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Climate Cycles, Habitat Stability, and Lineage Diversification in an African Biodiversity Hotspot. DIVERSITY 2023. [DOI: 10.3390/d15030394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The Eastern Arc Mountains of Tanzania and Kenya, a montane archipelago of 13 uplifted fault blocks (sky islands) isolated by lowland arid savanna, are a center of exceptional biological endemism. Under the influence of humid winds from the Indian Ocean, forests and associated species may have persisted in this region since the final uplift of these blocks in the late Miocene. Today, these mountains are inhabited by a remarkable diversity of bird species. To better understand the evolutionary processes behind this diversity, we combined molecular phylogenetic studies of East African montane birds with paleoclimate modeling of its montane forests. Across its largest lowland barrier, the 125 km between the Usambara and Nguru/Nguu Mountains, 10 of the 14 bird lineages exhibited a phylogeographic break. Using Bayesian methods, we established that at least three periods of forest contraction and expansion affected the diversification of Eastern Arc birds. Habitat distribution models suggest that lower-elevation hills may have acted as stepping-stones connecting isolated highlands to allow for the dispersal of montane forest-dependent species across them. Periods of vicariance during paleoclimatic cycles extending back through the Last Glacial Maximum would have then isolated these populations within the highlands they had reached. The broad distribution of neoendemic species across the mountains of East Africa provides evidence of climate cycling as a driver of lineage diversification. The high incidence of narrow-range endemism of paleoendemic species on the Usambara, Uluguru, and Udzungwa Mountains of this region is harder to explain. Our paleoclimate models retrodicted the persistence of montane forest during climate cycles on several Eastern Arc sky islands but not on the Southern Tanzania Volcanic Highlands. Consistent with recent theoretical work, different rates of local extinction rather than increased rates of lineage diversification may explain the pattern of excessive narrow-range endemism on some sky islands over others. Thus, a regional filtering effect is generated, with paleoendemics maintaining populations through time only in areas where habitat persisted, providing a credible explanation for the dramatic variance in levels of endemism among different East African sky islands.
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Lawson LP, Loader SP, Lyakurwa JV, Liedtke HC. Diversification of spiny-throated reed frogs (Anura: Hyperoliidae) with the description of a new, range-restricted species from the Ukaguru Mountains, Tanzania. PLoS One 2023; 18:e0277535. [PMID: 36730334 PMCID: PMC9894401 DOI: 10.1371/journal.pone.0277535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/28/2022] [Indexed: 02/03/2023] Open
Abstract
The spiny-throated reed frog species group is a small radiation of Hyperolius frogs from East Africa. Unlike many members of the genus which have relatively wide distributions, these species tend to be small-range endemics found in montane and submontane forests. Recent discovery of a golden-hued frog with the clade-specific traits of spines on their gular discs prompted a morphological and genetic exploration of the distinctness of this new lineage and relationships to other members of the clade. Genetic (mitochondrial and nuclear loci) results resolved many sister-relationships, but deeper nodes in the phylogeny were poorly resolved. A reduced-representation genome-wide Single Nucleotide Polymorphism (SNP) dataset was able to fully resolve the phylogenetic relationships within this clade, placing this new lineage, here named after the mountain range in which is it found-H. ukaguruensis sp. nov., as an early diverging lineage within the group. This new species is distinct from all other spiny-throated reed frogs, necessitating further understanding as a single-mountain endemics vulnerable to habitat loss and potential decline. Morphometric analyses identify clear morphological characteristics that are distinct for the herein described species, most noticeably in that the eyes are significantly smaller than other members of the genus for which we have samples.
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Affiliation(s)
- Lucinda P. Lawson
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
- Department of Zoology, Field Museum, Chicago, Illinois, United States of America
- * E-mail:
| | - Simon P. Loader
- Life Sciences Department, Natural History Museum, London, United Kingdom
| | - John V. Lyakurwa
- Department of Zoology and Wildlife Conservation, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - H. Christoph Liedtke
- Ecology, Evolution and Development Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
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Channing A, Schmitz A, Zancolli G, Conradie W, Rödel MO. Phylogeny and taxonomy of the African frog genus Strongylopus (Anura: Pyxicephalidae). REV SUISSE ZOOL 2022. [DOI: 10.35929/rsz.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Alan Channing
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa
| | - Andreas Schmitz
- Muséum d'histoire naturelle, UREC - Herpetology & Ichthyology, C.P. 6434, CH-1211 Genève 6, Switzerland
| | - Giulia Zancolli
- Department of Ecology and Evolution, Université de Lausanne, Quartier UNIL-Sorge Bâtiment Biophore, CH-1015 Lausanne, Switzerland
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Gqeberha 6013, South Africa
| | - Mark-Oliver Rödel
- Museum für Naturkunde – Leibnitz Institute for Evolution and Biodiversity Science, Invalidenstr. 43, D-10115 Berlin, Germany
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4
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McEntee JP, Zhelezov G, Werema C, Najar N, Peñalba JV, Mulungu E, Mbilinyi M, Karimi S, Chumakova L, Gordon Burleigh J, Bowie RCK. Punctuated evolution in the learned songs of African sunbirds. Proc Biol Sci 2021; 288:20212062. [PMID: 34784761 PMCID: PMC8595995 DOI: 10.1098/rspb.2021.2062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Learned traits are thought to be subject to different evolutionary dynamics than other phenotypes, but their evolutionary tempo and mode has received little attention. Learned bird song has been thought to be subject to rapid and constant evolution. However, we know little about the evolutionary modes of learned song divergence over long timescales. Here, we provide evidence that aspects of the territorial songs of Eastern Afromontane sky island sunbirds Cinnyris evolve in a punctuated fashion, with periods of stasis of the order of hundreds of thousands of years or more, broken up by evolutionary pulses. Stasis in learned songs is inconsistent with learned traits being subject to constant or frequent change, as would be expected if selection does not constrain song phenotypes over evolutionary timescales. Learned song may instead follow a process resembling peak shifts on adaptive landscapes. While much research has focused on the potential for rapid evolution in bird song, our results suggest that selection can tightly constrain the evolution of learned songs over long timescales. More broadly, these results demonstrate that some aspects of highly variable, plastic traits can exhibit punctuated evolution, with stasis over long time periods.
