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Ding C, Su C, Li Y, Zhao Y, Wang Y, Wang Y, Nie R, He B, Ma J, Hao J. Interspecific and Intraspecific Transcriptomic Variations Unveil the Potential High-Altitude Adaptation Mechanisms of the Parnassius Butterfly Species. Genes (Basel) 2024; 15:1013. [PMID: 39202373 PMCID: PMC11354221 DOI: 10.3390/genes15081013] [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: 06/19/2024] [Revised: 07/27/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
Parnassius butterflies have significantly advanced our understanding of biogeography, insect-plant interactions, and other fields of ecology and evolutionary biology. However, to date, little is known about the gene expression patterns related to the high-altitude adaptation of Parnassius species. In this study, we obtained high-throughput RNA-seq data of 48 adult Parnassius individuals covering 10 species from 12 localities in China, and deciphered their interspecific and intraspecific expression patterns based on comparative transcriptomic analyses. Though divergent transcriptional patterns among species and populations at different altitudes were found, a series of pathways related to genetic information processing (i.e., recombination, repair, transcription, RNA processing, and ribosome biogenesis), energy metabolism (i.e., oxidative phosphorylation, thermogenesis, and the citrate cycle), and cellular homeostasis were commonly enriched, reflecting similar strategies to cope with the high-altitude environments by activating energy metabolism, enhancing immune defense, and concurrently inhibiting cell growth and development. These findings deepen our understanding about the molecular mechanisms of adaptative evolution to extreme environments, and provide us with some theoretical criteria for the biodiversity conservation of alpine insects.
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Affiliation(s)
- Chen Ding
- College of Life Sciences, Anhui Normal University, Wuhu 241002, China; (C.D.); (C.S.); (Y.L.); (Y.Z.); (Y.W.); (Y.W.); (R.N.); (B.H.)
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu 241002, China; (C.D.); (C.S.); (Y.L.); (Y.Z.); (Y.W.); (Y.W.); (R.N.); (B.H.)
| | - Yali Li
- College of Life Sciences, Anhui Normal University, Wuhu 241002, China; (C.D.); (C.S.); (Y.L.); (Y.Z.); (Y.W.); (Y.W.); (R.N.); (B.H.)
| | - Youjie Zhao
- College of Life Sciences, Anhui Normal University, Wuhu 241002, China; (C.D.); (C.S.); (Y.L.); (Y.Z.); (Y.W.); (Y.W.); (R.N.); (B.H.)
| | - Yunliang Wang
- College of Life Sciences, Anhui Normal University, Wuhu 241002, China; (C.D.); (C.S.); (Y.L.); (Y.Z.); (Y.W.); (Y.W.); (R.N.); (B.H.)
- College of Physical Education, Anhui Normal University, Wuhu 241002, China
| | - Ying Wang
- College of Life Sciences, Anhui Normal University, Wuhu 241002, China; (C.D.); (C.S.); (Y.L.); (Y.Z.); (Y.W.); (Y.W.); (R.N.); (B.H.)
- College of Physical Education, Anhui Normal University, Wuhu 241002, China
| | - Ruie Nie
- College of Life Sciences, Anhui Normal University, Wuhu 241002, China; (C.D.); (C.S.); (Y.L.); (Y.Z.); (Y.W.); (Y.W.); (R.N.); (B.H.)
| | - Bo He
- College of Life Sciences, Anhui Normal University, Wuhu 241002, China; (C.D.); (C.S.); (Y.L.); (Y.Z.); (Y.W.); (Y.W.); (R.N.); (B.H.)
| | - Junye Ma
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu 241002, China; (C.D.); (C.S.); (Y.L.); (Y.Z.); (Y.W.); (Y.W.); (R.N.); (B.H.)
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Su C, Xie T, Jiang L, Wang Y, Wang Y, Nie R, Zhao Y, He B, Ma J, Yang Q, Hao J. Host genetics and larval host plant modulate microbiome structure and evolution underlying the intimate insect-microbe-plant interactions in Parnassius species on the Qinghai-Tibet Plateau. Ecol Evol 2024; 14:e11218. [PMID: 38606343 PMCID: PMC11007261 DOI: 10.1002/ece3.11218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Insects harbor a remarkable diversity of gut microbiomes critical for host survival, health, and fitness, but the mechanism of this structured symbiotic community remains poorly known, especially for the insect group consisting of many closely related species that inhabit the Qinghai-Tibet Plateau. Here, we firstly analyzed population-level 16S rRNA microbial dataset, comprising 11 Parnassius species covering 5 subgenera, from 14 populations mostly sampled in mountainous regions across northwestern-to-southeastern China, and meanwhile clarified the relative importance of multiple factors on gut microbial community structure and evolution. Our findings indicated that both host genetics and larval host plant modulated gut microbial diversity and community structure. Moreover, the effect analysis of host genetics and larval diet on gut microbiomes showed that host genetics played a critical role in governing the gut microbial beta diversity and the symbiotic community structure, while larval host plant remarkably influenced the functional evolution of gut microbiomes. These findings of the intimate insect-microbe-plant interactions jointly provide some new insights into the correlation among the host genetic background, larval host plant, the structure and evolution of gut microbiome, as well as the mechanisms of high-altitude adaptation in closely related species of this alpine butterfly group.
