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Jung T, Milenković I, Balci Y, Janoušek J, Kudláček T, Nagy Z, Baharuddin B, Bakonyi J, Broders K, Cacciola S, Chang TT, Chi N, Corcobado T, Cravador A, Đorđević B, Durán A, Ferreira M, Fu CH, Garcia L, Hieno A, Ho HH, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira L, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivuković Z, Tarigan M, Thu P, Tomić Z, Tomšovský M, Uematsu S, Webber J, Zeng HC, Zheng FC, Brasier C, Horta Jung M. Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Stud Mycol 2024; 107:251-388. [PMID: 38600961 PMCID: PMC11003442 DOI: 10.3114/sim.2024.107.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 04/12/2024] Open
Abstract
During 25 surveys of global Phytophthora diversity, conducted between 1998 and 2020, 43 new species were detected in natural ecosystems and, occasionally, in nurseries and outplantings in Europe, Southeast and East Asia and the Americas. Based on a multigene phylogeny of nine nuclear and four mitochondrial gene regions they were assigned to five of the six known subclades, 2a-c, e and f, of Phytophthora major Clade 2 and the new subclade 2g. The evolutionary history of the Clade appears to have involved the pre-Gondwanan divergence of three extant subclades, 2c, 2e and 2f, all having disjunct natural distributions on separate continents and comprising species with a soilborne and aquatic lifestyle and, in addition, a few partially aerial species in Clade 2c; and the post-Gondwanan evolution of subclades 2a and 2g in Southeast/East Asia and 2b in South America, respectively, from their common ancestor. Species in Clade 2g are soilborne whereas Clade 2b comprises both soil-inhabiting and aerial species. Clade 2a has evolved further towards an aerial lifestyle comprising only species which are predominantly or partially airborne. Based on high nuclear heterozygosity levels ca. 38 % of the taxa in Clades 2a and 2b could be some form of hybrid, and the hybridity may be favoured by an A1/A2 breeding system and an aerial life style. Circumstantial evidence suggests the now 93 described species and informally designated taxa in Clade 2 result from both allopatric non-adaptive and sympatric adaptive radiations. They represent most morphological and physiological characters, breeding systems, lifestyles and forms of host specialism found across the Phytophthora clades as a whole, demonstrating the strong biological cohesiveness of the genus. The finding of 43 previously unknown species from a single Phytophthora clade highlight a critical lack of information on the scale of the unknown pathogen threats to forests and natural ecosystems, underlining the risk of basing plant biosecurity protocols mainly on lists of named organisms. More surveys in natural ecosystems of yet unsurveyed regions in Africa, Asia, Central and South America are needed to unveil the full diversity of the clade and the factors driving diversity, speciation and adaptation in Phytophthora. Taxonomic novelties: New species: Phytophthora amamensis T. Jung, K. Kageyama, H. Masuya & S. Uematsu, Phytophthora angustata T. Jung, L. Garcia, B. Mendieta-Araica, & Y. Balci, Phytophthora balkanensis I. Milenković, Ž. Tomić, T. Jung & M. Horta Jung, Phytophthora borneensis T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora calidophila T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora catenulata T. Jung, T.-T. Chang, N.M. Chi & M. Horta Jung, Phytophthora celeris T. Jung, L. Oliveira, M. Tarigan & I. Milenković, Phytophthora curvata T. Jung, A. Hieno, H. Masuya & M. Horta Jung, Phytophthora distorta T. Jung, A. Durán, E. Sanfuentes von Stowasser & M. Horta Jung, Phytophthora excentrica T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora falcata T. Jung, K. Kageyama, S. Uematsu & M. Horta Jung, Phytophthora fansipanensis T. Jung, N.M. Chi, T. Corcobado & C.M. Brasier, Phytophthora frigidophila T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora furcata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora inclinata N.M. Chi, T. Jung, M. Horta Jung & I. Milenković, Phytophthora indonesiensis T. Jung, M. Tarigan, L. Oliveira & I. Milenković, Phytophthora japonensis T. Jung, A. Hieno, H. Masuya & J.F. Webber, Phytophthora limosa T. Corcobado, T. Majek, M. Ferreira & T. Jung, Phytophthora macroglobulosa H.-C. Zeng, H.-H. Ho, F.