1
|
Mottaghinia S, Stenzel S, Tsangaras K, Nikolaidis N, Laue M, Müller K, Hölscher H, Löber U, McEwen GK, Donnellan SC, Rowe KC, Aplin KP, Goffinet C, Greenwood AD. A recent gibbon ape leukemia virus germline integration in a rodent from New Guinea. Proc Natl Acad Sci U S A 2024; 121:e2220392121. [PMID: 38305758 PMCID: PMC10861895 DOI: 10.1073/pnas.2220392121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 11/30/2023] [Indexed: 02/03/2024] Open
Abstract
Germline colonization by retroviruses results in the formation of endogenous retroviruses (ERVs). Most colonization's occurred millions of years ago. However, in the Australo-Papuan region (Australia and New Guinea), several recent germline colonization events have been discovered. The Wallace Line separates much of Southeast Asia from the Australo-Papuan region restricting faunal and pathogen dispersion. West of the Wallace Line, gibbon ape leukemia viruses (GALVs) have been isolated from captive gibbons. Two microbat species from China appear to have been infected naturally. East of Wallace's Line, the woolly monkey virus (a GALV) and the closely related koala retrovirus (KoRV) have been detected in eutherians and marsupials in the Australo-Papuan region, often vertically transmitted. The detected vertically transmitted GALV-like viruses in Australo-Papuan fauna compared to sporadic horizontal transmission in Southeast Asia and China suggest the GALV-KoRV clade originates in the former region and further models of early-stage genome colonization may be found. We screened 278 samples, seven bat and one rodent family endemic to the Australo-Papuan region and bat and rodent species found on both sides of the Wallace Line. We identified two rodents (Melomys) from Australia and Papua New Guinea and no bat species harboring GALV-like retroviruses. Melomys leucogaster from New Guinea harbored a genomically complete replication-competent retrovirus with a shared integration site among individuals. The integration was only present in some individuals of the species indicating this retrovirus is at the earliest stages of germline colonization of the Melomys genome, providing a new small wild mammal model of early-stage genome colonization.
Collapse
Affiliation(s)
- Saba Mottaghinia
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
- Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, LyonF-69007, France
| | - Saskia Stenzel
- Institute of Virology Charité–Universitätsmedizin Berlin, BerlinD-10117, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, LiverpoolL3 5QA, United Kingdom
| | - Kyriakos Tsangaras
- Department of Life and Health Sciences, University of Nicosia, NicosiaCY-2417, Cyprus
| | - Nikolas Nikolaidis
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA92834-6850
| | - Michael Laue
- Advanced Light and Electron Microscopy (ZBS 4), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, BerlinD-13353, Germany
| | - Karin Müller
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
| | - Henriette Hölscher
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
| | - Ulrike Löber
- Max-Delbrük Center for Molecular Medicine Helmholtz Association, Berlin13125, Germany
| | - Gayle K. McEwen
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
| | | | - Kevin C. Rowe
- Sciences Department, Museums Victoria, Melbourne, VIC3001, Australia
| | - Ken P. Aplin
- South Australian Museum, North Terrace, Adelaide SA5000, Australia
| | - Christine Goffinet
- Institute of Virology Charité–Universitätsmedizin Berlin, BerlinD-10117, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, LiverpoolL3 5QA, United Kingdom
| | - Alex D. Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin14163, Germany
| |
Collapse
|
2
|
Mcguire JA, Huang X, Reilly SB, Iskandar DT, Wang-Claypool CY, Werning S, Chong RA, Lawalata SZS, Stubbs AL, Frederick JH, Brown RM, Evans BJ, Arifin U, Riyanto A, Hamidy A, Arida E, Koo MS, Supriatna J, Andayani N, Hall R. Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation. Syst Biol 2023; 72:885-911. [PMID: 37074804 PMCID: PMC10405571 DOI: 10.1093/sysbio/syad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/20/2023] Open
Abstract
The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].
Collapse
Affiliation(s)
- Jimmy A Mcguire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Xiaoting Huang
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qindao, Shandong, 266003, PR China
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060, USA
| | - Djoko T Iskandar
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Sarah Werning
- Department of Anatomy, Des Moines University, 3200 Grand Avenue, Des Moines, IA 50312-4198, USA
| | - Rebecca A Chong
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Shobi Z S Lawalata
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- United in Diversity Foundation, Jalan Hayam Wuruk, Jakarta, Indonesia
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey H Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, 1345 Jayhawk Blvd., University of Kansas, Lawrence, KS 66045, USA
| | - Ben J Evans
- Biology Department, McMaster University, Hamilton, Ontario, Canada
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
- Center for Taxonomy and Morphology, Zoologisches Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, R230 20146 Hamburg, Germany
| | - Awal Riyanto
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency of Indonesia (BRIN), Cibinong 16911, Indonesia
| | - Michelle S Koo
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA
| | - Jatna Supriatna
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Noviar Andayani
- Department of Biology, Institute for Sustainable Earth and Resources (I-SER), Gedung Laboratorium Multidisiplin, and Research Center for Climate Change (RCCC-UI), Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Robert Hall
- SE Asia Research Group (SEARG), Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| |
Collapse
|
3
|
Wu ZY, Milne RI, Liu J, Slik F, Yu Y, Luo YH, Monro AK, Wang WT, Wang H, Kessler PJA, Cadotte MW, Nathan R, Li DZ. Phylogenomics and evolutionary history of Oreocnide (Urticaceae) shed light on recent geological and climatic events in SE Asia. Mol Phylogenet Evol 2022; 175:107555. [PMID: 35724818 DOI: 10.1016/j.ympev.2022.107555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 11/26/2022]
Abstract
Climate change and geological events have long been known to shape biodiversity, implying that these can likewise be viewed from a biological perspective. To study whether plants can shed light on this, and how they responded to climate change there, we examined Oreocnide, a genus widely distributed in SE Asia. Based on broad geographic sampling with genomic data, we employed an integrative approach of phylogenomics, molecular dating, historical biogeography, and ecological analyses. We found that Oreocnide originated in mainland East Asia and began to diversify ∼6.06 Ma, probably in response to a distinct geographic and climatic transition in East Asia at around that time, implying that the last important geological change in mainland SE Asia might be 1 Ma older than previously suggested. Around four immigration events to the islands of Malesia followed, indicating that immigration from the mainland could be an underestimated factor in the assembly of biotic communities in the region. Two detected increases of diversification rate occurred 3.13 and 1.19 Ma, which strongly implicated climatic rather than geological changes as likely drivers of diversification, with candidates being the Pliocene intensification of the East Asian monsoons, and Pleistocene climate and sea level fluctuations. Distribution modelling indicated that Pleistocene sea level and climate fluctuations were inferred to enable inter-island dispersal followed by allopatric separation, underpinning radiation in the genus. Overall, our study, based on multiple lines of evidence, linked plant diversification to the most recent climatic and geological events in SE Asia. We highlight the importance of immigration in the assembly and diversification of the SE Asian flora, and underscore the utility of plant clades, as independent lines of evidence, for reconstructing recent climatic and geological events in the SE Asian region.
