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Buckley SJ, Brauer CJ, Unmack PJ, Hammer MP, Adams M, Beatty SJ, Morgan DL, Beheregaray LB. Long-term climatic stability drives accumulation and maintenance of divergent freshwater fish lineages in a temperate biodiversity hotspot. Heredity (Edinb) 2024; 133:149-159. [PMID: 38918613 PMCID: PMC11349885 DOI: 10.1038/s41437-024-00700-6] [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: 02/27/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
Anthropogenic climate change is forecast to drive regional climate disruption and instability across the globe. These impacts are likely to be exacerbated within biodiversity hotspots, both due to the greater potential for species loss but also to the possibility that endemic lineages might not have experienced significant climatic variation in the past, limiting their evolutionary potential to respond to rapid climate change. We assessed the role of climatic stability on the accumulation and persistence of lineages in an obligate freshwater fish group endemic to the southwest Western Australia (SWWA) biodiversity hotspot. Using 19,426 genomic (ddRAD-seq) markers and species distribution modelling, we explored the phylogeographic history of western (Nannoperca vittata) and little (Nannoperca pygmaea) pygmy perches, assessing population divergence and phylogenetic relationships, delimiting species and estimating changes in species distributions from the Pliocene to 2100. We identified two deep phylogroups comprising three divergent clusters, which showed no historical connectivity since the Pliocene. We conservatively suggest these represent three isolated species with additional intraspecific structure within one widespread species. All lineages showed long-term patterns of isolation and persistence owing to climatic stability but with significant range contractions likely under future climate change. Our results highlighted the role of climatic stability in allowing the persistence of isolated lineages in the SWWA. This biodiversity hotspot is under compounding threat from ongoing climate change and habitat modification, which may further threaten previously undetected cryptic diversity across the region.
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Affiliation(s)
- Sean James Buckley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
- School of Biological Sciences, University of Western Australia, Perth, WA, 6000, Australia
- Molecular Ecology and Evolution Group, School of Science, Edith Cowan University, Joondalup, WA, 6027, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, University of Canberra, Canberra, ACT 2601, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT, 0801, Australia
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Stephen J Beatty
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - David L Morgan
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia.
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Pallarés S, Ortego J, Carbonell JA, Franco-Fuentes E, Bilton DT, Millán A, Abellán P. Genomic, morphological and physiological data support fast ecotypic differentiation and incipient speciation in an alpine diving beetle. Mol Ecol 2024; 33:e17487. [PMID: 39108249 DOI: 10.1111/mec.17487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/31/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024]
Abstract
An intricate interplay between evolutionary and demographic processes has frequently resulted in complex patterns of genetic and phenotypic diversity in alpine lineages, posing serious challenges to species delimitation and biodiversity conservation planning. Here we integrate genomic data, geometric morphometric analyses and thermal tolerance experiments to explore the role of Pleistocene climatic changes and adaptation to alpine environments on patterns of genomic and phenotypic variation in diving beetles from the taxonomically complex Agabus bipustulatus species group. Genetic structure and phylogenomic analyses revealed the presence of three geographically cohesive lineages, two representing trans-Palearctic and Iberian populations of the elevation-generalist A. bipustulatus and another corresponding to the strictly-alpine A. nevadensis, a narrow-range endemic taxon from the Sierra Nevada mountain range in southeastern Iberia. The best-supported model of lineage divergence, along with the existence of pervasive genetic introgression and admixture in secondary contact zones, is consistent with a scenario of population isolation and connectivity linked to Quaternary climatic oscillations. Our results suggest that A. nevadensis is an alpine ecotype of A. bipustulatus, whose genotypic, morphological and physiological differentiation likely resulted from an interplay between population isolation and local altitudinal adaptation. Remarkably, within the Iberian Peninsula, such ecotypic differentiation is unique to Sierra Nevada populations and has not been replicated in other alpine populations of A. bipustulatus. Collectively, our study supports fast ecotypic differentiation and incipient speciation processes within the study complex and points to Pleistocene glaciations and local adaptation along elevational gradients as key drivers of biodiversity generation in alpine environments.
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Affiliation(s)
- Susana Pallarés
- Department of Zoology, University of Seville, Seville, Spain
| | - Joaquín Ortego
- Department of Ecology and Evolution, Estación Biológica de Doñana, EBD-CSIC, Seville, Spain
| | | | | | - David T Bilton
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
- Department of Zoology, University of Johannesburg, Johannesburg, South Africa
| | - Andrés Millán
- Department of Ecology and Hydrology, University of Murcia, Murcia, Spain
| | - Pedro Abellán
- Department of Zoology, University of Seville, Seville, Spain
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3
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Alexander N, de Flamingh A, Cosentino BJ, Schooley RL. Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies. J Hered 2024; 115:565-574. [PMID: 38982643 PMCID: PMC11334213 DOI: 10.1093/jhered/esae035] [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: 02/19/2024] [Accepted: 07/08/2024] [Indexed: 07/11/2024] Open
Abstract
Range contraction and expansion from glaciation have led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat loss, we recommend that G. b. illinoensis be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units.
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Affiliation(s)
- Nathan Alexander
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, United States
| | - Alida de Flamingh
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
| | - Bradley J Cosentino
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, United States
| | - Robert L Schooley
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, United States
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4
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Wu Y, Linan AG, Hoban S, Hipp AL, Ricklefs RE. Divergent ecological selection maintains species boundaries despite gene flow in a rare endemic tree, Quercus acerifolia (maple-leaf oak). J Hered 2024; 115:575-587. [PMID: 38881254 DOI: 10.1093/jhered/esae033] [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: 10/06/2023] [Accepted: 06/11/2024] [Indexed: 06/18/2024] Open
Abstract
Strong gene flow from outcrossing relatives tends to blur species boundaries, while divergent ecological selection can counteract gene flow. To better understand how these two forces affect the maintenance of species boundaries, we focused on a species complex including a rare species, maple-leaf oak (Quercus acerifolia), which is found in only four disjunct ridges in Arkansas. Its limited range and geographic proximity to co-occurring close relatives create the possibility for genetic swamping. In this study, we gathered genome-wide single nucleotide polymorphisms (SNPs) using restriction-site-associated DNA sequencing (RADseq) from 190 samples of Q. acerifolia and three of its close relatives, Q. shumardii, Q. buckleyi, and Q. rubra. We found that Q. shumardii and Q. acerifolia are reciprocally monophyletic with low support, suggesting incomplete lineage sorting, introgression between Q. shumardii and Q. acerifolia, or both. Analyses that model allele distributions demonstrate that admixture contributes strongly to this pattern. Populations of Q. acerifolia experience gene flow from Q. shumardii and Q. rubra, but we found evidence that divergent selection is likely maintaining species boundaries: 1) ex situ collections of Q. acerifolia have a higher proportion of hybrids compared to the mature trees of the wild populations, suggesting ecological selection against hybrids at the seed/seedling stage; 2) ecological traits co-vary with genomic composition; and 3) Q. acerifolia shows genetic differentiation at loci hypothesized to influence tolerance of radiation, drought, and high temperature. Our findings strongly suggest that in maple-leaf oak, selection results in higher divergence at regions of the genome despite gene flow from close relatives.
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Affiliation(s)
- Yingtong Wu
- Biology Department, University of Missouri-St. Louis, St. Louis, MO, United States
- Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO, United States
| | - Alexander G Linan
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, United States
| | - Sean Hoban
- Center for Tree Science, The Morton Arboretum, Lisle, IL, United States
| | - Andrew L Hipp
- Center for Tree Science, The Morton Arboretum, Lisle, IL, United States
- The Field Museum, Integrative Research Center, Chicago, IL, United States
| | - Robert E Ricklefs
- Biology Department, University of Missouri-St. Louis, St. Louis, MO, United States
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5
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Peñafiel Loaiza N, Chafe AH, Moraes R M, Oleas NH, Roncal J. Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products. Evol Appl 2024; 17:e13765. [PMID: 39091352 PMCID: PMC11291087 DOI: 10.1111/eva.13765] [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: 04/06/2023] [Revised: 06/30/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that P. cocoides is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild Parajubaea individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.
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Affiliation(s)
- Nicolás Peñafiel Loaiza
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
- Present address:
Chone y BabahoyoLojaEcuador
| | - Abigail H. Chafe
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Mónica Moraes R
- Herbario Nacional de Bolivia, Instituto de EcologíaUniversidad Mayor de San AndrésLa PazBolivia
| | - Nora H. Oleas
- Centro de Investigación de la Biodiversidad y Cambio Climático – BioCamb e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio AmbienteUniversidad IndoaméricaQuitoEcuador
| | - Julissa Roncal
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
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Rodríguez-Buján I, Díaz-Tapia P, Fagúndez J. Genetic and morphological evidence support the specific status of the endemic Ericaandevalensis (Ericales, Ericaceae). PHYTOKEYS 2024; 244:57-76. [PMID: 39006938 PMCID: PMC11245639 DOI: 10.3897/phytokeys.244.120914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/23/2024] [Indexed: 07/16/2024]
Abstract
Assessing the taxonomic status of closely related taxa is crucial in plant systematics and can have important implications for conservation and human plant use. Ericaandevalensis Cabezudo & Rivera is a metallophyte endemic species from highly metal-polluted soils of SW Iberian Peninsula, an area with a mining history going back more than 5,000 years. Ericaandevalensis is closely related to Ericamackayana Bab., a northern Iberian species also present in western Ireland. The status of E.andevalensis as a species or subspecies subordinated to E.mackayana is subject to debate. Here, we assessed the genetic and phenotypic relationship between both species, including the population structure of E.andevalensis. We used high throughput sequencing to determine genome-wide Single Nucleotide Polymorphisms (SNPs), and morphometric analyses from 35 reproductive and vegetative traits. The morphological analysis showed at least eight characters that can discriminate the two species, from which ovary hairiness and the size of leaf glandular hairs were the most informative. Genetic analyses showed that each species formed a monophyletic cluster with full support, separated by an interspecific genetic distance >4-fold higher than intra-specific distance. Population genetic analyses of E.andevalensis shows that populations are highly structured, with the Portuguese one as the most isolated and less variable. These results support the recognition of E.andevalensis as a distinct species with a highly constrained ecological requirements and a narrow geographic distribution, but with a limited gene flow between populations. We discuss the implications of these outcomes in conservation policies and potential uses of E.andevalensis such as decontamination of polluted soils.