-C. Zheng & T. Jung, Phytophthora montana T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora multipapillata T. Jung, M. Tarigan, I. Milenković & M. Horta Jung, Phytophthora multiplex T. Jung, Y. Balci, K. Broders & M. Horta Jung, Phytophthora nimia T. Jung, H. Masuya, A. Hieno & C.M. Brasier, Phytophthora oblonga T. Jung, S. Uematsu, K. Kageyama & C.M. Brasier, Phytophthora obovoidea T. Jung, Y. Balci, L. Garcia & B. Mendieta-Araica, Phytophthora obturata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora penetrans T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora platani T. Jung, A. Pérez-Sierra, S.O. Cacciola & M. Horta Jung, Phytophthora proliferata T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora pseudocapensis T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pseudocitrophthora T. Jung, S.O. Cacciola, J. Bakonyi & M. Horta Jung, Phytophthora pseudofrigida T. Jung, A. Durán, M. Tarigan & M. Horta Jung, Phytophthora pseudoccultans T. Jung, T.-T. Chang, I. Milenković & M. Horta Jung, Phytophthora pyriformis T. Jung, Y. Balci, K.D. Boders & M. Horta Jung, Phytophthora sumatera T. Jung, M. Tarigan, M. Junaid & A. Durán, Phytophthora transposita T. Jung, K. Kageyama, C.M. Brasier & H. Masuya, Phytophthora vacuola T. Jung, H. Masuya, K. Kageyama & J.F. Webber, Phytophthora valdiviana T. Jung, E. Sanfuentes von Stowasser, A. Durán & M. Horta Jung, Phytophthora variepedicellata T. Jung, Y. Balci, K. Broders & I. Milenković, Phytophthora vietnamensis T. Jung, N.M. Chi, I. Milenković & M. Horta Jung, Phytophthora ×australasiatica T. Jung, N.M. Chi, M. Tarigan & M. Horta Jung, Phytophthora ×lusitanica T. Jung, M. Horta Jung, C. Maia & I. Milenković, Phytophthora ×taiwanensis T. Jung, T.-T. Chang, H.-S. Fu & M. Horta Jung. Citation: Jung T, Milenković I, Balci Y, Janoušek J, Kudláček T, Nagy ZÁ, Baharuddin B, Bakonyi J, Broders KD, Cacciola SO, Chang T-T, Chi NM, Corcobado T, Cravador A, Đorđević B, Durán A, Ferreira M, Fu C-H, Garcia L, Hieno A, Ho H-H, Hong C, Junaid M, Kageyama K, Kuswinanti T, Maia C, Májek T, Masuya H, Magnano di San Lio G, Mendieta-Araica B, Nasri N, Oliveira LSS, Pane A, Pérez-Sierra A, Rosmana A, Sanfuentes von Stowasser E, Scanu B, Singh R, Stanivuković Z, Tarigan M, Thu PQ, Tomić Z, Tomšovský M, Uematsu S, Webber JF, Zeng H-C, Zheng F-C, Brasier CM, Horta Jung M (2024). Worldwide forest surveys reveal forty-three new species in Phytophthora major Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity. Studies in Mycology 107: 251-388. doi: 10.3114/sim.2024.107.04.
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Affiliation(s)
- T. Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- Phytophthora Research and Consultancy, 83131 Nussdorf, Germany
| | - I. Milenković
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- University of Belgrade, Faculty of Forestry, 11030 Belgrade, Serbia
| | - Y. Balci
- USDA-APHIS Plant Protection and Quarantine, 4700 River Road, Riverdale, Maryland, 20737 USA
| | - J. Janoušek
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - T. Kudláček
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- University of Greifswald, Institute for Mathematics and Computer Science & Center for Functional Genomics of Microbes, 17489 Greifswald, Germany
| | - Z.Á. Nagy
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - B. Baharuddin
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - J. Bakonyi
- HUN-REN Centre for Agricultural Research, Plant Protection Institute, ELKH, 1022 Budapest, Hungary
| | - K.D. Broders
- Smithsonian Tropical Research Institute, Apartado Panamá, República de Panamá
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, 61604, USA
| | - S.O. Cacciola
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - T.-T. Chang
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - N.M. Chi
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, 10000 Hanoi, Vietnam
| | - T. Corcobado
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - A. Cravador
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, University of Algarve, 8005-130 Faro, Portugal
| | - B. Đorđević
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - A. Durán
- Fiber Research and Development, Asia Pacific Resources International Limited (APRIL), 28300 Pangkalan Kerinci, Riau, Indonesia
| | - M. Ferreira
- Plant Diagnostic Center, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - C.-H. Fu
- Forest Protection Division, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - L. Garcia
- Universidad Nacional Agraria, Carretera Norte, Managua 11065, Nicaragua
| | - A. Hieno
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - H.-H. Ho
- Department of Biology, State University of New York, New Paltz, New York 12561, USA
| | - C. Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
| | - M. Junaid
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - K. Kageyama
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - T. Kuswinanti
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - C. Maia
- Centre of Marine Sciences (CCMAR), University of Algarve, 8005-139 Faro, Portugal
| | - T. Májek
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - H. Masuya
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki, 305-8687, Japan
