101
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Tran LAP. The role of ecological opportunity in shaping disparate diversification trajectories in a bicontinental primate radiation. Proc Biol Sci 2014; 281:20131979. [PMID: 24598417 DOI: 10.1098/rspb.2013.1979] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Exceptional species and phenotypic diversity commonly are attributed to ecological opportunity (EO). The conventional EO model predicts that rates of lineage diversification and phenotypic evolution are elevated early in a radiation only to decline later in response to niche availability. Foregut fermentation is hypothesized to be a key innovation that allowed colobine monkeys (subfamily Colobinae), the only primates with this trait, to successfully colonize folivore adaptive zones unavailable to other herbivorous species. Therefore, diversification rates also are expected to be strongly linked with the evolution of traits related to folivory in these monkeys. Using dated molecular phylogenies and a dataset of feeding morphology, I test predictions of the EO model to evaluate the role of EO conferred by foregut fermentation in shaping the African and Asian colobine radiations. Findings from diversification methods coupled with colobine biogeographic history provide compelling evidence that decreasing availability of new adaptive zones during colonization of Asia together with constraints presented by dietary specialization underlie temporal changes in diversification in the Asian but not African clade. Additionally, departures from the EO model likely reflect iterative diversification events in Asia.
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Affiliation(s)
- Lucy A P Tran
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, , 1109 Geddes Avenue, Ann Arbor, MI 48109-1079, USA
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102
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Ecology limits the diversity of the Cape flora: Phylogenetics and diversification of the genus Tetraria. Mol Phylogenet Evol 2014; 72:61-70. [DOI: 10.1016/j.ympev.2013.11.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/18/2013] [Accepted: 11/26/2013] [Indexed: 11/18/2022]
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103
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Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes. PLoS One 2014; 9:e88805. [PMID: 24586399 PMCID: PMC3930666 DOI: 10.1371/journal.pone.0088805] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/16/2014] [Indexed: 12/05/2022] Open
Abstract
Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process.
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104
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Santini F, Carnevale G, Sorenson L. First multi-locus timetree of seabreams and porgies (Percomorpha: Sparidae). ACTA ACUST UNITED AC 2014. [DOI: 10.1080/11250003.2013.878960] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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105
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Price SL, Powell S, Kronauer DJC, Tran LAP, Pierce NE, Wayne RK. Renewed diversification is associated with new ecological opportunity in the Neotropical turtle ants. J Evol Biol 2014; 27:242-58. [PMID: 24417316 DOI: 10.1111/jeb.12300] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 11/12/2013] [Indexed: 01/03/2023]
Abstract
Ecological opportunity, defined as access to new resources free from competitors, is thought to be a catalyst for the process of adaptive radiation. Much of what we know about ecological opportunity, and the larger process of adaptive radiation, is derived from vertebrate diversification on islands. Here, we examine lineage diversification in the turtle ants (Cephalotes), a species-rich group of ants that has diversified throughout the Neotropics. We show that crown group turtle ants originated during the Eocene (around 46 mya), coincident with global warming and the origin of many other clades. We also show a marked lineage-wide slowdown in diversification rates in the Miocene. Contrasting this overall pattern, a species group associated with the young and seasonally harsh Chacoan biogeographic region underwent a recent burst of diversification. Subsequent analyses also indicated that there is significant phylogenetic clustering within the Chacoan region and that speciation rates are highest there. Together, these findings suggest that recent ecological opportunity, from successful colonization of novel habitat, may have facilitated renewed turtle ant diversification. Our findings highlight a central role of ecological opportunity within a successful continental radiation.
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Affiliation(s)
- S L Price
- Department of Biological Sciences, George Washington University, Washington, DC, USA; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
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106
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Derryberry EP, Derryberry GE, Maley JM, Brumfield RT. hzar: hybrid zone analysis using an R software package. Mol Ecol Resour 2013; 14:652-63. [DOI: 10.1111/1755-0998.12209] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Elizabeth P. Derryberry
- Department of Ecology and Evolutionary Biology; Tulane University; New Orleans LA 70118 USA
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
| | | | - James M. Maley
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
- Moore Laboratory of Zoology; Occidental College; 1600 Campus Road Los Angeles, CA 90041 USA
| | - Robb T. Brumfield
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
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107
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Hollingsworth PR, Simons AM, Fordyce JA, Hulsey CD. Explosive diversification following a benthic to pelagic shift in freshwater fishes. BMC Evol Biol 2013; 13:272. [PMID: 24341464 PMCID: PMC3880099 DOI: 10.1186/1471-2148-13-272] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 12/11/2013] [Indexed: 12/05/2022] Open
Abstract
Background Interspecific divergence along a benthic to pelagic habitat axis is ubiquitous in freshwater fishes inhabiting lentic environments. In this study, we examined the influence of this habitat axis on the macroevolution of a diverse, lotic radiation using mtDNA and nDNA phylogenies for eastern North America’s most species-rich freshwater fish clade, the open posterior myodome (OPM) cyprinids. We used ancestral state reconstruction to identify the earliest benthic to pelagic transition in this group and generated fossil-calibrated estimates of when this shift occurred. This transition could have represented evolution into a novel adaptive zone, and therefore, we tested for a period of accelerated lineage accumulation after this historical habitat shift. Results Ancestral state reconstructions inferred a similar and concordant region of our mtDNA and nDNA based gene trees as representing the shift from benthic to pelagic habitats in the OPM clade. Two independent tests conducted on each gene tree suggested an increased diversification rate after this inferred habitat transition. Furthermore, lineage through time analyses indicated rapid early cladogenesis in the clade arising after the benthic to pelagic shift. Conclusions A burst of diversification followed the earliest benthic to pelagic transition during the radiation of OPM cyprinids in eastern North America. As such, the benthic/pelagic habitat axis has likely influenced the generation of biodiversity across disparate freshwater ecosystems.
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Affiliation(s)
- Phillip R Hollingsworth
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN 37996, USA.
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108
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Modeling lineage and phenotypic diversification in the New World monkey (Platyrrhini, Primates) radiation. Mol Phylogenet Evol 2013; 82 Pt B:375-85. [PMID: 24287474 DOI: 10.1016/j.ympev.2013.11.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 10/24/2013] [Accepted: 11/15/2013] [Indexed: 11/19/2022]
Abstract
Adaptive radiations that have taken place in the distant past can now be more thoroughly studied with the availability of large molecular phylogenies and comparative data drawn from extant and fossil species. Platyrrhines are a good example of a major mammalian evolutionary radiation confined to a single continent, involving a relatively large temporal scale and documented by a relatively small but informative fossil record. Here, we present comparative evidence using data on extant and fossil species to explore alternative evolutionary models in an effort to better understand the process of platyrrhine lineage and phenotypic diversification. Specifically, we compare the likelihood of null models of lineage and phenotypic diversification versus various models of adaptive evolution. Moreover, we statistically explore the main ecological dimension behind the platyrrhine diversification. Contrary to the previous proposals, our study did not find evidence of a rapid lineage accumulation in the phylogenetic tree of extant platyrrhine species. However, the fossil-based diversity curve seems to show a slowdown in diversification rates toward present times. This also suggests an early high rate of extinction among lineages within crown Platyrrhini. Finally, our analyses support the hypothesis that the platyrrhine phenotypic diversification appears to be characterized by an early and profound differentiation in body size related to a multidimensional niche model, followed by little subsequent change (i.e., stasis).
