut für Botanik, Technische Universität DresdenDresden, Germany
| | - Paul Goetghebeur
- Department of Biology, Research Group Spermatophytes, Ghent UniversityGent, Belgium
| | - Christoph Neinhuis
- Department of Biology, Institut für Botanik, Technische Universität DresdenDresden, Germany
| | | | - Stefan Wanke
- Department of Biology, Institut für Botanik, Technische Universität DresdenDresden, Germany
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40
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Papadopoulou A, Knowles LL. Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses. Proc Natl Acad Sci U S A 2016; 113:8018-24. [PMID: 27432974 PMCID: PMC4961141 DOI: 10.1073/pnas.1601069113] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
For three decades, comparative phylogeography has conceptually and methodologically relied on the concordance criterion for providing insights into the historical/biogeographic processes driving population genetic structure and divergence. Here we discuss how this emphasis, and the corresponding lack of methods for extracting information about biotic/intrinsic contributions to patterns of genetic variation, may bias our general understanding of the factors driving genetic structure. Specifically, this emphasis has promoted a tendency to attribute discordant phylogeographic patterns to the idiosyncracies of history, as well as an adherence to generic null expectations of concordance with reduced predictive power. We advocate that it is time for a paradigm shift in comparative phylogeography, especially given the limited utility of the concordance criterion as genomic data provide ever-increasing levels of resolution. Instead of adhering to the concordance-discordance dichotomy, comparative phylogeography needs to emphasize the contribution of taxon-specific traits that will determine whether concordance is a meaningful criterion for evaluating hypotheses or may predict discordant phylogeographic structure. Through reference to some case studies we illustrate how refined hypotheses based on taxon-specific traits can provide improved predictive frameworks to forecast species responses to climatic change or biogeographic barriers while gaining unique insights about the taxa themselves and their interactions with their environment. We outline a potential avenue toward a synthetic comparative phylogeographic paradigm that includes addressing some important conceptual and methodological challenges related to study design and application of model-based approaches for evaluating support of trait-based hypotheses under the proposed paradigm.
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Affiliation(s)
- Anna Papadopoulou
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109; Department of Integrative Ecology, Estación Biológica de Doñana, Consejo Superior de Investigaciones Cientificas, 41092 Seville, Spain
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109;
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41
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Yuan ZY, Zhou WW, Chen X, Poyarkov NA, Chen HM, Jang-Liaw NH, Chou WH, Matzke NJ, Iizuka K, Min MS, Kuzmin SL, Zhang YP, Cannatella DC, Hillis DM, Che J. Spatiotemporal Diversification of the True Frogs (GenusRana): A Historical Framework for a Widely Studied Group of Model Organisms. Syst Biol 2016; 65:824-42. [DOI: 10.1093/sysbio/syw055] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 05/31/2015] [Indexed: 11/12/2022] Open
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42
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Lagomarsino LP, Condamine FL, Antonelli A, Mulch A, Davis CC. The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae). THE NEW PHYTOLOGIST 2016; 210:1430-42. [PMID: 26990796 PMCID: PMC4950005 DOI: 10.1111/nph.13920] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/26/2016] [Indexed: 05/07/2023]
Abstract
The tropical Andes of South America, the world's richest biodiversity hotspot, are home to many rapid radiations. While geological, climatic, and ecological processes collectively explain such radiations, their relative contributions are seldom examined within a single clade. We explore the contribution of these factors by applying a series of diversification models that incorporate mountain building, climate change, and trait evolution to the first dated phylogeny of Andean bellflowers (Campanulaceae: Lobelioideae). Our framework is novel for its direct incorporation of geological data on Andean uplift into a macroevolutionary model. We show that speciation and extinction are differentially influenced by abiotic factors: speciation rates rose concurrently with Andean elevation, while extinction rates decreased during global cooling. Pollination syndrome and fruit type, both biotic traits known to facilitate mutualisms, played an additional role in driving diversification. These abiotic and biotic factors resulted in one of the fastest radiations reported to date: the centropogonids, whose 550 species arose in the last 5 million yr. Our study represents a significant advance in our understanding of plant evolution in Andean cloud forests. It further highlights the power of combining phylogenetic and Earth science models to explore the interplay of geology, climate, and ecology in generating the world's biodiversity.
