101
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Ericson PGP, Qu Y, Rasmussen PC, Blom MPK, Rheindt FE, Irestedt M. Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex. BMC Evol Biol 2019; 19:151. [PMID: 31340765 PMCID: PMC6657069 DOI: 10.1186/s12862-019-1481-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 07/16/2019] [Indexed: 01/01/2023] Open
Abstract
Background Allopatric speciation has played a particularly important role in archipelagic settings where populations evolve in isolation after colonizing different islands. The Indo-Australasian island realm is an unparalleled natural laboratory of biotic diversification. Here we explore how the level of earth-historic isolation has influenced genetic differentiation across the region by investigating phylogeographic patterns in the Pitta sordida species complex. Results We generated a de novo genome and compared population genomics of 29 individuals of Pitta sordida from the entire distributional range and we reconstructed phylogenetic relationship using mitogenomes, a multi-nuclear gene dataset and single nucleotide polymorphisms (SNPs). We found deep divergence between an eastern and a western group of taxa across Indo-Australasia. Within both groups we have identified major lineages that are geographically separated into Philippines, Borneo, western Sundaland, and New Guinea, respectively. Although these lineages are genetically well-differentiated, suggesting a long-term isolation, there are signatures of extensive gene flow within each lineage throughout the Pleistocene, despite the wide geographic range occupied by some of them. We found little evidence of hybridization or introgression among the studied taxa, but forsteni from Sulawesi makes an exception. This individual, belonging to the eastern clade, is genetically admixed between the western and eastern clades. Geographically this makes sense as Sulawesi is not far from Borneo that houses a population of hooded pittas that belongs to the western clade. Conclusions We found that geological vicariance events cannot explain the current genetic differentiation in the Pitta sordida species complex. Instead, the glacial-interglacial cycles may have played a major role therein. During glacials the sea level could be up to 120 m lower than today and land bridges formed within both the Sunda Shelf and the Sahul Shelf permitting dispersal of floral and faunal elements. The geographic distribution of hooded pittas shows the importance of overwater, “stepping-stone” dispersals not only to deep-sea islands, but also from one shelf to the other. The most parsimonious hypothesis is an Asian ancestral home of the Pitta sordida species complex and a colonization from west to east, probably via Wallacea. Electronic supplementary material The online version of this article (10.1186/s12862-019-1481-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden.
| | - Yanhua Qu
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pamela C Rasmussen
- Department of Integrative Biology and MSU Museum, Michigan State University, East Lansing, 48824, MI, USA.,Bird Group, The Natural History Museum, Akeman Street, Tring, HP23 6AP, UK
| | - Mozes P K Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 119077, Singapore
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, SE-104 05, Stockholm, Sweden
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102
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Diversification of bent-toed geckos (Cyrtodactylus) on Sumatra and west Java. Mol Phylogenet Evol 2019; 134:1-11. [DOI: 10.1016/j.ympev.2019.01.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 11/23/2022]
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103
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Jamaluddin JAF, Mohammed Akib NA, Ahmad SZ, Abdul Halim SAA, Abdul Hamid NK, Mohd Nor SA. DNA barcoding of shrimps from a mangrove biodiversity hotspot. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:618-625. [PMID: 31012766 DOI: 10.1080/24701394.2019.1597073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A total of 74 shrimp specimens were sequenced at a 584 bp segment of the cytochrome oxidase subunit I (COI) gene to examine patterns of DNA barcode variation in a mangrove biodiversity hotspot. The Maximum Likelihood tree, barcode gap analysis, Automatic Barcode Gap Discovery analysis and sequence comparisons with data available from Barcode of Life Data System and GenBank recovered 18 taxa of which 15 were identified to species level, 2 at genus level and a single taxon at order level. Two deep mitochondrial DNA lineage divergences were found in the giant tiger prawn, Penaeus monodon. It is suggested that one of the lineages is a consequence of an introduction from aquaculture activity. These results have provided a reliable barcode library for cataloguing shrimps in this area.
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Affiliation(s)
| | - Noor Adelyna Mohammed Akib
- a School of Biological Sciences , Universiti Sains Malaysia , Pulau Pinang , Malaysia.,b Centre for Global and Sustainability Studies (CGSS) , Universiti Sains Malaysia , Pulau Pinang , Malaysia
| | - Siti Zuliana Ahmad
- a School of Biological Sciences , Universiti Sains Malaysia , Pulau Pinang , Malaysia
| | | | | | - Siti Azizah Mohd Nor
- a School of Biological Sciences , Universiti Sains Malaysia , Pulau Pinang , Malaysia.,c Institute of Marine Biotechnology, Universiti Malaysia Terengganu , Terengganu , Malaysia
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104
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Guterres A, de Oliveira RC, Fernandes J, de Lemos ERS. The mystery of the phylogeographic structural pattern in rodent-borne hantaviruses. Mol Phylogenet Evol 2019; 136:35-43. [PMID: 30914396 DOI: 10.1016/j.ympev.2019.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/19/2022]
Abstract
Hantaviruses (order Bunyavirales, family Hantaviridae) are important zoonotic pathogens. Because of the great diversity of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. To understand the mechanisms behind the evolutionary history of hantaviruses through virus-reservoir interactions, it is important to know how the radiation and diversity of hantaviruses occurred. In this paper, we evaluate the pattern of hantavirus diversification based on a complete S segment representing major groups of hantaviruses found in the Americas. Phylogenetic analyses revealed a high degree of phylogeographic structure and a surprising pattern of geographical distribution of New World hantaviruses. The available data suggest that hantaviruses related to the Arvicolinae rodent subfamily in North America probably emerged and initially adapted from a shared common ancestor of the Tula virus. The first clade of hantaviruses associated with Neotominae occupied a stem lineage, especially those that emerged in Central America or Mexico. Hantaviruses from Central America and Mexico found in Neotominae rodents spread northward and probably gave rise to the first phylogroup of hantaviruses associated with Sigmodontinae in North America. Two preferential host-switching transmissions in hantaviruses apparently gave rise to two different paraphyletic group in Neotominae and Sigmodontinae. Our study supports a probable epicenter of diversification in Central America and/or Mexico for hantaviruses related to both the Neotominae and Sigmodontinae subfamilies.
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Affiliation(s)
- Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
| | - Renata Carvalho de Oliveira
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Jorlan Fernandes
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Elba Regina Sampaio de Lemos
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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105
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Riedel A, Narakusumo RP. One hundred and three new species of Trigonopterus weevils from Sulawesi. Zookeys 2019:1-153. [PMID: 30940991 PMCID: PMC6418079 DOI: 10.3897/zookeys.828.32200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/04/2019] [Indexed: 11/12/2022] Open
Abstract
The genus Trigonopterus Fauvel, 1862 is highly diverse in Melanesia, the Moluccas, and the Sunda Islands. Only one species, Trigonopterusfulvicornis (Pascoe, 1885) was so far recorded from Sulawesi. Based on focused field-work the fauna from Sulawesi and nearby islands is here revised. We redescribe T.allotopus Riedel newly recorded for Sulawesi and describe an additional 103 new species: T.abnormis sp. n., T.adspersus sp. n., T.ambangensis sp. n., T.ampanensis sp. n., T.analis sp. n., T.arachnobas sp. n., T.armipes sp. n., T.artemis sp. n., T.asterix sp. n., T.barbipes sp. n., T.bonthainensis sp. n., T.carinirostris sp. n., T.castaneipennis sp. n., T.celebensis sp. n., T.cirripes sp. n., T.collaris sp. n., T.costatulus sp. n., T.curvipes sp. n., T.crenulatus sp. n., T.cricki sp. n., T.darwini sp. n., T.ejaculatorius sp. n., T.fuscipes sp. n., T.gracilipes sp. n., T.heberti sp. n., T.hirsutus sp. n., T.humilis sp. n., T.hypocrita sp. n., T.idefix sp. n., T.impressicollis sp. n., T.incendium sp. n., T.incognitus sp. n., T.indigenus sp. n., T.inhonestus sp. n., T.invalidus sp. n., T.jasminae sp. n., T.klabatensis sp. n., T.kolakensis sp. n., T.kotamobagensis sp. n., T.laevigatus sp. n., T.lampros sp. n., T.latipennis sp. n., T.lompobattangensis sp. n., T.luwukensis sp. n., T.mahawuensis sp. n., T.manadensis sp. n., T.mangkutanensis sp. n., T.matalibaruensis sp. n., T.mesai sp. n., T.minahassae sp. n., T.moatensis sp. n., T.modoindingensis sp. n., T.nanus sp. n., T.nitidulus sp. n., T.obelix sp. n., T.ovalipunctatus sp. n., T.ovatulus sp. n., T.pagaranganensis sp. n., T.palopensis sp. n., T.paracollaris sp. n., T.pauper sp. n., T.pendolensis sp. n., T.posoensis sp. n., T.prismae sp. n., T.procurtus sp. n., T.pseudallotopus sp. n., T.pseudanalis, sp. n., T.pseudovatulus sp. n., T.pseudovalipunctatus sp. n., T.pseudofulvicornis sp. n., T.pseudomanadensis sp. n., T.pseudosimulans sp. n., T.pumilus sp. n., T.rantepao sp. n., T.reticulatus sp. n., T.rhombiformis sp. n., T.rotundatus sp. n., T.rotundulus sp. n., T.rudis sp. n., T.rufipes sp. n., T.sampunensis sp. n., T.sampuragensis sp. n., T.satyrus sp. n., T.scabripes sp. n., T.scaphiformis sp. n., T.scitulus sp. n., T.selayarensis sp. n., T.serripes sp. n., T.seticnemis sp. n., T.silvicola sp. n., T.squalidulus sp. n., T.sulawesiensis sp. n., T.suturatus sp. n., T.tatorensis sp. n., T.tenuipes sp. n., T.tomohonensis sp. n., T.toraja sp. n., T.vicinus sp. n., T.viduus sp. n., T.volcanorum sp. n., T.wangiwangiensis sp. n., T.watsoni sp. n., and T.yoda sp. n. All new species are authored by the taxonomist-in-charge, Alexander Riedel.
