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Karimi N, Krieg CP, Spalink D, Lemmon AR, Lemmon EM, Eifler E, Hernández AI, Chan PW, Rodríguez A, Landis JB, Strickler SR, Specht CD, Givnish TJ. Chromosomal evolution, environmental heterogeneity, and migration drive spatial patterns of species richness in Calochortus (Liliaceae). Proc Natl Acad Sci U S A 2024; 121:e2305228121. [PMID: 38394215 PMCID: PMC10927571 DOI: 10.1073/pnas.2305228121] [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: 03/31/2023] [Accepted: 12/20/2023] [Indexed: 02/25/2024] Open
Abstract
We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades-inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)-began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.
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Affiliation(s)
- Nisa Karimi
- Science and Conservation Division, Missouri Botanical Garden, St. Louis, MO63110
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| | | | - Daniel Spalink
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX77845
| | - Alan R. Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL32306
| | | | - Evan Eifler
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| | - Adriana I. Hernández
- School of Integrative Plant Science, Cornell University, Ithaca, NY14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY14853
| | - Patricia W. Chan
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
| | - Aarón Rodríguez
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco45200, Mexico
| | - Jacob B. Landis
- School of Integrative Plant Science, Cornell University, Ithaca, NY14853
- Departamento de Botánica y Zoología, Universidad de la Guadalajara, Zapopan, Jalisco45200, Mexico
- Boyce Thompson Institute for Plant Research, Ithaca, NY14853
| | | | - Chelsea D. Specht
- School of Integrative Plant Science, Cornell University, Ithaca, NY14853
- L. H. Bailey Hortorium, Cornell University, Ithaca, NY14853
| | - Thomas J. Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI53706
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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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Yang X, Zhang X, Xue T, Zhang X, Yang F, Yu J, Janssens SB, Bussmann RW, Yu S. Phylogenomics and historical biogeography of Hydrangeeae (Hydrangeaceae) elucidate the effects of geologic and climatic dynamics on diversification. Proc Biol Sci 2023; 290:20230659. [PMID: 37491959 PMCID: PMC10369024 DOI: 10.1098/rspb.2023.0659] [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: 03/21/2023] [Accepted: 07/03/2023] [Indexed: 07/27/2023] Open
Abstract
Demonstrating the process of transregional biogeography and mechanisms underlying evolutionary radiations is crucial to understanding biological evolution. Here, we use Hydrangeeae (Hydrangeaceae), a tribe with a unique disjunct distribution and complex trait variations, using a solid phylogenetic framework, to investigate how geographical and climatic factors interact with functional traits to trigger plant evolutionary radiations. We constructed the first highly supported and dated phylogenetic framework using 79 protein-coding genes obtained from 81 plastomes, representing 63 species and all major clades, and found that most extant species originated from asynchronous diversification of two lineages undergoing repeated expansion and retraction, at middle and high latitudes of the Northern Hemisphere between East Asia and North America, during the Eocene to Pleistocene (driven by geologic and climatic dynamics). In accordance with these drivers, interactions of flora between central-eastern China and Japan occurred frequently after the Late Tertiary. We found that resource limitation and range fragmentation probably accelerated the diversification of Hydrangeeae, which supports the resource-use hypothesis. Our study sheds light on the evolutionary radiation and assembly of flora within East Asia, and the East Asian-North American disjunction, through integration of phylogenomic and biogeographic data with functional trait and ecological data.