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109
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Pyron RA, Burbrink FT. Phylogenetic estimates of speciation and extinction rates for testing ecological and evolutionary hypotheses. Trends Ecol Evol 2013; 28:729-36. [PMID: 24120478 DOI: 10.1016/j.tree.2013.09.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 09/03/2013] [Accepted: 09/15/2013] [Indexed: 10/26/2022]
Abstract
Phylogenies are used to estimate rates of speciation and extinction, reconstruct historical diversification scenarios, and link these to ecological and evolutionary factors, such as climate or organismal traits. Recent models can now estimate the effects of binary, multistate, continuous, and biogeographic characters on diversification rates. Others test for diversity dependence (DD) in speciation and extinction, which has become recognized as an important process in numerous clades. A third class incorporates flexible time-dependent functions, enabling reconstruction of major periods of both expanding and contracting diversity. Although there are some potential problems (particularly for estimating extinction), these methods hold promise for answering many classic questions in ecology and evolution, such as the origin of adaptive radiations, and the latitudinal gradient in species richness.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, 2023 G St. NW, Washington, DC 20052, USA.
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110
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Bidegaray-Batista L, Ferrández MÁ, Arnedo MA. Winter is coming: Miocene and Quaternary climatic shifts shaped the diversification of Western-MediterraneanHarpactocrates(Araneae, Dysderidae) spiders. Cladistics 2013; 30:428-446. [DOI: 10.1111/cla.12054] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2013] [Indexed: 01/26/2023] Open
Affiliation(s)
- Leticia Bidegaray-Batista
- Institut de Recerca de la Biodiversitat and Departament de Biologia Animal; Universitat de Barcelona; Av. Diagonal 643 Barcelona 08028 Spain
| | - Miguel Á. Ferrández
- Sociedad para el Estudio y la Conservación de las Arañas; c/Villafranca 24, 1_C Madrid 28028 Spain
| | - Miquel A. Arnedo
- Institut de Recerca de la Biodiversitat and Departament de Biologia Animal; Universitat de Barcelona; Av. Diagonal 643 Barcelona 08028 Spain
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111
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Schenk JJ, Rowe KC, Steppan SJ. Ecological Opportunity and Incumbency in the Diversification of Repeated Continental Colonizations by Muroid Rodents. Syst Biol 2013; 62:837-64. [DOI: 10.1093/sysbio/syt050] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- John J. Schenk
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; and 2Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Kevin C. Rowe
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; and 2Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
| | - Scott J. Steppan
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; and 2Museum Victoria, GPO Box 666, Melbourne, Victoria 3001, Australia
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112
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Lorion J, Kiel S, Faure B, Kawato M, Ho SYW, Marshall B, Tsuchida S, Miyazaki JI, Fujiwara Y. Adaptive radiation of chemosymbiotic deep-sea mussels. Proc Biol Sci 2013; 280:20131243. [PMID: 24048154 PMCID: PMC3779325 DOI: 10.1098/rspb.2013.1243] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adaptive radiations present fascinating opportunities for studying the evolutionary process. Most cases come from isolated lakes or islands, where unoccupied ecological space is filled through novel adaptations. Here, we describe an unusual example of an adaptive radiation: symbiotic mussels that colonized island-like chemosynthetic environments such as hydrothermal vents, cold seeps and sunken organic substrates on the vast deep-sea floor. Our time-calibrated molecular phylogeny suggests that the group originated and acquired sulfur-oxidizing symbionts in the Late Cretaceous, possibly while inhabiting organic substrates and long before its major radiation in the Middle Eocene to Early Oligocene. The first appearance of intracellular and methanotrophic symbionts was detected only after this major radiation. Thus, contrary to expectations, the major radiation may have not been triggered by the evolution of novel types of symbioses. We hypothesize that environmental factors, such as increased habitat availability and/or increased dispersal capabilities, sparked the radiation. Intracellular and methanotrophic symbionts were acquired in several independent lineages and marked the onset of a second wave of diversification at vents and seeps. Changes in habitat type resulted in adaptive trends in shell lengths (related to the availability of space and energy, and physiological trade-offs) and in the successive colonization of greater water depths.
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Affiliation(s)
- Julien Lorion
- Marine Ecosystems Research Department, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), , 2-15 Natsushima, Yokosuka 237-0061, Japan, Geoscience Center, Geobiology Group, University of Göttingen, , Goldschmidtstrasse 3, Göttingen 37077, Germany, Department of Biology, Pennsylvania State University, , University Park, PA 16802, USA, School of Biological Sciences, University of Sydney, , Sydney, New South Wales 2006, Australia, Museum of New Zealand Te Papa Tongarewa, , PO Box 467, 169 Tory St., Te Aro, Wellington 6011, New Zealand, Faculty of Education and Human Sciences, University of Yamanashi, , Kofu, Yamanashi 400-8510, Japan
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113
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Delicado D, Machordom A, Ramos MA. Living on the mountains: Patterns and causes of diversification in the springsnail subgenus Pseudamnicola (Corrosella) (Mollusca: Caenogastropoda: Hydrobiidae). Mol Phylogenet Evol 2013; 68:387-97. [DOI: 10.1016/j.ympev.2013.04.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 04/17/2013] [Accepted: 04/23/2013] [Indexed: 11/30/2022]
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114
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McMahan CD, Chakrabarty P, Sparks JS, Smith WL, Davis MP. Temporal patterns of diversification across global cichlid biodiversity (Acanthomorpha: Cichlidae). PLoS One 2013; 8:e71162. [PMID: 23990936 PMCID: PMC3747193 DOI: 10.1371/journal.pone.0071162] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/01/2013] [Indexed: 11/26/2022] Open
Abstract
The contrasting distribution of species diversity across the major lineages of cichlids makes them an ideal group for investigating macroevolutionary processes. In this study, we investigate whether different rates of diversification may explain the disparity in species richness across cichlid lineages globally. We present the most taxonomically robust time-calibrated hypothesis of cichlid evolutionary relationships to date. We then utilize this temporal framework to investigate whether both species-rich and depauperate lineages are associated with rapid shifts in diversification rates and if exceptional species richness can be explained by clade age alone. A single significant rapid rate shift increase is detected within the evolutionary history of the African subfamily Pseudocrenilabrinae, which includes the haplochromins of the East African Great Lakes. Several lineages from the subfamilies Pseudocrenilabrinae (Australotilapiini, Oreochromini) and Cichlinae (Heroini) exhibit exceptional species richness given their clade age, a net rate of diversification, and relative rates of extinction, indicating that clade age alone is not a sufficient explanation for their increased diversity. Our results indicate that the Neotropical Cichlinae includes lineages that have not experienced a significant rapid burst in diversification when compared to certain African lineages (rift lake). Neotropical cichlids have remained comparatively understudied with regard to macroevolutionary patterns relative to African lineages, and our results indicate that of Neotropical lineages, the tribe Heroini may have an elevated rate of diversification in contrast to other Neotropical cichlids. These findings provide insight into our understanding of the diversification patterns across taxonomically disparate lineages in this diverse clade of freshwater fishes and one of the most species-rich families of vertebrates.
