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Pezzi PH, Wheeler LC, Freitas LB, Smith SD. Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae). Mol Phylogenet Evol 2024:108136. [PMID: 38909873 DOI: 10.1016/j.ympev.2024.108136] [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: 03/27/2024] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.
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Affiliation(s)
- Pedro H Pezzi
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
| | - Lucas C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
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2
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Bedoya AM. Botany and geogenomics: Constraining geological hypotheses in the neotropics with large-scale genetic data derived from plants. AMERICAN JOURNAL OF BOTANY 2024:e16306. [PMID: 38557829 DOI: 10.1002/ajb2.16306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 04/04/2024]
Abstract
Decades of empirical research have revealed how the geological history of our planet shaped plant evolution by establishing well-known patterns (e.g., how mountain uplift resulted in high rates of diversification and replicate radiations in montane plant taxa). This follows a traditional approach where botanical data are interpreted in light of geological events. In this synthesis, I instead describe how by integrating natural history, phylogenetics, and population genetics, botanical research can be applied alongside geology and paleontology to inform our understanding of past geological and climatic processes. This conceptual shift aligns with the goals of the emerging field of geogenomics. In the neotropics, plant geogenomics is a powerful tool for the reciprocal exploration of two long standing questions in biology and geology: how the dynamic landscape of the region came to be and how it shaped the evolution of the richest flora. Current challenges that are specific to analytical approaches for plant geogenomics are discussed. I describe the scale at which various geological questions can be addressed from biological data and what makes some groups of plants excellent model systems for geogenomics research. Although plant geogenomics is discussed with reference to the neotropics, the recommendations given here for approaches to plant geogenomics can and should be expanded to exploring long-standing questions on how the earth evolved with the use of plant DNA.
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Affiliation(s)
- Ana M Bedoya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, 70803, LA, USA
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3
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Sánchez KI, Recknagel H, Elmer KR, Avila LJ, Morando M. Tracing evolutionary trajectories in the presence of gene flow in South American temperate lizards (Squamata: Liolaemus kingii group). Evolution 2024; 78:716-733. [PMID: 38262697 DOI: 10.1093/evolut/qpae009] [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: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/17/2024] [Indexed: 01/25/2024]
Abstract
Evolutionary processes behind lineage divergence often involve multidimensional differentiation. However, in the context of recent divergences, the signals exhibited by each dimension may not converge. In such scenarios, incomplete lineage sorting, gene flow, and scarce phenotypic differentiation are pervasive. Here, we integrated genomic (RAD loci of 90 individuals), phenotypic (linear and geometric traits of 823 and 411 individuals, respectively), spatial, and climatic data to reconstruct the evolutionary history of a speciation continuum of liolaemid lizards (Liolaemus kingii group). Specifically, we (a) inferred the population structure of the group and contrasted it with the phenotypic variability; (b) assessed the role of postdivergence gene flow in shaping phylogeographic and phenotypic patterns; and (c) explored ecogeographic drivers of diversification across time and space. We inferred eight genomic clusters exhibiting leaky genetic borders coincident with geographic transitions. We also found evidence of postdivergence gene flow resulting in transgressive phenotypic evolution in one species. Predicted ancestral niches unveiled suitable areas in southern and eastern Patagonia during glacial and interglacial periods. Our study underscores integrating different data and model-based approaches to determine the underlying causes of diversification, a challenge faced in the study of recently diverged groups. We also highlight Liolaemus as a model system for phylogeographic and broader evolutionary studies.
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Affiliation(s)
- Kevin I Sánchez
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, Chubut, Argentina
| | - Hans Recknagel
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Kathryn R Elmer
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, Chubut, Argentina
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Consejo Nacional de Investigaciones Científicas y Técnicas (IPEEC-CONICET), Puerto Madryn, Chubut, Argentina
- Departamento de Biología y Ambiente, Universidad Nacional de la Patagonia San Juan Bosco, Sede Puerto Madryn, Puerto Madryn, Chubut, Argentina
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4
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Nevado B, Atchison GW, Bridges EL, Orzell S, Filatov D, Hughes CE. Pleistocene diversification of unifoliolate-leaved Lupinus (Leguminosae: Papilionoideae) in Florida. Mol Ecol 2024; 33:e17232. [PMID: 38205900 DOI: 10.1111/mec.17232] [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: 08/02/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
The importance and prevalence of recent ice-age and post-glacial speciation and species diversification during the Pleistocene across many organismal groups and physiographic settings are well established. However, the extent to which Pleistocene diversification can be attributed to climatic oscillations and their effects on distribution ranges and population structure remains debatable. In this study, we use morphologic, geographic and genetic (RADseq) data to document Pleistocene speciation and intra-specific diversification of the unifoliolate-leaved clade of Florida Lupinus, a small group of species largely restricted to inland and coastal sand ridges across the Florida peninsula and panhandle. Phylogenetic and demographic analyses alongside morphological and geographic evidence suggest that recent speciation and intra-specific divergence within this clade were driven by a combination of non-adaptive allopatric divergence caused by edaphic niche conservatism and opportunities presented by the emergence of new post-glacial sand ridge habitats. These results highlight the central importance of even modest geographic isolation and short periods of allopatric divergence following range expansion in the emergence of new taxa and add to the growing evidence that Pleistocene climatic oscillations may contribute to rapid diversification in a myriad of physiographic settings. Furthermore, our results shed new light on long-standing taxonomic debate surrounding the number of species in the Florida unifoliate Lupinus clade providing support for recognition of five species and a set of intra-specific variants. The important conservation implications for the narrowly restricted, highly endangered species Lupinus aridorum, which we show to be genetically distinct from its sister species Lupinus westianus, are discussed.
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Affiliation(s)
- Bruno Nevado
- Faculty of Sciences, cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, University of Lisbon, Lisbon, Portugal
- Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Guy W Atchison
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Edwin L Bridges
- Botanical and Ecological Consultant, Gig Harbor, Washington, USA
| | - Steve Orzell
- Avon Park Air Force Range, Avon Park, Florida, USA
| | | | - Colin E Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
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5
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San Jose M, Doorenweerd C, Geib S, Barr N, Dupuis JR, Leblanc L, Kauwe A, Morris KY, Rubinoff D. Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex. Mol Phylogenet Evol 2023; 188:107892. [PMID: 37524217 DOI: 10.1016/j.ympev.2023.107892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/07/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
As genomic data proliferates, the prevalence of post-speciation gene flow is making species boundaries and relationships increasingly ambiguous. Although current approaches inferring fully bifurcating phylogenies based on concatenated datasets provide simple and robust answers to many species relationships, they may be inaccurate because the models ignore inter-specific gene flow and incomplete lineage sorting. To examine the potential error resulting from ignoring gene flow, we generated both a RAD-seq and a 500 protein-coding loci highly multiplexed amplicon (HiMAP) dataset for a monophyletic group of 12 species defined as the Bactrocera dorsalis sensu lato clade. With some of the world's worst agricultural pests, the taxonomy of the B. dorsalis s.l. clade is important for trade and quarantines. However, taxonomic confusion confounds resolution due to intra- and interspecific phenotypic variation and convergence, mitochondrial introgression across half of the species, and viable hybrids. We compared the topological convergence of our datasets using concatenated phylogenetic and various multispecies coalescent approaches, some of which account for gene flow. All analyses agreed on species delimitation, but there was incongruence between species relationships. Under concatenation, both datasets suggest identical species relationships with mostly high statistical support. However, multispecies coalescent and multispecies network approaches suggest markedly different hypotheses and detected significant gene flow. We suggest that the network approaches are likely more accurate because gene flow violates the assumptions of the concatenated phylogenetic analyses, but the data-reductive requirements of network approaches resulted in reduced statistical support and could not unambiguously resolve gene flow directions. Our study highlights the importance of testing for gene flow, particularly with phylogenomic datasets, even when concatenated approaches receive high statistical support.
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Affiliation(s)
- Michael San Jose
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA.
| | - Camiel Doorenweerd
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | - Scott Geib
- Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Norman Barr
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, 22675 N. Moorefield Road, Edinburg, TX 78541, USA
| | - Julian R Dupuis
- University of Kentucky, Department of Entomology, S225 Ag Science Center North, 1100 South Limestone, Lexington, KY, 40546-0091, USA
| | - Luc Leblanc
- University of Idaho, Department of Entomology, Plant Pathology and Nematology, 875 Perimeter Drive, MS2329, Moscow, ID, 83844-2329, USA
| | - Angela Kauwe
- Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Kimberley Y Morris
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA; Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Daniel Rubinoff
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
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Tovar C, Hudson L, Cuesta F, Meneses RI, Muriel P, Hidalgo O, Palazzesi L, Suarez Ballesteros C, Hammond Hunt E, Diazgranados M, Hind DJN, Forest F, Halloy S, Aguirre N, Baker WJ, Beck S, Carilla J, Eguiguren P, Françoso E, Gámez LE, Jaramillo R, Llambí LD, Maurin O, Melcher I, Muller G, Roy S, Viñas P, Yager K, Viruel J. Strategies of diaspore dispersal investment in Compositae: the case of the Andean highlands. ANNALS OF BOTANY 2023; 132:255-267. [PMID: 37501620 PMCID: PMC10583198 DOI: 10.1093/aob/mcad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND AND AIMS Understanding diaspore morphology and how much a species invests on dispersal appendages is key for improving our knowledge of dispersal in fragmented habitats. We investigate diaspore morphological traits in high-Andean Compositae and their main abiotic and biotic drivers and test whether they play a role in species distribution patterns across the naturally fragmented high-Andean grasslands. METHODS We collected diaspore trait data for 125 Compositae species across 47 tropical high-Andean summits, focusing on achene length and pappus-to-achene length ratio, with the latter as a proxy of dispersal investment. We analysed the role of abiotic (temperature, elevation and latitude) and biotic factors (phylogenetic signal and differences between tribes) on diaspore traits and whether they are related to distribution patterns across the Andes, using phylogenomics, distribution modelling and community ecology analyses. KEY RESULTS Seventy-five percent of the studied species show small achenes (length <3.3 mm) and 67% have high dispersal investment (pappus length at least two times the achene length). Dispersal investment increases with elevation, possibly to compensate for lower air density, and achene length increases towards the equator, where non-seasonal climate prevails. Diaspore traits show significant phylogenetic signal, and higher dispersal investment is observed in Gnaphalieae, Astereae and Senecioneae, which together represent 72% of our species. High-Andean-restricted species found across the tropical Andes have, on average, the pappus four times longer than the achene, a significantly higher dispersal investment than species present only in the northern Andes or only in the central Andes. CONCLUSIONS Small achenes and high diaspore dispersal investment dominate among high-Andean Compositae, traits typical of mostly three tribes of African origin; but traits are also correlated with the environmental gradients within the high-Andean grasslands. Our results also suggest that diaspore dispersal investment is likely to shape species distribution patterns in naturally fragmented habitats.