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Affiliation(s)
- Chengyong Su
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Tingting Xie
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Lijun Jiang
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Yunliang Wang
- College of Life SciencesAnhui Normal UniversityWuhuChina
- College of Physical EducationAnhui Normal UniversityWuhuChina
| | - Ying Wang
- College of Life SciencesAnhui Normal UniversityWuhuChina
- College of Physical EducationAnhui Normal UniversityWuhuChina
| | - Ruie Nie
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Youjie Zhao
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Bo He
- College of Life SciencesAnhui Normal UniversityWuhuChina
| | - Junye Ma
- Key Laboratory of Palaeobiology and Petroleum Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and PaleontologyChinese Academy of SciencesNanjingChina
| | - Qun Yang
- Key Laboratory of Palaeobiology and Petroleum Stratigraphy, Center for Excellence in Life and Palaeoenvironment, Nanjing Institute of Geology and PaleontologyChinese Academy of SciencesNanjingChina
- Nanjing CollegeUniversity of Chinese Academy of SciencesNanjingChina
| | - Jiasheng Hao
- College of Life SciencesAnhui Normal UniversityWuhuChina
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Che X, Zhang Y, Wu A, Pan X, Wang M, Yang J, Wang X. Expansion and contraction of lake basin shape the genetic structure of Sinocyclocheilus (Osteichthyes: Cypriniformes: Cyprinidae) populations in Central Yunnan, China. Ecol Evol 2024; 14:e10840. [PMID: 38250223 PMCID: PMC10797211 DOI: 10.1002/ece3.10840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/10/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Geological events can strongly affect the genetic structures and differentiation of fish populations. Especially, as an endemic fish of the genus Sinocyclocheilus in the Yunnan-Guizhou Plateau, the effects of key geological events on the distributions and genetic structures remain poorly understood. Examining the phylogeographic patterns of Sinocyclocheilus fishes can be useful for elucidating the spatio-temporal dynamics of their population size, dispersal history and extent of geographical isolation, thereby providing a theoretical basis for their protection. Here, we used single nucleotide polymorphisms (SNP) method to investigate the phylogeographic patterns of Sinocyclocheilus fishes. Our analysis supports the endemicity of Sinocyclocheilus, but the samples of different regions of Sinocyclocheilus contain multiple ancestral components, which displayed more admixed and diversified genetic components, this may be due to the polymorphism of the ancestors themselves, or gene infiltration caused by hybridization between adjacent species of Sinocyclocheilus. We estimate that the most recent common ancestor (MRCA) of Sinocyclocheilus fish in the Central Yunnan Basin at approximately 3.75~3.11 Ma, and infer that the evolution of Sinocyclocheilus in the central Yunnan Basin is closely related to the formation of plateau lakes (around 4.0~0.02 Ma), and identifies the formation of Dianchi Lake and Fuxian Lake as key geological events shaping Sinocyclocheilus population structure. It is also the first time to prove that the altitude change has a great influence on the genetic variation among the populations of Sinocyclocheilus.
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Affiliation(s)
- Xing‐Jin Che
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuan‐Wei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - An‐Li Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Xiao‐Fu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Mo Wang
- Key Laboratory for Conserving Wildlife with Small Populations in Yunnan, Faculty of Biodiversity ConservationSouthwest Forestry UniversityKunmingChina
| | - Jun‐Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
| | - Xiao‐Ai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyThe Innovative Academy of Seed Design, Chinese Academy of SciencesKunmingChina
- Yunnan Key Laboratory of Plateau Fish BreedingYunnan Engineering Research Center for Plateau‐Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
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4
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Zhou G, YE RR, Zhao Z. A new troglobitic species of the genus Troglocoelotes Zhao & S. Li, 2019 (Araneae, Agelenidae, Coelotinae) from Guizhou, China. Biodivers Data J 2023; 11:e103265. [PMID: 38327381 PMCID: PMC10848803 DOI: 10.3897/bdj.11.e103265] [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: 03/09/2023] [Accepted: 07/12/2023] [Indexed: 02/09/2024] Open
Abstract
Background Troglocoelotes Zhao & S. Li, 2019 is the only known genus of Coelotinae of which all species have deep morphological adaptations to the subterranean environment, such as depigmentation of body, degenerated or absent eyes and, frequently, with attenuated bodies and/or appendages. Four species of Troglocoelotes have been reported from Guizhou Province, China. New information A new funnel-web spider of the genus Troglocoelotes is described and illustrated on the basis of a single female specimen from Tongren City, Guizhou: Troglocoelotessinanensis sp. nov. Additionally, photos of the collection site and a distribution map are also provided.
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Affiliation(s)
- Guchun Zhou
- School of life Sciences, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, ChinaSchool of life Sciences, National Navel Orange Engineering Research Center, Gannan Normal UniversityGanzhouChina
| | - Ru-rui YE
- Qiandongnan Cave & Rescue Association, Kaili, ChinaQiandongnan Cave & Rescue AssociationKailiChina
| | - Zhe Zhao
- Institute of Zoology, Chinese Academy of Sciences, Beijing, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
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5
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Li B, Zhao Z, Li S. Three new species of the genus Vappolotes Zhao & Li, 2019 (Araneae, Agelenidae) from southwest China. Zootaxa 2023; 5270:325-336. [PMID: 37518162 DOI: 10.11646/zootaxa.5270.2.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 08/01/2023]
Abstract
Three new species of Vappolotes Zhao & Li, 2019 (Araneae: Agelenidae) are described from Hunan and Sichuan provinces, China: V. longshan sp. n. (♀♂), V. tianjiayu sp. n. (♀), and V. hei sp. n. (♀♂). The diagnostic characters of this genus are amended based on the newly obtained data. Photographs of habitus and copulatory organs, as well as their distributions, are provided for all new Vappolotes species.