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Affiliation(s)
- Caleb D. McMahan
- LSU Museum of Natural Science (Ichthyology), Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Prosanta Chakrabarty
- LSU Museum of Natural Science (Ichthyology), Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - John S. Sparks
- American Museum of Natural History, Department of Ichthyology, Division of Vertebrate Zoology, New York, New York, United States of America
| | - Wm. Leo Smith
- The Field Museum, Division of Fishes, Chicago, Illinois, United States of America
| | - Matthew P. Davis
- The Field Museum, Division of Fishes, Chicago, Illinois, United States of America
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115
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Moura AE, Nielsen SCA, Vilstrup JT, Moreno-Mayar JV, Gilbert MTP, Gray HWI, Natoli A, Möller L, Hoelzel AR. Recent diversification of a marine genus (Tursiops spp.) tracks habitat preference and environmental change. Syst Biol 2013; 62:865-77. [PMID: 23929779 DOI: 10.1093/sysbio/syt051] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the evolution of diversity and the resulting systematics in marine systems is confounded by the lack of clear boundaries in oceanic habitats, especially for highly mobile species like marine mammals. Dolphin populations and sibling species often show differentiation between coastal and offshore habitats, similar to the pelagic/littoral or benthic differentiation seen for some species of fish. Here we test the hypothesis that lineages within the polytypic genus Tursiops track past changes in the environment reflecting ecological drivers of evolution facilitated by habitat release. We used a known recent time point for calibration (the opening of the Bosphorus) and whole mitochondrial genome (mitogenome) sequences for high phylogenetic resolution. The pattern of lineage formation suggested an origin in Australasia and several early divisions involving forms currently inhabiting coastal habitats. Radiation in pelagic environments was relatively recent, and was likely followed by a return to coastal habitat in some regions. The timing of some nodes defining different ecotypes within the genus clustered near the two most recent interglacial transitions. A signal for an increase in diversification was also seen for dates after the last glacial maximum. Together these data suggest the tracking of habitat preference during geographic expansions, followed by transition points reflecting habitat shifts, which were likely associated with periods of environmental change.
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Affiliation(s)
- Andre E Moura
- School of Biological and Biomedical Sciences, Durham University, South Road, DH1 3LE, UK; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark; Biological Department, UAE University, P.O.Box 17551, Al Ain, UAE; and School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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116
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Li S, He K, Yu FH, Yang QS. Molecular phylogeny and biogeography of Petaurista inferred from the cytochrome b gene, with implications for the taxonomic status of P. caniceps, P. marica and P. sybilla. PLoS One 2013; 8:e70461. [PMID: 23922995 PMCID: PMC3724786 DOI: 10.1371/journal.pone.0070461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 06/24/2013] [Indexed: 11/19/2022] Open
Abstract
The polymorphic genus Petaurista includes a group of diverse species and subspecies that are adapted for gliding and arboreal life. This morphological diversity has resulted in taxonomic discrepancies, and molecular phylogenetic studies have been limited by taxon sampling. To clarify this controversial taxonomy, we used the cytochrome b gene to reconstruct the phylogeny to obtain a more accurate picture of the evolutionary relationships, species differentiation and divergence pattern of Petaurista. The results revealed a significant inconsistency between taxonomic designations, phylogeny and genetic distances. When 6 recognized species were included, species delimitation revealed 15 putative species, a finding that warrants a comprehensive morphological diagnosis and a re-assessment of the species status. The validity of P. caniceps and P. marica was discussed. An estimation of the molecular divergence time demonstrated that the diversification and speciation of Petaurista began during the later Miocene and may have been affected by the uplifting of the Qinghai-Tibet plateau and subsequent climate change.
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Affiliation(s)
- Song Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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117
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Zhang JB, Li RQ, Xiang XG, Manchester SR, Lin L, Wang W, Wen J, Chen ZD. Integrated fossil and molecular data reveal the biogeographic diversification of the eastern Asian-eastern North American disjunct hickory genus (Carya Nutt.). PLoS One 2013; 8:e70449. [PMID: 23875028 PMCID: PMC3713062 DOI: 10.1371/journal.pone.0070449] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 06/18/2013] [Indexed: 12/01/2022] Open
Abstract
The hickory genus (Carya) contains ca. 17 species distributed in subtropical and tropical regions of eastern Asia and subtropical to temperate regions of eastern North America. Previously, the phylogenetic relationships between eastern Asian and eastern North American species of Carya were not fully confirmed even with an extensive sampling, biogeographic and diversification patterns had thus never been investigated in a phylogenetic context. We sampled 17 species of Carya and 15 species representing all other genera of the Juglandaceae as outgroups, with eight nuclear and plastid loci to reconstruct the phylogeny of Carya. The phylogenetic positions of seven extinct genera of the Juglandaceae were inferred using morphological characters and the molecular phylogeny as a backbone constraint. Divergence times within Carya were estimated with relaxed Bayesian dating. Biogeographic analyses were performed in DIVA and LAGRANGE. Diversification rates were inferred by LASER and APE packages. Our results support two major clades within Carya, corresponding to the lineages of eastern Asia and eastern North America. The split between the two disjunct clades is estimated to be 21.58 (95% HPD 11.07-35.51) Ma. Genus-level DIVA and LAGRANGE analyses incorporating both extant and extinct genera of the Juglandaceae suggested that Carya originated in North America, and migrated to Eurasia during the early Tertiary via the North Atlantic land bridge. Fragmentation of the distribution caused by global cooling in the late Tertiary resulted in the current disjunction. The diversification rate of hickories in eastern North America appeared to be higher than that in eastern Asia, which is ascribed to greater ecological opportunities, key morphological innovations, and polyploidy.
