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Myburgh AM, Barnes A, Henriques R, Daniels SR. Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki). Mol Phylogenet Evol 2024; 198:108132. [PMID: 38909874 DOI: 10.1016/j.ympev.2024.108132] [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: 03/22/2024] [Revised: 05/24/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.
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Affiliation(s)
- Angus Macgregor Myburgh
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Romina Henriques
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa
| | - Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa.
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Becker FS, Alexander GJ, Tolley KA. Substrate specialisation drives an unexpectedly diverse radiation in barking geckos (Ptenopus: Gekkonidae). Mol Phylogenet Evol 2024; 197:108104. [PMID: 38750676 DOI: 10.1016/j.ympev.2024.108104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/25/2024] [Accepted: 05/12/2024] [Indexed: 06/06/2024]
Abstract
Barking geckos (genus Ptenopus) are terrestrial, burrowing lizards endemic to southern Africa, currently with three recognised species. Two species are range-restricted (P. kochi and P. carpi) and display clear differences in substrate preference (soft sand vs. hard gravel). The third and most widespread species, P. garrulus, occurs on a variety of substrates of differing hardness, across potential geographic barriers, and over a steep climatic gradient. Variations in morphology and advertisement calls indicates that P. garrulus may be a species complex. Two subspecies of P. garrulus are currently recognised: P. g. maculatus and P. g. garrulus. To investigate species boundaries, we produced the first comprehensive phylogeny for the genus. We used a novel application of multiple regression on matrices models to assess multiple environmental drivers of diversification, as contrasted to isolation by distance. We show that P. kochi, P. carpi, and P. g. garrulus are valid species, but that P. g. maculatus is a paraphyletic complex of five previously unrecognised taxa. Specialisation onto different substrates was likely the main driver of divergence, with parapatric occurrence of two to four clades occurring at each of the three substrate transition zones identified a priori. The region encompasses diverse bioclimatic regions and potential geographic barriers, and these likely played a role in some divergence events.
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Affiliation(s)
- Francois S Becker
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, P.O. Wits, 2050 Johannesburg, South Africa; South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, Cape Town, South Africa; National Museum of Namibia, Ministry of Education, Arts and Culture, Private Bag 13186, Windhoek, Namibia; Gobabeb Namib Research Institute, PO Box 953, Walvis Bay 13103, Namibia.
| | - Graham J Alexander
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, P.O. Wits, 2050 Johannesburg, South Africa
| | - Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, Cape Town, South Africa; Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
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Lima RC, de Lima SR, Rocha MS, Dos Anjos HDB, Dantas YCA, Benites IDN, Queiroz CDCS, Fraga EDC, Batista JDS. Identification of fish specimens of the Tocantins River, Brazil, using DNA barcoding. JOURNAL OF FISH BIOLOGY 2024; 104:1924-1939. [PMID: 38551122 DOI: 10.1111/jfb.15721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 12/03/2023] [Accepted: 02/25/2024] [Indexed: 06/27/2024]
Abstract
The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues.
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Affiliation(s)
- Renato Corrêia Lima
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Laboratório Temático de Biologia Molecular (LTBM), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Sabrina Rufino de Lima
- Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Laboratório Temático de Biologia Molecular (LTBM), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
| | - Marcelo Salles Rocha
- Coordenação de Ciências Biológicas, Universidade do Estado do Amazonas (UEA), Manaus, Brazil
| | | | | | | | | | - Elmary da Costa Fraga
- Departamento de Química e Biologia, Universidade Estadual do Maranhão (UEMA), Caxias, Brazil
| | - Jacqueline da Silva Batista
- Coordenação de Biodiversidade (COBIO), Laboratório Temático de Biologia Molecular (LTBM), Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva (PPG-GCBEv), Instituto Nacional de Pesquisas da Amazônia (INPA), Manaus, Brazil
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Liu Y, Fu X, Wang Y, Liu J, Liu Y, Li C, Dong J. Exploring Barbronia species diversity and phylogenetic relationship within Suborder Erpobdelliformes (Clitellata: Annelida). PeerJ 2024; 12:e17480. [PMID: 38827288 PMCID: PMC11144392 DOI: 10.7717/peerj.17480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/07/2024] [Indexed: 06/04/2024] Open
Abstract
Background Barbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae. Methods Next-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method. Results The full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae.
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Affiliation(s)
- Yingkui Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Xinxin Fu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Yu Wang
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Jing Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Yong Liu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Chong Li
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
| | - Jiajia Dong
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry & Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
- School of Life Science, Xuzhou Medical University, Xuzhou, Jiangsu, People’s Republic of China
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Lo YY, Cheng RC, Lin CP. Integrative species delimitation and five new species of lynx spiders (Araneae, Oxyopidae) in Taiwan. PLoS One 2024; 19:e0301776. [PMID: 38722906 PMCID: PMC11081396 DOI: 10.1371/journal.pone.0301776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/21/2024] [Indexed: 05/13/2024] Open
Abstract
An accurate assessment of species diversity is a cornerstone of biology and conservation. The lynx spiders (Araneae: Oxyopidae) represent one of the most diverse and widespread cursorial spider groups, however their species richness in Asia is highly underestimated. In this study, we revised species diversity with extensive taxon sampling in Taiwan and explored species boundaries based on morphological traits and genetic data using a two-step approach of molecular species delimitation. Firstly, we employed a single COI dataset and applied two genetic distance-based methods: ABGD and ASAP, and two topology-based methods: GMYC and bPTP. Secondly, we further analyzed the lineages that were not consistently delimited, and incorporated H3 to the dataset for a coalescent-based analysis using BPP. A total of eight morphological species were recognized, including five new species, Hamataliwa cordivulva sp. nov., Hamat. leporauris sp. nov., Tapponia auriola sp. nov., T. parva sp. nov. and T. rarobulbus sp. nov., and three newly recorded species, Hamadruas hieroglyphica (Thorell, 1887), Hamat. foveata Tang & Li, 2012 and Peucetia latikae Tikader, 1970. All eight morphological species exhibited reciprocally monophyletic lineages. The results of molecular-based delimitation analyses suggested a variety of species hypotheses that did not fully correspond to the eight morphological species. We found that Hamat. cordivulva sp. nov. and Hamat. foveata showed shallow genetic differentiation in the COI, but they were unequivocally distinguishable according to their genitalia. In contrast, T. parva sp. nov. represented a deep divergent lineage, while differences of genitalia were not detected. This study highlights the need to comprehensively employ multiple evidence and methods to delineate species boundaries and the values of diagnostic morphological characters for taxonomic studies in lynx spiders.
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Affiliation(s)
- Ying-Yuan Lo
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Wild Animals Division, Biodiversity Research Institute, Nantou, Taiwan
| | - Ren-Chung Cheng
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Research Center for Global Change Biology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
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Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Podsiadlowski L, Niehuis O, Ahrens D. Metazoa-level USCOs as markers in species delimitation and classification. Mol Ecol Resour 2024; 24:e13921. [PMID: 38146909 DOI: 10.1111/1755-0998.13921] [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: 10/15/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.
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Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eckart Stolle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Paris-Lodron-University, Salzburg, Austria
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lars Podsiadlowski
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
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Magalhães RF, K S Ramos E, Bandeira LN, Ferreira JS, Werneck FP, Anciães M, Bruschi DP. Integrative species delimitation uncovers hidden diversity within the Pithecopus hypochondrialis species complex (Hylidae, Phyllomedusinae) and its phylogeography reveals Plio-Pleistocene connectivity among Neotropical savannas. Mol Phylogenet Evol 2024; 190:107959. [PMID: 37918682 DOI: 10.1016/j.ympev.2023.107959] [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: 05/12/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Despite their limited vagility and pronounced habitat heterogeneity in the tropics, many anuran species have unexpectedly extensive geographic ranges. One prominent example of this phenomenon is Pithecopus hypochondrialis, which is found in the Cerrado, Guianan savanna, and Llanos domains, as well as isolated tracts of savanna and open habitat within the Amazon Forest. The present study employs an integrative species delimitation approach to test the hypothesis that P. hypochondrialis is in fact a species complex. We also reconstruct the relationships among the lineages delimited here and other Pithecopus species. In this study, we employ Ecological Niche Modelling (ENM) and spatiotemporal phylogeographic reconstruction approaches to evaluate a multitude of scenarios of connectivity across the Neotropical savannas. We identified three divergent lineages, two of which have been described previously. The lineages were allocated to a lowland Pithecopus clade, although the relationships among these lineages are weakly supported. Both the ENM and the phylogeographic reconstruction highlight the occurrence of periods of connectivity among the Neotropical savannas over the course of the Pliocene and Pleistocene epochs. These processes extended from eastern Amazonia to the northern coast of Brazil. The findings of the present study highlight the presence of hidden diversity within P. hypochondrialis, and reinforce the need for a comprehensive taxonomic review. These findings also indicate intricate and highly dynamic patterns of connectivity across the Neotropical savannas that date back to the Pliocene.
