1
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Zhou N, Miao K, Liu C, Jia L, Hu J, Huang Y, Ji Y. Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics. PLANT DIVERSITY 2024; 46:219-228. [PMID: 38807906 PMCID: PMC11128834 DOI: 10.1016/j.pld.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/22/2023] [Accepted: 07/30/2023] [Indexed: 05/30/2024]
Abstract
Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.
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Affiliation(s)
- Nian Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ke Miao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changkun Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China
| | - Linbo Jia
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jinjin Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yongjiang Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Population, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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2
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Wu TR, Xu J, An MT, Yu JH, Liu F, Chen ZR. Hypericumliboense (Hypericaceae), a new species from Guizhou, China. PHYTOKEYS 2024; 237:37-49. [PMID: 38250524 PMCID: PMC10799301 DOI: 10.3897/phytokeys.237.110482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024]
Abstract
Hypericumliboense M.T.An & T.R.Wu, sp. nov. (Hypericaceae) is a newly described species found in the Maolan National Nature Reserve of Guizhou Province, where it grows in rocky habitats without soil on karst mountain tops. In this study, key morphological characters were compared between the new species and the other known Hypericum species of Hypericaceae. DNA sequences were extracted from the leaves of the new species, with nuclear gene sequences (ITS) generated to reconstruct phylogenetic trees and describe its phylogenetic position in relation to other species of Hypericum. Our results show that the proposed new species has the typical characteristics of the genus Hypericum in morphology being similar to Hypericummonogynum, but differing in its sessile and semi-clasped leaves, long elliptical to long circular leaf blades, thickly papery to thinly leathery, with entire and wavy leaf margins. The abaxial side of the leaves is covered with white powder, giving them a grey-white appearance. The main lateral veins of the leaves are 8-15-paired, and the midvein on both sides is convex. The main lateral veins and midvein branch are conspicuous, with tertiary venation forming a network on the leaf surface and appearing prominently sunken. The inflorescences are 1-3-flowered, with a large calyx and conspicuous veins. The molecular phylogenetic analysis (PP = 1.00) provided substantial evidence for the proposition of H.liboense as a new species within Hypericum. Morphological and molecular evidence is presented, corroborating the proposition of the new species, including a comprehensive account of the distinctive morphological attributes of H.liboense, along with its key distinguishing features from similar species.
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Affiliation(s)
- Tian-Rou Wu
- College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
| | - Jian Xu
- Guizhou Botanical Garden, Guiyang, 550000, Guizhou, China
| | - Ming-Tai An
- College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
| | - Jiang-Hong Yu
- College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
| | - Feng Liu
- College of Forestry, Guizhou University, Guiyang 550025, Guizhou, China
| | - Zheng-Ren Chen
- College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou, China
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3
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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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4
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Wu X, Wang M, Li X, Yan Y, Dai M, Xie W, Zhou X, Zhang D, Wen Y. Response of distribution patterns of two closely related species in Taxus genus to climate change since last inter-glacial. Ecol Evol 2022; 12:e9302. [PMID: 36177121 PMCID: PMC9475124 DOI: 10.1002/ece3.9302] [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: 01/19/2022] [Revised: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 02/02/2023] Open
Abstract
Climate change affects the species spatio-temporal distribution deeply. However, how climate affects the spatio-temporal distribution pattern of related species on the large scale remains largely unclear. Here, we selected two closely related species in Taxus genus Taxus chinensis and Taxus mairei to explore their distribution pattern. Four environmental variables were employed to simulate the distribution patterns using the optimized Maxent model. The results showed that the highly suitable area of T. chinensis and T. mairei in current period was 1.616 × 105 km2 and 3.093 × 105 km2, respectively. The distribution area of T. chinensis was smaller than that of T. mairei in different periods. Comparison of different periods shown that the distribution area of the two species was almost in stasis from LIG to the future periods. Temperature and precipitation were the main climate factors that determined the potential distribution of the two species. The centroids of T. chinensis and T. mairei were in Sichuan and Hunan provinces in current period, respectively. In the future, the centroid migration direction of the two species would shift towards northeast. Our results revealed that the average elevation distribution of T. chinensis was higher than that of T. mairei. This study sheds new insights into the habitat preference and limiting environment factors of the two related species and provides a valuable reference for the conservation of these two threatened species.
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Affiliation(s)
- Xingtong Wu
- Central South University of Forestry and Technology Hunan China
| | - Minqiu Wang
- Central South University of Forestry and Technology Hunan China
| | - Xinyu Li
- Central South University of Forestry and Technology Hunan China
| | - Yadan Yan
- Central South University of Forestry and Technology Hunan China
| | - Minjun Dai
- Central South University of Forestry and Technology Hunan China.,University of Georgia Athens Georgia USA
| | - Wanyu Xie
- Central South University of Forestry and Technology Hunan China
| | - Xiaofen Zhou
- Central South University of Forestry and Technology Hunan China
| | | | - Yafeng Wen
- Central South University of Forestry and Technology Hunan China
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5
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Global variation in diversification rate and species richness are unlinked in plants. Proc Natl Acad Sci U S A 2022; 119:e2120662119. [PMID: 35767644 PMCID: PMC9271200 DOI: 10.1073/pnas.2120662119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world's most important engineers of terrestrial ecosystems, we investigated the role of diversification rate as a link between the environment and global species richness patterns. Applying structural equation modeling to a comprehensive distribution dataset and phylogenetic tree covering all circa 332,000 seed plant species and 99.9% of the world's terrestrial surface (excluding Antarctica), we test five broad hypotheses postulating that diversification serves as a mechanistic link between species richness and climate, climatic stability, seasonality, environmental heterogeneity, or the distribution of biomes. Our results show that the global patterns of species richness and diversification rate are entirely independent. Diversification rates were not highest in warm and wet climates, running counter to the Metabolic Theory of Ecology, one of the dominant explanations for global gradients in species richness. Instead, diversification rates were highest in edaphically diverse, dry areas that have experienced climate change during the Neogene. Meanwhile, we confirmed climate and environmental heterogeneity as the main drivers of species richness, but these effects did not involve diversification rates as a mechanistic link, calling for alternative explanations. We conclude that high species richness is likely driven by the antiquity of wet tropical areas (supporting the "tropical conservatism hypothesis") or the high ecological carrying capacity of warm, wet, and/or environmentally heterogeneous environments.