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Affiliation(s)
- Iván Rodríguez-Buján
- Universidade da Coruña, BIOCOST research group, Centro Interdisciplinar de Química e Bioloxía (CICA), Rúa As Carballeiras, 15071, A Coruña, Spain
| | - Pilar Díaz-Tapia
- Universidade da Coruña, Facultade de Ciencias, Departamento de Bioloxía, 15071, A Coruña, Spain
| | - Jaime Fagúndez
- Universidade da Coruña, BIOCOST research group, Centro Interdisciplinar de Química e Bioloxía (CICA), Rúa As Carballeiras, 15071, A Coruña, Spain
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7
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Takada Y, Kanavillil N. Hierarchical diversity partitioning of microscopic epibiont community on intertidal molluscan shells and inert surfaces over three geographic regions in Japan. Oecologia 2024; 205:351-364. [PMID: 38831021 DOI: 10.1007/s00442-024-05575-2] [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: 10/30/2023] [Accepted: 05/27/2024] [Indexed: 06/05/2024]
Abstract
Microscopic epibionts on molluscan shells are a component of the biodiversity of intertidal coastal areas. Because molluscan shells are discrete habitats for the epibiont community, and the molluscan basibionts belong to the local community, epibiont diversity can be evaluated hierarchically by basibiont categories including species. To evaluate the structure of epibiont diversity and effects of taxonomic resolution on the evaluation, epibionts on molluscan shells and inert surfaces were investigated at three geographically distant sites in Japan. In total, 94 species-level taxonomic units of epibionts were obtained from 31 basibiont molluscan species and inert surfaces (plastics and rock chips). The density and the species richness at the site of the lowest latitude were significantly lower than those at the other sites. The epibiont community differed between the three sites, although the major portion of the epibionts were diatoms. Between-site diversity contributed most of the total diversity of the species richness and Simpson diversity in the five levels of the hierarchical partitioning: sample (individual basibiont), basibiont species (molluscan species), surface group (bivalves, chitons + limpets, and globose gastropods), site, and the total. The taxonomic resolution did not markedly affect the variability of communities between the three sites, although the taxon richness was reduced to 51 in the genus-level analysis. The lower taxonomic resolution (genus level); however, increased the contribution of the within-sample and decreased the contribution of β diversities at the higher hierarchies, leading to a possible overestimation of biotic homogenization between the communities.
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Affiliation(s)
- Yoshitake Takada
- Japan Fisheries Research and Education Agency, Fukuura 2-12-4, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan.
| | - Nandakumar Kanavillil
- Department of Sustainability Sciences, Lakehead University, 500 University Ave, Orillia, ON, L3V 0B9, Canada
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Zhang W, Lin K, Fu W, Xie J, Fan X, Zhang M, Luo H, Yin Y, Guo Q, Huang H, Chen T, Lin X, Yuan Y, Huang C, Du S. Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey. Genes (Basel) 2024; 15:398. [PMID: 38674333 PMCID: PMC11049310 DOI: 10.3390/genes15040398] [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: 02/17/2024] [Revised: 03/17/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from Meihuashan were divided into two groups; one group included three individuals who had a closer relationship with pureblood SCTs than another group. The three individuals shared more that 40% of their genome with pureblood SCTs and might be potential individuals for genetic rescuing in SCTs. A large-scale genetic survey based on 319 pureblood SCTs showed that the mean microsatellite inbreeding coefficient of pureblood SCTs decreased significantly from 0.1789 to 0.0600 (p = 0.000009) and the ratio of heterozygous loci increased significantly from 38.5% to 43.2% (p = 0.02) after one individual of the Chongqing line joined the Suzhou line and began to breed in the mid-1980s, which is a reason why the current SCTs keep a moderate level of microsatellite heterozygosity and nucleotide diversity. However, it is important to establish a back-up population based on the three individuals through introducing one pureblood SCT into the back-up population every year. The back-up population should be an important reserve in case the pureblood SCTs are in danger in the future.
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Affiliation(s)
- Wenping Zhang
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
| | - Kaixiong Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Wenyuan Fu
- Longyan Geopark Protection and Development Center, Longyan 364201, China
| | - Junjin Xie
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Xueyang Fan
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Mingchun Zhang
- China Conservation and Research Center for the Giant Panda, Chengdu 611830, China;
| | - Hongxing Luo
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | | | - Qiang Guo
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
| | - He Huang
- Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Tengteng Chen
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Xipan Lin
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | | | - Cheng Huang
- Fujian Meihuashan Institute of South China Tiger Breeding, Longyan 364201, China; (K.L.); (H.L.)
| | - Shizhang Du
- Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China; (W.Z.)
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Duran DP, Laroche RA, Roman SJ, Godwin W, Herrmann DP, Bull E, Egan SP. Species delimitation, discovery and conservation in a tiger beetle species complex despite discordant genetic data. Sci Rep 2024; 14:6617. [PMID: 38503840 PMCID: PMC10951344 DOI: 10.1038/s41598-024-56875-9] [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: 01/15/2024] [Accepted: 03/12/2024] [Indexed: 03/21/2024] Open
Abstract
In an age of species declines, delineating and discovering biodiversity is critical for both taxonomic accuracy and conservation. In recent years, there has been a movement away from using exclusively morphological characters to delineate and describe taxa and an increase in the use of molecular markers to describe diversity or through integrative taxonomy, which employs traditional morphological characters, as well as genetic or other data. Tiger beetles are charismatic, of conservation concern, and much work has been done on the morphological delineation of species and subspecies, but few of these taxa have been tested with genetic analyses. In this study, we tested morphologically based taxonomic hypotheses of polymorphic tiger beetles in the Eunota circumpicta (LaFerté-Sénectère, 1841) species complex using multilocus genomic and mtDNA analyses. We find multiple cryptic species within the previous taxonomic concept of Eunota circumpicta, some of which were historically recognized as subspecies. We found that the mtDNA and genomic datasets did not identify the same taxonomic units and that the mtDNA was most at odds with all other genetic and morphological patterns. Overall, we describe new cryptic diversity, which raises important conservation concerns, and provide a working example for testing species and subspecies validity despite discordant data.
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Affiliation(s)
- Daniel P Duran
- Department of Environmental Science, Rowan University, Glassboro, NJ, 08028, USA.
| | - Robert A Laroche
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - Stephen J Roman
- Florida State Collection of Arthropods, Gainesville, FL, 32608, USA
| | - William Godwin
- Sam Houston State Natural History Collection, Huntsville, TX, 77340, USA
| | | | - Ethan Bull
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
| | - Scott P Egan
- Department of BioSciences, Rice University, Houston, TX, 77005, USA
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10
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Meger J, Kozioł C, Pałucka M, Burczyk J, Chybicki IJ. Genetic resources of common ash (Fraxinus excelsior L.) in Poland. BMC PLANT BIOLOGY 2024; 24:186. [PMID: 38481155 PMCID: PMC10935948 DOI: 10.1186/s12870-024-04886-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND Knowledge of genetic structure and the factors that shape it has an impact on forest management practices. European ash (Fraxinus excelsior L.) has declined dramatically throughout its range as a result of a disease caused by the fungus Hymenoscyphus fraxineus. Despite the need for conservation and restoration of the species, genetic data required to guide these efforts at the country level are scarce. Thereofore, we studied the chloroplast and nuclear genetic diversity of 26 natural common ash populations (1269 trees) in Poland. RESULTS Chloroplast polymorphisms grouped the populations into two geographically structured phylogenetic lineages ascribed to different glacial refugia (the Balkans and the Eastern Alps). However, the populations demonstrated high genetic diversity (mean AR = 12.35; mean Ho = 0.769; mean He = 0.542) but low differentiation based on nuclear microsatellites (FST = 0.045). Significant spatial genetic structure, consistent with models of isolation by distance, was detected in 14 out of 23 populations. Estimated effective population size was moderate-to-high, with a harmonic mean of 57.5 individuals per population. CONCLUSIONS Genetic diversity was not homogeneously distributed among populations within phylogenetic gene pools, indicating that ash populations are not equal as potential sources of reproductive material. Genetic differences among populations could be related to their histories, including founder effects or gene flow between evolutionary lineages (admixture). Our results suggest that ash stands across Poland could be treated as two main management units (seed zones). Therefore, despite the homogenizing effect of pollen gene flow known for this species, the genetic structure should be taken into account in the management of the genetic resources of the common ash. Although ash dieback poses an additional challenge for the management of genetic resources, efforts should be directed towards protecting populations with high genetic diversity within defined phylogenetic units, as they may be an important source of adaptive variation for future stands.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, Bydgoszcz, 85-064, Poland.
| | - Czesław Kozioł
- Szklarska Poręba Forest District, Krasińskiego 6, Szklarska Poręba, 58-580, Poland
| | | | - Jarosław Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, Bydgoszcz, 85-064, Poland
| | - Igor J Chybicki
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, Bydgoszcz, 85-064, Poland.
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Hartig F, Abrego N, Bush A, Chase JM, Guillera-Arroita G, Leibold MA, Ovaskainen O, Pellissier L, Pichler M, Poggiato G, Pollock L, Si-Moussi S, Thuiller W, Viana DS, Warton DI, Zurell D, Yu DW. Novel community data in ecology-properties and prospects. Trends Ecol Evol 2024; 39:280-293. [PMID: 37949795 DOI: 10.1016/j.tree.2023.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023]
Abstract
New technologies for monitoring biodiversity such as environmental (e)DNA, passive acoustic monitoring, and optical sensors promise to generate automated spatiotemporal community observations at unprecedented scales and resolutions. Here, we introduce 'novel community data' as an umbrella term for these data. We review the emerging field around novel community data, focusing on new ecological questions that could be addressed; the analytical tools available or needed to make best use of these data; and the potential implications of these developments for policy and conservation. We conclude that novel community data offer many opportunities to advance our understanding of fundamental ecological processes, including community assembly, biotic interactions, micro- and macroevolution, and overall ecosystem functioning.