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Affiliation(s)
- Alexander Riedel
- Museum of Natural History Karlsruhe, Erbprinzenstr. 13, D-76133 Karlsruhe, Germany Museum of Natural History Karlsruhe Karlsruhe Germany
| | - Raden Pramesa Narakusumo
- Museum of Natural History Karlsruhe, Erbprinzenstr. 13, D-76133 Karlsruhe, Germany Museum of Natural History Karlsruhe Karlsruhe Germany.,Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jl. Raya Jakarta-Bogor km 46, Cibinong 16911, Indonesia Research Center for Biology, Indonesian Institute of Sciences Jl. Raya Jakarta-Bogor Indonesia
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106
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Jiruskova A, Motyka M, Bocek M, Bocak L. The Malacca Strait separates distinct faunas of poorly-flying Cautires net-winged beetles. PeerJ 2019; 7:e6511. [PMID: 30863675 PMCID: PMC6407506 DOI: 10.7717/peerj.6511] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 01/22/2019] [Indexed: 02/04/2023] Open
Abstract
We investigated the spatial and temporal patterns of Cautires diversification on the Malay Peninsula and Sumatra to understand if the narrow and frequently dry Malacca Strait separates different faunas. Moreover, we analyzed the origin of Cautires in Malayan and Sumatran mountains. We sampled 18 localities and present the mtDNA-based phylogeny of 76 species represented by 388 individuals. The phylogenetic tree was dated using mtDNA evolution rates and the ancestral ranges were estimated using the maximum likelihood approach. The phylogeny identified multiple lineages on the Malay Peninsula since the Upper Eocene (35 million years ago, mya) and a delayed evolution of diversity in Sumatra since the Upper Oligocene (26 mya). A limited number of colonization events across the Malacca Strait was identified up to the Pliocene and more intensive faunal exchange since the Pleistocene. The early colonization events were commonly followed by in situ diversification. As a result, the Malacca Strait now separates two faunas with a high species-level turnover. The montane fauna diversified in a limited space and seldom took part in colonization events across the Strait. Besides isolation by open sea or a savannah corridor, mimetic patterns could decrease the colonization capacity of Cautires. The Malay fauna is phylogenetically more diverse and has a higher value if conservation priorities should be defined.
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Affiliation(s)
- Alice Jiruskova
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Michal Motyka
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Matej Bocek
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
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107
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Revisiting species boundaries and distribution ranges of Nemacheilus spp. (Cypriniformes: Nemacheilidae) and Rasbora spp. (Cypriniformes: Cyprinidae) in Java, Bali and Lombok through DNA barcodes: implications for conservation in a biodiversity hotspot. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01152-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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108
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Bocek M, Bocak L. The origins and dispersal history of the trichaline net-winged beetles in Southeast Asia, Wallacea, New Guinea and Australia. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zly090] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Matej Bocek
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
| | - Ladislav Bocak
- Laboratory of Molecular Systematics, Department of Zoology, Faculty of Science, Palacky University, 17. listopadu 50, 771 46 Olomouc, Czech Republic
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109
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Cancian de Araujo B, Schmidt S, Schmidt O, von Rintelen T, von Rintelen K, Floren A, Ubaidillah R, Peggie D, Balke M. DNA barcoding data release for Coleoptera from the Gunung Halimun canopy fogging workpackage of the Indonesian Biodiversity Information System (IndoBioSys) project. Biodivers Data J 2019:e31432. [PMID: 30686928 PMCID: PMC6342863 DOI: 10.3897/bdj.7.e31432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/19/2018] [Indexed: 11/13/2022] Open
Abstract
We present the results of a DNA barcoding pipeline that was established as part of the German-Indonesian IndobioSys project - Indonesian Biodiversity Information System. Our data release provides the first large-scale diversity assessment of Indonesian coleoptera obtained by canopy fogging. The project combined extensive fieldwork with databasing, DNA barcode based species delineation and the release of results in collaboration with Indonesian counterparts, aimed at supporting further analyses of the data. Canopy fogging on 28 trees was undertaken at two different sites, Cikaniki and Gunung Botol, in the south-eastern area of the Gunung Halimun-Salak National Park in West Java, Indonesia. In total, 7,447 specimens of Coleoptera were processed, of which 3,836 specimens produced DNA barcode sequences that were longer than 300 bp. A total of 3,750 specimens were assigned a Barcode Index Number (BIN), including 2,013 specimens from Cikaniki and 1,737 specimens from Gunung Botol. The 747 BINs, that were obtained, represented 39 families of Coleoptera. The distribution of specimens with BINs per tree was quite heterogeneous in both sites even in terms of the abundance of specimens or diversity of BINs. The specimen distribution per taxon was heterogeneous as well. Some 416 specimens could not be identified to family level, corresponding to 72 BINs that lack a family level identification. The data have shown a large heterogeneity in terms of abundance and distribution of BINs between sites, trees and families of Coleoptera. From the total of 747 BINs that were recovered, 421 (56%) are exclusive from a single tree. Although the two study sites were in close proximity and separated by a distance of only about five kilometres, the number of shared BINs between sites is low, with 81 of the 747 BINs. With this data release, we expect to shed some light on the largely hidden diversity in the canopy of tropical forests in Indonesia and elsewhere.
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Affiliation(s)
- Bruno Cancian de Araujo
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
| | - Olga Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
| | | | | | - Andreas Floren
- The Biocenter of the University of Würzburg, Würzburg, Germany The Biocenter of the University of Würzburg Würzburg Germany
| | - Rosichon Ubaidillah
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences Cibinong Indonesia
| | - Djunijanti Peggie
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences Cibinong Indonesia
| | - Michael Balke
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
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110
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Oliver PM, Brown RM, Kraus F, Rittmeyer E, Travers SL, Siler CD. Lizards of the lost arcs: mid-Cenozoic diversification, persistence and ecological marginalization in the West Pacific. Proc Biol Sci 2019; 285:rspb.2017.1760. [PMID: 29343593 DOI: 10.1098/rspb.2017.1760] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 12/11/2017] [Indexed: 11/12/2022] Open
Abstract
Regions with complex geological histories often have diverse and highly endemic biotas, yet inferring the ecological and historical processes shaping this relationship remains challenging. Here, in the context of the taxon cycle model of insular community assembly, we investigate patterns of lineage diversity and habitat usage in a newly characterized vertebrate radiation centred upon the world's most geologically complex insular region: island arcs spanning from the Philippines to Fiji. On island arcs taxa are ecologically widespread, and provide evidence to support one key prediction of the taxon cycle, specifically that interior habitats (lowland rainforests, montane habitats) are home to a greater number of older or relictual lineages than are peripheral habitats (coastal and open forests). On continental fringes, however, the clade shows a disjunct distribution away from lowland rainforest, occurring in coastal, open or montane habitats. These results are consistent with a role for biotic interactions in shaping disjunct distributions (a central tenant of the taxon cycle), but we find this pattern most strongly on continental fringes not islands. Our results also suggest that peripheral habitats on islands, and especially island arcs, may be important for persistence and diversification, not just dispersal and colonization. Finally, new phylogenetic evidence for subaerial island archipelagos (with an associated biota) east of present-day Wallace's Line since the Oligocene has important implications for understanding long-term biotic interchange and assembly across Asia and Australia.
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Affiliation(s)
- Paul M Oliver
- Ecology, Evolution and Genetics, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eric Rittmeyer
- Ecology, Evolution and Genetics, Australian National University, Canberra, Australian Capital Territory 2601, Australia.,Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Scott L Travers
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7561, USA
| | - Cameron D Siler
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK 73072-7029, USA
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111
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Cancian de Araujo B, Schmidt S, Schmidt O, von Rintelen T, Ubaidillah R, Balke M. The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia. Biodivers Data J 2018:e29927. [PMID: 30598619 PMCID: PMC6306476 DOI: 10.3897/bdj.6.e29927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/28/2018] [Indexed: 11/12/2022] Open
Abstract
The Indonesian archipelago features an extraordinarily rich biota. However, the actual taxonomic inventory of the archipelago remains highly incomplete and there is hardly any significant taxonomic activity that utilises recent technological advances. The IndoBioSys project was established as a biodiversity information system aiming at, amongst other goals, creating inventories of the Indonesian entomofauna using DNA barcoding. Here, we release the first large scale assessment of the megadiverse insect groups that occur in the Mount Halimun-Salak National Park, one of the largest tropical rain-forest ecosystem in West Java, with a focus on Hymenoptera, Coleoptera, Diptera and Lepidoptera collected with Malaise traps. From September 2015 until April 2016, 34 Malaise traps were placed in different localities in the south-eastern part of the Halimun-Salak National Park. A total of 4,531 specimens were processed for DNA barcoding and in total, 2,382 individuals produced barcode compliant records, representing 1,195 exclusive BINs or putative species in 98 insect families. A total of 1,149 BINs were new to BOLD. Of 1,195 BINs detected, 804 BINs were singletons and more than 90% of the BINs incorporated less than five specimens. The astonishing heterogeneity of BINs, as high as 1.1 exclusive BIN per specimen of Diptera successfully processed, shows that the cost/benefit relationship of the discovery of new species in those areas is very low. In four genera of Chalcidoidea, a superfamily of the Hymenoptera, the number of discovered species was higher than the number of species known from Indonesia, suggesting that our samples contain many species that are new to science. Those numbers shows how fast molecular pipelines contribute substantially to the objective inventorying of the fauna giving us a good picture of how potentially diverse tropical areas might be.
