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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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Xiong Y, Xiong Y, Shu X, Yu Q, Lei X, Li D, Yan J, Bai S, Ma X. Molecular Phylogeography and Intraspecific Divergences in Siberian Wildrye ( Elymus sibiricus L.) Wild Populations in China, Inferred From Chloroplast DNA Sequence and cpSSR Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:862759. [PMID: 35665183 PMCID: PMC9161273 DOI: 10.3389/fpls.2022.862759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/30/2022] [Indexed: 05/27/2023]
Abstract
A detailed understanding of the distribution and degree of genetic variation within a species is important for determining their evolutionary potential, which in return facilitates the development of efficient conservation strategies aimed at preserving adaptive genetic variation. As an important perennial, cool-season grass in temperate Eurasia, increasing attention has been paid to Siberian wildrye (Elymus sibiricus) due to its excellent ecological utilization value and forage production potential in China, particularly in the Qinghai-Tibet Plateau (QTP) regions. In this study, we applied two chloroplast (cp) genes (matK and rbcL), three cp spacer regions (trnY-GUA∼trnD-GUC, atpH∼atpF, and rps4∼trnT-UGU), and six cpSSR markers to the genetic and phylogenetic analysis of 137 wild E. sibiricus accessions from 23 natural populations that represent the main distribution regions in China. The results show the highest genetic diversity (h = 0.913) and haplotype richness (10 haplotypes) for the QTP population, which indicates QTP as the probable diversity center and geographic origin of E. sibiricus in China. Population divergence was high, indicating a significant phylogeographic structure together with a significantly higher Nst value (Nst > Gst, P < 0.05) at the species level, QTP+XJ (combined populations from QTP and Xinjiang), QTP+NC (combined populations from QTP and North China), and XJ+NC (combined populations from Xinjiang and North China) group levels, respectively. An expansion was revealed in the distributional range of E. sibiricus in China from paleo times up to the recent past, while a dramatic range of contraction was predicted for the near future. The predicted main limiting factor for the further spread of E. sibiricus is an increasing global mean temperature. We recommend that the combination of Es-cpDNA1 and Es-cpDNA3+4+5 can be used as effective markers for phylogenetic analysis and phylogeographical history analysis of E. sibiricus. These findings shed new light on the historical population dynamics of cold-season herbs in the QTP region and the north of China and are of great significance for the future establishment of protection and collection strategies for wild E. sibiricus germplasm.
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Affiliation(s)
- Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xin Shu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Jiajun Yan
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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The formation of avian montane diversity across barriers and along elevational gradients. Nat Commun 2022; 13:268. [PMID: 35022441 PMCID: PMC8755808 DOI: 10.1038/s41467-021-27858-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 12/15/2021] [Indexed: 01/25/2023] Open
Abstract
Tropical mountains harbor exceptional concentrations of Earth's biodiversity. In topographically complex landscapes, montane species typically inhabit multiple mountainous regions, but are absent in intervening lowland environments. Here we report a comparative analysis of genome-wide DNA polymorphism data for population pairs from eighteen Indo-Pacific bird species from the Moluccan islands of Buru and Seram and from across the island of New Guinea. We test how barrier strength and relative elevational distribution predict population differentiation, rates of historical gene flow, and changes in effective population sizes through time. We find population differentiation to be consistently and positively correlated with barrier strength and a species' altitudinal floor. Additionally, we find that Pleistocene climate oscillations have had a dramatic influence on the demographics of all species but were most pronounced in regions of smaller geographic area. Surprisingly, even the most divergent taxon pairs at the highest elevations experience gene flow across barriers, implying that dispersal between montane regions is important for the formation of montane assemblages.