| | - G. Magnano di San Lio
- University Mediterranea of Reggio Calabria, Department of Agriculture, 89124 Reggio Calabria, Italy
| | | | - N. Nasri
- The United Graduate School of Agricultural Science, Ehime University, Matsuyama, 790-8566, Japan
| | - L.S.S. Oliveira
- Research and Development, Bracell, Alagoinhas, Bahia 48030-300, Brazil
| | - A. Pane
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy
| | - A. Pérez-Sierra
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - A. Rosmana
- Departement of Plant Pest and Disease, Faculty of Agriculture, Hasanuddin University, Makassar, 90245, South Sulawesi, Indonesia
| | - E. Sanfuentes von Stowasser
- Laboratorio de Patología Forestal, Facultad Ciencias Forestales y Centro de Biotecnología, Universidad de Concepción, 4030000 Concepción, Chile
| | - B. Scanu
- Department of Agricultural Sciences, University of Sassari, Viale Italia 39A, 07100 Sassari, Italy
| | - R. Singh
- Plant Diagnostic Center, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Z. Stanivuković
- University of Banja Luka, Faculty of Forestry, 78000 Banja Luka, Bosnia and Herzegovina
| | - M. Tarigan
- Fiber Research and Development, Asia Pacific Resources International Limited (APRIL), 28300 Pangkalan Kerinci, Riau, Indonesia
| | - P.Q. Thu
- Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, 10000 Hanoi, Vietnam
| | - Z. Tomić
- Center for Plant Protection, Croatian Agency for Agriculture and Food, 10000 Zagreb, Croatia
| | - M. Tomšovský
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
| | - S. Uematsu
- Laboratory of Molecular and Cellular Biology, Dept. of Bioregulation and Bio-interaction, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - J.F. Webber
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - H.-C. Zeng
- The Institute of Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, China
| | - F.-C. Zheng
- College of Environment and Plant Protection, Hainan University, Baodoa Xincun, Danzhou City, Hainan 571737, China
| | - C.M. Brasier
- Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH, UK
| | - M. Horta Jung
- Mendel University in Brno, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Phytophthora Research Centre, 613 00 Brno, Czech Republic
- Phytophthora Research and Consultancy, 83131 Nussdorf, Germany
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Dong PB, Wang LJ, Jia Y, Li ZH, Wang HY, Guo FX, Chen Y. Niche divergence at the intraspecific level in an endemic rare peony ( Paeonia rockii): A phylogenetic, climatic and environmental survey. FRONTIERS IN PLANT SCIENCE 2022; 13:978011. [PMID: 36388470 PMCID: PMC9663928 DOI: 10.3389/fpls.2022.978011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Ecological factors have received increasing attention as drivers of speciation but also in the maintenance of postspeciation divergence. However, the relative significance of the responses of species to climate oscillations for driving niche divergence or conservatism in the evolution of many species that pass through diverse environments and limited geographical boundaries remains poorly understood. Paeonia rockii (one of the ancient species of Paeonia) comprising two subspecies called Paeonia rockii subsp. rockii and Paeonia rockii subsp. taibaishanica is an endemic, rare, and endangered medicinal plant in China. In this study, we integrated whole chloroplast genomes, and ecological factors to obtain insights into ecological speciation and species divergence in this endemic rare peony. RAxML analysis indicated that the topological trees recovered from three different data sets were identical, where P. rockii subsp. rockii and P. rockii subsp. taibaishanica clustered together, and molecular dating analyses suggested that the two subspecies diverged 0.83 million years ago. In addition, ecological niche modeling showed that the predicted suitable distribution areas for P. rockii subsp. rockii and P. rockii subsp. taibaishanica differed considerably, although the predicted core distribution areas were similar, where the population contracted in the last interglacial and expanded in the last glacial maximum. Under the emissions scenarios for the 2050s and 2070s, the suitable distribution areas were predicted to contract significantly, where the migration routes of the two subspecies tended to migrate toward high latitudes and elevations, thereby suggesting strong responses of the distributions of the two subspecies to climate change. These findings combined with the phylogeographic relationships provide comprehensive insights into niche variation and differentiation in this endemic rare peony, and they highlight the importance of geological and climatic changes for species divergence and changes in the population geographic patterns of rare and endangered medicinal plants in East Asia.