Collapse
Affiliation(s)
- Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Jie Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ferry Slik
- Environmental and Life Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong, BE1410, Brunei Darussalam
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610207, China
| | - Ya-Huang Luo
- Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Alexandre K Monro
- Identification & Naming Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Wan-Ting Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Hong Wang
- Key Laboratory for Plant and Biodiversity of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Paul J A Kessler
- Uiversity of Leiden Hortus botanicus Leiden, PO Box 9500, 2300 RA Leiden, The Netherlands
| | - Marc W Cadotte
- Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Ran Nathan
- Movement Ecology Laboratory, Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| |
Collapse
|
4
|
Arfianti T, Costello MJ. The distribution of benthic amphipod crustaceans in Indonesian seas. PeerJ 2021; 9:e12054. [PMID: 34540368 PMCID: PMC8411938 DOI: 10.7717/peerj.12054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/04/2021] [Indexed: 11/20/2022] Open
Abstract
Amphipod crustaceans are an essential component of tropical marine biodiversity. However, their distribution and biogeography have not been analysed in one of the world’s largest tropical countries nested in the Coral Triangle, Indonesia. We collected and identified amphipod crustaceans from eight sites in Indonesian waters and combined the results with data from 32 additional sites in the literature. We analysed the geographic distribution of 147 benthic amphipod crustaceans using cluster analysis and the ‘Bioregions Infomaps’ neural network method of biogeographic discrimination. We found five groups of benthic amphipod crustaceans which show relationships with sampling methods, depth, and substrata. Neural network biogeographic analysis indicated there was only one biogeographic region that matched with the global amphipod regions and marine biogeographic realms defined for all marine taxa. There was no support for Wallaces or other lines being marine biogeographic boundaries in the region. Species richness was lower than expected considering the region is within the Coral Triangle. We hypothesise that this low richness might be due to the intense fish predation which may have limited amphipod diversification. The results indicated that habitat rather than biogeography determines amphipod distribution in Indonesia. Therefore, future research needs to sample more habitats, and consider habitat in conservation planning.
Collapse
Affiliation(s)
- Tri Arfianti
- Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Jawa Barat, Indonesia
| | - Mark John Costello
- School of Environment, University of Auckland, Auckland, New Zealand.,Faculty of Bioscience and Aquaculture, Nord University, Bodø, Norway
| |
Collapse
|
5
|
Termite transects from Buton Island, Sulawesi, have a low diversity compared with Sundaland sites. JOURNAL OF TROPICAL ECOLOGY 2021. [DOI: 10.1017/s0266467421000146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractWe used a standardised transect method to compare lowland forest termite assemblages in Buton Island, Sulawesi, with transects in Sundaland. The four Buton transects were extremely depauperate with species density ranging from 1 to 6 species, which is around 10% of the species density in 11 described Sundaland transects. Soil-feeding species were absent from the Buton transects but represent some 43% of species in the Sundaland transects. The Buton transects have relatively high soil pH (6.7–7.9), which may be associated with depauperate termite assemblages. Most termite genera recorded in Sulawesi are wood nesters that can raft in floating wood, which is probably how they arrived in Sulawesi. The Macrotermitinae (fungus-growers) do not raft and probably flew across serendipitously. Geographic isolation, both on Buton and in Sulawesi more generally, and Buton’s underlying geology causing high soil pH, may account for the near-absence of soil-nesters and soil-feeders, none of which are known to raft.
Collapse
|
6
|
Reilly SB, Stubbs AL, Arida E, Karin BR, Arifin U, Kaiser H, Bi K, Iskandar DT, McGuire JA. Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus Draco). Syst Biol 2021; 71:221-241. [PMID: 34117769 DOI: 10.1093/sysbio/syab043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder gene flow. Phylogenetic and species delimitation analyses of flying lizards (genus Draco) using single mitochondrial genes, complete mitochondrial genomes, and exome-capture data sets identified 9-11 deeply divergent lineages including single-island endemics, lineages that span multiple islands, and parapatrically-distributed non-sister lineages on the larger islands. Population clustering and PCA confirmed these genetic boundaries with isolation-by-distance playing a role in some islands or island sets. While gdi estimates place most candidate species comparisons in the ambiguous zone, migration estimates suggest 9 or 10 species exist with nuclear introgression detected across some intra-island contact zones. Initial entry of Draco into the archipelago occurred at 5.5-7.5 Ma, with most inter-island colonization events having occurred between 1-3 Ma. Biogeographical model testing favors scenarios integrating geographic distance and historical island connectivity, including an initial stepping-stone dispersal process from the Greater Sunda Shelf through the Sunda Arc as far eastward as Lembata Island. However, rather than reaching the adjacent island of Pantar by dispersing over the 15-km wide Alor Strait, Draco ultimately reached Pantar (and much of the rest of the archipelago) by way of a circuitous route involving at least five over-water dispersal events. These findings suggest that historical geological and oceanographic conditions heavily influenced dispersal pathways and gene flow, which in turn drove species formation and shaped species boundaries.