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Affiliation(s)
- Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany.
| | - Nerea Abrego
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014 Jyväskylä, Finland
| | - Alex Bush
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Jonathan M Chase
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014 Jyväskylä, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki 00014, Finland
| | - Loïc Pellissier
- Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, Department of Environmental Systems Science, ETH Zürich, 8092 Zurich, Switzerland; Unit of Land Change Science, Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), 8903 Birmensdorf, Switzerland
| | | | - Giovanni Poggiato
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | - Laura Pollock
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Sara Si-Moussi
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | - Wilfried Thuiller
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F38000, Grenoble, France
| | | | | | | | - Douglas W Yu
- Kunming Institute of Zoology; Yunnan, China; University of East Anglia, Norfolk, UK
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12
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Wang JC, Chen HH, Hsu TW, Hung KH, Huang CC. A taxonomic revision of the genus Angelica (Apiaceae) in Taiwan with a new species A. aliensis. BOTANICAL STUDIES 2024; 65:3. [PMID: 38252347 PMCID: PMC10803708 DOI: 10.1186/s40529-023-00407-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Angelica L. sensu lato is a taxonomically complex genus, and many studies have utilized morphological and molecular features to resolve its classification issues. In Taiwan, there are six taxa within Angelica, and their taxonomic treatments have been a subject of controversy. In this study, we conducted a comprehensive analysis incorporating morphological and molecular (cpDNA and nrDNA) characteristics to revise the taxonomic treatments of Angelica in Taiwan. RESULTS As a result of our research, we have revised the classification between A. dahurica var. formosana and A. pubescens and merged two varieties of A. morrisonicola into a single taxon. A new taxon, A. aliensis, has been identified and found to share a close relationship with A. tarokoensis. Based on the morphological and molecular characteristics data, it has been determined that the former three taxa should be grouped into the Eurasian Angelica clade, while the remaining four taxa should belong to the littoral Angelica clade. Furthermore, Angelica species in Taiwan distributed at higher altitudes displayed higher genetic diversity, implying that the central mountain range of Taiwan serves as a significant reservoir of plant biodiversity. Genetic drift, such as bottlenecks, has been identified as a potential factor leading to the fixation or reduction of genetic diversity of populations in most Angelica species. We provide key to taxa, synopsis, phenology, and distribution for each taxon of Taiwan. CONCLUSIONS Our comprehensive analysis of morphological and molecular features has shed light on the taxonomic complexities within Angelica in Taiwan, resolving taxonomic issues and providing valuable insights into the phylogenetic relationships of Angelica in Taiwan.
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Affiliation(s)
- Jenn-Che Wang
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
| | - Hung-Hsin Chen
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
| | - Tsai-Wen Hsu
- Wild Plants Division, Taiwan Biodiversity Research Institute, Nantou, 552, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
- Forestry and Biodiversity Research Center, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
| | - Chi-Chun Huang
- Wild Plants Division, Taiwan Biodiversity Research Institute, Nantou, 552, Taiwan.
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13
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Miller CV, Bossu CM, Sarraco JF, Toews DPL, Rushing CS, Roberto-Charron A, Tremblay JA, Chandler RB, DeSaix MG, Fiss CJ, Larkin JL, Haché S, Nebel S, Ruegg KC. Genomics-informed conservation units reveal spatial variation in climate vulnerability in a migratory bird. Mol Ecol 2024; 33:e17199. [PMID: 38018020 DOI: 10.1111/mec.17199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/18/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023]
Abstract
Identifying genetic conservation units (CUs) in threatened species is critical for the preservation of adaptive capacity and evolutionary potential in the face of climate change. However, delineating CUs in highly mobile species remains a challenge due to high rates of gene flow and genetic signatures of isolation by distance. Even when CUs are delineated in highly mobile species, the CUs often lack key biological information about what populations have the most conservation need to guide management decisions. Here we implement a framework for CU identification in the Canada Warbler (Cardellina canadensis), a migratory bird species of conservation concern, and then integrate demographic modelling and genomic offset to guide conservation decisions. We find that patterns of whole genome genetic variation in this highly mobile species are primarily driven by putative adaptive variation. Identification of CUs across the breeding range revealed that Canada Warblers fall into two evolutionarily significant units (ESU), and three putative adaptive units (AUs) in the South, East, and Northwest. Quantification of genomic offset, a metric of genetic changes necessary to maintain current gene-environment relationships, revealed significant spatial variation in climate vulnerability, with the Northwestern AU being identified as the most vulnerable to future climate change. Alternatively, quantification of past population trends within each AU revealed the steepest population declines have occurred within the Eastern AU. Overall, we illustrate that genomics-informed CUs provide a strong foundation for identifying current and future regional threats that can be used to inform management strategies for a highly mobile species in a rapidly changing world.
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Affiliation(s)
- Caitlin V Miller
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Christen M Bossu
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - James F Sarraco
- The Institute for Bird Populations, Petaluma, California, USA
| | - David P L Toews
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Clark S Rushing
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
| | | | - Junior A Tremblay
- Wildlife Research Division, Environment and Climate Change Canada, Québec, Quebec, Canada
| | - Richard B Chandler
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA
| | - Matthew G DeSaix
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Cameron J Fiss
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA
| | - Jeff L Larkin
- Department of Biology, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA
| | - Samuel Haché
- Canadian Wildlife Service, Environment Climate Change Canada, Yellowknife, Northwest Territories, Canada
| | | | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
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14
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Hu H, Wang Q, Hao G, Zhou R, Luo D, Cao K, Yan Z, Wang X. Insights into the phylogenetic relationships and species boundaries of the Myricaria squamosa complex (Tamaricaceae) based on the complete chloroplast genome. PeerJ 2023; 11:e16642. [PMID: 38099308 PMCID: PMC10720482 DOI: 10.7717/peerj.16642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/19/2023] [Indexed: 12/17/2023] Open
Abstract
Myricaria plants are widely distributed in Eurasia and are helpful for windbreak and embankment protection. Current molecular evidence has led to controversy regarding species boundaries within the Myricaria genus and interspecific phylogenetic relationships between three specific species-M. bracteata, M. paniculata and M. squamosa-which have remained unresolved. This study treated these three unresolved taxa as a species complex, named the M. squamosa complex. The genome skimming approach was used to determine 35 complete plastome sequences and nuclear ribosomal DNA sequences for the said complex and other closely related species, followed by de novo assembly. Comparative analyses were conducted across Myricaria to identify the genome size, gene content, repeat type and number, SSR (simple sequence repeat) abundance, and codon usage bias of chloroplast genomes. Tree-based species delimitation results indicated that M. bracteata, M. paniculata and M. squamosa could not be distinguished and formed two monophyletic lineages (P1 and P2) that were clustered together. Compared to plastome-based species delimitation, the standard nuclear DNA barcode had the lowest species resolution, and the standard chloroplast DNA barcode and group-specific barcodes delimitated a maximum of four out of the five species. Plastid phylogenomics analyses indicated that the monophyletic M. squamosa complex is comprised of two evolutionarily significant units: one in the western Tarim Basin and the other in the eastern Qinghai-Tibet Plateau. This finding contradicts previous species discrimination and promotes the urgent need for taxonomic revision of the threatened genus Myricaria. Dense sampling and plastid genomes will be essential in this effort. The super-barcodes and specific barcode candidates outlined in this study will aid in further studies of evolutionary history.
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Affiliation(s)
- Huan Hu
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Qian Wang
- Microbial Resources and Drug Development Key Laboratory of Guizhou Tertiary Institution, Zunyi Medical University, Zunyi, China
| | - Guoqian Hao
- School of Life Science and Food Engineering, Yibin University, Yibin, China
| | - Ruitao Zhou
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Dousheng Luo
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Kejun Cao
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Zhimeng Yan
- School of Medical Information Engineering, Zunyi Medical University, Zunyi, China
| | - Xinyu Wang
- Key Laboratory of Medical Electrophysiology, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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15
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Hoelzel AR. Where to now with the evolutionarily significant unit? Trends Ecol Evol 2023; 38:1134-1142. [PMID: 37596130 DOI: 10.1016/j.tree.2023.07.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/20/2023]
Abstract
The designation of units for conservation has been a necessary but challenging objective since conservation efforts began. Most species are divided, typically by environment, into populations with independent evolutionary trajectories. There are practical conservation objectives for defining these boundaries. Separate genetic clusters provide future evolutionary potential as environments change, and individuals in isolated populations may lose fitness when population size is reduced. The history of the effort to define units is briefly reviewed here, but I focus on finding a process that may facilitate uniform and effective application at a time when conservation urgency is great. I propose a refinement of the designated unit concept, distinguishing between conservation units (CUs) and evolutionarily sustaining conservation units (ESCUs).
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Affiliation(s)
- A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK.
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16
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Ni X, Chen Y, Deng G, Fu C. Pleistocene Landscape Dynamics Drives Lineage Divergence of a Temperate Freshwater Fish Gobio rivuloides in Coastal Drainages of Northern China. Genes (Basel) 2023; 14:2146. [PMID: 38136969 PMCID: PMC10743038 DOI: 10.3390/genes14122146] [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: 10/26/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Understanding historical processes underlying lineage distribution patterns is a primary goal of phylogeography. We selected Gobio rivuloides (Cypriniformes: Gobionidae) as a model to improve our knowledge about how intraspecific genetic divergence of freshwater fishes arises in coastal drainages of northern China via statistical analysis using cytochrome b gene. The time-calibrated phylogeny of G. rivuloides showed the divergence of two major lineages (I and II) at ~0.98 Ma (million years ago). Lineage I can be divided into two sub-lineages (I-A and I-B) with a divergence time of ~0.83 Ma. Sub-lineage I-A inhabits the Amur River, and sub-lineage I-B lives in the Luan River and Liao River. Lineage II is distributed in the Yellow River and Hai River, with close genetic relationships between the two drainages, and can be split into two sub-lineages (II-C and II-D) with a divergence time of ~0.60 Ma. Our findings indicate that the splitting of lineages and sub-lineages could be attributed to geographic isolation caused by the formation of the Bohai Sea, river capture, and the episodic hydrologic closing of a paleolake during the late Lower-Middle Pleistocene. It is also the first report we know of displaying a clear phylogeographic break for freshwater fishes across coastal drainages in northern China.
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Affiliation(s)
| | | | | | - Cuizhang Fu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China; (X.N.); (Y.C.); (G.D.)