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Affiliation(s)
- Bruno Cancian de Araujo
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
| | - Stefan Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
| | - Olga Schmidt
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung Berlin Germany
| | - Rosichon Ubaidillah
- Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences, Cibinong, Indonesia Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences Cibinong Indonesia
| | - Michael Balke
- SNSB-Zoologische Staatssammlung München, Munich, Germany SNSB-Zoologische Staatssammlung München Munich Germany
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112
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Dong J, Kergoat GJ, Vicente N, Rahmadi C, Xu S, Robillard T. Biogeographic patterns and diversification dynamics of the genus Cardiodactylus Saussure (Orthoptera, Grylloidea, Eneopterinae) in Southeast Asia. Mol Phylogenet Evol 2018; 129:1-14. [DOI: 10.1016/j.ympev.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/27/2018] [Accepted: 06/02/2018] [Indexed: 10/14/2022]
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113
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Shell WA, Rehan SM. Invasive range expansion of the small carpenter bee, Ceratina dentipes (Hymenoptera: Apidae) into Hawaii with implications for native endangered species displacement. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1892-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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114
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Yang CK, Chiang YC, Huang BH, Ju LP, Liao PC. Nuclear and chloroplast DNA phylogeography suggests an Early Miocene southward expansion of Lithocarpus (Fagaceae) on the Asian continent and islands. BOTANICAL STUDIES 2018; 59:27. [PMID: 30406863 PMCID: PMC6223401 DOI: 10.1186/s40529-018-0244-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 10/31/2018] [Indexed: 05/16/2023]
Abstract
BACKGROUND Most genera of Fagaceae are thought to have originated in the temperate regions except for the genus Lithocarpus, the stone oaks. Lithocarpus is distributed in subtropical and tropical Asia, and its ancestral population is hypothesized to be distributed in tropical regions in Borneo and Indochina. Borneo and the nearby islands (the Greater Sunda Islands) were connected to the Malay Peninsula and Indochina prior to the Pliocene epoch and formed the former Sundaland continent. The Southeast Asian Lithocarpus, is thought to have dispersed between continental Asia and the present Sundaland. The drastic climate changes during the Pliocene and Pleistocene epochs which caused periodic sea-level changes is often used to explain the cause of its diversity. The aim of this study was to establish phylogenetic relationships by analyzing nuclear (nrDNA) and chloroplast (cpDNA) DNA in order to describe and analyze the origin, causes of diversification and historical biogeography of Lithocarpus. RESULTS Phylogeny reconstructed through the multiple-species coalescent method with nrDNA and cpDNA revealed that the continental-Asian taxa were clustered at the basal lineages. The derived lineages of tropical Lithocarpus, with the inference of a subtropical ancestral state, imply a southward migration in the Early Miocene period with subsequent in situ diversification in the Greater Sunda Islands. The gradual decrease in temperature since the Middle Miocene period is proposed as a cause of the increase in the net diversification rate. CONCLUSIONS The historical ancestral origin of Lithocarpus has been suggested to be mainland Asia. Southward migration in the Early Miocene period with subsequent in situ diversification could explain the current diversity of stone oaks in Southeast Asia. This study also considered the multiple origins of stone oaks currently indigenous to the subtropical islands offshore and near mainland China. Our results provide phylogenetic evidence for a subtropical origin of Asian stone oaks and reveal the process of diversification and how it fits into the timeline of major geologic and climatic events rather than local, episodic, rate-shifting events.
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Affiliation(s)
- Chih-Kai Yang
- Department of Life Science, National Taiwan Normal University, 88, Ting-Chow Rd, Sec 4, Taipei, 116 Taiwan
- The Experimental Forest, College of Bio-Resources and Agriculture, National Taiwan University, 12, Sec. 1, Chien-Shan Rd., Nantou, 55750 Taiwan
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, 70, Lien-Hai Rd., Kaohsiung, 80424 Taiwan
| | - Bing-Hong Huang
- Department of Life Science, National Taiwan Normal University, 88, Ting-Chow Rd, Sec 4, Taipei, 116 Taiwan
| | - Li-Ping Ju
- Botanical Garden Division, Taiwan Forestry Research Institute, 53, Nan-Hai Rd., Taipei, 10066 Taiwan
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, 88, Ting-Chow Rd, Sec 4, Taipei, 116 Taiwan
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115
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Paijmans JLA, Barlow A, Förster DW, Henneberger K, Meyer M, Nickel B, Nagel D, Worsøe Havmøller R, Baryshnikov GF, Joger U, Rosendahl W, Hofreiter M. Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations. BMC Evol Biol 2018; 18:156. [PMID: 30348080 PMCID: PMC6198532 DOI: 10.1186/s12862-018-1268-0] [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: 02/16/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022] Open
Abstract
Background Resolving the historical biogeography of the leopard (Panthera pardus) is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts? Results In this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (~ 710 Ka), with the European ancient samples as sister to all Asian lineages (~ 483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (~ 122 Ka), and we find one Javan sample nested within these. Conclusions The phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies. Electronic supplementary material The online version of this article (10.1186/s12862-018-1268-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany.
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
| | - Daniel W Förster
- Leibniz Institute for Zoo- and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315, Berlin, Germany
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany
| | - Doris Nagel
- Institute for Paleontology, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria
| | - Rasmus Worsøe Havmøller
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Gennady F Baryshnikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034, St. Petersburg, Russia
| | - Ulrich Joger
- State Natural History Museum, Pockelsstr. 10, 38106, Braunschweig, Germany
| | - Wilfried Rosendahl
- Reiss-Engelhorn Museen and Curt-Engelhorn-Centre for Archaeometry, C4 8, 68159, Mannheim, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße 24-25, 14476, Potsdam, Germany
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116
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Landis MJ, Freyman WA, Baldwin BG. Retracing the Hawaiian silversword radiation despite phylogenetic, biogeographic, and paleogeographic uncertainty. Evolution 2018; 72:2343-2359. [PMID: 30198108 DOI: 10.1111/evo.13594] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/17/2018] [Indexed: 12/25/2022]
Abstract
The Hawaiian silversword alliance (Asteraceae) is an iconic adaptive radiation. However, like many island plant lineages, no fossils have been assigned to the clade. As a result, the clade's age and diversification rate are not known precisely, making it difficult to test biogeographic hypotheses about the radiation. In lieu of fossils, paleogeographically structured biogeographic processes may inform species divergence times; for example, an island must first exist for a clade to radiate upon it. We date the silversword clade and test biogeographic hypotheses about its radiation across the Hawaiian Archipelago by modeling interactions between species relationships, molecular evolution, biogeographic scenarios, divergence times, and island origination times using the Bayesian phylogenetic framework, RevBayes. The ancestor of living silverswords most likely colonized the modern Hawaiian Islands once from the mainland approximately 5.1 Ma, with the most recent common ancestor of extant silversword lineages first appearing approximately 3.5 Ma. Applying an event-based test of the progression rule of island biogeography, we found strong evidence that the dispersal process favors old-to-young directionality, but strong evidence for diversification continuing unabated into later phases of island ontogeny, particularly for Kaua'i. This work serves as a general example for how diversification studies benefit from incorporating biogeographic and paleogeographic components.
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Affiliation(s)
- Michael J Landis
- Department of Ecology & Evolution, Yale University, New Haven, Connecticut 06511
| | - William A Freyman
- Department of Ecology, Evolution, & Behavior, University of Minnesota, Saint Paul, Minnesota 55108.,Department of Integrative Biology, University of California, Berkeley, California 94720.,Jepson Herbarium, University of California, Berkeley, California 94720
| | - Bruce G Baldwin
- Department of Integrative Biology, University of California, Berkeley, California 94720.,Jepson Herbarium, University of California, Berkeley, California 94720
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117
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Li F, Li S. Paleocene–Eocene and Plio–Pleistocene sea-level changes as “species pumps” in Southeast Asia: Evidence from Althepus spiders. Mol Phylogenet Evol 2018; 127:545-555. [DOI: 10.1016/j.ympev.2018.05.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/28/2018] [Accepted: 05/13/2018] [Indexed: 01/03/2023]
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118
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Panettieri S, Gjinaj E, John G, Lohman DJ. Different ommochrome pigment mixtures enable sexually dimorphic Batesian mimicry in disjunct populations of the common palmfly butterfly, Elymnias hypermnestra. PLoS One 2018; 13:e0202465. [PMID: 30208047 PMCID: PMC6135364 DOI: 10.1371/journal.pone.0202465] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/04/2018] [Indexed: 11/18/2022] Open
Abstract
With varied, brightly patterned wings, butterflies have been the focus of much work on the evolution and development of phenotypic novelty. However, the chemical structures of wing pigments from few butterfly species have been identified. We characterized the orange wing pigments of female Elymnias hypermnestra butterflies (Lepidoptera: Nymphalidae: Satyrinae) from two Southeast Asian populations. This species is a sexually dimorphic Batesian mimic of several model species. Females are polymorphic: in some populations, females are dark, resemble conspecific males, and mimic Euploea spp. In other populations, females differ from males and mimic orange Danaus spp. Using LC-MS/MS, we identified nine ommochrome pigments: six from a population in Chiang Mai, Thailand, and five compounds from a population in Bali, Indonesia. Two ommochromes were found in both populations, and only two of the nine compounds have been previously reported. The sexually dimorphic Thai and Balinese populations are separated spatially by monomorphic populations in peninsular Malaysia, Singapore, and Sumatra, suggesting independent evolution of mimetic female wing pigments in these disjunct populations. These results indicate that other butterfly wing pigments remain to be discovered.
