1
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Reeve AH, Kennedy JD, Pujolar JM, Petersen B, Blom MPK, Alström P, Haryoko T, Ericson PGP, Irestedt M, Nylander JAA, Jønsson KA. The formation of the Indo-Pacific montane avifauna. Nat Commun 2023; 14:8215. [PMID: 38081809 PMCID: PMC10713610 DOI: 10.1038/s41467-023-43964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The processes generating the earth's montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species' ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region's montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.
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Affiliation(s)
- Andrew Hart Reeve
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark.
| | - Jonathan David Kennedy
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
| | - José Martín Pujolar
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Centre for Gelatinous Plankton Ecology and Evolution, DTU Aqua, Kemitorvet, Building 202, DK-2800, Kongens Lyngby, Denmark
| | - Bent Petersen
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, DK-1353, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Mozes P K Blom
- Museum für Naturkunde Berlin, Leibniz Institut für Evolutions- und Biodiversitätsforschung, 10115, Berlin, Germany
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Johan A A Nylander
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
| | - Knud Andreas Jønsson
- Natural History Museum of Denmark, University of Copenhagen, DK-2100, Copenhagen Ø, Denmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05, Stockholm, Sweden
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2
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Ng EYX, Li S, Zhang D, Garg KM, Song G, Martinez J, Hung LM, Tu VT, Fuchs J, Dong L, Olsson U, Huang Y, Alström P, Rheindt FE, Lei F. Genome‐wide
SNPs
confirm plumage polymorphism and hybridisation within a
Cyornis
flycatcher species complex. ZOOL SCR 2022. [DOI: 10.1111/zsc.12568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Elize Y. X. Ng
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Discipline of Biological Science, School of Natural Sciences University of Tasmania Hobart Tasmania Australia
| | - Siqi Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Sciences Shaanxi Normal University Xi'an China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Kritika M. Garg
- Department of Biological Sciences National University of Singapore Singapore Singapore
- Centre for Interdisciplinary Archaeological Research Ashoka University Sonipat India
- Department of Biology Ashoka University Sonipat India
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | | | - Le Manh Hung
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Vuong Tan Tu
- Institute of Ecology and Biological Resources, Graduate University of Science and Technology Vietnam Academy of Science and Technology Hanoi Vietnam
| | - Jérôme Fuchs
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle CNRS, 22 S U, EPHE, UA CP51 Paris France
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences Beijing Normal University Beijing China
| | - Urban Olsson
- Systematics and Biodiversity, Department of Biology and Environmental Sciences University of Gothenburg Gothenburg Sweden
- Gothenburg Global Biodiversity Center Göteborg Sweden
| | - Yuan Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre Uppsala University Uppsala Sweden
| | - Frank E. Rheindt
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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3
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Ibáñez C, Fukui D, Popa‐Lisseanu A.G, Pastor‐Beviá D, García‐Mudarra JL, Juste J. Molecular identification of bird species in the diet of the bird‐like noctule bat in Japan. J Zool (1987) 2020. [DOI: 10.1111/jzo.12855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. Ibáñez
- Estación Biológica de Doñana (CSIC) Sevilla Spain
| | - D. Fukui
- Graduate School of Agricultural and Life Sciences The University of Tokyo Hokkaido Forest The University of Tokyo Furano Hokkaido Japan
| | | | | | | | - J. Juste
- Estación Biológica de Doñana (CSIC) Sevilla Spain
- CIBER Epidemiology and Public Health (CIBERESP) Madrid Spain
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4
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Gyllenhaal EF, Mapel XM, Naikatini A, Moyle RG, Andersen MJ. A test of island biogeographic theory applied to estimates of gene flow in a Fijian bird is largely consistent with neutral expectations. Mol Ecol 2020; 29:4059-4073. [DOI: 10.1111/mec.15625] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/25/2023]
Affiliation(s)
- Ethan F. Gyllenhaal
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