Collapse
Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Evy Arida
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Umilaela Arifin
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, Indonesia
| | - Hinrich Kaiser
- Department of Vertebrate Zoology, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany; and Department of Biology, Victor Valley College, Victorville, California 92395, USA
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | | | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| |
Collapse
|
7
|
Ali JR, Heaney LR. Wallace's line,
Wallacea
, and associated divides and areas: history of a tortuous tangle of ideas and labels. Biol Rev Camb Philos Soc 2021; 96:922-942. [DOI: 10.1111/brv.12683] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 12/27/2022]
Affiliation(s)
- Jason R. Ali
- Department of Earth Sciences University of Hong Kong Pokfulam Road Hong Kong China
| | - Lawrence R. Heaney
- Field Museum of Natural History 1400 S Lake Shore Drive Chicago IL 60605‐2496 U.S.A
| |
Collapse
|
8
|
Richmond JQ, Ota H, Grismer LL, Fisher RN. Influence of niche breadth and position on the historical biogeography of seafaring scincid lizards. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Niche breadth and position can influence diversification among closely related species or populations, yet limited empirical data exist concerning the predictability of the outcomes. We explored the effects of these factors on the evolution of the Emoia atrocostata species group, an insular radiation of lizards in the western Pacific Ocean and Indo-Australasia composed of both endemic and widespread species that differ in niche occupancy. We used molecular data and phylogeographical diffusion models to estimate the timing and patterns of range expansion, and ancestral reconstruction methods to infer shifts in ecology. We show evidence of multidirectional spread from a centre of origin in western Micronesia, and that the phyletic diversity of the group is derived from a putative habitat specialist that survives in the littoral zone. This species is composed of paraphyletic lineages that represent stages or possible endpoints in the continuum toward speciation. Several descendant species have transitioned to either strand or interior forest habitat, but only on remote islands with depauperate terrestrial faunas. Our results suggest that the atrocostata group might be in the early phases of a Wilsonian taxon cycle and that the capacity to tolerate salt stress has promoted dispersal and colonization of remote oceanic islands. Divergence itself, however, is largely driven by geographical isolation rather than shifts in ecology.
Collapse
Affiliation(s)
| | - Hidetoshi Ota
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - L Lee Grismer
- Department of Biology, La Sierra University, Riverside, CA, USA
| | | |
Collapse
|
9
|
Hermogenes De Mendonça L, Ebach MC. A review of transition zones in biogeographical classification. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Transition zones are problematic in biogeographical classification as they represent artificial biotic areas. A review of transition zones into existing biogeographical classifications shows conflicting area taxonomies. While many authors consider transition zones as overlap zones or areas of biotic mixing, only a few have considered excluding them from biogeographical classification all together. One way of incorporating transition zones into a natural classification is by treating them as artefacts of geographically overlapping temporally disjunct biotic areas. In doing so, geographically overlapping biotic areas may occupy the same space but have different boundaries and histories. Temporally disjunct areas do form natural hierarchical classifications, as seen in the paleobiogeographical literature. A revision of each transition zone will determine whether they are artificial areas, areas within their own right or potentially geographically overlapping temporally disjunct regions.
Collapse
Affiliation(s)
- Lize Hermogenes De Mendonça
- Changing Earth, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Malte C Ebach
- Changing Earth, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| |
Collapse
|
10
|
Esquerré D, Donnellan S, Brennan IG, Lemmon AR, Moriarty Lemmon E, Zaher H, Grazziotin FG, Keogh JS. Phylogenomics, Biogeography, and Morphometrics Reveal Rapid Phenotypic Evolution in Pythons After Crossing Wallace’s Line. Syst Biol 2020; 69:1039-1051. [DOI: 10.1093/sysbio/syaa024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
Abstract
Ecological opportunities can be provided to organisms that cross stringent biogeographic barriers towards environments with new ecological niches. Wallace’s and Lyddeker’s lines are arguably the most famous biogeographic barriers, separating the Asian and Australo-Papuan biotas. One of the most ecomorphologically diverse groups of reptiles, the pythons, is distributed across these lines, and are remarkably more diverse in phenotype and ecology east of Lydekker’s line in Australo-Papua. We used an anchored hybrid enrichment approach, with near complete taxon sampling, to extract mitochondrial genomes and 376 nuclear loci to resolve and date their phylogenetic history. Biogeographic reconstruction demonstrates that they originated in Asia around 38-45 Ma and then invaded Australo-Papua around 23 Ma. Australo-Papuan pythons display a sizeable expansion in morphological space, with shifts towards numerous new adaptive optima in head and body shape, coupled with the evolution of new micro-habitat preferences. We provide an updated taxonomy of pythons and our study also demonstrates how ecological opportunity following colonization of novel environments can promote morphological diversification in a formerly ecomorphologically conservative group. [Adaptive radiation; anchored hybrid enrichment; biogeography; morphometrics; snakes.]
Collapse
Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Stephen Donnellan
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
- South Australian Museum, North Terrace, Adelaide SA 5000 Australia
| | - Ian G Brennan
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library Tallahassee, FL 32306-4120, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Hussam Zaher
- Museu de Zoologia, Universidade de São Paulo, Avenida Nazaré 481, CEP 04263-000, São Paulo, SP, Brazil
- CR2P – Centre de Recherche em Paléontologie – MNHN – Sorbonne Université – CNRS, 8 rue Buffon, CP 38, 75005 Paris, France
| | - Felipe G Grazziotin
- Laboratório de Coleções Zoológicas, Instituto Butantan, São Paulo, SP, Brazil
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| |
Collapse
|
11
|
Narakusumo RP, Balke M, Riedel A. Seven new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from the Tanimbar Archipelago. Zookeys 2019; 888:75-93. [PMID: 31754320 PMCID: PMC6861340 DOI: 10.3897/zookeys.888.38642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/08/2019] [Indexed: 11/12/2022] Open
Abstract
Based on recent fieldwork, the hyperdiverse weevil genus Trigonopterus Fauvel is recorded for the first time from the Indonesian Tanimbar Archipelago, halfway between Australia and Western New Guinea. All seven species discovered on Tanimbar are new to science, and described here: Trigonopterus atuf sp. nov., T. kumbang sp. nov., T. laratensis sp. nov., T. porg sp. nov., T. selaruensis sp. nov., T. tanimbarensis sp. nov., and T. triradiatus sp. nov. The new species are authored by the taxonomists-in-charge, Raden Pramesa Narakusumo and Alexander Riedel. This fauna appears discordant and established by relatively recent dispersal from New Guinea and other Moluccan islands.