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Affiliation(s)
- Silvio Panettieri
- Department of Chemistry and Biochemistry, City College of New York, City University of New York, New York, NY, United States of America
- Ph.D. Program in Chemistry, Graduate Center, City University of New York, New York, NY, United States of America
| | - Erisa Gjinaj
- Department of Chemistry and Biochemistry, City College of New York, City University of New York, New York, NY, United States of America
| | - George John
- Department of Chemistry and Biochemistry, City College of New York, City University of New York, New York, NY, United States of America
- Ph.D. Program in Chemistry, Graduate Center, City University of New York, New York, NY, United States of America
- * E-mail: (DJL); (GJ)
| | - David J. Lohman
- Biology Department, City College of New York, City University of New York, New York, NY, United States of America
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY, United States of America
- Entomology Section, National Museum of the Philippines, Manila, Philippines
- * E-mail: (DJL); (GJ)
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119
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Nakano T, Eto K, Nishikawa K, Hossman MY, Jeratthitikul E. Systematic revision of the Southeast Asian macrophagous leeches, with the description of two new gastrostomobdellid species (Hirudinida: Arhynchobdellida: Erpobdelliformes). Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zlx097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Takafumi Nakano
- Department of Science Education, Graduate School of Education, Hiroshima University, Higashihiroshima, Japan
| | - Koshiro Eto
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
- Kitakyushu Museum of Natural History and Human History, Kitakyushu, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Mohamad Yazid Hossman
- Fauna Biodiversity Section, Research, Development & Innovation Division, Forest Department Sarawak, Kuching, Sarawak, Malaysia
| | - Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
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120
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Huang JP, Knowles LL. Testing the impact of oceanic barriers on population subdivision, speciation and zoogeographical community assembly in Xylotrupes beetles across the Indo-Australian Archipelago. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Jen-Pan Huang
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
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121
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Coryell RL, Turnham KE, de Jesus Ayson EG, Lavilla‐Pltogo C, Alcala AC, Sotto F, Gonzales B, Nishiguchi MK. Phylogeographic patterns in the Philippine archipelago influence symbiont diversity in the bobtail squid -Vibrio mutualism. Ecol Evol 2018; 8:7421-7435. [PMID: 30151160 PMCID: PMC6106162 DOI: 10.1002/ece3.4266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 12/05/2022] Open
Abstract
Marine microbes encounter a myriad of biotic and abiotic factors that can impact fitness by limiting their range and capacity to move between habitats. This is especially true for environmentally transmitted bacteria that cycle between their hosts and the surrounding habitat. As geologic history, biogeography, and other factors such as water temperature, salinity, and physical barriers can inhibit bacterial movement to novel environments, we chose to examine the genetic architecture of Euprymna albatrossae (Mollusca: Cephalopoda) and their Vibrio fischeri symbionts in the Philippine archipelago using a combined phylogeographic approach. Eleven separate sites in the Philippine islands were examined using haplotype estimates that were examined via nested clade analysis to determine the relationship between E. albatrossae and V. fischeri populations and their geographic location. Identical analyses of molecular variance (AMOVA) were used to estimate variation within and between populations for host and symbiont genetic data. Host animals demonstrated a significant amount of variation within island groups, while symbiont variation was found within individual populations. Nested clade phylogenetic analysis revealed that hosts and symbionts may have colonized this area at different times, with a sudden change in habitat. Additionally, host data indicate restricted gene flow, whereas symbionts show range expansion, followed by periodic restriction to genetic flow. These differences between host and symbiont networks indicate that factors "outside the squid" influence distribution of Philippine V. fischeri. Our results shed light on how geography and changing environmental factors can impact marine symbiotic associations at both local and global scales.
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Affiliation(s)
- Randy L. Coryell
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico
| | - Kira E. Turnham
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico
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122
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Large-scale phylogenetic analyses provide insights into unrecognized diversity and historical biogeography of Asian leaf-litter frogs, genus Leptolalax (Anura: Megophryidae). Mol Phylogenet Evol 2018. [DOI: 10.1016/j.ympev.2018.02.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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123
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Spitsyn VM, Bolotov IN. Barsine podbolotskayae sp. n. from Flores Island, Lesser Sunda Archipelago, Indonesia (Lepidoptera, Erebidae, Arctiinae). Zookeys 2018:105-111. [PMID: 29955214 PMCID: PMC6019474 DOI: 10.3897/zookeys.768.24345] [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: 02/08/2018] [Accepted: 05/10/2018] [Indexed: 11/24/2022] Open
Abstract
Herein Barsinepodbolotskayaesp. n. (Lepidoptera: Erebidae: Arctiinae) is described from Flores Island, Lesser Sunda Archipelago, Indonesia. This local endemic species externally resembles Barsineexclusa Butler, 1877 from Sundaland and the Andaman Islands but differs by marking patterns and male genitalia structure.
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Affiliation(s)
- Vitaly M Spitsyn
- Northern Arctic Federal University, Severnoy Dviny Emb. 17, 163002, Arkhangelsk, Russia.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia
| | - Ivan N Bolotov
- Northern Arctic Federal University, Severnoy Dviny Emb. 17, 163002, Arkhangelsk, Russia.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, Northern Dvina Emb. 23, 163000, Arkhangelsk, Russia
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124
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Hausdorf B. Beyond Wallace’s line – dispersal of Oriental and Australo-Papuan land-snails across the Indo-Australian Archipelago. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bernhard Hausdorf
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz, Hamburg, Germany
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125
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Synchronous diversification of parachuting frogs (Genus Rhacophorus) on Sumatra and Java. Mol Phylogenet Evol 2018; 123:101-112. [DOI: 10.1016/j.ympev.2018.02.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/22/2022]
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126
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Frantz LAF, Rudzinski A, Nugraha AMS, Evin A, Burton J, Hulme-Beaman A, Linderholm A, Barnett R, Vega R, Irving-Pease EK, Haile J, Allen R, Leus K, Shephard J, Hillyer M, Gillemot S, van den Hurk J, Ogle S, Atofanei C, Thomas MG, Johansson F, Mustari AH, Williams J, Mohamad K, Damayanti CS, Wiryadi ID, Obbles D, Mona S, Day H, Yasin M, Meker S, McGuire JA, Evans BJ, von Rintelen T, Ho SYW, Searle JB, Kitchener AC, Macdonald AA, Shaw DJ, Hall R, Galbusera P, Larson G. Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events. Proc Biol Sci 2018; 285:rspb.2017.2566. [PMID: 29643207 PMCID: PMC5904307 DOI: 10.1098/rspb.2017.2566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/16/2018] [Indexed: 11/13/2022] Open
Abstract
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2–3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
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Affiliation(s)
- Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK .,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Anna Rudzinski
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Allowen Evin
- Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, Cedex 05, France.,Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - James Burton
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK.,IUCN SSC Asian Wild Cattle Specialist Group and Chester Zoo, Cedar House, Caughall Road, Upton by Chester, Chester CH2 1LH, UK
| | - Ardern Hulme-Beaman
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | - Ross Barnett
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Rodrigo Vega
- Ecology Research Group, Section of Life Sciences, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury CT1 1QU, Kent, UK
| | - Evan K Irving-Pease
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Richard Allen
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Kristin Leus
- Copenhagen Zoo, IUCN SSC Conservation Breeding Specialist Group-Europe, Roskildevej 38, Postboks 7, 2000 Frederiksberg, Denmark.,European Association of Zoos and Aquaria, PO Box 20164, 1000 HD Amsterdam, The Netherlands
| | - Jill Shephard
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium.,Environment and Conservation Sciences, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - Mia Hillyer
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium.,Molecular Systematics Unit/Terrestrial Zoology, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Sarah Gillemot
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Jeroen van den Hurk
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Sharron Ogle
- Edinburgh Medical School: BMTO, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Cristina Atofanei
- Ecology Research Group, Section of Life Sciences, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury CT1 1QU, Kent, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Abdul Haris Mustari
- Department of Forest Resources Conservation and Ecotourism, Faculty of Forestry, Bogor Agricultural University, PO Box 168, Bogor 16001, Indonesia
| | - John Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy, Southern Australia 5371, Australia
| | - Kusdiantoro Mohamad
- Faculty of Veterinary Medicine, Bogor Agricultural University, Jalan Agatis, IPB Campus, Darmaga, Bogor 16680, Indonesia
| | - Chandramaya Siska Damayanti
- Faculty of Veterinary Medicine, Bogor Agricultural University, Jalan Agatis, IPB Campus, Darmaga, Bogor 16680, Indonesia
| | | | - Dagmar Obbles
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - Stephano Mona
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005 Paris, France.,EPHE, PSL Research University, Paris, France
| | | | | | - Stefan Meker
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Thomas von Rintelen
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853, USA
| | - Andrew C Kitchener
- Department of Natural Sciences, Chambers Street, National Museums Scotland, Edinburgh EH1 1JF, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Alastair A Macdonald
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK
| | - Darren J Shaw
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK
| | - Robert Hall
- SE Asia Research Group, Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Peter Galbusera
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
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127
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Spitsyn VM, Kondakov AV, Bolotov NI, Thi Pham N, Gofarov MY, Bolotov IN. DNA barcoding unravels contrasting evolutionary history of two widespread Asian tiger moth species during the Late Pleistocene. PLoS One 2018; 13:e0194200. [PMID: 29617397 PMCID: PMC5884489 DOI: 10.1371/journal.pone.0194200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/27/2018] [Indexed: 12/02/2022] Open
Abstract
Populations of widespread pest insects in tropical areas are characterized by a complex evolutionary history, with overlapping natural and human-mediated dispersal events, sudden expansions, and bottlenecks. Here, we provide biogeographic reconstructions for two widespread pest species in the tiger moth genus Creatonotos (Lepidoptera: Erebidae: Arctiinae) based on the mitochondrial cytochrome c oxidase subunit I (COI) gene. The Asian Creatonotos transiens reveals shallow genetic divergence between distant populations that does not support its current intraspecific systematics with several local subspecies. In contrast, the more widespread Creatonotos gangis comprises at least three divergent subclades corresponding to certain geographic areas, i.e. Australia, Arabia + South Asia and Southeast Asia. With respect to our approximate Bayesian computation (ABC) model, the expansion of Creatonotos gangis into Australia is placed in the Late Pleistocene (~65–63 ka). This dating coincide with an approximate time of the earliest human migration into the continent (~65–54 ka) and the period of intervisibility between Timor and Australia (~65–62 ka). Our findings highlight that the drying Sunda and Sahul shelf areas likely support successful migrations of Asian taxa into Australia during the Pleistocene. The phylogeographic patterns discovered in this study can be used to improve the effectiveness of integrated pest control programs that is a task of substantial practical importance to a broad range of agricultural stakeholders.