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Affiliation(s)
- Rafael F Magalhães
- Department of Natural Sciences, Universidade Federal de São João del-Rei, Campus Dom Bosco, Praça Dom Helvécio, 70, São João del-Rei, MG 36301-160, Brazil; Postgraduate Programme in Zoology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Belo Horizonte, MG 31270-010, Brazil.
| | - Elisa K S Ramos
- Faculty of Philosophy and Natural Sciences, Department of Environmental Sciences, University of Basel, Bernoullistrasse 30, Basel 4056, Switzerland.
| | - Lucas N Bandeira
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Johnny S Ferreira
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
| | - Fernanda P Werneck
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Marina Anciães
- Postgraduate Programme in Ecology, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil; Scientific Biological Collections Program, Biodiversity Coordination, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Manaus, AM 69067-375, Brazil.
| | - Daniel P Bruschi
- Postgraduate Programme in Genetics, Department of Genetics, Biological Sciences Sector, Universidade Federal do Paraná, Caixa Postal 19071, Curitiba, PR 81531-980, Brazil.
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Zhou J, Wang S, Yu S, Li Y, Qiao M, Zhao Q, Hughes E, Liu H, Bu W. Limits of mitochondrial genes in delimiting species within a Carbula species complex (Hemiptera: Pentatomidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22075. [PMID: 38288487 DOI: 10.1002/arch.22075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/27/2023] [Accepted: 12/08/2023] [Indexed: 02/01/2024]
Abstract
Molecular data has become a powerful tool for species delimitation, particularly among those that present limited morphological differences; while the mitochondrial genome, with its moderate length, low cost of sequencing and fast lineage sorting, has emerged as a practical data set. Due to the limited morphological differences among the closely related species of Carbula Stål 1865, the species boundaries between Carbula abbreviata (Motschulsky, 1866), Carbula humerigera (Uhler, 1860), and Carbula putoni (Jakovlev, 1876) have remained particularly unclear. In this study, we applied two phylogenetic reconstruction methods to two data sets (mitogenome and COI) to assess the phylogeny of Carbula distributed in Asia, and five species delimitation methods to determine the boundaries between East Asian Carbula species. Our phylogenetic analyses showed Carbula to be paraphyletic; the seven known species distributed within East Asia to form a single monophyletic group, and within this, C. abbreviata, C. humerigera, C. putoni and middle-type to comprise a C. humerigera species complex. Our results show that mitogenome data alone, while effective in the differentiation of more distantly related Carbula species, is not sufficient to accurately delimit the species within this newly described complex.
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Affiliation(s)
- Jiayue Zhou
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Shujing Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Shengjie Yu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Yanfei Li
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Mu Qiao
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
| | - Qing Zhao
- College of Plant Protection, Shanxi Agricultural University, Taigu, PR China
| | | | - Huaxi Liu
- Department of Life Science, Natural History Museum, London, UK
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, PR China
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Fernández-Álvarez FÁ, Sanchez G, Deville D, Taite M, Villanueva R, Allcock AL. Atlantic Oceanic Squids in the "Grey Speciation Zone". Integr Comp Biol 2023; 63:1214-1225. [PMID: 37604791 PMCID: PMC10755182 DOI: 10.1093/icb/icad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 08/03/2023] [Accepted: 08/13/2023] [Indexed: 08/23/2023] Open
Abstract
Cryptic species complexes represent an important challenge for the adequate characterization of Earth's biodiversity. Oceanic organisms tend to have greater unrecognized cryptic biodiversity since the marine realm was often considered to lack hard barriers to genetic exchange. Here, we tested the effect of several Atlantic and Mediterranean oceanic barriers on 16 morphospecies of oceanic squids of the orders Oegopsida and Bathyteuthida using three mitochondrial and one nuclear molecular marker and five species delimitation methods. Number of species recognized within each morphospecies differed among different markers and analyses, but we found strong evidence of cryptic biodiversity in at least four of the studied species (Chtenopteryx sicula, Chtenopteryx canariensis, Ancistrocheirus lesueurii, and Galiteuthis armata). There were highly geographically structured units within Helicocranchia navossae that could either represent recently diverged species or population structure. Although the species studied here can be considered relatively passive with respect to oceanic currents, cryptic speciation patterns showed few signs of being related to oceanic currents. We hypothesize that the bathymetry of the egg masses and duration of the paralarval stage might influence the geographic distribution of oceanic squids. Because the results of different markers and different species delimitation methods are inconsistent and because molecular data encompassing broad geographic sampling areas for oceanic squids are scarce and finding morphological diagnostic characters for early life stages is difficult, it is challenging to assess the species boundaries for many of these species. Thus, we consider many to be in the "grey speciation zone." As many oceanic squids have cosmopolitan distributions, new studies combining genomic and morphological information from specimens collected worldwide are needed to correctly assess the actual oceanic squid biodiversity.
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Affiliation(s)
| | - Gustavo Sanchez
- Molecular Genetics Unit, Okinawa Institute of Science and Technology, Onna, Okinawa 904-0412, Japan
| | - Diego Deville
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima 739-8528, Japan
| | - Morag Taite
- Ryan Institute and School of Natural Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
| | - Roger Villanueva
- Institut de Ciències del Mar (ICM), CSIC, Passeig Marítim de la Barceloneta 37–49, 08003 Barcelona, Spain
| | - A Louise Allcock
- Ryan Institute and School of Natural Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
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Truszkowski J, Perrigo A, Broman D, Ronquist F, Antonelli A. Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics. Syst Biol 2023; 72:1199-1206. [PMID: 37498209 PMCID: PMC10627553 DOI: 10.1093/sysbio/syad045] [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: 10/20/2022] [Revised: 06/22/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
Bayesian phylogenetics is now facing a critical point. Over the last 20 years, Bayesian methods have reshaped phylogenetic inference and gained widespread popularity due to their high accuracy, the ability to quantify the uncertainty of inferences and the possibility of accommodating multiple aspects of evolutionary processes in the models that are used. Unfortunately, Bayesian methods are computationally expensive, and typical applications involve at most a few hundred sequences. This is problematic in the age of rapidly expanding genomic data and increasing scope of evolutionary analyses, forcing researchers to resort to less accurate but faster methods, such as maximum parsimony and maximum likelihood. Does this spell doom for Bayesian methods? Not necessarily. Here, we discuss some recently proposed approaches that could help scale up Bayesian analyses of evolutionary problems considerably. We focus on two particular aspects: online phylogenetics, where new data sequences are added to existing analyses, and alternatives to Markov chain Monte Carlo (MCMC) for scalable Bayesian inference. We identify 5 specific challenges and discuss how they might be overcome. We believe that online phylogenetic approaches and Sequential Monte Carlo hold great promise and could potentially speed up tree inference by orders of magnitude. We call for collaborative efforts to speed up the development of methods for real-time tree expansion through online phylogenetics.