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Affiliation(s)
- Jing-Bo Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Guo Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Steven R. Manchester
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Li Lin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America
- * E-mail: (ZDC); (JW)
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- * E-mail: (ZDC); (JW)
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118
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Shedko SV, Miroshnichenko IL, Nemkova GA. Phylogeny of salmonids (salmoniformes: Salmonidae) and its molecular dating: Analysis of mtDNA data. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413060112] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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119
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Litman JR, Praz CJ, Danforth BN, Griswold TL, Cardinal S. Origins, evolution, and diversification of cleptoparasitic lineages in long-tongued bees. Evolution 2013; 67:2982-98. [PMID: 24094348 DOI: 10.1111/evo.12161] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/03/2013] [Indexed: 11/30/2022]
Abstract
The evolution of parasitic behavior may catalyze the exploitation of new ecological niches yet also binds the fate of a parasite to that of its host. It is thus not clear whether evolutionary transitions from free-living organism to parasite lead to increased or decreased rates of diversification. We explore the evolution of brood parasitism in long-tongued bees and find decreased rates of diversification in eight of 10 brood parasitic clades. We propose a pathway for the evolution of brood parasitic strategy and find that a strategy in which a closed host nest cell is parasitized and the host offspring is killed by the adult parasite represents an obligate first step in the appearance of a brood parasitic lineage; this ultimately evolves into a strategy in which an open host cell is parasitized and the host offspring is killed by a specialized larval instar. The transition to parasitizing open nest cells expanded the range of potential hosts for brood parasitic bees and played a fundamental role in the patterns of diversification seen in brood parasitic clades. We address the prevalence of brood parasitic lineages in certain families of bees and examine the evolution of brood parasitism in other groups of organisms.
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Affiliation(s)
- Jessica R Litman
- Department of Entomology, Cornell University, Ithaca, New York, 14853.
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Into the deep: a phylogenetic approach to the bivalve subclass Protobranchia. Mol Phylogenet Evol 2013; 69:188-204. [PMID: 23742885 DOI: 10.1016/j.ympev.2013.05.018] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/14/2013] [Accepted: 05/21/2013] [Indexed: 01/19/2023]
Abstract
A molecular phylogeny of Protobranchia, the subclass of bivalve mollusks sister to the remaining Bivalvia, has long proven elusive, because many constituent lineages are deep-sea endemics, which creates methodological challenges for collecting and preserving genetic material. We obtained 74 representatives of all 12 extant protobranch families and investigated the internal phylogeny of this group using sequence data from five molecular loci (16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, and histone H3). Model-based and dynamic homology parsimony approaches to phylogenetic reconstruction unanimously supported four major clades of Protobranchia, irrespective of treatment of hypervariable regions in the nuclear ribosomal genes 18S rRNA and 28S rRNA. These four clades correspond to the superfamilies Nuculoidea (excluding Sareptidae), Nuculanoidea (including Sareptidae), Solemyoidea, and Manzanelloidea. Salient aspects of the phylogeny include (1) support for the placement of the family Sareptidae with Nuculanoidea; (2) the non-monophyly of the order Solemyida (Solemyidae+Nucinellidae); (3) and the non-monophyly of most nuculoid and nuculanoid genera and families. In light of this first family-level phylogeny of Protobranchia, we present a revised classification of the group. Estimation of divergence times in concert with analyses of diversification rates demonstrate the signature of the end-Permian mass extinction in the phylogeny of extant protobranchs.
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121
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Santini F, Carnevale G, Sorenson L. First molecular scombrid timetree (Percomorpha: Scombridae) shows recent radiation of tunas following invasion of pelagic habitat. ACTA ACUST UNITED AC 2013. [DOI: 10.1080/11250003.2013.775366] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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122
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Moreau CS, Bell CD. TESTING THE MUSEUM VERSUS CRADLE TROPICAL BIOLOGICAL DIVERSITY HYPOTHESIS: PHYLOGENY, DIVERSIFICATION, AND ANCESTRAL BIOGEOGRAPHIC RANGE EVOLUTION OF THE ANTS. Evolution 2013; 67:2240-57. [DOI: 10.1111/evo.12105] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 03/01/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Corrie S. Moreau
- Department of Zoology; Field Museum of Natural History; 1400 South Lake Shore Drive Chicago Illinois 60605
| | - Charles D. Bell
- Department of Biological Sciences; University of New Orleans; 2000 Lakeshore Drive New Orleans Louisiana 70148
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123
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Williams ST, Smith LM, Herbert DG, Marshall BA, Warén A, Kiel S, Dyal P, Linse K, Vilvens C, Kano Y. Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea). Ecol Evol 2013; 3:887-917. [PMID: 23610633 PMCID: PMC3631403 DOI: 10.1002/ece3.513] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 01/30/2013] [Accepted: 02/01/2013] [Indexed: 11/11/2022] Open
Abstract
Recent expeditions have revealed high levels of biodiversity in the tropical deep-sea, yet little is known about the age or origin of this biodiversity, and large-scale molecular studies are still few in number. In this study, we had access to the largest number of solariellid gastropods ever collected for molecular studies, including many rare and unusual taxa. We used a Bayesian chronogram of these deep-sea gastropods (1) to test the hypothesis that deep-water communities arose onshore, (2) to determine whether Antarctica acted as a source of diversity for deep-water communities elsewhere and (3) to determine how factors like global climate change have affected evolution on the continental slope. We show that although fossil data suggest that solariellid gastropods likely arose in a shallow, tropical environment, interpretation of the molecular data is equivocal with respect to the origin of the group. On the other hand, the molecular data clearly show that Antarctic species sampled represent a recent invasion, rather than a relictual ancestral lineage. We also show that an abrupt period of global warming during the Palaeocene Eocene Thermal Maximum (PETM) leaves no molecular record of change in diversification rate in solariellids and that the group radiated before the PETM. Conversely, there is a substantial, although not significant increase in the rate of diversification of a major clade approximately 33.7 Mya, coinciding with a period of global cooling at the Eocene-Oligocene transition. Increased nutrients made available by contemporaneous changes to erosion, ocean circulation, tectonic events and upwelling may explain increased diversification, suggesting that food availability may have been a factor limiting exploitation of deep-sea habitats. Tectonic events that shaped diversification in reef-associated taxa and deep-water squat lobsters in central Indo-West Pacific were also probably important in the evolution of solariellids during the Oligo-Miocene.