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Affiliation(s)
| | | | - Francisco Cuesta
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud – BIOMAS, Universidad de las Américas, Quito, Ecuador
| | - Rosa Isela Meneses
- Universidad Católica del Norte, San Pedro de Atacama, Chile
- Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, Bolivia
| | - Priscilla Muriel
- Laboratorio de Ecofisiología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica de Ecuador, Quito, Ecuador
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Luis Palazzesi
- Museo Argentino de Ciencias Naturales (CONICET), Buenos Aires, Argentina
| | | | | | | | | | | | - Stephan Halloy
- Biosecurity New Zealand, Ministry for Primary Industries, Wellington, New Zealand
| | - Nikolay Aguirre
- Centro de Investigaciones Tropicales del Ambiente y Biodiversidad, Carrera de Ingeniería Forestal, Universidad Nacional de Loja, Loja, Ecuador
| | | | - Stephan Beck
- Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, Bolivia
| | - Julieta Carilla
- Instituto de Ecología Regional (IER), Universidad Nacional de Tucumán (UNT), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán, Argentina
| | - Paúl Eguiguren
- Centro de Investigaciones Tropicales del Ambiente y Biodiversidad, Carrera de Ingeniería Forestal, Universidad Nacional de Loja, Loja, Ecuador
| | | | - Luis E Gámez
- Laboratorio de Dendrología, Facultad de Ciencias Forestales y Ambientales, Universidad de Los Andes, Mérida, Venezuela
| | - Ricardo Jaramillo
- Laboratorio de Ecofisiología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica de Ecuador, Quito, Ecuador
| | - Luis Daniel Llambí
- Instituto de Ciencias Ambientales y Ecologicas, Universidad de Los Andes, Mérida 5101, Venezuela
- Consorcio para el Desarrollo Sostenible de la Ecorregión Andina, Germán Alemán E12-123, Quito, Ecuador
| | | | - Inga Melcher
- Institute for Biodiversity & Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | | | | | - Karina Yager
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
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Escobari B, Borsch T, Kilian N. Generic concepts and species diversity within the Gynoxyoid clade (Senecioneae, Compositae). PHYTOKEYS 2023; 234:61-106. [PMID: 37860599 PMCID: PMC10582726 DOI: 10.3897/phytokeys.234.107750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/19/2023] [Indexed: 10/21/2023]
Abstract
The Gynoxyoid clade of the Senecioneae (Asteraceae) until now included the five genera Aequatorium, Gynoxys, Nordenstamia, Paracalia and Paragynoxys as diagnosed using selected morphological characters. In their pre-phylogenetic circumscription, the genera Aequatorium and Paragynoxys were considered to inhabit the northern Andes in contrast to Nordenstamia and Paracalia that occur in the central Andes. The most species-rich genus, Gynoxys, was believed to be distributed throughout the Andes. We use a recently established plastid phylogenomic framework that rendered Gynoxys paraphyletic to further evaluate the delimitation of genera in the Gynoxyoid clade. We examine the morphological variation of all members of the Gynoxyoid to identify characters potentially informative at genus level. This results in a matrix of eleven, mostly multistate characters, including those originally used to diagnose these genera. The ancestral character state inference displays a high level of homoplasy, but nevertheless supports the recognition of four genera. Aequatorium is characterised by white radiate capitula. Paracalia and Paragynoxys share white flowers and floral characteristics, such as flower opening and length of disc flowers lobes, as plesiomorphic states, but differ in habit (scandent shrubs vs. trees). Paracalia also retained white flowers, but its two species are characterised by the absence of outer phyllaries. The genera Gynoxys and Nordenstamia comprise species with yellow capitula which appear to be a derived feature in the Gynoxyoids. The genus Nordenstamia, with eight species, is synonymised under Gynoxys since molecular evidence shows its species nested within various parts of the Gynoxys subclade and the morphological variation of Nordenstamia falls well within that of Gynoxys. With the goal to assign all species to four genera (Aequatorium, Gynoxys, Paracalia and Paragynoxys), we assess the states for the eleven characters for all members of the Gynoxyoids and generate new ETS and ITS sequences for 171 specimens belonging to 49 species to further support their generic placement. We provide a taxonomic treatment for the four genera recognised here including amended diagnoses and morphological descriptions. Furthermore, a species-level taxonomic backbone is elaborated for all genera using electronic tools that list 158 currently accepted names and synonyms (209 names in total) with the respective protologue and type information, as well as notes on the current understanding of species limits. Eleven names are newly synonymised, two are lectotypified and eight are newly transferred to other genera.
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Affiliation(s)
- Belen Escobari
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin 14195, Germany
- Herbario Nacional de Bolivia, Universidad Mayor de San Andres, Casilla, La Paz, 10077, Bolivia
| | - Thomas Borsch
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin 14195, Germany
| | - Norbert Kilian
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Berlin 14195, Germany
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Arenas S, Búrquez A, Bustamante E, Scheinvar E, Eguiarte LE. Are 150 km of open sea enough? Gene flow and population differentiation in a bat-pollinated columnar cactus. PLoS One 2023; 18:e0282932. [PMID: 37384637 PMCID: PMC10309638 DOI: 10.1371/journal.pone.0282932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/26/2023] [Indexed: 07/01/2023] Open
Abstract
Genetic differentiations and phylogeographical patterns are controlled by the interplay between spatial isolation and gene flow. To assess the extent of gene flow across an oceanic barrier, we explored the effect of the separation of the peninsula of Baja California on the evolution of mainland and peninsular populations of the long-lived columnar cactus Stenocereus thurberi. We analyzed twelve populations throughout the OPC distribution range to assess genetic diversity and structure using chloroplast DNA sequences. Genetic diversity was higher (Hd = 0.81), and genetic structure was lower (GST = 0.143) in mainland populations vs peninsular populations (Hd = 0.71, GST = 0.358 respectively). Genetic diversity was negatively associated with elevation but positively with rainfall. Two mainland and one peninsular ancestral haplotypes were reconstructed. Peninsular populations were as isolated among them as with mainland populations. Peninsular haplotypes formed a group with one mainland coastal population, and populations across the gulf shared common haplotypes giving support to regular gene flow across the Gulf. Gene flow is likely mediated by bats, the main pollinators and seed dispersers. Niche modeling suggests that during the Last Glacial Maximum (c. 130 ka), OPC populations shrank to southern locations. Currently, Stenocereus thurberi populations are expanding, and the species is under population divergence despite ongoing gene flow. Ancestral populations are located on the mainland and although vicariant peninsular populations cannot be ruled out, they are likely the result of gene flow across the seemingly formidable barrier of the Gulf of California. Still, unique haplotypes occur in the peninsula and the mainland, and peninsular populations are more structured than those on the mainland.
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Affiliation(s)
- Sebastián Arenas
- DIADE, Université de Montpellier, IRD, Montpellier, France
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, México
| | - Alberto Búrquez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, México
| | - Enriquena Bustamante
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Sonora, México
| | - Enrique Scheinvar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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Vargas OM, Madriñán S, Simpson B. Allopatric speciation is more prevalent than parapatric ecological divergence in a recent high-Andean diversification ( Linochilus: Asteraceae). PeerJ 2023; 11:e15479. [PMID: 37312875 PMCID: PMC10259450 DOI: 10.7717/peerj.15479] [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: 01/09/2023] [Accepted: 05/08/2023] [Indexed: 06/15/2023] Open
Abstract
Elucidating how species accumulate in diversity hotspots is an ongoing debate in evolutionary biology. The páramo, in the Northern Andes, has remarkably high indices of plant diversity, endemicity, and diversification rates. A hypothesis for explaining such indices is that allopatric speciation is high in the páramo given its island-like distribution. An alternative hypothesis is that the altitudinal gradient of the Andean topography provides a variety of niches that drive vertical parapatric ecological speciation. A formal test for evaluating the relative roles of allopatric and parapatric ecological speciation is lacking. The main aim of our study is to test which kind of speciation is more common in an endemic páramo genus. We developed a framework incorporating phylogenetics, species' distributions, and a morpho-ecological trait (leaf area) to compare sister species and infer whether allopatric or parapatric ecological divergence caused their speciation. We applied our framework to the species-rich genus Linochilus (63 spp.) and found that the majority of recent speciation events in it (12 events, 80%) have been driven by allopatric speciation, while a smaller fraction (one event, 6.7%) is attributed to parapatric ecological speciation; two pairs of sister species produced inconclusive results (13.3%). We conclude that páramo autochthonous (in-situ) diversification has been primarily driven by allopatric speciation.
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Affiliation(s)
- Oscar M. Vargas
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA, United States
- Department of Integrative Biology and Billie Turner Plant Resources Center, The University of Texas at Austin, Austin, TX, USA
| | - Santiago Madriñán
- Department of Biological Sciences, University of the Andes, Bogotá, DC, Colombia
- Jardín Botánico de Cartagena, Turbaco, Bolívar, Colombia
| | - Beryl Simpson
- Department of Integrative Biology and Billie Turner Plant Resources Center, The University of Texas at Austin, Austin, TX, USA
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Chincoya DA, Arias S, Vaca-Paniagua F, Dávila P, Solórzano S. Phylogenomics and Biogeography of the Mammilloid Clade Revealed an Intricate Evolutionary History Arose in the Mexican Plateau. BIOLOGY 2023; 12:biology12040512. [PMID: 37106713 PMCID: PMC10135466 DOI: 10.3390/biology12040512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/31/2023]
Abstract
Mexico harbors ~45% of world’s cacti species richness. Their biogeography and phylogenomics were integrated to elucidate the evolutionary history of the genera Coryphantha, Escobaria, Mammillaria, Mammilloydia, Neolloydia, Ortegocactus, and Pelecyphora (Mammilloid Clade). We analyzed 52 orthologous loci from 142 complete genomes of chloroplast (103 taxa) to generate a cladogram and a chronogram; in the latter, the ancestral distribution was reconstructed with the Dispersal-Extinction-Cladogenesis model. The ancestor of these genera arose ~7 Mya on the Mexican Plateau, from which nine evolutionary lineages evolved. This region was the site of 52% of all the biogeographical processes. The lineages 2, 3 and 6 were responsible for the colonization of the arid southern territories. In the last 4 Mya, the Baja California Peninsula has been a region of prolific evolution, particularly for lineages 8 and 9. Dispersal was the most frequent process and vicariance had relevance in the isolation of cacti distributed in the south of Mexico. The 70 taxa sampled as Mammillaria were distributed in six distinct lineages; one of these presumably corresponded to this genus, which likely had its center of origin in the southern part of the Mexican Plateau. We recommend detailed studies to further determine the taxonomic circumscription of the seven genera.