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Affiliation(s)
- Peng-Bin Dong
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Ling-Juan Wang
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Jia
- Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) College of Life Sciences, Northwest University, Xi’an, China
| | - Hong-Yan Wang
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Feng-Xia Guo
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Yuan Chen
- College of Agronomy, College of Life Science and Technology, State Key Laboratory of Arid land Crop Science, Gansu Agricultural University, Lanzhou, China
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Vernygora OV, Campbell EO, Grishin NV, Sperling FA, Dupuis JR. Gauging ages of tiger swallowtail butterflies using alternate SNP analyses. Mol Phylogenet Evol 2022; 171:107465. [DOI: 10.1016/j.ympev.2022.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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Luo Y, Bourgoin T, Zhang JL, Feng JN. Distribution patterns of Chinese Cixiidae (Hemiptera, Fulgoroidea), highlight their high endemic diversity. Biodivers Data J 2022; 10:e75303. [PMID: 35110967 PMCID: PMC8803750 DOI: 10.3897/bdj.10.e75303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/13/2022] [Indexed: 11/12/2022] Open
Abstract
Background Cixiidae are small strictly phytophagous hemipteran insects worldwide distributed. Ecology and systematics of Chinese fauna remains poorly investigated. For instance, does their distribution follows the patterns of biogeogaphical distribution established for their host plants or other related-taxa because they are all obligatory phytophagous taxa? Do they follow the usual distributional Chinese realms and boundaries already recognized? Which zoogeographical Chinese regions and connections between them do they depict. To investigate these issues, we provide here a referenced and comprehensive checklist of the 250 cixiid species currently reported from China (77 new records), with their precise distribution at the regional level. In the 8 Chinese main zoogeographical regions usually recognized and 2 adjacent areas, we analyzed further their diversity at the tribal, generic, and specific levels using a non-metric multidimensional scaling and an unweighted pairwise group analysis using an arithmetic mean cluster analyses. The observed distribution patterns shown that an intercalary Sino-Japanese realm is recognisable between the Palaearctic and Oriental realms. At the regional level, the South China region clusters more closely with the Southwest, Central and North China regions. Taiwan, clearly separated from the South China region and mainland China, is more closely related to the Qinghai-Tibet region and Indochina countries. Although Central and South China regions remain close to each other, the Qinghai-Tibet region appears singularly different. New information An updated checklist of the 250 Cixiidae species, known to occur in China and counting for 10% of the Chinese planthopper fauna, is presented based on literature, recent collections, and museum records. More than 400 records distributed among the 28 provinces and 8 regions in China are extensively provided, including 77 new records. Of these, more than 80% of the species (205 species, 82%) have been only reported from China, and most of them are endemic species, which could reflects the great diversity degree of the Chinese regions and local biotypes highlights the uniqueness of this fauna. These species are found in 8 Chinese zoogeographical regions: The Taiwan region is the most diversified with 161 species and the highest rate of endemic species (69.57%), followed by South China (78 species, 17.95%), Central China (60 species, 33.33%), Southwest China (43 species, 39.53%), North China (29 species, 34.48%), Qinghai-Tibet region (10 species, 20%), Northeast China (8 species, 12.5%), and 5 species found in the Inner Mongolia-Xinjiang region that are not endemic ones. Endemism was analyzed for each region and repeated for species distribution patterns across them, 9 being bi-regionally and tri-regionally distributed. The South China-Taiwan pattern is the most richest one, followed by the Central-South China-Taiwan pattern. Semonini and Pentastirini tribes are widespread among all the zoological regions, representing respectively 21.20% and 17.20% of all the species, while Cixiini being is the most common tribe with 45.20%, remains absent from the North-Eastern China region. Andini with only 5.20% of the species is distributed in the Sino-Japanese - Oriental Region; Eucarpini (6.40%) and Borysthenini (2.00%) are mainly concentrated in the south of the Qingling Mountain-Huai River. The remaining four tribes, Bennini (0.40%), Briixini (0.80%), Oecleini (1.20%) and Stenophlepsiini (0.40%) are relatively rare and restricted to Taiwan. At the generic level, Kuvera (7.2%) is the most widely distributed genus in China while Cixius, Betacixius, Kuvera, Oecleopsis and Andes are the more diversified. One genus (Oliparisca) is distributed only in the Tibet region, while 10 genera are distributed only in the Taiwan region. In addition, nearly half of the genera (16 genera, 48.48%) are distributed south of the Palearctic/Oriental boundary. A non-metric multidimensional scaling and an unweighted pairwise group method analysis using arithmetic mean clustering based on the Jaccard similarity coefficient matrix support a Palaearctic/Sino-Japanese boundary and a South China region closer to the Southwest, Central and North China regions. The Taiwan region appears clearly separated from the South China region and to mainland China, and more closely related to the Qinghai-Tibet region and Indochina countries. The Central and South China regions appear close to each other, but the Qinghai-Tibet region is singularly isolated.
