1
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Cahill AE, Meglécz E, Chenuil A. Scientific history, biogeography, and biological traits predict presence of cryptic or overlooked species. Biol Rev Camb Philos Soc 2024; 99:546-561. [PMID: 38049930 DOI: 10.1111/brv.13034] [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: 01/03/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023]
Abstract
Genetic data show that many nominal species are composed of more than one biological species, and thus contain cryptic species in the broad sense (including overlooked species). When ignored, cryptic species generate confusion which, beyond biodiversity or vulnerability underestimation, blurs our understanding of ecological and evolutionary processes and may impact the soundness of decisions in conservation or medicine. However, very few hypotheses have been tested about factors that predispose a taxon to contain cryptic or overlooked species. To fill this gap, we surveyed the literature on free-living marine metazoans and built two data sets, one of 187,603 nominal species and another of 83 classes or phyla, to test several hypotheses, correcting for sequence data availability, taxon size and phylogenetic relatedness. We found a strong effect of scientific history: the probability of a taxon containing cryptic species was highest for the earliest described species and varied among time periods potentially consistently with an influence of prevailing scientific theories. The probability of cryptic species being present was also increased for species with large distribution ranges. They were more frequent in the north polar and south polar zones, contradicting previous predictions of more cryptic species in the tropics, and supporting the hypothesis that many cryptic species diverged recently. The number of cryptic species varied among classes, with an excess in hydrozoans and polychaetes, and a deficit in actinopterygians, for example, but precise class ranking was relatively sensitive to the statistical model used. For all models, biological traits, rather than phylum, appeared responsible for the variation among classes: there were fewer cryptic species than expected in classes with hard skeletons (perhaps because they provide good characters for taxonomy) and image-forming vision (in which selection against heterospecific mating may enhance morphological divergence), and more in classes with internal fertilisation. We estimate that among marine free-living metazoans, several thousand additional cryptic species complexes could be identified as more sequence data become available. The factors identified as important for marine animal cryptic species are likely important for other biomes and taxa and should aid many areas in biology that rely on accurate species identification.
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Affiliation(s)
- Abigail E Cahill
- Biology Department, Albion College, 611 East Porter St., Albion, MI, 49224, USA
| | - Emese Meglécz
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Station Marine d'Endoume, Chemin de la Batterie des Lions, Marseille, 13007, France
| | - Anne Chenuil
- Aix Marseille Univ, Avignon Univ, CNRS, IRD, IMBE, Station Marine d'Endoume, Chemin de la Batterie des Lions, Marseille, 13007, France
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2
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Wang HL, Lei T, Wang XW, Cameron S, Navas-Castillo J, Liu YQ, Maruthi MN, Omongo CA, Delatte H, Lee KY, Krause-Sakate R, Ng J, Seal S, Fiallo-Olivé E, Bushley K, Colvin J, Liu SS. A comprehensive framework for the delimitation of species within the Bemisia tabaci cryptic complex, a global pest-species group. INSECT SCIENCE 2024. [PMID: 38562016 DOI: 10.1111/1744-7917.13361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities. Bemisia tabaci is a cryptic species complex containing more than 44 putative species; several of which are currently among the world's most destructive crop pests. Interpreting and delimiting the evolution of this species complex has proved problematic. To develop a comprehensive framework for species delimitation and identification, we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B. tabaci species complex acquired worldwide. Distinct datasets include full mitogenomes, single-copy nuclear genes, restriction site-associated DNA sequencing, geographic range, host speciation, and reproductive compatibility datasets. Phylogenetically, our well-supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B. tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B. tabaci species diversity. Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples. Native geographic range information provides a complementary assessment of species recognition, while the host range datasets provide low rate of delimiting resolution. We further summarized different data performances in species classification when compared with reproductive compatibility, indicating that combination of mtCOI divergence, nuclear markers, geographic range provide a complementary assessment of species recognition. Finally, we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles.
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Affiliation(s)
- Hua-Ling Wang
- College of Forestry, Hebei Agricultural University, Baoding, Hebei Province, China
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Teng Lei
- College of Life Sciences, Taizhou University, Taizhou, Zhejiang Province, China
| | - Xiao-Wei Wang
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Stephen Cameron
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Malaga, Spain
| | - Yin-Quan Liu
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Kent, UK
| | | | - Hélène Delatte
- CIRAD, UMR PVBMT CIRAD, Pôle de Protection des Plantes, Saint-Pierre, France
| | - Kyeong-Yeoll Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | | | - James Ng
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Malaga, Spain
| | - Kathryn Bushley
- USDA Agricultural Research Service, 17123, Emerging Pests and Pathogens Research Unit, Ithaca, NY, USA
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - Shu-Sheng Liu
- The Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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3
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Ren Y, Zhang L, Yang X, Lin H, Sang Y, Feng L, Liu J, Kang M. Cryptic divergences and repeated hybridizations within the endangered "living fossil" dove tree ( Davidia involucrata) revealed by whole genome resequencing. PLANT DIVERSITY 2024; 46:169-180. [PMID: 38807904 PMCID: PMC11128880 DOI: 10.1016/j.pld.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 05/30/2024]
Abstract
The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a "living fossil" dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.
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Affiliation(s)
- Yumeng Ren
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Lushui Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xuchen Yang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Hao Lin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yupeng Sang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Landi Feng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Minghui Kang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
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4
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Lizano AMD, Kim KM, Juinio-Meñez MA, Ravago-Gotanco R. Pseudocryptic diversity and species boundaries in the sea cucumber Stichopus cf. horrens (Echinodermata: Stichopodidae) revealed by mitochondrial and microsatellite markers. Sci Rep 2024; 14:4886. [PMID: 38418859 PMCID: PMC10901784 DOI: 10.1038/s41598-024-54987-w] [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: 10/12/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
Morphologically cryptic and pseudo-cryptic species pose a challenge to taxonomic identification and assessments of species diversity and distributions. Such is the case for the sea cucumber Stichopus horrens, commonly confused with Stichopus monotuberculatus. Here, we used mitochondrial cytochrome oxidase subunit I (COI) and microsatellite markers to examine genetic diversity in Stichopus cf. horrens throughout the Philippine archipelago, to aid species identification and clarify species boundaries. Phylogenetic analysis reveals two recently diverged COI lineages (Clade A and Clade B; c. 1.35-2.54 Mya) corresponding to sequence records for specimens identified as S. monotuberculatus and S. horrens, respectively. Microsatellite markers reveal two significantly differentiated genotype clusters broadly concordant with COI lineages (Cluster 1, Cluster 2). A small proportion of individuals were identified as later-generation hybrids indicating limited contemporary gene flow between genotype clusters, thus confirming species boundaries. Morphological differences in papillae distribution and form are observed for the two species, however tack-like spicules from the dorsal papillae are not a reliable diagnostic character. An additional putative cryptic species was detected within Clade B-Cluster 2 specimens warranting further examination. We propose that these lineages revealed by COI and genotype data be referred to as Stichopus cf. horrens species complex.
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Affiliation(s)
- Apollo Marco D Lizano
- Faculty of Biosciences & Aquaculture, Nord University, Bodø, Norway.
- Marine Science Institute, University of the Philippines, 1101, Diliman Quezon City, Philippines.
| | - Kenneth M Kim
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Marine Science Institute, University of the Philippines, 1101, Diliman Quezon City, Philippines
| | | | - Rachel Ravago-Gotanco
- Marine Science Institute, University of the Philippines, 1101, Diliman Quezon City, Philippines
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5
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Miralles A, Puillandre N, Vences M. DNA Barcoding in Species Delimitation: From Genetic Distances to Integrative Taxonomy. Methods Mol Biol 2024; 2744:77-104. [PMID: 38683312 DOI: 10.1007/978-1-0716-3581-0_4] [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] [Indexed: 05/01/2024]
Abstract
Over the past two decades, DNA barcoding has become the most popular exploration approach in molecular taxonomy, whether for identification, discovery, delimitation, or description of species. The present contribution focuses on the utility of DNA barcoding for taxonomic research activities related to species delimitation, emphasizing the following aspects:(1) To what extent DNA barcoding can be a valuable ally for fundamental taxonomic research, (2) its methodological and theoretical limitations, (3) the conceptual background and practical use of pairwise distances between DNA barcode sequences in taxonomy, and (4) the different ways in which DNA barcoding can be combined with complementary means of investigation within a broader integrative framework. In this chapter, we recall and discuss the key conceptual advances that have led to the so-called renaissance of taxonomy, elaborate a detailed glossary for the terms specific to this discipline (see Glossary in Chap. 35 ), and propose a newly designed step-by-step species delimitation protocol starting from DNA barcode data that includes steps from the preliminary elaboration of an optimal sampling strategy to the final decision-making process which potentially leads to nomenclatural changes.
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Affiliation(s)
- Aurélien Miralles
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Nicolas Puillandre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Paris, France
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany.
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6
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Maltsev Y, Erst A. Recent Advances in the Integrative Taxonomy of Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:4097. [PMID: 38140423 PMCID: PMC10747101 DOI: 10.3390/plants12244097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 11/29/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023]
Abstract
Biodiversity conservation and management call for rapid and accurate global assessments at the species level [...].