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11
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Vallejos-Garrido P, Pino K, Espinoza-Aravena N, Pari A, Inostroza-Michael O, Toledo-Muñoz M, Castillo-Ravanal B, Romero-Alarcón V, Hernández CE, Palma RE, Rodríguez-Serrano E. The importance of the Andes in the evolutionary radiation of Sigmodontinae (Rodentia, Cricetidae), the most diverse group of mammals in the Neotropics. Sci Rep 2023; 13:2207. [PMID: 36750620 PMCID: PMC9905555 DOI: 10.1038/s41598-023-28497-0] [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: 05/10/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023] Open
Abstract
The Andean mountains stand out for their striking species richness and endemicity that characterize many emblematic Neotropical clades distributed in or around these mountains. The radiation of the Sigmodontinae subfamily, the most diversified mammalian group in the Neotropics, has been historically related to Andean orogenesis. We aim to evaluate this interplay between geological processes and biological responses through the diversification dynamics, the biogeographical history, and the range evolution of the subfamily. For these, we built the most comprehensive phylogeny and gathered 14,836 occurrences for the subfamily. We identified one shift in the speciation rate in the genus Akodon, which suffered their Andean radiation after the arrival of non-Andean ancestors. Our biogeographic analyses show multiple dispersal paths throughout the evolution that allowed this subfamily to colonize all Neotropics. The Northern Andes and Central-Southern Andes were the most important sources of diversity. In addition, the Central-Southern Andes were the most relevant sink, receiving the highest number of lineages. The Andean region exhibited higher speciation and turnover rates than non-Andean regions. Thus, our results support the crucial role of the Andean Mountains in the Sigmodontinae radiation, acting as a "macroevolutionary cradle" and "species attractor" for several sigmodontine lineages at different times, and as a "species pump" becoming the biogeographic source of multiple widely distributed neotropical lineages. Then, complex macroevolutionary dynamics would explain these rodents' high extant Andean diversity and their wide distribution in the Neotropics.
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Affiliation(s)
- Paulo Vallejos-Garrido
- Programa de Doctorado en Sistemática y Biodiversidad, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Vida Silvestre Investigadores Limitada, Concepción, Chile
| | - Kateryn Pino
- Programa de Doctorado en Sistemática y Biodiversidad, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Museo de Historia Natural, Universidad Nacional de San Agustín de Arequipa, Arequipa, Perú
| | - Nicolás Espinoza-Aravena
- Programa de Doctorado en Sistemática y Biodiversidad, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Laboratorio de Ecología Evolutiva y Filoinformática, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Alexander Pari
- Programa de Doctorado en Sistemática y Biodiversidad, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Museo de Historia Natural, Universidad Nacional de San Agustín de Arequipa, Arequipa, Perú
| | - Oscar Inostroza-Michael
- Laboratorio de Ecología Evolutiva y Filoinformática, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Macarena Toledo-Muñoz
- Programa de Magíster en Ciencias Mención Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Boris Castillo-Ravanal
- Programa de Magíster en Ciencias Mención Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | | | - Cristián E Hernández
- Laboratorio de Ecología Evolutiva y Filoinformática, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Universidad Católica de Santa María, Arequipa, Perú
| | - R Eduardo Palma
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Enrique Rodríguez-Serrano
- Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.
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12
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Harrington S, Burbrink F. Complex cycles of divergence and migration shape lineage structure in the common kingsnake species complex. JOURNAL OF BIOGEOGRAPHY 2023; 50:341-351. [PMID: 36817740 PMCID: PMC9937589 DOI: 10.1111/jbi.14536] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/17/2022] [Indexed: 06/18/2023]
Abstract
Aim The Nearctic is a complex patchwork of habitats and geologic features that form barriers to gene flow resulting in phylogeographic structure and speciation in many lineages. Habitats are rarely stable over geologic time, and the Nearctic has undergone major climatic changes in the past few million years. We use the common kingsnake species complex to study how climate, geography, and history influence lineage formation over a large, complex landscape. Location Nearctic/North America. Taxon Common kingsnake, Lampropeltis getula, species complex. Methods We analyzed genome-wide sequence data from 51 snakes spanning the majority of the species complex's range. We used population clustering, generalized dissimilarity modeling, and coalescent methods to identify the number of genetic clusters within the L. getula complex, infer the environmental correlates of genetic differentiation, and estimate models of divergence and gene flow among lineages. Results We identified three major lineages within the L. getula complex and further continuous spatial structure within lineages. The most important ecological correlates of genetic distance in the complex are related to aridity and precipitation, consistent with lineage breaks at the Great Plains/Desert ecotone and the Cochise Filter Barrier. Lineages are estimated to have undergone multiple rounds of isolation and secondary contact, with highly asymmetric migration occurring at present. Main conclusions Changing climates combined with a large and geologically complex landscape have resulted in a mosaic of discrete and spatially continuous genetic structure. Multiple rounds of isolation and secondary contact as climate fluctuated over the past ~4.4 My have likely driven the evolution of discrete lineages that maintain high levels of gene flow. Continuous structure is strongly shaped by aridity and precipitation, suggesting roles for major precipitation gradients in helping to maintain lineage identity in the face of gene flow when lineages are in geographic contact.
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Affiliation(s)
- Sean Harrington
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
- INBRE Data Science Core, University of Wyoming, Laramie, WY 82071, USA
| | - Frank Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
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13
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Ning Y, Li Y, Dong SB, Yang HG, Li CY, Xiong B, Yang J, Hu YK, Mu XY, Xia XF. The chromosome-scale genome of Kobresia myosuroides sheds light on karyotype evolution and recent diversification of a dominant herb group on the Qinghai-Tibet Plateau. DNA Res 2022; 30:6887608. [PMID: 36503982 PMCID: PMC9835760 DOI: 10.1093/dnares/dsac049] [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: 07/27/2022] [Revised: 11/15/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Kobresia species are common in meadows on the Qinghai-Tibet Plateau. They are important food resources for local livestock, and serve a critical foundation for ecosystem integration. Genetic resources of Kobresia species are scarce. Here, we generated a chromosome-level genome assembly for K. myosuroides (Cyperaceae), using PacBio long-reads, Illumina short-reads, and Hi-C technology. The final assembly had a total size of 399.9 Mb with a contig N50 value of 11.9 Mb. The Hi-C result supported a 29 pseudomolecules model which was in consistent with cytological results. A total of 185.5 Mb (44.89% of the genome) transposable elements were detected, and 26,748 protein-coding genes were predicted. Comparative analysis revealed that Kobresia plants have experienced recent diversification events during the late Miocene to Pliocene. Karyotypes analysis indicated that the fission and fusion of chromosomes have been a major driver of speciation, which complied with the lack of whole-genome duplication (WGD) in K. myosuroides genome. Generally, this high-quality reference genome provides insights into the evolution of alpine sedges, and may be helpful to endemic forage improvement and alpine ecosystem preservation.
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Affiliation(s)
- Yu Ning
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, China,Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Yang Li
- Huzhou University, Huzhou, China
| | - Shu Bin Dong
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hong Guo Yang
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, China,Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Chun Yi Li
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, China,Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Biao Xiong
- College of Tea Science, Guizhou University, Guiyang, China
| | - Jun Yang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yu Kun Hu
- Institute of Ecological Protection and Restoration, Chinese Academy of Forestry, Beijing, China,Institute of Wetland Research, Chinese Academy of Forestry, Beijing, China
| | - Xian Yun Mu
- College of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xiao Fei Xia
- To whom correspondence should be addressed. Tel. +86 010-67020687. Fax. +86 010-67021254.
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14
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Ma Y, Mao X, Wang J, Zhang L, Jiang Y, Geng Y, Ma T, Cai L, Huang S, Hollingsworth P, Mao K, Kang M, Li Y, Yang W, Wu H, Chen Y, Davis CC, Shrestha N, Ree RH, Xi Z, Hu Q, Milne RI, Liu J. Pervasive hybridization during evolutionary radiation of Rhododendron subgenus Hymenanthes in mountains of southwest China. Natl Sci Rev 2022; 9:nwac276. [PMID: 36687562 PMCID: PMC9844246 DOI: 10.1093/nsr/nwac276] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022] Open
Abstract
Radiations are especially important for generating species biodiversity in mountainous ecosystems. The contribution of hybridization to such radiations has rarely been examined. Here, we use extensive genomic data to test whether hybridization was involved in evolutionary radiation within Rhododendron subgenus Hymenanthes, whose members show strong geographic isolation in the mountains of southwest China. We sequenced genomes for 143 species of this subgenus and 93 species of four other subgenera, and found that Hymenanthes was monophyletic and radiated during the late Oligocene to middle Miocene. Widespread hybridization events were inferred within and between the identified clades and subclades. This suggests that hybridization occurred both early and late during diversification of subgenus Hymenanthes, although the extent to which hybridization, speciation through mixing-isolation-mixing or hybrid speciation, accelerated the diversification needs further exploration. Cycles of isolation and contact in such and other montane ecosystems may have together promoted species radiation through hybridization between diverging populations and species. Similar radiation processes may apply to other montane floras in this region and elsewhere.
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Affiliation(s)
| | | | | | - Lei Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yuying Geng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Liming Cai
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA 02138, USA
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | | | - Kangshan Mao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Minghui Kang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yiling Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wenlu Yang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Haolin Wu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yang Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA 02138, USA
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Richard H Ree
- Negaunee Integrative Research Center, Field Museum, Chicago, IL 60605, USA
| | - Zhenxiang Xi
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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15
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Pyrcz TW, Willmott KR, Lamas G, Boyer P, Florczyk K, Fåhraeus C, Mahecha O, Cerdeña J, Mrozek A, Farfán J, Zubek A. Considerations on the Systematics of Neotropical Pierina, with the Description of Two New Species of Phulia Herrich-Schäffer from the Peruvian Andes (Lepidoptera: Pieridae, Pierinae, Pierini). NEOTROPICAL ENTOMOLOGY 2022; 51:840-859. [PMID: 36378478 PMCID: PMC9705514 DOI: 10.1007/s13744-022-00999-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/20/2022] [Indexed: 05/29/2023]
Abstract
A comparative analysis of high-Andean Pierina was carried out, including a total of 25 species. Based on morphological evidence, with an emphasis on venation and genitalia and molecular data, using three genetic markers, we confirm the recent subjective synonymy of the generic names Tatochila Butler, 1870, Piercolias, Staudinger, 1894, Hypsochila Ureta, 1955, Infraphulia Field, 1958, Pierphulia Field, 1958, and Theochila Field, 1958 with Phulia Herrich-Schäffer, 1867. Two new species are described, namely Phulia stoddardi Pyrcz & Cerdeña n. sp., from the Andes of Central Peru, which occurs at an unusually high altitude of close to 5000 m a.s.l. in dry puna habitat, and Phulia phantasma Lamas, Willmott & Boyer n. sp., from dry montane forests in northern Peru and southern Ecuador. An overview of high-elevation butterflies is presented, with some discussion on adaptations to this environment.