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Affiliation(s)
- Jakub Truszkowski
- Department of Biological and Environmental Sciences, University of Gothenburg, P. O. Box 461, SE.405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden
| | - Allison Perrigo
- Department of Biological and Environmental Sciences, University of Gothenburg, P. O. Box 461, SE.405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden
| | - David Broman
- Department of Computer Science and Digital Futures, KTH Royal Institute of Technology, SE.100 44 Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P. O. Box 50007, SE.104 05 Stockholm, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, P. O. Box 461, SE.405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, 405 30 Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3 RB, UK
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11
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Martínez‐Borrego D, Arellano E, González‐Cózatl FX, Ospina‐Garcés SM, Rogers DS. Species delimitation and integrative taxonomy of the Reithrodontomys mexicanus (Rodentia: Cricetidae) cryptic complex. Ecol Evol 2023; 13:e10355. [PMID: 37529589 PMCID: PMC10387591 DOI: 10.1002/ece3.10355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/12/2023] [Accepted: 07/12/2023] [Indexed: 08/03/2023] Open
Abstract
Species boundaries are difficult to establish in groups with very similar morphology. As an alternative, it has been suggested to integrate multiple sources of data to clarify taxonomic problems in taxa where cryptic speciation processes have been reported. This is the case of the harvest mouse Reithrodontomys mexicanus, which has a problematic taxonomy history as it is considered a complex species. Here, we evaluate the cryptic diversity of R. mexicanus using an integrative taxonomy approach in order to detect candidate lineages at the species level. The molecular analysis used one mitochondrial (cytb) and two nuclear (Fgb-I7 and IRBP) genes. Species hypotheses were suggested based on three molecular delimitation methods (mPTP, bGMYC, and STACEY) and cytb genetic distance values. Skull and environmental space differences between the delimited species were also tested to complement the discrimination of candidate species. Based on the consensus across the delimitation methods and genetic distance values, four species were proposed, which were mostly supported by morphometric and ecological data: R. mexicanus clade I, R. mexicanus clade IIA, R. mexicanus clade IIIA, and R. mexicanus clade IIIB. In addition, the evolutionary relationships between the species that comprise the R. mexicanus group were discussed from a phylogenetic approach. Our findings present important taxonomic implications for Reithrodontomys, as the number of known species for this genus increases. Furthermore, we highlight the importance of the use of multiple sources of data in systematic studies to establish robust delimitations between species considered taxonomically complex.
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Affiliation(s)
- Daily Martínez‐Borrego
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMorelosMexico
| | - Elizabeth Arellano
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMorelosMexico
| | - Francisco X. González‐Cózatl
- Centro de Investigación en Biodiversidad y ConservaciónUniversidad Autónoma del Estado de MorelosCuernavacaMorelosMexico
| | | | - Duke S. Rogers
- Department of Biology and Monte L Bean Life Science MuseumBrigham Young UniversityProvoUtahUSA
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Thompson JB, Davis KE, Dodd HO, Wills MA, Priest NK. Speciation across the Earth driven by global cooling in terrestrial orchids. Proc Natl Acad Sci U S A 2023; 120:e2102408120. [PMID: 37428929 PMCID: PMC10629580 DOI: 10.1073/pnas.2102408120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/03/2023] [Indexed: 07/12/2023] Open
Abstract
Although climate change has been implicated as a major catalyst of diversification, its effects are thought to be inconsistent and much less pervasive than localized climate or the accumulation of species with time. Focused analyses of highly speciose clades are needed in order to disentangle the consequences of climate change, geography, and time. Here, we show that global cooling shapes the biodiversity of terrestrial orchids. Using a phylogeny of 1,475 species of Orchidoideae, the largest terrestrial orchid subfamily, we find that speciation rate is dependent on historic global cooling, not time, tropical distributions, elevation, variation in chromosome number, or other types of historic climate change. Relative to the gradual accumulation of species with time, models specifying speciation driven by historic global cooling are over 700 times more likely. Evidence ratios estimated for 212 other plant and animal groups reveal that terrestrial orchids represent one of the best-supported cases of temperature-spurred speciation yet reported. Employing >2.5 million georeferenced records, we find that global cooling drove contemporaneous diversification in each of the seven major orchid bioregions of the Earth. With current emphasis on understanding and predicting the immediate impacts of global warming, our study provides a clear case study of the long-term impacts of global climate change on biodiversity.
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Affiliation(s)
- Jamie B. Thompson
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
| | - Katie E. Davis
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | - Harry O. Dodd
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
| | - Matthew A. Wills
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
| | - Nicholas K. Priest
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
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13
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Magain N, Miadlikowska J, Goffinet B, Goward T, Pardo-De la Hoz C, Jüriado I, Simon A, Mercado-Díaz J, Barlow T, Moncada B, Lücking R, Spielmann A, Canez L, Wang L, Nelson P, Wheeler T, Lutzoni F, Sérusiaux E. High species richness in the lichen genus Peltigera ( Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. PERSOONIA 2023; 51:1-88. [PMID: 38665978 PMCID: PMC11041898 DOI: 10.3767/persoonia.2023.51.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/10/2022] [Indexed: 04/28/2024]
Abstract
Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza, P. neopolydactyla, P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification. Citation: Magain N, Miadlikowska J, Goffinet B, et al. 2023. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. Persoonia 51: 1-88. doi: 10.3767/persoonia.2023.51.01.
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Affiliation(s)
- N. Magain
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - J. Miadlikowska
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - B. Goffinet
- Ecology and Evolutionary Biology, Unit 3043, University of Connecticut, 75 North Eagleville road, Storrs CT, 06269-3043 USA
| | - T. Goward
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - C.J. Pardo-De la Hoz
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - I. Jüriado
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu 50409, Estonia; Institute of Agricultural & Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu 51006, Estonia
| | - A. Simon
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
- Ecology and Evolutionary Biology, Unit 3043, University of Connecticut, 75 North Eagleville road, Storrs CT, 06269-3043 USA
| | - J.A. Mercado-Díaz
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois, 60605 USA
| | - T. Barlow
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - B. Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26B-54, Torre de Laboratorios, Herbario, Bogotá, Colombia; current address: Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
| | - R. Lücking
- Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
| | - A. Spielmann
- Laboratòrio de Botanica / Liquenologia, Instituto de Biociencias, Universidade Federal de Mato Grosso do Sul, Campo Grande – MS, Brazil
| | - L. Canez
- Laboratòrio de Botanica / Liquenologia, Instituto de Biociencias, Universidade Federal de Mato Grosso do Sul, Campo Grande – MS, Brazil
| | - L.S. Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming 650201, China
| | - P. Nelson
- Natural and Behavioral Sciences Division, University of Maine – Fort Kent, Fort Kent, ME, USA
| | - T. Wheeler
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - F. Lutzoni
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - E. Sérusiaux
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
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14
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Kaiser S, Stransky B, Jennings RM, Kihara TC, Brix S. Combining morphological and mitochondrial DNA data to describe a new species of Austroniscus Vanhöffen, 1914 (Isopoda, Janiroidea, Nannoniscidae) linking abyssal and hadal depths of the Puerto Rico Trench. Zootaxa 2023; 5293:401-434. [PMID: 37518475 DOI: 10.11646/zootaxa.5293.3.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Indexed: 08/01/2023]
Abstract
Hadal trenches are perceived as a unique deep-sea ecosystem with fundamentally different communities compared to the nearby abyss. So far, however, scarce information exists about how populations are genetically linked within a trench and about mechanisms for species divergence. The present study presents the morphological and molecular-genetic characterization and description of a new nannoniscid species within the genus Austroniscus Vanhöffen, 1914 obtained from abyssal and hadal depths of the Puerto Rico Trench, NW Atlantic. Samples were collected as part of the Vema-TRANSIT expedition onboard RV Sonne in January 2015. Because of the large depth differences between sampling locations (4,552-8,338 m), we expected to find different species within the genus inhabiting abyssal and hadal sites. Initial morphological examination using traditional light microscopy and Confocal Laser Scanning Microscopy was paired with subsequent molecular analysis based on mtDNA (COI and 16S). Contrary to our assumptions, combined morphological and molecular species delimitation analyses (sGMYC, mPTP, ABGD) revealed the presence of only one species spanning the abyssal and hadal seafloor of the Puerto Rico Trench. In addition, comparison with type material could show that this species belongs to a new species, Austroniscus brandtae n. sp., which is described herein. Incongruence between some species delimitation methods suggesting the presence of multiple species is interpreted as strong genetic population structuring within the trench, which is also supported by the analysis of the haplotype networks. The geographic and bathymetric distribution of Austroniscus species is discussed. The species described herein represents the first in the genus Austroniscus from the Atlantic Ocean and the deepest record of the genus to date, and hence significantly expanding previously known limits of its geographic and bathymetric range.