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Affiliation(s)
- Xudong Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, People's Republic of China
| | - Tiantian Xue
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiaoxia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Fusheng Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jianghong Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- College of Forestry, Guizhou University, Guiyang 550025, People's Republic of China
| | - Steven B. Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven, Belgium
| | - Rainer W. Bussmann
- Institute of Botany and Bakuriani Alpine Botanical Garden, Ilia State University, Botanical Street 1, 0105 Tbilisi, Georgia
- Department of Botany, State Museum for Natural History Karlsruhe, Erbprinzenstraße 13, 76133 Karlsruhe, Germany
| | - Shengxiang Yu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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Peng HW, Xiang KL, Erst AS, Erst TV, Jabbour F, Ortiz RDC, Wang W. The synergy of abiotic and biotic factors correlated with diversification of Fumarioideae (Papaveraceae) in the Cenozoic. Mol Phylogenet Evol 2023:107868. [PMID: 37394080 DOI: 10.1016/j.ympev.2023.107868] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/04/2023]
Abstract
Rapid diversification of a group is often associated with exploiting an ecological opportunity and/or the evolution of a key innovation. However, how the interplay of such abiotic and biotic factors correlates with organismal diversification has been rarely documented in empirical studies, especially for organisms inhabiting drylands. Fumarioideae is the largest subfamily in Papaveraceae and is mainly distributed in temperate regions of the Northern Hemisphere. Here, we used one nuclear (ITS) and six plastid (rbcL, atpB, matK, rps16, trnL-F, and trnG) DNA sequences to investigate the spatio-temporal patterns of diversification and potential related factors of this subfamily. We first present the most comprehensive phylogenetic analysis of Fumarioideae to date. The results of our integrated molecular dating and biogeographic analyses indicate that the most recent common ancestor of Fumarioideae started to diversify in Asia during the Upper Cretaceous, and then dispersed multiple times out of Asia in the Cenozoic. In particular, we discover two independent dispersal events from Eurasia to East Africa in the late Miocene, suggesting that the Arabian Peninsula might be an important exchange corridor between Eurasia and East Africa in the late Miocene. Within the Fumarioideae, increased speciation rates were detected in two groups, Corydalis and Fumariinae. Corydalis first experienced a burst of diversification in its crown group at ∼42 Ma, and further accelerated diversification from the mid-Miocene onwards. During these two periods, Corydalis had evolved diverse life history types, which could have facilitated the colonization of diverse habitats originating from extensive orogenesis in the Northern Hemisphere as well as Asian interior desertification. Fumariinae underwent a burst of diversification at ∼15 Ma, which temporally coincides with the increasing aridification in central Eurasia, but is markedly posterior to the shifts in habitat (from moist to arid) and in life history (from perennial to annual) and to range expansion from Asia to Europe, suggesting that Fumariinae species may have been pre-adapted to invade European arid habitats by the acquisition of annual life history. Our study provides an empirical case that documents the importance of pre-adaptation on organismal diversification in drylands and highlights the significant roles of the synergy of abiotic and biotic factors in promoting plant diversification.
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Affiliation(s)
- Huan-Wen Peng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Andrey S Erst
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Tatyana V Erst
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, 57 rue Cuvier, CP39, Paris 75005, France
| | - Rosa Del C Ortiz
- Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, MO 63110, USA
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Vieira Lima L, Salino A, Kessler M, Rouhan G, Testo WL, Suzart Argolo C, Consortium G, Elias Almeida T. Phylogenomic evolutionary insights in the fern family Gleicheniaceae. Mol Phylogenet Evol 2023; 184:107782. [PMID: 37044191 DOI: 10.1016/j.ympev.2023.107782] [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: 09/26/2022] [Revised: 03/16/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
The pantropical fern family Gleicheniaceae comprises approximately 157 species. Seven genera are currently recognized in the family, although their monophyly is still uncertain due to low sampling in phylogenetic studies. We examined the monophyly of the genera through extended sampling, using the first phylogenomic inference of the family including data from both nuclear and plastid genomes. Seventy-six samples were sequenced (70 Gleicheniaceae species and six outgroups) using high throughput sequencing, including all seven currently recognized genera. Plastid and nuclear data were recovered and assembled; the nuclear data was phased to reduce paralogy as well as hybrid noise in the final recovered topology. Maximum likelihood trees were built for each locus, and a concatenated dataset was built for both datasets. A species tree based on a multispecies coalescent model was generated, and divergence time analyses performed. We here present the first genomic phylogenetic inferences concerning Gleicheniaceae, confirming the monophyly of most genera except Sticherus, which we recovered as paraphyletic. Although most of the extant genera of Gleicheniaceae originated during the Mesozoic, several genera show Neogene and even Quaternary diversifications, and our results suggest that reticulation and polyploidy may have played significant roles during this diversification. However, some genera, such as Rouxopteris and Stromatopteris, appear to represent evolutionary relicts.
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Affiliation(s)
- Lucas Vieira Lima
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Botânica, Laboratório de Sistemática Vegetal, Belo Horizonte, Minas Gerais, Brazil.
| | - Alexandre Salino
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departamento de Botânica, Laboratório de Sistemática Vegetal, Belo Horizonte, Minas Gerais, Brazil.
| | - Michael Kessler
- Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.
| | - Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France.
| | - Weston L Testo
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL, USA.
| | - Caio Suzart Argolo
- Universidade Estadual de Santa Cruz, Departamento de Ciências Biológicas, Centro de Biotecnologia e Genética, Rodovia Ilhéus-Itabuna, km 16, Ilhéus-BA, Brasil.
| | - GoFlag Consortium
- GoFlag is an NSF-funded project (DEB 1541506) based at the University of Florida, Field Museum, and the University of Arizona. Project personnel include (at UF), J. Gordon Burleigh, Emily Sessa, Stuart McDaniel, Christine Davis, Pavlo Antonenko, Sarah Carey, Lorena Endara, Weston Testo; (at Field), Matt von Konrat, Eve Gaus; (at UA): Hong Cui
| | - Thaís Elias Almeida
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Botânica, Avenida Professor Morais Rego 1235, CEP 50.670-420, Recife, PE, Brazil.
