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Wainwright BJ, Leon J, Vilela E, Hickman KJE, Caldwell J, Aimone B, Bischoff P, Ohran M, Morelli MW, Arlyza IS, Marwayana ON, Zahn G. Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria. ENVIRONMENTAL MICROBIOME 2024; 19:23. [PMID: 38637894 PMCID: PMC11027274 DOI: 10.1186/s40793-024-00568-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line. RESULTS We found significant differences in microbial community structure on either side of this boundary (R2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community. CONCLUSION Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.
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Affiliation(s)
- Benjamin J Wainwright
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
| | - Josh Leon
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Ernie Vilela
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - K J E Hickman
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Jensen Caldwell
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Behlee Aimone
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Porter Bischoff
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Marissa Ohran
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Magnolia W Morelli
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Irma S Arlyza
- Research Center for Oceanography, National Research and Innovation Agency (BRIN), Jl. Pasir Putih I, Ancol Timur, Jakarta, 14430, Indonesia
| | - Onny N Marwayana
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta-Bogor KM 46, Cibinong, Bogor, 16911, Indonesia
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA), 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
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2
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Steiner M, Huettmann F, Bryans N, Barker B. With super SDMs (machine learning, open access big data, and the cloud) towards more holistic global squirrel hotspots and coldspots. Sci Rep 2024; 14:5204. [PMID: 38433273 PMCID: PMC10909860 DOI: 10.1038/s41598-024-55173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Species-habitat associations are correlative, can be quantified, and used for powerful inference. Nowadays, Species Distribution Models (SDMs) play a big role, e.g. using Machine Learning and AI algorithms, but their best-available technical opportunities remain still not used for their potential e.g. in the policy sector. Here we present Super SDMs that invoke ML, OA Big Data, and the Cloud with a workflow for the best-possible inference for the 300 + global squirrel species. Such global Big Data models are especially important for the many marginalized squirrel species and the high number of endangered and data-deficient species in the world, specifically in tropical regions. While our work shows common issues with SDMs and the maxent algorithm ('Shallow Learning'), here we present a multi-species Big Data SDM template for subsequent ensemble models and generic progress to tackle global species hotspot and coldspot assessments for a more inclusive and holistic inference.
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Affiliation(s)
- Moriz Steiner
- IUCN Small Mammal Specialist Group (SMSG), IUCN, Rue Mauverney 28, 1196, Gland, Switzerland.
- IUCN Species Survival Commission (SSC), IUCN, Rue Mauverney 28, 1196, Gland, Switzerland.
- EWHALE Lab-Biology and Wildlife Department, Institute of Arctic Biology, University of Alaska Fairbanks (UAF), Fairbanks, AK, USA.
| | - F Huettmann
- EWHALE Lab-Biology and Wildlife Department, Institute of Arctic Biology, University of Alaska Fairbanks (UAF), Fairbanks, AK, USA
| | - N Bryans
- Oracle for Research, 2300 Oracle Wy, Austin, TX, 78741, USA
| | - B Barker
- Oracle for Research, 2300 Oracle Wy, Austin, TX, 78741, USA
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Skeels A, Boschman LM, McFadden IR, Joyce EM, Hagen O, Jiménez Robles O, Bach W, Boussange V, Keggin T, Jetz W, Pellissier L. Paleoenvironments shaped the exchange of terrestrial vertebrates across Wallace's Line. Science 2023; 381:86-92. [PMID: 37410831 DOI: 10.1126/science.adf7122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Faunal turnover in Indo-Australia across Wallace's Line is one of the most recognizable patterns in biogeography and has catalyzed debate about the role of evolutionary and geoclimatic history in biotic interchanges. Here, analysis of more than 20,000 vertebrate species with a model of geoclimate and biological diversification shows that broad precipitation tolerance and dispersal ability were key for exchange across the deep-time precipitation gradient spanning the region. Sundanian (Southeast Asian) lineages evolved in a climate similar to the humid "stepping stones" of Wallacea, facilitating colonization of the Sahulian (Australian) continental shelf. By contrast, Sahulian lineages predominantly evolved in drier conditions, hampering establishment in Sunda and shaping faunal distinctiveness. We demonstrate how the history of adaptation to past environmental conditions shapes asymmetrical colonization and global biogeographic structure.