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Affiliation(s)
- Bing Li
- College of Life Science; Langfang Normal University; Langfang 065000; China.
| | - Zhe Zhao
- Institute of Zoology; Chinese Academy of Sciences; Beijing 100101; China.
| | - Shuqiang Li
- Institute of Zoology; Chinese Academy of Sciences; Beijing 100101; China.
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Maul K, Wei Y, Iskandar EAP, Chantanaorrapint S, Ho B, Quandt D, Kessler M. Liverworts show a globally consistent mid‐elevation richness peak. Ecol Evol 2023; 13:e9862. [PMID: 36969936 PMCID: PMC10034488 DOI: 10.1002/ece3.9862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/26/2023] [Accepted: 02/07/2023] [Indexed: 03/25/2023] Open
Abstract
The study of elevational gradients allows to draw conclusions on the factors and mechanisms determining patterns in species richness distribution. Several earlier studies investigated liverwort diversity on single or few elevational transects. However, a comprehensive survey of the elevational distribution patterns of liverwort richness and their underlying factors is lacking so far. This study's purpose was to fill this gap by compiling an extensive data set of liverwort elevational patterns encompassing a broad diversity of mountains and mountain ranges around the world. Using polynomial regression analyses, we found a prevalence of hump‐shaped richness patterns (19 of 25 gradients), where liverwort species richness peaked at mid‐elevation and decreased towards both ends of the gradient. Against our expectation and unlike in other plant groups, in liverworts, this pattern also applies to elevational gradients at mid‐latitudes in temperate climates. Indeed, relative elevation, calculated as the percentage of the elevational range potentially inhabited by liverworts, was the most powerful predictor for the distribution of liverwort species richness. We conclude from these results that the admixture of low‐ and high‐elevation liverwort floras, in combination with steep ecological gradients, leads to a mid‐elevation floristic turnover shaping elevational patterns of liverwort diversity. Our analyses further detected significant effects of climatic variables (temperature of the warmest month, potential evapotranspiration, and precipitation of the warmest month) in explaining elevational liverwort richness patterns. This indicates that montane liverwort diversity is restricted by high temperatures and subsequent low water availability especially towards lower elevations, which presumably will lead to serious effects by temperature shifts associated with global warming.
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Affiliation(s)
- Karola Maul
- Nees Institute for Biodiversity of PlantsUniversity of BonnBonnGermany
| | - Yu‐Mei Wei
- Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of BotanyGuangxi Zhuang Autonomous Region and Chinese Academy of SciencesGuilinChina
| | - Eka Aditya Putri Iskandar
- Understanding Evolution Research GroupNaturalis Biodiversity CentreLeidenThe Netherlands
- Institute of Biology Leiden, Faculty of ScienceLeiden UniversityLeidenThe Netherlands
- Cibodas Botanic GardenNational Research and Innovation Agency (BRIN)BandungIndonesia
| | - Sahut Chantanaorrapint
- Division of Biological Sciences, Faculty of SciencePrince of Songkla UniversityHat YaiThailand
| | - Boon‐Chuan Ho
- Singapore Botanic GardensNational Parks BoardSingaporeRepublic of Singapore
| | - Dietmar Quandt
- Nees Institute for Biodiversity of PlantsUniversity of BonnBonnGermany
| | - Michael Kessler
- Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
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Li B, Zhao Z, Okumura KI, Meng K, Li S, Chen H. Yunguirius gen. nov., a new genus of Coelotinae (Araneae, Agelenidae) spiders from southwest China. Zookeys 2023; 1159:51-67. [PMID: 37213531 PMCID: PMC10193277 DOI: 10.3897/zookeys.1159.100786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/29/2023] [Indexed: 05/23/2023] Open
Abstract
A new genus of the subfamily Coelotinae F. O. Pickard-Cambridge, 1893, Yunguiriusgen. nov. is described, comprising two new species and three species previously described in Draconarius Ovtchinnikov, 1999, all from southwest China: Y.duogesp. nov. (♀), Y.xiangdingsp. nov. (♀), Y.ornatus (Wang, Yin, Peng & Xie, 1990) comb. nov. (♂♀) (the type species of Yunguiriusgen. nov.), Y.subterebratus (Zhang, Zhu & Wang, 2017) comb. nov. (♀), and Y.terebratus (Peng & Wang, 1997) comb. nov. (♂♀). Molecular analyses support Yunguiriusgen. nov. as a monophyletic group, with the Sinodraconarius clade as its sister group: Yunguiriusgen. nov. + (Hengconarius + (Nuconarius + Sinodraconarius)).