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Gao Y, Yin S, Chu H, Zhang Y, Wang H, Chen H, Liu C, Dai D, Tang L. Genome-Wide SNPs Provide Insights on the Cryptic Genetic Structure and Signatures of Climate Adaption in Amorphophallus albus Germplasms. FRONTIERS IN PLANT SCIENCE 2021; 12:683422. [PMID: 34367210 PMCID: PMC8343094 DOI: 10.3389/fpls.2021.683422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Domesticated species represent unique systems in which the evolutionary genomic consequences of intensive selective breeding and adaptation can be thoroughly investigated. Amorphophallus albus occurs naturally and is in cultivation throughout the downstream region of the Jinshajiang River in Southwest China. This species is characterised by high konjac glucomannan content, and has been cultivated in China for nearly 2,000 years. To study genetic differentiation and local adaption of A. albus, we sampled 13 distinct local cultivated populations of this species. Restriction site-associated DNA sequencing was conducted with 87 samples, resulting in 24,225 SNPs. The population structure analyses suggest two main genetic groups: one in the relatively upstream region, and one downstream. We found evidence of additional sub-structure within the upstream group, demonstrating the statistical power of genomic SNPs in discovering subtle genetic structure. The environmental and geographic factors were all identified as significant in shaping the genetic differentiation of this species. Notably, the proportion of environmental factors was larger than geographic factors in influencing the population genetic patterns of A. albus. We also discovered loci that were associated with local adaptation. These findings will help us understand the genetic differentiation of this newly domesticated species, thereby informing future breeding programs of A. albus.
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Zhang K, Qian Q, Mao Y, Xu Y, Yang Y, Chen Y, Wang X. Characterization of growth phenotypes and gastrointestinal tract microbiota in sheep fed with caragana. J Appl Microbiol 2021; 131:2763-2779. [PMID: 33998744 DOI: 10.1111/jam.15138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/22/2021] [Accepted: 05/10/2021] [Indexed: 01/15/2023]
Abstract
AIMS Using high-protein caragana as an unconventional feed supplement has promising application potential in livestock feeding programmes, and verifying its function is of great importance to guide efficient dietary management of livestock. METHODS AND RESULTS This study investigated the resulting changes in the growth, slaughter performance, serum physiological index, physical and chemical characteristics of meat, ruminal and intestine morphology and gastrointestinal tract microbiota in sheep fed with caragana (CAR), corn straw (COR) and alfalfa (ALF) diets. The CAR group showed an increased abundance of Christensenellaceae R-7 group, Marvinbryantia, Ruminococcaceae NK4A214, Lachnospiraceae UCG-002 and Desulfuromonas in the rumen compared with ALF, and CAR group mainly enhanced starch and sucrose metabolism, fructose and mannose metabolism, photosynthesis and d-alanine metabolism in the rumen compared with ALF. CONCLUSIONS CAR diet positively changed the fatty acid profile of longissimus dorsi muscle and significantly altered the composition and function of the microbiota in the rumen, ileum and cecum. SIGNIFICANCE AND IMPACT OF THE STUDY This study systematically demonstrated the feasibility of CAR as an alternative to ALF for animal fattening in a complete formula granulated feed and provided a fundamental basis for further research and development of CAR as an unconventional feed source for ruminants.