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Affiliation(s)
- Tomasz W Pyrcz
- Dept of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Jagiellonian Univ, Kraków, Poland.
| | - Keith R Willmott
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, Univ of Florida, FL, Gainesville, USA
| | - Gerardo Lamas
- Museo de Historia Natural, Univ Nacional Mayor de San Marcos, Lima, Perú
| | | | - Klaudia Florczyk
- Nature Education Centre of the Jagiellonian Univ, Kraków, Poland
| | | | - Oscar Mahecha
- Nature Education Centre of the Jagiellonian Univ, Kraków, Poland
- Grupo en Biogeografía y Ecología Evolutiva Neotropical BEEN, Univ Distrital F.J.C./Univ Incca de Colombia, Bogotá, Colombia
| | - José Cerdeña
- Univ Nacional de San Agustín de Arequipa, Museo de Historia Natural, Escuela de Biología UNSA, Arequipa, Perú
| | - Artur Mrozek
- Dept of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Jagiellonian Univ, Kraków, Poland
| | - Jackie Farfán
- Univ Nacional de San Agustín de Arequipa, Museo de Historia Natural, Escuela de Biología UNSA, Arequipa, Perú
| | - Anna Zubek
- Nature Education Centre of the Jagiellonian Univ, Kraków, Poland
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16
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Lu WX, Hu XY, Wang ZZ, Rao GY. Hyb-Seq provides new insights into the phylogeny and evolution of the Chrysanthemum zawadskii species complex in China. Cladistics 2022; 38:663-683. [PMID: 35766338 DOI: 10.1111/cla.12514] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 02/06/2023] Open
Abstract
A species complex is an assemblage of closely related species with blurred boundaries, and from which species could arise from different speciation processes and/or a speciation continuum. Such a complex can provide an opportunity to investigate evolutionary mechanisms acting on speciation. The Chrysanthemum zawadskii species complex in China, a monophyletic group of Chrysanthemum, consists of seven species with considerable morphological variation, diverse habitats and different distribution patterns. Here, we used Hyb-Seq data to construct a well-resolved phylogeny of the C. zawadskii complex. Then, we performed comparative analyses of variation patterns in morphology, ecology and distribution to investigate the roles of geography and ecology in this complex's diversification. Lastly, we implemented divergence time estimation, species distribution modelling and ancestral area reconstruction to trace the evolutionary history of this complex. We concluded that the C. zawadskii complex originated in the Qinling-Daba mountains during the early Pliocene and then spread west and northward along the mountain ranges to northern China. During this process, geographical and ecological factors imposing different influences resulted in the current diversification and distribution patterns of this species complex, which is composed of both well-diverged species and diverging lineages on the path of speciation.
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Affiliation(s)
- Wen-Xun Lu
- School of Life Sciences, Peking University, Beijing, China
| | - Xue-Ying Hu
- School of Life Sciences, Peking University, Beijing, China
| | - Zi-Zhao Wang
- School of Life Sciences, Peking University, Beijing, China
| | - Guang-Yuan Rao
- School of Life Sciences, Peking University, Beijing, China
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17
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Wang L, Liu S, Yang Y, Meng Z, Zhuang Z. Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers. Mol Ecol 2022; 31:5729-5744. [PMID: 36111361 PMCID: PMC9828471 DOI: 10.1111/mec.16693] [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: 04/24/2021] [Accepted: 09/06/2022] [Indexed: 01/13/2023]
Abstract
Understanding the mechanisms underlying heterogeneous genomic divergence is of particular interest in evolutionary biology. Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome-wide RAD sequencing in a pair of yellow croakers (genus: Larimichthys), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (FST ) and absolute sequence divergence (Dxy ), and elevated Dxy in genomic islands, indicating that the genomic landscape of divergence was not shaped by linked selection alone. Restricted gene flow in highly differentiated regions has probably remodelled the landscape of heterogeneous genomic divergence. This study highlights that highly differentiated genomic regions can also arise from a combination of linked selection and differential gene flow in interaction with varying recombination rates.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life SciencesSun Yat‐sen UniversityGuangzhouChina,Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research LinkNational University of SingaporeSingapore CitySingapore
| | - Shufang Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences & Function Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| | - Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life SciencesSun Yat‐sen UniversityGuangzhouChina
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and the Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life SciencesSun Yat‐sen UniversityGuangzhouChina,Southern Laboratory of Ocean Science and EngineeringZhuhaiChina
| | - Zhimeng Zhuang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences & Function Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
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18
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Liu L, Zhang Y, Tumi L, Suni ML, Arakaki M, Burgess KS, Ge X. Genetic markers in Andean
Puya
species (Bromeliaceae) with implications on plastome evolution and phylogeny. Ecol Evol 2022; 12:e9159. [PMID: 35919393 PMCID: PMC9336176 DOI: 10.1002/ece3.9159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/19/2022] [Accepted: 07/05/2022] [Indexed: 11/26/2022] Open
Abstract
The Andean plant endemic Puya is a striking example of recent and rapid diversification from central Chile to the northern Andes, tracking mountain uplift. This study generated 12 complete plastomes representing nine Puya species and compared them to five published plastomes for their features, genomic evolution, and phylogeny. The total size of the Puya plastomes ranged from 159,542 to 159,839 bp with 37.3%–37.4% GC content. The Puya plastomes were highly conserved in organization and structure with a typical quadripartite genome structure. Each of the 17 consensus plastomes harbored 133 genes, including 87 protein‐coding genes, 38 tRNA (transfer RNA) genes, and eight rRNA (ribosomal RNA) genes; we found 69–78 tandem repeats, 45–60 SSRs (simple sequence repeats), and 8–22 repeat structures among 13 species. Four protein‐coding genes were identified under positive site‐specific selection in Puya. The complete plastomes and hypervariable regions collectively provided pronounced species discrimination in Puya and a practical tool for future phylogenetic studies. The reconstructed phylogeny and estimated divergence time for the lineage suggest that the diversification of Puya is related to Andean orogeny and Pleistocene climatic oscillations. This study provides plastome resources for species delimitation and novel phylogenetic and biogeographic studies.
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Affiliation(s)
- Lu Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden Chinese Academy of Sciences Guangzhou China
- University of Chinese Academy of Sciences Beijing China
| | - Yu‐Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden Chinese Academy of Sciences Guangzhou China
- College of Pharmacy Shaanxi University of Chinese Medicine Xi'an China
| | - Liscely Tumi
- Facultad de Ciencias Biológicas Universidad Nacional Mayor de San Marcos Lima Peru
| | - Mery L. Suni
- Facultad de Ciencias Biológicas Universidad Nacional Mayor de San Marcos Lima Peru
| | - Mónica Arakaki
- Facultad de Ciencias Biológicas Universidad Nacional Mayor de San Marcos Lima Peru
| | - Kevin S. Burgess
- Department of Biology, Columbus State University University System of Georgia Columbus Georgia USA
| | - Xue‐Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden Chinese Academy of Sciences Guangzhou China
- Center of Conservation Biology, Core Botanical Gardens Chinese Academy of Sciences Guangzhou China
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19
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Smith ML, Wallace J, Tank DC, Sullivan J, Carstens BC. The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest. Mol Ecol 2022; 31:4402-4416. [PMID: 35780485 DOI: 10.1111/mec.16595] [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: 05/12/2021] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
Abstract
Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated Species Distribution Models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine-learning approach to compare models with and without gene flow between populations upon secondary contact after the Last Glacial Maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa, and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support a role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.
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Affiliation(s)
- Megan L Smith
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - Jessica Wallace
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - David C Tank
- Department of Botany and Rocky Mountain Herbarium, University of Wyoming, 1000 E. University Ave., Laramie, WY 82071, USA.,Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, 875 Perimeter Dr. MS 3051, Moscow, ID 83844-3051, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
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20
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Brito J, Tinoco N, Pinto CM, García R, Koch C, Fernandez V, Burneo S, Pardiñas UFJ. Unlocking Andean sigmodontine diversity: five new species of Chilomys (Rodentia: Cricetidae) from the montane forests of Ecuador. PeerJ 2022; 10:e13211. [PMID: 35462758 PMCID: PMC9029390 DOI: 10.7717/peerj.13211] [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: 12/15/2021] [Accepted: 03/11/2022] [Indexed: 01/12/2023] Open
Abstract
The Andean cloud forests of Ecuador are home to several endemic mammals. Members of the Thomasomyini rodents are well represented in the Andes, with Thomasomys being the largest genus (47 species) of the subfamily Sigmodontinae. Within this tribe, however, there are genera that have escaped a taxonomic revision, and Chilomys Thomas, 1897, constitutes a paradigmatic example of these "forgotten" Andean cricetids. Described more than a century ago, current knowledge of this externally unmistakable montane rodent is very limited, and doubts persist as to whether or not it is monotypic. After several years of field efforts in Ecuador, a considerable quantity of specimens of Chilomys were collected from various localities representing both Andean chains. Based on an extensive genetic survey of the obtained material, we can demonstrate that what is currently treated as C. instans in Ecuador is a complex comprising at least five new species which are described in this paper. In addition, based on these noteworthy new evidence, we amend the generic diagnosis in detail, adding several key craniodental traits such as incisor procumbency and microdonty. These results indicate that Chilomys probably has a hidden additional diversity in large parts of the Colombian and Peruvian territories, inviting a necessary revision of the entire genus.