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Garg KM, Chattopadhyay B, Cros E, Tomassi S, Benedick S, Edwards DP, Rheindt FE. Island Biogeography Revisited: Museomics Reveals Affinities of Shelf Island Birds Determined by Bathymetry and Paleo-Rivers, Not by Distance to Mainland. Mol Biol Evol 2022; 39:msab340. [PMID: 34893875 PMCID: PMC8789277 DOI: 10.1093/molbev/msab340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Island biogeography is one of the most powerful subdisciplines of ecology: its mathematical predictions that island size and distance to mainland determine diversity have withstood the test of time. A key question is whether these predictions follow at a population-genomic level. Using rigorous ancient-DNA protocols, we retrieved approximately 1,000 genomic markers from approximately 100 historic specimens of two Southeast Asian songbird complexes from across the Sunda Shelf archipelago collected 1893-1957. We show that the genetic affinities of populations on small shelf islands defy the predictions of geographic distance and appear governed by Earth-historic factors including the position of terrestrial barriers (paleo-rivers) and persistence of corridors (Quaternary land bridges). Our analyses suggest that classic island-biogeographic predictors may not hold well for population-genomic dynamics on the thousands of shelf islands across the globe, which are exposed to dynamic changes in land distribution during Quaternary climate change.
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Affiliation(s)
- Kritika M Garg
- Department of Biological Sciences, National University of Singapore, Singapore
- Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat, India
- Department of Biology, Ashoka University, Sonipat, India
| | - Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, Singapore
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Emilie Cros
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Suzanne Tomassi
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Suzan Benedick
- Faculty of Sustainable Agriculture, University of Malaysia, Sabah, Malaysia
| | - David P Edwards
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore
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Teixeira H, Salmona J, Arredondo A, Mourato B, Manzi S, Rakotondravony R, Mazet O, Chikhi L, Metzger J, Radespiel U. Impact of model assumptions on demographic inferences: the case study of two sympatric mouse lemurs in northwestern Madagascar. BMC Ecol Evol 2021; 21:197. [PMID: 34727890 PMCID: PMC8561976 DOI: 10.1186/s12862-021-01929-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Quaternary climate fluctuations have been acknowledged as major drivers of the geographical distribution of the extraordinary biodiversity observed in tropical biomes, including Madagascar. The main existing framework for Pleistocene Malagasy diversification assumes that forest cover was strongly shaped by warmer Interglacials (leading to forest expansion) and by cooler and arid glacials (leading to forest contraction), but predictions derived from this scenario for forest-dwelling animals have rarely been tested with genomic datasets. RESULTS We generated genomic data and applied three complementary demographic approaches (Stairway Plot, PSMC and IICR-simulations) to infer population size and connectivity changes for two forest-dependent primate species (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. The analyses suggested major demographic changes in both species that could be interpreted in two ways, depending on underlying model assumptions (i.e., panmixia or population structure). Under panmixia, the two species exhibited larger population sizes across the Last Glacial Maximum (LGM) and towards the African Humid Period (AHP). This peak was followed by a population decline in M. ravelobensis until the present, while M. murinus may have experienced a second population expansion that was followed by a sharp decline starting 3000 years ago. In contrast, simulations under population structure suggested decreasing population connectivity between the Last Interglacial and the LGM for both species, but increased connectivity during the AHP exclusively for M. murinus. CONCLUSION Our study shows that closely related species may differ in their responses to climatic events. Assuming that Pleistocene climatic conditions in the lowlands were similar to those in the Malagasy highlands, some demographic dynamics would be better explained by changes in population connectivity than in population size. However, changes in connectivity alone cannot be easily reconciled with a founder effect that was shown for M. murinus during its colonization of the northwestern Madagascar in the late Pleistocene. To decide between the two alternative models, more knowledge about historic forest dynamics in lowland habitats is necessary. Altogether, our study stresses that demographic inferences strongly depend on the underlying model assumptions. Final conclusions should therefore be based on a comparative evaluation of multiple approaches.