Collapse
Affiliation(s)
- Raden Pramesa Narakusumo
- State Museum of Natural History Karlsruhe, Erbprinzenstr. 13, D-76133 Karlsruhe, Germany.,Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Gd. Widyasatwaloka, Jl. Raya Jakarta-Bogor km 46, Cibinong 16911, Indonesia
| | - Michael Balke
- SNSB-Zoological State Collection (ZSM), Münchhausenstr. 21, D-81247 Munich, Germany
| | - Alexander Riedel
- State Museum of Natural History Karlsruhe, Erbprinzenstr. 13, D-76133 Karlsruhe, Germany
| |
Collapse
|
12
|
Trethowan LA, Arif A, Clark RP, Girmansyah D, Kintamani E, Prychid CJ, Pujirahayu N, Rosmarlinasiah, Brearley FQ, Utteridge TMA, Lewis GP. An enigmatic genus on an enigmatic island: the re-discovery of Kalappia on Sulawesi. Ecology 2019; 100:e02793. [PMID: 31228253 DOI: 10.1002/ecy.2793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/13/2019] [Accepted: 05/29/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Liam A Trethowan
- Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom.,Royal Botanic Gardens Kew, Richmond, TW9 3AE, United Kingdom
| | | | - Ruth P Clark
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, United Kingdom
| | - Deden Girmansyah
- Herbarium Bogoriense, Indonesian Institute of Sciences, Cibinong, 16911, Indonesia
| | - Endang Kintamani
- Herbarium Bogoriense, Indonesian Institute of Sciences, Cibinong, 16911, Indonesia
| | | | | | | | | | | | - Gwilym P Lewis
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, United Kingdom
| |
Collapse
|
13
|
O’Connell DP, Kelly DJ, Lawless N, O’Brien K, Marcaigh FÓ, Karya A, Analuddin K, Marples NM. A sympatric pair of undescribed white-eye species (Aves: Zosteropidae: Zosterops) with different origins. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Darren P O’Connell
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
- School of Biology & Environment Science, University College Dublin, Dublin, Ireland
| | - David J Kelly
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Naomi Lawless
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Katie O’Brien
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Fionn Ó Marcaigh
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Adi Karya
- Department of Biology and Biotechnology, Universitas Halu Oleo, Kendari, South-east Sulawesi, Indonesia
| | - Kangkuso Analuddin
- Department of Biology and Biotechnology, Universitas Halu Oleo, Kendari, South-east Sulawesi, Indonesia
| | - Nicola M Marples
- Department of Zoology, School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| |
Collapse
|
14
|
Turvey ST, Crees JJ, Hansford J, Jeffree TE, Crumpton N, Kurniawan I, Setiyabudi E, Guillerme T, Paranggarimu U, Dosseto A, van den Bergh GD. Quaternary vertebrate faunas from Sumba, Indonesia: implications for Wallacean biogeography and evolution. Proc Biol Sci 2018; 284:rspb.2017.1278. [PMID: 28855367 PMCID: PMC5577490 DOI: 10.1098/rspb.2017.1278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/21/2017] [Indexed: 12/03/2022] Open
Abstract
Historical patterns of diversity, biogeography and faunal turnover remain poorly understood for Wallacea, the biologically and geologically complex island region between the Asian and Australian continental shelves. A distinctive Quaternary vertebrate fauna containing the small-bodied hominin Homo floresiensis, pygmy Stegodon proboscideans, varanids and giant murids has been described from Flores, but Quaternary faunas are poorly known from most other Lesser Sunda Islands. We report the discovery of extensive new fossil vertebrate collections from Pleistocene and Holocene deposits on Sumba, a large Wallacean island situated less than 50 km south of Flores. A fossil assemblage recovered from a Pleistocene deposit at Lewapaku in the interior highlands of Sumba, which may be close to 1 million years old, contains a series of skeletal elements of a very small Stegodon referable to S. sumbaensis, a tooth attributable to Varanus komodoensis, and fragmentary remains of unidentified giant murids. Holocene cave deposits at Mahaniwa dated to approximately 2000–3500 BP yielded extensive material of two new genera of endemic large-bodied murids, as well as fossils of an extinct frugivorous varanid. This new baseline for reconstructing Wallacean faunal histories reveals that Sumba's Quaternary vertebrate fauna, although phylogenetically distinctive, was comparable in diversity and composition to the Quaternary fauna of Flores, suggesting that similar assemblages may have characterized Quaternary terrestrial ecosystems on many or all of the larger Lesser Sunda Islands.
Collapse
Affiliation(s)
- Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Jennifer J Crees
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - James Hansford
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK.,Ocean and Earth Science, National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, UK
| | - Timothy E Jeffree
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Nick Crumpton
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | | | | | - Thomas Guillerme
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot SL5 7PY, UK
| | | | - Anthony Dosseto
- Wollongong Isotope Geochronology Laboratory, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Gerrit D van den Bergh
- Centre for Archaeological Science, School of Earth and Environmental Sciences, University of Wollongong, Wollongong, New South Wales 2522, Australia
| |
Collapse
|
15
|
Establishing a Framework for a Natural Area Taxonomy. Acta Biotheor 2017; 65:167-177. [PMID: 28493088 DOI: 10.1007/s10441-017-9310-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
The identification of areas of endemism is essential in building an area classification, but plays little role in how natural areas are discovered. Rather area monophyly, derived from cladistics, is essential in the discovery of natural area classifications or area taxonomy. We propose Area Taxonomy to be a new sub-discipline of historical biogeography, one that can be revised and debated, and which has its own area nomenclature. Separately to area taxonomy, we outline how natural areas may be discovered by transcribing the concepts of homology and monophyly from biological systematics to historical biogeography, in the form of area homologues, area homologies and area monophyly.