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Affiliation(s)
- Jorge Brito
- Sección de Mastozoología, Instituto Nacional de Biodiversidad (INABIO), Quito, Pichincha, Ecuador
| | - Nicolás Tinoco
- Sección de Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Pichincha, Ecuador
| | - C. Miguel Pinto
- Observatorio de Biodiversidad Ambiente y Salud (OBBAS), Quito, Pichincha, Ecuador. Current address: Charles Darwin Research Station, Charles Darwin Foundation, Puerto Ayora, Galápagos, Ecuador
| | - Rubí García
- Sección de Mastozoología, Instituto Nacional de Biodiversidad (INABIO), Quito, Pichincha, Ecuador
| | - Claudia Koch
- Leibniz Institute for the Analysis of Biodiversity Change/Museum Koenig, Bonn, Germany
| | - Vincent Fernandez
- Imaging and Analysis Centre, Natural History Museum (NHM), London, United Kingdom
| | - Santiago Burneo
- Sección de Mastozoología, Museo de Zoología, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Pichincha, Ecuador
| | - Ulyses F. J. Pardiñas
- Sección de Mastozoología, Instituto Nacional de Biodiversidad (INABIO), Quito, Pichincha, Ecuador,Instituto de Diversidad y Evolución Austral (IDEAus – CONICET), Puerto Madryn, Chubut, Argentina
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21
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Pérez-Escobar OA, Zizka A, Bermúdez MA, Meseguer AS, Condamine FL, Hoorn C, Hooghiemstra H, Pu Y, Bogarín D, Boschman LM, Pennington RT, Antonelli A, Chomicki G. The Andes through time: evolution and distribution of Andean floras. TRENDS IN PLANT SCIENCE 2022; 27:364-378. [PMID: 35000859 DOI: 10.1016/j.tplants.2021.09.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/03/2021] [Accepted: 09/30/2021] [Indexed: 05/12/2023]
Abstract
The Andes are the world's most biodiverse mountain chain, encompassing a complex array of ecosystems from tropical rainforests to alpine habitats. We provide a synthesis of Andean vascular plant diversity by estimating a list of all species with publicly available records, which we integrate with a phylogenetic dataset of 14 501 Neotropical plant species in 194 clades. We find that (i) the Andean flora comprises at least 28 691 georeferenced species documented to date, (ii) Northern Andean mid-elevation cloud forests are the most species-rich Andean ecosystems, (iii) the Andes are a key source and sink of Neotropical plant diversity, and (iv) the Andes, Amazonia, and other Neotropical biomes have had a considerable amount of biotic interchange through time.
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Affiliation(s)
| | - Alexander Zizka
- Biodiversity of Plants, Philipps University Marburg, 35043 Marburg, Germany; German Center for Integrative Biodiversity Research Halle-Jena-Leipzig (iDiv), 04103 Leipzig, Germany
| | - Mauricio A Bermúdez
- Escuela de Ingeniería Geológica, Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
| | - Andrea S Meseguer
- Real Jardín Botánico de Madrid (RJB)-Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Fabien L Condamine
- Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier), 34095 Montpellier, France
| | - Carina Hoorn
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Henry Hooghiemstra
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Yuanshu Pu
- German Center for Integrative Biodiversity Research Halle-Jena-Leipzig (iDiv), 04103 Leipzig, Germany
| | - Diego Bogarín
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, Costa Rica; Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Lydian M Boschman
- Department of Environmental Systems Science, Eidgenössische Technische Hochschule (ETH) Zurich, 8092 Zurich, Switzerland
| | - R Toby Pennington
- Department of Geography, University of Exeter, Exeter EX4 4RJ, UK; Royal Botanic Garden, Edinburgh EH3 5LR, UK
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew TW9 3AB, Surrey, UK; Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | - Guillaume Chomicki
- Ecology and Evolutionary Biology, University of Sheffield, Sheffield S10 2TN, UK.
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22
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Dellinger AS, Paun O, Baar J, Temsch EM, Fernández-Fernández D, Schönenberger J. Population structure in Neotropical plants: integrating pollination biology, topography and climatic niches. Mol Ecol 2022; 31:2264-2280. [PMID: 35175652 PMCID: PMC9310734 DOI: 10.1111/mec.16403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/29/2022]
Abstract
Animal pollinators mediate gene flow among plant populations, but in contrast to well‐studied topographic and (Pleistocene) environmental isolating barriers, their impact on population genetic differentiation remains largely unexplored. Comparing how these multifarious factors drive microevolutionary histories is, however, crucial for better resolving macroevolutionary patterns of plant diversification. Here we combined genomic analyses with landscape genetics and niche modelling across six related Neotropical plant species (424 individuals across 33 localities) differing in pollination strategy to test the hypothesis that highly mobile (vertebrate) pollinators more effectively link isolated localities than less mobile (bee) pollinators. We found consistently higher genetic differentiation (FST) among localities of bee‐ than vertebrate‐pollinated species with increasing geographical distance, topographic barriers and historical climatic instability. High admixture among montane populations further suggested relative climatic stability of Neotropical montane forests during the Pleistocene. Overall, our results indicate that pollinators may differentially impact the potential for allopatric speciation, thereby critically influencing diversification histories at macroevolutionary scales.
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Affiliation(s)
- Agnes S Dellinger
- Department of Botany and Biodiversity Research, University of Vienna, Austria.,Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Austria
| | - Juliane Baar
- Department of Botany and Biodiversity Research, University of Vienna, Austria
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Austria
| | | | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Austria
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23
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Jacobs SJ, Grundler MC, Henriquez CL, Zapata F. An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae). Sci Rep 2021; 11:24013. [PMID: 34907249 PMCID: PMC8671583 DOI: 10.1038/s41598-021-03419-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species (\documentclass[12pt]{minimal}
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\begin{document}$$< 20\%$$\end{document}<20%). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.
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Affiliation(s)
- Sarah J Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.,Department of Botany, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
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24
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Linan AG, Myers JA, Edwards CE, Zanne AE, Smith SA, Arellano G, Cayola L, Farfan-Ríos W, Fuentes AF, García-Cabrera K, González-Caro S, Loza MI, Macía MJ, Malhi Y, Nieto-Ariza B, Salinas N, Silman M, Tello JS. The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades? THE NEW PHYTOLOGIST 2021; 232:2506-2519. [PMID: 34379801 DOI: 10.1111/nph.17674] [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: 01/11/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Recent studies have demonstrated that ecological processes that shape community structure and dynamics change along environmental gradients. However, much less is known about how the emergence of the gradients themselves shape the evolution of species that underlie community assembly. In this study, we address how the creation of novel environments leads to community assembly via two nonmutually exclusive processes: immigration and ecological sorting of pre-adapted clades (ISPC), and recent adaptive diversification (RAD). We study these processes in the context of the elevational gradient created by the uplift of the Central Andes. We develop a novel approach and method based on the decomposition of species turnover into within- and among-clade components, where clades correspond to lineages that originated before mountain uplift. Effects of ISPC and RAD can be inferred from how components of turnover change with elevation. We test our approach using data from over 500 Andean forest plots. We found that species turnover between communities at different elevations is dominated by the replacement of clades that originated before the uplift of the Central Andes. Our results suggest that immigration and sorting of clades pre-adapted to montane habitats is the primary mechanism shaping tree communities across elevations.
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Affiliation(s)
- Alexander G Linan
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
| | - Jonathan A Myers
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Christine E Edwards
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
| | - Amy E Zanne
- Department of Biological Sciences, The George Washington University, Washington, DC, 20052, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gabriel Arellano
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Leslie Cayola
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - William Farfan-Ríos
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Alfredo F Fuentes
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Karina García-Cabrera
- Escuela Profesional de Biología, Universidad Nacional de San Antonio Abad del Cusco, Cusco, Peru
| | - Sebastián González-Caro
- Departamento de Ciencias Forestales, Universidad Nacional de Colombia Sede Medellín, Universidad Nacional de Colombia, Medellín, Colombia
| | - M Isabel Loza
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
- Herbario Nacional de Bolivia, Universidad Mayor de San Andrés, La Paz, Bolivia
- Department of Biology, University of Missouri-St Louis, St Louis, MO, 63121, USA
| | - Manuel J Macía
- Departamento de Biología, Área de Botánica, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
| | | | - Norma Salinas
- Institute for Nature Earth and Energy, Pontificia Universidad Catolica del Peru, Lima, Peru
| | - Miles Silman
- Center for Energy, Environment and Sustainability, Winston-Salem, NC, 27109, USA
| | - J Sebastián Tello
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St Louis, MO, 63110, USA
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25
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Miao J, Farhat P, Wang W, Ruhsam M, Milne R, Yang H, Tso S, Li J, Xu J, Opgenoorth L, Miehe G, Mao K. Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau. ANNALS OF BOTANY 2021; 128:903-918. [PMID: 34472580 PMCID: PMC8577208 DOI: 10.1093/aob/mcab114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP). METHODS The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow-endemic junipers from the QTP that are sister to each other, was surveyed using RNA-sequencing data. Coalescent-based analyses were used to test speciation, migration and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species. KEY RESULTS Analyses of 149 052 single nucleotide polymorphisms showed that the two species are well differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma but only one for J. erectopatens. The identified positively selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter. CONCLUSIONS This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in understanding the current distribution pattern and genetic diversity of threatened species in mountainous regions.
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Affiliation(s)
- Jibin Miao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Perla Farhat
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Wentao Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Richard Milne
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Heng Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Sonam Tso
- College of Science, Tibet University, Lhasa 850000, PR China
| | - Jialiang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Jingjing Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Lars Opgenoorth
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Georg Miehe
- Faculty of Biology and Geology, University of Marburg, 35032 Marburg, Germany
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610065, Sichuan, PR China
- College of Science, Tibet University, Lhasa 850000, PR China
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26
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Liu W, Xie J, Zhou H, Kong H, Hao G, Fritsch PW, Gong W. Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China. Evol Appl 2021; 14:2647-2663. [PMID: 34815745 PMCID: PMC8591333 DOI: 10.1111/eva.13301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
The mountains of subtropical China are an excellent system for investigating the processes driving the geographical distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the major mountain ranges in subtropical China have affected the evolution of plant species in the subtropical evergreen broadleaved forest is an issue with long-term concern. Here, we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. The orientation and physiography of the mountain ranges of subtropical China appear to have contributed to the geographical pattern of genetic variation between the eastern and western populations of C. chuniana. Complex physiography plus long-term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. The Nanling Mts. are thus considered as a suitable area for preserving population diversity and large population sizes of C. chuniana compared with other regions. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan-Tali Interglacial period, with intensified East Asia summer monsoon and continuous habitat available for occupation. Our data support the strong influence of both climatic history and topographic characteristics on the high regional phytodiversity of the subtropical evergreen broadleaved forest in subtropical China.