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Affiliation(s)
- Stefanie Kaiser
- University of Łódź; Faculty of Biology and Environmental Protection; Department of Invertebrate Zoology and Hydrobiology; Banacha St. 12/16; Łódź; 90-237; Poland; Senckenberg Research Institute; Department of Marine Zoology; Section Crustacea; Senckenberganlage 25; 60325 Frankfurt; Germany.
| | - Bente Stransky
- Museum of Nature; Leibniz Institute for the Analysis of Biodiversity Change (LIB); Centre for Taxonomy and Morphology; Martin- Luther-King-Platz 3; 20146 Hamburg; Germany.
| | - Robert M Jennings
- Temple University; Biology Department; 1900 North 12th Street; Philadelphia; PA 19122; USA.
| | - Terue Cristina Kihara
- Integrated Environmental Solutions UG-INES; c/o DZMB; Südstrand 44; 26382 Wilhelmshaven; Germany.
| | - Saskia Brix
- German Centre for Marine Biodiversity Research (DZMB); Senckenberg am Meer; Martin-Luther-King-Platz 3; 20146 Hamburg; Germany.
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15
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Day JJ, Steell EM, Vigliotta TR, Withey LA, Bills R, Friel JP, Genner MJ, Stiassny MLJ. Exceptional levels of species discovery ameliorate inferences of the biogeography and diversification of an Afrotropical catfish family. Mol Phylogenet Evol 2023; 182:107754. [PMID: 36906193 DOI: 10.1016/j.ympev.2023.107754] [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: 11/07/2022] [Revised: 02/24/2023] [Accepted: 03/05/2023] [Indexed: 03/13/2023]
Abstract
Endeavours in species discovery, particularly the characterisation of cryptic species, have been greatly aided by the application of DNA molecular sequence data to phylogenetic reconstruction and inference of evolutionary and biogeographic processes. However, the extent of cryptic and undescribed diversity remains unclear in tropical freshwaters, where biodiversity is declining at alarming rates. To investigate how data on previously undiscovered biodiversity impacts inferences of biogeography and diversification dynamics, we generated a densely sampled species-level family tree of Afrotropical Mochokidae catfishes (220 valid species) that was ca. 70 % complete. This was achieved through extensive continental sampling specifically targeting the genus Chiloglanis a specialist of the relatively unexplored fast-flowing lotic habitat. Applying multiple species-delimitation methods, we report exceptional levels of species discovery for a vertebrate genus, conservatively delimiting a staggering ca. 50 putative new Chiloglanis species, resulting in a near 80 % increase in species richness for the genus. Biogeographic reconstructions of the family identified the Congo Basin as a critical region in the generation of mochokid diversity, and further revealed complex scenarios for the build-up of continental assemblages of the two most species rich mochokid genera, Synodontis and Chiloglanis. While Syndontis showed most divergence events within freshwater ecoregions consistent with largely in situ diversification, Chiloglanis showed much less aggregation of freshwater ecoregions, suggesting dispersal as a key diversification process in this older group. Despite the significant increase in mochokid diversity identified here, diversification rates were best supported by a constant rate model consistent with patterns in many other tropical continental radiations. While our findings highlight fast-flowing lotic freshwaters as potential hotspots for undescribed and cryptic species diversity, a third of all freshwater fishes are currently threatened with extinction, signifying an urgent need to increase exploration of tropical freshwaters to better characterise and conserve its biodiversity.
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Affiliation(s)
- Julia J Day
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | - Elizabeth M Steell
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Thomas R Vigliotta
- Department of Ichthyology, American Museum of Natural History, New York, NY, USA
| | - Lewis A Withey
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Roger Bills
- South African Institute for Aquatic Biodiversity, Private Bag, 1015, 6140 Grahamstown, South Africa
| | - John P Friel
- Alabama Museum of Natural History, The University of Alabama, Box 870340, 35487-0340 Tuscaloosa, AL, USA
| | - Martin J Genner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, NY, USA
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16
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Zhao Z, Conradie W, Pietersen DW, Jordaan A, Nicolau G, Edwards S, Riekert S, Heideman N. Diversification of the African legless skinks in the subfamily Acontinae (Family Scincidae). Mol Phylogenet Evol 2023; 182:107747. [PMID: 36849095 DOI: 10.1016/j.ympev.2023.107747] [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: 08/11/2022] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily's biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered "ghost introgression" in A. occidentalis. Our inferred species tree revealed a signal of gene flow, which implies possible cross-over in some groups. Fossil evidence calibration dating results showed that the divergence between Typhlosaurus and Acontias was likely influenced by cooling and increasing aridity along the southwest coast in the mid-Oligocene caused by the opening of the Drake Passage. Further cladogenesis observed in Typhlosaurus and Acontias was likely influenced by Miocene cooling, expansion of open habitat, uplifting of the eastern Great Escarpment (GE), and variation in rainfall patterns, together with the effect of the warm Agulhas Current since the early Miocene, the development of the cold Benguela Current since the late Miocene, and their co-effects. The biogeographic pattern of the Acontinae bears close resemblance to that of other herpetofauna (e.g., rain frogs and African vipers) in southern Africa.
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Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa; Department of Genetics, University of the Free State, Bloemfontein, South Africa.
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), P.O. Box 13147, Humewood, Port Elizabeth 6013, South Africa; Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Darren W Pietersen
- Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Gary Nicolau
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Shelley Edwards
- Zoology & Entomology Molecular Lab, Department of Zoology and Entomology, Rhodes University, Makhanda, South Africa
| | - Stephanus Riekert
- Department of Information and Communication Technology Services, University of the Free State, Bloemfontein, South Africa
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
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17
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Ortiz AS, Rubio RM, de Freina JJ, Guerrero JJ, Garre M, Yela JL. DNA barcoding and morphology reveal European and western Asian Arctiavillica (Linnaeus, 1758) as a complex of species (Lepidoptera, Erebidae, Arctiinae). Zookeys 2023; 1159:69-86. [PMID: 37234560 PMCID: PMC10208439 DOI: 10.3897/zookeys.1159.95225] [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: 09/22/2022] [Accepted: 02/23/2023] [Indexed: 05/28/2023] Open
Abstract
Currently, the genus Arctia Schrank, 1802 includes approximately 16 species in the Palaearctic region, depending on the taxonomic interpretation. Here, populations of the Arctiavillica (Linnaeus, 1758) morphospecies complex were studied from Europe to the Middle East (Turkey, northern Iran) by molecular methods. Morphological treatment has traditionally revealed the presence of five nominal taxa: A.villica (Linnaeus, 1758), A.angelica (Boisduval, 1829), A.konewkaii (Freyer, 1831), A.marchandi de Freina, 1983, and A.confluens Romanoff, 1884. The molecular approach tests whether they represent well-delimited species. Subsequently, this study corroborates the suitability of the mitochondrial cytochrome c oxidase subunit 1 (COI) marker sequence for species delimitation. In total, 55 barcodes of the Arctiavillica complex were compared, and two molecular species delimitation algorithms were applied to reveal the potential Molecular Operational Taxonomic Units (MOTUs), namely the distance-based Barcode Index Number (BIN) System, and the hierarchical clustering algorithm based on a pairwise genetic distances approach using the Assemble Species by Automatic Partitioning (ASAP). The applied ASAP distance-based species delimitation method for the analysed dataset revealed an interspecific threshold of 2.0-3.5% K2P distance as suitable for species identification purposes of the Iberian A.angelica and the Sicilian A.konewkaii and less than 2% for the three taxa of the A.villica clade: A.villica, A.confluens, and A.marchandi. This study contributes to a better understanding of the taxonomy of the genus Arctia and challenges future revision of this genus in Turkey, the Caucasus, Transcaucasia as well as northern Iran using standard molecular markers.