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17
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Rutherford S, Rossetto M, Bragg JG, Wan JSH. Where to draw the boundaries? Using landscape genomics to disentangle the scribbly gum species complex. AMERICAN JOURNAL OF BOTANY 2023; 110:e16245. [PMID: 37747108 DOI: 10.1002/ajb2.16245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
PREMISE Species delimitation is an integral part of evolution and ecology and is vital in conservation science. However, in some groups, species delimitation is difficult, especially where ancestral relationships inferred from morphological or genetic characters are discordant, possibly due to a complicated demographic history (e.g., recent divergences between lineages). Modern genetic techniques can take into account complex histories to distinguish species at a reasonable cost and are increasingly used in numerous applications. We focus on the scribbly gums, a group of up to five closely related and morphologically similar "species" within the eucalypts. METHODS Multiple populations of each recognized scribbly gum species were sampled over a wide region across climates, and genomewide scans were used to resolve species boundaries. RESULTS None of the taxa were completely divergent, and there were two genetically distinct entities: the inland distributed Eucalyptus rossii and a coastal conglomerate consisting of four species forming three discernible, but highly admixed groups. Divergence among taxa was likely driven by temporal vicariant processes resulting in partial separation across biogeographic barriers. High interspecific gene flow indicated separated taxa reconnected at different points in time, blurring species boundaries. CONCLUSIONS Our results highlight the need for genetic screening when dealing with closely related taxonomic entities, particularly those with modest morphological differences. We show that high-throughput sequencing can be effective at identifying species groupings and processes driving divergence, even in the most taxonomically complex groups, and be used as a standard practice for disentangling species complexes.
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Affiliation(s)
- Susan Rutherford
- Department of Environmental Science, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Department of Environmental and Sustainability Sciences, The Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, Union, NJ, USA
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou, Zhejiang Province, China
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
| | - Jason G Bragg
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
| | - Justin S H Wan
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Royal Botanic Garden Sydney, Mrs Macquaries Road, Sydney, New South Wales, Australia
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18
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Kägi C, Petitpierre B, Meyer P, Lötscher Y, Eggenberg S, Aubry S. Fostering in situ conservation of wild relatives of forage crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1287430. [PMID: 38023832 PMCID: PMC10643147 DOI: 10.3389/fpls.2023.1287430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Most plant conservation strategies generally overlook the intra-specific genetic diversity of crop gene pools. Focusing on forage crops and their wild relatives, we present a novel approach to address the conservation of these species on meadows. Two-thirds of Swiss agricultural land is green land, mostly used for forage purposes, and their genetic diversity is being threatened. We focused here on eight plant associations gathering at least 18 taxa considered priority crop wild relatives of forage crops. Since 2020, about 1,217 high-quality surfaces (representing 1,566 hectares) nationwide have been integrated into an innovative auction-based policy instrument dedicated to conserving these populations. Here, we report the benefits and hurdles of implementing this bottom-up approach and try to estimate the quality of conservation of the forage plants' CWR gene pool. Although we focus on the Swiss case, our approach to in situ conservation offers opportunities to effectively guide conservation in other contexts. We also discuss possible ways to improve CWR conservation policy, particularly the need to better consider the populations and habitat levels.
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Affiliation(s)
- Christina Kägi
- Federal Office for Agriculture (FOAG), Federal Department of Economic Affairs, Education and Research EAER, Bern, Switzerland
| | | | - Philipp Meyer
- Federal Office for Agriculture (FOAG), Federal Department of Economic Affairs, Education and Research EAER, Bern, Switzerland
| | - Yvonne Lötscher
- Federal Office for Agriculture (FOAG), Federal Department of Economic Affairs, Education and Research EAER, Bern, Switzerland
| | | | - Sylvain Aubry
- Federal Office for Agriculture (FOAG), Federal Department of Economic Affairs, Education and Research EAER, Bern, Switzerland
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19
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Coimbra RTF, Winter S, Muneza A, Fennessy S, Otiende M, Mijele D, Masiaine S, Stacy-Dawes J, Fennessy J, Janke A. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biol 2023; 21:215. [PMID: 37833744 PMCID: PMC10576358 DOI: 10.1186/s12915-023-01722-y] [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: 02/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. RESULTS We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. CONCLUSIONS Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | | | | | | | | | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
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20
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Chen X, Feng Y, Chen S, Yang K, Wen X, Sun Y. Species Delimitation and Genetic Relationship of Castanopsis hainanensis and Castanopsis wenchangensis (Fagaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:3544. [PMID: 37896008 PMCID: PMC10609670 DOI: 10.3390/plants12203544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Castanopsis is one of the most common genus of trees in subtropical evergreen broad-leaved forests and tropical monsoon rainforests in China. Castanopsis hainanensis and Castanopsis wenchangensis are endemic to Hainan Island, but they were once confused as the same species due to very similar morphologies. In this study, nuclear microsatellite markers and chloroplast genomes were used to delimit C. hainanensis and C. wenchangensis. The allelic variations of nuclear microsatellites revealed that C. hainanensis and C. wenchangensis were highly genetically differentiated with very limited gene admixture. Both showed higher genetic diversity within populations and lower genetic diversity among populations, and neither had further population genetic structure. Furthermore, C. wenchangensis and C. hainanensis had very different chloroplast genomes. The independent genetic units, very limited gene admixture, different distribution ranges, and distinct habitats all suggest that C. wenchangensis and C. hainanensis are independent species, thus they should be treated as distinct conservation units.
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Affiliation(s)
- Xing Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Yi Feng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Shuang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Kai Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Xiangying Wen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
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21
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Wylie MJ, Kitson J, Russell K, Yoshizaki G, Yazawa R, Steeves TE, Wellenreuther M. Fish germ cell cryobanking and transplanting for conservation. Mol Ecol Resour 2023. [PMID: 37712134 DOI: 10.1111/1755-0998.13868] [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: 01/05/2023] [Revised: 05/26/2023] [Accepted: 07/18/2023] [Indexed: 09/16/2023]
Abstract
The unprecedented loss of global biodiversity is linked to multiple anthropogenic stressors. New conservation technologies are urgently needed to mitigate this loss. The rights, knowledge and perspectives of Indigenous peoples in biodiversity conservation-including the development and application of new technologies-are increasingly recognised. Advances in germplasm cryopreservation and germ cell transplantation (termed 'broodstock surrogacy') techniques offer exciting tools to preserve biodiversity, but their application has been underappreciated. Here, we use teleost fishes as an exemplar group to outline (1) the power of these techniques to preserve genome-wide genetic diversity, (2) the need to apply a conservation genomic lens when selecting individuals for germplasm cryobanking and broodstock surrogacy and (3) the value of considering the cultural significance of these genomic resources. We conclude by discussing the opportunities and challenges of these techniques for conserving biodiversity in threatened teleost fish and beyond.
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Affiliation(s)
- Matthew J Wylie
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
| | - Jane Kitson
- Kitson Consulting Ltd, Invercargill, New Zealand
| | - Khyla Russell
- Kāti Huirapa Rūnaka ki Puketeraki, Karitane, New Zealand
| | - Goro Yoshizaki
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Ryosuke Yazawa
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Limited, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Lehnert SJ, Bradbury IR, Wringe BF, Van Wyngaarden M, Bentzen P. Multifaceted framework for defining conservation units: An example from Atlantic salmon ( Salmo salar) in Canada. Evol Appl 2023; 16:1568-1585. [PMID: 37752960 PMCID: PMC10519414 DOI: 10.1111/eva.13587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/12/2023] [Accepted: 07/26/2023] [Indexed: 09/28/2023] Open
Abstract
Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at-risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed "designatable units"; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet criteria of discreteness and significance, and increasing access to "big data" is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non-model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. Here, we develop a framework that uses a multifaceted, weight of evidence approach to incorporate multiple data types, including genetic and genomic data, to inform COSEWIC DUs. We apply this framework to delineate DUs of Atlantic salmon (Salmo salar, L.), an economically, culturally, and ecologically significant species, that is also characterized by complex hierarchical population structure. Specifically, we focus on an in-depth example of how our approach was applied to a previously data limited region of northern Canada that was defined by a single large DU. Application of our framework with newly available genetic and genomic data led to subdividing this DU into three new DUs. Although our approach was developed to meet criteria of COSEWIC, it is widely applicable given similarities in the definitions of a conservation unit.
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Affiliation(s)
- Sarah J. Lehnert
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Brendan F. Wringe
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | | | - Paul Bentzen
- Biology DepartmentDalhousie UniversityHalifaxNova ScotiaCanada
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23
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Sánchez-Barreiro F, De Cahsan B, Westbury MV, Sun X, Margaryan A, Fontsere C, Bruford MW, Russo IRM, Kalthoff DC, Sicheritz-Pontén T, Petersen B, Dalén L, Zhang G, Marquès-Bonet T, Gilbert MTP, Moodley Y. Historic Sampling of a Vanishing Beast: Population Structure and Diversity in the Black Rhinoceros. Mol Biol Evol 2023; 40:msad180. [PMID: 37561011 PMCID: PMC10500089 DOI: 10.1093/molbev/msad180] [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: 09/16/2022] [Revised: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 08/11/2023] Open
Abstract
The black rhinoceros (Diceros bicornis L.) is a critically endangered species historically distributed across sub-Saharan Africa. Hunting and habitat disturbance have diminished both its numbers and distribution since the 19th century, but a poaching crisis in the late 20th century drove them to the brink of extinction. Genetic and genomic assessments can greatly increase our knowledge of the species and inform management strategies. However, when a species has been severely reduced, with the extirpation and artificial admixture of several populations, it is extremely challenging to obtain an accurate understanding of historic population structure and evolutionary history from extant samples. Therefore, we generated and analyzed whole genomes from 63 black rhinoceros museum specimens collected between 1775 and 1981. Results showed that the black rhinoceros could be genetically structured into six major historic populations (Central Africa, East Africa, Northwestern Africa, Northeastern Africa, Ruvuma, and Southern Africa) within which were nested four further subpopulations (Maasailand, southwestern, eastern rift, and northern rift), largely mirroring geography, with a punctuated north-south cline. However, we detected varying degrees of admixture among groups and found that several geographical barriers, most prominently the Zambezi River, drove population discontinuities. Genomic diversity was high in the middle of the range and decayed toward the periphery. This comprehensive historic portrait also allowed us to ascertain the ancestry of 20 resequenced genomes from extant populations. Lastly, using insights gained from this unique temporal data set, we suggest management strategies, some of which require urgent implementation, for the conservation of the remaining black rhinoceros diversity.