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Affiliation(s)
- Bing Li
- College of Life Sciences, Langfang Normal University, Langfang, Hebei 065000, ChinaLangfang Normal UniversityLangfangChina
| | - Zhe Zhao
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Ken-ichi Okumura
- Department of Zoology, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, JapanNational Museum of Nature and ScienceIbarakiJapan
| | - Kaibayier Meng
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Shuqiang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, ChinaInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Haifeng Chen
- College of Life Sciences, Langfang Normal University, Langfang, Hebei 065000, ChinaLangfang Normal UniversityLangfangChina
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Dimitrov D, Bolzern A, Arnedo M. Bringing Tegenaria boitanii stat. rev. back to life with a review of the Tegenaria percuriosa-complex (Araneae: Agelenidae), description of a new species and insight into their phylogenetic relationships and evolutionary history. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2021.2012297] [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]
Affiliation(s)
- Dragomir Dimitrov
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Avinguda Diagonal 645, Barcelona, 08028, Spain
| | - Angelo Bolzern
- Naturhistorisches Museum Basel, Augustinergasse 2, Basel, 4001, Switzerland
| | - Miquel Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Avinguda Diagonal 645, Barcelona, 08028, Spain
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9
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Wen H, Luo T, Wang Y, Wang S, Liu T, Xiao N, Zhou J. Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China. Integr Zool 2021; 17:311-325. [PMID: 34958525 DOI: 10.1111/1749-4877.12624] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modern accumulations of genetic data offer unprecedented opportunities for understanding the systematic classification and origins of specific groups of organisms. The genus Sinocyclocheilus is among the most cave abundant genera in Cyprinidae, with 76 recognized species, belonging to four species groups. Recent phylogenetic studies have shown that the classification of species groups within the genus Sinocyclocheilus remains controversial. In this study, we constructed a sequence supermatrix of 26 species from four species groups of the genus Sinocyclocheilus using the mitochondrial genome to reveal phylogenetic relationships, historical biogeography and patterns of species diversification in the genus Sinocyclocheilus. Phylogenetic analysis strongly supports the monophyletic groups of the three species groups (S. jii, S. cyphotergous, and S. tingi groups) except the S. angularis group. Phylogenetic analysis showed that S. anshuiensis and S. microphthalmus, which were recognized as numbers of S. angularis group, formed a strongly supported independent clade. Therefore, we propose a new species group, the S. microphthalmus group, which contains S. anshuiensis and S. microphthalmus. Biogeographic reconstruction suggests that the living Sinocyclocheilus may have originated in north-central Guangxi at the late Eocene and dispersed outward after a vicariance at 32.31 Million years ago (Ma). Early diversification is focused on the late Oligocene (ca. 25 Ma), which is related to the second uplift of the Qinghai-Tibetan Plateau and the lateral extrusion of the Indochina at the Oligocene/Miocene boundary. Our results suggest that two uplifts of the Qinghai-Tibetan Plateau and climate change in the Miocene may have influenced the diversification of the Sinocyclocheilus lineage. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Huamei Wen
- School of Life Sciences, Central China Normal University, Wuhan, China.,School of Karst Sciences, Guizhou Normal University, Guiyang, China
| | - Tao Luo
- School of Karst Sciences, Guizhou Normal University, Guiyang, China
| | - Yali Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Siwei Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Tao Liu
- Liupanshui No. 4 Higth School, Liupanshui, China
| | - Ning Xiao
- Guiyang Nursing Vocational College, Guiyang, China
| | - Jiang Zhou
- School of Karst Sciences, Guizhou Normal University, Guiyang, China
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10
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Liang J, Pecoraro L, Cai L, Yuan Z, Zhao P, Tsui CKM, Zhang Z. Phylogenetic Relationships, Speciation, and Origin of Armillaria in the Northern Hemisphere: A Lesson Based on rRNA and Elongation Factor 1-Alpha. J Fungi (Basel) 2021; 7:1088. [PMID: 34947070 PMCID: PMC8705980 DOI: 10.3390/jof7121088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 01/09/2023] Open
Abstract
Armillaria species have a global distribution and play various roles in the natural ecosystems, e.g., pathogens, decomposers, and mycorrhizal associates. However, their taxonomic boundaries, speciation processes, and origin are poorly understood. Here, we used a phylogenetic approach with 358 samplings from Europe, East Asia, and North America to delimit the species boundaries and to discern the evolutionary forces underpinning divergence and evolution. Three species delimitation methods indicated multiple unrecognized phylogenetic species, and biological species recognition did not reflect the natural evolutionary relationships within Armillaria; for instance, biological species of A. mellea and D. tabescens are divergent and cryptic species/lineages exist associated with their geographic distributions in Europe, North America, and East Asia. While the species-rich and divergent Gallica superclade might represent three phylogenetic species (PS I, PS II, and A. nabsnona) that undergo speciation. The PS II contained four lineages with cryptic diversity associated with the geographic distribution. The genus Armillaria likely originated from East Asia around 21.8 Mya in early Miocene when Boreotropical flora (56-33.9 Mya) and the Bering land bridge might have facilitated transcontinental dispersal of Armillaria species. The Gallica superclade arose at 9.1 Mya and the concurrent vicariance events of Bering Strait opening and the uplift of the northern Tibetan plateau might be important factors in driving the lineage divergence.
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Affiliation(s)
- Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
| | - Lorenzo Pecoraro
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
| | - Zhilin Yuan
- Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 310029, China;
| | - Peng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
| | - Clement K. M. Tsui
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
- Department of Pathology, Sidra Medicine, Doha 2713, Qatar
| | - Zhifeng Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (L.P.); (L.C.); (P.Z.); (Z.Z.)