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Diversity of the Pteridoflora of Montane Northwestern Mexico. DIVERSITY 2023. [DOI: 10.3390/d15030324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
This study compiles and updates the checklist of ferns and lycophytes from the Sierra Madre Occidental (SMOc). For this, we revised information on these taxa from regional floristic studies, databases, and herbaria. Our updated list includes 312 species, of which 276 are ferns and 36 are lycophytes integrated into 27 families and 75 genera. The richest families are Pteridaceae (118), Polypodiaceae (31), Selaginellaceae (30), Aspleniaceae (25), and Dryopteridaceae (25). The three most diverse genera were Selaginella (30), Asplenium (25), and Myriopteris (22). The species-rich Mexican states that include the SMOc are Durango (166 species), Chihuahua (149), and Jalisco (146). As in other tropical mountains, species richness in the SMOc is concentrated at the elevation interval of 1500 to 2000 m (236 species). The mid-mountain vegetation forests (Quercus and Pinus-Quercus forests) harbor the most pteridoflora richness (52% of the species). Four species of ferns are listed as threatened in the Mexican Official Norm NOM-059-SEMARNAT-2010, 17 species are listed in the IUCN, and only one tree ferns are in CITES. The SMOc has a Nearctic affinity, and its fern and lycophyte diversity are lower than in other Mexican Transition Zone mountain chains, such as the Sierra Madre del Sur, the Trans-Mexican Volcanic Belt, and the Sierra Madre Oriental. Notwithstanding, its biological composition is unique and distinctive. The species number reported in the SMOc represents 31% of the pteridoflora diversity recorded in Mexico.
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León B, Acuña-Tarazona M, Mellado F. Pteridofitas: helechos y licófitos de El mundo vegetal de los Andes peruanos en el contexto actual. REVISTA PERUANA DE BIOLOGÍA 2022. [DOI: 10.15381/rpb.v29i3.22890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Los helechos y licófitos mencionados en El mundo Vegetal de los Andes peruanos de Weberbauer brindan una breve información de su riqueza y sustento a las observaciones ambientales para cada categoría de su esquema fitogeográfico del Perú. Este estudio actualiza tanto el concepto y características de los pteridofitos mencionados en el capítulo Unidades Sistemáticas, como la nomenclatura de los 126 nombres de los taxones mencionados en la obra. Además, se ofrece una breve historia del estudio del grupo en el Perú, para proveer el contexto de la inclusión de estas plantas por Weberbauer. Y se mencionan las colecciones que Weberbauer realizara del grupo y, en particular, las citadas como ejemplos. Se ofrece un perfil de las tareas por realizar para completar la labor biogeográfica iniciada por Weberbauer.
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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: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [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 GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yu‐Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- College of PharmacyShaanxi University of Chinese MedicineXi'anChina
| | - Liscely Tumi
- Facultad de Ciencias BiológicasUniversidad Nacional Mayor de San MarcosLimaPeru
| | - Mery L. Suni
- Facultad de Ciencias BiológicasUniversidad Nacional Mayor de San MarcosLimaPeru
| | - Mónica Arakaki
- Facultad de Ciencias BiológicasUniversidad Nacional Mayor de San MarcosLimaPeru
| | - Kevin S. Burgess
- Department of Biology, Columbus State UniversityUniversity System of GeorgiaColumbusGeorgiaUSA
| | - Xue‐Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation Biology, Core Botanical GardensChinese Academy of SciencesGuangzhouChina
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Chen S, Wang T, Shu J, Xiang Q, Yang T, Zhang X, Yan Y. Plastid Phylogenomics and Plastomic Diversity of the Extant Lycophytes. Genes (Basel) 2022; 13:genes13071280. [PMID: 35886063 PMCID: PMC9316050 DOI: 10.3390/genes13071280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
Although extant lycophytes represent the most ancient surviving lineage of early vascular plants, their plastomic diversity has long been neglected. The ancient evolutionary history and distinct genetic diversity patterns of the three lycophyte families, each with its own characteristics, provide an ideal opportunity to investigate the interfamilial relationships of lycophytes and their associated patterns of evolution. To compensate for the lack of data on Lycopodiaceae, we sequenced and assembled 14 new plastid genomes (plastomes). Combined with other lycophyte plastomes available online, we reconstructed the phylogenetic relationships of the extant lycophytes based on 93 plastomes. We analyzed, traced, and compared the plastomic diversity and divergence of the three lycophyte families (Isoëtaceae, Lycopodiaceae, and Selaginellaceae) in terms of plastomic diversity by comparing their plastome sizes, GC contents, substitution rates, structural rearrangements, divergence times, ancestral states, RNA editings, and gene losses. Comparative analysis of plastid phylogenomics and plastomic diversity of three lycophyte families will set a foundation for further studies in biology and evolution in lycophytes and therefore in vascular plants.