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6
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Hsieh CL, Yu CC, Huang YL, Chung KF. Mahonia vs. Berberis Unloaded: Generic Delimitation and Infrafamilial Classification of Berberidaceae Based on Plastid Phylogenomics. FRONTIERS IN PLANT SCIENCE 2022; 12:720171. [PMID: 35069611 PMCID: PMC8770955 DOI: 10.3389/fpls.2021.720171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/15/2021] [Indexed: 05/12/2023]
Abstract
The early-diverging eudicot family Berberidaceae is composed of a morphologically diverse assemblage of disjunctly distributed genera long praised for their great horticultural and medicinal values. However, despite century-long studies, generic delimitation of Berberidaceae remains controversial and its tribal classification has never been formally proposed under a rigorous phylogenetic context. Currently, the number of accepted genera in Berberidaceae ranges consecutively from 13 to 19, depending on whether to define Berberis, Jeffersonia, and Podophyllum broadly, or to segregate these three genera further and recognize Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Dysosma, Diphylleia, and Sinopodophyllum, respectively. To resolve Berberidaceae's taxonomic disputes, we newly assembled 23 plastomes and, together with 85 plastomes from the GenBank, completed the generic sampling of the family. With 4 problematic and 14 redundant plastome sequences excluded, robust phylogenomic relationships were reconstructed based on 93 plastomes representing all 19 genera of Berberidaceae and three outgroups. Maximum likelihood phylogenomic relationships corroborated with divergence time estimation support the recognition of three subfamilies Berberidoideae, Nandinoideae, and Podophylloideae, with tribes Berberideae and Ranzanieae, Leonticeae and Nandineae, and Podophylleae, Achlydeae, Bongardieae tr. nov., Epimedieae, and Jeffersonieae tr. nov. in the former three subfamilies, respectively. By applying specifically stated criteria, our phylogenomic data also support the classification of 19 genera, recognizing Alloberberis, Mahonia, and Moranothamnus, Plagiorhegma, and Diphylleia, Dysosma, and Sinopodophyllum that are morphologically and evolutionarily distinct from Berberis, Jeffersonia, and Podophyllum, respectively. Comparison of plastome structures across Berberidaceae confirms inverted repeat expansion in the tribe Berberideae and reveals substantial length variation in accD gene caused by repeated sequences in Berberidoideae. Comparison of plastome tree with previous studies and nuclear ribosomal DNA (nrDNA) phylogeny also reveals considerable conflicts at different phylogenetic levels, suggesting that incomplete lineage sorting and/or hybridization had occurred throughout the evolutionary history of Berberidaceae and that Alloberberis and Moranothamnus could have resulted from reciprocal hybridization between Berberis and Mahonia in ancient times prior to the radiations of the latter two genera.
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Affiliation(s)
- Chia-Lun Hsieh
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Chieh Yu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Yu-Lan Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuo-Fang Chung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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7
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Bitencourt C, Nürk NM, Rapini A, Fishbein M, Simões AO, Middleton DJ, Meve U, Endress ME, Liede-Schumann S. Evolution of Dispersal, Habit, and Pollination in Africa Pushed Apocynaceae Diversification After the Eocene-Oligocene Climate Transition. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.719741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Apocynaceae (the dogbane and milkweed family) is one of the ten largest flowering plant families, with approximately 5,350 species and diverse morphology and ecology, ranging from large trees and lianas that are emblematic of tropical rainforests, to herbs in temperate grasslands, to succulents in dry, open landscapes, and to vines in a wide variety of habitats. Despite a specialized and conservative basic floral architecture, Apocynaceae are hyperdiverse in flower size, corolla shape, and especially derived floral morphological features. These are mainly associated with the development of corolline and/or staminal coronas and a spectrum of integration of floral structures culminating with the formation of a gynostegium and pollinaria—specialized pollen dispersal units. To date, no detailed analysis has been conducted to estimate the origin and diversification of this lineage in space and time. Here, we use the most comprehensive time-calibrated phylogeny of Apocynaceae, which includes approximately 20% of the species covering all major lineages, and information on species number and distributions obtained from the most up-to-date monograph of the family to investigate the biogeographical history of the lineage and its diversification dynamics. South America, Africa, and Southeast Asia (potentially including Oceania), were recovered as the most likely ancestral area of extant Apocynaceae diversity; this tropical climatic belt in the equatorial region retained the oldest extant lineages and these three tropical regions likely represent museums of the family. Africa was confirmed as the cradle of pollinia-bearing lineages and the main source of Apocynaceae intercontinental dispersals. We detected 12 shifts toward accelerated species diversification, of which 11 were in the APSA clade (apocynoids, Periplocoideae, Secamonoideae, and Asclepiadoideae), eight of these in the pollinia-bearing lineages and six within Asclepiadoideae. Wind-dispersed comose seeds, climbing growth form, and pollinia appeared sequentially within the APSA clade and probably work synergistically in the occupation of drier and cooler habitats. Overall, we hypothesize that temporal patterns in diversification of Apocynaceae was mainly shaped by a sequence of morphological innovations that conferred higher capacity to disperse and establish in seasonal, unstable, and open habitats, which have expanded since the Eocene-Oligocene climate transition.
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8
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Eyres A, Eronen JT, Hagen O, Böhning-Gaese K, Fritz SA. Climatic effects on niche evolution in a passerine bird clade depend on paleoclimate reconstruction method. Evolution 2021; 75:1046-1060. [PMID: 33724456 DOI: 10.1111/evo.14209] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/29/2021] [Accepted: 02/12/2021] [Indexed: 01/08/2023]
Abstract
Climatic niches describe the climatic conditions in which species can persist. Shifts in climatic niches have been observed to coincide with major climatic change, suggesting that species adapt to new conditions. We test the relationship between rates of climatic niche evolution and paleoclimatic conditions through time for 65 Old-World flycatcher species (Aves: Muscicapidae). We combine niche quantification for all species with dated phylogenies to infer past changes in the rates of niche evolution for temperature and precipitation niches. Paleoclimatic conditions were inferred independently using two datasets: a paleoelevation reconstruction and the mammal fossil record. We find changes in climatic niches through time, but no or weak support for a relationship between niche evolution rates and rates of paleoclimatic change for both temperature and precipitation niche and for both reconstruction methods. In contrast, the inferred relationship between climatic conditions and niche evolution rates depends on paleoclimatic reconstruction method: rates of temperature niche evolution are significantly negatively related to absolute temperatures inferred using the paleoelevation model but not those reconstructed from the fossil record. We suggest that paleoclimatic change might be a weak driver of climatic niche evolution in birds and highlight the need for greater integration of different paleoclimate reconstructions.