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Affiliation(s)
| | - Binia De Cahsan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Xin Sun
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Fontsere
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
| | | | | | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Love Dalén
- Department of Zoology, Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, People's Republic of China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, People's Republic of China
- BGI Research, BGI-Shenzhen, Shenzhen, People's Republic of China
| | - Tomás Marquès-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas–Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Catalonia, Spain
- National Centre for Genomic Analysis–Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Life & Medical Sciences, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - M Thomas P Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Trondheim, Norway
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Thohoyandou, Republic of South Africa
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24
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Jourdan J, Bundschuh M, Copilaș-Ciocianu D, Fišer C, Grabowski M, Hupało K, Jemec Kokalj A, Kabus J, Römbke J, Soose LJ, Oehlmann J. Cryptic Species in Ecotoxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2023; 42:1889-1914. [PMID: 37314101 DOI: 10.1002/etc.5696] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023]
Abstract
The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Jonas Jourdan
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Mirco Bundschuh
- iES Landau, Institute for Environmental Sciences, University of Kaiserslautern-Landau, Landau, Germany
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Denis Copilaș-Ciocianu
- Laboratory of Evolutionary Ecology of Hydrobionts, Nature Research Centre, Vilnius, Lithuania
| | - Cene Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michał Grabowski
- Invertebrate Zoology and Hydrobiology, University of Lodz, Łódź, Poland
| | - Kamil Hupało
- Department of Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Anita Jemec Kokalj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Kabus
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Römbke
- ECT Oekotoxikologie, Flörsheim am Main, Germany
| | - Laura J Soose
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Department of Aquatic Ecotoxicology, Goethe University, Frankfurt am Main, Germany
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25
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Ibrahim AA, Alwutayd KM, Safhi FA, Alshegaihi RM, Alqurashi M, Alyamani A, Aloufi S, Alharthi B, Fayad E, Abd El-Moneim D. Characterization and comparative genomic analyses of complete chloroplast genome on Trema orientalis L. GENETIC RESOURCES AND CROP EVOLUTION 2023. [DOI: 10.1007/s10722-023-01678-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/06/2023] [Indexed: 09/02/2023]
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26
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Turbek SP, Funk WC, Ruegg KC. Where to draw the line? Expanding the delineation of conservation units to highly mobile taxa. J Hered 2023; 114:300-311. [PMID: 36815497 DOI: 10.1093/jhered/esad011] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species' range for protection when implementing conservation and management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patterns of isolation by distance (IBD), frequently the primary signal of population structure in highly mobile taxa, such as birds, bats, and marine organisms with pelagic larval stages. While individuals located on either end of a species' distribution may exhibit clear genetic, phenotypic, and ecological differences, IBD produces subtle changes in allele frequencies across space, making it difficult to draw clear boundaries for conservation purposes in the absence of discrete population structure. Here, we highlight potential pitfalls that arise when applying common methods for delineating CUs to continuously distributed organisms and review existing methods for detecting subtle breakpoints in patterns of IBD that can indicate barriers to gene flow in highly mobile taxa. In addition, we propose a new framework for identifying CUs in all organisms, including those characterized by continuous genomic differentiation, and suggest several possible ways to harness the information contained in patterns of IBD to guide conservation and management decisions.
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Affiliation(s)
- Sheela P Turbek
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Fort Collins, CO, United States
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27
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Islam SU, Mangral ZA, Hussain K, Tariq L, Bhat BA, Khuroo AA, Hassan Dar TU. Unravelling diversity, drivers, and indicators of soil microbiome of Trillium govanianum, an endangered plant species of the Himalaya. ENVIRONMENTAL RESEARCH 2023; 227:115819. [PMID: 37011799 DOI: 10.1016/j.envres.2023.115819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/19/2023] [Accepted: 03/30/2023] [Indexed: 05/08/2023]
Abstract
In an era of global environmental change, conservation of threatened biodiversity and ecosystem restoration are formidable ecological challenges. The forest understory strata and the belowground soil environment including rhizospheric microbial communities, which are crucial for ecosystem functioning and overall forest biodiversity maintenance, have remained understudied. Here, we investigate the soil microbiome of Trillium govanianum - an endangered Himalayan Forest herb, to unravel the underground diversity, drivers, and potential indicators of the microbial community. We collected rhizospheric and bulk soil samples for microbiome and physicochemical analysis at three sites along an elevation gradient (2500-3300 m) in Kashmir Himalaya. Amplicon sequencing of 16 S rRNA and ITS was used to identify the bacterial and fungal soil microorganisms. We found significant differences in the structure and diversity of microbial community (bacterial and fungal) between the rhizosphere and bulk soil along the altitudinal gradient, and noticeable shifts in the nutrient level in dominant microbial phyla associated with T. govanianum. A significant difference between soil physicochemical parameters and increasing altitude suggests that microbial community structure is determined by altitude and soil type. Similarly, the microbial communities showed a significant (P < 0.05) correlation with soil physicochemical variables along the altitudinal gradient. The moisture content in bacterial and total organic carbon in fungal communities showed the most substantial impact on the physiochemical drivers. We also identify potential bacterial and fungal plant growth promoter indicator species in the soil microbiome of T. govanianum. Overall, our findings provide novel research insights that can be pivotal in designing integrated species recovery programs and long-term restoration plans for T. govanianum, with learnings for biodiversity conservation elsewhere.
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Affiliation(s)
- Shahid Ul Islam
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Zahid Ahmed Mangral
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Khalid Hussain
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Lubna Tariq
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Basharat Ahmad Bhat
- Department of Bio-Resources, School of Biological Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Anzar Ahmad Khuroo
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Tanvir Ul Hassan Dar
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India.
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28
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Zhang W, Hu Y, Zhang S, Shao J. Integrative taxonomy in a rapid speciation group associated with mating system transition: A case study in the Primula cicutariifolia complex. Mol Phylogenet Evol 2023:107840. [PMID: 37279815 DOI: 10.1016/j.ympev.2023.107840] [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: 02/17/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023]
Abstract
Accurate species delimitation is the key to biodiversity conservation and is fundamental to most branches of biology. However, species delimitation remains challenging in those evolutionary radiations associated with mating system transition from outcrossing to self-fertilization, which have frequently occurred in angiosperms and are usually accompanied by rapid speciation. Here, using the Primula cicutariifolia complex as a case, we integrated molecular, morphological and reproductive isolation evidence to test and verify whether its outcrossing (distylous) and selfing (homostylous) populations have developed into independent evolutionary lineages. Phylogenetic trees based on whole plastomes and SNPs of the nuclear genome both indicated that the distylous and homostylous populations grouped into two different clades. Multispecies coalescent, gene flow and genetic structure analyses all supported such two clades as two different genetic entities. In morphology, as expected changes in selfing syndrome, homostylous populations have significantly fewer umbel layers and smaller flower and leaf sizes compared to distylous populations, and the variation range of some floral traits, such as corolla diameter and umbel layers, show obvious discontinuity. Furthermore, hand-pollinated hybridization between the two clades produced almost no seeds, indicating that well post-pollination reproductive isolation has been established between them. Therefore, the distylous and homostylous populations in this studied complex are two independent evolutionary lineages, and thus these distylous populations should be treated as a distinct species, here named Primula qiandaoensis W. Zhang & J.W. Shao sp. nov.. Our empirical study of the P. cicutariifolia complex highlights the importance of applying multiple lines of evidence, in particular genomic data, to delimit species in pervasive evolutionary plant radiations associated with mating system transition.
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Affiliation(s)
- Wei Zhang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China; College of Life Sciences, Anqing Normal University, Anqing 246011, Anhui, China
| | - Yingfeng Hu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Siyu Zhang
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Jianwen Shao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China; Provincial Key Laboratory of Conservation and Utilization of Biological Resources, Wuhu 241000, Anhui, China.
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29
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Hughes A, Auliya M, Altherr S, Scheffers B, Janssen J, Nijman V, Shepherd CR, D'Cruze N, Sy E, Edwards DP. Determining the sustainability of legal wildlife trade. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 341:117987. [PMID: 37178541 DOI: 10.1016/j.jenvman.2023.117987] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/19/2023] [Accepted: 04/18/2023] [Indexed: 05/15/2023]
Abstract
Exploitation of wildlife represents one of the greatest threats to species survival according to the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Whilst detrimental impacts of illegal trade are well recognised, legal trade is often equated to being sustainable despite the lack of evidence or data in the majority of cases. We review the sustainability of wildlife trade, the adequacy of tools, safeguards, and frameworks to understand and regulate trade, and identify gaps in data that undermine our ability to truly understand the sustainability of trade. We provide 183 examples showing unsustainable trade in a broad range of taxonomic groups. In most cases, neither illegal nor legal trade are supported by rigorous evidence of sustainability, with the lack of data on export levels and population monitoring data precluding true assessments of species or population-level impacts. We propose a more precautionary approach to wildlife trade and monitoring that requires those who profit from trade to provide proof of sustainability. We then identify four core areas that must be strengthened to achieve this goal: (1) rigorous data collection and analyses of populations; (2) linking trade quotas to IUCN and international accords; (3) improved databases and compliance of trade; and (4) enhanced understanding of trade bans, market forces, and species substitutions. Enacting these core areas in regulatory frameworks, including CITES, is essential to the continued survival of many threatened species. There are no winners from unsustainable collection and trade: without sustainable management not only will species or populations become extinct, but communities dependent upon these species will lose livelihoods.
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Affiliation(s)
- Alice Hughes
- School of Biological Sciences, University of Hong Kong, China.
| | - Mark Auliya
- Department of Herpetology, Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Brett Scheffers
- Department of Wildlife Ecology and Conservation, University of Florida/IFAS, Gainesville, FL, USA
| | - Jordi Janssen
- Monitor Conservation Research Society, PO BOX 200, Big Lake Ranch, BC, V0L 1G0, Canada
| | - Vincent Nijman
- Oxford Wildlife Trade Research Group, Oxford Brookes University, Oxford, OX3 0BP, UK.
| | - Chris R Shepherd
- Monitor Conservation Research Society, PO BOX 200, Big Lake Ranch, BC, V0L 1G0, Canada
| | - Neil D'Cruze
- The Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Tubney, UK; World Animal Protection, 222 Greys Inn Road, London, WC1X 8HB, UK
| | - Emerson Sy
- Philippine Center for Terrestrial & Aquatic Research, Manila, Philippines
| | - David P Edwards
- Ecology and Evolutionary Biology, School of Biosciences University of Sheffield, Sheffield, S10 2TN, UK.