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Affiliation(s)
- Jay P McEntee
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.,Department of Biology, Missouri State University, Springfield, MO 65897, USA
| | - Gleb Zhelezov
- School of Mathematics, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - Chacha Werema
- Department of Zoology and Wildlife Conservation, University of Dar-es-salaam, PO Box 35064, Tanzania
| | - Nadje Najar
- School of Natural Resources, University of Nebraska, Lincoln, NE 68503, USA
| | - Joshua V Peñalba
- Museum für Naturkunde, Center for Integrative Biodiversity Discovery, Invalidenstrasse 43, 10115 Berlin, Germany
| | | | | | | | - Lyubov Chumakova
- School of Mathematics, University of Edinburgh, Edinburgh EH9 3FD, UK
| | - J Gordon Burleigh
- Biology Department, University of Florida, Gainesville, FL 32611, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
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Highly divergent karyotypes and barcoding of the East African genus Gonatoxia Karsch (Orthoptera: Phaneropterinae). Sci Rep 2021; 11:22781. [PMID: 34815452 PMCID: PMC8610994 DOI: 10.1038/s41598-021-02110-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/20/2021] [Indexed: 11/09/2022] Open
Abstract
East Africa is a hotspot of biodiversity of many orthopteran taxa, including bushcrickets. Gonatoxia Karsch, 1889 species are fully alate Phaneropterinae, which are perfectly adapted to the foliage of forests. We examined five species using combined cytogenetic and molecular data to determine the inter- and intraspecific genetic diversity. The variation in the diploid number of chromosomes in males ranged from 2n = 28 + X0 and 26 + X0 to 2n = 6 + X0. Fluorescence in situ hybridization showed from one to many 18S rDNA loci as well as interstitial sequences, especially in G. helleri. 18S rDNA loci coincided with active NOR and C-banding patterns. The isolation of populations of the species explains differences in the number of chromosomes (G. maculata), chromosomal polymorphism and chromosomal heterozygosity (G. helleri). Our molecular phylogeny based on the COI locus supported the monophyly of the genus Gonatoxia and separateness of the five examined species in accordance with their morphological features and chromosome numbers as well as the species' distribution.
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Busschau T, Conradie W, Daniels SR. One species hides many: Molecular and morphological evidence for cryptic speciation in a thread snake (Leptotyphlopidae:
Leptotyphlops sylvicolus
Broadley & Wallach, 1997). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Theo Busschau
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
| | - Werner Conradie
- Port Elizabeth Museum Humewood South Africa
- School of Natural Resource Management, George Campus Nelson Mandela University George South Africa
| | - Savel R. Daniels
- Department of Botany & Zoology University of Stellenbosch Matieland South Africa
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Bwong BA, Barratt CD, Loader SP, Nyamache JO, Menegon M, Malonza PK, Nagel P, Lawson LP. Systematics of Hyperolius mitchelli Loveridge, 1953 and Hyperolius rubrovermiculatus Schiøtz, 1975 (Anura: Hyperoliidae) and assignment of populations from northern Tanzania. AFR J HERPETOL 2020. [DOI: 10.1080/21564574.2020.1768155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Beryl A Bwong
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
| | - Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Simon P Loader
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | | | - Michele Menegon
- Science Museo of Trento, Via della Scienza e del lavoro, Trento, Italy
| | | | - Peter Nagel
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Lucinda P Lawson
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States
- Field Museum of Natural History, Chicago, Illinois, United States
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Mahulu A, Clewing C, Stelbrink B, Chibwana FD, Tumwebaze I, Russell Stothard J, Albrecht C. Cryptic intermediate snail host of the liver fluke Fasciola hepatica in Africa. Parasit Vectors 2019; 12:573. [PMID: 31801595 PMCID: PMC6894237 DOI: 10.1186/s13071-019-3825-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/23/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Snails such as Galba truncatula are hosts for trematode flukes causing fascioliasis, a zoonosis that is a major public health problem. Galba truncatula has recently been shown to be a cryptic species complex. African populations of Galba spp. are not yet studied using molecular assessments and is imperative to do so and reconstruct the centre of origin of Galba and to understand when and by what means it may have colonized the highlands of Africa and to what extent humans might have been involved in that process. METHODS Samples from all known sub-ranges throughout Africa and new samples from Europe and Asia were obtained. We used a combination of two mitochondrial (cox1 and 16S) and one nuclear (ITS2) markers and phylogenetic, divergence time estimates and phylogeographical methods to determine the identity and biogeographical affinities. We also reconstructed the colonization history including the likely mode of dispersal and tested for the presence of cryptic Galba species in Africa. RESULTS Galba truncatula is restricted to the Palaearctic region of the continent, namely Morocco. All sub-Saharan populations proved to be a distinct species according to the phylogenetic analyses and genetic distance. We propose to use the existing name Galba mweruensis (Connolly, 1929) for this species which is morphologically indistinguishable from the other two species hitherto known to occur in northern Africa, i.e. G. truncatula and G. schirazensis. Sub-tropical Africa has been colonized only once in either the Pliocene and possibly Miocene. Diversification within G. mweruensis is dated to the Plio-Pleistocene and thus human-mediated dispersal can be ruled out for the initial colonization of the isolated mountain ranges. There are potentially even more cryptic species in high altitude areas of Africa as outlined by the distinctness of the population found at the top of Mt. Elgon, Uganda. CONCLUSIONS From a novel genetic inspection of available African material, a hitherto neglected distinct species, G. mweruensis, now appears a major host of F. hepatica throughout sub-Saharan Africa. A closer examination of trematode parasites hosted by this species is needed in order to understand transmission patterns in highlands throughout eastern and southern Africa. We encourage future studies to inspect other high altitudes areas in Africa in light of parasites of either veterinary or medical importance.
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Affiliation(s)
- Anna Mahulu
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Catharina Clewing
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Björn Stelbrink
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Fred D. Chibwana
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
- Department of Zoology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Immaculate Tumwebaze
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - J. Russell Stothard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Giessen, Germany
- Department of Biology, Mbarara University of Science and Technology, Mbarara, Uganda
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9
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Portillo F, Stanley EL, Branch WR, Conradie W, Rödel MO, Penner J, Barej MF, Kusamba C, Muninga WM, Aristote MM, Bauer AM, Trape JF, Nagy ZT, Carlino P, Pauwels OSG, Menegon M, Ineich I, Burger M, Zassi-Boulou AG, Mazuch T, Jackson K, Hughes DF, Behangana M, Greenbaum E. Evolutionary history of burrowing asps (Lamprophiidae: Atractaspidinae) with emphasis on fang evolution and prey selection. PLoS One 2019; 14:e0214889. [PMID: 30995262 PMCID: PMC6469773 DOI: 10.1371/journal.pone.0214889] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/22/2019] [Indexed: 11/18/2022] Open
Abstract
Atractaspidines are poorly studied, fossorial snakes that are found throughout Africa and western Asia, including the Middle East. We employed concatenated gene-tree analyses and divergence dating approaches to investigate evolutionary relationships and biogeographic patterns of atractaspidines with a multi-locus data set consisting of three mitochondrial (16S, cyt b, and ND4) and two nuclear genes (c-mos and RAG1). We sampled 91 individuals from both atractaspidine genera (Atractaspis and Homoroselaps). Additionally, we used ancestral-state reconstructions to investigate fang and diet evolution within Atractaspidinae and its sister lineage (Aparallactinae). Our results indicated that current classification of atractaspidines underestimates diversity within the group. Diversification occurred predominantly between the Miocene and Pliocene. Ancestral-state reconstructions suggest that snake dentition in these taxa might be highly plastic within relatively short periods of time to facilitate adaptations to dynamic foraging and life-history strategies.