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Affiliation(s)
- Antonio S. Ortiz
- Department of Zoology and Physical Anthropology, University of Murcia, Campus de Espinardo, 30100 Murcia, SpainUniversity of MurciaMurciaSpain
| | - Rosa M. Rubio
- Department of Zoology and Physical Anthropology, University of Murcia, Campus de Espinardo, 30100 Murcia, SpainUniversity of MurciaMurciaSpain
| | - Josef J. de Freina
- Eduard Schmid-Str. 10, D-81541, München, GermanyUnaffiliatedMunichGermany
| | - Juan J. Guerrero
- Department of Zoology and Physical Anthropology, University of Murcia, Campus de Espinardo, 30100 Murcia, SpainUniversity of MurciaMurciaSpain
| | - Manuel Garre
- Department of Zoology and Physical Anthropology, University of Murcia, Campus de Espinardo, 30100 Murcia, SpainUniversity of MurciaMurciaSpain
| | - José Luis Yela
- Grupo DITEG, Área de Zoología, Facultad de Ciencias Ambientales, Universidad de Castilla-La Mancha, Avda, Carlos III, s.n., Campus Real Fábrica de Armas, E-45071, Toledo, SpainUniversidad de Castilla-La ManchaToledoSpain
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18
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DNA Barcoding of Fish Species Diversity in Guizhou, China. DIVERSITY 2023. [DOI: 10.3390/d15020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Guizhou is an important ecological barrier in the upper reaches of the Yangtze River and the Pearl River basins with abundant fish species. However, fish from these regions are threatened by anthropogenic activities, including overfishing and habitat destruction. Here, we assessed the fish diversity including more than half of the species from the region using DNA barcoding (partial sequence of cytochrome c oxidase subunit I (COI) gene). We obtained 800 mitochondrial COI barcode sequences from 82 genera, 18 families and 8 orders of fishes. The average Kimura two-parameter (K2P) distances within species and genera were 0.35% and 5.44%, respectively. The average interspecific distance was 15.54 times higher than the mean intraspecific distance. Moreover, DNA barcodes revealed 175 operational taxonomic units (OTUs) based on consensus demarcation schemes. Barcoding gaps were detected in 94.81% of morphospecies. Three fish species (Schistura fasciolata, Vanmanenia pingchowensis, and Misgurnus dabryanus) have considerable intraspecific variability, and each was divided into multiple molecular operational taxonomic units (MOTUs) using molecular definition methods (Automatic Barcode Gap Discovery, Refined Single Linkage, General Mixed Yule Coalescent, and Poisson Tree Processes), possibly indicating the occurrence of cryptic species. Altogether, our study reveals the complex diversity of fish species in Guizhou Province, serving as a reference for the conservation and monitoring of fish species in this region.
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Molecular ecology meets systematic conservation planning. Trends Ecol Evol 2023; 38:143-155. [PMID: 36210287 DOI: 10.1016/j.tree.2022.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 08/29/2022] [Accepted: 09/12/2022] [Indexed: 01/06/2023]
Abstract
Integrative and proactive conservation approaches are critical to the long-term persistence of biodiversity. Molecular data can provide important information on evolutionary processes necessary for conserving multiple levels of biodiversity (genes, populations, species, and ecosystems). However, molecular data are rarely used to guide spatial conservation decision-making. Here, we bridge the fields of molecular ecology (ME) and systematic conservation planning (SCP) (the 'why') to build a foundation for the inclusion of molecular data into spatial conservation planning tools (the 'how'), and provide a practical guide for implementing this integrative approach for both conservation planners and molecular ecologists. The proposed framework enhances interdisciplinary capacity, which is crucial to achieving the ambitious global conservation goals envisioned for the next decade.
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de Araújo AD, Carvalho ODS, Gava SG, Caldeira RL. DNA barcoding as a valuable tool for delimiting mollusk species of the genus Biomphalaria Preston, 1910 (Gastropoda: Planorbidae). Front Cell Infect Microbiol 2023; 13:1167787. [PMID: 37168391 PMCID: PMC10165093 DOI: 10.3389/fcimb.2023.1167787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/22/2023] [Indexed: 05/13/2023] Open
Abstract
Introduction The genus Biomphalaria in Brazil includes 11 species and one subspecies, three of which are intermediate hosts of Schistosoma mansoni. Due to the recent evolution of this group, some species are difficult to identify based on morphological characters, making the use of genetic markers necessary for species identification. This study aimed to evaluate the use of partial sequences of the cytochrome c oxidase I (coi) gene for the identification of Biomphalaria species using phylogenetic reconstruction and species delimitation algorithms. The study tested the use of DNA barcoding technique for species delimitation within the genus. Methods DNA barcoding was performed by sequencing a partial region of the coi gene from specimens, and the sequences were analyzed using phylogenetic reconstruction and algorithms to delimit Operational Taxonomic Units (OTUs). Results The study found that the use of the coi gene in the reconstruction of the phylogeny of the genus might be an alternative for understanding the evolution and dispersion of species. However, this marker alone is not enough to solve complex taxonomic problems within the genus. A total of 223 sequences were analyzed, 102 of which could be separated using the barcode gap, enabling the correct identification of seven taxa. Discussion The study demonstrated that accurate mollusk identification is necessary for effective schistosomiasis control. The DNA barcoding methodology was found to be promising for accurate mollusk identification, which is crucial for concentrating schistosomiasis control efforts in places where it is needed.
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Sampaio FL, Day JJ, Mendis Wickramasinghe LJ, Cyriac VP, Papadopoulou A, Brace S, Rajendran A, Simon-Nutbrown C, Flouris T, Kapli P, Ranga Vidanapathirana D, Kotharambath R, Kodandaramaiah U, Gower DJ. A near-complete species-level phylogeny of uropeltid snakes harnessing historical museum collections as a DNA source. Mol Phylogenet Evol 2023; 178:107651. [PMID: 36306995 DOI: 10.1016/j.ympev.2022.107651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Uropeltidae is a clade of small fossorial snakes (ca. 64 extant species) endemic to peninsular India and Sri Lanka. Uropeltid taxonomy has been confusing, and the status of some species has not been revised for over a century. Attempts to revise uropeltid systematics and undertake evolutionary studies have been hampered by incompletely sampled and incompletely resolved phylogenies. To address this issue, we take advantage of historical museum collections, including type specimens, and apply genome-wide shotgun (GWS) sequencing, along with recent field sampling (using Sanger sequencing) to establish a near-complete multilocus species-level phylogeny (ca. 87% complete at species level). This results in a phylogeny that supports the monophyly of all genera (if Brachyophidium is considered a junior synonym of Teretrurus), and provides a firm platform for future taxonomic revision. Sri Lankan uropeltids are probably monophyletic, indicating a single colonisation event of this island from Indian ancestors. However, the position of Rhinophis goweri (endemic to Eastern Ghats, southern India) is unclear and warrants further investigation, and evidence that it may nest within the Sri Lankan radiation indicates a possible recolonisation event. DNA sequence data and morphology suggest that currently recognised uropeltid species diversity is substantially underestimated. Our study highlights the benefits of integrating museum collections in molecular genetic analyses and their role in understanding the systematics and evolutionary history of understudied organismal groups.
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Affiliation(s)
- Filipa L Sampaio
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
| | - Julia J Day
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Vivek P Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695 551, India
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, 2109 Nicosia, Cyprus
| | - Selina Brace
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Albert Rajendran
- Research Department of Zoology, St. John's College, Tirunelveli, Tamil Nadu, India
| | - Cornelia Simon-Nutbrown
- The Lyell Centre for Earth and Marine Science and Technology, Heriot-Watt University, Edinburgh EH14 4BA, UK; Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Tomas Flouris
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Paschalia Kapli
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Ramachandran Kotharambath
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution, Indian Institute of Science Education and Research Thiruvananthapuram, Kerala 695 551, India
| | - David J Gower
- Natural History Museum, Cromwell Road, London SW7 5BD, UK; Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India.