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Affiliation(s)
- Alison Eyres
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, 60325, Germany.,Department of Biological Sciences, Goethe University Frankfurt, Frankfurt, 60438, Germany.,RSPB Centre for Conservation Science, Cambridge, CB2 3QZ, United Kingdom
| | - Jussi T Eronen
- Ecosystems and Environment Research Program and Helsinki Institute of Sustainability Science (HELSUS), Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,BIOS Research Unit, Helsinki, 00170, Finland
| | - Oskar Hagen
- Landscape Ecology, Institute of Terrestrial Ecosystems, D-USYS, ETH Zürich, Zürich, CH-8092, Switzerland.,Swiss Federal Research Institute WSL, Birmensdorf, CH-8903, Switzerland
| | - Katrin Böhning-Gaese
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, 60325, Germany.,Department of Biological Sciences, Goethe University Frankfurt, Frankfurt, 60438, Germany
| | - Susanne A Fritz
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, 60325, Germany.,Department of Biological Sciences, Goethe University Frankfurt, Frankfurt, 60438, Germany.,Institut für Geowissenschaften, Goethe University Frankfurt, Frankfurt, 60438, Germany
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9
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Ecological and spatial patterns associated with diversification of South American Physaria (Brassicaceae) through the general concept of species. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00486-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Villastrigo A, Abellán P, Ribera I. Habitat preference and diversification rates in a speciose lineage of diving beetles. Mol Phylogenet Evol 2021; 159:107087. [PMID: 33545273 DOI: 10.1016/j.ympev.2021.107087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/24/2022]
Abstract
The long-term geological stability of aquatic habitats has been demonstrated to be a determinant in the evolution of macroinvertebrate fauna, with species in running (lotic) waters having lower dispersal abilities, smaller ranges and higher gene flow between populations than species in standing (lentic) environments. Lotic species have been hypothesized to be more specialised, but the diversification dynamics of both habitat types have not been studied in detail. Using a speciose lineage of water beetles we test here whether diversification rates are related to the habitat preference of the species and its consequences on turnover, which we expect to be higher for lotic taxa. Moreover, we tested whether life in lotic environments is acting as an evolutionary dead-end as it is considered an ecological specialisation. We built a comprehensive molecular phylogeny with 473 terminals representing 421 of the 689 known species of the tribe Hydroporini (Coleoptera, Dytiscidae), using a combination of sequences from four mitochondrial and two nuclear genes plus 69 mitogenomes obtained with NGS. We found a general pattern of gradual acceleration of diversification rate with time, with 2-3 significant diversification shifts. However, habitat is not the main factor driving diversification in Hydroporini based on SecSSE analyses. The most recent common ancestor of Hydroporini was reconstructed as a lotic species, with multiple shifts to lentic environments. Most frequent transitions were estimated from lentic and lotic habitats to the category "both", followed by transitions from lotic to lentic and lentic to lotic respectively, although with very similar rates. Contrary to expectations, we found little evidence for differences in diversification dynamics between habitats, with lotic environments clearly not acting as evolutionary dead-ends in Hydroporini.
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Affiliation(s)
- Adrián Villastrigo
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| | | | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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11
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Jenfaoui H, Uras ME, Bahri BA, Ozyigit II, Souissi T. Morphological variation, genetic diversity and phylogenetic relationships of Hypericum triquetrifolium Turra populations from Tunisia. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1977180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Houda Jenfaoui
- Department of Plant Health and Environment, National Agronomic Institute of Tunisia, University of Carthage, Tunis, Tunisia
- Department of Plant Health and Environment, Laboratory of Bioagressor and Integrated Management in Agriculture (LR14AGR02), National Agronomic Institute of Tunisia, University of Carthage, Tunis, Tunisia
| | - Mehmet Emin Uras
- Faculty of Arts & Science, Department of Biology, Marmara University, Istanbul, Turkey
| | - Bochra Amina Bahri
- Department of Plant Health and Environment, Laboratory of Bioagressor and Integrated Management in Agriculture (LR14AGR02), National Agronomic Institute of Tunisia, University of Carthage, Tunis, Tunisia
- Institute of Plant Breeding, Genetics and Genomics and Department of Plant Pathology, University of Georgia, Griffin, Georgia, USA; eFaculty of Science, Department of Biology, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Ibrahim Ilker Ozyigit
- Faculty of Arts & Science, Department of Biology, Marmara University, Istanbul, Turkey
- Faculty of Science, Department of Biology, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Thouraya Souissi
- Department of Plant Health and Environment, National Agronomic Institute of Tunisia, University of Carthage, Tunis, Tunisia
- Department of Plant Health and Environment, Laboratory of Bioagressor and Integrated Management in Agriculture (LR14AGR02), National Agronomic Institute of Tunisia, University of Carthage, Tunis, Tunisia
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12
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Folk RA, Siniscalchi CM, Soltis DE. Angiosperms at the edge: Extremity, diversity, and phylogeny. PLANT, CELL & ENVIRONMENT 2020; 43:2871-2893. [PMID: 32926444 DOI: 10.1111/pce.13887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/21/2020] [Accepted: 08/13/2020] [Indexed: 05/26/2023]
Abstract
A hallmark of flowering plants is their ability to invade some of the most extreme and dynamic habitats, including cold and dry biomes, to a far greater extent than other land plants. Recent work has provided insight to the phylogenetic distribution and evolutionary mechanisms which have enabled this success, yet needed is a synthesis of evolutionary perspectives with plant physiological traits, morphology, and genomic diversity. Linking these disparate components will not only lead to better understand the evolutionary parallelism and diversification of plants with these two strategies, but also to provide the framework needed for directing future research. We summarize the primary physiological and structural traits involved in response to cold- and drought stress, outline the phylogenetic distribution of these adaptations, and describe the recurring association of these changes with rapid diversification events that occurred in multiple lineages over the past 15 million years. Across these threefold facets of dry-cold correlation (traits, phylogeny, and time) we stress the contrast between (a) the amazing diversity of solutions flowering plants have developed in the face of extreme environments and (b) a broad correlation between cold and dry adaptations that in some cases may hint at deep common origins.
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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13
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Sun M, Folk RA, Gitzendanner MA, Soltis PS, Chen Z, Soltis DE, Guralnick RP. Recent accelerated diversification in rosids occurred outside the tropics. Nat Commun 2020; 11:3333. [PMID: 32620894 PMCID: PMC7335165 DOI: 10.1038/s41467-020-17116-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/05/2020] [Indexed: 01/28/2023] Open
Abstract
Conflicting relationships have been found between diversification rate and temperature across disparate clades of life. Here, we use a supermatrix comprising nearly 20,000 species of rosids-a clade of ~25% of all angiosperm species-to understand global patterns of diversification and its climatic association. Our approach incorporates historical global temperature, assessment of species' temperature niche, and two broad-scale characterizations of tropical versus non-tropical niche occupancy. We find the diversification rates of most subclades dramatically increased over the last 15 million years (Myr) during cooling associated with global expansion of temperate habitats. Climatic niche is negatively associated with diversification rates, with tropical rosids forming older communities and experiencing speciation rates ~2-fold below rosids in cooler climates. Our results suggest long-term cooling had a disproportionate effect on non-tropical diversification rates, leading to dynamic young communities outside of the tropics, while relative stability in tropical climes led to older, slower-evolving but still species-rich communities.
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Affiliation(s)
- Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. .,Department of Bioscience, Aarhus University, Aarhus, 8000C, Denmark. .,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA.
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32608, USA
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA.,Department of Biology, University of Florida, Gainesville, FL, 32611, USA.,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.,Genetics Institute, University of Florida, Gainesville, FL, 32608, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA. .,Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA.
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14
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Liede-Schumann S, Grimm GW, Nürk NM, Potts AJ, Meve U, Hartmann HE. Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae). PeerJ 2020; 8:e8999. [PMID: 32426182 PMCID: PMC7213013 DOI: 10.7717/peerj.8999] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/26/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Drosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum, together with the highly succulent and species-rich tribe Ruschieae, constitute the 'core ruschioids' in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution. METHODS Using chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence dataset comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole. RESULTS Phylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.