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Affiliation(s)
- A Skeels
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Research School of Biology, Australian National University, Canberra 0200, Australia
| | - L M Boschman
- Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, Netherlands
| | - I R McFadden
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, Netherlands
| | - E M Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, 80331 Munich, Germany
| | - O Hagen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - O Jiménez Robles
- Research School of Biology, Australian National University, Canberra 0200, Australia
- Institute of Biology, École Normale Supérieure, 75005 Paris, France
| | - W Bach
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - V Boussange
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - T Keggin
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - W Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, CT 06520, USA
| | - L Pellissier
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
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4
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Velde MF, Besozzi EM, Krochuk BA, Henderson KM, Tsuru BR, Restrepo SV, Garrod HM, Cooper JC. What constitutes a community? A co-occurrence exploration of the Costa Rican avifauna. NEOTROPICAL BIODIVERSITY 2023; 9:64-75. [PMID: 37275476 PMCID: PMC10237366 DOI: 10.1080/23766808.2023.2204549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/11/2023] [Indexed: 06/07/2023] Open
Abstract
The concept of a "community" as a form of organization for natural biological systems is both widespread and widely accepted within the ecological and biological sciences. Communities have been defined as groups of organisms that interact in ways that denote interdependence between individuals and taxa (e.g. as defined by "food webs") but they have also been defined as groups of co-occurring organisms that are assumed to interact by virtue of their shared spatiotemporal existence. The latter definition has been debated and challenged in the literature, with mounting evidence for co-occurrence being more indicative of coincident ecological niches in space and time rather than being evidence of ecological interaction or dependency. Using a dataset of 460 Costa Rican bird species divided into breeding and non-breeding season datasets, we empirically demonstrate the ways in which co-occurrence can create illusory communities based on similar occupied ecological niches and similar patterns of co-occurrence at different times of year. We discuss the importance of discerning coincidental co-occurrence from true ecological interactions that would manifest a true community, and further address the importance of differentiating communities of co-occurrence from communities of demonstrable ecological interaction. While co-occurrence is a necessary aspect of interspecific interactions, we discuss and demonstrate here that such co-occurrence does not make a community, nor should explicit patterns of co-occurrence be seen as evidence for evolutionarily important ecological interactions.
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Affiliation(s)
- Mélusine F. Velde
- Division of Birds, Negaunee Integrative Research Center, Chicago, IL, USA
- Faculty of Natural Sciences, Imperial College London Silwood Park, Ascot, UK
- Biological Sciences Division, The College at University of Chicago, Chicago, IL, USA
| | | | - Billi A. Krochuk
- Biodiversity Research Centre and Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Kate M. Henderson
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, USA
| | - Brian R. Tsuru
- School of Environment and Natural Resources, Ohio State University, Columbus, OH, USA
| | | | - Holly M. Garrod
- BirdsCaribbean, Natick, MA, USA
- Department of Biology, Villanova University, Villanova, PA, USA
| | - Jacob C. Cooper
- Division of Birds, Negaunee Integrative Research Center, Chicago, IL, USA
- Biodiversity Institute & Natural History Museum, University of Kansas, Lawrence, KS, USA
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA
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5
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Arrieta-Bolaños E, Hernández-Zaragoza DI, Barquera R. An HLA map of the world: A comparison of HLA frequencies in 200 worldwide populations reveals diverse patterns for class I and class II. Front Genet 2023; 14:866407. [PMID: 37035735 PMCID: PMC10076764 DOI: 10.3389/fgene.2023.866407] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
HLA frequencies show widespread variation across human populations. Demographic factors as well as selection are thought to have shaped HLA variation across continents. In this study, a worldwide comparison of HLA class I and class II diversity was carried out. Multidimensional scaling techniques were applied to 50 HLA-A and HLA-B (class I) as well as 13 HLA-DRB1 (class II) first-field frequencies in 200 populations from all continents. Our results confirm a strong effect of geography on the distribution of HLA class I allele groups, with principal coordinates analysis closely resembling geographical location of populations, especially those of Africa-Eurasia. Conversely, class II frequencies stratify populations along a continuum of differentiation less clearly correlated to actual geographic location. Double clustering analysis revealed finer intra-continental sub-clusters (e.g., Northern and Western Europe vs. South East Europe, North Africa and Southwest Asia; South and East Africa vs. West Africa), and HLA allele group patterns characteristic of these clusters. Ancient (Austronesian expansion) and more recent (Romani people in Europe) migrations, as well as extreme differentiation (Taiwan indigenous peoples, Native Americans), and interregional gene flow (Sámi, Egyptians) are also reflected by the results. Barrier analysis comparing DST and geographic location identified genetic discontinuities caused by natural barriers or human behavior explaining inter and intra-continental HLA borders for class I and class II. Overall, a progressive reduction in HLA diversity from African to Oceanian and Native American populations is noted. This analysis of HLA frequencies in a unique set of worldwide populations confirms previous findings on the remarkable similarity of class I frequencies to geography, but also shows a more complex development for class II, with implications for both human evolutionary studies and biomedical research.