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Affiliation(s)
- Sisi Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Jiangping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Qiaoping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
| | - Tuo Yang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
- Correspondence: (X.Z.); (Y.Y.)
| | - Yuehong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- Correspondence: (X.Z.); (Y.Y.)
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10
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Hay EM, McGee MD, Chown SL. Geographic range size and speciation in honeyeaters. BMC Ecol Evol 2022; 22:86. [PMID: 35768772 PMCID: PMC9245323 DOI: 10.1186/s12862-022-02041-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Darwin and others proposed that a species' geographic range size positively influences speciation likelihood, with the relationship potentially dependent on the mode of speciation and other contributing factors, including geographic setting and species traits. Several alternative proposals for the influence of range size on speciation rate have also been made (e.g. negative or a unimodal relationship with speciation). To examine Darwin's proposal, we use a range of phylogenetic comparative methods, focusing on a large Australasian bird clade, the honeyeaters (Aves: Meliphagidae). RESULTS We consider the influence of range size, shape, and position (latitudinal and longitudinal midpoints, island or continental species), and consider two traits known to influence range size: dispersal ability and body size. Applying several analytical approaches, including phylogenetic Bayesian path analysis, spatiophylogenetic models, and state-dependent speciation and extinction models, we find support for both the positive relationship between range size and speciation rate and the influence of mode of speciation. CONCLUSIONS Honeyeater speciation rate differs considerably between islands and the continental setting across the clade's distribution, with range size contributing positively in the continental setting, while dispersal ability influences speciation regardless of setting. These outcomes support Darwin's original proposal for a positive relationship between range size and speciation likelihood, while extending the evidence for the contribution of dispersal ability to speciation.
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Affiliation(s)
- Eleanor M Hay
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia.
| | - Matthew D McGee
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Melbourne, VIC, 3800, Australia
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11
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Bedoya AM, Leaché AD, Olmstead RG. Andean uplift, drainage basin formation, and the evolution of plants living in fast-flowing aquatic ecosystems in northern South America. THE NEW PHYTOLOGIST 2021; 232:2175-2190. [PMID: 34318482 DOI: 10.1111/nph.17649] [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: 06/21/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Northern South America is a geologically dynamic and species-rich region. Fossil and stratigraphic data show that mountain uplift in the tropical Andes reconfigured river drainages. These landscape changes shaped the evolution of the flora in the region, yet the impacts on aquatic taxa have been overlooked. We explore the role of landscape change on the evolution of plants living strictly in rivers across drainage basins in northern South America by conducting population structure, phylogenetic inference, and divergence-dating analyses for two species in the genus Marathrum (Podostemaceae). Mountain uplift and drainage basin formation isolated populations of M. utile and M. foeniculaceum in northern South America and created barriers to gene flow across river drainages. Sympatric species hybridize and the hybrids show the phenotype of one parental line. We propose that the pattern of divergence of populations reflects the formation of river drainages, which was not complete until < 4.1 million yr ago (Ma). Our study provides a clear picture of the role of landscape change on the evolution of plants living strictly in rivers in northern South America. By shifting the focus to aquatic taxa, we provide a novel perspective on the processes shaping the evolution of the Neotropical flora.