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30
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Li C, Xiao H, Zhang X, Lin H, Elmer KR, Zhao J. Deep genome-wide divergences among species in White Cloud Mountain minnow Tanichthys albonubes (Cypriniformes: Tanichthyidae) complex: Conservation and species management implications. Mol Phylogenet Evol 2023; 182:107734. [PMID: 36804428 DOI: 10.1016/j.ympev.2023.107734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Abstract
Identifying cryptic species is important for the assessments of biodiversity. Further, untangling mechanisms underlying the origins of cryptic species can facilitate our understanding of evolutionary processes. Advancements in genomic approaches for non-model systems have offered unprecedented opportunities to investigate these areas. The White Cloud Mountain minnow (Tanichthys albonubes) is a popular freshwater pet fish worldwide but its wild populations in China are critically endangered. Recent research based on a few molecular markers suggested that this species in fact comprised seven cryptic species, of which six were previously unknown. Here, we tested six of these cryptic species and quantified genomic interspecific divergences between species in the T. albonubes complex by analyzing genome-wide restriction site-associated DNA sequencing (RADseq) data generated from 189 individuals sampled from seven populations (including an outgroup congeneric species, T. micagemmae). We found that six cryptic species previously suggested were well supported by RADseq data. The genetic diversity of each species in the T. albonubes complex was low compared with T. micagemmae and the contemporary effective population sizes (Ne) of each cryptic species were small. Phylogenetic analysis showed seven clades with high support values confirmed with Neighbor-Net trees. The pairwise divergences between species in T. albonubes complex were deep and the highly differentiated loci were evenly distributed across the genome. We proposed that the divergence level of T. albonubes complex is at a late stage of cryptic speciation and lacking gene flow. Our findings provide new insights into cryptic speciation and have important implications for conservation and species management of T. albonubes complex.
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Affiliation(s)
- Chao Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China; Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Han Xiao
- Institute of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Xiuxia Zhang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Hungdu Lin
- The Affiliated School of National Tainan First Senior High School, Tainan, Taiwan
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jun Zhao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Guangdong Provincial Engineering Technology Research Center for Environmentally Friendly Aquaculture, School of Life Sciences, South China Normal University, Guangzhou, China.
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31
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Whelan NV, Strong EE, Gladstone NS, Mays JW. Using genomics, morphometrics, and environmental niche modeling to test the validity of a narrow-range endemic snail, Pateranantahala (Gastropoda, Polygyridae). Zookeys 2023; 1158:91-120. [PMID: 37234252 PMCID: PMC10208601 DOI: 10.3897/zookeys.1158.94152] [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: 08/27/2022] [Accepted: 03/13/2023] [Indexed: 05/27/2023] Open
Abstract
Terrestrial gastropods are among the most imperiled groups of organisms on Earth. Many species have a complex taxonomic history, often including poorly defined subspecies, most of which have not been the focus of modern systematics research. Genomic tools, geometric morphometrics, and environmental niche modeling were used to assess the taxonomic status of Pateraclarkiinantahala (Clench & Banks, 1932), a subspecies of high conservation concern with a restricted range of approximately 3.3 km2 in North Carolina, USA. A genome-scale dataset was generated that included individuals with morphologies matching P.c.nantahala, P.c.clarkii, and one individual with an intermediate form between P.c.nantahala and P.c.clarkii that was initially hypothesized as a potential hybrid. Mitochondrial phylogenetics, nuclear species tree inference, and phylogenetic networks were used to assess relationships and gene flow. Differences in shell shape via geometric morphometrics and whether the environmental niches of the two subspecies were significantly different were also examined. Molecular analyses indicated an absence of gene flow among lineages of P.clarkii sensu lato. Analyses rejected our hypothesis that the intermediate shelled form represented a hybrid, but instead indicated that it was a distinct lineage. Environmental niche models indicated significant differences in environmental niche between P.c.clarkii and P.c.nantahala, and geometric morphometrics indicated that P.c.nantahala had a significantly different shell shape. Given multiple lines of evidence, species-level recognition of P.nantahala is warranted.
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Affiliation(s)
- Nathan V. Whelan
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, US Fish and Wildlife Service, 203 Swingle Hall, Auburn, Alabama, 36849, USAAuburn UniversityAuburnUnited States of America
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USAWarm Springs Fish Technology Center, US Fish and Wildlife ServiceAuburnUnited States of America
| | - Ellen E. Strong
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 163, Washington, DC 20013, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Nicholas S. Gladstone
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USAWarm Springs Fish Technology Center, US Fish and Wildlife ServiceAuburnUnited States of America
| | - Jason W. Mays
- Asheville Ecological Services Field Office, United States Fish and Wildlife Service, 160 Zillicoa ST, Asheville, NC 28801, USAAsheville Ecological Services Field Office, United States Fish and Wildlife ServiceAshevilleUnited States of America
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32
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Genetic Diversity and Insights about Distribution of Brown Howler Monkeys (Alouatta guariba Group) (Atelidae, Alouattinae). INT J PRIMATOL 2023. [DOI: 10.1007/s10764-023-00352-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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Investigating an Unknown Biodiversity: Evidence of Distinct Lineages of the Endemic Chola Guitarfish Pseudobatos percellens Walbaum, 1792 in the Western Atlantic Ocean. DIVERSITY 2023. [DOI: 10.3390/d15030344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Anthropogenic actions have affected marine species for a long time, through overexploitation of natural stocks and habitat degradation, influencing the life strategies of several taxa, especially rays and sharks, which have suffered significant population declines in recent years. Therefore, conservation actions and stock management have become paramount. In this regard, chola guitarfish, Pseudobatos percellens, distributed throughout the Brazilian coast, is often commercially fished by local artisanal fleets or as by-catch in shrimp trawl fisheries. Therefore, this study aimed to understand the genetic diversity of P. percellens throughout the Brazilian coast, using single nucleotide polymorphisms (SNPs). Genetic analyses employing 3329 SNPs revealed a hidden biodiversity within P. percellens, with at least one lineage occurring in the Northern and Northeastern regions and another distributed in the Southeastern/Southern Brazilian coast, with high genetic differentiation between them. However, the Discriminant Analysis of Principal Components (DAPC) indicated the presence of in fact three lineages distributed in these regions that must still be better investigated. Therefore, to ensure adequate conservation of chola guitarfish biodiversity, populations must be managed separately along the Brazilian coast. Furthermore, the need for a taxonomic review for this group is noted.
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Chung MY, Merilä J, Li J, Mao K, López-Pujol J, Tsumura Y, Chung MG. Neutral and adaptive genetic diversity in plants: An overview. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1116814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Genetic diversity is a prerequisite for evolutionary change in all kinds of organisms. It is generally acknowledged that populations lacking genetic variation are unable to evolve in response to new environmental conditions (e.g., climate change) and thus may face an increased risk of extinction. Although the importance of incorporating genetic diversity into the design of conservation measures is now well understood, less attention has been paid to the distinction between neutral (NGV) and adaptive (AGV) genetic variation. In this review, we first focus on the utility of NGV by examining the ways to quantify it, reviewing applications of NGV to infer ecological and evolutionary processes, and by exploring its utility in designing conservation measures for plant populations and species. Against this background, we then summarize the ways to identify and estimate AGV and discuss its potential use in plant conservation. After comparing NGV and AGV and considering their pros and cons in a conservation context, we conclude that there is an urgent need for a better understanding of AGV and its role in climate change adaptation. To date, however, there are only a few AGV studies on non-model plant species aimed at deciphering the genetic and genomic basis of complex trait variation. Therefore, conservation researchers and practitioners should keep utilizing NGV to develop relevant strategies for rare and endangered plant species until more estimates of AGV are available.
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Zozaya SM, Teasdale LC, Tedeschi LG, Higgie M, Hoskin CJ, Moritz C. Initiation of speciation across multiple dimensions in a rock-restricted, tropical lizard. Mol Ecol 2023; 32:680-695. [PMID: 36394360 PMCID: PMC10099344 DOI: 10.1111/mec.16787] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
Population isolation and concomitant genetic divergence, resulting in strong phylogeographical structure, is a core aspect of speciation initiation. If and how speciation then proceeds and ultimately completes depends on multiple factors that mediate reproductive isolation, including divergence in genomes, ecology and mating traits. Here we explored these multiple dimensions in two young (Plio-Pleistocene) species complexes of gekkonid lizards (Heteronotia) from the Kimberley-Victoria River regions of tropical Australia. Using mitochondrial DNA screening and exon capture phylogenomics, we show that the rock-restricted Heteronotia planiceps exhibits exceptional fine-scale phylogeographical structure compared to the codistributed habitat generalist Heteronotia binoei. This indicates pervasive population isolation and persistence in the rock-specialist, and thus a high rate of speciation initiation across this geographically complex region, with levels of genomic divergence spanning the "grey zone" of speciation. Proximal lineages of H. planiceps were often separated by different rock substrates, suggesting a potential role for ecological isolation; however, phylogenetic incongruence and historical introgression were inferred between one such pair. Ecomorphological divergence among lineages within both H. planiceps and H. binoei was limited, except that limestone-restricted lineages of H. planiceps tended to be larger than rock-generalists. By contrast, among-lineage divergence in the chemical composition of epidermal pore secretions (putative mating trait) exceeded ecomorphology in both complexes, but with less trait overlap among lineages in H. planiceps. This system-particularly the rock-specialist H. planiceps-highlights the role of multidimensional divergence during incipient speciation, with divergence in genomes, ecomorphology and chemical signals all at play at very fine spatial scales.