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Affiliation(s)
- Frank Portillo
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Edward L. Stanley
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - William R. Branch
- Port Elizabeth Museum, Humewood, South Africa
- Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Werner Conradie
- Port Elizabeth Museum, Humewood, South Africa
- School of Natural Resource Management, George Campus, Nelson Mandela University, George, South Africa
| | - Mark-Oliver Rödel
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Johannes Penner
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- Department of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Germany
| | - Michael F. Barej
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Chifundera Kusamba
- Laboratoire d’Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, Lwiro, South Kivu, Democratic Republic of the Congo
| | - Wandege M. Muninga
- Laboratoire d’Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, Lwiro, South Kivu, Democratic Republic of the Congo
| | - Mwenebatu M. Aristote
- Institut Supérieur d'Écologie pour la Conservation de la Nature, Katana Campus, South Kivu, Democratic Republic of the Congo
| | - Aaron M. Bauer
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Jean-François Trape
- Laboratoire de Paludologie et Zoologie Médicale, Institut de Recherche pour le Développement, Dakar, Senegal
| | | | - Piero Carlino
- Museo di Storia naturale del Salento, Calimera, Italy
| | - Olivier S. G. Pauwels
- Département des Vertébrés Récents, Institut Royal des Sciences naturelles de Belgique, Brussels, Belgium
| | - Michele Menegon
- Division of Biology and Conservation Ecology, School of Science and the Environment, Manchester Metropolitan University, Manchester, United Kingdom
| | - Ivan Ineich
- Muséum National d’Histoire Naturelle, Sorbonne Universités, Département Systématique et Evolution (Reptiles), ISyEB (Institut de Systématique, Évolution, Biodiversité), Paris, France
| | - Marius Burger
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
- Flora Fauna & Man, Ecological Services Ltd. Tortola, British Virgin Islands
| | | | | | - Kate Jackson
- Department of Biology, Whitman College, Walla Walla, Washington, United States of America
| | - Daniel F. Hughes
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Mathias Behangana
- Department of Environmental Sciences, Makerere University, Kampala, Uganda
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
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Differentiation underground: Range-wide multilocus genetic structure of the silvery mole-rat does not support current taxonomy based on mitochondrial sequences. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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Portillo F, Branch WR, Conradie W, Rödel MO, Penner J, Barej MF, Kusamba C, Muninga WM, Aristote MM, Bauer AM, Trape JF, Nagy ZT, Carlino P, Pauwels OS, Menegon M, Burger M, Mazuch T, Jackson K, Hughes DF, Behangana M, Zassi-Boulou AG, Greenbaum E. Phylogeny and biogeography of the African burrowing snake subfamily Aparallactinae (Squamata: Lamprophiidae). Mol Phylogenet Evol 2018; 127:288-303. [DOI: 10.1016/j.ympev.2018.03.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 01/16/2018] [Accepted: 03/14/2018] [Indexed: 11/24/2022]
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Manthey JD, Reyes-Velasco J, Freilich X, Boissinot S. Diversification in a biodiversity hotspot: genomic variation in the river frog Amietia nutti across the Ethiopian Highlands. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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13
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Impact of species delimitation and sampling on niche models and phylogeographical inference: A case study of the East African reed frog Hyperolius substriatus Ahl, 1931. Mol Phylogenet Evol 2017; 114:261-270. [DOI: 10.1016/j.ympev.2017.06.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 06/29/2017] [Accepted: 06/29/2017] [Indexed: 11/24/2022]
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14
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Bowie RCK, Pasquet E, McEntee JP, Njilima F, Fjeldså J. The systematics and biogeography of African tailorbirds (Cisticolidae: Artisornis) with comment on the choice of Bayesian branch-length prior when analyzing heterogeneous data. Mol Phylogenet Evol 2017; 118:172-183. [PMID: 28834700 DOI: 10.1016/j.ympev.2017.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/15/2017] [Indexed: 11/28/2022]
Abstract
The Long-billed Tailorbird (Artisornis moreaui), one of Africa's rarest birds, has a strikingly disjunct distribution, the origin of which has long puzzled biogeographers. One small population (subspecies moreaui) occurs in sub-montane forest in the East Usambara Mountains, a sky island near the coast of northern Tanzania, and another (subspecies sousae) on Serra Jeci in northwestern Mozambique, 950km away. The African Tailorbird, the putative sister-species of Long-billed Tailorbird, also occurs in the East Usambara Mountains and on Serra Jeci, but in addition occupies all the Eastern Arc Mountain forests between these disjunct sites. Stuart (1981) hypothesized that the two tailorbird distributions could be explained by strong ecological competition, with African Tailorbird populations having eliminated Long-billed Tailorbird populations via competitive exclusion in montane forests between the East Usambara and Serra Jeci. If such competitive exclusion explains these geographic distributions, the co-occurrence of the two species in the East Usambara and at Serra Jeci may be ephemeral, with the status of Long-billed Tailorbird especially in doubt. We sought to (1) determine whether the two species of African tailorbirds are indeed sister-species, and (2) test predictions from Stuart's (1981) competitive exclusion hypothesis using genetic data. Phylogenetic analyses of our seven gene dataset (3 mtDNA, 4 introns; 4784bp) indeed place these two species together in the genus Artisornis. Instead of finding shallow divergence among African Tailorbird populations and deep divergence between Long-billed Tailorbird populations as expected from Stuart's hypothesis, we recover deep genetic divergence and geographic structure among populations of both tailorbird species. This result is consistent with long-term co-existence of the two species at East Usambara and Serra Jeci. Observational data from both the East Usambara and Serra Jeci suggest that the two species have diverged in use of forest canopy strata. From a conservation standpoint, our results suggest that extinction of the Long-billed Tailorbird as a function of competition with African Tailorbird is highly unlikely, and should not be viewed as imminent. Threats to its survival are instead anthropogenic, and conservation measures should take this into account. Finally, our empirical results suggest that mis-specification of the branch-length prior in Bayesian analyses of mitochondrial DNA data can have a profound effect on the overall tree-length (sum of branch-lengths), whereas the topology and support values tend to remain more stable. In contrast, mis-specification of the branch-length prior had a lesser impact on all aspects of the nuclear-only DNA analyses. This problem may be exacerbated when mitochondrial and nuclear DNA analyses are combined in a total evidence approach.