| | - Xena M. Mapel
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
| | - Alivereti Naikatini
- South Pacific Regional Herbarium Institute of Applied Sciences University of the South Pacific Suva Fiji Islands
| | - Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology University of Kansas Lawrence KS USA
| | - Michael J. Andersen
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
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5
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Fuchs J, Alström P, Yosef R, Olsson U. Miocene diversification of an open‐habitat predatorial passerine radiation, the shrikes (Aves: Passeriformes: Laniidae). ZOOL SCR 2019. [DOI: 10.1111/zsc.12363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jérôme Fuchs
- UMR7205 Institut de Systématique, Evolution, Biodiversité CNRS MNHN UPMC EPHE, Muséum National d’Histoire Naturelle Sorbonne Université Paris France
| | - Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre Uppsala University Uppsala Sweden
- Swedish Species Information Centre Swedish University of Agricultural Sciences Uppsala Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology Chinese Academy of Sciences Beijing China
| | | | - Urban Olsson
- Department of Biology and Environmental Science University of Gothenburg Gothenburg Sweden
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6
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Wei C, Dong L, Li SH, Alström P, Liu Y, Xia C, Yao CT, Zhang Y. From the Himalayas to a continental Island: Integrative species delimitation in the Brownish-flanked Bush Warbler Horornis fortipes complex. Mol Phylogenet Evol 2018; 131:219-227. [PMID: 30316948 DOI: 10.1016/j.ympev.2018.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/06/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022]
Abstract
As species serve as basic units of study in many fields of biology, assessments of species limits are fundamental for such studies. Here, we used a multilocus dataset and different coalescent-based methods to analyze species delimitation and phylogenetic relationships in the Brownish-flanked Bush Warbler Horornis fortipes complex, which is widespread in the Sino-Himalayan region. We also examined the vocal and morphometric divergence within this complex. Our genetic results suggested that Horornis fortipes is composed of at least three independently evolving lineages, which diverged 1.1-1.8 million years ago. However, these lineages have hardly diverged in song or morphometrics and only very slightly in plumage. Our result indicate that there are three incipient species in Horonis fortipes complex diverged in central Himalayas and Hengduan Mountains, but not between the continent and Taiwan island.
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Affiliation(s)
- Chentao Wei
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lu Dong
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
| | - Shou-Hsien Li
- Department of Life Science, National Taiwan Normal University, Taipei 11677, Taiwan, China
| | - Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden; Swedish Species Information Centre, Swedish University of Agricultural Sciences, Box 7007, SE-75007 Uppsala, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Yang Liu
- State Key Laboratory of Biocontrol and Department of Ecology/School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Cheng-Te Yao
- Medium Altitude Experimental Station, Endemic Species Research Institute, Chichi, 15, Nantou 552, Taiwan, China
| | - Yanyun Zhang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.
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7
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Comprehensive molecular phylogeny of the grassbirds and allies (Locustellidae) reveals extensive non-monophyly of traditional genera, and a proposal for a new classification. Mol Phylogenet Evol 2018; 127:367-375. [DOI: 10.1016/j.ympev.2018.03.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/21/2018] [Accepted: 03/28/2018] [Indexed: 11/17/2022]
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8
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Alström P, Rheindt FE, Zhang R, Zhao M, Wang J, Zhu X, Gwee CY, Hao Y, Ohlson J, Jia C, Prawiradilaga DM, Ericson PGP, Lei F, Olsson U. Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation. Mol Phylogenet Evol 2018; 126:141-152. [PMID: 29631054 DOI: 10.1016/j.ympev.2018.03.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/24/2018] [Accepted: 03/28/2018] [Indexed: 10/17/2022]
Abstract
The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment,and we argue againstproliferation of taxonomic names,and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.