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Affiliation(s)
| | | | - Nicolai M. Nürk
- Department of Plant Systematics, University of Bayreuth, Bayreuth, Germany
| | - Alastair J. Potts
- African Centre for Coastal Palaeoscience, Nelson Mandela University, Port Elizabeth, Eastern Cape, South Africa
| | - Ulrich Meve
- Department of Plant Systematics, University of Bayreuth, Bayreuth, Germany
| | - Heidrun E.K. Hartmann
- Department of Systematics and Evolution of Plants, University of Hamburg, Hamburg, Germany
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15
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Pirie MD, Kandziora M, Nürk NM, Le Maitre NC, Mugrabi de Kuppler A, Gehrke B, Oliver EGH, Bellstedt DU. Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica. BMC Evol Biol 2019; 19:222. [PMID: 31805850 PMCID: PMC6896773 DOI: 10.1186/s12862-019-1545-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 11/21/2019] [Indexed: 12/28/2022] Open
Abstract
Background The coincidence of long distance dispersal (LDD) and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica (Ericaceae) across the Afrotemperate. We quantify similarity of Erica climate niches per biogeographic area using direct observations of species, and test various colonisation scenarios while estimating ancestral areas for the Erica clade using parametric biogeographic model testing. Results We infer that the overall dispersal history of Erica across the Afrotemperate is the result of infrequent colonisation limited by geographic proximity and niche similarity. However, the Drakensberg Mountains represent a colonisation sink, rather than acting as a “stepping stone” between more distant and ecologically dissimilar Cape and Tropical African regions. Strikingly, the most dramatic examples of species radiations in Erica were the result of single unique dispersals over longer distances between ecologically dissimilar areas, contradicting the rule of phylogenetic biome conservatism. Conclusions These results highlight the roles of geographical and ecological distance in limiting LDD, but also the importance of rare biome shifts, in which a unique dispersal event fuels evolutionary radiation.
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Affiliation(s)
- Michael D Pirie
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany. .,Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa. .,Current address: University Museum, The University of Bergen, Postboks 7800, N-5020, Bergen, Norway.
| | - Martha Kandziora
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany.,Life and Environmental Sciences, School of Natural Sciences, University of California, Merced, USA
| | - Nicolai M Nürk
- Department of Plant Systematics, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, Germany
| | - Nicholas C Le Maitre
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.,Department of Plant Science, University of the Free State, QwaQwa, Bloemfontein, South Africa
| | - Ana Mugrabi de Kuppler
- INRES Pflanzenzüchtung, Rheinische Friedrich-Wilhelms-Universität Bonn, Katzenburgweg 5, 53115, Bonn, Germany
| | - Berit Gehrke
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany.,Current address: University Museum, The University of Bergen, Postboks 7800, N-5020, Bergen, Norway
| | - Edward G H Oliver
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
| | - Dirk U Bellstedt
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa
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16
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Arnal P, Coeur d'acier A, Favret C, Godefroid M, Qiao G, Jousselin E, Sanchez Meseguer A. The evolution of climate tolerance in conifer-feeding aphids in relation to their host's climatic niche. Ecol Evol 2019; 9:11657-11671. [PMID: 31695876 PMCID: PMC6822038 DOI: 10.1002/ece3.5652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/15/2019] [Accepted: 07/28/2019] [Indexed: 01/09/2023] Open
Abstract
Climate adaptation has major consequences in the evolution and ecology of all living organisms. Though phytophagous insects are an important component of Earth's biodiversity, there are few studies investigating the evolution of their climatic preferences. This lack of research is probably because their evolutionary ecology is thought to be primarily driven by their interactions with their host plants. Here, we use a robust phylogenetic framework and species-level distribution data for the conifer-feeding aphid genus Cinara to investigate the role of climatic adaptation in the diversity and distribution patterns of these host-specialized insects. Insect climate niches were reconstructed at a macroevolutionary scale, highlighting that climate niche tolerance is evolutionarily labile, with closely related species exhibiting strong climatic disparities. This result may suggest repeated climate niche differentiation during the evolutionary diversification of Cinara. Alternatively, it may merely reflect the use of host plants that occur in disparate climatic zones, and thus, in reality the aphid species' fundamental climate niches may actually be similar but broad. Comparisons of the aphids' current climate niches with those of their hosts show that most Cinara species occupy the full range of the climatic tolerance exhibited by their set of host plants, corroborating the hypothesis that the observed disparity in Cinara species' climate niches can simply mirror that of their hosts. However, 29% of the studied species only occupy a subset of their hosts' climatic zone, suggesting that some aphid species do indeed have their own climatic limitations. Our results suggest that in host-specialized phytophagous insects, host associations cannot always adequately describe insect niches and abiotic factors must be taken into account.
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Affiliation(s)
- Pierre Arnal
- CBGPINRACIRADIRDMontpellier SupAgroUniv MontpellierMontpellierFrance
- Institut Systématique Evolution Biodiversité (ISYEB)Muséum national d'Histoire naturelleCNRSEPHESorbonne UniversitéParisFrance
| | | | - Colin Favret
- Department of Biological SciencesBiodiversity CentreUniversity of MontrealMontrealQCCanada
| | - Martin Godefroid
- CBGPINRACIRADIRDMontpellier SupAgroUniv MontpellierMontpellierFrance
| | - Ge‐Xia Qiao
- Key Laboratory of Zoological Systematics and EvolutionInstitute of ZoologyChinese Academy of SciencesBeijingChina
| | | | - Andrea Sanchez Meseguer
- CBGPINRACIRADIRDMontpellier SupAgroUniv MontpellierMontpellierFrance
- CNRSUMR 5554 Institut des Sciences de l'Evolution (ISEM)Univ MontpellierMontpellierFrance
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17
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Marin J, Hedges SB. Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life. Mol Biol Evol 2019; 35:2077-2084. [PMID: 29846659 DOI: 10.1093/molbev/msy103] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Genomic data drive evolutionary research on the relationships and timescale of life but the genomes of most species remain poorly sampled. Phylogenetic trees can be reconstructed reliably using small data sets and the same has been assumed for the estimation of divergence time with molecular clocks. However, we show here that undersampling of molecular data results in a bias expressed as disproportionately shorter branch lengths and underestimated divergence times in the youngest nodes and branches, termed the small sample artifact. In turn, this leads to increasing speciation and diversification rates towards the present. Any evolutionary analyses derived from these biased branch lengths and speciation rates will be similarly biased. The widely used timetrees of the major species-rich studies of amphibians, birds, mammals, and squamate reptiles are all data-poor and show upswings in diversification rate, suggesting that their results were biased by undersampling. Our results show that greater sampling of genomes is needed for accurate time and rate estimation, which are basic data used in ecological and evolutionary research.