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Affiliation(s)
- Wanzhen Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jianguang Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hui Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Gang Hao
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | | | - Wei Gong
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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27
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Xia XM, Yang MQ, Li CL, Huang SX, Jin WT, Shen TT, Wang F, Li XH, Yoichi W, Zhang LH, Zheng YR, Wang XQ. Spatiotemporal evolution of the global species diversity of Rhododendron. Mol Biol Evol 2021; 39:6413646. [PMID: 34718707 PMCID: PMC8760938 DOI: 10.1093/molbev/msab314] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Evolutionary radiation is a widely recognized mode of species diversification, but its underlying mechanisms have not been unambiguously resolved for species-rich cosmopolitan plant genera. In particular, it remains largely unknown how biological and environmental factors have jointly driven its occurrence in specific regions. Here, we use Rhododendron, the largest genus of woody plants in the Northern Hemisphere, to investigate how geographic and climatic factors, as well as functional traits, worked together to trigger plant evolutionary radiations and shape the global patterns of species richness based on a solid species phylogeny. Using 3,437 orthologous nuclear genes, we reconstructed the first highly supported and dated backbone phylogeny of Rhododendron comprising 200 species that represent all subgenera, sections, and nearly all multispecies subsections, and found that most extant species originated by evolutionary radiations when the genus migrated southward from circumboreal areas to tropical/subtropical mountains, showing rapid increases of both net diversification rate and evolutionary rate of environmental factors in the Miocene. We also found that the geographically uneven diversification of Rhododendron led to a much higher diversity in Asia than in other continents, which was mainly driven by two environmental variables, that is, elevation range and annual precipitation, and were further strengthened by the adaptation of leaf functional traits. Our study provides a good example of integrating phylogenomic and ecological analyses in deciphering the mechanisms of plant evolutionary radiations, and sheds new light on how the intensification of the Asian monsoon has driven evolutionary radiations in large plant genera of the Himalaya-Hengduan Mountains.
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Affiliation(s)
- Xiao-Mei Xia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao-Qin Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Cong-Li Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si-Xin Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Tao Jin
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ting-Ting Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fei Wang
- West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Sichuan 611834, China
| | - Xiao-Hua Li
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiangxi 332900, China
| | - Watanabe Yoichi
- Graduate School of Horticulture, Chiba University, Chiba 271-8510, Japan
| | - Le-Hua Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiangxi 332900, China
| | - Yuan-Run Zheng
- West China Subalpine Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Sichuan 611834, China.,State Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Ortego J, Knowles LL. Geographical isolation versus dispersal: Relictual alpine grasshoppers support a model of interglacial diversification with limited hybridization. Mol Ecol 2021; 31:296-312. [PMID: 34651368 DOI: 10.1111/mec.16225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/21/2021] [Accepted: 10/08/2021] [Indexed: 01/25/2023]
Abstract
Alpine biotas are paradigmatic of the countervailing roles of geographical isolation and dispersal during diversification. In temperate regions, repeated distributional shifts driven by Pleistocene climatic oscillations produced both recurrent pulses of population fragmentation and opportunities for gene flow during range expansions. Here, we test whether a model of divergence in isolation vs. with gene flow is more likely in the diversification of flightless alpine grasshoppers of the genus Podisma from the Iberian Peninsula. The answer to this question can also provide key insights about the pace of evolution. Specifically, if the data fit a divergence in isolation model, this suggests rapid evolution of reproductive isolation. Genomic data confirm a Pleistocene origin of the species complex, and multiple analytical approaches revealed limited asymmetric historical hybridization between two taxa. Genomic-based demographic reconstructions, spatial patterns of genetic structure and range shifts inferred from palaeodistribution modelling suggest severe range contraction accompanied by declines in effective population sizes during interglacials (i.e., contemporary populations confined to sky islands are relicts) and expansions during the coldest stages of the Pleistocene in each taxon. Although limited hybridization during secondary contact leads to phylogenetic uncertainty if gene flow is not accommodated when estimating evolutionary relationships, all species exhibit strong genetic cohesiveness. Our study lends support to the notion that the accumulation of incipient differences during periods of isolation were sufficient to lead to lineage persistence, but also that the demographic changes, dispersal constraints and spatial distribution of the sky islands themselves mediated species diversification in temperate alpine biotas.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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29
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Bator J, Marshall DC, Hill KBR, Cooley JR, Leston A, Simon C. Phylogeography of the endemic red-tailed cicadas of New Zealand (Hemiptera: Cicadidae: Rhodopsalta), and molecular, morphological and bioacoustical confirmation of the existence of Hudson’s Rhodopsalta microdora. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
Why do some genera radiate, whereas others do not? The genetic structure of present-day populations can provide clues for developing hypotheses. In New Zealand, three Cicadidae genera are depauperate [Amphipsalta (three species), Notopsalta (one species) and Rhodopsalta (three species)], whereas two have speciated extensively [Kikihia (~30 species/subspecies) and Maoricicada (~20 species/subspecies). Here, we examine the evolution of Rhodopsalta, the last New Zealand genus to be studied phylogenetically and phylogeographically. We use Bayesian and maximum-likelihood analyses of mitochondrial cox1 and nuclear EF1α gene sequences. Concatenated and single-gene phylogenies for 70 specimens (58 localities) support its monophyly and three described species: Rhodopsalta cruentata, Rhodopsalta leptomera and Rhodopsalta microdora, the last taxon previously regarded as uncertain. We provide distribution maps, biological notes and the first descriptions of diagnostic songs. We show that both R. cruentata and R. microdora exhibit northern and southern genetic subclades. Subclades of the dry-adapted R. microdora clade show geographical structure, whereas those of the mesic R. cruentata and sand-dune specialist R. leptomera have few discernible patterns. Genetic, bioacoustical and detailed distributional evidence for R. microdora add to the known biodiversity of New Zealand. We designate a lectotype for Tettigonia cruentata Fabricius, 1775, the type species of Rhodopsalta.
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Affiliation(s)
- John Bator
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - David C Marshall
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Kathy B R Hill
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - John R Cooley
- Department of Ecology and Evolutionary Biology, University of Connecticut, 10 South Prospect Street, Hartford, CT 06103, USA
| | - Adam Leston
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
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30
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Dynamic Capabilities and Their Impact on Intellectual Capital and Innovation Performance. SUSTAINABILITY 2021. [DOI: 10.3390/su131810028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
There is a high tendency for conversion from a statistical economy based on measuring tangible assets into investigating non-tangible capital drive in the present economic status worldwide. The implications of intellectual capital on innovation performance have widely attracted attention among researchers in the global arena. The present study investigated the impacts of intellectual capital on innovation performance in the banking sector as influencing non-tangible assets. Besides, the role of dynamic capabilities in moderating the relationship between intellectual capital and innovation performance was examined. A purposive sampling technique was applied to 364 participants from Iraqi commercial banks as the research context. Thereafter, structural equation modelling (SEM) was utilised to analyse the collected data from the survey questionnaire using SPSS.v25 and AMOS.v24. The study found that the employees’ levels of intellectual capital significantly increased toward innovativeness through the moderating role of dynamic capabilities between intellectual capital and innovation performance in the commercial banking sector for better competitive advantages. Consequently, the study provides valuable insights and guidance for academicians and practitioners on the impacts of developing intellectual capital on enhancing competitive performance, especially in the context of Iraqi commercial banks.
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31
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Moré M, Soteras F, Ibañez AC, Dötterl S, Cocucci AA, Raguso RA. Floral Scent Evolution in the Genus Jaborosa (Solanaceae): Influence of Ecological and Environmental Factors. PLANTS (BASEL, SWITZERLAND) 2021; 10:1512. [PMID: 34451557 PMCID: PMC8398055 DOI: 10.3390/plants10081512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/05/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Floral scent is a key communication channel between plants and pollinators. However, the contributions of environment and phylogeny to floral scent composition remain poorly understood. In this study, we characterized interspecific variation of floral scent composition in the genus Jaborosa Juss. (Solanaceae) and, using an ecological niche modelling approach (ENM), we assessed the environmental variables that exerted the strongest influence on floral scent variation, taking into account pollination mode and phylogenetic relationships. Our results indicate that two major evolutionary themes have emerged: (i) a 'warm Lowland Subtropical nectar-rewarding clade' with large white hawkmoth pollinated flowers that emit fragrances dominated by oxygenated aromatic or sesquiterpenoid volatiles, and (ii) a 'cool-temperate brood-deceptive clade' of largely fly-pollinated species found at high altitudes (Andes) or latitudes (Patagonian Steppe) that emit foul odors including cresol, indole and sulfuric volatiles. The joint consideration of floral scent profiles, pollination mode, and geoclimatic context helped us to disentangle the factors that shaped floral scent evolution across "pollinator climates" (geographic differences in pollinator abundance or preference). Our findings suggest that the ability of plants in the genus Jaborosa to colonize newly formed habitats during Andean orogeny was associated with striking transitions in flower scent composition that trigger specific odor-driven behaviors in nocturnal hawkmoths and saprophilous fly pollinators.
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Affiliation(s)
- Marcela Moré
- Laboratorio de Ecología Evolutiva y Biología Floral, Instituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba), Córdoba CP 5000, Argentina; (F.S.); (A.C.I.); (A.A.C.)
| | - Florencia Soteras
- Laboratorio de Ecología Evolutiva y Biología Floral, Instituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba), Córdoba CP 5000, Argentina; (F.S.); (A.C.I.); (A.A.C.)
| | - Ana C. Ibañez
- Laboratorio de Ecología Evolutiva y Biología Floral, Instituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba), Córdoba CP 5000, Argentina; (F.S.); (A.C.I.); (A.A.C.)
| | - Stefan Dötterl
- Department of Biosciences, Paris-Lodron-University of Salzburg, 5020 Salzburg, Austria;
| | - Andrea A. Cocucci
- Laboratorio de Ecología Evolutiva y Biología Floral, Instituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba), Córdoba CP 5000, Argentina; (F.S.); (A.C.I.); (A.A.C.)
| | - Robert A. Raguso
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
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32
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Acha S, Linan A, MacDougal J, Edwards C. The evolutionary history of vines in a neotropical biodiversity hotspot: Phylogenomics and biogeography of a large passion flower clade (Passiflora section Decaloba). Mol Phylogenet Evol 2021; 164:107260. [PMID: 34273502 DOI: 10.1016/j.ympev.2021.107260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
Because of their extraordinary flower and leaf morphology, passion flowers (Passifloraceae) have fascinated naturalists since their discovery. Within the large, diverse (600 species) genus Passiflora is an especially enigmatic and species-rich (120 spp.) subclade, Section Decaloba, which occurs in the Neotropics and has its center of diversity in Andean montane forests. A recent phylogenetic study of Passifloraceae showed that Section Decaloba was monophyletic, but was unable to resolve relationships within the clade, thus preventing inferences of evolutionary history and biogeography. The goal of this study was to elucidate the phylogeny and biogeography of Section Decaloba. We sampled 206 accessions representing 91 of the ~ 120 known species in section Decaloba and four outgroups, with samples derived predominantly from herbarium specimens. We generated DNA sequences using a high-throughput DNA sequencing technique called 2b-RAD, reconstructed the phylogeny, and conducted ancestral area reconstructions to infer the biogeographic history of the group. We recovered predominantly well-supported trees in which species were grouped into two main clades: 1) the Central American clade, within which the majority of nodes well supported and species were monophyletic and 2) the South American clade, a large clade that showed overall lower resolution and included several polyphyletic species and species complexes that need additional research. RASP analysis showed that section Decaloba originated in Central America around 10.4 Ma, and then dispersed to South America, the Greater Antilles, and the Bahamas. The South American clade diversified in the Northern Andes and then dispersed to the rest of South America, and Lesser Antilles. Results suggest that both long-distance dispersal and colonization of newly available habitats (i.e., in the Andes) likely promoted diversification of this clade. This study also illustrates how using herbarium specimens and a RAD-seq approach can produce phylogenies for broadly distributed, highly diverse, and poorly accessible groups of plants where field collections would be unfeasible.