Collapse
|
16
|
Morinaka S, Erniwati, Minaka N, Miyata T, Hoshizaki S. Phylogeography of the Delias hyparete species group (Lepidoptera: Pieridae): complex historical dispersals into and out of Wallacea. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
17
|
Döring B, Mecke S, Kieckbusch M, O’Shea M, Kaiser H. Food spectrum analysis of the Asian toad,Duttaphrynus melanostictus(Schneider, 1799) (Anura: Bufonidae), from Timor Island, Wallacea. J NAT HIST 2017. [DOI: 10.1080/00222933.2017.1293182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
18
|
Abstract
Ontological understanding of biological units (i.e. what kinds of things are they) is crucial to their use in experimental design, analysis, and interpretation. Conceptualizing fundamental units in biology as individuals or classes is important for subsequent development of discovery operations. While the criteria for diagnosing individuals are acknowledged, temporal boundedness is often misinterpreted and temporal minima are applied to units in question. This results in misdiagnosis or abandonment of ontological interpretation altogether. Biological units such as areas of endemism in biogeography and species in evolutionary biology fall victim to such problems. Our goal here is to address the misconception that biological individuals such as species and areas of endemism have a temporal minimum. Areas of endemism can persist within small temporal boundaries in the context of metapopulation dynamics, island biogeography, and range expansion and contraction. Similarly, lineage reticulation illustrates examples of short-lived species. Here, examples of known entities are provided to illustrate their persistence on short time scales in attempt to rescue future interpretation of biological units from ontological misdiagnosis, elucidate the philosophical individuality of areas of endemism and species with short lifespans, and provide justification for the "snapshot in time" diagnostic approach.
Collapse
Affiliation(s)
- Christopher M Murray
- Department of Biological Sciences, Auburn University, 331 Funchess Hall, Auburn, AL, 36849, USA.
| | - Brian I Crother
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, 70402, USA.
| |
Collapse
|
19
|
Driller C, Merker S, Perwitasari-Farajallah D, Sinaga W, Anggraeni N, Zischler H. Stop and Go - Waves of Tarsier Dispersal Mirror the Genesis of Sulawesi Island. PLoS One 2015; 10:e0141212. [PMID: 26559527 PMCID: PMC4641617 DOI: 10.1371/journal.pone.0141212] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/05/2015] [Indexed: 11/18/2022] Open
Abstract
The Indonesian island of Sulawesi harbors a highly endemic and diverse fauna sparking fascination since long before Wallace’s contemplation of biogeographical patterns in the region. Allopatric diversification driven by geological or climatic processes has been identified as the main mechanism shaping present faunal distribution on the island. There is both consensus and conflict among range patterns of terrestrial species pointing to the different effects of vicariant events on once co-distributed taxa. Tarsiers, small nocturnal primates with possible evidence of an Eocene fossil record on the Asian mainland, are at present exclusively found in insular Southeast Asia. Sulawesi is hotspot of tarsier diversity, whereby island colonization and subsequent radiation of this old endemic primate lineage remained largely enigmatic. To resolve the phylogeographic history of Sulawesi tarsiers we analyzed an island-wide sample for a set of five approved autosomal phylogenetic markers (ABCA1, ADORA3, AXIN1, RAG1, and TTR) and the paternally inherited SRY gene. We constructed ML and Bayesian phylogenetic trees and estimated divergence times between tarsier populations. We found that their arrival at the Proto-Sulawesi archipelago coincided with initial Miocene tectonic uplift and hypothesize that tarsiers dispersed over the region in distinct waves. Intra-island diversification was spurred by land emergence and a rapid succession of glacial cycles during the Plio-Pleistocene. Some tarsier range boundaries concur with spatial limits in other taxa backing the notion of centers of faunal endemism on Sulawesi. This congruence, however, has partially been superimposed by taxon-specific dispersal patterns.
Collapse
Affiliation(s)
- Christine Driller
- Institute of Anthropology, Johannes-Gutenberg University Mainz, Mainz, Germany
- * E-mail:
| | - Stefan Merker
- Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | - Dyah Perwitasari-Farajallah
- Primate Research Center, Bogor Agricultural University, Bogor, Indonesia
- Department of Biology, Bogor Agricultural University, Bogor, Indonesia
| | - Walberto Sinaga
- Primate Research Center, Bogor Agricultural University, Bogor, Indonesia
| | - Novita Anggraeni
- School of Graduate Studies, Bogor Agricultural University, Bogor, Indonesia
| | - Hans Zischler
- Institute of Anthropology, Johannes-Gutenberg University Mainz, Mainz, Germany
| |
Collapse
|
20
|
Ung V, Zaragueta-Bagils R, Williams DM. Comparative biogeography of Southeast Asia and the West Pacific region. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12670] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Visotheary Ung
- Institut de Systématique, Evolution, Biodiversité (ISYEB, UMR 7205); Sorbonne Universités; Museum National d'Histoire Naturelle; Université Pierre et Marie Curie, CNRS, EPHE; 57 rue Cuvier CP48 75005 Paris France
- Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P, UMR 7207); Sorbonne Universités; Museum National d'Histoire Naturelle; Université Pierre et Marie Curie, CNRS; 57 rue Cuvier CP48 75005 Paris France
| | - René Zaragueta-Bagils
- Institut de Systématique, Evolution, Biodiversité (ISYEB, UMR 7205); Sorbonne Universités; Museum National d'Histoire Naturelle; Université Pierre et Marie Curie, CNRS, EPHE; 57 rue Cuvier CP48 75005 Paris France
- Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements (CR2P, UMR 7207); Sorbonne Universités; Museum National d'Histoire Naturelle; Université Pierre et Marie Curie, CNRS; 57 rue Cuvier CP48 75005 Paris France
| | - David M. Williams
- Department of Life Sciences; The Natural History Museum; Cromwell Road London SW7 5 BD UK
| |
Collapse
|
21
|
Dalsgaard B, Carstensen DW, Fjeldså J, Maruyama PK, Rahbek C, Sandel B, Sonne J, Svenning JC, Wang Z, Sutherland WJ. Determinants of bird species richness, endemism, and island network roles in Wallacea and the West Indies: is geography sufficient or does current and historical climate matter? Ecol Evol 2014; 4:4019-31. [PMID: 25505528 PMCID: PMC4242583 DOI: 10.1002/ece3.1276] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 09/01/2014] [Indexed: 11/26/2022] Open
Abstract
Island biogeography has greatly contributed to our understanding of the processes determining species' distributions. Previous research has focused on the effects of island geography (i.e., island area, elevation, and isolation) and current climate as drivers of island species richness and endemism. Here, we evaluate the potential additional effects of historical climate on breeding land bird richness and endemism in Wallacea and the West Indies. Furthermore, on the basis of species distributions, we identify island biogeographical network roles and examine their association with geography, current and historical climate, and bird richness/endemism. We found that island geography, especially island area but also isolation and elevation, largely explained the variation in island species richness and endemism. Current and historical climate only added marginally to our understanding of the distribution of species on islands, and this was idiosyncratic to each archipelago. In the West Indies, endemic richness was slightly reduced on islands with historically unstable climates; weak support for the opposite was found in Wallacea. In both archipelagos, large islands with many endemics and situated far from other large islands had high importance for the linkage within modules, indicating that these islands potentially act as speciation pumps and source islands for surrounding smaller islands within the module and, thus, define the biogeographical modules. Large islands situated far from the mainland and/or with a high number of nonendemics acted as links between modules. Additionally, in Wallacea, but not in the West Indies, climatically unstable islands tended to interlink biogeographical modules. The weak and idiosyncratic effect of historical climate on island richness, endemism, and network roles indicates that historical climate had little effects on extinction-immigration dynamics. This is in contrast to the strong effect of historical climate observed on the mainland, possibly because surrounding oceans buffer against strong climate oscillations and because geography is a strong determinant of island richness, endemism and network roles.