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Affiliation(s)
- Julie Marin
- Center for Biodiversity, 502 SERC Building, Temple University, Philadelphia, PA
- Institut de Systématique, Evolution, Biodiversité UMR 7205, Département Systématique et Evolution, Muséum national d'Histoire naturelle, Sorbonne-Universités, Paris Cedex 05 75231, France
| | - S Blair Hedges
- Center for Biodiversity, 502 SERC Building, Temple University, Philadelphia, PA
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18
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Rates of niche and phenotype evolution lag behind diversification in a temperate radiation. Proc Natl Acad Sci U S A 2019; 116:10874-10882. [PMID: 31085636 PMCID: PMC6561174 DOI: 10.1073/pnas.1817999116] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Alternative models of evolutionary processes suggest different associations between species diversification and trait evolution, but limited empirical evidence is available to test these models across large clades at global extents. Here we investigate the relative timing of species diversification and niche and phenotypic evolution across a global plant radiation (Saxifragales) with enormous phenotypic and habitat variation. We demonstrate strong temporal lags among rates, with increased diversification occurring first, followed by niche and phenotype. Accelerated diversification rates are coincident with mid-Miocene expansion of temperate biomes. Later increases in niche and phenotypic evolutionary rates argue against density-dependent diversification alone, indicating a major role for ecological opportunity. These results have broad implications for understanding diversification processes and the origin of present-day temperate biotas. Environmental change can create opportunities for increased rates of lineage diversification, but continued species accumulation has been hypothesized to lead to slowdowns via competitive exclusion and niche partitioning. Such density-dependent models imply tight linkages between diversification and trait evolution, but there are plausible alternative models. Little is known about the association between diversification and key ecological and phenotypic traits at broad phylogenetic and spatial scales. Do trait evolutionary rates coincide with rates of diversification, are there lags among these rates, or is diversification niche-neutral? To address these questions, we combine a deeply sampled phylogeny for a major flowering plant clade—Saxifragales—with phenotype and niche data to examine temporal patterns of evolutionary rates. The considerable phenotypic and habitat diversity of Saxifragales is greatest in temperate biomes. Global expansion of these habitats since the mid-Miocene provided ecological opportunities that, with density-dependent adaptive radiation, should result in simultaneous rate increases for diversification, niche, and phenotype, followed by decreases with habitat saturation. Instead, we find that these rates have significantly different timings, with increases in diversification occurring at the mid-Miocene Climatic Optimum (∼15 Mya), followed by increases in niche and phenotypic evolutionary rates by ∼5 Mya; all rates increase exponentially to the present. We attribute this surprising lack of temporal coincidence to initial niche-neutral diversification followed by ecological and phenotypic divergence coincident with more extreme cold and dry habitats that proliferated into the Pleistocene. A lack of density-dependence contrasts with investigations of other cosmopolitan lineages, suggesting alternative patterns may be common in the diversification of temperate lineages.
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19
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Widhelm TJ, Bertoletti FR, Asztalos MJ, Mercado-Díaz JA, Huang JP, Moncada B, Lücking R, Magain N, Sérusiaux E, Goffinet B, Crouch N, Mason-Gamer R, Lumbsch HT. Oligocene origin and drivers of diversification in the genus Sticta (Lobariaceae, Ascomycota). Mol Phylogenet Evol 2018; 126:58-73. [PMID: 29656104 DOI: 10.1016/j.ympev.2018.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 02/19/2018] [Accepted: 04/05/2018] [Indexed: 11/24/2022]
Abstract
A major challenge to evolutionary biologists is to understand how biodiversity is distributed through space and time and across the tree of life. Diversification of organisms is influenced by many factors that act at different times and geographic locations but it is still not clear which have a significant impact and how drivers interact. To study diversification, we chose the lichen genus Sticta, by sampling through most of the global range and producing a time tree. We estimate that Sticta originated about 30 million years ago, but biogoegraphic analysis was unclear in estimating the origin of the genus. Furthermore, we investigated the effect of dispersal ability finding that Sticta has a high dispersal rate, as collections from Hawaii showed that divergent lineages colonized the islands at least four times. Symbiont interactions were investigated using BiSSE to understand if green-algal or cyanobacterial symbiont interactions influenced diversification, only to find that the positive results were driven almost completely by Type I error. On the other hand, another BiSSE analysis found that an association with Andean tectonic activity increases the speciation rate of species.
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Affiliation(s)
- Todd J Widhelm
- Science & Education, The Field Museum, Chicago, IL, USA; Biological Sciences, Ecology and Evolution, University of Illinois at Chicago, Chicago, IL, USA.
| | | | | | | | - Jen-Pan Huang
- Science & Education, The Field Museum, Chicago, IL, USA
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Bogotá, Colombia
| | - Robert Lücking
- Kustos Herbarium, Botanischer Garten und Botanisches Museum, Berlin, Germany
| | | | | | - Bernard Goffinet
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Nicholas Crouch
- Biological Sciences, Ecology and Evolution, University of Illinois at Chicago, Chicago, IL, USA
| | - Roberta Mason-Gamer
- Biological Sciences, Ecology and Evolution, University of Illinois at Chicago, Chicago, IL, USA
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20
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Navaud O, Barbacci A, Taylor A, Clarkson JP, Raffaele S. Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens. Mol Ecol 2018; 27:1309-1323. [PMID: 29421852 PMCID: PMC5900718 DOI: 10.1111/mec.14523] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 01/07/2023]
Abstract
The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite cophylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.
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Affiliation(s)
- Olivier Navaud
- LIPM, Université de Toulouse, INRA, CNRSCastanet‐TolosanFrance
| | - Adelin Barbacci
- LIPM, Université de Toulouse, INRA, CNRSCastanet‐TolosanFrance
| | - Andrew Taylor
- Warwick Crop CentreSchool of Life SciencesUniversity of WarwickCoventryUK
| | - John P. Clarkson
- Warwick Crop CentreSchool of Life SciencesUniversity of WarwickCoventryUK
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21
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Diversification dynamics and transoceanic Eurasian-Australian disjunction in the genus Picris (Compositae) induced by the interplay of shifts in intrinsic/extrinsic traits and paleoclimatic oscillations. Mol Phylogenet Evol 2018; 119:182-195. [DOI: 10.1016/j.ympev.2017.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 11/22/2022]
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22
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Scheriau CL, Nuerk NM, Sharbel TF, Koch MA. Cryptic gene pools in the Hypericum perforatum-H. maculatum complex: diploid persistence versus trapped polyploid melting. ANNALS OF BOTANY 2017; 120:955-966. [PMID: 29182722 PMCID: PMC5710527 DOI: 10.1093/aob/mcx110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/09/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS In Central Europe Hypericum perforatum and Hypericum maculatum show significant hybridization and introgression as a consequence of Pleistocene range fluctuations, and their gene pools are merging on higher ploidy levels. This paper discusses whether polyploid hybrid gene pools are trapped in the ecological climatic niche space of their diploid ancestors, and tests the idea of geographical parthenogenesis. METHODS DNA sequence information of nuclear ribosomal DNA and plastid loci, ploidy level estimates and ecological niche modelling are used to characterize the various diploid and polyploid gene pools and unravel spatio-temporal patterns of gene flow among them. KEY RESULTS On the diploid level, the three gene pools are clearly distinct between and within species of H. perforatum (two gene pools) and H. maculatum, and their divergence dates back to the first half of the Pleistocene. All polyploids in Central Europe show high levels of past and contemporary gene flow between all three gene pools. The correlation of genetic and geographical distances breaks down if the latter is larger than 250 km, indicating recent and ongoing gene flow. The two species are ecologically differentiated, but in particular hybrids among all three gene pools do not show significant niche differences compared to their parental gene pools, except for some combinations with H. maculatum. CONCLUSIONS Inter- and intraspecific gene flow between inter- and intra-species gene pools is limited on the diploid level, and the geographical distribution of the diploids largely reflects Pleistocene evolutionary history. Secondary contact promoted hybridization and introgression on the polyploid level, enabling offspring to escape the diploid gene pools. However, the hybrid polyploids do not show significant niche differences compared to their diploid progenitors. It is concluded that the observed absence of niche divergence has precluded further differentiation and geographical partitioning of new polyploid lineages being effectively separated from the parental lines. The predominantly apomictic reproducing polyploids are trapped in the polyploid gene pool and the ecological climatic niche space of their diploid ancestors.