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Affiliation(s)
- Serena Acha
- Department of Biology, University of Missouri-St. Louis, One University Blvd, Research Hall St. Louis, MO 63121, USA; Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO 63110, USA; University of Florida Herbarium, Florida Museum of Natural History,1659 Museum Rd, Gainesville, FL 32611-7800, USA.
| | - Alexander Linan
- Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO 63110, USA
| | - John MacDougal
- Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO 63110, USA; Harris-Stowe State University, 3026 Laclede Ave, St. Louis, MO 63103, USA
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33
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Lu J, Lu H, Brusseau ML, He L, Gorlier A, Yao T, Tian P, Feng S, Yu Q, Nie Q, Yang Y, Yin C, Tang M, Feng W, Xue Y, Yin F. Interaction of climate change, potentially toxic elements (PTEs), and topography on plant diversity and ecosystem functions in a high-altitude mountainous region of the Tibetan Plateau. CHEMOSPHERE 2021; 275:130099. [PMID: 33667772 DOI: 10.1016/j.chemosphere.2021.130099] [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: 11/05/2020] [Revised: 02/03/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Potentially toxic elements (PTEs) generated from mining activities have affected ecological diversity and ecosystem functions around the world. Accurately assessing the long-term effects of PTEs is critical to classifying recoverable areas and proposing management strategies. Mining activities that shape geographical patterns of biodiversity in individual regions are increasingly understood, but the complex interactions on broad scales and in changing environments are still unclear. In this study, we developed a series of empirical models that simulate the changes in biodiversity and ecosystem functions in mine-affected regions along elevation gradients (1500-3600 m a.s.l) in the metal-rich Qilian Mountains (∼800 km) on the northeastern Tibetan Plateau (China). Our results confirmed the crucial role of PTEs dispersal, topography, and climatic heterogeneity in the diversification of plant community composition. On average, 54% of the changes in ecosystem functions were explained by the interactions among topography, climate, and PTEs. However, merely 30% of the changes were correlated with a single driver. The changes in species composition (explained variables = 94.8%) in the PTE-polluted habitats located in the warm and humid low-elevation deserts and grasslands were greater than those occurring in the dry alpine deserts and grasslands. The ecosystem functions (soil characteristics, nutrient migration, and plant biomass) experienced greater changes in the humid low-elevation grasslands and alpine deserts. Our results suggest that the processes driven by climate or other factors can result in high-altitude PTE-affected habitat facing greater threats.
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Affiliation(s)
- Jingzhao Lu
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China; College of Science and Technology, Hebei Agricultural University, Cangzhou, 061100, China; Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Hongwei Lu
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China.
| | - Mark L Brusseau
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, USA; Department of Hydrology and Atmospheric Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Li He
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300072, China
| | - Alessandra Gorlier
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, 85721, USA
| | - Tianci Yao
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China
| | - Peipei Tian
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China; School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Sansan Feng
- School of Renewable Energy, North China Electric Power University, Beijing, 102206, China
| | - Qing Yu
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China
| | - Qianwen Nie
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China
| | - Yiyang Yang
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China
| | - Chuang Yin
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China
| | - Meng Tang
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China
| | - Wei Feng
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China
| | - Yuxuan Xue
- Key Laboratory of Water Cycle and Related Land Surface Processes, Institute of Geographic Science and Natural Resources Research, Chinese Academy of Science, Beijing, 100101, China
| | - Fangping Yin
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300072, China
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Liu L, Tumi L, Suni ML, Arakaki M, Wang ZF, Ge XJ. Draft genome of Puya raimondii (Bromeliaceae), the Queen of the Andes. Genomics 2021; 113:2537-2546. [PMID: 34089785 DOI: 10.1016/j.ygeno.2021.05.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/16/2021] [Accepted: 05/31/2021] [Indexed: 01/20/2023]
Abstract
Puya raimondii, the Queen of the Andes, is an endangered high Andean species in the Bromeliaceae family. Here, we report its first genome to promote its conservation and evolutionary study. Comparative genomics showed P. raimondii diverged from Ananas comosus about 14.8 million years ago, and the long terminal repeats were likely to contribute to the genus diversification in last 3.5 million years. The gene families related to plant reproductive development and stress responses significantly expanded in the genome. At the same time, gene families involved in disease defense, photosynthesis and carbohydrate metabolism significantly contracted, which may be an evolutionary strategy to adapt to the harsh conditions in high Andes. The demographic history analysis revealed the P. raimondii population size sharply declined in the Pleistocene and then increased in the Holocene. We also designed and tested 46 pairs of universal primers for amplifying orthologous single-copy nuclear genes in Puya species.
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Affiliation(s)
- Lu Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Liscely Tumi
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Mery L Suni
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Monica Arakaki
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Zheng-Feng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China; South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China; South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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35
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Aquino D, Moreno‐Letelier A, González‐Botello MA, Arias S. The importance of environmental conditions in maintaining lineage identity in Epithelantha (Cactaceae). Ecol Evol 2021; 11:4520-4531. [PMID: 33976827 PMCID: PMC8093668 DOI: 10.1002/ece3.7347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 11/17/2022] Open
Abstract
The use of environmental variables to explain the evolution of lineages has gained relevance in recent studies. Additionally, it has allowed the recognition of species by adding more characters to morphological and molecular information. This study focuses on identifying environmental and landscape variables that have acted as barriers that could have influenced the evolution of Epithelantha species and its close genera.Our results show that soil pH, isothermality, temperature seasonality, and annual precipitation have a significant phylogenetic signal for Epithelantha. Soil type and landforms are also relevant as ecological barriers that maintain the identity of Epithelantha species.The variables associated with the soil (pH) have influenced the evolution of Epithelantha and probably in other genera of Cactaceae. Additionally, Epithelantha is frequent in the piedmont and haplic kastanozems. Bioclimatic variables reinforce the recognition of E. micromeris, and E. cryptica as independent species. Therefore, ecology can be considered as a factor to explain the high level of endemism in Cactaceae.
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Affiliation(s)
- David Aquino
- Jardín BotánicoInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | | | | | - Salvador Arias
- Jardín BotánicoInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
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36
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Padilla-González GF, Diazgranados M, Da Costa FB. Effect of the Andean Geography and Climate on the Specialized Metabolism of Its Vegetation: The Subtribe Espeletiinae (Asteraceae) as a Case Example. Metabolites 2021; 11:220. [PMID: 33916648 PMCID: PMC8065660 DOI: 10.3390/metabo11040220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/28/2021] [Accepted: 04/02/2021] [Indexed: 01/02/2023] Open
Abstract
The Andean mountains are 'center stage' to some of the most spectacular examples of plant diversifications, where geographic isolation and past climatic fluctuations have played a major role. However, the influence of Andean geography and climate as drivers of metabolic variation in Andean plants is poorly elucidated. Here, we studied the influence of those factors on the metabolome of the subtribe Espeletiinae (Asteraceae) using liquid chromatography coupled to high-resolution mass spectrometry data of over two hundred samples from multiple locations. Our results demonstrate that metabolic profiles can discriminate Espeletiinae taxa at different geographic scales, revealing inter- and intraspecific metabolic variations: at the country level, segregation between Colombian and Venezuelan taxa was observed; regionally, between páramo massifs; and locally, between páramo complexes. Metabolic differences in Espeletiinae were mainly explained by geographic isolation, although differences in taxonomic genera, temperature, and elevation, were also important. Furthermore, we found that different species inhabiting the same páramo complex showed stronger chemical similarities than the same species at different locations, corroborating that geographic isolation represents the main driver of metabolic change in Espeletiinae. The current study serves as a starting point to fill in the gaps in how Andean geography and climate have shaped the metabolism of its vegetation and reveal the potential of untargeted metabolomics to study the environmental physiology of plants.
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Affiliation(s)
- Guillermo F. Padilla-González
- AsterBioChem Research Team, Laboratory of Pharmacognosy, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto SP 14040-903, Brazil;
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Kew Road, London TW9 3AB, UK
| | - Mauricio Diazgranados
- Millennium Seed Bank, Royal Botanic Gardens, Kew, Ardingly, West Sussex, Haywards Heath RH17 6TN, UK;
| | - Fernando B. Da Costa
- AsterBioChem Research Team, Laboratory of Pharmacognosy, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto SP 14040-903, Brazil;
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37
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Pouchon C, Lavergne S, Fernández Á, Alberti A, Aubert S, Mavárez J. Phylogenetic signatures of ecological divergence and leapfrog adaptive radiation in Espeletia. AMERICAN JOURNAL OF BOTANY 2021; 108:113-128. [PMID: 33426651 DOI: 10.1002/ajb2.1591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 09/21/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Events of accelerated species diversification represent one of Earth's most celebrated evolutionary outcomes. Northern Andean high-elevation ecosystems, or páramos, host some plant lineages that have experienced the fastest diversification rates, likely triggered by ecological opportunities created by mountain uplifts, local climate shifts, and key trait innovations. However, the mechanisms behind rapid speciation into the new adaptive zone provided by these opportunities have long remained unclear. METHODS We address this issue by studying the Venezuelan clade of Espeletia, a species-rich group of páramo-endemics showing a dazzling ecological and morphological diversity. We performed several comparative analyses to study both lineage and trait diversification, using an updated molecular phylogeny of this plant group. RESULTS We showed that sets of either vegetative or reproductive traits have conjointly diversified in Espeletia along different vegetation belts, leading to adaptive syndromes. Diversification in vegetative traits occurred earlier than in reproductive ones. The rate of species and morphological diversification showed a tendency to slow down over time, probably due to diversity dependence. We also found that closely related species exhibit significantly more overlap in their geographic distributions than distantly related taxa, suggesting that most events of ecological divergence occurred at close geographic proximity within páramos. CONCLUSIONS These results provide compelling support for a scenario of small-scale ecological divergence along multiple ecological niche dimensions, possibly driven by competitive interactions between species, and acting sequentially over time in a leapfrog pattern.