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Affiliation(s)
- Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Heidelberg, Germany
- *Correspondence: Esteban Arrieta-Bolaños,
| | | | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology (MPI-EVA), Leipzig, Germany
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6
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Marcaigh FÓ, Kelly DJ, O’connell DP, Analuddin K, Karya A, Mccloughan J, Tolan E, Lawless N, Marples NM. Small islands and large biogeographic barriers have driven contrasting speciation patterns in Indo-Pacific sunbirds (Aves: Nectariniidae). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Birds of the Indo-Pacific have provided biologists with many foundationalinsights. This study presents evidence for strong phylogeographic structure in two sunbird species from the heart of this region, the olive-backed sunbird, Cinnyris jugularis, and the black sunbird, Leptocoma aspasia. We assessed population divergence using morphological, plumage, bioacoustic and molecular data (mitochondrial ND2/ND3). Our findings indicate that the olive-backed sunbird should be recognized as multiple species, because birds from Sulawesi and the Sahul Shelf are closely related to each other, but widely separated from those in other regions. In addition, we provide evidence for an endemic species on the Wakatobi Islands, an archipelago of deep-sea islands off south-east Sulawesi. That a small bird could exhibit a range all the way from Sulawesi to Australia, while diverging on a small archipelago within this range, illustrates the complex interplay between dispersal and speciation. Our black sunbird genetic data also suggest unrecognized population structure, despite relatively weak plumage divergence. Black sunbirds in Sulawesi are likely to be a separate species from those in New Guinea, with a mean genetic distance of 9.1%. Current taxonomy suggests these sunbird species transcend classic biogeographic barriers, but our results suggest that these barriers are not easily bypassed.
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Affiliation(s)
- Fionn Ó Marcaigh
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - David J Kelly
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Darren P O’connell
- School of Biology and Environmental Science, University College Dublin , Dublin D04 N2E5 , Ireland
| | - Kangkuso Analuddin
- Department of Biology and Biotechnology, Universitas Halu Oleo , Kendari 93132, South-east Sulawesi , Indonesia
| | - Adi Karya
- Department of Biology and Biotechnology, Universitas Halu Oleo , Kendari 93132, South-east Sulawesi , Indonesia
| | - Jennifer Mccloughan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Ellen Tolan
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Naomi Lawless
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
| | - Nicola M Marples
- Department of Zoology, School of Natural Sciences, Trinity College Dublin , Dublin D02 CX56 , Ireland
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7
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Reilly SB, Karin BR, Stubbs AL, Arida E, Arifin U, Kaiser H, Bi K, Hamidy A, Iskandar DT, McGuire JA. Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago. Evolution 2022; 76:2281-2301. [PMID: 35932243 DOI: 10.1111/evo.14592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 01/22/2023]
Abstract
The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semipermeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation, rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence capture to generate a dataset of 1154 nuclear genes (∼1.8 Mb) plus complete mitochondrial genomes. Phylogenomic analyses recovered many deeply divergent lineages, three pairs of which are now sympatric, that began to diversify in the late Miocene shortly after the oldest islands are thought to have become emergent. We infer a complex and nonstepping-stone pattern of island colonization, with the group having originated in the Sunda Arc islands before using Sumba as a springboard for colonization of the Banda Arcs. Estimates of population structure and gene flow across the region suggest total isolation except between two Pleistocene Aggregate Island Complexes that become episodically land-bridged during glacial maxima. These historical processes have resulted in at least 11 Sphenomorphus species in the region, nine of which require formal description. This fine-scale geographic partitioning of undescribed species highlights the importance of utilizing comprehensive genomic studies for defining biodiversity hotspots to be considered for conservation protection.