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Affiliation(s)
- K Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Q Qian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Mao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Y Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - X Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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7
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Jung T, Horta Jung M, Webber JF, Kageyama K, Hieno A, Masuya H, Uematsu S, Pérez-Sierra A, Harris AR, Forster J, Rees H, Scanu B, Patra S, Kudláček T, Janoušek J, Corcobado T, Milenković I, Nagy Z, Csorba I, Bakonyi J, Brasier CM. The Destructive Tree Pathogen Phytophthora ramorum Originates from the Laurosilva Forests of East Asia. J Fungi (Basel) 2021; 7:jof7030226. [PMID: 33803849 PMCID: PMC8003361 DOI: 10.3390/jof7030226] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022] Open
Abstract
As global plant trade expands, tree disease epidemics caused by pathogen introductions are increasing. Since ca 2000, the introduced oomycete Phytophthora ramorum has caused devastating epidemics in Europe and North America, spreading as four ancient clonal lineages, each of a single mating type, suggesting different geographical origins. We surveyed laurosilva forests for P. ramorum around Fansipan mountain on the Vietnam-China border and on Shikoku and Kyushu islands, southwest Japan. The surveys yielded 71 P. ramorum isolates which we assigned to eight new lineages, IC1 to IC5 from Vietnam and NP1 to NP3 from Japan, based on differences in colony characteristics, gene x environment responses and multigene phylogeny. Molecular phylogenetic trees and networks revealed the eight Asian lineages were dispersed across the topology of the introduced European and North American lineages. The deepest node within P. ramorum, the divergence of lineages NP1 and NP2, was estimated at 0.5 to 1.6 Myr. The Asian lineages were each of a single mating type, and at some locations, lineages of "opposite" mating type were present, suggesting opportunities for inter-lineage recombination. Based on the high level of phenotypic and phylogenetic diversity in the sample populations, the coalescence results and the absence of overt host symptoms, we conclude that P. ramorum comprises many anciently divergent lineages native to the laurosilva forests between eastern Indochina and Japan.
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Affiliation(s)
- Thomas Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
- Phytophthora Research and Consultancy, 83131 Nußdorf, Germany
- Correspondence: (T.J.); (C.M.B.); Tel.: +420-545136172 (T.J.)
| | - Marília Horta Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
- Phytophthora Research and Consultancy, 83131 Nußdorf, Germany
| | - Joan F. Webber
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan; (K.K.); (A.H.)
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan; (K.K.); (A.H.)
| | - Hayato Masuya
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki 305-8687, Japan;
| | - Seiji Uematsu
- Departament of Bioregulation and Biointeraction, Laboratory of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan;
| | - Ana Pérez-Sierra
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Anna R. Harris
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Jack Forster
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Helen Rees
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Bruno Scanu
- Department of Agricultural Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Sneha Patra
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
- Laboratory of Ecological Plant Physiology, CzechGlobe, Global Change Research Institute of the Czech Academy of Sciences, 603 00 Brno, Czech Republic
| | - Tomáš Kudláček
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Josef Janoušek
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Tamara Corcobado
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Ivan Milenković
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Zoltán Nagy
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Ildikó Csorba
- Centre for Agricultural Research, Plant Protection Institute, ELKH, H-1022 Budapest, Hungary; (I.C.); (J.B.)
| | - József Bakonyi
- Centre for Agricultural Research, Plant Protection Institute, ELKH, H-1022 Budapest, Hungary; (I.C.); (J.B.)
| | - Clive M. Brasier
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
- Correspondence: (T.J.); (C.M.B.); Tel.: +420-545136172 (T.J.)
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8
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Pezzotti G, Ohgitani E, Shin‐Ya M, Adachi T, Marin E, Boschetto F, Zhu W, Mazda O. Instantaneous "catch-and-kill" inactivation of SARS-CoV-2 by nitride ceramics. Clin Transl Med 2020; 10:e212. [PMID: 33135340 PMCID: PMC7568850 DOI: 10.1002/ctm2.212] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/17/2022] Open
Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics LaboratoryKyoto Institute of TechnologyKyotoJapan
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
| | - Eriko Ohgitani
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
| | - Masaharu Shin‐Ya
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
| | - Tetsuya Adachi
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
| | - Elia Marin
- Ceramic Physics LaboratoryKyoto Institute of TechnologyKyotoJapan
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
| | - Francesco Boschetto
- Ceramic Physics LaboratoryKyoto Institute of TechnologyKyotoJapan
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
| | - Wenliang Zhu
- Ceramic Physics LaboratoryKyoto Institute of TechnologyKyotoJapan
| | - Osam Mazda
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKyotoJapan
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9
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Sahibzada S, Pang S, Hernández-Jover M, Jordan D, Abraham S, O'Dea M, Heller J. Prevalence and antimicrobial resistance of MRSA across different pig age groups in an intensive pig production system in Australia. Zoonoses Public Health 2020; 67:576-586. [PMID: 32458580 DOI: 10.1111/zph.12721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/21/2019] [Accepted: 04/14/2020] [Indexed: 01/22/2023]
Abstract