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Affiliation(s)
- Charlotte L Scheriau
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Nicolai M Nuerk
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Timothy F Sharbel
- Global Institute for Food Security, Seed Developmental Biology Program, University of Saskatchewan, Canada
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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23
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Molecular phylogeny and divergence times of Astragalus section Hymenostegis: An analysis of a rapidly diversifying species group in Fabaceae. Sci Rep 2017; 7:14033. [PMID: 29070910 PMCID: PMC5656595 DOI: 10.1038/s41598-017-14614-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/11/2017] [Indexed: 11/29/2022] Open
Abstract
The taxa of Astragalus section Hymenostegis are an important element of mountainous and steppe habitats in Southwest Asia. A phylogenetic hypothesis of sect. Hymenostegis has been obtained from nuclear ribosomal DNA internal transcribed spacer (ITS) and plastid ycf1 sequences of up to 303 individuals from 106 species, including all 89 taxa currently assigned to sect. Hymenostegis, 14 species of other Astragalus sections, and two species of Oxytropis and one Biserrula designated as outgroups. Bayesian phylogenetic inference and parsimony analyses reveal that three species from two other closely related sections group within sect. Hymenostegis, making the section paraphyletic. DNA sequence diversity is generally very low among Hymenostegis taxa, which is consistent with recent diversification of the section. We estimate that diversification in sect. Hymenostegis occurred in the middle to late Pleistocene, with many species arising only during the last one million years, when environmental conditions in the mountain regions of Southwest and Central Asia cycled repeatedly between dry and more humid conditions.
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24
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Ebersbach J, Schnitzler J, Favre A, Muellner-Riehl AN. Evolutionary radiations in the species-rich mountain genus Saxifraga L. BMC Evol Biol 2017; 17:119. [PMID: 28545386 PMCID: PMC5445344 DOI: 10.1186/s12862-017-0967-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/12/2017] [Indexed: 11/10/2022] Open
Abstract
Background A large number of taxa have undergone evolutionary radiations in mountainous areas, rendering alpine systems particularly suitable to study the extrinsic and intrinsic factors that have shaped diversification patterns in plants. The species-rich genus Saxifraga L. is widely distributed throughout the Northern Hemisphere, with high species numbers in the regions adjacent to the Qinghai-Tibet Plateau (QTP) in particular the Hengduan Mountains and the Himalayas. Using a dataset of 297 taxa (representing at least 60% of extant Saxifraga species), we explored the variation of infrageneric diversification rates. In addition, we used state-dependent speciation and extinction models to test the effects of geographic distribution in the Hengduan Mountains and the entire QTP region as well as of two morphological traits (cushion habit and specialized lime-secreting glands, so-called hydathodes) on the diversification of this genus. Results We detected two to three rate shifts across the Saxifraga phylogeny and two of these shifts led to radiations within two large subclades of Saxifraga, sect. Ciliatae Haworth subsect. Hirculoideae Engl. & Irmsch. and sect. Porphyrion Tausch subsect. Kabschia Engl. GEOSSE analyses showed that presence in the Hengduan Mountains had a positive effect on diversification across Saxifraga. Influence of these mountains was strongest in Saxifraga sect. Ciliatae subsect. Hirculoideae given its pronounced distribution there, and thus the radiation in this group can be classified at least partially as geographic. In contrast, the evolution of the cushion life form and lime-secreting hydathodes had positive effects on diversification only in selected Saxifraga sections, including sect. Porphyrion subsect. Kabschia. We therefore argue that radiation in this group was likely adaptive. Conclusions Our study underlines the complexity of processes and factors underpinning plant radiations: Even in closely related lineages occupying the same life zone, shifts in diversification are not necessarily governed by similar factors. In conclusion, alpine plant radiations result from a complex interaction among geographical settings and/or climatic modifications providing key opportunities for diversification as well as the evolution of key innovations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0967-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Ebersbach
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, D-04103, Leipzig, Germany.
| | - J Schnitzler
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, D-04103, Leipzig, Germany
| | - A Favre
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, D-04103, Leipzig, Germany
| | - A N Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, D-04103, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
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Tusiime FM, Gizaw A, Wondimu T, Masao CA, Abdi AA, Muwanika V, Trávníček P, Nemomissa S, Popp M, Eilu G, Brochmann C, Pimentel M. Sweet vernal grasses (Anthoxanthum) colonized African mountains along two fronts in the Late Pliocene, followed by secondary contact, polyploidization and local extinction in the Pleistocene. Mol Ecol 2017; 26:3513-3532. [PMID: 28390111 DOI: 10.1111/mec.14136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/24/2017] [Accepted: 03/29/2017] [Indexed: 11/28/2022]
Abstract
High tropical mountains harbour remarkable and fragmented biodiversity thought to a large degree to have been shaped by multiple dispersals of cold-adapted lineages from remote areas. Few dated phylogenetic/phylogeographic analyses are however available. Here, we address the hypotheses that the sub-Saharan African sweet vernal grasses have a dual colonization history and that lineages of independent origins have established secondary contact. We carried out rangewide sampling across the eastern African high mountains, inferred dated phylogenies from nuclear ribosomal and plastid DNA using Bayesian methods, and performed flow cytometry and AFLP (amplified fragment length polymorphism) analyses. We inferred a single Late Pliocene western Eurasian origin of the eastern African taxa, whose high-ploid populations in one mountain group formed a distinct phylogeographic group and carried plastids that diverged from those of the currently allopatric southern African lineage in the Mid- to Late Pleistocene. We show that Anthoxanthum has an intriguing history in sub-Saharan Africa, including Late Pliocene colonization from southeast and north, followed by secondary contact, hybridization, allopolyploidization and local extinction during one of the last glacial cycles. Our results add to a growing body of evidence showing that isolated tropical high mountain habitats have a dynamic recent history involving niche conservatism and recruitment from remote sources, repeated dispersals, diversification, hybridization and local extinction.