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Affiliation(s)
- Vitaly M. Spitsyn
- Lab for Molecular Ecology and Phylogenetics, Northern Arctic Federal University, Arkhangelsk, Russian Federation
- Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russian Federation
- * E-mail:
| | - Alexander V. Kondakov
- Lab for Molecular Ecology and Phylogenetics, Northern Arctic Federal University, Arkhangelsk, Russian Federation
- Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russian Federation
| | - Nikita I. Bolotov
- Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russian Federation
| | - Nhi Thi Pham
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mikhail Y. Gofarov
- Lab for Molecular Ecology and Phylogenetics, Northern Arctic Federal University, Arkhangelsk, Russian Federation
- Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russian Federation
| | - Ivan N. Bolotov
- Lab for Molecular Ecology and Phylogenetics, Northern Arctic Federal University, Arkhangelsk, Russian Federation
- Institute of Biogeography and Genetic Resources, Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Arkhangelsk, Russian Federation
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128
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Garg KM, Chattopadhyay B, Wilton PR, Malia Prawiradilaga D, Rheindt FE. Pleistocene land bridges act as semipermeable agents of avian gene flow in Wallacea. Mol Phylogenet Evol 2018; 125:196-203. [PMID: 29625230 DOI: 10.1016/j.ympev.2018.03.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 03/18/2018] [Accepted: 03/29/2018] [Indexed: 11/16/2022]
Abstract
Cyclical periods of global cooling have been important drivers of biotic differentiation throughout the Quaternary. Ice age-induced sea level fluctuations can lead to changing patterns of land connections, both facilitating and disrupting gene flow. In this study, we test if species with differing life histories are differentially affected by Quaternary land connections. We used genome-wide SNPs in combination with mitochondrial gene sequences to analyse levels of divergence and gene flow between two songbird complexes across two Wallacean islands that have been repeatedly connected during glaciations. Although the two bird complexes are similar in ecological attributes, the forest and edge-inhabiting golden whistler Pachycephala pectoralis is comparatively flexible in its diet and niche requirements as compared to the henna-tailed jungle-flycatcher Cyornis colonus, which is largely restricted to the forest interior. Using population-genomic and coalescent approaches, we estimated levels of gene flow, population differentiation and divergence time between the two island populations. We observed higher levels of differentiation, an approximately two to four times deeper divergence time and near-zero levels of gene flow between the two island populations of the more forest-dependent henna-tailed jungle-flycatcher as compared to the more generalist golden whistler. Our results suggest that Quaternary land bridges act as semipermeable agents of gene flow in Wallacea, allowing only certain taxa to connect between islands while others remain isolated. Quaternary land bridges do not accommodate all terrestrial species equally, differing in suitability according to life history and species biology. More generalist species are likely to use Quaternary land connections as a conduit for gene flow between islands whereas island populations of more specialist species may continue to be reproductively isolated even during periods of Quaternary land bridges.
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Affiliation(s)
- Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | - Peter R Wilton
- Department of Organismic and Evolutionary Biology, Harvard University, USA
| | - Dewi Malia Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Bogor-Cibinong, West Java, Indonesia
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore.
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129
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Uva V, Päckert M, Cibois A, Fumagalli L, Roulin A. Comprehensive molecular phylogeny of barn owls and relatives (Family: Tytonidae), and their six major Pleistocene radiations. Mol Phylogenet Evol 2018. [PMID: 29535030 DOI: 10.1016/j.ympev.2018.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The owl family Tytonidae comprises two genera: Phodilus, limited to the forests of central Africa and South-East Asia, and the ubiquitous Tyto. The genus Tyto is majorly represented by the cosmopolitan Common Barn Owl group, with more than 30 subspecies worldwide. Discrete differences in body size and plumage colouration have led to the classification of this family into many species and subspecies, but the taxonomic status and phylogenetic relationships between taxa remain unclear, and in some groups controversial. Although several previous studies attempted to resolve this problem, they have been limited in their taxonomic and geographical coverage, or have relied on restricted molecular evidence and low sample sizes. Based on the most comprehensive sampling to date (16 out of 17 Tyto species, and one out of three Phodilus species), a multi-locus approach using seven mitochondrial and two nuclear markers, and taking advantage of field data and museum collections available worldwide, our main questions in this study were: (1) what are the phylogenetic relationships and classification status of the whole family; (2) when and where did the most important speciation events occur? We confirm that the Common Barn Owl, Tyto alba is divided into three main evolutionary units: the American Barn Owl, T. furcata; the Western Barn Owl, T. alba; and the Eastern Barn Owl, T. javanica, and suggest a Late Miocene (ca. 6 mya) Australasian and African origin of the group. Our results are supported by fossil age information, given that the most recent common ancestor between the Tytonidae genera Phodilus and Tyto was probably from the Oligocene (ca. 28 mya) of Australasia. We finally reveal six major Pleistocene radiations of Tyto, all resulting in wide-range distributions.
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Affiliation(s)
- Vera Uva
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Martin Päckert
- Senckenberg Natural History Collections, Königsbrücker, Landstraße 159, 01109 Dresden, Germany.
| | - Alice Cibois
- Museum of Natural History of Geneva, Route de Managnou 1, 1208 Geneva, Switzerland.
| | - Luca Fumagalli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland; Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Rue du Bugnon 21, 1011 Lausanne, Switzerland.
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
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130
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Matos-Maraví P, Clouse RM, Sarnat EM, Economo EP, LaPolla JS, Borovanska M, Rabeling C, Czekanski-Moir J, Latumahina F, Wilson EO, Janda M. An ant genus-group (Prenolepis) illuminates the biogeography and drivers of insect diversification in the Indo-Pacific. Mol Phylogenet Evol 2018; 123:16-25. [PMID: 29448063 DOI: 10.1016/j.ympev.2018.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 11/16/2017] [Accepted: 02/06/2018] [Indexed: 11/25/2022]
Abstract
The Malay Archipelago and the tropical South Pacific (hereafter the Indo-Pacific region) are considered biodiversity hotspots, yet a general understanding of the origins and diversification of species-rich groups in the region remains elusive. We aimed to test hypotheses for the evolutionary processes driving insect species diversity in the Indo-Pacific using a higher-level and comprehensive phylogenetic hypothesis for an ant clade consisting of seven genera. We estimated divergence times and reconstructed the biogeographical history of ant species in the Prenolepis genus-group (Formicidae: Formicinae: Lasiini). We used a fossil-calibrated phylogeny to infer ancestral geographical ranges utilizing a biogeographic model that includes founder-event speciation. Ancestral state reconstructions of the ants' ecological preferences, and diversification rates were estimated for selected Indo-Pacific clades. Overall, we report that faunal interchange between Asia and Australia has occurred since at least 20-25 Ma, and early dispersal to the Fijian Basin happened during the early and mid-Miocene (ca. 10-20 Ma). Differences in diversification rates across Indo-Pacific clades may be related to ecological preference breadth, which in turn may have facilitated geographical range expansions. Ancient dispersal routes suggested by our results agree with the palaeogeography of the region. For this particular group of ants, the rapid orogenesis in New Guinea and possibly subsequent ecological shifts may have promoted their rapid diversification and widespread distribution across the Indo-Pacific.
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Affiliation(s)
- Pável Matos-Maraví
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Department of Zoology, Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic; Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden; The Gothenburg Global Biodiversity Centre, Göteborg, Sweden.
| | - Ronald M Clouse
- Division of Invertebrate Zoology, American Museum of Natural History, New York City, NY, USA
| | - Eli M Sarnat
- Department of Entomology, University of Illinois, IL, USA
| | - Evan P Economo
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - John S LaPolla
- Deparment of Biological Sciences, Towson University, Towson, MD, USA
| | - Michaela Borovanska
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Christian Rabeling
- School of Life Sciences, Arizona State University, Tempe, AZ, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Jesse Czekanski-Moir
- Department of Environmental and Forest Biology, 1 Forestry Drive, State University of New York, Syracuse, NY, USA
| | - Fransina Latumahina
- Department of Forestry, Agriculture Faculty, Pattimura University, Ambon, Indonesia
| | - Edward O Wilson
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Milan Janda
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Cátedras CONACYT, Laboratorio Nacional de Análisis y Síntesis Ecológica, ENES, UNAM, Morelia, Mexico
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131
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Chomicki G, Janda M, Renner SS. The assembly of ant-farmed gardens: mutualism specialization following host broadening. Proc Biol Sci 2018; 284:rspb.2016.1759. [PMID: 28298344 DOI: 10.1098/rspb.2016.1759] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/19/2016] [Indexed: 11/12/2022] Open
Abstract
Ant-gardens (AGs) are ant/plant mutualisms in which ants farm epiphytes in return for nest space and food rewards. They occur in the Neotropics and Australasia, but not in Africa, and their evolutionary assembly remains unclear. We here use phylogenetic frameworks for important AG lineages in Australasia, namely the ant genus Philidris and domatium-bearing ferns (Lecanopteris) and flowering plants in the Apocynaceae (Hoya and Dischidia) and Rubiaceae (Myrmecodia, Hydnophytum, Anthorrhiza, Myrmephytum and Squamellaria). Our analyses revealed that in these clades, diaspore dispersal by ants evolved at least 13 times, five times in the Late Miocene and Pliocene in Australasia and seven times during the Pliocene in Southeast Asia, after Philidris ants had arrived there, with subsequent dispersal between these two areas. A uniquely specialized AG system evolved in Fiji at the onset of the Quaternary. The farming in the same AG of epiphytes that do not offer nest spaces suggests that a broadening of the ants' plant host spectrum drove the evolution of additional domatium-bearing AG-epiphytes by selecting on pre-adapted morphological traits. Consistent with this, we found a statistical correlation between the evolution of diaspore dispersal by ants and domatia in all three lineages. Our study highlights how host broadening by a symbiont has led to new farming mutualisms.