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Tavares VDC, Gardner AL, Mcdonough MM, Maldonado JE, Gutiérrez EE, Velazco PM, Garbino GST. Historical DNA of rare yellow-eared bats Vampyressa Thomas, 1900 (Chiroptera, Phyllostomidae) clarifies phylogeny and species boundaries within the genus. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2117247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Valéria da C. Tavares
- Instituto Tecnológico Vale (ITV), Belém, 66055-090, PA, Brazil
- Laboratório de Mamíferos, Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba (UFPB), João Pessoa, 58059-900, PB, Brazil
| | - Alfred L. Gardner
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Molly M. Mcdonough
- Department of Biological Sciences, Chicago State University, Chicago, IL, USA
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Jesús E. Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | | | - Paúl M. Velazco
- Department of Biology, Arcadia University, Glenside, PA, USA
- Department of Mammalogy, American Museum of Natural History, New York, NY, USA
| | - Guilherme S. T. Garbino
- Museu de Zoologia João Moojen, Departamento de Biologia Animal, Universidade Federal de Viçosa, Viçosa, 36570-900, MG, Brazil
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Carmelet‐Rescan D, Morgan‐Richards M, Pattabiraman N, Trewick SA. Time-calibrated phylogeny and ecological niche models indicate Pliocene aridification drove intraspecific diversification of brushtail possums in Australia. Ecol Evol 2022; 12:e9633. [PMID: 36540081 PMCID: PMC9755819 DOI: 10.1002/ece3.9633] [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: 10/21/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Major aridification events in Australia during the Pliocene may have had significant impact on the distribution and structure of widespread species. To explore the potential impact of Pliocene and Pleistocene climate oscillations, we estimated the timing of population fragmentation and past connectivity of the currently isolated but morphologically similar subspecies of the widespread brushtail possum (Trichosurus vulpecula). We use ecological niche modeling (ENM) with the current fragmented distribution of brushtail possums to estimate the environmental envelope of this marsupial. We projected the ENM on models of past climatic conditions in Australia to infer the potential distribution of brushtail possums over 6 million years. D-loop haplotypes were used to describe population structure. From shotgun sequencing, we assembled whole mitochondrial DNA genomes and estimated the timing of intraspecific divergence. Our projections of ENMs suggest current possum populations were unlikely to have been in contact during the Pleistocene. Although lowered sea level during glacial periods enabled connection with habitat in Tasmania, climate fluctuation during this time would not have facilitated gene flow over much of Australia. The most recent common ancestor of sampled intraspecific diversity dates to the early Pliocene when continental aridification caused significant changes to Australian ecology and Trichosurus vulpecula distribution was likely fragmented. Phylogenetic analysis revealed that the subspecies T. v. hypoleucus (koomal; southwest), T. v. arnhemensis (langkurr; north), and T. v. vulpecula (bilda; southeast) correspond to distinct mitochondrial lineages. Despite little phenotypic differentiation, Trichosurus vulpecula populations probably experienced little gene flow with one another since the Pliocene, supporting the recognition of several subspecies and explaining their adaptations to the regional plant assemblages on which they feed.
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Affiliation(s)
- David Carmelet‐Rescan
- Wildlife and Ecology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Mary Morgan‐Richards
- Wildlife and Ecology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Nimeshika Pattabiraman
- Wildlife and Ecology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Steven A. Trewick
- Wildlife and Ecology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
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24
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Guo B, Kong L. Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda). Genes (Basel) 2022; 13:genes13122273. [PMID: 36553540 PMCID: PMC9778293 DOI: 10.3390/genes13122273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed biodiverse species have been paid increasing attention. DNA sequence-based species delimitation methods are mainly classified into two categories, namely, distance-based and tree-based methods, and have been widely adopted in many studies. In the present study, we performed three distance-based (ad hoc threshold, ABGD, and ASAP) and four tree-based (sGMYC, mGMYC, PTP, and mPTP) analyses based on Trochoidea COI data and analyzed the discordance between them. Moreover, we also observed the performance of these methods at different taxonomic ranks (the genus, subfamily, and family ranks). The results suggested that the distance-based approach is generally superior to the tree-based approach, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version performed better than the multiple threshold version of GMYC, and PTP showed higher efficiency than mPTP in delimiting species. Additionally, GMYC was found to be significantly influenced by taxonomic rank, showing poorer efficiency in datasets at the genus level than at higher levels. Finally, our results highlighted that cryptic diversity within Trochoidea (Mollusca: Vetigastropoda) might be underestimated, which provides quantitative evidence for excavating the cryptic lineages of these species.
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Affiliation(s)
- Bingyu Guo
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China
- Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
- Correspondence:
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25
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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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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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Othman SN, Shin Y, Kim HT, Chuang MF, Bae Y, Hoti J, Zhang Y, Jang Y, Borzée A. Evaluating the efficiency of popular species identification analytical methods, and integrative workflow using morphometry and barcoding bioinformatics for taxonomy and origin of traded cryptic brown frogs. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
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Pinochet R, Pardo LM, Cárdenas L. Assessing diversity of King Crab
Lithodes
spp. in the south‐eastern pacific using phylogeny and molecular species delimitation methods. Ecol Evol 2022; 12:e9143. [PMID: 35923941 PMCID: PMC9339758 DOI: 10.1002/ece3.9143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 11/08/2022] Open
Abstract
The purpose of this study was to test the hypothesis that the genetic diversity of commercially significant species of King Crabs (Lithodes spp.) along the south‐eastern Pacific (SEP) comprises different independent evolutionary units (IEUs) with spatially isolated distribution. Nine localities from inner and open waters along the SEP Chilean coast (39°S‐55°S) were sampled. We analyzed sequences from 173 individuals for the mitochondrial gene Cytochrome oxidase I (COX‐I), 151 individuals for the Internal Transcribed Spacer 1 (ITS) and 135 for the structural ribosomal RNA (28S). Genetic delimitation was performed through three analytical methods: ABGD, GMYC, and its Bayesian implementation, bGMYC. Bayesian phylogenetic analyses and haplotype networks were also performed. Divergence time between clades was assessed for the COX‐I marker and estimated from known evolutionary rates for this marker in other crustacean species and fossil calibration from other Anomuran species. Delimitation analyses, phylogenetic analyses, and mitochondrial haplotype networks suggested the presence of two deeply divergent mitochondrial lineages of Lithodes in the SEP, referred to as Clade1 and Clade 2. Nuclear markers showed low phylogenetic resolution and therefore were unsuitable for molecular species delimitation. Divergence time analysis of the mitochondrial lineages suggests a separation between Clades of approximately 2.3 Mya. The divergence time obtained suggested that Pliocene glaciations and deglaciations cycles could be involved in hybridization events between Lithodes IEUs at southern tip of South American coasts. The different frequencies of Lithodes haplotypes in inner and open water environments along SEP coasts could be explained by events such as the last glacial maximum or by differences in the adaptation of each clade to different environments. These findings support the necessity of evaluating the taxonomic status of Lithodes individuals found along SEP coasts under an integrative taxonomy approach or through markers with other evolution rates than those already used.
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Affiliation(s)
- Ramona Pinochet
- Programa de Doctorado en Biología Marina, Facultad de Ciencias Universidad Austral de Chile Valdivia Chile
- Centro de Investigación de Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) Valdivia Chile
| | - Luis Miguel Pardo
- Centro de Investigación de Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) Valdivia Chile
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias Universidad Austral de Chile Valdivia Chile
| | - Leyla Cárdenas
- Centro de Investigación de Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) Valdivia Chile
- Instituto de Ciencias ambientales y evolutivas, Facultad de Ciencias Universidad Austral de Chile Valdivia Chile
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Lozano AP, Lasso-Alcalá OM, Bittencourt PS, Taphorn DC, Perez N, Farias IP. A new species of Astronotus (Teleostei, Cichlidae) from the Orinoco River and Gulf of Paria basins, northern South America. Zookeys 2022; 1113:111-152. [PMID: 36762228 PMCID: PMC9848875 DOI: 10.3897/zookeys.1113.81240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/15/2022] [Indexed: 11/12/2022] Open
Abstract
Based on morphological and molecular analysis of Astronotus species, a new species is described from the Orinoco River and Gulf of Paria basins in Venezuela and Colombia. Morphologically, it differs from Astronotuscrassipinnis and Astronotusocellatus in pre-orbital depth, caudal peduncle depth, head width, and caudal peduncle length, with significant differences in average percentage values. Osteologically, it differs from the two described species by lacking a hypurapophysis on the parahypural bone (hypural complex) and having two or three supraneural bones. Another characteristic that helps diagnose the new species is the morphology of the sagitta otolith, which is oval with crenulated dorsal and ventral margins and a rounded posterior edge. Genetically, the new species is distinct from all the other lineages previously proposed for the genus, delimited by five single locus species delimitation methods, and also has unique diagnostic nucleotides. Phylogenetic analyses support the monophyly of the new species as well as all other species/lineages. Astronotus species have considerable genetic, anatomical, and sagitta otolith shape differences, but have few significant traditional morphometric and meristic differences, because there is high variability in counts of spines, soft dorsal-fin rays, and lateral-line scales. It is clear that this new species is genetically and anatomically differentiated from all other species within the genus, and deserves recognition as a new valid species.