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Affiliation(s)
- S T Williams
- Department of Life Sciences, Natural History Museum Cromwell Road, London, SW7 5BD, UK
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124
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Bloom DD, Weir JT, Piller KR, Lovejoy NR. DO FRESHWATER FISHES DIVERSIFY FASTER THAN MARINE FISHES? A TEST USING STATE-DEPENDENT DIVERSIFICATION ANALYSES AND MOLECULAR PHYLOGENETICS OF NEW WORLD SILVERSIDES (ATHERINOPSIDAE). Evolution 2013; 67:2040-57. [DOI: 10.1111/evo.12074] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 02/04/2013] [Indexed: 12/17/2022]
Affiliation(s)
- Devin D. Bloom
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario M1C 1A4 Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Jason T. Weir
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario M1C 1A4 Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Kyle R. Piller
- Department of Biological Sciences; Southeastern Louisiana University; Hammond Louisiana 70402
| | - Nathan R. Lovejoy
- Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario M1C 1A4 Canada
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
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125
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Santini F, Nguyen MTT, Sorenson L, Waltzek TB, Lynch Alfaro JW, Eastman JM, Alfaro ME. Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae). J Evol Biol 2013; 26:1003-18. [DOI: 10.1111/jeb.12112] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 12/18/2012] [Accepted: 12/19/2012] [Indexed: 11/28/2022]
Affiliation(s)
- F. Santini
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
| | - M. T. T. Nguyen
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
| | - L. Sorenson
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
| | - T. B. Waltzek
- Department of Infectious Diseases and Pathology; College of Veterinary Medicine, University of Florida; Gainesville FL USA
| | - J. W. Lynch Alfaro
- Institute for Society and Genetics & Department of Anthropology; University of California Los Angeles; Los Angeles CA USA
| | - J. M. Eastman
- Department of Biological Sciences & the Institute of Bioinformatics and Evolutionary Study; University of Idaho; Moscow ID USA
| | - M. E. Alfaro
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; Los Angeles CA USA
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126
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Day JJ, Peart CR, Brown KJ, Friel JP, Bills R, Moritz T. Continental Diversification of an African Catfish Radiation (Mochokidae: Synodontis). Syst Biol 2013; 62:351-65. [DOI: 10.1093/sysbio/syt001] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Julia J. Day
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - Claire R. Peart
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - Katherine J. Brown
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - John P. Friel
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - Roger Bills
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
| | - Timo Moritz
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK; 2Department of Zoology, The Natural History Museum, Cromwell Road, South Kensington, London SW7 5BD, UK; 3Cornell University Museum of Vertebrates, 159 Sapsucker Woods Road, Ithaca 14850-1923, NY, USA; 4South African Institute for Aquatic Biodiversity, Private Bag 1015, 6140 Grahamstown, South Africa; 5Deutsches Meeresmuseum, Katharinenberg 14–20, 18439 Stralsund, Germany
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127
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van Velzen R, Wahlberg N, Sosef MSM, Bakker FT. Effects of changing climate on species diversification in tropical forest butterflies of the genusCymothoe(Lepidoptera: Nymphalidae). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Robin van Velzen
- Biosystematics Group; Wageningen University; PO box 647 6708PB Wageningen the Netherlands
- Naturalis Biodiversity Centre (Section NHN); Wageningen University; Generaal Foulkesweg 37, 6703 BL Wageningen the Netherlands
| | - Niklas Wahlberg
- Laboratory of Genetics; Department of Biology; University of Turku; Turku 20014 Finland
| | - Marc S. M. Sosef
- Biosystematics Group; Wageningen University; PO box 647 6708PB Wageningen the Netherlands
- Naturalis Biodiversity Centre (Section NHN); Wageningen University; Generaal Foulkesweg 37, 6703 BL Wageningen the Netherlands
| | - Freek T. Bakker
- Biosystematics Group; Wageningen University; PO box 647 6708PB Wageningen the Netherlands
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128
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Le Rouzic A, Payen T, Hua-Van A. Reconstructing the evolutionary history of transposable elements. Genome Biol Evol 2013; 5:77-86. [PMID: 23275488 PMCID: PMC3595040 DOI: 10.1093/gbe/evs130] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2012] [Indexed: 01/03/2023] Open
Abstract
The impact of transposable elements (TEs) on genome structure, plasticity, and evolution is still not well understood. The recent availability of complete genome sequences makes it possible to get new insights on the evolutionary dynamics of TEs from the phylogenetic analysis of their multiple copies in a wide range of species. However, this source of information is not always fully exploited. Here, we show how the history of transposition activity may be qualitatively and quantitatively reconstructed by considering the distribution of transposition events in the phylogenetic tree, along with the tree topology. Using statistical models developed to infer speciation and extinction rates in species phylogenies, we demonstrate that it is possible to estimate the past transposition rate of a TE family, as well as how this rate varies with time. This methodological framework may not only facilitate the interpretation of genomic data, but also serve as a basis to develop new theoretical and statistical models.
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Affiliation(s)
- Arnaud Le Rouzic
- Laboratoire Évolution, Génomes, Spéciation, CNRS-LEGS-UPR9034, CNRS-IDEEV-FR3284, Gif sur Yvette, France.
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129
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Roquet C, Thuiller W, Lavergne S. Building megaphylogenies for macroecology: taking up the challenge. ECOGRAPHY 2013; 36:13-26. [PMID: 24790290 PMCID: PMC4001083 DOI: 10.1111/j.1600-0587.2012.07773.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The last decades have seen an upsurge in ecological studies incorporating phylogenetic information with increasing species samples, motivated by the common conjecture that species with common ancestors should share some ecological characteristics due to niche conservatism. This has been carried out using various methods of increasing complexity and reliability: using only taxonomical classification; constructing supertrees that incorporate only topological information from previously published phylogenies; or building supermatrices of molecular data that are used to estimate phylogenies with evolutionary meaningful branch lengths. Although the latter option is more informative than the others, it remains under-used in ecology because ecologists are generally unaware of or unfamiliar with modern molecular phylogenetic methods. However, a solid phylogenetic hypothesis is necessary to conduct reliable ecological analysis integrating evolutive aspects. Our aim here is to clarify the concepts and methodological issues associated with the reconstruction of dated megaphylogenies, and to show that it is nowadays possible to obtain accurate and well sampled megaphylogenies with informative branch-lengths on large species samples. This is possible thanks to improved phylogenetic methods, vast amounts of molecular data available from databases such as Genbank, and consensus knowledge on deep phylogenetic relationships for an increasing number of groups of organisms. Finally, we include a detailed step-by-step workflow pipeline (Supplementary material), from data acquisition to phylogenetic inference, mainly based on the R environment (widely used by ecologists) and the use of free web-servers, that has been applied to the reconstruction of a species-level phylogeny of all breeding birds of Europe.
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Affiliation(s)
- Cristina Roquet
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Univ. Joseph Fourier, Grenoble 1, BP 53, FR-38041 Grenoble Cedex 9, France
| | - Wilfried Thuiller
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Univ. Joseph Fourier, Grenoble 1, BP 53, FR-38041 Grenoble Cedex 9, France
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine, UMR-CNRS 5553, Univ. Joseph Fourier, Grenoble 1, BP 53, FR-38041 Grenoble Cedex 9, France
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130
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Frédérich B, Sorenson L, Santini F, Slater GJ, Alfaro ME. Iterative Ecological Radiation and Convergence during the Evolutionary History of Damselfishes (Pomacentridae). Am Nat 2013; 181:94-113. [DOI: 10.1086/668599] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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131
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Giribet G, Edgecombe GD. Stable phylogenetic patterns in scutigeromorph centipedes (Myriapoda : Chilopoda : Scutigeromorpha): dating the diversification of an ancient lineage of terrestrial arthropods. INVERTEBR SYST 2013. [DOI: 10.1071/is13019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Although stable and well-supported relationships are in place for the three main clades (families) of Scutigeromorpha, the interrelationships of particular taxa within the most diverse family, Scutigeridae, are less clearly resolved. Novel molecular data for taxa from Mesoamerica, the Caribbean, southern Africa, New Guinea and previously unsampled parts of the Pacific are incorporated into phylogenetic analyses. Relationships across the tree are stable under variable analytical conditions, whether these are homology-based (multiple sequence alignment versus implied alignment; untrimmed versus trimmed datasets) or method-based (parsimony versus maximum likelihood). Hypervariable regions, contrary to common belief, add phylogenetic structure to the data, as measured by the increased support for many nodes when compared with the same alignments trimmed with Gblocks. Our analyses show that a Yule-3-rate model best explained the diversification of Scutigeromorpha during their 400 million years of history. More complete molecular data for the New Guinea genus Ballonema stabilise its position as sister group to Thereuoneminae. To reconcile scutigeromorph systematics with the phylogeny, the monotypic genus Madagassophora Verhoeff, 1936, is placed in synonymy with Scutigerina Silvestri, 1901 (n. syn.), its type species M. hova becoming Scutigerina hova (de Saussure & Zehntner, 1902) new comb. (from Scutigera), and Lassophora Verhoeff, 1905, is re-established for an Afro-Malagasy clade containing Lassophora nossibei (de Saussure & Zehntner, 1902) new comb. (from Scutigera) and a newly sequenced species from Mozambique that diverged at the base of the lineage to Thereuoneminae. The dated phylogeny of Scutigeromorpha is more consistent with ancient vicariant splits between Madagascar–southern Africa and Australia–New Caledonia than with younger dispersal scenarios, though some geologically young Pacific islands that harbour lineages dating to the Cretaceous demonstrate the potential for trans-oceanic dispersal.