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
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11
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Xiang KL, Erst AS, Yang J, Peng HW, Ortiz RDC, Jabbour F, Erst TV, Wang W. Biogeographic diversification of Eranthis (Ranunculaceae) reflects the geological history of the three great Asian plateaus. Proc Biol Sci 2021; 288:20210281. [PMID: 33823668 PMCID: PMC8059577 DOI: 10.1098/rspb.2021.0281] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
The evolutionary history of organisms with poor dispersal abilities usually parallels geological events. Collisions of the Indian and Arabian plates with Eurasia greatly changed Asian topography and affected regional and global climates as well as biotic evolution. However, the geological evolution of Asia related to these two collisions remains debated. Here, we used Eranthis, an angiosperm genus with poor seed dispersal ability and a discontinuous distribution across Eurasia, to shed light on the orogenesis of the Qinghai-Tibetan, Iranian and Mongolian Plateaus. Our phylogenetic analyses show that Eranthis comprises four major geographical clades: east Qinghai-Tibetan Plateau clade (I-1), North Asian clade (I-2), west Qinghai-Tibetan Plateau clade (II-1) and Mediterranean clade (II-2). Our molecular dating and biogeographic analyses indicate that within Eranthis, four vicariance events correlate well with the two early uplifts of the Qinghai-Tibetan Plateau during the Late Eocene and the Oligocene-Miocene boundary and the two uplifts of the Iranian Plateau during the Middle and Late Miocene. The origin and divergence of the Mongolian Plateau taxa are related to the two uplifts of the Mongolian Plateau during the Middle and Late Miocene. Additionally, our results are in agreement with the hypothesis that the central part of Tibet only reached an altitude of less than 2.3 km at approximately 40 Ma. This study highlights that organismal evolution could be related to the formation of the three great Asian plateaus, hence contributing to the knowledge on the timing of the key tectonic events in Asia.
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Affiliation(s)
- Kun-Li Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Andrey S. Erst
- Laboratory of Herbarium, Central Siberian Botanical Garden, Russian Academy of Sciences, Zolotodolinskaya Street 101, Novosibirsk 630090, Russia
- Laboratory of Herbarium, Tomsk State University, Tomsk 634050, Russia
| | - Jian Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Huan-Wen Peng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Rosa del C. Ortiz
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, MO 63166-0299, USA
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris 75005, France
| | - Tatyana V. Erst
- Laboratory of Herbarium, Tomsk State University, Tomsk 634050, Russia
- Laboratory of Molecular Plant Pathology, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Wei Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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12
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Xu H, Zhang X, Yao Z, Ali A, Li S. Thirty-five new species of the spider genus Pimoa (Araneae, Pimoidae) from Pan-Himalaya. Zookeys 2021; 1029:1-92. [PMID: 33935549 PMCID: PMC8050015 DOI: 10.3897/zookeys.1029.64080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/26/2021] [Indexed: 11/12/2022] Open
Abstract
Thirty-five new species of the Pimoa Chamberlin & Ivie, 1943 are described from Pan-Himalaya: P.anning Zhang & Li, sp. nov. (♂♀), P.bomi Zhang & Li, sp. nov. (♂♀), P.cawarong Zhang & Li, sp. nov. (♀), P.daman Zhang & Li, sp. nov. (♀), P.danba Zhang & Li, sp. nov. (♀), P.deqen Zhang & Li, sp. nov. (♀), P.dongjiu Zhang & Li, sp. nov. (♂♀), P.guiqing Zhang & Li, sp. nov. (♀), P.gyaca Zhang & Li, sp. nov. (♀), P.gyara Zhang & Li, sp. nov. (♂♀), P.gyirong Zhang & Li, sp. nov. (♂♀), P.heishui Zhang & Li, sp. nov. (♂♀), P.jinchuan Zhang & Li, sp. nov. (♂♀), P.khaptad Zhang & Li, sp. nov. (♀), P.koshi Zhang & Li, sp. nov. (♀), P.lhatog Zhang & Li, sp. nov. (♀), P.mechi Zhang & Li, sp. nov. (♂♀), P.miandam Zhang & Li, sp. nov. (♂♀), P.miero Zhang & Li, sp. nov. (♂♀), P.mude Zhang & Li, sp. nov. (♀), P.muli Zhang & Li, sp. nov. (♂♀), P.naran Zhang & Li, sp. nov. (♀), P.ninglang Zhang & Li, sp. nov. (♀), P.nyalam Zhang & Li, sp. nov. (♂♀), P.phaplu Zhang & Li, sp. nov. (♂♀), P.putou Zhang & Li, sp. nov. (♀), P.rara Zhang & Li, sp. nov. (♀), P.sangri Zhang & Li, sp. nov. (♂♀), P.shigatse Zhang & Li, sp. nov. (♀), P.tengchong Zhang & Li, sp. nov. (♂♀), P.xiahe Zhang & Li, sp. nov. (♂♀), P.yejiei Zhang & Li, sp. nov. (♀), P.yele Zhang & Li, sp. nov. (♂♀), P.zayu Zhang & Li, sp. nov. (♂♀), P.zhigangi Zhang & Li, sp. nov. (♀). The DNA barcodes of the thirty-five new species are provided.