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Affiliation(s)
- Yevhen Maltsev
- K.A. Timiryazev Institute of Plant Physiology Russian Academy of Sciences, IPP RAS, Moscow 127276, Russia;
| | - Andrey Erst
- Central Siberian Botanical Garden, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
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7
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Alexander Pyron R. Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation. Mol Phylogenet Evol 2023; 189:107939. [PMID: 37804960 DOI: 10.1016/j.ympev.2023.107939] [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: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Integrative taxonomy, combining data from multiple axes of biologically relevant variation, is a major goal of systematics. Ideally, such taxonomies will derive from similarly integrative species-delimitation analyses. Yet, most current methods rely solely or primarily on molecular data, with other layers often incorporated only in a post hoc qualitative or comparative manner. A major limitation is the difficulty of devising quantitative parametric models linking different datasets in a unified ecological and evolutionary framework. Machine Learning (ML) methods offer flexibility in this arena by easily learning high-dimensional associations between observations (e.g., individual specimens) across a wide array of input features (e.g., genetics, geography, environment, and phenotype) to delimit statistically meaningful clusters. Here, I implement an unsupervised method using Self-Organizing (or "Kohonen") Maps (SOMs) for such purposes. Recent extensions called "SuperSOMs" can integrate multiple layers, each of which exerts independent influence on a two-dimensional output grid via empirically estimated weights. The grid cells are then delimited into K distinct units that can be interpreted as species or other entities. I show empirical examples in salamanders (Desmognathus) and snakes (Storeria) with layers representing alleles, space, climate, and traits. Simulations reveal that the SuperSOM approach can detect K = 1, tends not to over-split, reflects contributions from all layers, and limits large layers (e.g., genetic matrices) from overwhelming other datasets, desirable properties addressing major concerns from previous studies. Finally, I suggest that these and similar methods could integrate conservation-relevant layers such as population trends and human encroachment to delimit management units from an explicitly quantitative framework grounded in the ecology and evolution of species limits and boundaries.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052 USA.
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8
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Fiesinger A, Held C, Schmidt AL, Putchim L, Melzner F, Wall M. Dominance of the coral Pocillopora acuta around Phuket Island in the Andaman Sea, Thailand. Ecol Evol 2023; 13:e10724. [PMID: 38020692 PMCID: PMC10643679 DOI: 10.1002/ece3.10724] [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: 05/17/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
Pocillopora damicornis (Linnaeus, 1758), a species complex, consists of several genetic lineages, some of which likely represent reproductively isolated species, including the species Pocillopora acuta Lamarck, 1816. Pocillopora acuta can exhibit similar morphological characteristics as P. damicornis, thus making it difficult to identify species-level taxonomic units. To determine whether the P. damicornis-like colonies on the reefs in the Andaman Sea (previously often identified as P. damicornis) consist of different species, we sampled individual colonies at five sites along a 50 km coastal stretch at Phuket Island and four island sites towards Krabi Province, Thailand. We sequenced 210 coral samples for the mitochondrial open reading frame and identified six distinct haplotypes, all belonging to P. acuta according to the literature. Recently, P. acuta was observed to efficiently recolonize heat-damaged reefs in Thailand as well as globally, making it a potentially important coral species in future reefs. Specifically in the light of global change, this study underscores the importance of high-resolution molecular species recognition, since taxonomic units are important factors for population genetic studies, and the latter are crucial for management and conservation efforts.
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Affiliation(s)
- Anna Fiesinger
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - Christoph Held
- Alfred‐Wegener‐InstitutHelmholtz‐Zentrum für Polar‐ und MeeresforschungBremerhavenGermany
| | - Andrea L. Schmidt
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
- Cooperative Institute for Marine and Atmospheric ResearchUniversity of Hawai‘i at ManoaHonoluluHonoluluUSA
| | | | - Frank Melzner
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
| | - Marlene Wall
- GEOMAR Helmholtz Centre for Ocean Research KielKielGermany
- Alfred‐Wegener‐InstitutHelmholtz‐Zentrum für Polar‐ und MeeresforschungBremerhavenGermany
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9
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Ansari L, Asgari B, Zare R, Zamanizadeh HR. Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran. Int J Syst Evol Microbiol 2023; 73. [PMID: 37676702 DOI: 10.1099/ijsem.0.006028] [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] [Indexed: 09/08/2023] Open
Abstract
During a survey of species diversity of Penicillium and Talaromyces in sugarcane (Saccharum officinarum) rhizosphere in the Khuzestan province of Iran [1], 195 strains were examined, from which 187 belonged to Penicillium (11 species) and eight to Talaromyces (one species). In the present study, three strains of Penicillium belonging to section Exilicaulis series Restricta, identified as P. restrictum by Ansari et al. [1], were subjected to a phylogenetic study. The multilocus phylogeny of partial β-tubulin, calmodulin and RNA polymerase II second largest subunit genes enabled the recognition of one new phylogenetic species that is here formally described as Penicillium rhizophilum sp. nov. This species is phylogenetically distinct in series Restricta, but it does not show significant morphological differences from other species previously classified in the series. Therefore, we here placed bias on the phylogenetic species concept. The holotype of Penicillium rhizophilum sp. nov. is IRAN 18169F and the ex-type culture is LA30T (=IRAN 4042CT=CBS 149737T).
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Affiliation(s)
- Laleh Ansari
- Department of Plant Protection, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Bita Asgari
- Department of Botany, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Rasoul Zare
- Department of Botany, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Hamid Reza Zamanizadeh
- Department of Plant Protection, Science and Research Branch, Islamic Azad University, Tehran, Iran
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10
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Abalde S, Crocetta F, Tenorio MJ, D'Aniello S, Fassio G, Rodríguez-Flores PC, Uribe JE, M L Afonso C, Oliverio M, Zardoya R. Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus. Mol Phylogenet Evol 2023:107838. [PMID: 37286063 DOI: 10.1016/j.ympev.2023.107838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 05/15/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red+blue+orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
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Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Fabio Crocetta
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Giulia Fassio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Paula C Rodríguez-Flores
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge MA 02138, USA
| | - Juan E Uribe
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal
| | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
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11
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Gu YF, Shu JP, Lu YJ, Shen H, Shao W, Zhou Y, Sun QM, Chen JB, Liu BD, Yan YH. Insights into cryptic speciation of quillworts in China. PLANT DIVERSITY 2023; 45:284-301. [PMID: 37397601 PMCID: PMC10311115 DOI: 10.1016/j.pld.2022.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/24/2022] [Accepted: 11/08/2022] [Indexed: 07/04/2023]
Abstract
Cryptic species are commonly misidentified because of high morphological similarities to other species. One group of plants that may harbor large numbers of cryptic species is the quillworts (Isoëtes spp.), an ancient aquatic plant lineage. Although over 350 species of Isoëtes have been reported globally, only ten species have been recorded in China. The aim of this study is to better understand Isoëtes species diversity in China. For this purpose, we systematically explored the phylogeny and evolution of Isoëtes using complete chloroplast genome (plastome) data, spore morphology, chromosome number, genetic structure, and haplotypes of almost all Chinese Isoëtes populations. We identified three ploidy levels of Isoëtes in China-diploid (2n = 22), tetraploid (2n = 44), and hexaploid (2n = 66). We also found four megaspore and microspore ornamentation types in diploids, six in tetraploids, and three in hexaploids. Phylogenetic analyses confirmed that I. hypsophila as the ancestral group of the genus and revealed that Isoëtes diploids, tetraploids, and hexaploids do not form monophyletic clades. Most individual species possess a single genetic structure; however, several samples have conflicting positions on the phylogenetic tree based on SNPs and the tree based on plastome data. All 36 samples shared 22 haplotypes. Divergence time analysis showed that I. hypsophila diverged in the early Eocene (∼48.05 Ma), and most other Isoëtes species diverged 3-20 Ma. Additionally, different species of Isoëtes were found to inhabit different water systems and environments along the Yangtze River. These findings provide new insights into the relationships among Isoëtes species in China, where highly similar morphologic populations may harbor many cryptic species.
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Affiliation(s)
- Yu-Feng Gu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, 150025, China
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Jiang-Ping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Yi-Jun Lu
- Zhejiang University City College, Hangzhou, 310015, China
| | - Hui Shen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Wen Shao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yan Zhou
- Jiande Xin'anjiang Forest Farm, Jiande, 311600, China
| | - Qi-Meng Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Jian-Bing Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Bao-Dong Liu
- Life Science and Technology College, Harbin Normal University, Key Laboratory of Plant Biology in Colleges of Heilongjiang Province, Harbin, 150025, China
| | - Yue-Hong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, and Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
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12
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Arakaki N, Flores Ramos L, Oscanoa Huaynate AI, Ruíz Soto A, Ramírez ME. Biochemical and Nutritional Characterization of Edible Seaweeds from the Peruvian Coast. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091795. [PMID: 37176854 PMCID: PMC10181002 DOI: 10.3390/plants12091795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
In Peru, the number of species of edible seaweeds within the genera Chondracanthus, Porphyra (hereafter P.), Pyropia (hereafter Py.), and Ulva has not been fully established, nor is there a significant level of information available related to their chemical and nutritional composition. This study involved the biochemical analysis of species belonging to ten genera of macroalgae, known edible and some of which have the potential to be used as food, including six red (Callophyllis, Chondracanthus, Mazzaella, Porphyra, Pyropia, and Rhodymenia), two green (Ulva and Codium), and two brown (Eisenia and Lessonia) species collected along the Peruvian coast (6°-17° S). In the evaluation of 37 specimens, differences were found in the proximal composition, amino acid composition, and fatty acid profiles, which were specific to subgroups and supported their taxonomic classification, mainly at the order level. The red algae Porphyra/Pyropia (Bangiales) had the highest average percentage of protein (24.10%) and carbohydrates (59.85%) and the lowest percentage of ash (7.95%). Conversely, the brown alga Eisenia (Laminariales) had the lowest average percentage of protein, with different values related to the structure: 14.11% at the level of the frond and 9.46% at the level of the stipe. On the other hand, Bryopsidales green algae showed the highest average percentages of lipids (5.38%). The moisture percentages ranged from 4 to 16%, and no relevant significant differences were shown between the orders. The characteristic amino acids in all of the studied groups were glutamic acid, aspartic acid, alanine, and leucine. The highest average of the essential amino acids ratio was obtained for the Gigartinales red algae (48.65%), and the highest values of the essential amino acid index (EAAI) were obtained for the Ulvales, Laminariales, Gigartinales, and Rhodymeniales algae (EAAI > 0.92). The highest average relative percentage of fatty acids was obtained for polyunsaturated fatty acids, followed by saturated fatty acids. The major component of the ω6 fatty acids from red and brown algae was arachidonic acid (C20:4n - 6). The highest level of ω3 fatty acids was observed for the eicosapentaenoic acids (EPA) in red algae. The highest median ω6/ω3 ratio was displayed by the red alga Callophyllis variegata (Gigartinales). A detailed knowledge of edible seaweeds, and those considered potentially edible, would help to diversify the diet based on macroalgae in Peru.