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Affiliation(s)
- Per Alström
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden; Swedish Species Information Centre, Swedish University of Agricultural Sciences (SLU), Box 7007, Uppsala SE-750 07, Sweden; Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558 Singapore, Singapore
| | - Ruiying Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaojia Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, 117558 Singapore, Singapore
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jan Ohlson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm SE-10405, Sweden
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dewi M Prawiradilaga
- Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong Science Centre, Jalan Raya Jakarta Bogor KM 46, Bogor 16911, Indonesia
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, Stockholm SE-10405, Sweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden
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9
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Ren G, Conti E, Salamin N. Phylogeny and biogeography of Primula sect. Armerina: implications for plant evolution under climate change and the uplift of the Qinghai-Tibet Plateau. BMC Evol Biol 2015; 15:161. [PMID: 26275399 PMCID: PMC4537560 DOI: 10.1186/s12862-015-0445-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The historical orogenesis and associated climatic changes of mountain areas have been suggested to partly account for the occurrence of high levels of biodiversity and endemism. However, their effects on dispersal, differentiation and evolution of many groups of plants are still unknown. In this study, we examined the detailed diversification history of Primula sect. Armerina, and used biogeographic analysis and macro-evolutionary modeling to investigate a series of different questions concerning the evolution of the geographical and ecological distribution of the species in this section. RESULTS We sequenced five chloroplast and one nuclear genes for species of Primula sect. Armerina. Neither chloroplast nor nuclear trees support the monophyly of the section. The major incongruences between the two trees occur among closely related species and may be explained by hybridization. Our dating analyses based on the chloroplast dataset suggest that this section began to diverge from its relatives around 3.55 million years ago, largely coinciding with the last major uplift of the Qinghai-Tibet Plateau (QTP). Biogeographic analysis supports the origin of the section in the Himalayan Mountains and dispersal from the Himalayas to Northeastern QTP, Western QTP and Hengduan Mountains. Furthermore, evolutionary models of ecological niches show that the two P. fasciculata clades have significantly different climatic niche optima and rates of niche evolution, indicating niche evolution under climatic changes and further providing evidence for explaining their biogeographic patterns. CONCLUSION Our results support the hypothesis that geologic and climatic events play important roles in driving biological diversification of organisms in the QTP area. The Pliocene uplift of the QTP and following climatic changes most likely promoted both the inter- and intraspecific divergence of Primula sect. Armerina. This study also illustrates how niche evolution under climatic changes influences biogeographic patterns.
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Affiliation(s)
- Guangpeng Ren
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland.
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou, 730000, , Gansu, China.
| | - Elena Conti
- Institute for Systematic Botany, University of Zurich, Zollikerstrasse 107, 8008, ZURICH, Switzerland.
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge, 1015, Lausanne, Switzerland.
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10
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Sangster G, Luksenburg JA. Declining rates of species described per taxonomist: slowdown of progress or a side-effect of improved quality in taxonomy? Syst Biol 2014; 64:144-51. [PMID: 25190593 DOI: 10.1093/sysbio/syu069] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- George Sangster
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden; and Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, Virginia 22030 4444, USA Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden; and Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, Virginia 22030 4444, USA
| | - Jolanda A Luksenburg
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden; and Department of Environmental Science and Policy, George Mason University, 4400 University Drive, Fairfax, Virginia 22030 4444, USA
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11
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Abstract
This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.