This observational study aimed to determine MRSA prevalence using strain-specific real-time PCR at the pig level, stratified by age groupings, within a pig enterprise. A total of 658 samples were collected from individual pigs (n = 618) and the piggery environment (n = 40), distributed amongst five different pig age groups. Presumptive MRSA isolates were confirmed by the presence of mecA, and MALDI-TOF was performed for species verification. All isolates were tested against 18 different antimicrobials. MRSA was isolated from 75.2% (95% CI 71.8-78.6) of samples collected from pigs, and 71% of the MRSA isolates from this source were identified as community-associated (CA)-MRSA ST93, while the remainder were livestock-associated (LA)-MRSA ST398. Amongst environmental isolates, 80% (CI 64.3-95.7) were ST93 and the remainder ST398. All MRSA isolates from pigs and the environment were susceptible to ciprofloxacin, gentamicin, linezolid, mupirocin, rifampicin, sulfamethoxazole-trimethoprim, teicoplanin and vancomycin. Phenotypic rates of resistance were penicillin (100%), clindamycin (97.6%), erythromycin (96.3%), ceftiofur (93.7%), chloramphenicol (81.2%), tetracycline (63.1%) and amoxicillin-clavulanate (63.9%). A low prevalence of resistance (9.2%) was observed against neomycin and quinupristin-dalfopristin. The probability of MRSA carriage in dry sows (42.2%) was found to be significantly lower (p < .001) when compared to other age groups: farrowing sows (76.8%, RR1.82), weaners (97.8%, RR 2.32), growers (94.2%, RR 2.23) and finishers (98.3%, RR 2.33). Amongst different production age groups, a significant difference was also found in antimicrobial resistance for amoxicillin-clavulanate, neomycin, chloramphenicol and tetracycline. Using the RT-PCR assay adopted in this study, filtering of highly prevalent ST93 and non-ST93 isolates was performed at high throughput and low cost. In conclusion, this study found that weaner pigs presented a higher risk for CA-MRSA and antimicrobial resistance compared to other age groups. These findings have major implications for how investigations of MRSA outbreaks should be approached under the One-Health context.
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Affiliation(s)
- Shafi Sahibzada
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia.,School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.,Graham Centre for Agricultural Innovation, Wagga Wagga, NSW, Australia
| | - Stanley Pang
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia.,PathWest Laboratory Medicine - WA, Fiona Stanley Hospital, Murdoch, Australia
| | - Marta Hernández-Jover
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.,Graham Centre for Agricultural Innovation, Wagga Wagga, NSW, Australia
| | - David Jordan
- New South Wales Department of Primary Industries, Wollongbar, NSW, Australia
| | - Sam Abraham
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Mark O'Dea
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Jane Heller
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.,Graham Centre for Agricultural Innovation, Wagga Wagga, NSW, Australia
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10
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Chen Z, Li H, Zhai X, Zhu Y, He Y, Wang Q, Li Z, Jiang J, Xiong R, Chen X. Phylogeography, speciation and demographic history: Contrasting evidence from mitochondrial and nuclear markers of the Odorrana graminea sensu lato (Anura, Ranidae) in China. Mol Phylogenet Evol 2020; 144:106701. [DOI: 10.1016/j.ympev.2019.106701] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/21/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
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11
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Rambo IM, Dombrowski N, Constant L, Erdner D, Baker BJ. Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus. Environ Microbiol 2019; 22:1764-1783. [PMID: 31775181 DOI: 10.1111/1462-2920.14878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 11/13/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.
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Affiliation(s)
- Ian M Rambo
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA.,NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, Den Burg, The Netherlands
| | - Lauren Constant
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Deana Erdner
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin, 750 Channel View Drive, Port Aransas, TX, 78373, USA
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12
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Pan T, Sun Z, Lai X, Orozcoterwengel P, Yan P, Wu G, Wang H, Zhu W, Wu X, Zhang B. Hidden species diversity in Pachyhynobius: A multiple approaches species delimitation with mitogenomes. Mol Phylogenet Evol 2019; 137:138-145. [PMID: 31085325 DOI: 10.1016/j.ympev.2019.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 01/16/2023]
Abstract
The lack of distinct morphological features of cryptic species is a hard problem for taxonomy, especially when the taxa are closely related with considerable amounts of ancestral polymorphism. Lately, intensive coalescent-based analyses involving multiple loci have become the preferred method to assess the extent of genetic distinctiveness in otherwise phenotypically similar populations. Previously, phylogenetic studies on Pachyhynobius shangchengensis uncovered five extremely deeply divergent clades, which suggested that this species may be a cryptic species complex. In this study, we used the complete mitochondrial genome data and samples from the entire range of stout salamander (Pachyhynobius), as well as publicly available mitochondrial genomes to assess species boundaries within this genus using a suite of diverse methodologies (e.g. general mixed Yule coalescent model, Automatic Barcode Gap Discovery). The phylogenetic relationships recovered two major groups within P. shangchengensis, with one group formed by four of the six extant populations and corresponding to the central and eastern range of the Dabie mountains, while the other group encompassed two other lineages in the north west of the Dabie mountain range. The species delimitation comparison within Pachyhynobius supported the presence of recognized species within the genus, and consensus was observed across methods for the existence of up to five cryptic species within what has been traditionally considered to be P. shangchengensis. While this implies the existence of four taxa in addition to the described P. shangchengensis species, morphological data and life history information are further required to contribute to the species definition. The observed pattern of genetic variation is likely the outcome of a discontinuous habitat combined with niche conservatism, which produced the sky-island effect observed in Pachyhynobius, and which led to formation of a hidden species diversity in this genus.