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Affiliation(s)
- Guillaume Chomicki
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany
| | - Milan Janda
- Biology Centre of the Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic.,Laboratorio Nacional de Análisis y Síntesis Ecológica, ENES, UNAM, Antigua Carretera a Pátzcuaro 8701, Morelia, Mexico
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Str. 67, 80638 Munich, Germany
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132
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Eldridge RA, Achmadi AS, Giarla TC, Rowe KC, Esselstyn JA. Geographic isolation and elevational gradients promote diversification in an endemic shrew on Sulawesi. Mol Phylogenet Evol 2018; 118:306-317. [DOI: 10.1016/j.ympev.2017.09.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 08/08/2017] [Accepted: 09/25/2017] [Indexed: 01/06/2023]
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133
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O'Connell KA, Smith EN, Shaney KJ, Arifin U, Kurniawan N, Sidik I, Fujita MK. Coalescent species delimitation of a Sumatran parachuting frog. ZOOL SCR 2017. [DOI: 10.1111/zsc.12248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kyle A O'Connell
- Department of Biology The University of Texas at Arlington Arlington TX USA
- The Amphibian and Reptile Diversity Research Center University of Texas at Arlington Arlington TX USA
| | - Eric N Smith
- Department of Biology The University of Texas at Arlington Arlington TX USA
- The Amphibian and Reptile Diversity Research Center University of Texas at Arlington Arlington TX USA
| | - Kyle J Shaney
- Department of Biology The University of Texas at Arlington Arlington TX USA
- The Amphibian and Reptile Diversity Research Center University of Texas at Arlington Arlington TX USA
| | - Umilaela Arifin
- Biozentrum Grindel & Zopolofisches Museum Universität Hamburg Hamburg Germany
| | - Nia Kurniawan
- Department of Biology Universitas Brawijaya Malang East Java Indonesia
| | - Irvan Sidik
- Research and Development Center for Biology Indonesian Institute of Science (LIPI) Cibinong West Java Indonesia
| | - Matthew K Fujita
- Department of Biology The University of Texas at Arlington Arlington TX USA
- The Amphibian and Reptile Diversity Research Center University of Texas at Arlington Arlington TX USA
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134
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Vicariance and Oceanic Barriers Drive Contemporary Genetic Structure of Widespread Mangrove Species Sonneratia alba J. Sm in the Indo-West Pacific. FORESTS 2017. [DOI: 10.3390/f8120483] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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135
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Heatwole H, Grech A, Marsh H. Paleoclimatology, Paleogeography, and the Evolution and Distribution of Sea Kraits (Serpentes; Elapidae;Laticauda). HERPETOLOGICAL MONOGRAPHS 2017. [DOI: 10.1655/herpmonographs-d-16-00003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Harold Heatwole
- School of Earth and Environmental Sciences, James Cook University, Townsville, Queensland 4811, Australia
| | - Alana Grech
- Department of Environmental Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Helene Marsh
- College of Marine and Environmental Sciences, Centre for Tropical Water and Aquatic Ecosystem Research, James Cook University, Townsville, Queensland 4811, Australia
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136
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Li Y, Chen J, Jiang L, Qiao G. Islands conserve high species richness and areas of endemism of Hormaphidinae aphids. Curr Zool 2017; 63:623-632. [PMID: 29492023 PMCID: PMC5804216 DOI: 10.1093/cz/zox004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/12/2016] [Indexed: 11/29/2022] Open
Abstract
Patterns of biodiversity and endemism are important and form the foundation for biogeography and conservation studies. Hormaphidinae is an aphid group mainly distributed in the Sino-Japanese, Oriental, and Nearctic zoogeographic realms. To infer the areas of endemism of Hormaphidinae aphids in the Sino-Japanese and Oriental realms, we employed a geographical distribution dataset covering all 225 species in subfamily Hormaphidinae. In total, 1,245 distribution occurrence records for all species were analyzed in addition to the number of species in a certain grid cell to calculate species richness. Two methods (parsimony analysis of endemicity (PAE) and the use of an optimization criterion-NDM/VNDM) using a total of 6 grid sizes were applied to detect possible areas of endemism and to assess the probable effects of the 2 different methods and 6 grid sizes on the results of the patterns of the areas of endemism. The results revealed that islands presented most of the areas with high species richness and endemic species, particularly Japan, Taiwan Island, Java Island, the Malaysian Peninsula, southeast Himalaya, and the Hengduan Mountains. Most of these areas of endemism were located on islands or a peninsula. Islands were therefore shown to play an essential role in facilitating the formation of high species richness and endemism. Different grid sizes directly determined the regions of the areas of endemism, with small grid sizes tending to detect small and discrete areas of endemism and large grid sizes identifying continuous areas of endemism. In terms of the two methods, NDM/VNDM was found to identify more areas of endemism than PAE.
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Affiliation(s)
- Yang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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137
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Pan T, Zhang Y, Wang H, Wu J, Kang X, Qian L, Chen J, Rao D, Jiang J, Zhang B. The reanalysis of biogeography of the Asian tree frog, Rhacophorus (Anura: Rhacophoridae): geographic shifts and climatic change influenced the dispersal process and diversification. PeerJ 2017; 5:e3995. [PMID: 29177111 PMCID: PMC5701547 DOI: 10.7717/peerj.3995] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/16/2017] [Indexed: 11/20/2022] Open
Abstract
Rapid uplifts of the Tibetan Plateau and climate change in Asia are thought to have profoundly modulated the diversification of most of the species distributed throughout Asia. The ranoid tree frog genus Rhacophorus, the largest genus in the Rhacophoridae, is widely distributed in Asia and especially speciose in the areas south and east of the Tibetan Plateau. Here, we infer phylogenetic relationships among species and estimate divergence times, asking whether the spatiotemporal characteristics of diversification within Rhacophorus were related to rapid uplifts of the Tibetan Plateau and concomitant climate change. Phylogenetic analysis recovered distinct lineage structures in Rhacophorus, which indicated a clear distribution pattern from Southeast Asia toward East Asia and India. Molecular dating suggests that the first split within the genus date back to the Middle Oligocene (approx. 30 Ma). The Rhacophorus lineage through time (LTT) showed that there were periods of increased speciation rate: 14–12 Ma and 10–4 Ma. In addition, ancestral area reconstructions supported Southeast Asia as the ancestral area of Rhacophorus. According to the results of molecular dating, ancestral area reconstructions and LTT we think the geographic shifts, the staged rapid rises of the Tibetan Plateau with parallel climatic changes and reinforcement of the Asian monsoons (15 Ma, 8 Ma and 4–3 Ma), possibly prompted a burst of diversification in Rhacophorus.
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Affiliation(s)
- Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Yanan Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Jun Wu
- Ministry of Environmental Protection, Nanjing Institute of Environmental Sciences, Nanjing, Jiangsu, China
| | - Xing Kang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Lifu Qian
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China
| | - Jinyun Chen
- Department of Life Science, Huainan Normal University, Huainan, Anhui, China
| | - Dingqi Rao
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, Anhui Province, China.,School of Biosciences, Cardiff University, Cardiff, United Kingdom
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138
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Wassermann M, Raisch L, Lyons JA, Natusch DJD, Richter S, Wirth M, Preeprem P, Khoprasert Y, Ginting S, Mackenstedt U, Jäkel T. Examination of Sarcocystis spp. of giant snakes from Australia and Southeast Asia confirms presence of a known pathogen - Sarcocystis nesbitti. PLoS One 2017; 12:e0187984. [PMID: 29131856 PMCID: PMC5683627 DOI: 10.1371/journal.pone.0187984] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/30/2017] [Indexed: 11/18/2022] Open
Abstract
We examined Sarcocystis spp. in giant snakes from the Indo-Australian Archipelago and Australia using a combination of morphological (size of sporocyst) and molecular analyses. We amplified by PCR nuclear 18S rDNA from single sporocysts in order to detect mixed infections and unequivocally assign the retrieved sequences to the corresponding parasite stage. Sarcocystis infection was generally high across the study area, with 78 (68%) of 115 examined pythons being infected by one or more Sarcocystis spp. Among 18 randomly chosen, sporocyst-positive samples (11 from Southeast Asia, 7 from Northern Australia) the only Sarcocystis species detected in Southeast Asian snakes was S. singaporensis (in reticulated pythons), which was absent from all Australian samples. We distinguished three different Sarcocystis spp. in the Australian sample set; two were excreted by scrub pythons and one by the spotted python. The sequence of the latter is an undescribed species phylogenetically related to S. lacertae. Of the two Sarcocystis species found in scrub pythons, one showed an 18S rRNA gene sequence similar to S. zamani, which is described from Australia for the first time. The second sequence was identical/similar to that of S. nesbitti, a known human pathogen that was held responsible for outbreaks of disease among tourists in Malaysia. The potential presence of S. nesbitti in Australia challenges the current hypothesis of a snake-primate life cycle, and would have implications for human health in the region. Further molecular and biological characterizations are required to confirm species identity and determine whether or not the Australian isolate has the same zoonotic potential as its Malaysian counterpart. Finally, the absence of S. nesbitti in samples from reticulated pythons (which were reported to be definitive hosts), coupled with our phylogenetic analyses, suggest that alternative snake hosts may be responsible for transmitting this parasite in Malaysia.