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Affiliation(s)
- Gergely J Szöllősi
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France
| | - Eric Tannier
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France
| | - Vincent Daubin
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France
| | - Bastien Boussau
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France;
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12
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Poor Fit to the Multispecies Coalescent is Widely Detectable in Empirical Data. Syst Biol 2013; 63:322-33. [DOI: 10.1093/sysbio/syt057] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Höhna S. Fast simulation of reconstructed phylogenies under global time-dependent birth–death processes. Bioinformatics 2013; 29:1367-74. [DOI: 10.1093/bioinformatics/btt153] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Olsson U, Irestedt M, Sangster G, Ericson PG, Alström P. Systematic revision of the avian family Cisticolidae based on a multi-locus phylogeny of all genera. Mol Phylogenet Evol 2013; 66:790-9. [DOI: 10.1016/j.ympev.2012.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 09/28/2012] [Accepted: 11/02/2012] [Indexed: 10/27/2022]
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15
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Sheldon FH, Oliveros CH, Taylor SS, McKay B, Lim HC, Rahman MA, Mays H, Moyle RG. Molecular phylogeny and insular biogeography of the lowland tailorbirds of Southeast Asia (Cisticolidae: Orthotomus). Mol Phylogenet Evol 2012; 65:54-63. [DOI: 10.1016/j.ympev.2012.05.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 05/20/2012] [Accepted: 05/21/2012] [Indexed: 10/28/2022]
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Fregin S, Haase M, Olsson U, Alström P. New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers. BMC Evol Biol 2012; 12:157. [PMID: 22920688 PMCID: PMC3462691 DOI: 10.1186/1471-2148-12-157] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 08/17/2012] [Indexed: 11/20/2022] Open
Abstract
Background The circumscription of the avian superfamily Sylvioidea is a matter of long ongoing debate. While the overall inclusiveness has now been mostly agreed on and 20 families recognised, the phylogenetic relationships among the families are largely unknown. We here present a phylogenetic hypothesis for Sylvioidea based on one mitochondrial and six nuclear markers, in total ~6.3 kbp, for 79 ingroup species representing all currently recognised families and some species with uncertain affinities, making this the most comprehensive analysis of this taxon. Results The resolution, especially of the deeper nodes, is much improved compared to previous studies. However, many relationships among families remain uncertain and are in need of verification. Most families themselves are very well supported based on the total data set and also by indels. Our data do not support the inclusion of Hylia in Cettiidae, but do not strongly reject a close relationship with Cettiidae either. The genera Scotocerca and Erythrocercus are closely related to Cettiidae, but separated by relatively long internodes. The families Paridae, Remizidae and Stenostiridae clustered among the outgroup taxa and not within Sylvioidea. Conclusions Although the phylogenetic position of Hylia is uncertain, we tentatively support the recognition of the family Hyliidae Bannerman, 1923 for this genus and Pholidornis. We propose new family names for the genera Scotocerca and Erythrocercus, Scotocercidae and Erythrocercidae, respectively, rather than including these in Cettiidae, and we formally propose the name Macrosphenidae, which has been in informal use for some time. We recommend that Paridae, Remizidae and Stenostiridae are not included in Sylvioidea. We also briefly discuss the problems of providing a morphological diagnosis when proposing a new family-group name (or genus-group name) based on a clade.
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Affiliation(s)
- Silke Fregin
- Vogelwarte Hiddensee, Zoological Institute and Museum, Ernst Moritz Arndt University of Greifswald, Greifswald, 17489, Germany.
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Eight independent nuclear genes support monophyly of the plovers: the role of mutational variance in gene trees. Mol Phylogenet Evol 2012; 65:631-41. [PMID: 22842291 DOI: 10.1016/j.ympev.2012.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 07/18/2012] [Accepted: 07/19/2012] [Indexed: 01/25/2023]
Abstract
Molecular phylogenies of Charadriiformes based on mtDNA genes and one to three nuclear loci do not support the traditional placement of Pluvialis in the plovers (Charadriidae), assigning it instead to oystercatchers, stilts, and avocets (Haematopodidae and Recurvirostridae). To investigate this hypothesis of plover paraphyly, the relationships among Pluvialis and closely related families were revisited by sequencing two individuals of all taxa except Peltohyas for eight independent single copy nuclear protein-coding loci selected for their informativeness at this phylogenetic depth. The species tree estimated jointly with the gene trees in the coalescent programme (*)BEAST strongly supported plover monophyly, as did Bayesian analysis of the concatenated matrix. The data sets that supported plover paraphyly in Baker et al. (2007) and Fain and Houde (2007) reflect two to four independent gene histories, and thus discordance with the plover monophyly species tree might have arisen by chance through stochastic mutational variance. For the plovers we conclude there is no conclusive evidence of coalescent variance from ancient incomplete lineage sorting across the interior branch leading to Pluvialis in the species tree. Rather, earlier studies seem have been misled by faster evolving mtDNA genes with high mutational variance, and a few nuclear genes that had low resolving power at the Pluvialis sister group level. These findings are of general relevance in avian phylogenetics, as they show that careful attention needs to be paid to the number and the phylogenetic informativeness of genes required to obtain accurate estimates of the species tree, especially where there is mutational heterogeneity in gene trees.
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