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Affiliation(s)
- Rauri C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Science Building, University of California, Berkeley, CA 94720-3160, USA.
| | - Eric Pasquet
- UMR7205 CNRS, «Origine, Structure et Evolution de la Biodiversité», Muséum National d'Histoire Naturelle, 55 Rue Buffon, 75005 Paris, France; UMS2700 CNRS, «Outils et Méthodes de la Systématique Intégrative», Muséum National d'Histoire Naturelle, 43, rue Cuvier, 75005 Paris, France
| | - Jay P McEntee
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Science Building, University of California, Berkeley, CA 94720-3160, USA
| | - Fadhili Njilima
- Udzungwa Forest Project, P.O. Box 99, Mangúla-Morogoro, Tanzania
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Zoological Museum, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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15
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The roles of barriers, refugia, and chromosomal clines underlying diversification in Atlantic Forest social wasps. Sci Rep 2017; 7:7689. [PMID: 28794485 PMCID: PMC5550474 DOI: 10.1038/s41598-017-07776-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/03/2017] [Indexed: 12/11/2022] Open
Abstract
Phylogeographic studies have sought to explain the genetic imprints of historical climatic changes and geographic barriers within the Brazilian Atlantic Forest (AF) biota, and consequently two processes of diversification (refugia and barriers) have been proposed. Additionally, there is evidence that eustatic changes influenced the biogeographic history of the AF. Here we evaluate these contrasting diversification processes using two AF social wasp species – the mid-montane Synoeca cyanea and the lowland Synoeca aff. septentrionalis. We analyzed several sources of data including multilocus DNA sequence, climatic niche models and chromosomal features. We find support for idiosyncratic phylogeographic patterns between these wasps, involving different levels of population structure and genetic diversity, contrary suitable climatic conditions during the last glaciation, and contrasting historical movements along the AF. Our data indicate that neotectonics and refugia played distinct roles in shaping the genetic structure of these wasps. However, we argue that eustatic changes influenced the demographic expansion but not population structure in AF biota. Notably, these wasps exhibited chromosomal clines, involving chromosome number and decreasing of GC content, latitudinally oriented along the AF. Together, these results reinforce the need to consider individual organismal histories and indicate that barriers and refugia are significant factors in understanding AF evolution.
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Carlen EJ, Rathbun GB, Olson LE, Sabuni CA, Stanley WT, Dumbacher JP. Reconstructing the molecular phylogeny of giant sengis (Macroscelidea; Macroscelididae; Rhynchocyon). Mol Phylogenet Evol 2017; 113:150-160. [PMID: 28552433 DOI: 10.1016/j.ympev.2017.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 05/05/2017] [Accepted: 05/12/2017] [Indexed: 11/18/2022]
Abstract
Giant sengis (Macroscelidea; Macroscelididae; Rhynchocyon), also known as giant elephant-shrews, are small-bodied mammals that range from central through eastern Africa. Previous research on giant sengi systematics has relied primarily on pelage color and geographic distribution. Because some species have complex phenotypic variation and large geographic ranges, we used molecular markers to evaluate the phylogeny and taxonomy of the genus, which currently includes four species: R. chrysopygus, R. cirnei (six subspecies), R. petersi (two subspecies), and R. udzungwensis. We extracted DNA from fresh and historical museum samples from all taxa except one R. cirnei subspecies, and we generated and analyzed approximately 4700 aligned nucleotides (2685 bases of mitochondrial DNA and 2019 bases of nuclear DNA) to reconstruct a molecular phylogeny. We genetically evaluate Rhynchocyon spp. sequences previously published on GenBank, propose that the captive R. petersi population in North American zoos is likely R. p. adersi, and suggest that hybridization among taxa is not widespread in Rhynchocyon. The DNA sample we have from the distinctive but undescribed giant sengi from the Boni forest of northern coastal Kenya is unexpectedly nearly identical to R. chrysopygus, which will require further study. Our analyses support the current morphology-based taxonomy, with each recognized species forming a monophyletic clade, but we propose elevating R. c. stuhlmanni to a full species.
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Affiliation(s)
- Elizabeth J Carlen
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA 94118, United States; Department of Biology, San Francisco State University, San Francisco, CA 94132, United States
| | - Galen B Rathbun
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA 94118, United States
| | - Link E Olson
- University of Alaska Museum, Fairbanks, AK 99775, United States
| | - Christopher A Sabuni
- Pest Management Centre, African Centre of Excellence, Sokoine University of Agriculture, Morogoro, Tanzania
| | - William T Stanley
- Science & Education, Field Museum of Natural History, Chicago, IL 60605, United States
| | - John P Dumbacher
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA 94118, United States; Department of Biology, San Francisco State University, San Francisco, CA 94132, United States.
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17
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Weirauch C, Forthman M, Grebennikov V, Baňař P. From Eastern Arc Mountains to extreme sexual dimorphism: systematics of the enigmatic assassin bug genus Xenocaucus (Hemiptera: Reduviidae: Tribelocephalinae). ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0314-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Lawson LP, Bates JM, Menegon M, Loader SP. Divergence at the edges: peripatric isolation in the montane spiny throated reed frog complex. BMC Evol Biol 2015; 15:128. [PMID: 26126573 PMCID: PMC4487588 DOI: 10.1186/s12862-015-0384-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/20/2015] [Indexed: 11/17/2022] Open
Abstract
Background Peripatric speciation and peripheral isolation have uncertain importance in species accumulation, and are largely overshadowed by assumed dominance of allopatric modes of speciation. Understanding the role of different speciation mechanisms within biodiversity hotspots is central to understanding the generation of biological diversity. Here, we use a phylogeographic analysis of the spiny-throated reed frogs and examine sister pairings with unbalanced current distributional ranges for characteristics of peripatric speciation. We further investigate whether forest/grassland mosaic adapted species are more likely created through peripatric speciation due to instability of this habitat type. Results We reconstructed a multi-locus molecular phylogeny of spiny-throated reed frogs which we then combined with comparative morphologic data to delimit species and analyze historical demographic change; identifying three new species. Three potential peripatric speciation events were identified along with one case of allopatric speciation. Peripatric speciation is supported through uneven potential and realized distributions and uneven population size estimates based on field collections. An associated climate shift was observed in most potentially peripatric splits. Morphological variation was highest in sexually dimorphic traits such as body size and gular shape, but this variation was not limited to peripatric species pairs as hypothesized. The potentially allopatric species pair showed no niche shifts and equivalent effective population sizes, ruling out peripatry in that speciation event. Two major ecological niche shifts were recovered within this radiation, possibly as adaptations to occupy areas of grassland that became more prevalent in the last 5 million years. Restricted and fluctuating grassland mosaics within forests might promote peripatric speciation in the Eastern Arc Biodiversity Hotspot (EABH). Conclusions In our case study, peripatric speciation appears to be an important driver of diversity within the EABH biodiversity hotspot, implying it could be a significant speciation mechanism in highly fragmented ecosystems. Extensive peripatric speciation in this montane archipelago may explain the abundance of discrete lineages within the limited area of the EABH, as inferred in remote island archipelagos. Future phylogenetic studies incorporating demographic and spatial analyses will clarify the role of peripatric speciation in creating biodiversity hotspots. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0384-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lucinda P Lawson
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St. Culver Hall 402, Chicago, IL, 60637, USA. .,Life Sciences, Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL, 60605, USA. .,Department of Biological Sciences, University of Cincinnati, 614 Rieveschl Hall, Cincinnati, OH, 45220, USA.
| | - John M Bates
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th St. Culver Hall 402, Chicago, IL, 60637, USA. .,Life Sciences, Field Museum of Natural History, 1400 S. Lake Shore Dr., Chicago, IL, 60605, USA.
| | - Michele Menegon
- Tropical Biodiversity Section, Science Museo of Trento, Via della Scienza e del lavoro, 38122, Trento, Italy.
| | - Simon P Loader
- Biogeography Research Group, Department of Environmental Sciences, University of Basel, Basel, 4056, Switzerland.