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Affiliation(s)
- Felly Mugizi Tusiime
- School of Forestry, Geographical and Environmental Sciences, Department of Forestry, Biodiversity and Tourism, Makerere University, Kampala, Uganda.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Abel Gizaw
- Natural History Museum, University of Oslo, Oslo, Norway.,Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tigist Wondimu
- Natural History Museum, University of Oslo, Oslo, Norway.,Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Catherine Aloyce Masao
- Natural History Museum, University of Oslo, Oslo, Norway.,Department of Forest Biology, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ahmed Abdikadir Abdi
- Natural History Museum, University of Oslo, Oslo, Norway.,National Museums of Kenya, Nairobi, Kenya
| | - Vincent Muwanika
- School of Forestry, Geographical and Environmental Sciences, Department of Forestry, Biodiversity and Tourism, Makerere University, Kampala, Uganda
| | - Pavel Trávníček
- Department of Flow Cytometry, Institute of Botany, Průhonice, Czech Republic
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Addis Ababa, Ethiopia
| | - Magnus Popp
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Gerald Eilu
- School of Forestry, Geographical and Environmental Sciences, Department of Forestry, Biodiversity and Tourism, Makerere University, Kampala, Uganda
| | | | - Manuel Pimentel
- Natural History Museum, University of Oslo, Oslo, Norway.,CICA, Centro de Investigacións Científicas Avanzadas, Universidade da Coruña, Galicia, Spain
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26
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Uribe-Convers S, Carlsen MM, Lagomarsino LP, Muchhala N. Phylogenetic relationships of Burmeistera (Campanulaceae: Lobelioideae): Combining whole plastome with targeted loci data in a recent radiation. Mol Phylogenet Evol 2017; 107:551-563. [DOI: 10.1016/j.ympev.2016.12.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/06/2016] [Accepted: 12/09/2016] [Indexed: 11/24/2022]
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27
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Soták M, Czeranková O, Klein D, Jurčacková Z, Li L, Čellárová E. Comparative Transcriptome Reconstruction of Four Hypericum Species Focused on Hypericin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2016; 7:1039. [PMID: 27468294 PMCID: PMC4942478 DOI: 10.3389/fpls.2016.01039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/01/2016] [Indexed: 05/10/2023]
Abstract
Next generation sequencing technology rapidly developed research applications in the field of plant functional genomics. Several Hypericum spp. with an aim to generate and enhance gene annotations especially for genes coding the enzymes supposedly included in biosynthesis of valuable bioactive compounds were analyzed. The first de novo transcriptome profiling of Hypericum annulatum Moris, H. tomentosum L., H. kalmianum L., and H. androsaemum L. leaves cultivated in vitro was accomplished. All four species with only limited genomic information were selected on the basis of differences in ability to synthesize hypericins and presence of dark nodules accumulating these metabolites with purpose to enrich genomic background of Hypericum spp. H. annulatum was chosen because of high number of the dark nodules and high content of hypericin. H. tomentosum leaves are typical for the presence of only 1-2 dark nodules localized in the apical part. Both H. kalmianum and H. androsaemum lack hypericin and have no dark nodules. Four separated datasets of the pair-end reads were gathered and used for de novo assembly by Trinity program. Assembled transcriptomes were annotated to the public databases Swiss-Prot and non-redundant protein database (NCBI-nr). Gene ontology analysis was performed. Differences of expression levels in the marginal tissues with dark nodules and inner part of leaves lacking these nodules indicate a potential genetic background for hypericin formation as the presumed site of hypericin biosynthesis is in the cells adjacent to these structures. Altogether 165 contigs in H. annulatum and 100 contigs in H. tomentosum were detected as significantly differentially expressed (P < 0.05) and upregulated in the leaf rim tissues containing the dark nodules. The new sequences homologous to octaketide synthase and enzymes catalyzing phenolic oxidative coupling reactions indispensable for hypericin biosynthesis were discovered. The presented transcriptomic sequence data will improve current knowledge about the selected Hypericum spp. with proposed relation to hypericin biosynthesis and will provide a useful resource of genomic information for consequential studies in the field of functional genomics, proteomics and metabolomics.
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Affiliation(s)
- Miroslav Soták
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik UniversityKošice, Slovakia
| | - Odeta Czeranková
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik UniversityKošice, Slovakia
| | - Daniel Klein
- Institute of Mathematics, Faculty of Science, Pavol Jozef Šafárik UniversityKošice, Slovakia
| | - Zuzana Jurčacková
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik UniversityKošice, Slovakia
| | - Ling Li
- Department of Genetics, Development, and Cell Biology, Iowa State University, AmesIA, USA
- Center for Metabolic Biology, Iowa State University, AmesIA, USA
| | - Eva Čellárová
- Department of Genetics, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik UniversityKošice, Slovakia
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28
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Gizaw A, Brochmann C, Nemomissa S, Wondimu T, Masao CA, Tusiime FM, Abdi AA, Oxelman B, Popp M, Dimitrov D. Colonization and diversification in the African 'sky islands': insights from fossil-calibrated molecular dating of Lychnis (Caryophyllaceae). THE NEW PHYTOLOGIST 2016; 211:719-34. [PMID: 27037925 DOI: 10.1111/nph.13937] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/18/2016] [Indexed: 05/10/2023]
Abstract
The flora on the isolated high African mountains or 'sky islands' is remarkable for its peculiar adaptations, local endemism and striking biogeographical connections to remote parts of the world. Ages of the plant lineages and the timing of their radiations have frequently been debated but remain contentious as there are few estimates based on explicit models and fossil-calibrated molecular clocks. We used the plastid region maturaseK (matK) and a Caryophylloflora paleogenica fossil to infer the age of the genus Lychnis, and constructed a data set of three plastid (matK; a ribosomal protein S16 (rps16); and an intergenic spacer (psbE-petL)) and two nuclear (internal transcribed spacer (ITS) and a region spanning exon 18-24 in the second largest subunit of RNA polymerase II (RPB2)) loci for joint estimation of the species tree and divergence time of the African representatives. The time of divergence of the African high-altitude Lychnis was placed in the late Miocene to early Pliocene. A single speciation event was inferred in the early Pliocene; subsequent speciation took place sporadically from the late Pliocene to the middle Pleistocene. We provide further support for a Eurasian origin of the African 'sky islands' floral elements, which seem to have been recruited via dispersals at different times: some old, as in Lychnis, and others very recent. We show that dispersal and diversification within Africa play an important role in shaping these isolated plant communities.