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Affiliation(s)
- Hao Xu
- College of Life Science, Shenyang Normal University, Shenyang 110034, Liaoning, China Shenyang Normal University Shenyang China
| | - Xiaoqing Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Zhiyuan Yao
- College of Life Science, Shenyang Normal University, Shenyang 110034, Liaoning, China Shenyang Normal University Shenyang China
| | - Abid Ali
- Department of Entomology, Faculty of Agriculture, University of Agriculture, Faisalabad-38040, Punjab, Pakistan University of Agriculture Faisalabad Pakistan.,College of Life Science, Shenyang Normal University, Shenyang 110034, Liaoning, China Shenyang Normal University Shenyang China
| | - Shuqiang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
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Yuan D, Chen X, Gu H, Zou M, Zou Y, Fang J, Tao W, Dai X, Xiao S, Wang Z. Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation. Gigascience 2020; 9:giaa132. [PMID: 33231676 PMCID: PMC7684707 DOI: 10.1093/gigascience/giaa132] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/18/2020] [Accepted: 10/30/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Intense stresses caused by high-altitude environments may result in noticeable genetic adaptions in native species. Studies of genetic adaptations to high elevations have been largely limited to terrestrial animals. How fish adapt to high-elevation environments is largely unknown. Triplophysa bleekeri, an endemic fish inhabiting high-altitude regions, is an excellent model to investigate the genetic mechanisms of adaptation to the local environment. Here, we assembled a chromosomal genome sequence of T. bleekeri, with a size of ∼628 Mb (contig and scaffold N50 of 3.1 and 22.9 Mb, respectively). We investigated the origin and environmental adaptation of T. bleekeri based on 21,198 protein-coding genes in the genome. RESULTS Compared with fish species living at low altitudes, gene families associated with lipid metabolism and immune response were significantly expanded in the T. bleekeri genome. Genes involved in DNA repair exhibit positive selection for T. bleekeri, Triplophysa siluroides, and Triplophysa tibetana, indicating that adaptive convergence in Triplophysa species occurred at the positively selected genes. We also analyzed whole-genome variants among samples from 3 populations. The results showed that populations separated by geological and artificial barriers exhibited obvious differences in genetic structures, indicating that gene flow is restricted between populations. CONCLUSIONS These results will help us expand our understanding of environmental adaptation and genetic diversity of T. bleekeri and provide valuable genetic resources for future studies on the evolution and conservation of high-altitude fish species such as T. bleekeri.
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Affiliation(s)
- Dengyue Yuan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xuehui Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ming Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Yu Zou
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Jian Fang
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiangyan Dai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shijun Xiao
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei 430000, China
- College of Plant Protection, Jilin Agriculture University, Changchun, Jilin 130118, China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
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Miocene Diversification and High-Altitude Adaptation of Parnassius Butterflies (Lepidoptera: Papilionidae) in Qinghai-Tibet Plateau Revealed by Large-Scale Transcriptomic Data. INSECTS 2020; 11:insects11110754. [PMID: 33153157 PMCID: PMC7693471 DOI: 10.3390/insects11110754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 12/01/2022]
Abstract
Simple Summary Parnassius butterflies have contributed to fundamental studies in biogeography, insect–plant interactions, and other fields of conservation biology and ecology. However, the early evolutionary pattern and molecular adaptation mechanism of this alpine butterfly group to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now. In this study, we report for the first time, a relatively large-scale transcriptomic dataset of eight Parnassius species and their two closely related papilionid species, a dated phylogeny based on hundreds of gene sequences, and potential genetic mechanisms underlying the high-altitude adaptation by investigating changes in evolutionary rates and positively selected genes. Overall, our findings indicate that the transcriptome data sets reported here can provide some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, and will support further expressional and functional studies that will help interested researchers to address evolution, biodiversity and conservation questions concerning Parnassius and other butterfly species. Abstract The early evolutionary pattern and molecular adaptation mechanism of alpine Parnassius butterflies to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now, due to difficulties in sampling, limited sequence data, and time calibration issues. Here, we present large-scale transcriptomic datasets of eight representative Parnassius species to reveal the phylogenetic timescale and potential genetic basis for high-altitude adaptation with multiple analytic strategies using 476 orthologous genes. Our phylogenetic results strongly supported that the subgenus Parnassius formed a well-resolved basal clade, and the subgenera Tadumia and Kailasius were closely related in the phylogenetic trees. In addition, molecular dating analyses showed that the Parnassius began to diverge at about 13.0 to 14.3 million years ago (middle Miocene), correlated with their hostplant’s spatiotemporal distributions, as well as geological and palaeoenvironmental changes of the Qinghai–Tibet Plateau. Moreover, the accelerated evolutionary rate, candidate positively selected genes and their potentially functional changes were detected, probably contributed to the high-altitude adaptation of Parnassius species. Overall, our study provided some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, which will help to address evolution, biodiversity, and conservation questions concerning Parnassius and other butterfly species.
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15
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Zhang X, Lan T, Nie L, Li S. Eight new species of the spider genus Pimoa (Araneae, Pimoidae) from Tibet, China. Zookeys 2020; 940:79-104. [PMID: 32581632 PMCID: PMC7303224 DOI: 10.3897/zookeys.940.49793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/27/2020] [Indexed: 11/12/2022] Open
Abstract
Eight new species of the spider genus Pimoa Chamberlin & Ivie, 1943 are described from Tibet, China: P.cona Zhang & Li, sp. nov. (♂♀), P.duiba Zhang & Li, sp. nov. (♂♀), P.lemenba Zhang & Li, sp. nov. (♀), P.mainling Zhang & Li, sp. nov. (♂♀), P.nyingchi Zhang & Li, sp. nov. (♂♀), P.rongxar Zhang & Li, sp. nov. (♂♀), P.samyai Zhang & Li, sp. nov. (♂♀), and P.yadong Zhang & Li, sp. nov. (♂♀). The DNA barcodes of the eight new species are documented.