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Affiliation(s)
- Charles Pouchon
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
| | - Sébastien Lavergne
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
| | - Ángel Fernández
- Herbario IVIC. Instituto Venezolano de Investigaciones Científicas, Apartado 20632, Caracas, 1020-A, Venezuela
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, 91057, Evry, France
| | - Serge Aubert
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
- Université Grenoble Alpes, CNRS, Université Savoie Mont Blanc, SAJF, Station Alpine Joseph Fourier, 38000, Grenoble, France
| | - Jesús Mavárez
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, F-38000, Grenoble, France
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Kandziora M, Sklenář P, Kolář F, Schmickl R. How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example. FRONTIERS IN PLANT SCIENCE 2021; 12:765719. [PMID: 35069621 PMCID: PMC8777076 DOI: 10.3389/fpls.2021.765719] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/22/2021] [Indexed: 05/17/2023]
Abstract
A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.
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Affiliation(s)
- Martha Kandziora
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- *Correspondence: Martha Kandziora,
| | - Petr Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
| | - Roswitha Schmickl
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czechia
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Vega-Polo P, Cobo MM, Argudo A, Gutierrez B, Rowntree J, Torres MDL. Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands. PLoS One 2020; 15:e0243420. [PMID: 33284832 PMCID: PMC7721170 DOI: 10.1371/journal.pone.0243420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 11/18/2022] Open
Abstract
The Ecuadorian páramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortiño, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortiño could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortiño populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 species-specific SSR (simple sequence repeats) markers and used 16 of these to characterize 100 mortiño individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE = 0.73) for the Ecuadorian mortiño, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated with the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortiño populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist in the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystem as a whole.
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Affiliation(s)
- Pamela Vega-Polo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Maria Mercedes Cobo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Andrea Argudo
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Bernardo Gutierrez
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jennifer Rowntree
- Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Oxford, United Kingdom
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- * E-mail:
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40
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Valencia JB, Mesa J, León JG, Madriñán S, Cortés AJ. Climate Vulnerability Assessment of the Espeletia Complex on Páramo Sky Islands in the Northern Andes. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.565708] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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41
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Abstract
Parasites are interesting models for studying speciation processes because they have a high potential for specialization, thanks to the intimate ecological association with their hosts and vectors. Yet little is known about the circumstances under which new parasite lineages emerge. Here we studied the genome diversity of parasites of the Leishmania braziliensis species complex that inhabit both Amazonian and Andean biotas in Peru. We identify three major parasite lineages that occupy particular ecological niches and show that these emerged during forestation changes over the past 150,000 y. We furthermore discovered that meiotic recombination between Amazonian and Andean lineages resulted in full-genome hybrids presenting mixed mitochondrial genomes, providing insights into the genetic consequences of hybridization in parasitic protozoa. The tropical Andes are an important natural laboratory to understand speciation in many taxa. Here we examined the evolutionary history of parasites of the Leishmania braziliensis species complex based on whole-genome sequencing of 67 isolates from 47 localities in Peru. We first show the origin of Andean Leishmania as a clade of near-clonal lineages that diverged from admixed Amazonian ancestors, accompanied by a significant reduction in genome diversity and large structural variations implicated in host–parasite interactions. Within the Andean species, patterns of population structure were strongly associated with biogeographical origin. Molecular clock and ecological niche modeling suggested that the history of diversification of the Andean lineages is limited to the Late Pleistocene and intimately associated with habitat contractions driven by climate change. These results suggest that changes in forestation over the past 150,000 y have influenced speciation and diversity of these Neotropical parasites. Second, genome-scale analyses provided evidence of meiotic-like recombination between Andean and Amazonian Leishmania species, resulting in full-genome hybrids. The mitochondrial genome of these hybrids consisted of homogeneous uniparental maxicircles, but minicircles originated from both parental species. We further show that mitochondrial minicircles—but not maxicircles—show a similar evolutionary pattern to the nuclear genome, suggesting that compatibility between nuclear-encoded mitochondrial genes and minicircle-encoded guide RNA genes is essential to maintain efficient respiration. By comparing full nuclear and mitochondrial genome ancestries, our data expand our appreciation on the genetic consequences of diversification and hybridization in parasitic protozoa.
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Schley RJ, Pennington RT, Pérez-Escobar OA, Helmstetter AJ, de la Estrella M, Larridon I, Sabino Kikuchi IAB, Barraclough TG, Forest F, Klitgård B. Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity. Mol Ecol 2020; 29:4170-4185. [PMID: 32881172 DOI: 10.1111/mec.15616] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/03/2023]
Abstract
Hybridization has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing interspecific gene flow. However, hybridization in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (Brownea, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridization among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between Brownea lineages and indicated that gene tree incongruence in Brownea is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridization using ~19,000 ddRAD loci recovered a high degree of shared variation between two Brownea species that co-occur in the Ecuadorian Amazon. Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and persistent hybridization. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridization's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.
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Affiliation(s)
- Rowan J Schley
- Royal Botanic Gardens, Kew, Richmond, UK.,Department of Life Sciences, Imperial College London, Ascot, Berkshire, London, UK
| | - R Toby Pennington
- Geography, University of Exeter, Exeter, UK.,Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Andrew J Helmstetter
- Institut de Recherche pour le Développement (IRD), UMR-DIADE, Montpellier, France
| | - Manuel de la Estrella
- Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, UK.,Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L, Gent, Belgium
| | | | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, London, UK.,Department of Zoology, University of Oxford, Oxford, UK
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Vasconcelos TNC, Alcantara S, Andrino CO, Forest F, Reginato M, Simon MF, Pirani JR. Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient Neotropical mountains. Proc Biol Sci 2020; 287:20192933. [PMID: 32183631 DOI: 10.1098/rspb.2019.2933] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mountains are among the most biodiverse areas on the globe. In young mountain ranges, exceptional plant species richness is often associated with recent and rapid radiations linked to the mountain uplift itself. In ancient mountains, however, orogeny vastly precedes the evolution of vascular plants, so species richness has been explained by species accumulation during long periods of low extinction rates. Here we evaluate these assumptions by analysing plant diversification dynamics in the campo rupestre, an ecosystem associated with pre-Cambrian mountaintops and highlands of eastern South America, areas where plant species richness and endemism are among the highest in the world. Analyses of 15 angiosperm clades show that radiations of endemics exhibit fastest rates of diversification during the last 5 Myr, a climatically unstable period. However, results from ancestral range estimations using different models disagree on the age of the earliest in situ speciation events and point to a complex floristic assembly. There is a general trend for higher diversification rates associated with these areas, but endemism may also increase or reduce extinction rates, depending on the group. Montane habitats, regardless of their geological age, may lead to boosts in speciation rates by accelerating population isolation in archipelago-like systems, circumstances that can also result in higher extinction rates and fast species turnover, misleading the age estimates of endemic lineages.
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Affiliation(s)
- Thais N C Vasconcelos
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil.,Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Suzana Alcantara
- Laboratório de Sistemática de Plantas Vasculares, Departmento de Botânica, Universidade Federal de Santa Catarina, Florianópolis, SC 88040-090, Brazil
| | - Caroline O Andrino
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil.,Instituto Tecnológico Vale, Rua Boaventura da Silva, 955, Nazaré, Belém, PA 66055-090, Brazil
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Marcelo Reginato
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 90650-001, Brazil
| | - Marcelo F Simon
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF 70770-917, Brazil
| | - José R Pirani
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
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Wong ELY, Nevado B, Osborne OG, Papadopulos AST, Bridle JR, Hiscock SJ, Filatov DA. Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna. Mol Ecol 2019; 29:394-412. [PMID: 31793091 DOI: 10.1111/mec.15319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022]
Abstract
Recently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome-wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection. We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly-differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs' allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16-0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species - pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.
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Affiliation(s)
- Edgar L Y Wong
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, UK
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Rahbek C, Borregaard MK, Antonelli A, Colwell RK, Holt BG, Nogues-Bravo D, Rasmussen CMØ, Richardson K, Rosing MT, Whittaker RJ, Fjeldså J. Building mountain biodiversity: Geological and evolutionary processes. Science 2019; 365:1114-1119. [DOI: 10.1126/science.aax0151] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/26/2019] [Indexed: 01/04/2023]
Abstract
Mountain regions are unusually biodiverse, with rich aggregations of small-ranged species that form centers of endemism. Mountains play an array of roles for Earth’s biodiversity and affect neighboring lowlands through biotic interchange, changes in regional climate, and nutrient runoff. The high biodiversity of certain mountains reflects the interplay of multiple evolutionary mechanisms: enhanced speciation rates with distinct opportunities for coexistence and persistence of lineages, shaped by long-term climatic changes interacting with topographically dynamic landscapes. High diversity in most tropical mountains is tightly linked to bedrock geology—notably, areas comprising mafic and ultramafic lithologies, rock types rich in magnesium and poor in phosphate that present special requirements for plant physiology. Mountain biodiversity bears the signature of deep-time evolutionary and ecological processes, a history well worth preserving.
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46
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Distinctiveness, speciation and demographic history of the rare endemic conifer Juniperus erectopatens in the eastern Qinghai-Tibet Plateau. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01211-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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47
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Testo WL, Sessa E, Barrington DS. The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae). THE NEW PHYTOLOGIST 2019; 222:604-613. [PMID: 30326543 DOI: 10.1111/nph.15544] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Tropical mountains are disproportionately biodiverse relative to their surface area, but the processes underlying their exceptional diversity require further study. Here, we use comparative phylogenetic methods to examine the impact of the Andean orogeny on the diversification of Neotropical Phlegmariurus, a species-rich lycophyte clade. We generated a time-calibrated phylogeny of 105 species of Neotropical Phlegmariurus and estimated lineage diversification rates. We tested for correlations between lineage diversification rates and species range size, niche breadth, elevational range amplitude, and mean elevation of occurrence. A recently developed macroevolutionary model was used to incorporate geological data and test for an association between diversification rates and the Andean uplift. Diversification rates of Neotropical Phlegmariurus are negatively correlated with species range size and positively correlated with mean elevation of species occurrence. The rise of the Andes is strongly associated with increased rates of diversification in Neotropical Phlegmariurus during the last 10 Myr. Our study demonstrates the importance of mountain-building events and geographical isolation of alpine populations as drivers of rapid diversification, even in spore-dispersed plants. This work also highlights the usefulness of combined phylogenetic, geological and ecological datasets, and the promise of comparative environment-dependent diversification models in better understanding the evolutionary origins of biodiversity.
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Affiliation(s)
- Weston L Testo
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611, USA
| | - David S Barrington
- Department of Plant Biology, University of Vermont, 63 Carrigan Drive, Burlington, VT, 05405, USA
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