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Affiliation(s)
- Laura P. Lagomarsino
- Department of Organismic and Evolutionary BiologyHarvard University HerbariaHarvard UniversityCambridgeMA02138USA
| | - Fabien L. Condamine
- Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSE 405 30Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of GothenburgGöteborgSE 405 30Sweden
- Gothenburg Botanical GardenGöteborgSE 413 19Sweden
| | - Andreas Mulch
- Senckenberg Biodiversity and Climate Research Centre (BiK‐F)SenckenbergFrankfurt/Main60325Germany
- Institute for GeosciencesGoethe University FrankfurtFrankfurt/Main60438Germany
| | - Charles C. Davis
- Department of Organismic and Evolutionary BiologyHarvard University HerbariaHarvard UniversityCambridgeMA02138USA
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43
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May MR, Höhna S, Moore BR. A Bayesian approach for detecting the impact of mass‐extinction events on molecular phylogenies when rates of lineage diversification may vary. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12563] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Michael R. May
- Department of Evolution and Ecology University of California Davis CA95616USA
| | - Sebastian Höhna
- Department of Evolution and Ecology University of California Davis CA95616USA
- Department of Integrative Biology University of California Berkeley CA94720USA
- Department of Statistics University of California Berkeley CA94720USA
- Department of Mathematics Stockholm University Stockholm SE‐106 91Sweden
| | - Brian R. Moore
- Department of Evolution and Ecology University of California Davis CA95616USA
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44
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Chen Y. Does the diversification rate of endemic birds of mainland China follow abrupt, gradual shifting or constant patterns? Integr Zool 2016; 12:165-171. [PMID: 27135435 DOI: 10.1111/1749-4877.12205] [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: 11/29/2022]
Abstract
In this brief report, time-varying (including both gradual and abrupt change) and time-constant diversification models are fitted on a phylogeny of endemic birds of mainland China to test the diversification patterns of endemic birds in the region. The results show that phylogeny of endemic birds is best quantified by a constant-rate diversification model through model comparison. Limitations of the study are discussed. In particular, ignorance of non-endemic taxa and the limited sampling of endemic taxa could influence the conclusions of the study.
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Affiliation(s)
- Youhua Chen
- Department of Renewable Resources, University of Alberta, Edmonton, Canada
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May MR, Moore BR. How Well Can We Detect Lineage-Specific Diversification-Rate Shifts? A Simulation Study of Sequential AIC Methods. Syst Biol 2016; 65:1076-1084. [PMID: 27037081 PMCID: PMC5066061 DOI: 10.1093/sysbio/syw026] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/25/2016] [Indexed: 11/26/2022] Open
Abstract
Evolutionary biologists have long been fascinated by the extreme differences in species numbers across branches of the Tree of Life. This has motivated the development of statistical methods for detecting shifts in the rate of lineage diversification across the branches of phylogenic trees. One of the most frequently used methods, MEDUSA, explores a set of diversification-rate models, where each model assigns branches of the phylogeny to a set of diversification-rate categories. Each model is first fit to the data, and the Akaike information criterion (AIC) is then used to identify the optimal diversification model. Surprisingly, the statistical behavior of this popular method is uncharacterized, which is a concern in light of: (1) the poor performance of the AIC as a means of choosing among models in other phylogenetic contexts; (2) the ad hoc algorithm used to visit diversification models, and; (3) errors that we reveal in the likelihood function used to fit diversification models to the phylogenetic data. Here, we perform an extensive simulation study demonstrating that MEDUSA (1) has a high false-discovery rate (on average, spurious diversification-rate shifts are identified ≈30% of the time), and (2) provides biased estimates of diversification-rate parameters. Understanding the statistical behavior of MEDUSA is critical both to empirical researchers—in order to clarify whether these methods can make reliable inferences from empirical datasets—and to theoretical biologists—in order to clarify the specific problems that need to be solved in order to develop more reliable approaches for detecting shifts in the rate of lineage diversification. [Akaike information criterion; extinction; lineage-specific diversification rates; phylogenetic model selection; speciation.]