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Affiliation(s)
- Xiaoqing Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Tianqi Lan
- College of Life Science, Shenyang Normal University, Shenyang 110034, Liaoning, China Shenyang Normal University Liaoning China
| | - Lei Nie
- College of Life Science, Hebei University, Baoding, Hebei 071002, China Hebei University Baoding China
| | - Shuqiang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
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16
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Chang WJ, Li S. Thirty-one new species of the spider genus Leclercera from Southeast Asia (Araneae, Psilodercidae). Zookeys 2020; 913:1-87. [PMID: 32132849 PMCID: PMC7044255 DOI: 10.3897/zookeys.913.48650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 01/27/2020] [Indexed: 12/03/2022] Open
Abstract
Thirty-one new species of the genus Leclercera Deeleman-Reinhold, 1995 from China, Indonesia, Malaysia, Myanmar, Nepal, and Thailand are described: L.mianqiusp. nov. (♂♀), L.thamsangensissp. nov. (♂♀), L.yandousp. nov. (♂♀), L.thamkaewensissp. nov. (♂♀), L.xiangbabangsp. nov. (♂♀), L.jianzuiyusp. nov. (♂♀), L.yamaensissp. nov. (♂♀), L.banensissp. nov. (♂♀), L.dumuzhousp. nov. (♀), L.suwanensissp. nov. (♂♀), L.maochongsp. nov. (♀), L.shanzisp. nov. (♀), L.duandaisp. nov. (♂♀), L.hponensissp. nov. (♂♀), L.lizisp. nov. (♂), L.xiaodaisp. nov. (♀), L.yanjingsp. nov. (♀), L.ekteenensissp. nov. (♂), L.zhamensissp. nov. (♂), L.sanjiaosp. nov. (♀), L.selasihensissp. nov. (♂♀), L.paiensissp. nov. (♀), L.yuanzhuisp. nov. (♀), L.zanggaensissp. nov. (♀), L.aniensissp. nov. (♂♀), L.renqinensissp. nov. (♂♀), L.shergylaensissp. nov. (♂♀), L.pulongensissp. nov. (♂), L.tudaosp. nov. (♂♀), L.duibaensissp. nov. (♂), and L.jiazhongensissp. nov. (♂♀). Types are deposited in the Institute of Zoology, Chinese Academy of Sciences (IZCAS) in Beijing.
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Affiliation(s)
- Wan-Jin Chang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Shuqiang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
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17
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Magalhaes ILF, Azevedo GHF, Michalik P, Ramírez MJ. The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic. Biol Rev Camb Philos Soc 2020; 95:184-217. [PMID: 31713947 DOI: 10.1111/brv.12559] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 01/24/2023]
Abstract
Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long-standing debate in spider evolution - we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous-Paleogene (K-Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA-clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA-clade spiders.
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Affiliation(s)
- Ivan L F Magalhaes
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Guilherme H F Azevedo
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
| | - Peter Michalik
- Zoologisches Institut und Museum, Universität Greifswald, Loitzer Straβe 26, Greifswald, D-17489, Germany
| | - Martín J Ramírez
- División Aracnología, Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" - CONICET, Av. Ángel Gallardo 470, Buenos Aires, C1405DJR, Argentina
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An integrative phylogenomic approach illuminates the evolutionary history of Old World tree frogs (Anura: Rhacophoridae). Mol Phylogenet Evol 2019; 145:106724. [PMID: 31881327 DOI: 10.1016/j.ympev.2019.106724] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/14/2019] [Accepted: 12/23/2019] [Indexed: 11/24/2022]
Abstract
Rhacophoridae are one of the most speciose and ecologically diverse families of amphibians. Resolution of their evolutionary relationships is key to understanding the accumulation of biodiversity, yet previous hypotheses based on Sanger sequencing exhibit much discordance amongst generic relationships. This conflict precludes the making of sound macroevolutionary conclusions. Herein, we conduct the first phylogenomic study using broad-scale sampling and sequences of 352 nuclear DNA loci obtained using anchored hybrid enrichment targeted sequencing. The robust time-calibrated phylogenetic hypothesis clarifies several long-disputed relationships and facilitates the testing of evolutionary hypotheses on spatiotemporal diversification and reproductive modes. The major extant lineages of Rhacophoridae appear to have radiated in mainland Asia, and the spatiotemporal process corresponds with several common accumulations of biodiversity in Asia. Analyses do not detect any case of "Out of Himalaya" in Rhacophoridae. All transitions of reproductive modes appear to have evolved in an ordered, gradual sequence associated with gaining independence of standing water for larval development. The different reproductive modes are phylogenetically conserved and the completion of their transitions appear to have occurred over a period of ~30 Ma, which does not fit a pattern of a rapid burst of diversification. Innovations in reproductive modes associate statistically with the uneven distribution of species-richness between clades, where higher diversification is linked to increased terrestrial modes of reproduction. These results strengthen the hypothesis that breeding innovations drive diversification by providing new opportunities for ecological release and dispersion.