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Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin R Karin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Alexander L Stubbs
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Evy Arida
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Umilaela Arifin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Zoology Museum Hamburg, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany
| | - Hinrich Kaiser
- Department of Biology, Victor Valley College, 18422 Bear Valley Road, Victorville, California, 92395, USA.,Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.,Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Amir Hamidy
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, Indonesia
| | - Djoko T Iskandar
- Basic Sciences Commission, Indonesian Academy of Sciences, 11, Jl. Medan Merdeka, Selatan Jakarta, 10110, Indonesia.,School of Life Sciences and Technology, Institut Teknologi Bandung, 10 Jalan Ganesha, Bandung, 40132, Indonesia
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
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8
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Li Q, Sun H, Boufford DE, Bartholomew B, Fritsch PW, Chen J, Deng T, Ree RH. Grade of Membership models reveal geographical and environmental correlates of floristic structure in a temperate biodiversity hotspot. THE NEW PHYTOLOGIST 2021; 232:1424-1435. [PMID: 33932292 DOI: 10.1111/nph.17443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Identifying the contours and correlates of species turnover is central to understanding the nature of biogeographical regions. The Hengduan Mountains region of south-central China (HMR) is well known for its high diversity of plants, but its boundaries and internal floristic structure are poorly understood, especially in relation to geographical and environmental factors. With data on occurrences and elevational ranges of seed plants across the HMR and adjacent areas of the greater Qinghai-Tibet Plateau, we identified motifs (distinct species assemblages) by Grade of Membership models, and characterized relative contributions of geography, elevation, and climate to their spatial patterns. Motifs segregate primarily by latitude, elevation, and correlated environmental variables, most sharply across the tropical-temperate divide. Secondarily, they segregate by longitude and geographical features, and reveal a novel divide across the Jinsha River. A core set of motifs corresponds to previous delineations of the HMR. The HMR biodiversity hotspot is more a mosaic of floristic elements than a cohesive entity. Grade of Membership models effectively reveal the geographical contours of biotic structure, and are a valuable new tool for biogeographical analysis.
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Affiliation(s)
- Qin Li
- Department of Science and Education, Field Museum, Chicago, IL, 60605, USA
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | | | - Bruce Bartholomew
- Department of Botany, California Academy of Sciences, Golden Gate Park, San Francisco, CA, 94118, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, Fort Worth, TX, 76017, USA
| | - Jiahui Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Richard H Ree
- Department of Science and Education, Field Museum, Chicago, IL, 60605, USA
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9
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Cooper JC. Hierarchical analyses of avian community biogeography in the Afromontane highlands. FRONTIERS OF BIOGEOGRAPHY 2021; 13:e51310. [PMID: 36844190 PMCID: PMC9956335 DOI: 10.21425/f5fbg51310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The Afromontane mountains are a complex series of highlands that have intermittently been connected by habitat corridors during climatic cycles, resulting in a mosaic of range disjunctions and allospecies complexes in the present day. Patterns of community relatedness between geographic regions are often determined through single-species analyses or spatial analyses of diversity and nestedness at the species level. To understand patterns of Afromontane community evolution and to assess the effects of taxonomy on our understanding of biogeographic patterns, I concatenated three lists of Afromontane bird taxa divided into five taxonomic hierarchies. These lists were converted into a presence-absence matrix across 42 montane regions and analyzed using a variety of clustering techniques based on a replicable coding pipeline. I used these lists and methods to determine patterns of relatedness between montane blocks, to assess the consistency with which biogeographic regions were recovered, and to shed light on the patterns of connectivity within the Afromontane region. My results reaffirm the distinctiveness of many biogeographic regions (e.g., the Cameroon Highlands) while also clarifying regional relationships and the presence of 'transition zones' between regions. Differences between lists illustrated how our understanding of taxonomy and distribution in the Afromontane highlands can also change our understanding of Afromontane biogeography. Most notably, I found evidence for an Expanded Eastern Arc that included the Eastern Arc Mountains and highlands in Malawi, Mozambique, and Zimbabwe. This study presents a rigorous yet easily adjustable pipeline for studying regional biogeography from multiple taxonomic perspectives using both traditional and novel approaches.
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Affiliation(s)
- Jacob C Cooper
- University of Chicago Committee on Evolutionary Biology, 1025 E. 57th Street, Chicago, IL 60637, USA.,Division of Birds, Negaunee Integrative Research Center, Field Museum, Chicago, IL 60605, USA.,Current Address: University of Kansas Biodiversity Institute, 1345 Jayhawk Boulevard, Lawrence, KS 66045, USA
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