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Affiliation(s)
- Ana M Bedoya
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195, USA
| | - Adam D Leaché
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195, USA
| | - Richard G Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, 98195, USA
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12
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Zhang X, Landis JB, Sun Y, Zhang H, Lin N, Kuang T, Huang X, Deng T, Wang H, Sun H. Macroevolutionary pattern of Saussurea (Asteraceae) provides insights into the drivers of radiating diversification. Proc Biol Sci 2021; 288:20211575. [PMID: 34727720 DOI: 10.1098/rspb.2021.1575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Evolutionary radiations have intrigued biologists for more than a century, yet our understanding of the drivers of radiating diversification is still limited. We investigate the roles of environmental and species-intrinsic factors in driving the rapid radiation of Saussurea (Asteraceae) by deploying a number of palaeoenvironment-, diversity- and trait-dependent models, as well as ecological distribution data. We show that three main clades of Saussurea began to diversify in the Miocene almost simultaneously, with increasing diversification rates (DRs) negatively dependent on palaeotemperature but not dependent on species diversity. Our trait-dependent models detect some adaptive morphological innovations associated with DR shifts, while indicating additional unobserved traits are also likely driving diversification. Accounting for ecological niche data, we further reveal that accelerations in DRs are correlated with niche breadth and the size of species' range. Our results point out a macroevolutionary scenario where both adaptive morphological evolution and ecological opportunities provided by palaeoenvironmental fluctuations triggered an exceptionally radiating diversification. Our study highlights the importance of integrating phylogenomic, morphological, ecological and model-based approaches to illustrate evolutionary dynamics of lineages in biodiversity hotspots.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, Hubei, People's Republic of China.,Center of Conservation Biology, Chinese Academy of Sciences, Core Botanical Gardens, Wuhan 430074, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, Ithaca, NY 14850, USA.,BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, Hubei, People's Republic of China.,Center of Conservation Biology, Chinese Academy of Sciences, Core Botanical Gardens, Wuhan 430074, People's Republic of China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, Hubei, People's Republic of China.,Center of Conservation Biology, Chinese Academy of Sciences, Core Botanical Gardens, Wuhan 430074, People's Republic of China
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, Hubei, People's Republic of China.,Center of Conservation Biology, Chinese Academy of Sciences, Core Botanical Gardens, Wuhan 430074, People's Republic of China
| | - Tianhui Kuang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, People's Republic of China
| | - Xianhan Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, People's Republic of China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, People's Republic of China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan 430074, Hubei, People's Republic of China.,Center of Conservation Biology, Chinese Academy of Sciences, Core Botanical Gardens, Wuhan 430074, People's Republic of China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, People's Republic of China
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13
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Earth history events shaped the evolution of uneven biodiversity across tropical moist forests. Proc Natl Acad Sci U S A 2021; 118:2026347118. [PMID: 34599095 PMCID: PMC8501849 DOI: 10.1073/pnas.2026347118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 02/07/2023] Open
Abstract
Tropical moist forests harbor much of the world’s biodiversity, but this diversity is not evenly distributed globally, with tropical moist forests in the Neotropics and Indomalaya generally exhibiting much greater diversity than in the Afrotropics. Here, we assess the ubiquity of this “pantropical diversity disparity” (PDD) using the present-day distributions of over 150,000 species of plants and animals, and we compare these distributions with a spatial model of diversification combined with reconstructions of plate tectonics, temperature, and aridity. Our study demonstrates that differences in paleoenvironmental dynamics between continents, including mountain building, aridification, and global temperature fluxes, can explain the PDD by shaping spatial and temporal patterns of species origination and extinction, providing a close match to observed distributions of plants and animals. Far from a uniform band, the biodiversity found across Earth’s tropical moist forests varies widely between the high diversity of the Neotropics and Indomalaya and the relatively lower diversity of the Afrotropics. Explanations for this variation across different regions, the “pantropical diversity disparity” (PDD), remain contentious, due to difficulty teasing apart the effects of contemporary climate and paleoenvironmental history. Here, we assess the ubiquity of the PDD in over 150,000 species of terrestrial plants and vertebrates and investigate the relationship between the present-day climate and patterns of species richness. We then investigate the consequences of paleoenvironmental dynamics on the emergence of biodiversity gradients using a spatially explicit model of diversification coupled with paleoenvironmental and plate tectonic reconstructions. Contemporary climate is insufficient in explaining the PDD; instead, a simple model of diversification and temperature niche evolution coupled with paleoaridity constraints is successful in reproducing the variation in species richness and phylogenetic diversity seen repeatedly among plant and animal taxa, suggesting a prevalent role of paleoenvironmental dynamics in combination with niche conservatism. The model indicates that high biodiversity in Neotropical and Indomalayan moist forests is driven by complex macroevolutionary dynamics associated with mountain uplift. In contrast, lower diversity in Afrotropical forests is associated with lower speciation rates and higher extinction rates driven by sustained aridification over the Cenozoic. Our analyses provide a mechanistic understanding of the emergence of uneven diversity in tropical moist forests across 110 Ma of Earth’s history, highlighting the importance of deep-time paleoenvironmental legacies in determining biodiversity patterns.