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Zhang X, Li S. On three species of the spider genus Pimoa (Araneae, Pimoidae) from China. Zookeys 2019; 855:1-13. [PMID: 31244538 PMCID: PMC6586717 DOI: 10.3897/zookeys.855.33501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/13/2019] [Indexed: 12/27/2022] Open
Abstract
Two new species of the spider genus Pimoa Chamberlin & Ivie, 1943 are described from Hunan and Yunnan Provinces, China: P.binchuanensissp. nov. (♂♀) and P.xinjianensissp. nov. (♂♀). In addition, the male of P.lata Xu & Li, 2009 is described for the first time. The DNA barcodes of the two new species are documented.
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Affiliation(s)
- Xiaoqing Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Shuqiang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
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20
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Ma X, Petrusek A, Wolinska J, Hu W, Yin M. Lineage diversity and reproductive modes of the Daphnia pulex group in Chinese lakes and reservoirs. Mol Phylogenet Evol 2019; 130:424-433. [DOI: 10.1016/j.ympev.2018.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 07/24/2018] [Accepted: 08/03/2018] [Indexed: 12/27/2022]
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Li B, Zhao Z, Chen H, Wu Z, Zhang C, Li S. Guilotes, a new genus of Coelotinae spiders from Guangxi Zhuang Autonomous Region, China (Araneae, Agelenidae). Zookeys 2018:1-17. [PMID: 30568527 PMCID: PMC6290050 DOI: 10.3897/zookeys.802.29913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/03/2018] [Indexed: 11/24/2022] Open
Abstract
A new genus of the subfamily Coelotinae F.O. Pickard-Cambridge, 1893, Guilotes Z. Zhao & S. Li, gen. n. from China is described, as well as four new species: G.ludiensis Z. Zhao & S. Li, sp. n. (♂♀, type species), G.qingshitanensis Z. Zhao & S. Li, sp. n. (♂♀), G.xingpingensis Z. Zhao & S. Li, sp. n. (♂♀) and G.yandongensis Z. Zhao & S. Li, sp. n. (♀). The DNA barcodes of all species are documented for future use.
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Affiliation(s)
- Bing Li
- College of Life Science, Langfang Normal University, Langfang 065000, Hebei Province, China Langfang Normal University Langfang China.,College of Life Science, Shenyang Normal University, Shenyang, Liaoning 110034, China Shenyang Normal University Liaoning China
| | - Zhe Zhao
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
| | - Haifeng Chen
- College of Life Science, Langfang Normal University, Langfang 065000, Hebei Province, China Langfang Normal University Langfang China
| | - Zhiyan Wu
- College of Life Science, Langfang Normal University, Langfang 065000, Hebei Province, China Langfang Normal University Langfang China
| | - Chuntian Zhang
- College of Life Science, Shenyang Normal University, Shenyang, Liaoning 110034, China Shenyang Normal University Liaoning China
| | - Shuqiang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China Institute of Zoology, Chinese Academy of Sciences Beijing China
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22
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Li F, Li S. Paleocene–Eocene and Plio–Pleistocene sea-level changes as “species pumps” in Southeast Asia: Evidence from Althepus spiders. Mol Phylogenet Evol 2018; 127:545-555. [DOI: 10.1016/j.ympev.2018.05.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/28/2018] [Accepted: 05/13/2018] [Indexed: 01/03/2023]
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Li B, Zhao Z, Zhang C, Li S. Sinodraconarius gen. n., a new genus of Coelotinae spiders from Southwest China (Araneae, Agelenidae). Zookeys 2018:117-135. [PMID: 30002592 PMCID: PMC6041365 DOI: 10.3897/zookeys.770.22470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 05/12/2018] [Indexed: 11/18/2022] Open
Abstract
A new genus of the subfamily Coelotinae F.O. Pickard-Cambridge, 1893, Sinodraconariusgen. n., with four new species, S.cawarongensissp. n. (♂♀), S.muruoensissp. n. (♂♀), S.sangjiuensissp. n. (♂♀, type species), S.yuisp. n. (♂♀) and S.patellabifidus (Wang, 2003) comb. n., ex. Draconarius Ovtchinnikov, 1999 is described. The genus is restricted to Southwest China. Sinodraconariusgen. n. is most similar to Draconarius but can be distinguished by the shape of the copulatory organs. The DNA barcodes of all species were documented for future use.
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Affiliation(s)
- Bing Li
- College of Life Science, Shenyang Normal University, Shenyang, Liaoning 110034, China
| | - Zhe Zhao
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuntian Zhang
- College of Life Science, Shenyang Normal University, Shenyang, Liaoning 110034, China
| | - Shuqiang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Fernández R, Kallal RJ, Dimitrov D, Ballesteros JA, Arnedo MA, Giribet G, Hormiga G. Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life. Curr Biol 2018; 28:1489-1497.e5. [PMID: 29706520 DOI: 10.1016/j.cub.2018.03.064] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 03/27/2018] [Indexed: 12/22/2022]
Abstract
Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic. We find no significant association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade-the most diverse araneomorph spider lineage-shows enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle.
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Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA.
| | - Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA
| | - Dimitar Dimitrov
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway; Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Jesús A Ballesteros
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA
| | - Miquel A Arnedo
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA; Department of Evolutionary Biology, Ecology and Environmental Sciences, & Biodiversity Research Institute (IRBio) Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, D.C. 20052, USA
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