Collapse
Affiliation(s)
- Bo Dalsgaard
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen Universitetsparken 15, DK-2100, Copenhagen Ø, Denmark ; Conservation Science Group, Department of Zoology, University of Cambridge Downing Street, Cambridge, CB2 3EJ, UK
| | - Daniel W Carstensen
- Department of Biological Sciences, Aarhus University Ny Munkegade 114, DK-8000, Aarhus C, Denmark ; Plant Phenology and Seed Dispersal Group, Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista (UNESP) Avenida 24-A n° 1515, Rio Claro, SP, 13506-900, Brazil
| | - Jon Fjeldså
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen Universitetsparken 15, DK-2100, Copenhagen Ø, Denmark
| | - Pietro K Maruyama
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen Universitetsparken 15, DK-2100, Copenhagen Ø, Denmark ; Programa de Pós-Graduacão em Ecologia, Universidade Estadual de Campinas (UNICAMP) Cx. Postal 6109, Campinas, SP, 13083-865, Brazil
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen Universitetsparken 15, DK-2100, Copenhagen Ø, Denmark
| | - Brody Sandel
- Department of Biological Sciences, Aarhus University Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Jesper Sonne
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen Universitetsparken 15, DK-2100, Copenhagen Ø, Denmark
| | - Jens-Christian Svenning
- Department of Biological Sciences, Aarhus University Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Zhiheng Wang
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen Universitetsparken 15, DK-2100, Copenhagen Ø, Denmark
| | - William J Sutherland
- Conservation Science Group, Department of Zoology, University of Cambridge Downing Street, Cambridge, CB2 3EJ, UK
| |
Collapse
|
22
|
von Rintelen T, Stelbrink B, Marwoto RM, Glaubrecht M. A snail perspective on the biogeography of Sulawesi, Indonesia: origin and intra-island dispersal of the viviparous freshwater gastropod Tylomelania. PLoS One 2014; 9:e98917. [PMID: 24971564 PMCID: PMC4090239 DOI: 10.1371/journal.pone.0098917] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/09/2014] [Indexed: 11/25/2022] Open
Abstract
The complex geological history of the Indonesian island Sulawesi has shaped the origin and subsequent diversification of its taxa. For the endemic freshwater snail Tylomelania a vicariant origin from the Australian margin has been hypothesized. Divergence time estimates from a mtDNA phylogeny based on a comprehensive island-wide sampling of Tylomelania fit regional tectonic constraints and support the ‘out-of-Australia’ vicariance hypothesis. The Banggai-Sula region of the Sula Spur, the Australian promontory colliding with West Sulawesi during the Miocene, is identified as a possible source area for the colonization of Sulawesi by the ancestor of Tylomelania. The molecular phylogeny also shows a rapid diversification of Tylomelania into eight major lineages with very little overlap in their distribution on the island. Haplotype networks provide further evidence for a strong spatial structure of genetic diversity in Tylomelania. Distribution boundaries of the major lineages do at best partially coincide with previously identified contact zones for other endemic species groups on Sulawesi. This pattern has likely been influenced by the poor dispersal capabilities and altitudinal distribution limits of this strict freshwater inhabitant. We suggest that late Miocene and Pliocene orogeny in large parts of Sulawesi has been the vicariant event driving primary diversification in Tylomelania.
Collapse
Affiliation(s)
- Thomas von Rintelen
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
- * E-mail:
| | - Björn Stelbrink
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Ristiyanti M. Marwoto
- Zoology Division (Museum Zoologicum Bogoriense), Research Center for Biology, LIPI, Cibinong, Bogor, Indonesia
| | - Matthias Glaubrecht
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| |
Collapse
|
23
|
Ogawa R, Loebl I, Maeto K. Three new species of the genus Scaphicoma Motschulsky, 1863 (Coleoptera, Staphylinidae, Scaphidiinae) from Northern Sulawesi, Indonesia. Zookeys 2014:1-13. [PMID: 24843264 PMCID: PMC4023237 DOI: 10.3897/zookeys.403.7200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 04/02/2014] [Indexed: 11/30/2022] Open
Abstract
Three new species of the genus Scaphicoma Motschulsky, 1863 from Sulawesi, Indonesia are illustrated and described: Scaphicoma subflava Ogawa & Löbl, sp. n., S. bidentia Ogawa & Löbl, sp. n., and S. quadrifasciata Ogawa & Löbl, sp. n.Lepteroscapha pallens Achard, 1921 is designated as the type species of the genus Lepteroscapha Achard, 1921.