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14
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Kong H, Condamine FL, Yang L, Harris AJ, Feng C, Wen F, Kang M. Phylogenomic and Macroevolutionary Evidence for an Explosive Radiation of a Plant Genus in the Miocene. Syst Biol 2021; 71:589-609. [PMID: 34396416 PMCID: PMC9016594 DOI: 10.1093/sysbio/syab068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/02/2022] Open
Abstract
Mountain systems harbor a substantial fraction of global biodiversity and, thus, provide excellent opportunities to study rapid diversification and to understand the historical processes underlying the assembly of biodiversity hotspots. The rich biodiversity in mountains is widely regarded as having arisen under the influence of geological and climatic processes as well as the complex interactions among them. However, the relative contribution of geology and climate in driving species radiation is seldom explored. Here, we studied the evolutionary radiation of Oreocharis (Gesneriaceae), which has diversified extensively throughout East Asia, especially within the Hengduan Mountains (HDM), using transcriptomic data and a time calibrated phylogeny for 88% (111/126) of all species of the genus. In particular, we applied phylogenetic reconstructions to evaluate the extent of incomplete lineage sorting accompanying the early and rapid radiation in the genus. We then fit macroevolutionary models to explore its spatial and diversification dynamics in Oreocharis and applied explicit birth–death models to investigate the effects of past environmental changes on its diversification. Evidence from 574 orthologous loci suggest that Oreocharis underwent an impressive early burst of speciation starting ca. 12 Ma in the Miocene, followed by a drastic decline in speciation toward the present. Although we found no evidence for a shift in diversification rate across the phylogeny of Oreocharis, we showed a difference in diversification dynamics between the HDM and non-HDM lineages, with higher diversification rates in the HDM. The diversification dynamic of Oreocharis is most likely positively associated with temperature-dependent speciation and dependency on the Asian monsoons. We suggest that the warm and humid climate of the mid-Miocene was probably the primary driver of the rapid diversification in Oreocharis, while mountain building of the HDM might have indirectly affected species diversification of the HDM lineage. This study highlights the importance of past climatic changes, combined with mountain building, in creating strong environmental heterogeneity and driving diversification of mountain plants, and suggests that the biodiversity in the HDM cannot directly be attributed to mountain uplift, contrary to many recent speculations.[East Asian monsoons; environmental heterogeneity; Hengduan Mountains; incomplete lineage sorting; Oreocharis; past climate change; rapid diversification; transcriptome.]
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Affiliation(s)
- Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095 Montpellier, France
| | - Lihua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China
| | - Fang Wen
- Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, 541006 Guilin, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, 510650 Guangzhou, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, 510650 Guangzhou, China
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15
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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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16
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Igea J, Tanentzap AJ. Global topographic uplift has elevated speciation in mammals and birds over the last 3 million years. Nat Ecol Evol 2021; 5:1530-1535. [PMID: 34475571 PMCID: PMC8560637 DOI: 10.1038/s41559-021-01545-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023]
Abstract
Topographic change shapes the evolution of biodiversity by influencing both habitat connectivity and habitat diversity as well as abiotic factors like climate. However, its role in creating global biodiversity gradients remains poorly characterized because geology, climate and evolutionary data have rarely been integrated across concordant timescales. Here we show that topographic uplift over the last 3 million years explains more spatial variation in the speciation of all mammals and birds than do the direct effects of palaeoclimate change and both present-day elevation and present-day temperature. By contrast, the effects of topographic changes are much smaller than those of present-day temperatures in eroded areas. Together, our results stress that historical geological processes rather than traditionally studied macroecological gradients may ultimately generate much of the world's biodiversity. More broadly, as the Earth's surface continues to rise and fall, topography will remain an important driver of evolutionary change and novelty.
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Affiliation(s)
- Javier Igea
- grid.5335.00000000121885934Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Andrew J. Tanentzap
- grid.5335.00000000121885934Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, UK
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17
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Hay EM, Poulin R, Jorge F. Macroevolutionary dynamics of parasite diversification: A reality check. J Evol Biol 2020; 33:1758-1769. [PMID: 33047407 DOI: 10.1111/jeb.13714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 12/21/2022]
Abstract
Parasitism is often invoked as a factor explaining the variation in diversification rates across the tree of life, while also representing up to half of Earth's diversity. Yet, patterns and processes of parasite diversification remain mostly unknown. In this study, we assess the patterns of parasite diversification and specifically determine the role of life-history traits (i.e. life cycle complexity and host range) and major coevolutionary events in driving diversification across eight phylogenetic datasets spanning taxonomically different parasite groups. Aware of the degree of incomplete sampling among all parasite phylogenies, we also tested the impact of sampling bias on estimates of diversification. We show that the patterns and rates of parasite diversification differ among taxa according to life cycle complexity and to some extent major host transitions. Only directly transmitted parasites were found to be influenced by an effect of major host transitions on diversification rates. Although parasitism may be a main factor responsible for heterogeneity in diversification among the tree of life, the high degree of incomplete parasite phylogenies remains an obstacle when modelling diversification dynamics. Nevertheless, we provide the first comparative test of parasite diversification, revealing some consistent patterns and insight into the processes that shape it.