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Affiliation(s)
- Marion Wassermann
- Department of Zoology, Division of Parasitology, University of Hohenheim, Stuttgart, Germany
| | - Lisa Raisch
- Department of Zoology, Division of Parasitology, University of Hohenheim, Stuttgart, Germany
| | | | | | - Sarah Richter
- Department of Zoology, Division of Parasitology, University of Hohenheim, Stuttgart, Germany
| | - Mareike Wirth
- Department of Zoology, Division of Parasitology, University of Hohenheim, Stuttgart, Germany
| | - Piyarat Preeprem
- Plant Protection Research and Development Office, Department of Agriculture, Bangkok, Thailand
| | - Yuvaluk Khoprasert
- Plant Protection Research and Development Office, Department of Agriculture, Bangkok, Thailand
| | | | - Ute Mackenstedt
- Department of Zoology, Division of Parasitology, University of Hohenheim, Stuttgart, Germany
| | - Thomas Jäkel
- Department of Zoology, Division of Parasitology, University of Hohenheim, Stuttgart, Germany
- Plant Protection Research and Development Office, Department of Agriculture, Bangkok, Thailand
- * E-mail:
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139
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Tethyan changes shaped aquatic diversification. Biol Rev Camb Philos Soc 2017; 93:874-896. [DOI: 10.1111/brv.12376] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 01/19/2023]
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140
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Hutama A, Dahruddin H, Busson F, Sauri S, Keith P, Hadiaty RK, Hanner R, Suryobroto B, Hubert N. Identifying spatially concordant evolutionary significant units across multiple species through DNA barcodes: Application to the conservation genetics of the freshwater fishes of Java and Bali. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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141
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Bolotov IN, Kondakov AV, Spitsyn VM, Gofarov MY, Kolosova YS. Leptocneria vinarskii sp. nov. (Lepidoptera: Erebidae: Lymantriinae), an overlooked Wallacean lineage of the Australian genus. Sci Rep 2017; 7:12430. [PMID: 28963487 PMCID: PMC5622091 DOI: 10.1038/s41598-017-12797-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/15/2017] [Indexed: 11/28/2022] Open
Abstract
The tussock moth genus Leptocneria Butler, 1886 (Lepidoptera: Erebidae: Lymantriinae) has been considered an entirely Australian taxon that includes two species: L. reducta (Walker, 1855) and L. binotata Butler, 1886. However, we discovered a divergent lineage of Leptocneria inhabiting Flores Island, Lesser Sundas, Indonesia. Here, we describe this lineage as the third species of the genus, L. vinarskii Bolotov, Kondakov et Spitsyn sp. nov. The new species is sister to L. reducta but differs from it by dark gray marking patterns of the forewing that lack orange or dark yellow marks. The mean COI genetic distance between L. vinarskii sp. nov. and L. reducta sensu lato is 2.9%. Our findings confirm that the Wallacean region was a faunal exchange area between Sundaland and Sahul during the Pleistocene but highlight that the vicariance events may have played a crucial role in origin of the endemic faunas on the islands of East Nusa Tenggara. Additionally, we show that both Australian species most likely represent cryptic species complexes, which are in need of further taxonomic revision.
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Affiliation(s)
- Ivan N Bolotov
- Northern Arctic Federal University, 163002, Arkhangelsk, Russia. .,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, 163000, Arkhangelsk, Russia.
| | - Alexander V Kondakov
- Northern Arctic Federal University, 163002, Arkhangelsk, Russia.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, 163000, Arkhangelsk, Russia
| | - Vitaly M Spitsyn
- Northern Arctic Federal University, 163002, Arkhangelsk, Russia.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, 163000, Arkhangelsk, Russia
| | - Mikhail Yu Gofarov
- Northern Arctic Federal University, 163002, Arkhangelsk, Russia.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, 163000, Arkhangelsk, Russia
| | - Yulia S Kolosova
- Northern Arctic Federal University, 163002, Arkhangelsk, Russia.,Federal Center for Integrated Arctic Research of the Russian Academy of Sciences, 163000, Arkhangelsk, Russia
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142
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von Rintelen K, Arida E, Häuser C. A review of biodiversity-related issues and challenges in megadiverse Indonesia and other Southeast Asian countries. RESEARCH IDEAS AND OUTCOMES 2017. [DOI: 10.3897/rio.3.e20860] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Indonesia is one of the ten member states of the economically and politically diverse regional organization of the Association of Southeast Asian Nations (ASEAN). Southeast Asia comprises four of the 25 global biodiversity hotspots, three of the 17 global megadiverse countries (Indonesia, Malaysia, and the Philippines) and the most diverse coral reefs in the world. All member states are Parties to the Convention on Biological Diversity (CBD). We discuss ASEAN-wide joint activities on nature conservation and sustainable use of biodiversity that do not stop at national borders.
The Indonesian archipelago comprises two of the world’s biodiversity hotspots (areas with a high degree of endemic species that are highly threatened by loss of habitats): Its insular character and complex geological history led to the evolution of a megadiverse fauna and flora on the global scale. The importance of biodiversity, e.g., in traditional medicine and agriculture, is deep-rooted in Indonesian society. Modern biodiversity pathways include new fields of application in technology, pharmacy and economy along with environmental policies. This development occurred not only in Indonesia but also in other biodiversity-rich tropical countries.
This review summarizes and discusses the unique biodiversity of Indonesia from different angles (science, society, environmental policy, and bioeconomy) and brings it into context within the ASEAN region. The preconditions of each member state for biodiversity-related activities are rather diverse. Much was done to improve the conditions for biodiversity research and use in several countries, primarily in those with a promising economic development. However, ASEAN as a whole still has further potential for more joint initiatives. Especially Indonesia has the highest biodiversity potential within the ASEAN and beyond, but likewise the highest risk of biodiversity loss.
We conclude that Indonesia has not taken full advantage of this potential yet. A growing national interest in local biodiversity as a natural resource is a welcome development on one hand, but the risk of too many restrictions for, e.g., the science community (high level of bureaucracy at all project stages from planning phase, visa procedures, field work permits, scientific exchange and project managment issues, governmental budget cuts for basic research and restricted access to international literature for Indonesian researchers) does significantly hamper the internationalization of biodiversity-related science. In the long run, Indonesia has to find a balance between protectionism and sensible access to its national biodiversity to tackle global challenges in biodiversity conservation, health issues, food security, and climate change.
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143
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Patel RP, Wutke S, Lenz D, Mukherjee S, Ramakrishnan U, Veron G, Fickel J, Wilting A, Förster DW. Genetic Structure and Phylogeography of the Leopard Cat (Prionailurus bengalensis) Inferred from Mitochondrial Genomes. J Hered 2017; 108:349-360. [PMID: 28498987 DOI: 10.1093/jhered/esx017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/21/2017] [Indexed: 01/02/2023] Open
Abstract
The Leopard cat Prionailurus bengalensis is a habitat generalist that is widely distributed across Southeast Asia. Based on morphological traits, this species has been subdivided into 12 subspecies. Thus far, there have been few molecular studies investigating intraspecific variation, and those had been limited in geographic scope. For this reason, we aimed to study the genetic structure and evolutionary history of this species across its very large distribution range in Asia. We employed both PCR-based (short mtDNA fragments, 94 samples) and high throughput sequencing based methods (whole mitochondrial genomes, 52 samples) on archival, noninvasively collected and fresh samples to investigate the distribution of intraspecific genetic variation. Our comprehensive sampling coupled with the improved resolution of a mitochondrial genome analyses provided strong support for a deep split between Mainland and Sundaic Leopard cats. Although we identified multiple haplogroups within the species' distribution, we found no matrilineal evidence for the distinction of 12 subspecies. In the context of Leopard cat biogeography, we cautiously recommend a revision of the Prionailurus bengalensis subspecific taxonomy: namely, a reduction to 4 subspecies (2 mainland and 2 Sundaic forms).
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Affiliation(s)
- Riddhi P Patel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany.,Freie Universität Berlin, Berlin, Germany
| | - Saskia Wutke
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany
| | - Shomita Mukherjee
- Salim Ali Centre for Ornithology and Natural History, Coimbatore, India.,);National Centre for Biological Sciences, GKVK Campus, Bangalore, India
| | - Uma Ramakrishnan
- );National Centre for Biological Sciences, GKVK Campus, Bangalore, India
| | - Géraldine Veron
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS MNHN UPMC EPHE, Muséum National d'Histoire Naturelle, Sorbonne Universités, CP 51, Paris, France
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Andreas Wilting
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany
| | - Daniel W Förster
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke Str.17, 10315 Berlin, Germany
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144
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Bernardes SC, Pepato AR, von Rintelen T, von Rintelen K, Page TJ, Freitag H, de Bruyn M. The complex evolutionary history and phylogeography of Caridina typus (Crustacea: Decapoda): long-distance dispersal and cryptic allopatric species. Sci Rep 2017; 7:9044. [PMID: 28831142 PMCID: PMC5567278 DOI: 10.1038/s41598-017-08494-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/30/2017] [Indexed: 11/09/2022] Open
Abstract
The evolutionary history of the old, diverse freshwater shrimp genus Caridina is still poorly understood, despite its vast distribution – from Africa to Polynesia. Here, we used nuclear and mitochondrial DNA to infer the phylogeographic and evolutionary history of C. typus, which is one of only four species distributed across the entire range of the genus. Despite this species’ potential for high levels of gene flow, questions have been raised regarding its phylogeographic structure and taxonomic status. We identified three distinct lineages that likely diverged in the Miocene. Molecular dating and ancestral range reconstructions are congruent with C. typus’ early dispersal to Africa, possibly mediated by the Miocene Indian Ocean Equatorial Jet, followed by back dispersal to Australasia after the Jet’s closure. Furthermore, several different species delimitation methods indicate each lineage represents a distinct (cryptic) species, contradicting current morphospecies delimitation of a single C. typus taxon. The evolutionary history of C. typus lineages is complex, in which ancient oceanic current systems and (currently unrecognised) speciation events preceded secondary sympatry of these cryptic species.
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Affiliation(s)
- Samuel C Bernardes
- Laboratório de Acarologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, 31270-901, Brazil.
| | - Almir R Pepato
- Laboratório de Acarologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte, 31270-901, Brazil
| | - Thomas von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin, 10115, Germany
| | - Kristina von Rintelen
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, Berlin, 10115, Germany
| | - Timothy J Page
- Australian Rivers Institute, Griffith University, Nathan, Queensland 4111, Australia.,Water Planning Ecology, Queensland Department of Science, Information Technology and Innovation, Dutton Park, Queensland 4102, Australia
| | - Hendrik Freitag
- Department of Biology, School of Science & Engineering, Ateneo de Manila University, Quezon City, 1108, Philippines
| | - Mark de Bruyn
- School of Biological Sciences, Bangor University, Bangor, LL57 2UW, UK. .,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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145
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Murray-Dickson G, Ghazali M, Ogden R, Brown R, Auliya M. Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds' most traded snake species. PLoS One 2017; 12:e0182049. [PMID: 28817588 PMCID: PMC5560690 DOI: 10.1371/journal.pone.0182049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/11/2017] [Indexed: 11/19/2022] Open
Abstract
As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python's native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley's modification of Wallace's line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans.