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Affiliation(s)
- Helena Teixeira
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
| | - Jordi Salmona
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Armando Arredondo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Beatriz Mourato
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Sophie Manzi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Romule Rakotondravony
- Ecole Doctorale Ecosystèmes Naturels (EDEN), University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
| | - Olivier Mazet
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Lounès Chikhi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Julia Metzger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, 30559, Hannover, Germany
- Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
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6
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Teixeira H, Montade V, Salmona J, Metzger J, Bremond L, Kasper T, Daut G, Rouland S, Ranarilalatiana S, Rakotondravony R, Chikhi L, Behling H, Radespiel U. Past environmental changes affected lemur population dynamics prior to human impact in Madagascar. Commun Biol 2021; 4:1084. [PMID: 34526636 PMCID: PMC8443640 DOI: 10.1038/s42003-021-02620-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/31/2021] [Indexed: 02/08/2023] Open
Abstract
Quaternary climatic changes have been invoked as important drivers of species diversification worldwide. However, the impact of such changes on vegetation and animal population dynamics in tropical regions remains debated. To overcome this uncertainty, we integrated high-resolution paleoenvironmental reconstructions from a sedimentary record covering the past 25,000 years with demographic inferences of a forest-dwelling primate species (Microcebus arnholdi), in northern Madagascar. Result comparisons suggest that climate changes through the African Humid Period (15.2 - 5.5 kyr) strongly affected the demographic dynamics of M. arnholdi. We further inferred a population decline in the last millennium which was likely shaped by the combination of climatic and anthropogenic impacts. Our findings demonstrate that population fluctuations in Malagasy wildlife were substantial prior to a significant human impact. This provides a critical knowledge of climatically driven, environmental and ecological changes in the past, which is essential to better understand the dynamics and resilience of current biodiversity.
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Affiliation(s)
- Helena Teixeira
- grid.412970.90000 0001 0126 6191Institute of Zoology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
| | - Vincent Montade
- grid.7450.60000 0001 2364 4210University of Goettingen, Department of Palynology and Climate Dynamics, Untere Karspüle 2, 37073 Goettingen, Germany ,grid.462058.d0000 0001 2188 7059ISEM, Université Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier, France
| | - Jordi Salmona
- grid.15781.3a0000 0001 0723 035XCNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France
| | - Julia Metzger
- grid.412970.90000 0001 0126 6191Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559 Hannover, Germany ,grid.419538.20000 0000 9071 0620Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Laurent Bremond
- grid.462058.d0000 0001 2188 7059ISEM, Université Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier, France
| | - Thomas Kasper
- grid.9613.d0000 0001 1939 2794Friedrich-Schiller-University Jena, Department of Physical Geography, Loebdergraben 32, 07743 Jena, Germany
| | - Gerhard Daut
- grid.9613.d0000 0001 1939 2794Friedrich-Schiller-University Jena, Department of Physical Geography, Loebdergraben 32, 07743 Jena, Germany
| | - Sylvie Rouland
- grid.462058.d0000 0001 2188 7059ISEM, Université Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, Montpellier, France
| | - Sandratrinirainy Ranarilalatiana
- grid.440419.c0000 0001 2165 5629Université d’Antananarivo, Faculté des Sciences, Mention Biologie et Ecologie Végétale, Laboratoire de Palynologie Appliquée, B.P 905 - 101, Antananarivo, Madagascar
| | - Romule Rakotondravony
- Ecole Doctorale Ecosystèmes Naturels (EDEN), University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, Mahajanga, 401 Madagascar ,Faculté des Sciences, de Technologies et de l’Environnement, University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, Mahajanga, 401 Madagascar
| | - Lounès Chikhi
- grid.418346.c0000 0001 2191 3202Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, P-2780-156 Oeiras, Portugal ,grid.4399.70000000122879528Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 route de Narbonne, Bât. 4R1, 31062 Toulouse cedex 9, France
| | - Hermann Behling
- grid.7450.60000 0001 2364 4210University of Goettingen, Department of Palynology and Climate Dynamics, Untere Karspüle 2, 37073 Goettingen, Germany
| | - Ute Radespiel
- grid.412970.90000 0001 0126 6191Institute of Zoology, University of Veterinary Medicine Hannover, Bünteweg 17, 30559 Hannover, Germany
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