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132
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Schoville SD, Uchifune T, Machida R. Colliding fragment islands transport independent lineages of endemic rock-crawlers (Grylloblattodea: Grylloblattidae) in the Japanese archipelago. Mol Phylogenet Evol 2012; 66:915-27. [PMID: 23220515 DOI: 10.1016/j.ympev.2012.11.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/09/2012] [Accepted: 11/23/2012] [Indexed: 11/24/2022]
Abstract
Fragment islands, viewed from the paradigm of island biogeographic theory, depend on continual immigration from continental sources to maintain levels of species diversity, or otherwise undergo a period of relaxation where species diversity declines to a lower equilibrium. Japan is a recently derived fragment island with a rich endemic flora and fauna. These endemic species have been described as paleoendemics, and conversely as recently derived Pleistocene colonists. Geological events in the Miocene period, notably the fragmentation and collision of islands, and the subsequent uplift of mountains in central Japan, provided opportunities for genetic isolation. More recently, cyclical climatic change during the Pliocene and Pleistocene periods led to intermittent land bridge connections to continental Asia. Here we investigate the pattern and timing of diversification in a diverse endemic lineage in order to test whether ongoing migration has sustained species diversity, whether there is evidence of relaxation, and how geological and climatic events are associated with lineage diversification. Using multi-locus genetic data, we test these hypotheses in a poorly dispersing, cold-adapted terrestrial insect lineage (Grylloblattodea: Grylloblattidae) sampled from Japan, Korea, and Russia. In phylogenetic analyses of concatenated data and a species tree approach, we find evidence of three deeply divergent lineages of rock-crawlers in Japan consistent with the pattern of island fragmentation from continental Asia. Tests of lineage diversification rates suggest that relaxation has not occurred and instead endemism has increased in the Japanese Grylloblattidae following mountain-building events in the Miocene. Although the importance of climate change in generating species diversity is a commonly held paradigm in Japanese biogeography, our analyses, including analyses of demographic change and phylogeographic range shifts in putative species, suggests that Pleistocene climatic change has had a limited effect on the diversification of rock-crawlers.
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Affiliation(s)
- Sean D Schoville
- Sugadaira Montane Research Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan.
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133
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Smith BT, Ribas CC, Whitney BM, HernÁndez-baÑos BE, Klicka J. Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genusForpus. Mol Ecol 2012. [DOI: 10.1111/mec.12118] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brian Tilston Smith
- Museum of Natural Science; Louisiana State University; 119 Foster Hall Baton Rouge LA 70803 USA
- Marjorie Barrick Museum of Natural History; University of Nevada; Las Vegas, 4505 S. Maryland Parkway Box 454012 Las Vegas NV 89154-4012 USA
- School of Life Sciences; University of Nevada; Las Vegas, 4505 S. Maryland Parkway Las Vegas NV 89154 USA
| | - Camila C. Ribas
- Coordenação de Biodiversidade; Instituto Nacional de Pesquisas da Amazônia; Av. André Araújo Manaus AM 2936 Brasil
| | - Bret M. Whitney
- Museum of Natural Science; Louisiana State University; 119 Foster Hall Baton Rouge LA 70803 USA
| | - Blanca E. HernÁndez-baÑos
- Museo de Zoología, Facultad de Ciencias; Universidad Nacional Autónoma de México; Apartado Postal 70-399 México DF 04510 México
| | - John Klicka
- Marjorie Barrick Museum of Natural History; University of Nevada; Las Vegas, 4505 S. Maryland Parkway Box 454012 Las Vegas NV 89154-4012 USA
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134
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Bell CD, Mavrodiev EV, Soltis PS, Calaminus AK, Albach DC, Cellinese N, Garcia-Jacas N, Soltis DE. Rapid diversification ofTragopogonand ecological associates in Eurasia. J Evol Biol 2012; 25:2470-80. [DOI: 10.1111/j.1420-9101.2012.02616.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/28/2012] [Accepted: 08/08/2012] [Indexed: 11/28/2022]
Affiliation(s)
- C. D. Bell
- Department of Biological Sciences; University of New Orleans; New Orleans; LA; USA
| | | | - P. S. Soltis
- Florida Museum of Natural History; University of Florida; Gainesville; FL; USA
| | - A. K. Calaminus
- Department of Biology; University of Florida; Gainesville; FL; USA
| | - D. C. Albach
- AG Biodiversitat und Evolution der Pflanzen; Institut fur Biologie und Umweltwissenschaften; Carl von Ossietzky-Universitat; Oldenburg; Germany
| | - N. Cellinese
- Florida Museum of Natural History; University of Florida; Gainesville; FL; USA
| | - N. Garcia-Jacas
- Institut Botànic de Barcelona (IBB - CSIC - ICUB); Barcelona; Spain
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135
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Pedraza-Lara C, Doadrio I, Breinholt JW, Crandall KA. Phylogeny and evolutionary patterns in the Dwarf crayfish subfamily (Decapoda: Cambarellinae). PLoS One 2012; 7:e48233. [PMID: 23155379 PMCID: PMC3498282 DOI: 10.1371/journal.pone.0048233] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 09/27/2012] [Indexed: 11/18/2022] Open
Abstract
The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group) and into Central México (Mexican Group), has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp) using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group) and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047), resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric divergence in freshwater organisms can be promoted through diverse vicariant factors.
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Affiliation(s)
- Carlos Pedraza-Lara
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain.