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Loader SP, Lawson LP, Portik DM, Menegon M. Three new species of spiny throated reed frogs (Anura: Hyperoliidae) from evergreen forests of Tanzania. BMC Res Notes 2015; 8:167. [PMID: 25909565 PMCID: PMC4409744 DOI: 10.1186/s13104-015-1050-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/11/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The East African spiny-throated reed frog complex (Hyperolius spinigularis, H. tanneri, and H. minutissimus) is comprised of morphologically similar species with highly fragmented populations across the Eastern Afromontane Region. Recent genetic evidence has supported the distinctiveness of populations suggesting a number of cryptic species. We analyse newly collected morphological data and evaluate the taxonomic distinctiveness of populations. RESULTS We find three new distinct species on the basis of morphological and molecular evidence. The primary morphological traits distinguishing species within the Hyperolius spinigularis complex include the proportions and degree of spinosity of the gular flap in males and snout-urostyle length in females. Other features allow the three species to be distinguished from each other (genetics). We refine the understanding of H. minutissimus which can be found in both forest and grassland habitats of the Udzungwa Mountains, and provide more details on the call of this species. Further details on ecology are noted for all species where known. CONCLUSIONS Three new species are described and we narrow the definition and distribution of Hyperolius spinigularis and H. minutissimus in East Africa. The spiny-throated reed frogs have highly restricted distributions across the fragmented mountains of the Eastern Afromontane region. Given the newly defined and substantially narrower distributions of these spiny-throated reed frog species, conservation concerns are outlined.
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Affiliation(s)
- Simon P Loader
- Department of Environmental Sciences, University of Basel, Biogeography Research Group, Basel, 4056, Switzerland.
| | - Lucinda P Lawson
- Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th Street, Culver Hall 402, Chicago, IL, 60637, USA. .,Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA. .,University of Cincinnati, 614 Rieveschl Hall, Cincinnati, OH, 45221, USA.
| | - Daniel M Portik
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, California, 94720, USA.
| | - Michele Menegon
- Tropical Biodiversity Section, Science Museo of Trento, Via della Scienza e del lavoro, 38122, Trento, Italy.
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Stanley WT, Hutterer R, Giarla TC, Esselstyn JA. Phylogeny, phylogeography and geographical variation in theCrocidura monax(Soricidae) species complex from the montane islands of Tanzania, with descriptions of three new species. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12230] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- William T. Stanley
- Science and Education; Field Museum of Natural History; 1400 South Lake Shore Drive Chicago IL 60605 USA
| | - Rainer Hutterer
- Zoologisches Forschungsmuseum Alexander Koenig; Adenauerallee 160 53113 Bonn Germany
| | - Thomas C. Giarla
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; 119 Foster Hall Baton Rouge LA 70803 USA
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences; Louisiana State University; 119 Foster Hall Baton Rouge LA 70803 USA
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21
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An B, Zhang L, Liu N, Wang Y. Refugia persistence of Qinghai-Tibetan plateau by the cold-tolerant bird Tetraogallus tibetanus (Galliformes: Phasianidae). PLoS One 2015; 10:e0121118. [PMID: 25822918 PMCID: PMC4378977 DOI: 10.1371/journal.pone.0121118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/10/2015] [Indexed: 11/19/2022] Open
Abstract
Most of the temperate species are expected to have moved to lower altitudes during the glacial periods of the Quaternary. Here we tested this hypothesis in a cold-tolerant avian species Tibetan snowcock (Tetraogallus tibetanus) using two segments of mitochondrial gene (a 705bp Cytochrome-b; abbrev. Cyt-b and an 854 bp Control Region; abbrev. CR) and eight microsatellite loci by characterizing population differentiation and gene flow across its range. Combined (Cyt-b + CR) datasets detected several partially lineages with poor support. Microsatellite data, however, identified two distinct lineages congruent with the geographically separated western and central regions of Qinghai-Tibetan Plateau (QTP). The phylogeographic patterns that we observed might be explained by a combination of vicariance events that led to local isolation of T. tibetanus during warm periods and range expansions and population intermixing during cold periods. The results of this study add to our knowledge of population differentiation and connectivity in high altitude mountain ecosystems.
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Affiliation(s)
- Bei An
- School of Basic Medicine Sciences, Lanzhou University, Lanzhou, China
| | - Lixun Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou, China
- * E-mail: (LZ); (NL)
| | - Naifa Liu
- School of Life Sciences, Lanzhou University, Lanzhou, China
- * E-mail: (LZ); (NL)
| | - Ying Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, Shandong, China
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22
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Menegon M, Loader S, Marsden S, Branch W, Davenport T, Ursenbacher S. The genus Atheris (Serpentes: Viperidae) in East Africa: Phylogeny and the role of rifting and climate in shaping the current pattern of species diversity. Mol Phylogenet Evol 2014; 79:12-22. [DOI: 10.1016/j.ympev.2014.06.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 05/03/2014] [Accepted: 06/05/2014] [Indexed: 11/30/2022]
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23
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Cytonuclear discordance and historical demography of two brown frogs, Rana tagoi and R. sakuraii (Amphibia: Ranidae). Mol Phylogenet Evol 2014; 79:231-9. [DOI: 10.1016/j.ympev.2014.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 11/19/2022]
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24
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Jump AS, Carr M, Ahrends A, Marchant R. Genetic Divergence During Long-term Isolation in Highly Diverse Populations of Tropical Trees Across the Eastern Arc Mountains of Tanzania. Biotropica 2014. [DOI: 10.1111/btp.12139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Alistair S. Jump
- Tropical Ecology and Conservation Group; Biological and Environmental Sciences; School of Natural Sciences; University of Stirling; Stirling FK9 4LA U.K
| | - Martin Carr
- School of Applied Sciences; University of Huddersfield; Huddersfield HD1 3DH U.K
| | - Antje Ahrends
- Royal Botanic Garden Edinburgh; 20A Inverleith Row Edinburgh EH3 5LR U.K
| | - Rob Marchant
- York Institute for Tropical Ecosystem Dynamics; Environment Department; University of York; York YO10 5DD U.K
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25
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Cox SC, Prys-Jones RP, Habel JC, Amakobe BA, Day JJ. Niche divergence promotes rapid diversification of East African sky island white-eyes (Aves: Zosteropidae). Mol Ecol 2014; 23:4103-18. [PMID: 24954273 PMCID: PMC4255762 DOI: 10.1111/mec.12840] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 12/01/2022]
Abstract
The Eastern Afromontane biodiversity hotspot composed of highly fragmented forested highlands (sky islands) harbours exceptional diversity and endemicity, particularly within birds. To explain their elevated diversity within this region, models founded on niche conservatism have been offered, although detailed phylogeographic studies are limited to a few avian lineages. Here, we focus on the recent songbird genus Zosterops, represented by montane and lowland members, to test the roles of niche conservatism versus niche divergence in the diversification and colonization of East Africa's sky islands. The species-rich white-eyes are a typically homogeneous family with an exceptional colonizing ability, but in contrast to their diversity on oceanic islands, continental diversity is considered depauperate and has been largely neglected. Molecular phylogenetic analysis of ~140 taxa reveals extensive polyphyly among different montane populations of Z. poliogastrus. These larger endemic birds are shown to be more closely related to taxa with divergent habitat types, altitudinal distributions and dispersal abilities than they are to populations of restricted endemics that occur in neighbouring montane forest fragments. This repeated transition between lowland and highland habitats over time demonstrate that diversification of the focal group is explained by niche divergence. Our results also highlight an underestimation of diversity compared to morphological studies that has implications for their taxonomy and conservation. Molecular dating suggests that the spatially extensive African radiation arose exceptionally rapidly (1-2.5 Ma) during the fluctuating Plio-Pleistocene climate, which may have provided the primary driver for lineage diversification.