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Affiliation(s)
- Natalia Arakaki
- Banco de Germoplasma de Organismos Acuáticos, Área Funcional de Investigaciones en Acuicultura, Instituto del Mar del Perú, Esquina Gamarra y General Valle S/N, Chucuito, Callao 07021, Peru
| | - Leenin Flores Ramos
- Laboratorio de Análisis Instrumental, Área Funcional de Investigaciones en Acuicultura, Instituto del Mar del Perú, Esquina Gamarra y General Valle S/N, Chucuito, Callao 07021, Peru
| | - Alberto Isidoro Oscanoa Huaynate
- Laboratorio de Análisis Instrumental, Área Funcional de Investigaciones en Acuicultura, Instituto del Mar del Perú, Esquina Gamarra y General Valle S/N, Chucuito, Callao 07021, Peru
| | - Anthony Ruíz Soto
- Laboratorio de Análisis Instrumental, Área Funcional de Investigaciones en Acuicultura, Instituto del Mar del Perú, Esquina Gamarra y General Valle S/N, Chucuito, Callao 07021, Peru
| | - María Eliana Ramírez
- Museo Nacional de Historia Natural, Área Botánica, Casilla 787, Santiago 8500000, Chile
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13
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Oury N, Noël C, Mona S, Aurelle D, Magalon H. From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 2023; 184:107803. [PMID: 37120114 DOI: 10.1016/j.ympev.2023.107803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France.
| | - Cyril Noël
- IFREMER - IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; EPHE, PSL Research University, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
| | - Didier Aurelle
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
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14
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A comprehensive phylogeny and revised taxonomy illuminate the origin and diversification of the global radiation of Papilio (Lepidoptera: Papilionidae). Mol Phylogenet Evol 2023; 183:107758. [PMID: 36907224 DOI: 10.1016/j.ympev.2023.107758] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/28/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
The swallowtail genus Papilio (Lepidoptera: Papilionidae) is species rich, distributed worldwide, and has broad morphological habits and ecological niches. Because of its elevated species richness, it has been historically difficult to reconstruct a densely sampled phylogeny for this clade. Here we provide a taxonomic working list for the genus, resulting in 235 Papilio species, and assemble a molecular dataset of seven gene fragments representing ca. 80% of the currently described diversity. Phylogenetic analyses reconstructed a robust tree with highly supported relationships within subgenera, although a few nodes in the early history of the Old World Papilio remain unresolved. Contrasting with previous results, we found that Papilio alexanor is sister to all Old World Papilio and that the subgenus Eleppone is no longer monotypic. The latter includes the recently described Fijian Papilio natewa with the Australian Papilio anactus and is sister to subgenus Araminta (formerly included in subgenus Menelaides) occurring in Southeast Asia. Our phylogeny also includes rarely studied (P. antimachus, P. benguetana) or endangered species (P. buddha, P. chikae). Taxonomic changes resulting from this study are elucidated. Molecular dating and biogeographic analyses indicate that Papilio originated ca. 30 million years ago (Oligocene), in a northern region centered on Beringia. A rapid early Miocene radiation in the Paleotropics is revealed within Old World Papilio, potentially explaining their low early branch support. Most subgenera originated in the early to middle Miocene followed by synchronous southward biogeographic dispersals and repeated local extirpations in northern latitudes. This study provides a comprehensive phylogenetic framework for Papilio with clarification of subgeneric systematics and species taxonomic changes enumerated, which will facilitate further studies to address questions on their ecology and evolutionary biology using this model clade.
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15
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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16
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Eyer PA, Finand B, Mona S, Khimoun A, D'ettorre P, Fédérici P, Leroy C, Cornette R, Chifflet-Belle P, Monnin T, Doums C. Integrative characterization of genetic and phenotypic differentiation in an ant species complex with strong hierarchical population structure and low dispersal abilities. Heredity (Edinb) 2023; 130:163-176. [PMID: 36585503 PMCID: PMC9981590 DOI: 10.1038/s41437-022-00590-6] [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: 12/07/2021] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Low dispersal, occurrence of asexual reproduction and geographic discontinuity increase genetic differentiation between populations, which ultimately can lead to speciation. In this work, we used a multidisciplinary framework to characterize the genetic and phenotypic differentiation between and within two cryptic ant species with restricted dispersal, Cataglyphis cursor and C. piliscapa and used behavioral experiments to test for reproductive isolation. Their distribution is segregated by the Rhône River and they have been traditionally distinguished only by hair numbers, although a statistical assessment is still lacking. We found strong genetic (microsatellites, nuclear and mitochondrial sequences), morphological (number of hairs, tibia length, male genitalia) and chemical (cuticular hydrocarbons) differentiation not only between species but also among localities within species. However, inter-specific differentiation was slightly higher than intra-specific differentiation for most markers. Overall, this pattern could either reflect reproductive isolation or could result from a longer period of geographic isolation between species than among localities within species without necessarily involving reproductive isolation. Interestingly, our behavioral experiments showed an absence of mating between species associated to a higher aggressiveness of workers towards heterospecific males. This suggests that sexual selection may, at least partially, fuel reproductive isolation. We also showed that cuticular hydrocarbons, mtDNA sequences and number of hairs provide reliable criteria allowing species discrimination. Overall, this species complex offers a case study to further investigate varying stages of a speciation continuum by estimating reproductive isolation between pairs of localities varying by their level of genetic differentiation.
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Affiliation(s)
- P A Eyer
- Department of Entomology, 2143 TAMU, Texas A&M University, College Station, TX, 77843-2143, USA.
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France.
- EPHE, PSL University, 75005, Paris, France.
| | - B Finand
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
| | - S Mona
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
- EPHE, PSL University, 75005, Paris, France
| | - A Khimoun
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
- EPHE, PSL University, 75005, Paris, France
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - P D'ettorre
- Laboratory of Experimental and Comparative Ethology, University of Paris 13, Sorbonne Paris Cité, 93430, Villetaneuse, France
| | - P Fédérici
- Sorbonne Université, Université Paris Est Créteil, CNRS, INRAe, IRD, Institute of Ecology and Environmental sciences of Paris, iEES-Paris, 75005, Paris, France
| | - C Leroy
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne Franche-Comté, 6 Boulevard Gabriel, 21000, Dijon, France
| | - R Cornette
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
| | - P Chifflet-Belle
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
- EPHE, PSL University, 75005, Paris, France
| | - T Monnin
- Sorbonne Université, Université Paris Est Créteil, CNRS, INRAe, IRD, Institute of Ecology and Environmental sciences of Paris, iEES-Paris, 75005, Paris, France
| | - C Doums
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205, MNHN, CNRS, EPHE-PSL, Sorbonne Université, Université des Antilles, 75005, Paris, France
- EPHE, PSL University, 75005, Paris, France
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17
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Mammola S, Viel N, Amiar D, Mani A, Hervé C, Heard SB, Fontaneto D, Pétillon J. Taxonomic practice, creativity and fashion: what’s in a spider name? Zool J Linn Soc 2023. [DOI: 10.1093/zoolinnean/zlac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Abstract
There is a secret pleasure in naming new species. Besides traditional etymologies recalling the sampling locality, habitat or morphology of the species, names may be tributes to some meaningful person, pop culture references and even exercises of enigmatography. Using a dataset of 48 464 spider etymologies, we tested the hypothesis that species names given by taxonomists are deeply influenced by their cultural background. Specifically, we asked whether naming practices change through space or have changed through time. In absolute terms, etymologies referring to morphology were the most frequently used. In relative terms, references to morphology peaked in 1850–1900 and then began to decline, with a parallel increase in etymologies dedicated to people and geography. We also observed a dramatic increase in etymologies referring to pop culture and other cultural aspects in 2000–2020, especially in Europe and the Americas. While such fashionable names often carry no biological information regarding the species itself, they help give visibility to taxonomy, a discipline currently facing a profound crisis in academia. Taxonomy is among the most unchanged disciplines across the last centuries in terms of tools, rules and writing style. Yet, our analysis suggests that taxonomists remain deeply influenced by their living time and space.