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Affiliation(s)
- Alfredo Perez Lozano
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Alagoas (UFAL), Maceió, BrazilUniversidade Federal de AlagoasMaceióBrazil
| | - Oscar M. Lasso-Alcalá
- Museo de Historia Natural La Salle, Fundación La Salle de Ciencias Naturales (MHNLS), Caracas, VenezuelaMuseo de Historia Natural La SalleCaracasVenezuela
| | - Pedro S. Bittencourt
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas (UFAM), Manaus, BrazilUniversidade Federal do AmazonasManausBrazil
| | - Donald C. Taphorn
- BioCentro, Universidad Nacional Experimental de los Llanos Occidentales Ezequiel Zamora (UNELLEZ), Guanare, Portuguesa, VenezuelaUniversidad Nacional Experimental de los Llanos Occidentales Ezequiel ZamoraGuanareVenezuela
| | - Nayibe Perez
- BioCentro, Universidad Nacional Experimental de los Llanos Occidentales Ezequiel Zamora (UNELLEZ), Guanare, Portuguesa, VenezuelaUniversidad Nacional Experimental de los Llanos Occidentales Ezequiel ZamoraGuanareVenezuela
| | - Izeni Pires Farias
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas (UFAM), Manaus, BrazilUniversidade Federal do AmazonasManausBrazil
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Main DC, van Vuuren BJ, Tilbury CR, Tolley KA. Out of southern Africa: Origins and cryptic speciation in Chamaeleo, the most widespread chameleon genus. Mol Phylogenet Evol 2022; 175:107578. [PMID: 35809854 DOI: 10.1016/j.ympev.2022.107578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/18/2022] [Accepted: 07/01/2022] [Indexed: 11/19/2022]
Abstract
Molecular phylogenetics and the application of species delimitation methods have proven useful in addressing limitations associated with morphology based taxonomy and have highlighted the inconsistencies in the current taxonomy for many groups. For example, the genus Chamaeleo, which comprises 14 species with large distributions across mainland Africa and parts of Eurasia, exhibits relatively minor phenotypic differentiation between species, leading to speculation regarding the presence of cryptic diversity in the genus. Therefore, the aims of the present study were to construct a robust and comprehensive phylogeny of the genus and highlight potential species-level cryptic diversity. Additionally, we sought to ascertain the most likely biogeographic origin of the genus and understand its spatio-temporal diversification. Accordingly, we made use of species delimitation methods (Bayesian and divergence based) to investigate the extent of cryptic diversity in Chamaeleo, and applied an ancestral area reconstruction to examine the biogeographic origin of the group. Our phylogenetic analyses suggested the presence of at least 18 taxa within Chamaeleo. Notably, three taxa could be recognised within C. dilepis, none of which are equivalent in context with any of the currently described subspecies. There were also three taxa within C. gracilis and two within C. anchietae. The single available tissue specimen identified as C. necasi was embedded within the C. gracilis clade. Our ancestral area reconstruction points to a southern African/Zambezian origin for Chamaeleo, with diversification beginning during the cooling and aridification of Africa that characterised the Oligocene Epoch, ca. 34-23 Mya (Million years ago). Species-level diversification began in the Miocene Epoch (ca. 23-5 Mya), possibly tracking the aridification that triggered the shift from forest to more open, mesic savanna for most clades, but with tectonic events influencing speciation in a Palearctic clade. These findings lay the foundation for a future integrative taxonomic re-evaluation of Chamaeleo, which will be supported with additional lines of evidence before implementing any taxonomic changes.
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Affiliation(s)
- Devon C Main
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa
| | - Colin R Tilbury
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, South Africa
| | - Krystal A Tolley
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, 2006 Johannesburg, South Africa; South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7 Claremont, Cape Town, South Africa.
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Pfingstl T, Schäffer S, Bardel-Kahr I, Baumann J. A closer look reveals hidden diversity in the intertidal Caribbean Fortuyniidae (Acari, Oribatida). PLoS One 2022; 17:e0268964. [PMID: 35704591 PMCID: PMC9200316 DOI: 10.1371/journal.pone.0268964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 05/10/2022] [Indexed: 11/19/2022] Open
Abstract
A molecular genetic and morphometric investigation revealed the supposedly widespread Caribbean and Western Atlantic intertidal oribatid mite species Fortuynia atlantica to comprise at least two different species. Although there are no distinct morphological differences separating these taxa, COI and 18S sequence divergence data, as well as different species delimitation analyses, clearly identify the two species. Fortuynia atlantica is distributed in the northern Caribbean and the Western Atlantic and the new Fortuynia antillea sp. nov. is presently endemic to Barbados. Vicariance is supposed to be responsible for their genetic diversification and stabilizing selection caused by the extreme intertidal environment is suggested to be the reason for the found morphological stasis. The genetic structure of Fortuynia atlantica indicates that Bermudian populations are derived from the northern Caribbean and thus support the theory of dispersal by drifting on the Gulf Stream. Haplotype network data suggest that Bermudian and Bahamian populations were largely shaped by colonization, expansion and extinction events caused by dramatic sea level changes during the Pleistocene. A preliminary phylogenetic analysis based on 18S gene sequences indicates that the globally distributed genus Fortuynia may be a monophyletic group, whereas Caribbean and Western Atlantic members are distinctly separated from the Indo-Pacific and Western Pacific species.
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Affiliation(s)
- Tobias Pfingstl
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
- * E-mail:
| | - Sylvia Schäffer
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
| | - Iris Bardel-Kahr
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
| | - Julia Baumann
- Institute of Biology, Karl-Franzens University of Graz, Graz, Austria
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Chang JT, Chao CT, Nakamura K, Liu HL, Luo MX, Liao PC. Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data. FRONTIERS IN PLANT SCIENCE 2022; 13:824158. [PMID: 35615129 PMCID: PMC9125193 DOI: 10.3389/fpls.2022.824158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The divergence process of incipient species is fascinating but elusive by incomplete lineage sorting or gene flow. Species delimitation is also challenging among those morphologically similar allopatric species, especially when lacking comprehensive data. Cycas sect. Asiorientales, comprised of C. taitungensis and C. revoluta in the Ryukyu Archipelago and Taiwan, diverged recently with continuous gene flow, resulting in a reciprocal paraphyletic relationship. Their previous evolutionary inferences are questioned from few genetic markers, incomplete sampling, and incomprehensive morphological comparison by a long-term taxonomic misconception. By whole range sampling, this study tests the geographic mode of speciation in the two species of Asiorientales by approximate Bayesian computation (ABC) using genome-wide single nucleotide polymorphisms (SNPs). The individual tree was reconstructed to delimit the species and track the gene-flow trajectory. With the comparison of diagnostic morphological traits and genetic data, the allopatric speciation was rejected. Alternatively, continuous but spatially heterogeneous gene flow driven by transoceanic vegetative dispersal and pollen flow with contrasting population sizes blurred their species boundary. On the basis of morphological, genetic, and evolutionary evidence, we synonymized these two Cycas species. This study highlights not only the importance of the Kuroshio Current to species evolution but also the disadvantage of using species with geographically structured genealogies as conservation units.