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Affiliation(s)
- Stephen M Zozaya
- Research School of Biology, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Luisa C Teasdale
- Research School of Biology, Australian National University, Australian Capital Territory, Canberra, Australia.,Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Leonardo G Tedeschi
- Research School of Biology, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Megan Higgie
- College of Science and Engineering, James Cook University, Queensland, Townsville, Australia
| | - Conrad J Hoskin
- College of Science and Engineering, James Cook University, Queensland, Townsville, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, Australian Capital Territory, Canberra, Australia
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Ferrer Obiol J, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, González-Solís J. Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds. Mol Phylogenet Evol 2023; 179:107671. [PMID: 36442764 DOI: 10.1016/j.ympev.2022.107671] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/28/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species.
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Affiliation(s)
- Joan Ferrer Obiol
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Department of Environmental Science and Policy, University of Milan, Milan, Italy.
| | - Jose M Herranz
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, Madrid, Spain; Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Josephine R Paris
- Department of Health, Life and Environmental Sciences, University of l'Aquila, Coppito, Italy; Department of Biosciences, University of Exeter, Exeter, UK
| | - James R Whiting
- Department of Biosciences, University of Exeter, Exeter, UK; Department of Biological Sciences, Faculty of Sciences, University of Calgary, Calgary, Canada
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
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37
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Molecular ecology meets systematic conservation planning. Trends Ecol Evol 2023; 38:143-155. [PMID: 36210287 DOI: 10.1016/j.tree.2022.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 08/29/2022] [Accepted: 09/12/2022] [Indexed: 01/06/2023]
Abstract
Integrative and proactive conservation approaches are critical to the long-term persistence of biodiversity. Molecular data can provide important information on evolutionary processes necessary for conserving multiple levels of biodiversity (genes, populations, species, and ecosystems). However, molecular data are rarely used to guide spatial conservation decision-making. Here, we bridge the fields of molecular ecology (ME) and systematic conservation planning (SCP) (the 'why') to build a foundation for the inclusion of molecular data into spatial conservation planning tools (the 'how'), and provide a practical guide for implementing this integrative approach for both conservation planners and molecular ecologists. The proposed framework enhances interdisciplinary capacity, which is crucial to achieving the ambitious global conservation goals envisioned for the next decade.
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38
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Adkins P, Harley J, Darbyshire T, Holmes A, Scott-Somme K, Mieskowska N. The genome sequence of the turban top shell, Gibbula magus (Linnaeus, 1758). Wellcome Open Res 2023; 8:35. [PMID: 37538380 PMCID: PMC10394393 DOI: 10.12688/wellcomeopenres.18792.1] [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] [Accepted: 01/03/2023] [Indexed: 08/05/2023] Open
Abstract
We present a genome assembly from an individual Gibbula magus (the turban top shell; Mollusca; Gastropoda; Trochida; Trochidae). The genome sequence is 1,470 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 41,167 protein coding genes.
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39
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Population Subdivision in the Gopher Frog (Rana capito) across the Fragmented Longleaf Pine-Wiregrass Savanna of the Southeastern USA. DIVERSITY 2023. [DOI: 10.3390/d15010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Delineating genetically distinct population segments of threatened species and quantifying population connectivity are important steps in developing effective conservation and management strategies aimed at preventing extinction. The gopher frog (Rana capito) is a xeric-adapted, pond-breeding species endemic to the Gulf and Atlantic coastal plains of the southeastern United States. This species has experienced extensive habitat loss and fragmentation in the formerly widespread longleaf pine-wiregrass savanna where it lives, resulting in individual abundance declines and population extinctions throughout its range. We used individual-based clustering methods along with Bayesian inference of historical migration based on almost 1500 multilocus microsatellite genotypes to examine genetic structure in this taxon. Clustering analyses identified panhandle and peninsular populations in Florida as distinct genetic clusters separated by the Aucilla River, consistent with the division between the Coastal Plain and peninsular mitochondrial lineages, respectively. Analysis of historical migration indicated an east–west population divergence event followed by immigration to the east. Together, our results indicate that the genetically distinct Coastal Plain and peninsular Florida lineages should be considered separately for conservation and management purposes.
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40
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Li M, Yang X, Ni X, Fu C. The role of landscape evolution in the genetic diversification of a stream fish Sarcocheilichthys parvus from Southern China. Front Genet 2023; 13:1075617. [PMID: 36685913 PMCID: PMC9853433 DOI: 10.3389/fgene.2022.1075617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
Sarcocheilichthys parvus (Cypriniformes: Gobionidae) is a stream fish which is endemic to sub-tropical coastal drainages in southern China, thus offering a valuable model for understanding how genetic divergence arises in stream-adapting freshwater fishes in this region. Using the mitochondrial Cyt b gene, integrative analyses of phylogeny, population demography, and ancestral area and paleo-drainage reconstructions are carried out to explicitly explore the role of landscape evolution in genetic diversification of S. parvus. The time-calibrated phylogeny of S. parvus indicates the splitting of two major lineages (A and B) at ∼3.66 Ma. Lineage A inhabits the Poyang Lake sub-drainage of the middle Yangtze River, Han River and Pearl River, and can be split into two sub-lineages (A-I and A-II), where sub-lineage A-II can be further sub-divided into three infra-sub-lineages (A-IIa, A-IIb and A-IIc). Except for the infra-sub-lineage A-IIc, which is restricted to the Han River and Pearl River, the other sub-lineages and infra-sub-lineages live exclusively in the Poyang Lake sub-drainage. Lineage B lives in the lower Yangtze River, Qiantang River, Jiaojiang River and Ou River, displaying close genetic relationships among the drainages. Rapid population expansion has occurred since the Late Pleistocene. Our findings indicate that the splitting of lineages A and B could be attributed to geographic isolation due to the Zhe-Min Uplift, acting as a biogeographic barrier before the late Early Pleistocene. Furthermore, the strong genetic divergence within Lineage A could be explained by the isolation role of the Nanling Mountains and Poyang Lake acting as an ecological barrier; while the lack of phylogenetic structure within Lineage B may have been the result of paleo-drainage connections or episodic freshwater connections during the eustatic low stand of sea level in the late Middle-Late Pleistocene.
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Affiliation(s)
| | | | - Xiaomin Ni
- *Correspondence: Xiaomin Ni, ; Cuizhang Fu,
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41
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Molinari J. A bare-bones scheme to choose between the species, subspecies, and ‘evolutionarily significant unit’ categories in taxonomy and conservation. J Nat Conserv 2023. [DOI: 10.1016/j.jnc.2023.126335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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42
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Klunzinger MW, Whisson C, Zieritz A, Benson JA, Stewart BA, Kirkendale L. Integrated taxonomy reveals new threatened freshwater mussels (Bivalvia: Hyriidae: Westralunio) from southwestern Australia. Sci Rep 2022; 12:20385. [PMID: 36437370 PMCID: PMC9701689 DOI: 10.1038/s41598-022-24767-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The freshwater mussel Westralunio carteri (Iredale, 1934) has long been considered the sole Westralunio species in Australia, limited to the Southwest and listed as vulnerable on the IUCN Red List and under Australian legislation. Here, we used species delimitation models based on COI mtDNA sequences to confirm existence of three evolutionarily significant units (ESUs) within this taxon and conducted morphometric analyses to investigate whether shell shape differed significantly among these ESUs. "W. carteri" I was found to be significantly larger and more elongated than "W. carteri" II and "W. carteri" II + III combined, but not different from "W. carteri" III alone. We recognise and redescribe "W. carteri" I as Westralunio carteri (Iredale, 1934) from western coastal drainages and describe "W. carteri" II and "W. carteri" III as Westralunio inbisi sp. nov. from southern and lower southwestern drainages. Two subspecies are further delineated: "W. carteri" II is formally described as Westralunio inbisi inbisi subsp. nov. from southern coastal drainages, and "W. carteri" III as Westralunio inbisi meridiemus subsp. nov. from the southwestern corner. Because this study profoundly compresses the range of Westralunio carteri northward and introduces additional southern and southwestern taxa with restricted distributions, new threatened species nominations are necessary.
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Affiliation(s)
- Michael W Klunzinger
- Australian Rivers Institute, Griffith University, Nathan, QLD, 6111, Australia.
- Mollusc Section, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA, 6163, Australia.
| | - Corey Whisson
- Mollusc Section, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA, 6163, Australia
| | - Alexandra Zieritz
- School of Geography, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Justin A Benson
- Centre for Natural Resource Management, UWA School of Agriculture and the Environment, The University of Western Australia, Albany, WA, 6330, Australia
| | - Barbara A Stewart
- Centre for Natural Resource Management, UWA School of Agriculture and the Environment, The University of Western Australia, Albany, WA, 6330, Australia
| | - Lisa Kirkendale
- Mollusc Section, Department of Aquatic Zoology, Western Australian Museum, Welshpool, WA, 6163, Australia
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43
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Wang Y, Ma X, Lu Y, Hu X, Lou L, Tong Z, Zhang J. Assessing the current genetic structure of 21 remnant populations and predicting the impacts of climate change on the geographic distribution of Phoebe sheareri in southern China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157391. [PMID: 35850348 DOI: 10.1016/j.scitotenv.2022.157391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Phoebe sheareri is a valuable tree species known as "Golden Nanmu" and is one of the most important protected tree species in China. However, natural populations are decreasing because of climate change and anthropogenic factors. To evaluate the genetic diversity and structure of remnant populations and the impacts of climate change on the distribution of potential suitable habitats, we conducted a field investigation and sampled 21 P. sheareri natural populations to evaluate their genetic diversity and structure using simple sequence repeat (SSR) molecular markers. Then, we predicted the distribution of suitable P. sheareri habitats across China under future scenarios (RCP 2.6 and RCP 8.5) and periods (2050 and 2070) using multivariate modeling methods-the MaxEnt model. The results showed a medium level of genetic diversity and low inbreeding in the 21 P. sheareri natural populations, and genetic differentiation among populations was significant, with 21.2 % genetic variation among populations. The remnant populations of P. sheareri were grouped into four genetic clusters based on genetic structure; five environmental variables involving four temperature variables and precipitation seasonality (Bio12) might determine the distribution of P. sheareri populations. In the future, the suitable habitats of P. sheareri are manifested as northward migration, and the highly suitable habitats are expected to increase. Our results highlight the importance of conservation units in situ, giving priority to populations with higher genetic diversity (e.g., TMS, FJS, and THY populations); sampling strategies for ex situ conservation, breeding and reforestation should consider climate change, especially Bio1 (annual mean temperature) and Bio12 (annual precipitation). Overall, this study may provide useful genetic information for strategies for the protection, management, and utilization of P. sheareri.