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Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, University of Helsinki , Pohjoinen Rautatiekatu 13, Helsinki 00100 , Finland
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council (CNR) , Corso Tonolli 50, 28922 Verbania Pallanza , Italy
| | - Nathan Viel
- UMR 65532 CNRS ECOBIO (Ecosystèmes, Biodiversité, Evolution), Université de Rennes , F-35000, Rennes , France
| | - Dylan Amiar
- UMR 65532 CNRS ECOBIO (Ecosystèmes, Biodiversité, Evolution), Université de Rennes , F-35000, Rennes , France
| | - Atishya Mani
- Department of Biology, University of New Brunswick , Fredericton , NB Canada E3B 5A3
| | - Christophe Hervé
- Muséum d‘Histoire Naturelle de Paris , 45 Rue de Buffon, 75005 Paris , France
| | - Stephen B Heard
- Department of Biology, University of New Brunswick , Fredericton , NB Canada E3B 5A3
| | - Diego Fontaneto
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council (CNR) , Corso Tonolli 50, 28922 Verbania Pallanza , Italy
| | - Julien Pétillon
- UMR 65532 CNRS ECOBIO (Ecosystèmes, Biodiversité, Evolution), Université de Rennes , F-35000, Rennes , France
- Institute for Coastal and Marine Research, Nelson Mandela University , Port Elizabeth 6001 , South Africa
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18
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Touchard F, Simon A, Bierne N, Viard F. Urban rendezvous along the seashore: Ports as Darwinian field labs for studying marine evolution in the Anthropocene. Evol Appl 2023; 16:560-579. [PMID: 36793678 PMCID: PMC9923491 DOI: 10.1111/eva.13443] [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: 01/10/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 11/30/2022] Open
Abstract
Humans have built ports on all the coasts of the world, allowing people to travel, exploit the sea, and develop trade. The proliferation of these artificial habitats and the associated maritime traffic is not predicted to fade in the coming decades. Ports share common characteristics: Species find themselves in novel singular environments, with particular abiotic properties-e.g., pollutants, shading, protection from wave action-within novel communities in a melting pot of invasive and native taxa. Here, we discuss how this drives evolution, including setting up of new connectivity hubs and gateways, adaptive responses to exposure to new chemicals or new biotic communities, and hybridization between lineages that would have never come into contact naturally. There are still important knowledge gaps, however, such as the lack of experimental tests to distinguish adaptation from acclimation processes, the lack of studies to understand the putative threats of port lineages to natural populations or to better understand the outcomes and fitness effects of anthropogenic hybridization. We thus call for further research examining "biological portuarization," defined as the repeated evolution of marine species in port ecosystems under human-altered selective pressures. Furthermore, we argue that ports act as giant mesocosms often isolated from the open sea by seawalls and locks and so provide replicated life-size evolutionary experiments essential to support predictive evolutionary sciences.
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Affiliation(s)
| | - Alexis Simon
- ISEM, EPHE, IRDUniversité MontpellierMontpellierFrance
- Center of Population Biology and Department of Evolution and EcologyUniversity of California DavisDavisCaliforniaUSA
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19
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Coelho MAG, Pearson GA, Boavida JRH, Paulo D, Aurelle D, Arnaud‐Haond S, Gómez‐Gras D, Bensoussan N, López‐Sendino P, Cerrano C, Kipson S, Bakran‐Petricioli T, Ferretti E, Linares C, Garrabou J, Serrão EA, Ledoux J. Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification. Ecol Evol 2023; 13:e9740. [PMID: 36789139 PMCID: PMC9912747 DOI: 10.1002/ece3.9740] [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: 11/28/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/31/2023] Open
Abstract
The accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals.
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Affiliation(s)
- Márcio A. G. Coelho
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal,MARE – Marine and Environmental Sciences CentreISPA‐Instituto UniversitárioLisboaPortugal
| | | | | | - Diogo Paulo
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal
| | - Didier Aurelle
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRSSorbonne UniversitéParisFrance
| | - Sophie Arnaud‐Haond
- MARBEC (Marine Biodiversity, Exploitation and Conservation)Univ. Montpellier, IFREMER, CNRS, IRDSète CedexFrance
| | - Daniel Gómez‐Gras
- Hawai‘i Institute of Marine BiologyUniversity of Hawai‘i at MānoaKaneoheHawaiiUSA,Departament de Biologia Evolutiva, Ecologia i Ciències AmbientalsUniversitat de Barcelona (UB)BarcelonaSpain,Institut de Recerca de la Biodiversitat (IRBio)Universitat de Barcelona (UB)BarcelonaSpain
| | - Nathaniel Bensoussan
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Paula López‐Sendino
- Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Carlo Cerrano
- Dipartimento di Scienze della Vita e dell’Ambiente (DiSVA)Università Politecnica delle MarcheAnconaItaly,Consorzio Nazionale Interuniversitario per le Scienze del Mare (CoNISMa)RomeItaly,Stazione Zoologica Anton DohrnNaplesItaly,Fano Marine CenterFanoItaly
| | - Silvija Kipson
- Department of Biology, Faculty of ScienceUniversity of ZagrebZagrebCroatia,SEAFAN – Marine Research & ConsultancyZagrebCroatia
| | | | - Eliana Ferretti
- Studio Associato GAIA s.n.c.GenoaItaly,Institute of Marine ScienceThe University of AucklandAucklandNew Zealand
| | - Cristina Linares
- Departament de Biologia Evolutiva, Ecologia i Ciències AmbientalsUniversitat de Barcelona (UB)BarcelonaSpain,Institut de Recerca de la Biodiversitat (IRBio)Universitat de Barcelona (UB)BarcelonaSpain
| | - Joaquim Garrabou
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIOMarseilleFrance,Departament de Biologia MarinaInstitut de Ciències del Mar (CSIC)BarcelonaSpain
| | - Ester A. Serrão
- Centre for Marine Sciences (CCMAR)University of AlgarveFaroPortugal,CIBIO/InBIO‐Centro de Investigação em Biodiversidade e Recursos GenéticosVairãoPortugal
| | - Jean‐Baptiste Ledoux
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e AmbientalUniversidade do PortoPortoPortugal
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20
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Knauber H, Silberberg JR, Brandt A, Riehl T. Evolution and biogeography of the Haploniscus belyaevi species complex (Isopoda: Haploniscidae) revealed by means of integrative taxonomy. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2099477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Henry Knauber
- Department of Marine Zoology, Senckenberg Research Institute and Natural History Museum, Section Crustacea, Senckenberganlage 25, Frankfurt, 60325, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt, 60438, Germany
| | - Jona R. Silberberg
- Department of Marine Zoology, Senckenberg Research Institute and Natural History Museum, Section Crustacea, Senckenberganlage 25, Frankfurt, 60325, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt, 60438, Germany
| | - Angelika Brandt
- Department of Marine Zoology, Senckenberg Research Institute and Natural History Museum, Section Crustacea, Senckenberganlage 25, Frankfurt, 60325, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt, 60438, Germany
| | - Torben Riehl
- Department of Marine Zoology, Senckenberg Research Institute and Natural History Museum, Section Crustacea, Senckenberganlage 25, Frankfurt, 60325, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Johann Wolfgang Goethe University Frankfurt, Max-von-Laue-Str. 13, Frankfurt, 60438, Germany
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21
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Conjectures and refutations: Species diversity and phylogeny of Australoheros from coastal rivers of southern South America (Teleostei: Cichlidae). PLoS One 2022; 17:e0261027. [PMID: 36490238 PMCID: PMC9733902 DOI: 10.1371/journal.pone.0261027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
Morphological and genetic analyses of species of Australoheros focusing on those distributed in coastal rivers from the Rio de La Plata north to the Rio Buranhém, support recognition of 17 valid species in the genus. Eight species are represented in coastal rivers: A acaroides, A. facetus, A. ipatinguensis, A. oblongus, A. ribeirae, and A. sanguineus are validated from earlier descriptions. Australoheros mboapari is a new species from the Rio Taquari in the Rio Jacuí drainage. Australoheros ricani is a new species from the upper Rio Jacuí. Specimens from the Rio Yaguarón and Rio Tacuary, affluents of Laguna Merín, and tributaries of the Rio Negro, tributary of the Rio Uruguay are assigned to A. minuano pending critical data on specimens from the type locality of A. minuano. Australoheros taura is a junior synonym of A. acaroides. Australoheros autrani, A. saquarema, A. capixaba, A. macaensis, A. perdi, and A. muriae are junior synonyms of A. ipatinguensis. Heros autochthon, A. mattosi, A. macacuensis, A. montanus, A. tavaresi, A. paraibae, and A. barbosae, are junior synonyms of A. oblongus. Heros jenynsii is a junior synonym of A. facetus.
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22
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Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson R, Visagie C, Yilmaz N, Gené J, Cano J, Chen A, Nováková A, Yaguchi T, Kolařík M, Hubka V. Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Stud Mycol 2022; 102:53-93. [PMID: 36760461 PMCID: PMC9903908 DOI: 10.3114/sim.2022.102.02] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera. Citation: Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102 : 53-93. doi: 10.3114/sim.2022.102.02.