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Affiliation(s)
- Abel Gizaw
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Department of Plant Biology and Biodiversity Management, College of Natural Science, Addis Ababa University, PO Box 3434, Addis Ababa, Ethiopia
| | - Christian Brochmann
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
| | - Sileshi Nemomissa
- Department of Plant Biology and Biodiversity Management, College of Natural Science, Addis Ababa University, PO Box 3434, Addis Ababa, Ethiopia
| | - Tigist Wondimu
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Department of Plant Biology and Biodiversity Management, College of Natural Science, Addis Ababa University, PO Box 3434, Addis Ababa, Ethiopia
| | - Catherine Aloyce Masao
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Department of Forest Biology, Sokoine University of Agriculture, PO Box 3010, Morogoro, Tanzania
- Institute of Resource Assessment, University of Dar es Salaam, Box 35097, Dar es Salaam, Tanzania
| | - Felly Mugizi Tusiime
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Department of Forestry Biodiversity and Tourism, School of Forestry Geographical and Environmental Sciences, Makerere University, PO Box 7062, Kampala, Uganda
| | - Ahmed Abdikadir Abdi
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
- Botany Department, National Museums of Kenya, PO Box 40658, 00100, Nairobi, Kenya
| | - Bengt Oxelman
- Department of Biology and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30, Gothenburg, Sweden
| | - Magnus Popp
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
| | - Dimitar Dimitrov
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
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29
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Ruhfel BR, Bove CP, Philbrick CT, Davis CC. Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade. AMERICAN JOURNAL OF BOTANY 2016; 103:1117-1128. [PMID: 27335391 DOI: 10.3732/ajb.1500537] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 05/18/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY The clusioid clade (Malpighiales) has an ancient fossil record (∼90 Ma) and extant representatives exhibit a pantropical distribution represented on all former Gondwanan landmasses (Africa, Australia, India, Madagascar, and South America) except Antarctica. Several biogeographers have hypothesized that the clusioid distribution is an example of Gondwanan vicariance. Our aim is to test the hypothesis that the modern distribution of the clusioid clade is largely explained by Gondwanan fragmentation. METHODS Using a four gene, 207-taxon data set we simultaneously estimated the phylogeny and divergence times of the clusioid clade using a Bayesian Markov chain Monte Carlo approach. Ancestral Area Reconstructions (AARs) were then conducted on a distribution of 1000 trees and summarized on a reduced phylogeny. KEY RESULTS Divergence time estimates and AARs revealed only two or four cladogenic events that are potentially consistent with Gondwanan vicariance, depending on the placement of the ancient fossil Paleoclusia. In contrast, dispersal occurred on > 25% of the branches, indicating the current distribution of the clade likely reflects extensive recent dispersal during the Cenozoic (< 65 Ma), most of which occurred after the beginning of the Eocene (∼56 Ma). CONCLUSIONS These results support growing evidence that suggests many traditionally recognized angiosperm clades (families and genera) are too young for their distributions to have been influenced strictly by Gondwanan fragmentation. Instead, it appears that corridors of dispersal may be the best explanation for numerous angiosperm clades with Gondwanan distributions.
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Affiliation(s)
- Brad R Ruhfel
- Department of Biological Sciences, Eastern Kentucky University, 521 Lancaster Avenue, Richmond, Kentucky 40475 USA Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138 USA
| | - Claudia P Bove
- Departamento de Botânica, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, Rio de Janeiro 20940-040, Brazil
| | - C Thomas Philbrick
- Biological & Environmental Sciences, Western Connecticut State University, 181 White Street, Danbury, Connecticut 06810 USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138 USA
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30
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Schwallier R, Raes N, de Boer HJ, Vos RA, van Vugt RR, Gravendeel B. Phylogenetic analysis of niche divergence reveals distinct evolutionary histories and climate change implications for tropical carnivorous pitcher plants. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12382] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Rachel Schwallier
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
| | - Niels Raes
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
| | - Hugo J. de Boer
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- Uppsala University; Norbyvägen 18D SE 75236 Uppsala Sweden
- The Natural History Museum; University of Oslo; P.O. Box 1172 NO-0318 Oslo Norway
| | - Rutger A. Vos
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
| | - Rogier R. van Vugt
- Hortus Botanicus of Leiden University; Rapenburg 73 2311 GJ Leiden The Netherlands
| | - Barbara Gravendeel
- Naturalis Biodiversity Center; Darwinweg 2 2333 CR Leiden The Netherlands
- University of Applied Sciences Leiden; Zernikedreef 11 2333 CK Leiden The Netherlands
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31
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Nürk NM, Uribe-Convers S, Gehrke B, Tank DC, Blattner FR. Oligocene niche shift, Miocene diversification - cold tolerance and accelerated speciation rates in the St. John's Worts (Hypericum, Hypericaceae). BMC Evol Biol 2015; 15:80. [PMID: 25944090 PMCID: PMC4422466 DOI: 10.1186/s12862-015-0359-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/22/2015] [Indexed: 12/03/2022] Open
Abstract
Background Our aim is to understand the evolution of species-rich plant groups that shifted from tropical into cold/temperate biomes. It is well known that climate affects evolutionary processes, such as how fast species diversify, species range shifts, and species distributions. Many plant lineages may have gone extinct in the Northern Hemisphere due to Late Eocene climate cooling, while some tropical lineages may have adapted to temperate conditions and radiated; the hyper-diverse and geographically widespread genus Hypericum is one of these. Results To investigate the effect of macroecological niche shifts on evolutionary success we combine historical biogeography with analyses of diversification dynamics and climatic niche shifts in a phylogenetic framework. Hypericum evolved cold tolerance c. 30 million years ago, and successfully colonized all ice-free continents, where today ~500 species exist. The other members of Hypericaceae stayed in their tropical habitats and evolved into ~120 species. We identified a 15–20 million year lag between the initial change in temperature preference in Hypericum and subsequent diversification rate shifts in the Miocene. Conclusions Contrary to the dramatic niche shift early in the evolution of Hypericum most extant species occur in temperate climates including high elevations in the tropics. These cold/temperate niches are a distinctive characteristic of Hypericum. We conclude that the initial release from an evolutionary constraint (from tropical to temperate climates) is an important novelty in Hypericum. However, the initial shift in the adaptive landscape into colder climates appears to be a precondition, and may not be directly related to increased diversification rates. Instead, subsequent events of mountain formation and further climate cooling may better explain distribution patterns and species-richness in Hypericum. These findings exemplify important macroevolutionary patterns of plant diversification during large-scale global climate change. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0359-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolai M Nürk
- Centre for Organismal Studies Heidelberg, University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany.
| | - Simon Uribe-Convers
- Department of Biological Sciences, Institute for Bioinformatics & Evolutionary Studies, University of Idaho, 875 Perimeter MS 3051, Moscow, ID, 83844-3051, USA.
| | - Berit Gehrke
- Institute of Special Botany, Johannes Gutenberg University, Anselm-Franz-von-Bentzelweg 9a, 55099, Mainz, Germany.
| | - David C Tank
- Department of Biological Sciences, Institute for Bioinformatics & Evolutionary Studies, University of Idaho, 875 Perimeter MS 3051, Moscow, ID, 83844-3051, USA.
| | - Frank R Blattner
- Institute of Plant Genetics and Crop Research (IPK), Correnzstrasse 3, 06466, Gatersleben, Germany. .,German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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