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Affiliation(s)
- Siobhan C Cox
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK; Bird Group, Department of Life Sciences, The Natural History Museum, Akeman Street, Tring, Hertfordshire, HP23 6AP, UK
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26
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Demos TC, Kerbis Peterhans JC, Agwanda B, Hickerson MJ. Uncovering cryptic diversity and refugial persistence among small mammal lineages across the Eastern Afromontane biodiversity hotspot. Mol Phylogenet Evol 2014; 71:41-54. [DOI: 10.1016/j.ympev.2013.10.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 10/11/2013] [Accepted: 10/17/2013] [Indexed: 01/04/2023]
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27
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Zancolli G, Steffan-Dewenter I, Rödel MO. Amphibian diversity on the roof of Africa: unveiling the effects of habitat degradation, altitude and biogeography. DIVERS DISTRIB 2013. [DOI: 10.1111/ddi.12161] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Giulia Zancolli
- Department of Animal Ecology and Tropical Biology; Biocentre; University of Würzburg; Am Hubland 97074 Würzburg Germany
| | - Ingolf Steffan-Dewenter
- Department of Animal Ecology and Tropical Biology; Biocentre; University of Würzburg; Am Hubland 97074 Würzburg Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde; Leibniz Institute for Research on Evolution and Biodiversity; Invalidenstr. 43 10115 Berlin Germany
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28
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Alvarado-Serrano DF, Knowles LL. Ecological niche models in phylogeographic studies: applications, advances and precautions. Mol Ecol Resour 2013; 14:233-48. [DOI: 10.1111/1755-0998.12184] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Diego F. Alvarado-Serrano
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
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29
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Hickerson MJ, Stone GN, Lohse K, Demos TC, Xie X, Landerer C, Takebayashi N. Recommendations for using msBayes to incorporate uncertainty in selecting an abc model prior: a response to oaks et Al. Evolution 2013; 68:284-94. [PMID: 24102483 DOI: 10.1111/evo.12241] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 07/04/2013] [Indexed: 01/06/2023]
Abstract
Prior specification is an essential component of parameter estimation and model comparison in Approximate Bayesian computation (ABC). Oaks et al. present a simulation-based power analysis of msBayes and conclude that msBayes has low power to detect genuinely random divergence times across taxa, and suggest the cause is Lindley's paradox. Although the predictions are similar, we show that their findings are more fundamentally explained by insufficient prior sampling that arises with poorly chosen wide priors that critically undersample nonsimultaneous divergence histories of high likelihood. In a reanalysis of their data on Philippine Island vertebrates, we show how this problem can be circumvented by expanding upon a previously developed procedure that accommodates uncertainty in prior selection using Bayesian model averaging. When these procedures are used, msBayes supports recent divergences without support for synchronous divergence in the Oaks et al. data and we further present a simulation analysis that demonstrates that msBayes can have high power to detect asynchronous divergence under narrower priors for divergence time. Our findings highlight the need for exploration of plausible parameter space and prior sampling efficiency for ABC samplers in high dimensions. We discus potential improvements to msBayes and conclude that when used appropriately with model averaging, msBayes remains an effective and powerful tool.
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Affiliation(s)
- Michael J Hickerson
- Biology Department, City College of New York, New York, New York, 10031; The Graduate Center, City University of New York, New York, New York, 10016.
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30
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Lawson LP, Vernesi C, Ricci S, Rovero F. Evolutionary history of the grey-faced Sengi, Rhynchocyon udzungwensis, from Tanzania: a molecular and species distribution modelling approach. PLoS One 2013; 8:e72506. [PMID: 24015252 PMCID: PMC3754996 DOI: 10.1371/journal.pone.0072506] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/10/2013] [Indexed: 11/18/2022] Open
Abstract
Rhynchocyon udzungwensis is a recently described and poorly understood sengi (giant elephant-shrew) endemic to two small montane forests in Southern Tanzania, and surrounded in lower forests by R. cirnei reichardi. In this study, we investigate the molecular genetic relationship between R. udzungwensis and R. c. reichardi, and the possible role that shifting species distributions in response to climate fluctuations may have played in shaping their evolutionary history. Rhynchocyon udzungwensis and R. c. reichardi individuals were sampled from five localities for genetic analyses. Three mitochondrial and two nuclear loci were used to construct species trees for delimitation and to determine whether introgression was detectable either from ancient or ongoing hybridization. All species-tree results show R. udzungwensis and R. c. reichardi as distinct lineages, though mtDNA shows evidence of introgression in some populations. Nuclear loci of each species were monophyletic, implying introgression is exclusively historical. Because we found evidence of introgression, we used distribution data and species distribution modelling for present, glacial, and interglacial climate cycles to predict how shifting species distributions may have facilitated hybridization in some populations. Though interpretations are affected by the limited range of these species, a likely scenario is that the mtDNA introgression found in eastern mid-elevation populations was facilitated by low numbers of R. udzungwensis that expanded into lowland heavily occupied R. c. reichardi areas during interglacial climate cycles. These results imply that relationships within the genus Rhynchocyon may be confounded by porous species boundaries and introgression, even if species are not currently sympatric.