Collapse
|
24
|
Meijer HJM. The avian fossil record in Insular Southeast Asia and its implications for avian biogeography and palaeoecology. PeerJ 2014; 2:e295. [PMID: 24688871 PMCID: PMC3961167 DOI: 10.7717/peerj.295] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 02/07/2014] [Indexed: 11/20/2022] Open
Abstract
Excavations and studies of existing collections during the last decades have significantly increased the abundance as well as the diversity of the avian fossil record for Insular Southeast Asia. The avian fossil record covers the Eocene through the Holocene, with the majority of bird fossils Pleistocene in age. Fossil bird skeletal remains represent at least 63 species in 54 genera and 27 families, and two ichnospecies are represented by fossil footprints. Birds of prey, owls and swiftlets are common elements. Extinctions seem to have been few, suggesting continuity of avian lineages since at least the Late Pleistocene, although some shifts in species ranges have occurred in response to climatic change. Similarities between the Late Pleistocene avifaunas of Flores and Java suggest a dispersal route across southern Sundaland. Late Pleistocene assemblages of Niah Cave (Borneo) and Liang Bua (Flores) support the rainforest refugium hypothesis in Southeast Asia as they indicate the persistence of forest cover, at least locally, throughout the Late Pleistocene and Holocene.
Collapse
Affiliation(s)
- Hanneke J M Meijer
- Institut Català de Paleontologia Miquel Crusafont , Cerdanyola del Vallès , Spain
| |
Collapse
|
25
|
Ebach MC. Tewkesbury Walks: An Exploration of Biogeography and Evolution.— By Bernard Michaux. Syst Biol 2014. [DOI: 10.1093/sysbio/syu014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
26
|
An evaluation of taxonomic concepts of the widespread plant genus Aglaia and its allies across Wallace's Line (tribe Aglaieae, Meliaceae). Mol Phylogenet Evol 2014; 73:65-76. [PMID: 24495856 DOI: 10.1016/j.ympev.2014.01.025] [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] [Received: 08/30/2013] [Revised: 11/28/2013] [Accepted: 01/14/2014] [Indexed: 11/22/2022]
Abstract
Similar to other species-rich taxa in the Indo-Australian Archipelago, taxonomy of the genus Aglaia (mahogany family, Meliaceae) remains problematic. This study aims to evaluate taxonomic concepts within Aglaia based on the largest dataset to-date. We analyzed sequences of 237 accessions of Aglaia and representatives of all other genera of the tribe Aglaieae, including nuclear ribosomal ITS, the trnL-trnF intron and intergenic spacer, the atpF intron and the petD region comprising the petB-petD spacer, the petD-5' exon and the petD intron (all but the first from the plastid genome). Our analyses were set both in maximum likelihood and Bayesian frameworks, which (1) supported paraphyly of Aglaia and Aphanamixis; (2) demonstrated polyphyly of previously described sections for Aglaia; and (3) suggested delimitation problems with 57% of the morphologically "variable species" and all "complex species". In general, there were more genetic entities than species described, which shows that the taxonomy of this group is more complex than has sometimes been previously assumed. For some species, morphological variation suggests the existence of more variants, subspecies or species within various taxa. Furthermore, our study detected additional phylogenetic entities that were geographically distinct, occurring on either side of Wallace's Line but not on both sides. The delineation of these inter-specific taxa needs further investigation by taking into account the morphological variation within and between populations across the entire distribution.
Collapse
|
27
|
van Welzen PC, Strijk JS, van Konijnenburg-van Cittert JHA, Nucete M, Merckx VSFT. Dated phylogenies of the sister genera Macaranga and Mallotus (Euphorbiaceae): congruence in historical biogeographic patterns? PLoS One 2014; 9:e85713. [PMID: 24465660 PMCID: PMC3894986 DOI: 10.1371/journal.pone.0085713] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 12/01/2013] [Indexed: 11/18/2022] Open
Abstract
Molecular phylogenies and estimates of divergence times within the sister genera Macaranga and Mallotus were estimated using Bayesian relaxed clock analyses of two generic data sets, one per genus. Both data sets were based on different molecular markers and largely different samples. Per genus three calibration points were utilised. The basal calibration point (crown node of all taxa used) was taken from literature and used for both taxa. The other three calibrations were based on fossils of which two were used per genus. We compared patterns of dispersal and diversification in Macaranga and Mallotus using ancestral area reconstruction in RASP (S-DIVA option) and contrasted our results with biogeographical and geological records to assess accuracy of inferred age estimates. A check of the fossil calibration point showed that the Japanese fossil, used for dating the divergence of Mallotus, probably had to be attached to a lower node, the stem node of all pioneer species, but even then the divergence time was still younger than the estimated age of the fossil. The African (only used in the Macaranga data set) and New Zealand fossils (used for both genera) seemed reliably placed. Our results are in line with existing geological data and the presence of stepping stones that provided dispersal pathways from Borneo to New Guinea-Australia, from Borneo to mainland Asia and additionally at least once to Africa and Madagascar via land and back to India via Indian Ocean island chains. The two genera show congruence in dispersal patterns, which corroborate divergence time estimates, although the overall mode and tempo of dispersal and diversification differ significantly as shown by distribution patterns of extant species.