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Affiliation(s)
- Eleanor M Hay
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Robert Poulin
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Fátima Jorge
- Department of Zoology, University of Otago, Dunedin, New Zealand
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18
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Patino LH, Muñoz M, Cruz-Saavedra L, Muskus C, Ramírez JD. Genomic Diversification, Structural Plasticity, and Hybridization in Leishmania (Viannia) braziliensis. Front Cell Infect Microbiol 2020; 10:582192. [PMID: 33178631 PMCID: PMC7596589 DOI: 10.3389/fcimb.2020.582192] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/28/2020] [Indexed: 01/12/2023] Open
Abstract
Leishmania (Viannia) braziliensis is an important Leishmania species circulating in several Central and South American countries. Among Leishmania species circulating in Brazil, Argentina and Colombia, L. braziliensis has the highest genomic variability. However, genomic variability at the whole genome level has been only studied in Brazilian and Peruvian isolates; to date, no Colombian isolates have been studied. Considering that in Colombia, L. braziliensis is a species with great clinical and therapeutic relevance, as well as the role of genetic variability in the epidemiology of leishmaniasis, we analyzed and evaluated intraspecific genomic variability of L. braziliensis from Colombian and Bolivian isolates and compared them with Brazilian isolates. Twenty-one genomes were analyzed, six from Colombian patients, one from a Bolivian patient, and 14 Brazilian isolates downloaded from public databases. The results obtained of Phylogenomic analysis showed the existence of four well-supported clades, which evidenced intraspecific variability. The whole-genome analysis revealed structural variations in the somy, mainly in the Brazilian genomes (clade 1 and clade 3), low copy number variations, and a moderate number of single-nucleotide polymorphisms (SNPs) in all genomes analyzed. Interestingly, the genomes belonging to clades 2 and 3 from Colombia and Brazil, respectively, were characterized by low heterozygosity (~90% of SNP loci were homozygous) and regions suggestive of loss of heterozygosity (LOH). Additionally, we observed the drastic whole genome loss of heterozygosity and possible hybridization events in one genome belonging to clade 4. Unique/shared SNPs between and within the four clades were identified, revealing the importance of some of them in biological processes of L. braziliensis. Our analyses demonstrate high genomic variability of L. braziliensis in different regions of South America, mainly in Colombia and suggest that this species exhibits striking genomic diversity and a capacity of genomic hybridization; additionally, this is the first study to report whole-genome sequences of Colombian L. braziliensis isolates.
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Affiliation(s)
- Luz H Patino
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Lissa Cruz-Saavedra
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Carlos Muskus
- Programa de Estudio y Control de Enfermedades Tropicales (PECET), Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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Yang J, Guo YF, Chen XD, Zhang X, Ju MM, Bai GQ, Liu ZL, Zhao GF. Framework Phylogeny, Evolution and Complex Diversification of Chinese Oaks. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1024. [PMID: 32823635 PMCID: PMC7464331 DOI: 10.3390/plants9081024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022]
Abstract
Oaks (Quercus L.) are ideal models to assess patterns of plant diversity. We integrated the sequence data of five chloroplast and two nuclear loci from 50 Chinese oaks to explore the phylogenetic framework, evolution and diversification patterns of the Chinese oak's lineage. The framework phylogeny strongly supports two subgenera Quercus and Cerris comprising four infrageneric sections Quercus, Cerris, Ilex and Cyclobalanopsis for the Chinese oaks. An evolutionary analysis suggests that the two subgenera probably split during the mid-Eocene, followed by intergroup divergence within the subgenus Cerris around the late Eocene. The initial diversification of sections in the subgenus Cerris was dated between the mid-Oligocene and the Oligocene-Miocene boundary, while a rapid species radiation in section Quercus started in the late Miocene. Diversification simulations indicate a potential evolutionary shift on section Quercus, while several phenotypic shifts likely occur among all sections. We found significant negative correlations between rates of the lineage diversification and phenotypic turnover, suggesting a complex interaction between the species evolution and morphological divergence in Chinese oaks. Our infrageneric phylogeny of Chinese oaks accords with the recently proposed classification of the genus Quercus. The results point to tectonic activity and climatic change during the Tertiary as possible drivers of evolution and diversification in the Chinese oak's lineage.
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Affiliation(s)
- Jia Yang
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Yu-Fan Guo
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Xiao-Dan Chen
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Xiao Zhang
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Miao-Miao Ju
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Guo-Qing Bai
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
- Institute of Botany of Shaanxi Province, Xi’an 710061, China
| | - Zhan-Lin Liu
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
| | - Gui-Fang Zhao
- College of Life Sciences, Northwest University, Xi’an 710069, China; (Y.-F.G.); (X.-D.C.); (X.Z.); (M.-M.J.); (G.-Q.B.); (Z.-L.L.)