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Affiliation(s)
- Michael R May
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
| | - Brian R Moore
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
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Pulido-Santacruz P, Weir JT. Extinction as a driver of avian latitudinal diversity gradients. Evolution 2016; 70:860-72. [DOI: 10.1111/evo.12899] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 12/22/2022]
Affiliation(s)
| | - Jason T. Weir
- Current Address: Department of Ecology and Evolutionary Biology; University of Toronto; 1265 Military Trail Scarborough Ontario M1C 1A4 Canada
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario Canada
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Sanmartín I, Meseguer AS. Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage. Front Genet 2016; 7:35. [PMID: 27047538 PMCID: PMC4802293 DOI: 10.3389/fgene.2016.00035] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 02/29/2016] [Indexed: 01/03/2023] Open
Abstract
Global climate change and its impact on biodiversity levels have made extinction a relevant topic in biological research. Yet, until recently, extinction has received less attention in macroevolutionary studies than speciation; the reason is the difficulty to infer an event that actually eliminates rather than creates new taxa. For example, in biogeography, extinction has often been seen as noise, introducing homoplasy in biogeographic relationships, rather than a pattern-generating process. The molecular revolution and the possibility to integrate time into phylogenetic reconstructions have allowed studying extinction under different perspectives. Here, we review phylogenetic (temporal) and biogeographic (spatial) approaches to the inference of extinction and the challenges this process poses for reconstructing evolutionary history. Specifically, we focus on the problem of discriminating between alternative high extinction scenarios using time trees with only extant taxa, and on the confounding effect introduced by asymmetric spatial extinction – different rates of extinction across areas – in biogeographic inference. Finally, we identify the most promising avenues of research in both fields, which include the integration of additional sources of evidence such as the fossil record or environmental information in birth–death models and biogeographic reconstructions, the development of new models that tie extinction rates to phenotypic or environmental variation, or the implementation within a Bayesian framework of parametric non-stationary biogeographic models.
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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
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Uribe-Convers S, Tank DC. Shifts in diversification rates linked to biogeographic movement into new areas: An example of a recent radiation in the Andes. AMERICAN JOURNAL OF BOTANY 2015; 102:1854-69. [PMID: 26542843 DOI: 10.3732/ajb.1500229] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/24/2015] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Clade-specific bursts in diversification are often associated with the evolution of key innovations. However, in groups with no obvious morphological innovations, observed upticks in diversification rates have also been attributed to the colonization of a new geographic environment. In this study, we explore the systematics, diversification dynamics, and historical biogeography of the plant clade Rhinantheae in the Orobanchaceae, with a special focus on the Andean clade of the genus Bartsia. METHODS We sampled taxa from across Rhinantheae, including a representative sample of Andean Bartsia species. Using standard phylogenetic methods, we reconstructed evolutionary relationships, inferred divergence times among the clades of Rhinantheae, elucidated their biogeographic history, and investigated diversification dynamics. KEY RESULTS We confirmed that the South American Bartsia species form a highly supported monophyletic group. The median crown age of Rhinantheae was determined to be ca. 30 Myr, and Europe played an important role in the biogeographic history of the lineages. South America was first reconstructed in the biogeographic analyses around 9 Myr ago, and with a median age of 2.59 Myr, this clade shows a significant uptick in diversification. CONCLUSIONS Increased net diversification of the South American clade corresponds to biogeographic movement into the New World. This movement happened at a time when the Andes were reaching the necessary elevation to host an alpine environment. Although a specific route could not be identified with certainty, we provide plausible hypotheses to how the group colonized the New World.