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136
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Wang L, Schneider H, Zhang XC, Xiang QP. The rise of the Himalaya enforced the diversification of SE Asian ferns by altering the monsoon regimes. BMC PLANT BIOLOGY 2012; 12:210. [PMID: 23140168 PMCID: PMC3508991 DOI: 10.1186/1471-2229-12-210] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/06/2012] [Indexed: 05/24/2023]
Abstract
BACKGROUND The rise of high mountain chains is widely seen as one of the factors driving rapid diversification of land plants and the formation of biodiversity hotspots. Supporting evidence was reported for the impact of the rapid rise of the Andean mountains but this hypothesis has so far been less explored for the impact of the "roof of the world". The formation of the Himalaya, and especially the rise of the Qinghai-Tibetan Plateau in the recent 20 million years, altered the monsoon regimes that dominate the current climates of South East Asia. Here, we infer the hypothesis that the rise of Himalaya had a strong impact on the plant diversity in the biodiversity hotspot of the Southwest Chinese Mountains. RESULTS Our analyses of the diversification pattern of the derived fern genus Lepisorus recovered evidence for changes in plant diversity that correlated with the strengthening of South East Asian monsoon. Southwest China or Southwest China and Japan was recovered as the putative area of origin of Lepisorus and enhancing monsoon regime were found to shape the early diversification of the genus as well as subsequent radiations during the late Miocene and Pliocene. CONCLUSIONS We report new evidence for a coincidence of plant diversification and changes of the climate caused by the uplift of the Himalaya. These results are discussed in the context of the impact of incomplete taxon sampling, uncertainty of divergence time estimates, and limitations of current methods used to assess diversification rates.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Harald Schneider
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- Department of Botany, The Natural History Museum London, London, SW7 5BD, UK
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
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137
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Nattier R, Grandcolas P, Elias M, Desutter-Grandcolas L, Jourdan H, Couloux A, Robillard T. Secondary sympatry caused by range expansion informs on the dynamics of microendemism in a biodiversity hotspot. PLoS One 2012; 7:e48047. [PMID: 23139758 PMCID: PMC3490955 DOI: 10.1371/journal.pone.0048047] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 09/20/2012] [Indexed: 12/31/2022] Open
Abstract
Islands are bounded areas where high endemism is explained either by allopatric speciation through the fragmentation of the limited amount of space available, or by sympatric speciation and accumulation of daughter species. Most empirical evidence point out the dominant action of allopatric speciation. We evaluate this general view by looking at a case study where sympatric speciation is suspected. We analyse the mode, tempo and geography of speciation in Agnotecous, a cricket genus endemic to New Caledonia showing a generalized pattern of sympatry between species making sympatric speciation plausible. We obtained five mitochondrial and five nuclear markers (6.8 kb) from 37 taxa corresponding to 17 of the 21 known extant species of Agnotecous, and including several localities per species, and we conducted phylogenetic and dating analyses. Our results suggest that the diversification of Agnotecous occurred mostly through allopatric speciation in the last 10 Myr. Highly microendemic species are the most recent ones (<2 Myr) and current sympatry is due to secondary range expansion after allopatric speciation. Species distribution should then be viewed as a highly dynamic process and extreme microendemism only as a temporary situation. We discuss these results considering the influence of climatic changes combined with intricate soil diversity and mountain topography. A complex interplay between these factors could have permitted repeated speciation events and range expansion.
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Affiliation(s)
- Romain Nattier
- Muséum national d'Histoire naturelle, Département Systématique et Evolution, UMR 7205 CNRS OSEB, Case postale 50 (Entomologie), Paris, France.
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138
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Blair C, Davy CM, Ngo A, Orlov NL, Shi HT, Lu SQ, Gao L, Rao DQ, Murphy RW. Genealogy and Demographic History of a Widespread Amphibian throughout Indochina. J Hered 2012; 104:72-85. [PMID: 23125408 DOI: 10.1093/jhered/ess079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Relatively little is known about spatial patterns of cryptic diversity in tropical species and the processes that generate them. Few studies examine the geographic distribution of genetic lineages in Southeast Asia, an area hypothesized to harbor substantial cryptic diversity. We investigated the evolutionary history of Asian tree frogs of the Polypedates leucomystax complex (n = 172) based on 1800 bp of the mtDNA genes ND1 and cytochrome b and tested hypotheses pertaining to climate, geology, and dispersal patterns. Analyses revealed substantial genetic diversity and lineage divergence throughout the region with evidence for widespread sympatric lineages and a general north versus south clustering. Relaxed molecular clock analysis and tests for demographic expansion identified an initial cladogenesis during the Miocene with subsequent Plio-Pleistocene diversification, with the former corresponding to periods of increased aridity and the onset of monsoonal weather systems. Rates of diversification were relatively constant until the Early Pleistocene when rates increased exponentially. We found equivocal evidence for isolation-by-distance and a potential role of some landscape features as partial barriers to dispersal. Finally, our analyses showed that divergence between insular and mainland populations occurred before Homo sapiens colonized Southeast Asia, suggesting that historical human-mediated dispersal did not drive insular diversification. Our results suggested that demographic expansion in the Late Pleistocene resulted in widespread sympatric lineages in the P. leucomystax complex throughout southern China and Indochina and further clarified the evolutionary history of lineages within P. leucomystax.
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Affiliation(s)
- Christopher Blair
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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139
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Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO. The global diversity of birds in space and time. Nature 2012; 491:444-8. [PMID: 23123857 DOI: 10.1038/nature11631] [Citation(s) in RCA: 1859] [Impact Index Per Article: 154.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 09/28/2012] [Indexed: 11/09/2022]
Abstract
Current global patterns of biodiversity result from processes that operate over both space and time and thus require an integrated macroecological and macroevolutionary perspective. Molecular time trees have advanced our understanding of the tempo and mode of diversification and have identified remarkable adaptive radiations across the tree of life. However, incomplete joint phylogenetic and geographic sampling has limited broad-scale inference. Thus, the relative prevalence of rapid radiations and the importance of their geographic settings in shaping global biodiversity patterns remain unclear. Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective. Overall, whereas constituent clades may exhibit slowdowns, the adaptive zone into which modern birds have diversified since the Cretaceous may still offer opportunities for diversification.
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Affiliation(s)
- W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, Connecticut 06520-8106, USA.
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140
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Burbrink FT, Chen X, Myers EA, Brandley MC, Pyron RA. Evidence for determinism in species diversification and contingency in phenotypic evolution during adaptive radiation. Proc Biol Sci 2012; 279:4817-26. [PMID: 23034709 DOI: 10.1098/rspb.2012.1669] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Adaptive radiation (AR) theory predicts that groups sharing the same source of ecological opportunity (EO) will experience deterministic species diversification and morphological evolution. Thus, deterministic ecological and morphological evolution should be correlated with deterministic patterns in the tempo and mode of speciation for groups in similar habitats and time periods. We test this hypothesis using well-sampled phylogenies of four squamate groups that colonized the New World (NW) in the Late Oligocene. We use both standard and coalescent models to assess species diversification, as well as likelihood models to examine morphological evolution. All squamate groups show similar early pulses of speciation, as well as diversity-dependent ecological limits on clade size at a continental scale. In contrast, processes of morphological evolution are not easily predictable and do not show similar pulses of early and rapid change. Patterns of morphological and species diversification thus appear uncoupled across these groups. This indicates that the processes that drive diversification and disparification are not mechanistically linked, even among similar groups of taxa experiencing the same sources of EO. It also suggests that processes of phenotypic diversification cannot be predicted solely from the existence of an AR or knowledge of the process of diversification.