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Affiliation(s)
- F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic;,*Corresponding author: V. Hubka, ; F. Sklenář,
| | - K. Glässnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ž. Jurjević
- EMSL Analytical, Cinnaminson, New Jersey, USA
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - C.M. Visagie
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - J. Cano
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - A.J. Chen
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, China
| | - A. Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
| | - M. Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic;, Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan,*Corresponding author: V. Hubka, ; F. Sklenář,
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23
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Bian C, Kusuya Y, Sklenář F, D’hooge E, Yaguchi T, Ban S, Visagie C, Houbraken J, Takahashi H, Hubka V. Reducing the number of accepted species in Aspergillus series Nigri. Stud Mycol 2022; 102:95-132. [PMID: 36760462 PMCID: PMC9903907 DOI: 10.3114/sim.2022.102.03] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The Aspergillus series Nigri contains biotechnologically and medically important species. They can produce hazardous mycotoxins, which is relevant due to the frequent occurrence of these species on foodstuffs and in the indoor environment. The taxonomy of the series has undergone numerous rearrangements, and currently, there are 14 species accepted in the series, most of which are considered cryptic. Species-level identifications are, however, problematic or impossible for many isolates even when using DNA sequencing or MALDI-TOF mass spectrometry, indicating a possible problem in the definition of species limits or the presence of undescribed species diversity. To re-examine the species boundaries, we collected DNA sequences from three phylogenetic markers (benA, CaM and RPB2) for 276 strains from series Nigri and generated 18 new whole-genome sequences. With the three-gene dataset, we employed phylogenetic methods based on the multispecies coalescence model, including four single-locus methods (GMYC, bGMYC, PTP and bPTP) and one multilocus method (STACEY). From a total of 15 methods and their various settings, 11 supported the recognition of only three species corresponding to the three main phylogenetic lineages: A. niger, A. tubingensis and A. brasiliensis. Similarly, recognition of these three species was supported by the GCPSR approach (Genealogical Concordance Phylogenetic Species Recognition) and analysis in DELINEATE software. We also showed that the phylogeny based on benA, CaM and RPB2 is suboptimal and displays significant differences from a phylogeny constructed using 5 752 single-copy orthologous proteins; therefore, the results of the delimitation methods may be subject to a higher than usual level of uncertainty. To overcome this, we randomly selected 200 genes from these genomes and performed ten independent STACEY analyses, each with 20 genes. All analyses supported the recognition of only one species in the A. niger and A. brasiliensis lineages, while one to four species were inconsistently delimited in the A. tubingensis lineage. After considering all of these results and their practical implications, we propose that the revised series Nigri includes six species: A. brasiliensis, A. eucalypticola, A. luchuensis (syn. A. piperis), A. niger (syn. A. vinaceus and A. welwitschiae), A. tubingensis (syn. A. chiangmaiensis, A. costaricensis, A. neoniger and A. pseudopiperis) and A. vadensis. We also showed that the intraspecific genetic variability in the redefined A. niger and A. tubingensis does not deviate from that commonly found in other aspergilli. We supplemented the study with a list of accepted species, synonyms and unresolved names, some of which may threaten the stability of the current taxonomy. Citation: Bian C, Kusuya Y, Sklenář F, D'hooge E, Yaguchi T, Ban S, Visagie CM, Houbraken J, Takahashi H, Hubka V (2022). Reducing the number of accepted species in Aspergillus series Nigri. Studies in Mycology 102: 95-132. doi: 10.3114/sim.2022.102.03.
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Affiliation(s)
- C. Bian
- Graduate School of Medical and Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Y. Kusuya
- Medical Mycology Research Center, Chiba University, Chiba, Japan;, Biological Resource Center, National Institute of Technology and Evaluation, Kisarazu, Japan
| | - F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - E. D’hooge
- BCCM/IHEM collection, Mycology and Aerobiology, Sciensano, Bruxelles, Belgium
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - S. Ban
- Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - C.M. Visagie
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands
| | - H. Takahashi
- Medical Mycology Research Center, Chiba University, Chiba, Japan;, Molecular Chirality Research Center, Chiba University, Chiba, Japan;, Plant Molecular Science Center, Chiba University, Chiba, Japan,*Corresponding authors: H. Takahashi, ; V. Hubka,
| | - V. Hubka
- Medical Mycology Research Center, Chiba University, Chiba, Japan;, Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic;,*Corresponding authors: H. Takahashi, ; V. Hubka,
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24
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Integrative taxonomy helps to revise systematics and questions the purported cosmopolitan nature of the type species within the genus Diaforobiotus (Eutardigrada: Richtersiusidae). ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Recent advances in tardigrade taxonomy have been greatly enhanced by the redescriptions of the type species for particular taxa or species groups. De novo characterisation of these key taxa now allows to describe tardigrade species diversity with improved precision and at higher rate, increasing the momentum towards resolving the taxonomic impediment in these micro-invertebrates. Since its description, Diaforobiotus islandicus (Richters, 1904) has been reported from many distinct localities around the world. This suggested, perhaps falsely, a cosmopolitan nature of the species. However, potential erroneous assignment of newly found populations to this species could be a result of the very general and superficial original description. In order to properly recognise and name species diversity within the genus, I provide here an integrative redescription of the type species (D. islandicus) with a neotype designation, a description of a new species, Diaforbiotus svalbardicus sp. nov, and dichotomous key for the genus. Both descriptions are based on detailed morphological and morphometric data associated with standard DNA sequences of four genetic markers (18S rRNA, 28S rRNA, ITS-2, and COI). The genus composition and diagnosis amendments of the family Richtersiuside are also discussed. The presented study constitutes a starting point for further systematic studies on the genus Diaforobiotus and new taxa discoveries.
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25
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Daniels SR, Busschau T, Gullacksen G, Marais H, Gouws G, Barnes A. Cryptic and widespread: a recipe for taxonomic misidentification in a freshwater crab species (Decapoda: Potamonautidae: Potamonautes sidneyi) as evident from species delimitation methods. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
AbstractWe examined the systematics of a ubiquitously distributed southern African freshwater crab, Potamonautes sidneyi s.l. species complex. Specimens were subjected to DNA sequence analyses of two mitochondrial loci (16S rRNA + COI). We applied three species delimitations methods (ASAP, bGMYC and bPTP) to test their utility in delineating species boundaries in Potamonautes and three additional Afrotropical genera (Liberonautes, Nesonautes and Seychellum). The combined mtDNA dataset retrieved five clades. Clade 1 comprised of P. barbarai, clade 2 comprised of specimens from the interior of the Great Karoo Basin, sister to P. sidneyi s.s. in clade 3. Clade 4 was confined to Eswatini and the Mpumalanga Province of South Africa, and sister to clade 5 that comprised P. danielsi. The three species delimitation methods either over- or underestimated the number of species. Phylogenetically, specimens from the Great Karoo Basin (clade 2) were equidistant to P. sidneyi s.s. and P. perlatus, while the Eswatini and Mpumalanga specimens (clade 4) were sister to P. danielsi. Clades 2 and 4 are herein described as P. karooensis sp. nov. and P. valles sp. nov., respectively.
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Affiliation(s)
- Savel R Daniels
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
| | - Theo Busschau
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
| | | | - Hannes Marais
- Mpumalanga Tourism and Parks Agency, Aquatic Unit , Lydenburg, 1120 , South Africa
| | - Gavin Gouws
- National Research Foundation - South African Institute for Aquatic Biodiversity , Private Bag 1015, Makhanda, 6140 , South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, University of Stellenbosch , Private Bag X1, Matieland, 7602 , South Africa
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26
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Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia). Genetica 2022; 150:247-262. [PMID: 36083388 DOI: 10.1007/s10709-022-00165-7] [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: 05/27/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RAD-sequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e., PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.
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Shilling MD, Krueger-Hadfield SA, McClintock JB. Genetic Evidence Supports Species Delimitation of Luidia in the Northern Gulf of Mexico. THE BIOLOGICAL BULLETIN 2022; 243:28-37. [PMID: 36108035 DOI: 10.1086/720972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
AbstractAccurate species delimitation is crucial to understanding biodiversity. In the northern Gulf of Mexico, recent genetic evidence has suggested that the tricolor Luidia lawrencei is not a species distinct from the gray Luidia clathrata. We collected Luidia specimens from Apalachee Bay, Florida, and morphologically identified 11 as L. clathrata and 16 as L. lawrencei. We sequenced 1074 bp of the cytochrome c oxidase subunit I (COI) and found ~14% divergence between L. clathrata and L. lawrencei, suggesting two distinct species (within-species divergence was <1%). Two specimens were phenotypically L. lawrencei (i.e., tricolor morph) but mitochondrially were L. clathrata. Our findings lend support to maintaining L. clathrata and L. lawrencei as distinct species. However, the species boundary between these two taxa may be porous, and ongoing hybridization may occur when the two species are found in sympatry. Future work with nuclear markers is warranted to determine the frequency of hybridization and the extent of introgression. Clarifying the genetic relationship between these species will provide a baseline for assessing ongoing changes in connectivity of these two highly abundant sea stars in the rapidly warming northern Gulf of Mexico.