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Affiliation(s)
- Lucinda P. Lawson
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Centre for Research and Innovation, Michele all’Adige, Italy
| | - Silvia Ricci
- Tropical Biodiversity Section, Museo delle Scienze, Trento, Italy
| | - Francesco Rovero
- Tropical Biodiversity Section, Museo delle Scienze, Trento, Italy
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31
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Guarnizo CE, Cannatella DC. Genetic divergence within frog species is greater in topographically more complex regions. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carlos E. Guarnizo
- Section of Integrative Biology; University of Texas at Austin; Austin TX USA
| | - David C. Cannatella
- Section of Integrative Biology; University of Texas at Austin; Austin TX USA
- Texas Natural Science Center; University of Texas at Austin; Austin TX USA
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32
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Affiliation(s)
- John C. Poynton
- a Department of Zoology , Natural History Museum , London , UK
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33
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Loader SP, Ceccarelli FS, Wilkinson M, Menegon M, Mariaux J, de Sá RO, Howell KM, Gower DJ. Species boundaries and biogeography of East African torrent frogs of the genus Petropedetes (Amphibia: Anura: Petropeditidae). AFR J HERPETOL 2013. [DOI: 10.1080/21564574.2013.781549] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Simon P. Loader
- a Department of Environmental Science (Biogeography) , University of Basel , Switzerland
| | - F. Sara Ceccarelli
- a Department of Environmental Science (Biogeography) , University of Basel , Switzerland
| | - Mark Wilkinson
- b Department of Zoology , The Natural History Museum , London , UK
| | - Michele Menegon
- c Tropical Biodiversity Section , Museo Tridentino di Scienze Naturali , Trento , Italy
| | - Jean Mariaux
- d Department of Invertebrates , Muséum d'Histoire Naturelle , Geneva , Switzerland
| | - Rafael O. de Sá
- e Department of Biology , University of Richmond , Richmond , VA , USA
| | - Kim M. Howell
- f Department of Zoology and Marine Biology , University of Dar es Salaam , Dar es Salaam , Tanzania
| | - David J. Gower
- b Department of Zoology , The Natural History Museum , London , UK
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The genus Aerotegmina (Orthoptera, Tettigoniidae, Hexacentrinae): chromosomes, morphological relations, phylogeographical patterns and description of a new species. ORG DIVERS EVOL 2013. [DOI: 10.1007/s13127-013-0133-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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35
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Ornelas JF, Sosa V, Soltis DE, Daza JM, González C, Soltis PS, Gutiérrez-Rodríguez C, de los Monteros AE, Castoe TA, Bell C, Ruiz-Sanchez E. Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica. PLoS One 2013; 8:e56283. [PMID: 23409165 PMCID: PMC3567015 DOI: 10.1371/journal.pone.0056283] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 01/12/2013] [Indexed: 12/01/2022] Open
Abstract
Comparative phylogeography can elucidate the influence of historical events on current patterns of biodiversity and can identify patterns of co-vicariance among unrelated taxa that span the same geographic areas. Here we analyze temporal and spatial divergence patterns of cloud forest plant and animal species and relate them to the evolutionary history of naturally fragmented cloud forests–among the most threatened vegetation types in northern Mesoamerica. We used comparative phylogeographic analyses to identify patterns of co-vicariance in taxa that share geographic ranges across cloud forest habitats and to elucidate the influence of historical events on current patterns of biodiversity. We document temporal and spatial genetic divergence of 15 species (including seed plants, birds and rodents), and relate them to the evolutionary history of the naturally fragmented cloud forests. We used fossil-calibrated genealogies, coalescent-based divergence time inference, and estimates of gene flow to assess the permeability of putative barriers to gene flow. We also used the hierarchical Approximate Bayesian Computation (HABC) method implemented in the program msBayes to test simultaneous versus non-simultaneous divergence of the cloud forest lineages. Our results show shared phylogeographic breaks that correspond to the Isthmus of Tehuantepec, Los Tuxtlas, and the Chiapas Central Depression, with the Isthmus representing the most frequently shared break among taxa. However, dating analyses suggest that the phylogeographic breaks corresponding to the Isthmus occurred at different times in different taxa. Current divergence patterns are therefore consistent with the hypothesis of broad vicariance across the Isthmus of Tehuantepec derived from different mechanisms operating at different times. This study, coupled with existing data on divergence cloud forest species, indicates that the evolutionary history of contemporary cloud forest lineages is complex and often lineage-specific, and thus difficult to capture in a simple conservation strategy.
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Affiliation(s)
- Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología, AC, Xalapa, Veracruz, Mexico.
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Devitt TJ, Devitt SEC, Hollingsworth BD, McGuire JA, Moritz C. Montane refugia predict population genetic structure in the Large-blotched Ensatina salamander. Mol Ecol 2013; 22:1650-65. [PMID: 23379992 DOI: 10.1111/mec.12196] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Revised: 11/20/2012] [Accepted: 11/26/2012] [Indexed: 11/26/2022]
Abstract
Understanding the biotic consequences of Pleistocene range shifts and fragmentation remains a fundamental goal in historical biogeography and evolutionary biology. Here, we combine species distribution models (SDM) from the present and two late Quaternary time periods with multilocus genetic data (mitochondrial DNA and microsatellites) to evaluate the effect of climate-induced habitat shifts on population genetic structure in the Large-blotched Ensatina (Ensatina eschscholtzii klauberi), a plethodontid salamander endemic to middle and high-elevation conifer forest in the Transverse and Peninsular Ranges of southern California and northern Baja California. A composite SDM representing the range through time predicts two disjunct refugia, one in southern California encompassing the core of the species range and the other in the Sierra San Pedro Mártir of northern Baja California at the southern limit of the species range. Based on our spatial model, we would expect a pattern of high connectivity among populations within the northern refugium and, conversely, a pattern of isolation due to long-term persistence of the Sierra San Pedro Mártir population. Our genetic results are consistent with these predictions based on the hypothetical refugia in that (i) historical measures of population connectivity among stable areas are correlated with gene flow estimates; and (ii) there is strong geographical structure between separate refugia. These results provide evidence for the role of recent climatic change in shaping patterns of population persistence and connectivity within the Transverse and Peninsular Ranges, an evolutionary hotspot.
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Affiliation(s)
- Thomas J Devitt
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720-3160, USA.
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Lawson LP. Diversification in a biodiversity hot spot: landscape correlates of phylogeographic patterns in the African spotted reed frog. Mol Ecol 2013; 22:1947-60. [DOI: 10.1111/mec.12229] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 12/05/2012] [Accepted: 12/20/2012] [Indexed: 12/25/2022]
Affiliation(s)
- Lucinda P. Lawson
- Committee on Evolutionary Biology; University of Chicago; Chicago IL 60637 USA
- Zoology Department; Field Museum of Natural History; Chicago IL 60605 USA
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Oaks JR, Sukumaran J, Esselstyn JA, Linkem CW, Siler CD, Holder MT, Brown RM. Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events. Evolution 2012; 67:991-1010. [PMID: 23550751 DOI: 10.1111/j.1558-5646.2012.01840.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co-distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea-level oscillations during the Pleistocene caused diversification across the islands. To guide interpretation of our results, we perform a suite of simulation-based power analyses. Our empirical results strongly support a recent simultaneous divergence event for all 22 taxon pairs, consistent with the prediction of the Pleistocene-driven diversification hypothesis. However, our empirical estimates are sensitive to changes in prior distributions, and our simulations reveal low power of the method to detect random variation in divergence times and bias toward supporting clustered divergences. Our results demonstrate that analyses exploring power and prior sensitivity should accompany ABC model selection inferences. The problems we identify are potentially mitigable with uniform priors over divergence models (rather than classes of models) and more flexible prior distributions on demographic and divergence-time parameters.
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Affiliation(s)
- Jamie R Oaks
- Department of Ecology and Evolutionary Biology, Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.