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Affiliation(s)
- Yang Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Bio-technology, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Xiaohua Ma
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Bio-technology, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Yunfeng Lu
- The Seeding Breeding Center of Ningbo Forestry Bureau, Ningbo 315012, Zhejiang, China
| | - Xiange Hu
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Bio-technology, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Luhuan Lou
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Bio-technology, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Bio-technology, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
| | - Junhong Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry & Bio-technology, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
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Penna A, Dillon R, Bearder SK, Karlsson J, Perkin A, Pozzi L. Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
Assessing the true lineage diversity in elusive nocturnal organisms is particularly challenging due to their subtle phenotypic variation in diagnostic traits. The cryptic small-eared greater galago (Otolemur garnettii) offers a great opportunity to test if currently recognized subspecies, suggested by discontinuities in coat colour pattern and geographic barriers, represent distinct evolutionary lineages. To answer this question, we conducted the first population-level phylogeographic study of the species, sampling wild specimens from across almost its entire latitudinal range, including the Zanzibar Archipelago. We applied five species-delimitation algorithms to investigate the genetic diversity and distribution pattern of mitochondrial DNA across the geographic range of three out of four subspecies. Our results suggest that far-northern populations of O. g. lasiotis potentially represent an independently evolving lineage, but populations assigned to O. g. garnettii from Zanzibar Island and of O. g panganiensis from mainland Tanzania do not constitute two independent lineages. A dated phylogeny suggests that this northern clade diverged from all remaining samples approximately 4 Mya. Such old divergence age is in line with the split between many galagid species. This northern lineage could potentially represent an incipient species; however, there is not yet enough evidence to support a new taxonomic status for this unique mitochondrial group.
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Affiliation(s)
- Anna Penna
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Rosemarie Dillon
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
| | - Simon K Bearder
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Johan Karlsson
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Andrew Perkin
- Nocturnal Primate Research Group, Oxford Brookes University , Oxford , UK
| | - Luca Pozzi
- Department of Anthropology, University of Texas at San Antonio , San Antonio, Texas , USA
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Lovrenčić L, Temunović M, Bonassin L, Grandjean F, Austin CM, Maguire I. Climate change threatens unique genetic diversity within the Balkan biodiversity hotspot – The case of the endangered stone crayfish. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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46
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Population structure of threatened caribou in western Canada inferred from genome-wide SNP data. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01475-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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47
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Prates I, Doughty P, Rabosky DL. Subspecies at crossroads: the evolutionary significance of genomic and phenotypic variation in a wide-ranging Australian lizard ( Ctenotus pantherinus). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Many subspecies were described to capture phenotypic variation in wide-ranging taxa, with some later being found to correspond to divergent genetic lineages. We investigate whether currently recognized subspecies correspond to distinctive and coherent evolutionary lineages in the widespread Australian lizard Ctenotus pantherinus based on morphological, mitochondrial and genome-wide nuclear variation. We find weak and inconsistent correspondence between morphological patterns and the presumed subspecies ranges, with character polymorphism within regions and broad morphological overlap across regions. Phylogenetic analyses suggest paraphyly of populations assignable to each subspecies, mitonuclear discordance and little congruence between subspecies ranges and the distribution of inferred clades. Genotypic clustering supports admixture across regions. These results undermine the presumed phenotypic and genotypic coherence and distinctiveness of C. pantherinus subspecies. Based on our findings, we comment on the operational and conceptual shortcomings of morphologically defined subspecies and discuss practical challenges in applying the general notion of subspecies as incompletely separated population lineages. We conclude by highlighting a historical asymmetry that has implications for ecology, evolution and conservation: subspecies proposed in the past are difficult to falsify even in the face of new data that challenge their coherence and distinctiveness, whereas modern researchers appear hesitant to propose new subspecies.
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Affiliation(s)
- Ivan Prates
- Department of Ecology and Evolutionary Biology, University of Michigan , Ann Arbor, MI , USA
- Museum of Zoology, University of Michigan , Ann Arbor, MI , USA
| | - Paul Doughty
- Collections & Research, Western Australian Museum , Welshpool , WA 6106 , Australia
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48
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Jiang N, Li Z, Dai Y, Liu Z, Han X, Li Y, Li Y, Xiong H, Xu J, Zhang G, Xiao S, Yuan X, Fu Y. Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma. Mol Ecol Resour 2022. [PMID: 36214617 DOI: 10.1111/1755-0998.13718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022]
Abstract
Genome introgression is one of the driving forces that can increase species and genetic diversity and facilitate the adaptive evolution of organisms and biodiversity conservation. However, the genomic introgression and its contribution to biodiversity of macrofungi are still unclear. The genus Ganoderma is a typical macrofungal group that plays crucial roles in forest ecosystem as saprophytic organisms and plant pathogens, and is also involved in human health as medicinal mushrooms. Most public Ganoderma genomes are fragmented, and reference genomes and whole-genome information of diverse germplasm resources for many Ganoderma species are lacking, thus hindering functional and evolutionary genomic investigations among Ganoderma species. In this study, we provide high-quality genomes of 10 Ganoderma species and whole-genome variants data of 224 individuals from various ecoregions, enabling us to infer the phylogeny of Ganoderma species and their historical population dynamics. Based on whole-genome variants, widespread and genome-wide introgression among Ganoderma species is revealed. Genes with significant introgression signals were related to stress response, digestive absorption, and secondary metabolite synthesis, factors that may contribute to environmental adaptation and important biocomponent metabolism. CYP512U6, an essential functional gene in the CYP450 family related to Ganoderma triterpene synthesis, was detected with significant introgression and selection signals combined with Ganoderma metabolomic analysis, indicating that both ancient gene exchange and recent domestication have contributed to the categories and content of secondary metabolites of Ganoderma. The reference genomes, whole-genome variants, and metabolite profiles could serve as abundant and valuable genetic resources for evolution, ecology, and conservation investigations of Ganoderma species and other macrofungi.
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Affiliation(s)
- Nan Jiang
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
- College of Plant Protection, Jilin Agricultural University, Jilin, Changchun, China
| | - Zhenhao Li
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Yueting Dai
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhenhua Liu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Xuerong Han
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu Li
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yong Li
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Hui Xiong
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Jing Xu
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Guoliang Zhang
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Shijun Xiao
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, Zhejiang, China
| | - Xiaohui Yuan
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yongping Fu
- College of Plant Protection, Jilin Agricultural University, Jilin, Changchun, China
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Mohr JJ, Harrison PA, Stanhope J, Breed MF. Is the genomics 'cart' before the restoration ecology 'horse'? Insights from qualitative interviews and trends from the literature. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210381. [PMID: 35757881 PMCID: PMC9234818 DOI: 10.1098/rstb.2021.0381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/26/2022] [Indexed: 12/21/2022] Open
Abstract
Harnessing new technologies is vital to achieve global imperatives to restore degraded ecosystems. We explored the potential of genomics as one such tool. We aimed to understand barriers hindering the uptake of genomics, and how to overcome them, via exploratory interviews with leading scholars in both restoration and its sister discipline of conservation-a discipline that has successfully leveraged genomics. We also conducted an examination of research trends to explore some insights that emerged from the interviews, including publication trends that have used genomics to address restoration and conservation questions. Our qualitative findings revealed varied perspectives on harnessing genomics. For example, scholars in restoration without genomics experience felt genomics was over-hyped. Scholars with genomics experience emphatically emphasized the need to proceed cautiously in using genomics in restoration. Both genomics-experienced and less-experienced scholars called for case studies to demonstrate the benefits of genomics in restoration. These qualitative data contrasted with our examination of research trends, which revealed 70 restoration genomics studies, particularly studies using environmental DNA as a monitoring tool. We provide a roadmap to facilitate the uptake of genomics into restoration, to help the restoration sector meet the monumental task of restoring huge areas to biodiverse and functional ecosystems. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'.
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Affiliation(s)
- Jakki J. Mohr
- College of Business, Institute on Ecosystems, University of Montana, Missoula, MT 59812, USA
| | - Peter A. Harrison
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Jessica Stanhope
- School of Allied Health Science and Practice, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Martin F. Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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Discerning the global phylogeographic distribution of Phyllosticta citricarpa by means of whole genome sequencing. Fungal Genet Biol 2022; 162:103727. [PMID: 35870700 DOI: 10.1016/j.fgb.2022.103727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/08/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022]
Abstract
Phyllosticta citricarpa is a fungal pathogen causing citrus black spot (CBS). As a regulated pest in some countries, the presence of the pathogen limits the export of fruit and is therefore of agricultural and economic importance. In this study, we used high throughput sequencing data to infer the global phylogeographic distribution of this pathogen, including 71 isolates from eight countries, Argentina, Australia, Brazil, China, Cuba, Eswatini, South Africa and the United States of America. We assembled draft genomes and used a pairwise read mapping approach for the detection and enumeration of variants between isolates. We performed SSR marker discovery based on the assembled genome with the best assembly statistics, and generated genotype profiles for all isolates with 1987 SSR markers in silico. Furthermore, we identified 32,560 SNPs relative to a reference sequence followed by population genetic analyses based on the three datasets; pairwise variant counts, SSR genotypes and SNP genotypes. All three analysis approaches gave similar overall results. Possible pathways of dissemination among the populations from China, Australia, southern Africa and the Americas are postulated. The Chinese population is the most diverse, and is genetically the furthest removed from all other populations, and is therefore considered the closest to the origin of the pathogen. Isolates from Australia, Eswatini and the South African province Mpumalanga are closely associated and clustered together with those from Argentina and Brazil. The Eastern Cape, North West, and KwaZulu-Natal populations in South Africa grouped in another cluster, while isolates from Limpopo are distributed between the two aforementioned clusters. Southern African populations showed a close relationship to populations in North America, and could be a possible source of P. citricarpa populations that are now found in North America. This study represents the largest whole genome sequencing survey of P. citricarpa to date and provides a more comprehensive assessment of the population genetic diversity and connectivity of P. citricarpa from different geographic origins. This information could further assist in a better understanding of the epidemiology of the CBS pathogen, its long-distance dispersal and dissemination pathways, and can be used to refine phytosanitary regulations and management programmes for the disease.
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