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Zamani A, Dal Pos D, Fric ZF, Orfinger AB, Scherz MD, Bartoňová AS, Gante HF. The future of zoological taxonomy is integrative, not minimalist. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2063964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alireza Zamani
- Zoological Museum, Biodiversity Unit, University of Turku, 20500 Turku, Finland
| | - Davide Dal Pos
- Department of Biology, University of Central Florida, 4110 Libra dr. Rm 442, Orlando, FL 32816, USA
| | - Zdenek Faltýnek Fric
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Alexander B. Orfinger
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA
- Center for Water Resources, Florida A&M University, Tallahassee, FL 32301, USA
| | - Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Alena Sucháčková Bartoňová
- Department of Biodiversity and Conservation Biology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, CZ-37005, Czech Republic
| | - Hugo F. Gante
- cE3c—Center for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Lisboa, Portugal
- Department of Biology, KU Leuven, Section Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 32 box 2439, Leuven, B-3000, Belgium
- Royal Museum for Central Africa, Leuvensesteenweg 17, Tervuren, 3080, Belgium
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29
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Pavón-Vázquez CJ, Esquerré D, Fitch AJ, Maryan B, Doughty P, Donnellan SC, Scott Keogh J. Between a rock and a dry place: phylogenomics, biogeography, and systematics of ridge-tailed monitors (Squamata: Varanidae: Varanus acanthurus complex). Mol Phylogenet Evol 2022; 173:107516. [DOI: 10.1016/j.ympev.2022.107516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
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30
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Titus BM, Daly M. Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes? Heredity (Edinb) 2022; 128:338-351. [PMID: 35418670 PMCID: PMC9076904 DOI: 10.1038/s41437-022-00531-3] [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: 09/09/2020] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 11/08/2022] Open
Abstract
Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.
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Affiliation(s)
- Benjamin M Titus
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
- Dauphin Island Sea Lab, Dauphin Island, AL, USA.
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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31
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Phillips JD, Gillis DJ, Hanner RH. Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.859099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially in size, there is now the need to identify novel ways of meaningfully analyzing vast amounts of available DNA barcode data. This is an important issue to address promptly for the routine tasks of specimen identification and species discovery, which have seen broad adoption in areas as diverse as regulatory forensics and resource conservation. Here, it is demonstrated that the interpretation of DNA barcoding data is lacking in statistical rigor. To highlight this, focus is set specifically on one key concept that has become a household name in the field: the DNA barcode gap. Arguments outlined herein specifically center on DNA barcoding in animal taxa and stem from three angles: (1) the improper allocation of specimen sampling effort necessary to capture adequate levels of within-species genetic variation, (2) failing to properly visualize intra-specific and interspecific genetic distances, and (3) the inconsistent, inappropriate use, or absence of statistical inferential procedures in DNA barcoding gap analyses. Furthermore, simple statistical solutions are outlined which can greatly propel the use of DNA barcoding as a tool to irrefutably match unknowns to knowns on the basis of the barcoding gap with a high degree of confidence. Proposed methods examined herein are illustrated through application to DNA barcode sequence data from Canadian Pacific fish species as a case study.
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Species delimitation and mitonuclear discordance within a species complex of biting midges. Sci Rep 2022; 12:1730. [PMID: 35110675 PMCID: PMC8810881 DOI: 10.1038/s41598-022-05856-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/17/2022] [Indexed: 12/11/2022] Open
Abstract
The inability to distinguish between species can be a serious problem in groups responsible for pathogen transmission. Culicoides biting midges transmit many pathogenic agents infecting wildlife and livestock. In North America, the C. variipennis species complex contains three currently recognized species, only one of which is a known vector, but limited species-specific characters have hindered vector surveillance. Here, genomic data were used to investigate population structure and genetic differentiation within this species complex. Single nucleotide polymorphism data were generated for 206 individuals originating from 17 locations throughout the United States and Canada. Clustering analyses suggest the occurrence of two additional cryptic species within this complex. All five species were significantly differentiated in both sympatry and allopatry. Evidence of hybridization was detected in three different species pairings indicating incomplete reproductive isolation. Additionally, COI sequences were used to identify the hybrid parentage of these individuals, which illuminated discordance between the divergence of the mitochondrial and nuclear datasets.
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Fedosov A, Achaz G, Gontchar A, Puillandre N. MOLD, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions. Mol Ecol Resour 2022; 22:2038-2053. [DOI: 10.1111/1755-0998.13590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Leninsky prospect 33 119071 Moscow Russia
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
| | - Guillaume Achaz
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
- UMR7206 Eco‐Anthropologie Université de Paris‐CNRS‐MNHN Paris
- UMR7241 Centre Interdisciplinaire de Recherche en Biologie Collége de France‐CNRS‐INSERM Paris
| | - Andrey Gontchar
- Molecular Immunology Laboratory Dmitry Rogachev National Medical Research Center of Pediatric Hematology Oncology and Immunology Samory Mashela street 1 117997 Moscow Russia
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB) Muséum national d'Histoire naturelle CNRS Sorbonne Université EPHE Université des Antilles 57 rue Cuvier, CP 26 75005 Paris France
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Dartois M, Pante E, Viricel A, Becquet V, Sauriau PG. Molecular genetic diversity of seaweeds morphologically related to Ulva rigida at three sites along the French Atlantic coast. PeerJ 2022; 9:e11966. [PMID: 35036110 PMCID: PMC8711279 DOI: 10.7717/peerj.11966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/04/2021] [Indexed: 11/21/2022] Open
Abstract
Foliose species of the genus Ulva are notoriously difficult to identify due to their variable morphological characteristics and high phenotypic plasticity. We reassessed the taxonomic status of several distromatic foliose Ulva spp., morphologically related to Ulva rigida, using DNA barcoding with the chloroplastic tufA and rbcL (for a subset of taxa) genes for 339 selected attached Ulva specimens collected from three intertidal rocky sites. Two of the collection sites were in Brittany and one site was in Vendée, along the Atlantic coast of France. Molecular analyses included several museum specimens and the holotype of Ulva armoricana Dion, Reviers & Coat. We identified five different tufA haplotypes using a combination of phylogenetic analysis, with the support of several recently sequenced holotypes and lectotypes, and a species delimitation method based on hierarchical clustering. Four haplotypes were supported by validly named species: Ulva australis Areschoug, Ulva fenestrata Postels & Ruprecht, Ulva lacinulata (Kützing) Wittrock and U. rigida C. Agardh. The later was additionally investigated using rbcL. The fifth haplotype represented exact sequence matches to an unnamed species from European Atlantic coasts. Our results support: (1) the synonymy of both U. rigida sensu Bliding non C. Agardh and U. armoricana with U. lacinulata. This finding is based on current genetic analysis of tufA from the U. armoricana holotype and recent molecular characterization of the lectotype of U. laetevirens, which is synonymous to U. australis, (2) the presence of U. australis as a misidentified introduced species in Brittany, and (3) the presence of U. fenestrata and U. rigida in southern Brittany. The taxonomic history of each species is discussed, highlighting issues within distromatic foliose taxa of the genus Ulva and the need to genetically characterize all its available type specimens.
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Affiliation(s)
- Manon Dartois
- Littoral, Environnement et Sociétés, UMR 7266, CNRS - La Rochelle Université, La Rochelle, France
| | - Eric Pante
- Littoral, Environnement et Sociétés, UMR 7266, CNRS - La Rochelle Université, La Rochelle, France.,Institut Systématique Evolution Biodiversité (ISYEB), CNRS, Sorbonne Université, EPHE, Université des Antilles, Museum national d'Histoire naturelle, Paris, France
| | - Amélia Viricel
- Littoral, Environnement et Sociétés, UMR 7266, CNRS - La Rochelle Université, La Rochelle, France
| | - Vanessa Becquet
- Littoral, Environnement et Sociétés, UMR 7266, CNRS - La Rochelle Université, La Rochelle, France
| | - Pierre-Guy Sauriau
- Littoral, Environnement et Sociétés, UMR 7266, CNRS - La Rochelle Université, La Rochelle, France
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Wei Z, Xia Z, Shu J, Shang H, Maxwell SJ, Chen L, Zhou X, Xi W, Adjie B, Yuan Q, Cao J, Yan Y. Phylogeny and Taxonomy on Cryptic Species of Forked Ferns of Asia. FRONTIERS IN PLANT SCIENCE 2021; 12:748562. [PMID: 34975938 PMCID: PMC8718997 DOI: 10.3389/fpls.2021.748562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Cryptic species comprise two or more taxa that are grounded under a single name because they are more-or-less indistinguishable morphologically. These species are potentially important for detailed assessments of biodiversity, but there now appear to be many more cryptic species than previously estimated. One taxonomic group likely to contain many cryptic species is Dicranopteris, a genus of forked ferns that occurs commonly along roadsides in Asia. The genus has a complex taxonomical history, and D. linearis has been particularly challenging with many intra-specific taxa dubiously erected to accommodate morphological variation that lacks clear discontinuities. To resolve species boundaries within Dicranopteris, we applied a molecular phylogenetic approach as complementary to morphology. Specifically, we used five chloroplast gene regions (rbcL, atpB, rps4, matK, and trnL-trnF) to generate a well-resolved phylogeny based on 37 samples representing 13 taxa of Dicranopteris, spanning the major distributional area in Asia. The results showed that Dicranopteris consists of ten highly supported clades, and D. linearis is polyphyletic, suggesting cryptic diversity within the species. Further through morphological comparison, we certainly erected Dicranopteris austrosinensis Y.H. Yan & Z.Y. Wei sp. nov. and Dicranopteris baliensis Y.H. Yan & Z.Y. Wei sp. nov. as distinct species and proposed five new combinations. We also inferred that the extant diversity of the genus Dicranopteris may result from relatively recent diversification in the Miocene based on divergence time dating. Overall, our study not only provided additional insights on the Gleicheniaceae tree of life, but also served as a case of integrating molecular and morphological approaches to elucidate cryptic diversity in taxonomically difficult groups.