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Affiliation(s)
- Simon Uribe-Convers
- Department of Biological Sciences, University of Idaho, 875 Perimeter MS 3051, Moscow, Idaho 83844-3051, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter MS 3051, Moscow, Idaho 83844-3051, USA
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Marshall DC, Hill KBR, Moulds M, Vanderpool D, Cooley JR, Mohagan AB, Simon C. Inflation of Molecular Clock Rates and Dates: Molecular Phylogenetics, Biogeography, and Diversification of a Global Cicada Radiation from Australasia (Hemiptera: Cicadidae: Cicadettini). Syst Biol 2015; 65:16-34. [PMID: 26493828 DOI: 10.1093/sysbio/syv069] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 09/17/2015] [Indexed: 11/13/2022] Open
Abstract
Dated phylogenetic trees are important for studying mechanisms of diversification, and molecular clocks are important tools for studies of organisms lacking good fossil records. However, studies have begun to identify problems in molecular clock dates caused by uncertainty of the modeled molecular substitution process. Here we explore Bayesian relaxed-clock molecular dating while studying the biogeography of ca. 200 species from the global cicada tribe Cicadettini. Because the available fossils are few and uninformative, we calibrate our trees in part with a cytochrome oxidase I (COI) clock prior encompassing a range of literature estimates for arthropods. We show that tribe-level analyses calibrated solely with the COI clock recover extremely old dates that conflict with published estimates for two well-studied New Zealand subclades within Cicadettini. Additional subclade analyses suggest that COI relaxed-clock rates and maximum-likelihood branch lengths become inflated relative to EF-1[Formula: see text] intron and exon rates and branch lengths as clade age increases. We present corrected estimates derived from: (i) an extrapolated EF-1[Formula: see text] exon clock derived from COI-calibrated analysis within the largest New Zealand subclade; (ii) post hoc scaling of the tribe-level chronogram using results from subclade analyses; and (iii) exploitation of a geological calibration point associated with New Caledonia. We caution that considerable uncertainty is generated due to dependence of substitution estimates on both the taxon sample and the choice of model, including gamma category number and the choice of empirical versus estimated base frequencies. Our results suggest that diversification of the tribe Cicadettini commenced in the early- to mid-Cenozoic and continued with the development of open, arid habitats in Australia and worldwide. We find that Cicadettini is a rare example of a global terrestrial animal group with an Australasian origin, with all non-Australasian genera belonging to two distal clades. Within Australia, we show that Cicadettini is more widely distributed than any other cicada tribe, diverse in temperate, arid and monsoonal habitats, and nearly absent from rainforests. We comment on the taxonomic implications of our findings for thirteen cicada genera.
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Affiliation(s)
- David C Marshall
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA;
| | - Kathy B R Hill
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA
| | - Max Moulds
- Entomology Department, Australian Museum, 6 College Street, Sydney NSW 2010, Australia
| | - Dan Vanderpool
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA; Division of Biological Sciences, Health Sciences 304, U. Montana, Missoula, MT 59812
| | - John R Cooley
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA
| | - Alma B Mohagan
- Central Mindanao University, Sayre Highway, Bukidnon, Philippines
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, 75 N. Eagleville Rd., Storrs, CT 06269, USA
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50
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Cox CL, Cox RM. Evolutionary shifts in habitat aridity predict evaporative water loss across squamate reptiles. Evolution 2015; 69:2507-16. [DOI: 10.1111/evo.12742] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 06/26/2015] [Accepted: 07/13/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Christian L. Cox
- Department of Biology; Georgia Southern University; Statesboro Georgia 30458
- Department of Biology; University of Virginia; Charlottesville Virginia 22904
| | - Robert M. Cox
- Department of Biology; Georgia Southern University; Statesboro Georgia 30458
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