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Affiliation(s)
- Frank T Burbrink
- Department of Biology, The College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA.
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141
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Hardy NB, Cook LG. Testing for Ecological Limitation of Diversification: A Case Study Using Parasitic Plants. Am Nat 2012; 180:438-49. [DOI: 10.1086/667588] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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142
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Weir JT, Mursleen S. DIVERSITY-DEPENDENT CLADOGENESIS AND TRAIT EVOLUTION IN THE ADAPTIVE RADIATION OF THE AUKS (AVES: ALCIDAE). Evolution 2012; 67:403-16. [DOI: 10.1111/j.1558-5646.2012.01786.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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143
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Sharma PP, Giribet G. Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods. Proc Biol Sci 2012; 279:3501-9. [PMID: 22628468 PMCID: PMC3396899 DOI: 10.1098/rspb.2012.0675] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 05/03/2012] [Indexed: 11/12/2022] Open
Abstract
The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous (ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.
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Affiliation(s)
- Prashant P Sharma
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
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144
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145
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Condamine FL, Toussaint EF, Cotton AM, Genson GS, Sperling FA, Kergoat GJ. Fine-scale biogeographical and temporal diversification processes of peacock swallowtails (PapiliosubgenusAchillides) in the Indo-Australian Archipelago. Cladistics 2012; 29:88-111. [DOI: 10.1111/j.1096-0031.2012.00412.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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146
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Weber MG, Agrawal AA. Phylogeny, ecology, and the coupling of comparative and experimental approaches. Trends Ecol Evol 2012; 27:394-403. [DOI: 10.1016/j.tree.2012.04.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 04/20/2012] [Accepted: 04/23/2012] [Indexed: 11/27/2022]
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147
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Ryberg M, Matheny PB. Asynchronous origins of ectomycorrhizal clades of Agaricales. Proc Biol Sci 2012; 279:2003-11. [PMID: 22171078 PMCID: PMC3311903 DOI: 10.1098/rspb.2011.2428] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 11/24/2011] [Indexed: 11/12/2022] Open
Abstract
The ectomycorrhizal (ECM) symbiosis is the most widespread biotrophic nutritional mode in mushroom-forming fungi. ECM fungi include, though are not limited to, about 5000 described species of Agaricales from numerous, independently evolved lineages. Two central hypotheses suggest different explanations for the origin of ECM fungal diversity: (i) dual origins, initially with the Pinaceae in the Jurassic and later with angiosperms during the Late Cretaceous, and (ii) a simultaneous and convergent radiation of ECM lineages in response to cooling climate during the Palaeogene and advancing temperate ECM plant communities. Neither of these hypotheses is supported here. While we demonstrate support for asynchronous origins of ECM Agaricales, the timing of such events appears to have occurred more recently than suggested by the first hypothesis, first during the Cretaceous and later during the Palaeogene. We are also unable to reject models of rate constancy, which suggests that the diversity of ECM Agaricales is not a consequence of convergent rapid radiations following evolutionary transitions from saprotrophic to ECM habits. ECM lineages of Agaricales differ not only in age, but also in rates of diversification and rate of substitution at nuclear ribosomal RNA loci. These results question the biological uniformity of the ECM guild.
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Affiliation(s)
- Martin Ryberg
- Department of Ecology and Evolutionary Biology, University of Tennessee, 332 Hesler, Knoxville, TN 37996, USA.
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148
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Claramunt S, Derryberry EP, Brumfield RT, Remsen JV. Ecological Opportunity and Diversification in a Continental Radiation of Birds: Climbing Adaptations and Cladogenesis in the Furnariidae. Am Nat 2012; 179:649-66. [DOI: 10.1086/664998] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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149
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Jønsson KA, Fabre PH, Fritz SA, Etienne RS, Ricklefs RE, Jørgensen TB, Fjeldså J, Rahbek C, Ericson PGP, Woog F, Pasquet E, Irestedt M. Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas. Proc Natl Acad Sci U S A 2012; 109:6620-5. [PMID: 22505736 PMCID: PMC3340096 DOI: 10.1073/pnas.1115835109] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adaptive radiation is the rapid diversification of a single lineage into many species that inhabit a variety of environments or use a variety of resources and differ in traits required to exploit these. Why some lineages undergo adaptive radiation is not well-understood, but filling unoccupied ecological space appears to be a common feature. We construct a complete, dated, species-level phylogeny of the endemic Vangidae of Madagascar. This passerine bird radiation represents a classic, but poorly known, avian adaptive radiation. Our results reveal an initial rapid increase in evolutionary lineages and diversification in morphospace after colonizing Madagascar in the late Oligocene some 25 Mya. A subsequent key innovation involving unique bill morphology was associated with a second increase in diversification rates about 10 Mya. The volume of morphospace occupied by contemporary Madagascan vangas is in many aspects as large (shape variation)--or even larger (size variation)--as that of other better-known avian adaptive radiations, including the much younger Galapagos Darwin's finches and Hawaiian honeycreepers. Morphological space bears a close relationship to diet, substrate use, and foraging movements, and thus our results demonstrate the great extent of the evolutionary diversification of the Madagascan vangas.
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Affiliation(s)
- Knud A Jønsson
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, 2100 Copenhagen Ø, Denmark.
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150
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Cabezas P, Sanmartín I, Paulay G, Macpherson E, Machordom A. Deep under the sea: unraveling the evolutionary history of the deep-sea squat lobster Paramunida (Decapoda, Munididae). Evolution 2012; 66:1878-96. [PMID: 22671553 DOI: 10.1111/j.1558-5646.2011.01560.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The diversification of Indo-Pacific marine fauna has long captivated the attention of evolutionary biologists. Previous studies have mainly focused on coral reef or shallow water-associated taxa. Here, we present the first attempt to reconstruct the evolutionary history--phylogeny, diversification, and biogeography--of a deep-water lineage. We sequenced the molecular markers 16S, COI, ND1, 18S, and 28S for nearly 80% of the nominal species of the squat lobster genus Paramunida. Analyses of the molecular phylogeny revealed an accelerated diversification in the late Oligocene-Miocene followed by a slowdown in the rate of lineage accumulation over time. A parametric biogeographical reconstruction showed the importance of the southwest Pacific area, specifically the island arc of Fiji, Tonga, Vanuatu, Wallis, and Futuna, for diversification of squat lobsters, probably associated with the global warming, high tectonic activity, and changes in oceanic currents that took place in this region during the Oligocene-Miocene period. These results add strong evidence to the hypothesis that the Neogene was a period of major diversification for marine organisms in both shallow and deep waters.
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Affiliation(s)
- Patricia Cabezas
- Museo Nacional de Ciencias Naturales, MNCN-CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain.
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