Collapse
Affiliation(s)
- Peter C. van Welzen
- Naturalis Biodiversity Center, sector Herbarium, Leiden, The Netherlands
- Institute Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Joeri S. Strijk
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan Province, P.R. China
| | | | - Monica Nucete
- Naturalis Biodiversity Center, sector Herbarium, Leiden, The Netherlands
| | | |
Collapse
|
28
|
Brown RM, Siler CD, Oliveros CH, Esselstyn JA, Diesmos AC, Hosner PA, Linkem CW, Barley AJ, Oaks JR, Sanguila MB, Welton LJ, Blackburn DC, Moyle RG, Townsend Peterson A, Alcala AC. Evolutionary Processes of Diversification in a Model Island Archipelago. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110411-160323] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rafe M. Brown
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Cameron D. Siler
- Sam Noble Museum and Department of Biology, University of Oklahoma, Norman, Oklahoma 73073-7029;
| | - Carl H. Oliveros
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803;
| | - Arvin C. Diesmos
- Herpetology Section, Zoology Division, National Museum of the Philippines, Manila, Philippines;
| | - Peter A. Hosner
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Charles W. Linkem
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
- Current address: Department of Biology, University of Washington, Seattle, Washington 98195;
| | - Anthony J. Barley
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Jamie R. Oaks
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | | | - Luke J. Welton
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
- Department of Biology, Brigham Young University, Provo, Utah 84602;
| | - David C. Blackburn
- Department of Vertebrate Zoology and Anthropology, California Academy of Sciences, San Francisco, California 94118;
| | - Robert G. Moyle
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - A. Townsend Peterson
- Department of Ecology and Evolution and Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045; , , , , , ,
| | - Angel C. Alcala
- Silliman University-Angelo King Center for Research and Environmental Management (SUAKCREM), SU-Marine Laboratory, 6200 Dumaguete City, Philippines;
| |
Collapse
|
29
|
Ung V. Biotic Evolution and Environmental Change in Southeast Asia.— Edited by David Gower, Kenneth Johnson, James Richardson, Brian Rosen, Lukas Rüber, and Suzanne Williams. Syst Biol 2013. [DOI: 10.1093/sysbio/syt042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Visotheary Ung
- Centre de Recherche en Paléobiodiversité et Paléoenvironnements (UMR 7207: CNRS MNHN UPMC), 57 rue Cuvier CP 48, 75005 Paris, France; E-mail:
| |
Collapse
|
30
|
Tweedley JR, Bird DJ, Potter IC, Gill HS, Miller PJ, O'Donovan G, Tjakrawidjaja AH. Species compositions and ecology of the riverine ichthyofaunas in two Sulawesian islands in the biodiversity hotspot of Wallacea. JOURNAL OF FISH BIOLOGY 2013; 82:1916-1950. [PMID: 23731145 DOI: 10.1111/jfb.12121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/11/2013] [Indexed: 06/02/2023]
Abstract
This account of the riverine ichthyofaunas from the islands of Buton and Kabaena, off south-eastern mainland Sulawesi, represents the first detailed quantitative checklist and ecological study of the riverine fish faunas in the biological hotspot of Wallacea. The results are based on analysis of samples collected by electrofishing at a wide range of sites from July to September in both 2001 and 2002. While the fauna was diverse, with the 2179 fishes caught comprising 64 species representing 43 genera and 22 families, the catches were dominated by the Gobiidae (26 species and 25% by numbers), Eleotridae (seven species and 27% by numbers), Zenarchopteridae (three species and 22% by numbers) and Anguillidae (two species and 12% by numbers). The most abundant species were the eleotrids Eleotris aff. fusca-melanosoma and Ophieleotris aff. aporos, the anguillid Anguilla celebesensis, the zenarchopterids Nomorhamphus sp. and Nomorhamphus ebrardtii and the gobiids Sicyopterus sp. and Glossogobius aff. celebius-kokius. The introduced catfish Clarias batrachus was moderately abundant at a few sites. Cluster analysis, allied with the similarity profiles routine SIMPROF, identified seven discrete groups, which represented samples from sites entirely or predominantly in either Buton (five clusters) or Kabaena (two clusters). Species composition was related to geographical location, distance from river mouth, per cent contribution of sand and silt, altitude and water temperature. The samples from the two islands contained only one species definitively endemic to Sulawesi, i.e. N. ebrardtii and another presumably so, i.e. Nomorhamphus sp., contrasting starkly with the 57 species that are endemic to Sulawesi and, most notably, its large central and deep lake systems on the mainland. This accounts for the ichthyofaunas of these two islands, as well as those of rivers in northern mainland Sulawesi and Flores, being more similar to each other than to those of the central mainland lake systems. This implies that the major adaptive radiation of freshwater fishes in Sulawesi occurred in those lacustrine environments rather than in rivers.
Collapse
Affiliation(s)
- J R Tweedley
- Centre for Fish and Fisheries Research, School of Biological Sciences and Biotechnology, Murdoch University, Perth, WA 6150, Australia.
| | | | | | | | | | | | | |
Collapse
|
31
|
Affiliation(s)
- John A. Allen
- Centre for Biological Sciences; University of Southampton; Life Sciences Building 85; Southampton; SO17 1BJ; UK
| |
Collapse
|
32
|
Stelbrink B, Albrecht C, Hall R, von Rintelen T. THE BIOGEOGRAPHY OF SULAWESI REVISITED: IS THERE EVIDENCE FOR A VICARIANT ORIGIN OF TAXA ON WALLACE'S “ANOMALOUS ISLAND”? Evolution 2012; 66:2252-71. [DOI: 10.1111/j.1558-5646.2012.01588.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
33
|
Lohman DJ, de Bruyn M, Page T, von Rintelen K, Hall R, Ng PK, Shih HT, Carvalho GR, von Rintelen T. Biogeography of the Indo-Australian Archipelago. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2011. [DOI: 10.1146/annurev-ecolsys-102710-145001] [Citation(s) in RCA: 331] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David J. Lohman
- Department of Biology, The City College of New York, The City University of New York, New York, NY 10031;
| | - Mark de Bruyn
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW United Kingdom; ,
| | - Timothy Page
- Australian Rivers Institute, Griffith University, Nathan, Queensland 4111, Australia;
| | - Kristina von Rintelen
- Museum für Naturkunde—Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, 10115 Berlin, Germany; ,
| | - Robert Hall
- Southeast Asia Research Group, Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, United Kingdom;
| | - Peter K.L. Ng
- Department of Biological Sciences and Raffles Museum of Biodiversity Research, National University of Singapore, Singapore 117546;
| | - Hsi-Te Shih
- Department of Life Science, National Chung Hsing University, Taichung 402, Taiwan;
| | - Gary R. Carvalho
- School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW United Kingdom; ,
| | - Thomas von Rintelen
- Museum für Naturkunde—Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, 10115 Berlin, Germany; ,
| |
Collapse
|
34
|
|
35
|
VAN WELZEN PETERC, PARNELL JOHNAN, SLIK JWFERRY. Wallace's Line and plant distributions: two or three phytogeographical areas and where to group Java? Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01647.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|