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Affiliation(s)
- Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; School of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Zhonglou Sun
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Department of Medicine, University of Utah, Salt Lake City 84112, UT, United States
| | - Xinlei Lai
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China
| | | | - Peng Yan
- School of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Guiyou Wu
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China
| | - Weiquan Zhu
- Department of Medicine, University of Utah, Salt Lake City 84112, UT, United States
| | - Xiaobing Wu
- School of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei 230601, Anhui, China.
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13
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Gao C, Chen J, Li Y, Jiang LY, Qiao GX. Congruent patterns between species richness and areas of endemism of the Greenideinae aphids (Hemiptera: Aphididae) revealed by global-scale data. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Chao Gao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, P.R. China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
| | - Yang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
| | - Li-Yun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, P.R. China
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14
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Wang J, Feng C, Jiao T, Von Wettberg EB, Kang M. Genomic Signature of Adaptive Divergence despite Strong Nonadaptive Forces on Edaphic Islands: A Case Study of Primulina juliae. Genome Biol Evol 2017; 9:3495-3508. [PMID: 29272422 PMCID: PMC5751081 DOI: 10.1093/gbe/evx263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2017] [Indexed: 12/28/2022] Open
Abstract
Both genetic drift and divergent selection are expected to be strong evolutionary forces driving population differentiation on edaphic habitat islands. However, the relative contribution of genetic drift and divergent selection to population divergence has rarely been tested simultaneously. In this study, restriction-site associated DNA-based population genomic analyses were applied to assess the relative importance of drift and divergent selection on population divergence of Primulina juliae, an edaphic specialist from southern China. All populations were found with low standing genetic variation, small effective population size (NE), and signatures of bottlenecks. Populations with the lowest genetic variation were most genetically differentiated from other populations and the extent of genetic drift increased with geographic distance from other populations. Together with evidence of isolation by distance, these results support neutral drift as a critical evolutionary driver. Nonetheless, redundancy analysis revealed that genomic variation is significantly associated with both edaphic habitats and climatic factors independently of spatial effects. Moreover, more genomic variation was explained by environmental factors than by geographic variables, suggesting that local adaptation might have played an important role in driving population divergence. Finally, outlier tests and environment association analyses identified 31 single-nucleotide polymorphisms as candidates for adaptive divergence. Among these candidates, 26 single-nucleotide polymorphisms occur in/near genes that potentially play a role in adaptation to edaphic specialization. This study has important implications that improve our understanding of the joint roles of genetic drift and adaptation in generating population divergence and diversity of edaphic specialists.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chao Feng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tenglong Jiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Myanmar
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15
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Sun Z, Pan T, Hu C, Sun L, Ding H, Wang H, Zhang C, Jin H, Chang Q, Kan X, Zhang B. Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses. PLoS One 2017; 12:e0184529. [PMID: 28892502 PMCID: PMC5593203 DOI: 10.1371/journal.pone.0184529] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/25/2017] [Indexed: 11/29/2022] Open
Abstract
The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.
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Affiliation(s)
- Zhonglou Sun
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| | - Tao Pan
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| | - Chaochao Hu
- School of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Lu Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hengwu Ding
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Hui Wang
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
| | - Chenling Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, China
| | - Hong Jin
- School of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
- Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Qing Chang
- School of Life Science, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xianzhao Kan
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui, China
| | - Baowei Zhang
- School of Life Sciences, Anhui Key Laboratory of Eco-engineering and Bio-technique, Anhui University, Hefei, Anhui, China
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