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Fjeldså J, Bowie RC, Rahbek C. The Role of Mountain Ranges in the Diversification of Birds. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2012. [DOI: 10.1146/annurev-ecolsys-102710-145113] [Citation(s) in RCA: 257] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jon Fjeldså
- Center for Macroecology, Evolution, and Climate, Natural History Museum of Denmark, University of Copenhagen, DK-2100 Copenhagen, Denmark;
| | - Rauri C.K. Bowie
- Museum of Vertebrate Zoology & Department of Integrative Biology, University of California, Berkeley, California 94720;
| | - Carsten Rahbek
- Center for Macroecology, Evolution, and Climate, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark;
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Four new bat species (Rhinolophus hildebrandtii complex) reflect Plio-Pleistocene divergence of dwarfs and giants across an Afromontane archipelago. PLoS One 2012; 7:e41744. [PMID: 22984399 PMCID: PMC3440430 DOI: 10.1371/journal.pone.0041744] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 06/28/2012] [Indexed: 11/19/2022] Open
Abstract
Gigantism and dwarfism evolve in vertebrates restricted to islands. We describe four new species in the Rhinolophus hildebrandtii species-complex of horseshoe bats, whose evolution has entailed adaptive shifts in body size. We postulate that vicissitudes of palaeoenvironments resulted in gigantism and dwarfism in habitat islands fragmented across eastern and southern Africa. Mitochondrial and nuclear DNA sequences recovered two clades of R. hildebrandtii senso lato which are paraphyletic with respect to a third lineage (R. eloquens). Lineages differ by 7.7 to 9.0% in cytochrome b sequences. Clade 1 includes R. hildebrandtii sensu stricto from the east African highlands and three additional vicariants that speciated across an Afromontane archipelago through the Plio-Pleistocene, extending from the Kenyan Highlands through the Eastern Arc, northern Mozambique and the Zambezi Escarpment to the eastern Great Escarpment of South Africa. Clade 2 comprises one species confined to lowland savanna habitats (Mozambique and Zimbabwe). A third clade comprises R. eloquens from East Africa. Speciation within Clade 1 is associated with fixed differences in echolocation call frequency, and cranial shape and size in populations isolated since the late Pliocene (ca 3.74 Mya). Relative to the intermediate-sized savanna population (Clade 2), these island-populations within Clade 1 are characterised by either gigantism (South African eastern Great Escarpment and Mts Mabu and Inago in Mozambique) or dwarfism (Lutope-Ngolangola Gorge, Zimbabwe and Soutpansberg Mountains, South Africa). Sympatry between divergent clades (Clade 1 and Clade 2) at Lutope-Ngolangola Gorge (NW Zimbabwe) is attributed to recent range expansions. We propose an "Allometric Speciation Hypothesis", which attributes the evolution of this species complex of bats to divergence in constant frequency (CF) sonar calls. The origin of species-specific peak frequencies (overall range = 32 to 46 kHz) represents the allometric effect of adaptive divergence in skull size, represented in the evolution of gigantism and dwarfism in habitat islands.
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Zimkus BM, Lawson L, Loader SP, Hanken J. Terrestrialization, miniaturization and rates of diversification in African puddle frogs (Anura: Phrynobatrachidae). PLoS One 2012; 7:e35118. [PMID: 22509392 PMCID: PMC3325629 DOI: 10.1371/journal.pone.0035118] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 03/13/2012] [Indexed: 11/29/2022] Open
Abstract
Terrestrialization, the evolution of non-aquatic oviposition, and miniaturization, the evolution of tiny adult body size, are recurring trends in amphibian evolution, but the relationships among the traits that characterize these phenomena are not well understood. Furthermore, these traits have been identified as possible "key innovations" that are predicted to increase rates of speciation in those lineages in which they evolve. We examine terrestrialization and miniaturization in sub-Saharan puddle frogs (Phrynobatrachidae) in a phylogenetic context to investigate the relationship between adaptation and diversification through time. We use relative dating techniques to ascertain if character trait shifts are associated with increased diversification rates, and we evaluate the likelihood that a single temporal event can explain the evolution of those traits. Results indicate alternate reproductive modes evolved independently in Phrynobatrachus at least seven times, including terrestrial deposition of eggs and terrestrial, non-feeding larvae. These shifts towards alternate reproductive modes are not linked to a common temporal event. Contrary to the "key innovations" hypothesis, clades that exhibit alternate reproductive modes have lower diversification rates than those that deposit eggs aquatically. Adult habitat, pedal webbing and body size have no effect on diversification rates. Though these traits putatively identified as key innovations for Phrynobatrachus do not seem to be associated with increased speciation rates, they may still provide opportunities to extend into new niches, thus increasing overall diversity.
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Affiliation(s)
- Breda M Zimkus
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
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Demographic processes in the montane Atlantic rainforest: Molecular and cytogenetic evidence from the endemic frog Proceratophrys boiei. Mol Phylogenet Evol 2012; 62:880-8. [DOI: 10.1016/j.ympev.2011.11.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 11/04/2011] [Accepted: 11/07/2011] [Indexed: 01/27/2023]
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Measey GJ, Tolley KA. Sequential fragmentation of Pleistocene forests in an East Africa biodiversity hotspot: chameleons as a model to track forest history. PLoS One 2011; 6:e26606. [PMID: 22053198 PMCID: PMC3203880 DOI: 10.1371/journal.pone.0026606] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 09/29/2011] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The Eastern Arc Mountains (EAM) is an example of naturally fragmented tropical forests, which contain one of the highest known concentrations of endemic plants and vertebrates. Numerous paleo-climatic studies have not provided direct evidence for ancient presence of Pleistocene forests, particularly in the regions in which savannah presently occurs. Knowledge of the last period when forests connected EAM would provide a sound basis for hypothesis testing of vicariance and dispersal models of speciation. Dated phylogenies have revealed complex patterns throughout EAM, so we investigated divergence times of forest fauna on four montane isolates in close proximity to determine whether forest break-up was most likely to have been simultaneous or sequential, using population genetics of a forest restricted arboreal chameleon, Kinyongia boehmei. METHODOLOGY/PRINCIPAL FINDINGS We used mitochondrial and nuclear genetic sequence data and mutation rates from a fossil-calibrated phylogeny to estimate divergence times between montane isolates using a coalescent approach. We found that chameleons on all mountains are most likely to have diverged sequentially within the Pleistocene from 0.93-0.59 Ma (95% HPD 0.22-1.84 Ma). In addition, post-hoc tests on chameleons on the largest montane isolate suggest a population expansion ∼182 Ka. CONCLUSIONS/SIGNIFICANCE Sequential divergence is most likely to have occurred after the last of three wet periods within the arid Plio-Pleistocene era, but was not correlated with inter-montane distance. We speculate that forest connection persisted due to riparian corridors regardless of proximity, highlighting their importance in the region's historic dispersal events. The population expansion coincides with nearby volcanic activity, which may also explain the relative paucity of the Taita's endemic fauna. Our study shows that forest chameleons are an apposite group to track forest fragmentation, with the inference that forest extended between some EAM during the Pleistocene 1.1-0.9 Ma.
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Affiliation(s)
- G John Measey
- Applied Biodiversity Research Division, South African National Biodiversity Institute, Cape Town, South Africa.
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