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Affiliation(s)
- Gillian Murray-Dickson
- Royal Zoological Society of Scotland (RZSS) WildGenes Laboratory, Edinburgh, United Kingdom
- * E-mail:
| | - Muhammad Ghazali
- Royal Zoological Society of Scotland (RZSS) WildGenes Laboratory, Edinburgh, United Kingdom
| | - Rob Ogden
- Trace Wildlife Forensics Network, Edinburgh, United Kingdom
| | - Rafe Brown
- KU Biodiversity Institute, 1345 Jayhawk Blvd, Dyche, Lawrence, KS, United States of America
| | - Mark Auliya
- Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany
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146
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Beck SV, Carvalho GR, Barlow A, Rüber L, Hui Tan H, Nugroho E, Wowor D, Mohd Nor SA, Herder F, Muchlisin ZA, de Bruyn M. Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax. PLoS One 2017; 12:e0179557. [PMID: 28742862 PMCID: PMC5526567 DOI: 10.1371/journal.pone.0179557] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/30/2017] [Indexed: 11/19/2022] Open
Abstract
The complex climatic and geological history of Southeast Asia has shaped this region’s high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods.
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Affiliation(s)
- Samantha V. Beck
- Hólar University College, Department of Aquaculture and Fish Biology, Háskólinn á Hólum, Sauðárkrókur, Iceland
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
- * E-mail: (MdB); (SVB)
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor, United Kingdom
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse, Potsdam (Golm), Germany
| | - Lukas Rüber
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse, Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse, Bern, Switzerland
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Estu Nugroho
- Indonesian Research Institute for Freshwater Aquaculture, Bogor, Java, Indonesia
| | - Daisy Wowor
- Research Center for Biology (Puslit Biologi), Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | | | - Fabian Herder
- Sektion Ichthyologie, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee, Bonn, Germany
| | - Zainal A. Muchlisin
- Department of Aquaculture, Marine & Fishery Sciences, Syiah Kuala University, Banda Aceh, Indonesia
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor, United Kingdom
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
- * E-mail: (MdB); (SVB)
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147
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New record of Melomys burtoni (Mammalia, Rodentia, Murinae) from Halmahera (North Moluccas, Indonesia): a review of Moluccan Melomys. MAMMALIA 2017. [DOI: 10.1515/mammalia-2016-0137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Mosaic-tailed rodents of the genus Melomys belong to the Australasian old endemic murine radiation and exhibit a rat-like morphology with arboreal or scansorial specializations. Here we report a new population of Melomys burtoni from the island of Halmahera (in the North Moluccas, Indonesia). Our molecular phylogenetic results highlight close relationships and recent evolutionary divergences among M. burtoni from Halmahera and the Australo-Papuan taxa M. burtoni and M. lutillus and other Moluccan taxa, including M. paveli. Multivariate as well as geometric morphometric analyses of cranial, and dental features support the recognition of M. burtoni from Halmahera as a slightly distinctive insular population, preventing us from elevating it as a new taxa. This population is recorded from lowland secondary forest and forest edge habitats in south-central Halmahera. As with other Moluccan endemic murines, colonization by an Australo-Papuan ancestor and subsequent isolation is the probable mode of diversification for M. burtoni in Halmahera. The discovery of Melomys in Halmahera fills a previously puzzling gap in knowledge of the murine fauna of the Moluccas and the biogeography of the Wallacean region.
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148
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Selvatti AP, Galvão A, Pereira AG, Pedreira Gonzaga L, Russo CADM. An African Origin of the Eurylaimides (Passeriformes) and the Successful Diversification of the Ground-Foraging Pittas (Pittidae). Mol Biol Evol 2017; 34:483-499. [PMID: 28069777 DOI: 10.1093/molbev/msw250] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The Eurylaimides is one of the few passerine groups with a pantropical distribution. In this study, we generated a multi-calibrated tree with 83% of eurylaimid species diversity based on 30 molecular loci. Particular attention was given to the monotypic Sapayoidae to reconstruct the biogeography of this radiation. We conducted several topological tests including nonoverlapping subsampling of the concatenated alignment and coalescent species tree reconstruction. These tests firmly placed the South American Sapayoidae as the sister group to all other Eurylaimides families (split at ∼28 Ma), with increasing branch support as highly variable sites were removed. This topology is consistent with the breakup of the insular connection between Africa and South America (Atlantogea) that took place between the middle Eocene and the early Oligocene. We recovered Africa as the cradle of the core Eurylaimides, and this result is supported by all African lineages corresponding to the oldest splits within each family in this group. Our timescale suggests that desertification and the uplift of the Tibetan Plateau caused a parallel divergence between African and Asian lineages in all major clades in the core Eurylaimides at 22-9 Ma. We also propose that the ground-foraging behavior in the Pittidae ancestor allowed the pitta lineage to thrive and coexist with the older arboreal lineages of the core Eurylaimides. In contrast, the diversification of pittas in Australia was likely hindered by direct competition with the endemic ground-foraging oscines that had been well established in that continent since the Eocene.
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Affiliation(s)
- Alexandre Pedro Selvatti
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Ana Galvão
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Anieli Guirro Pereira
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Instituto de Biologia, Rio de Janeiro, RJ, Brazil
| | - Luiz Pedreira Gonzaga
- Departamento de Zoologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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149
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Wei CH, Lohman DJ, Peggie D, Yen SH. An illustrated checklist of the genus Elymnias Hübner, 1818 (Nymphalidae, Satyrinae). Zookeys 2017:47-152. [PMID: 28769686 PMCID: PMC5523206 DOI: 10.3897/zookeys.676.12579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 04/19/2017] [Indexed: 11/12/2022] Open
Abstract
We review the genus Elymnias Hübner, 1818, a morphologically diverse satyrine butterfly clade involved in multifarious Batesian mimicry relationships throughout Asia and Africa. A variety of different model species are mimicked, and many Elymnias species are sexually dimorphic mimics, with males and females resembling different model species. We revise species and subspecies delimitations in light of an integrative taxonomic investigation using external morphology, male and female genital morphology, and a multi-locus molecular phylogeny. There is little interspecific genitalic variation among species in this group, and previous taxonomists therefore relied almost entirely on wing patterns. Our molecular phylogenetic analysis reveals several examples of polymorphism or wing pattern divergence within a single species currently classified as two or more different species. We also found examples of wing pattern convergence among disparate lineages that mimic the same widespread model species. Frequently, two or more phenotypically similar species were classified as a single species. This comprehensive checklist reviews all names associated with Elymnias to align its taxonomy with the evolutionary history of the group. All available information on nomenclature, type localities, repositories of type specimens, and geographical distributions is summarized, and images of adult specimens and genitalia are provided along with distribution maps of all species and selected subspecies. We identify 2 species incertae sedis, establish 15 monophyletic species groups (including 1 species unplaced in any species group), and make 49 taxonomic changes, including 35 new synonyms, 7 new combinations (2 of which have new status), 1 resurrected combination, 1 resurrected subspecies, and 7 status changes.
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Affiliation(s)
- Chia-Hsuan Wei
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - David J Lohman
- Department of Biology, City College of New York, City University of New York, New York, NY, 10031, USA.,Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY, 10016, USA.,Entomology Section, National Museum of the Philippines, Manila, 1000, Philippines
| | - Djunijanti Peggie
- Division of Zoology, Research Centre for Biology-LIPI, Cibinong-Bogor, 16911, Indonesia
| | - Shen-Horn Yen
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
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150
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Bolotov IN, Kondakov AV, Vikhrev IV, Aksenova OV, Bespalaya YV, Gofarov MY, Kolosova YS, Konopleva ES, Spitsyn VM, Tanmuangpak K, Tumpeesuwan S. Ancient River Inference Explains Exceptional Oriental Freshwater Mussel Radiations. Sci Rep 2017; 7:2135. [PMID: 28522869 PMCID: PMC5437074 DOI: 10.1038/s41598-017-02312-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 04/07/2017] [Indexed: 11/18/2022] Open
Abstract
The concept of long-lived (ancient) lakes has had a great influence on the development of evolutionary biogeography. According to this insight, a number of lakes on Earth have existed for several million years (e.g., Baikal and Tanganyika) and represent unique evolutionary hotspots with multiple intra-basin radiations. In contrast, rivers are usually considered to be variable systems, and the possibility of their long-term existence during geological epochs has never been tested. In this study, we reconstruct the history of freshwater basin interactions across continents based on the multi-locus fossil-calibrated phylogeny of freshwater mussels (Unionidae). These mussels most likely originated in Southeast and East Asia in the Jurassic, with the earliest expansions into North America and Africa (since the mid-Cretaceous) following the colonization of Europe and India (since the Paleocene). We discovered two ancient monophyletic mussel radiations (mean age ~51–55 Ma) within the paleo-Mekong catchment (i.e., the Mekong, Siam, and Malacca Straits paleo-river drainage basins). Our findings reveal that the Mekong may be considered a long-lived river that has existed throughout the entire Cenozoic epoch.
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Affiliation(s)
- Ivan N Bolotov
- Department of Science, Northern Arctic Federal University, Arkhangelsk, Russian Federation.
| | - Alexander V Kondakov
- Department of Science, Northern Arctic Federal University, Arkhangelsk, Russian Federation
| | - Ilya V Vikhrev
- Department of Science, Northern Arctic Federal University, Arkhangelsk, Russian Federation
| | - Olga V Aksenova
- Department of Science, Northern Arctic Federal University, Arkhangelsk, Russian Federation
| | - Yulia V Bespalaya
- Department of Science, Northern Arctic Federal University, Arkhangelsk, Russian Federation
| | - Mikhail Yu Gofarov
- Department of Science, Northern Arctic Federal University, Arkhangelsk, Russian Federation
| | - Yulia S Kolosova
- Department of Science, Northern Arctic Federal University, Arkhangelsk, Russian Federation
| | - Ekaterina S Konopleva
- Department of Science, Northern Arctic Federal University, Arkhangelsk, Russian Federation
| | - Vitaly M Spitsyn
- Department of Science, Northern Arctic Federal University, Arkhangelsk, Russian Federation
| | - Kitti Tanmuangpak
- Department of Science, Faculty of Science and Technology, Loei Rajabhat University, Loei, Thailand
| | - Sakboworn Tumpeesuwan
- Department of Biology, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand
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