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Affiliation(s)
- Zuoying Wei
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zengqiang Xia
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jiangping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hui Shang
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Stephen J. Maxwell
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
| | - Lijun Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Xile Zhou
- Xiangxi Tujia and Miao Autonomous Prefecture Forest Resources Monitoring Center, Jishou, China
| | - Wang Xi
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Bayu Adjie
- Research Center for Plants Conservation and Botanic Gardens, National Research and Innovation Agency of Indonesia, Bali, Indonesia
| | - Quan Yuan
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jianguo Cao
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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Morrison CL, Johnson NA, Jones JW, Eackles MS, Aunins AW, Fitzgerald DB, Hallerman EM, King TL. Genetic and morphological characterization of the freshwater mussel clubshell species complex ( Pleurobema clava and Pleurobema oviforme) to inform conservation planning. Ecol Evol 2021; 11:15325-15350. [PMID: 34765181 PMCID: PMC8571583 DOI: 10.1002/ece3.8219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/14/2021] [Accepted: 08/26/2021] [Indexed: 11/09/2022] Open
Abstract
The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding.
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Affiliation(s)
- Cheryl L. Morrison
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Nathan A. Johnson
- U.S. Geological Survey, Wetland and Aquatic Research CenterGainesvilleFloridaUSA
| | - Jess W. Jones
- U.S. Fish and Wildlife Service, Department of Fish and Wildlife Conservation, Virginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Michael S. Eackles
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Aaron W. Aunins
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Daniel B. Fitzgerald
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Eric M. Hallerman
- Department of Fish and Wildlife ConservationVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Tim L. King
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
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Samarasinghe H, Lu Y, Aljohani R, Al-Amad A, Yoell H, Xu J. Global patterns in culturable soil yeast diversity. iScience 2021; 24:103098. [PMID: 34622153 PMCID: PMC8479693 DOI: 10.1016/j.isci.2021.103098] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/09/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Yeasts, broadly defined as unicellular fungi, fulfill essential roles in soil ecosystems as decomposers and nutrition sources for fellow soil-dwellers. Broad-scale investigations of soil yeasts pose a methodological challenge as metagenomics are of limited use for identifying this group of fungi. Here we characterize global soil yeast diversity using fungal DNA barcoding on 1473 yeasts cultured from 3826 soil samples obtained from nine countries in six continents. We identify mean annual precipitation and international air travel as two significant correlates with soil yeast community structure and composition worldwide. Evidence for anthropogenic influences on soil yeast communities, directly via travel and indirectly via altered rainfall patterns resulting from climate change, is concerning as we found common infectious yeasts frequently distributed in soil in several countries. Our discovery of 41 putative novel species highlights the continued need for culture-based studies to advance our knowledge of environmental yeast diversity. Mean annual rainfall is a positive predictor of global soil yeast diversity International travel predicts number of shared yeast species between countries 41 novel yeast species were discovered from soils in eight countries Continued culture-based studies are needed to investigate soil yeast populations
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Affiliation(s)
| | - Yi Lu
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Renad Aljohani
- Department of Biology, McMaster University, Hamilton, ON, Canada.,Department of Infectious Diseases, South Kensington Campus, Imperial College London, London, UK
| | - Ahmad Al-Amad
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Heather Yoell
- Department of Biology, McMaster University, Hamilton, ON, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Afiq‐Rosli L, Wainwright BJ, Gajanur AR, Lee AC, Ooi SK, Chou LM, Huang D. Barriers and corridors of gene flow in an urbanized tropical reef system. Evol Appl 2021; 14:2502-2515. [PMID: 34745340 PMCID: PMC8549622 DOI: 10.1111/eva.13276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
Information about the distribution of alleles among marine populations is critical for determining patterns of genetic connectivity that are essential in modern conservation planning. To estimate population connectivity in Singapore's urbanized equatorial reef system, we analysed single nucleotide polymorphisms (SNPs) from two species of reef-building corals with distinct life histories. For Porites sp., a broadcast-spawning coral, we found cryptic lineages that were differentially distributed at inshore and central-offshore sites that could be attributed to contemporary surface current regimes. Near panmixia was observed for Pocillopora acuta with differentiation of colonies at the farthest site from mainland Singapore, a possible consequence of the brooding nature and relatively long pelagic larval duration of the species. Furthermore, analysis of recent gene flow showed that 60-80% of colonies in each population were nonmigrants, underscoring self-recruitment as an important demographic process in this reef system. Apart from helping to enhance the management of Singapore's coral reef ecosystems, findings here pave the way for better understanding of the evolution of marine populations in South-East Asia.
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Affiliation(s)
- Lutfi Afiq‐Rosli
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
| | - Benjamin John Wainwright
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Yale‐NUS CollegeNational University of SingaporeSingaporeSingapore
| | - Anya Roopa Gajanur
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Ai Chin Lee
- Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
| | - Seng Keat Ooi
- Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
| | - Loke Ming Chou
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
- Centre for Nature‐based Climate SolutionsNational University of SingaporeSingaporeSingapore
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Chafin TK, Douglas MR, Bangs MR, Martin BT, Mussmann SM, Douglas ME. Taxonomic Uncertainty and the Anomaly Zone: Phylogenomics Disentangle a Rapid Radiation to Resolve Contentious Species (Gila robusta Complex) in the Colorado River. Genome Biol Evol 2021; 13:evab200. [PMID: 34432005 PMCID: PMC8449829 DOI: 10.1093/gbe/evab200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 12/18/2022] Open
Abstract
Species are indisputable units for biodiversity conservation, yet their delimitation is fraught with both conceptual and methodological difficulties. A classic example is the taxonomic controversy surrounding the Gila robusta complex in the lower Colorado River of southwestern North America. Nominal species designations were originally defined according to weakly diagnostic morphological differences, but these conflicted with subsequent genetic analyses. Given this ambiguity, the complex was re-defined as a single polytypic unit, with the proposed "threatened" status under the U.S. Endangered Species Act of two elements being withdrawn. Here we re-evaluated the status of the complex by utilizing dense spatial and genomic sampling (n = 387 and >22 k loci), coupled with SNP-based coalescent and polymorphism-aware phylogenetic models. In doing so, we found that all three species were indeed supported as evolutionarily independent lineages, despite widespread phylogenetic discordance. To juxtapose this discrepancy with previous studies, we first categorized those evolutionary mechanisms driving discordance, then tested (and subsequently rejected) prior hypotheses which argued phylogenetic discord in the complex was driven by the hybrid origin of Gila nigra. The inconsistent patterns of diversity we found within G. robusta were instead associated with rapid Plio-Pleistocene drainage evolution, with subsequent divergence within the "anomaly zone" of tree space producing ambiguities that served to confound prior studies. Our results not only support the resurrection of the three species as distinct entities but also offer an empirical example of how phylogenetic discordance can be categorized within other recalcitrant taxa, particularly when variation is primarily partitioned at the species level.
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Affiliation(s)
- Tyler K Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Marlis R Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Max R Bangs
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Bradley T Martin
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Global Campus, University of Arkansas, Fayetteville, Arkansas, USA
| | - Steven M Mussmann
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish & Wildlife Service, Dexter, New Mexico, USA
| | - Michael E Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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Buckley SJ, Brauer C, Unmack PJ, Hammer MP, Beheregaray LB. The roles of aridification and sea level changes in the diversification and persistence of freshwater fish lineages. Mol Ecol 2021; 30:4866-4883. [PMID: 34265125 DOI: 10.1111/mec.16082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/29/2022]
Abstract
While the influence of Pleistocene climatic changes on divergence and speciation has been well-documented across the globe, complex spatial interactions between hydrology and eustatics over longer timeframes may also determine species evolutionary trajectories. Within the Australian continent, glacial cycles were not associated with changes in ice cover and instead largely resulted in fluctuations from moist to arid conditions across the landscape. We investigated the role of hydrological and coastal topographic changes brought about by Plio-Pleistocene climatic changes on the biogeographic history of a small Australian freshwater fish, the southern pygmy perch Nannoperca australis. Using 7958 ddRAD-seq (double digest restriction-site associated DNA) loci and 45,104 filtered SNPs, we combined phylogenetic, coalescent and species distribution analyses to assess the various roles of aridification, sea level and tectonics and associated biogeographic changes across southeast Australia. Sea-level changes since the Pliocene and reduction or disappearance of large waterbodies throughout the Pleistocene were determining factors in strong divergence across the clade, including the initial formation and maintenance of a cryptic species, N. 'flindersi'. Isolated climatic refugia and fragmentation due to lack of connected waterways maintained the identity and divergence of inter- and intraspecific lineages. Our historical findings suggest that predicted increases in aridification and sea level due to anthropogenic climate change might result in markedly different demographic impacts, both spatially and across different landscape types.
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Affiliation(s)
- Sean James Buckley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Chris Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, ACT, Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, NT, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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Parker E, Dornburg A, Struthers CD, Jones CD, Near TJ. Phylogenomic species delimitation dramatically reduces species diversity in an Antarctic adaptive radiation. Syst Biol 2021; 71:58-77. [PMID: 34247239 DOI: 10.1093/sysbio/syab057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 07/06/2021] [Accepted: 06/30/2021] [Indexed: 11/14/2022] Open
Abstract
Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously-undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.