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Chamberland L, Salgado-Roa FC, Basco A, Crastz-Flores A, Binford GJ, Agnarsson I. Phylogeography of the widespread Caribbean spiny orb weaver Gasteracantha cancriformis. PeerJ 2020; 8:e8976. [PMID: 32391201 PMCID: PMC7196328 DOI: 10.7717/peerj.8976] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/24/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Modern molecular analyses are often inconsistent with pre-cladistic taxonomic hypotheses, frequently indicating higher richness than morphological taxonomy estimates. Among Caribbean spiders, widespread species are relatively few compared to the prevalence of single island endemics. The taxonomic hypothesis Gasteracantha cancriformis circumscribes a species with profuse variation in size, color and body form. Distributed throughout the Neotropics, G. cancriformis is the only morphological species of Gasteracantha in the New World in this globally distributed genus. METHODS We inferred phylogenetic relationships across Neotropical populations of Gasteracantha using three target genes. Within the Caribbean, we estimated genetic diversity, population structure, and gene flow among island populations. RESULTS Our findings revealed a single widespread species of Gasteracantha throughout the Caribbean, G. cancriformis, while suggesting two recently divergent mainland populations that may represent separate species, diverging linages, or geographically isolated demes. The concatenated and COI (Cytochrome c oxidase subunit 1) phylogeny supported a Caribbean clade nested within the New World. Genetic variability was high between island populations for our COI dataset; however, gene flow was also high, especially between large, adjacent islands. We found structured genetic and morphological variation within G. cancriformis island populations; however, this variation does not reflect genealogical relationships. Rather, isolation by distance and local morphological adaptation may explain the observed variation.
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Affiliation(s)
- Lisa Chamberland
- Department of Biology, University of Vermont, Burlington, VT, USA
| | - Fabian C. Salgado-Roa
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogota, Colombia
| | - Alma Basco
- University of Puerto Rico at Rio Piedras, San Juan, Puerto Rico
| | | | | | - Ingi Agnarsson
- Department of Biology, University of Vermont, Burlington, VT, USA
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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Pérez-Escobar OA, Lucas E, Jaramillo C, Monro A, Morris SK, Bogarín D, Greer D, Dodsworth S, Aguilar-Cano J, Sanchez Meseguer A, Antonelli A. The Origin and Diversification of the Hyperdiverse Flora in the Chocó Biogeographic Region. FRONTIERS IN PLANT SCIENCE 2019; 10:1328. [PMID: 31867022 PMCID: PMC6910151 DOI: 10.3389/fpls.2019.01328] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Extremely high levels of plant diversity in the American tropics are derived from multiple interactions between biotic and abiotic factors. Previous studies have focused on macro-evolutionary dynamics of the Tropical Andes, Amazonia, and Brazil's Cerrado and Atlantic forests during the last decade. Yet, other equally important Neotropical biodiversity hotspots have been severely neglected. This is particularly true for the Chocó region on the north-western coast of South and Central America. This geologically complex region is Earth's ninth most biodiverse hotspot, hosting approximately 3% of all known plant species. Here, we test Gentry's [1982a,b] hypothesis of a northern Andean-Central American Pleistocene origin of the Chocoan flora using phylogenetic reconstructions of representative plant lineages in the American tropics. We show that plant diversity in the Chocó is derived mostly from Andean immigrants. Contributions from more distant biogeographical areas also exist but are fewer. We also identify a strong floristic connection between the Chocó and Central America, revealed by multiple migrations into the Chocó during the last 5 Ma. The dated phylogenetic reconstructions suggest a Plio-Pleistocene onset of the extant Chocó flora. Taken together, these results support to a limited extend Gentry's hypothesis of a Pleistocene origin and of a compound assembly of the Chocoan biodiversity hotspot. Strong Central American-Chocoan floristic affinity may be partly explained by the accretion of a land mass derived from the Caribbean plate to north-western South America. Additional densely sampled phylogenies of Chocoan lineages also well represented across the Neotropics could enlighten the role of land mass movements through time in the assembly of floras in Neotropical biodiversity hotspots.
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Affiliation(s)
- Oscar Alejandro Pérez-Escobar
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Eve Lucas
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Panama, Panama
- ISEM, U. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Alexandre Monro
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Sarah K. Morris
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Diego Bogarín
- Universidad de Costa Rica, Jardín Botánico Lankester, Cartago, Costa Rica
| | - Deborah Greer
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Department of Environment, Food and Rural Affairs, London, United Kingdom
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
| | | | | | - Alexandre Antonelli
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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Muchhala N. Quantum dots shed light on angiosperm speciation. THE NEW PHYTOLOGIST 2019; 224:1005-1008. [PMID: 31631364 DOI: 10.1111/nph.16211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Nathan Muchhala
- Biology Department, University of Missouri - St Louis, One University Boulevard, 223 Research Hall, St Louis, MO, 63121, USA
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23
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Lagomarsino LP. Rapid plant diversification in the Andes does not require flowers. THE NEW PHYTOLOGIST 2019; 222:11-13. [PMID: 30815947 DOI: 10.1111/nph.15619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Laura P Lagomarsino
- Shirley C. Tucker Herbarium, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
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