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Affiliation(s)
- Elyse Parker
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, NC 28223, USA
| | - Carl D Struthers
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Christopher D Jones
- Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.,Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA
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45
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Long-term stasis in acariform mites provides evidence for morphologically stable evolution: Molecular vs. morphological differentiation in Linopodes (Acariformes; Prostigmata). Mol Phylogenet Evol 2021; 163:107237. [PMID: 34147656 DOI: 10.1016/j.ympev.2021.107237] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 11/21/2022]
Abstract
Molecular species delimitation, usually by COI DNA barcoding, shows that cryptic speciation is a common phenomenon observed in most animal phyla. Cryptic species have frequently been observed among all major taxa of mites. The mites of the eupodoid genus Linopodes are cosmopolitan in distribution and are most often found in soil-related habitats. Currently, the genus consists of 22 morphologically similar species, which, in practice, are indistinguishable on the basis of their morphological features. The diagnostic issue of the Linopodes species may be caused by the poor delineation of the species, which need taxonomic revision, or the low morphological variability among cryptic species. In this paper, we present the results of molecular species delimitation carried out using sampled Linopodes populations and the level of morphological inter/intraspecific variation within defined groups. We compared COI, 18S and 28S sequence data together with morphological characters. The molecular delimitation revealed seven well-defined species of Linopodes based on DNA sequences. A well-supported phylogenetic tree revealed the same seven species, while morphological analysis showed negligible phenotypic differentiation among the species revealed. We demonstrate that mites can undergo changes in their DNA accompanied by morphological stasis lasting at least 80 MY.
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46
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Wüster W, Thomson SA, O’shea M, Kaiser H. Confronting taxonomic vandalism in biology: conscientious community self-organization can preserve nomenclatural stability. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Self-published taxon descriptions, bereft of a basis of evidence, are a long-standing problem in taxonomy. The problem derives in part from the Principle of Priority in the International Code of Zoological Nomenclature, which forces the use of the oldest available nomen irrespective of scientific merit. This provides a route to ‘immortality’ for unscrupulous individuals through the mass-naming of taxa without scientific basis, a phenomenon referred to as taxonomic vandalism. Following a flood of unscientific taxon namings, in 2013 a group of concerned herpetologists organized a widely supported, community-based campaign to treat these nomina as lying outside the permanent scientific record, and to ignore and overwrite them as appropriate. Here, we review the impact of these proposals over the past 8 years. We identified 59 instances of unscientific names being set aside and overwritten with science-based names (here termed aspidonyms), and 1087 uses of these aspidonyms, compared to one instance of preference for the overwritten names. This shows that when there is widespread consultation and agreement across affected research communities, setting aside certain provisions of the Code can constitute an effective last resort defence against taxonomic vandalism and enhance the universality and stability of the scientific nomenclature.
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Affiliation(s)
- Wolfgang Wüster
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Scott A Thomson
- Museu de Zoologia da Universidade de São Paulo, Divisão de Vertebrados (Herpetologia), Avenida Nazaré, 481, Ipiranga, 04263-000, São Paulo, SP, Brazil
- Chelonian Research Institute, 401 South Central Avenue, Oviedo, FL 32765, USA
| | - Mark O’shea
- Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Hinrich Kaiser
- Department of Vertebrate Zoology, Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
- Department of Biology, Victor Valley College, 18422 Bear Valley Road, Victorville, CA 92395, USA
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47
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Cerca J, Rivera-Colón AG, Ferreira MS, Ravinet M, Nowak MD, Catchen JM, Struck TH. Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species. PeerJ 2021; 9:e10896. [PMID: 33614296 PMCID: PMC7879940 DOI: 10.7717/peerj.10896] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.
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Affiliation(s)
- José Cerca
- Department of Environmental Science, Policy, and Management, University of California, University of California, Berkeley, Berkeley, CA, United States of America
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Angel G. Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
| | - Mafalda S. Ferreira
- Division of Biological Sciences, University of Montana, Missoula, MT, United States of America
- Departamento de Biologia, Universidade do Porto, Porto, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Porto, Porto, Portugal
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | | | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana Champaign, IL, United States of America
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48
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Burbrink FT, Gehara M, McKelvy AD, Myers EA. Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex). Evolution 2021; 75:260-277. [PMID: 33346918 DOI: 10.1111/evo.14141] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 01/04/2023]
Abstract
Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the "gray zone" of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes in the environment between lineages. Using population genomic data from the North American ratsnake complex (Pantherophis obsoletus), we connected phylogeographic estimates of lineage structure, migration, historical demography, and timing of divergence with hybrid zone dynamics. We examined the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches were applied to understand how landscape features and past climate have influenced population genetic structure among these lineages. We found that rates of migration between lineages were associated with the overall width of hybrid zones. Timing of divergence was not related to migration rate or hybrid zone width across species pairs but may be related to the number of alleles weakly introgressing through hybrid zones. This research underscores how incomplete reproductive isolation can be better understood by considering differential allelic introgression and the effects of historical and contemporary landscape features on the formation of lineages as well as overall genomic estimates of migration rates through time.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024
| | - Marcelo Gehara
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, New Jersey, 07102
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, New York, 10016
| | - Edward A Myers
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC
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49
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Corrêa de Barros R, Moreira da Rocha R. Genetic analyses reveal cryptic diversity in the widely distributed Styela canopus (Ascidiacea:Styelidae). INVERTEBR SYST 2021. [DOI: 10.1071/is20058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The routine use of DNA sequencing techniques and phylogenetic analysis has resulted in the discovery of many cryptic species, especially in the oceans. The common, globally introduced species Styela canopus is suspected to be a complex of cryptic species because of its widespread distribution and variable external morphology. We tested this possibility using COI and ANT marker sequences to uncover the phylogenetic relationship among 19 populations, and to examine genetic variability as well as gene flow. We obtained 271 COI and 67 ANT sequences and found surprising diversity among the 19 populations (COI: π = 0.18, hd = 0.99; ANT: π = 0.13, hd = 0.95). Corresponding topologies were found using Bayesian inference and maximum likelihood for both simple locus (COI) and multilocus (COI + ANT) analyses and so the clades received strong support. We used simple (ABGD, bPTP, GMYC) and multiple (BSD) locus methods to delimit species. The simple locus methods indicated that the current Styela canopus comprises at least 15 species. The BSD method for concatenated data supported 7 of the 15 species. We suggest that S. canopus should be treated as the Styela canopus complex. The large number of cryptic species found, often with more than one clade found in sympatry, creates opportunities for better understanding reproductive isolation, hybridisation or speciation. As several lineages have already been introduced widely around the world, we must quickly understand their diversity and invasive abilities.
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50
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Padial JM, De la Riva I. A paradigm shift in our view of species drives current trends in biological classification. Biol Rev Camb Philos Soc 2020; 96:731-751. [PMID: 33368983 DOI: 10.1111/brv.12676] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022]
Abstract
Discontent about changes in species classifications has grown in recent years. Many of these changes are seen as arbitrary, stemming from unjustified conceptual and methodological grounds, or leading to species that are less distinct than those recognised in the past. We argue that current trends in species classification are the result of a paradigm shift toward which systematics and population genetics have converged and that regards species as the phylogenetic lineages that form the branches of the Tree of Life. Species delimitation now consists of determining which populations belong to which individual phylogenetic lineage. This requires inferences on the process of lineage splitting and divergence, a process to which we have only partial access through incidental evidence and assumptions that are themselves subject to refutation. This approach is not free of problems, as horizontal gene transfer, introgression, hybridisation, incorrect assumptions, sampling and methodological biases can mislead inferences of phylogenetic lineages. Increasing precision is demanded through the identification of both sister relationships and processes blurring or mimicking phylogeny, which has triggered, on the one hand, the development of methods that explicitly address such processes and, on the other hand, an increase in geographical and character data sampling necessary to infer/test such processes. Although our resolving power has increased, our knowledge of sister relationships - what we designate as species resolution - remains poor for many taxa and areas, which biases species limits and perceptions about how divergent species are or ought to be. We attribute to this conceptual shift the demise of trinominal nomenclature we are witnessing with the rise of subspecies to species or their rejection altogether; subspecies are raised to species if they are found to correspond to phylogenetic lineages, while they are rejected as fabricated taxa if they reflect arbitrary partitions of continuous or non-hereditary variation. Conservation strategies, if based on taxa, should emphasise species and reduce the use of subspecies to avoid preserving arbitrary partitions of continuous variation; local variation is best preserved by focusing on biological processes generating ecosystem resilience and diversity rather than by formally naming diagnosable units of any kind. Since many binomials still designate complexes of species rather than individual species, many species have been discovered but not named, geographical sampling is sparse, gene lineages have been mistaken for species, plenty of species limits remain untested, and many groups and areas lack adequate species resolution, we cannot avoid frequent changes to classifications as we address these problems. Changes will not only affect neglected taxa or areas, but also popular ones and regions where taxonomic research remained dormant for decades and old classifications were taken for granted.
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Affiliation(s)
- José M Padial
- Department of Herpetology, American Museum of Natural History, Central Park West & 79th St., New York, NY, 10024, U.S.A.,Department of Biology, Bronx Community College, City University of New York, 2155 University Avenue, Bronx, NY, 10453, U.S.A
| | - Ignacio De la Riva
- Museo Nacional de Ciencias Naturales-CSIC, José Gutiérrez Abascal 2, Madrid, 28006, Spain
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