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Affiliation(s)
- Jui-Tse Chang
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Chien-Ti Chao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Koh Nakamura
- Botanic Garden, Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Hsiao-Lei Liu
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
| | - Min-Xin Luo
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Pei-Chun Liao
- School of Life Science, National Taiwan Normal University, Taipei, Taiwan
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Gregorio Martínez J, David Rangel-Medrano J, Johanna Yepes-Acevedo A, Restrepo-Escobar N, Judith Márquez E. Species limits and introgression in Pimelodus from the Magdalena-Cauca River basin. Mol Phylogenet Evol 2022; 173:107517. [DOI: 10.1016/j.ympev.2022.107517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 03/20/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022]
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Cruz DD, Arellano E. Molecular data confirm Triatoma pallidipennis Stål, 1872 (Hemiptera: Reduviidae: Triatominae) as a novel cryptic species complex. Acta Trop 2022; 229:106382. [PMID: 35189124 DOI: 10.1016/j.actatropica.2022.106382] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/17/2022] [Accepted: 02/17/2022] [Indexed: 12/11/2022]
Abstract
Triatoma pallidipennis constitues one of the most important Chagas disease vector in Mexico. Previous studies based on molecular data suggest T. pallidipennis as a complex of cryptic species. For that reason, we analyzed the phylogenetic relationships of T. pallidipennis using DNA sequences from the mitochondrial ND4 gene and the ITS-2 gene. In addition, the divergence times were estimated, and possible new taxa were delimited with three species delimitation methods. Finally, genetic distances and possible connectivity routes based on shared haplotypes were obtained among the T. pallidipennis populations. Five haplogroups (possible cryptic species) were found, based on delimitation methods and genetic distances. Haplogroup divergence began about 3 Ma, in the Pleistocene. Moreover, none of the haplogroups showed potential connectivity routes between them, evidencing lack of gene flow. Our results suggest the existence of a new cryptic species complex within what is currently recognized as a T. pallidipennis.
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Affiliation(s)
- Daryl D Cruz
- Centro de Investigación en Biodiversidad y Conservación (CIByC), UAEM, Cuernavaca, Morelos, Mexico
| | - Elizabeth Arellano
- Centro de Investigación en Biodiversidad y Conservación (CIByC), UAEM, Cuernavaca, Morelos, Mexico.
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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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Coelho FEA, Camurugi F, Marques R, Magalhães FDM, Werneck FP, Garda AA. Historical connections between Atlantic Forest and Amazonia drove genetic and ecological diversity in Lithobates palmipes (Anura, Ranidae). SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2046657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Felipe Eduardo Alves Coelho
- Programa de Pós-Graduação em Ecologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Avenida Senador Salgado Filho, S/N, Lagoa Nova, Natal 59078-900, RN, Brazil
| | - Felipe Camurugi
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Avenida Senador Salgado Filho, S/N, Lagoa Nova, Natal 59078-900, RN, Brazil
| | - Ricardo Marques
- Programa de Pós-Graduação em Ciências Biológicas (Zoologia, Universidade Federal da Paraíba, Centro de Ciências Exatas e da Natureza, Departamento de Sistemática e Ecologia, Campus I – Cidade Universitaria, S/N, Cidade Universitária, João Pessoa 58051-900, Paraíba, Brasil
| | - Felipe De Medeiros Magalhães
- Programa de Pós-Graduação em Ciências Biológicas (Zoologia, Universidade Federal da Paraíba, Centro de Ciências Exatas e da Natureza, Departamento de Sistemática e Ecologia, Campus I – Cidade Universitaria, S/N, Cidade Universitária, João Pessoa 58051-900, Paraíba, Brasil
- Earth and Environmental Sciences, Ecology and Evolution, Rutgers University-Newark, 195 University Ave, Newark 07102, New Jersey NJ, USA
| | - Fernanda P. Werneck
- Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo 2936, Aleixo, Manaus 69067-375, Amazonas, Brazil
| | - Adrian Antonio Garda
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Centro de Biociências, Avenida Senador Salgado Filho, S/N, Lagoa Nova, Natal 59078-900, RN, Brazil
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Dissecting a Geographical Colourful Tapestry: Phylogeography of the Colour Polymorphic Spider Gasteracantha cancriformis. J ZOOL SYST EVOL RES 2022. [DOI: 10.1155/2022/8112945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Species with large distributions provide unique opportunities to test how geography has influenced biotic diversification. In this work, we aimed to explore the effect of geographic barriers on the distribution of the phenotypic and genetic variation of a spider species that is widespread in continental and insular America. We obtained an alignment of the mitochondrial locus Cytochrome Oxidase I (COI) for 408 individuals across the geographic range of Gasteracantha cancriformis. We used phylogenetics, population genetics, and morphology to explore the genetic and phenotypic variation of this species. We found five genetically differentiated and geographically structured populations. Three of them are distributed in continental America, separated by the Andes mountains, and two are in the Caribbean and Galapagos Islands. Some of these geographic clades shared haplotypes between them, which may be a consequence of dispersal. We detected at least 20 phenotypes of G. cancriformis, some of which were exclusive to a geographic region, while others occurred in multiple regions. We did not observe well-defined morphological differences across male genitalia. This evidence suggests that G. cancriformis is a widespread species with high phenotypic variation that should be explored in more depth.
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Malleret MM, Freire MD, Lemes P, Brum FT, Camargo A, Verrastro L. Phylogeography and species delimitation of the Neotropical frog complex (Hylidae:
Scinax granulatus
). ZOOL SCR 2022. [DOI: 10.1111/zsc.12537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matías M. Malleret
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Marcelo D. Freire
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
| | - Priscila Lemes
- Laboratório de Ecologia e Conservação Departamento de Botânica e Ecologia, Insituto de Biociências, Universidade Federal do Mato Grosso Cuiabá Mato Grosso Brazil
| | - Fernanda T. Brum
- Programa de Pós‐graduação em Ecologia e Conservação Universidade Federal do Paraná Curitiba Paraná Brazil
| | - Arley Camargo
- Laboratorio de Biogeografía y Evolución Programa de Desarrollo Universitario, Centro Universitario Regional Noreste, Universidad de la República Rivera Uruguay
| | - Laura Verrastro
- Laboratório de Herpetologia Programa de Pós‐graduação em Biologia Animal Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Rio Grande do Sul Brazil
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Tolley KA, Tilbury CR, Burger M. Convergence and vicariance: speciation of chameleons in the Cape Fold Mountains, South Africa, and the description of three new species of Bradypodion Fitzinger, 1843. AFR J HERPETOL 2022. [DOI: 10.1080/21564574.2021.1998236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Krystal A Tolley
- South African National Biodiversity Institute, Claremont, Cape Town, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Auckland Park, Johannesburg, South Africa
| | - Colin R Tilbury
- Department of Botany and Zoology, University of Stellenbosch, Matieland, South Africa
| | - Marius Burger
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
- Flora Fauna & Man, Ecological Services Ltd., Tortola, British Virgin Islands
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Delicado D, Hauffe T. Shell features and anatomy of the springsnail genus Radomaniola (Caenogastropoda: Hydrobiidae) show a different pace and mode of evolution over five million years. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
Shell features are key factors for systematics and evolutionary biology studies of freshwater gastropods. Based mostly on shell morphology, 19 species of the springsnail genus Radomaniola (family Hydrobiidae) have been described. Although the scarce differentiation of various shell dimensions suggests morphological stasis, the evolutionary dynamics of shell and other anatomical structures have not yet been explored fully. By inferring a phylogeny and a time-calibrated species tree from mitochondrial (COI and 16S) and nuclear (28S) sequences of 15 recognized species, we initially examine the species diversity of the Radomaniola dataset and then, through phylogenetic comparative methods, assess the evolutionary correlation, pace and mode of 40 continuous shell and anatomical characters. By synthesizing the results of four species delimitation methods and through morphological examinations, we recognize 21 groups, for which taxonomy is discussed here. Seven new species are described. We reveal a high degree of correlated evolution between characters of the shell, which are constrained by a single morphological optimum, consistent with the morphological stasis model. Anatomical traits diverged rapidly in an unconstrained manner or toward multiple optima. These findings indicate that in order to understand the morphological evolution of springsnails, it is essential to examine different organs in detail.
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Affiliation(s)
- Diana Delicado
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32 IFZ, D-35392, Giessen, Germany
| | - Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
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Multiple Recent Colonizations of the Australian Region by the Chydorus sphaericus Group (Crustacea: Cladocera). WATER 2022. [DOI: 10.3390/w14040594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Biotic introductions are an ongoing disruption for many ecosystems. For passively dispersed freshwater zooplankton, transcontinental introductions have been common but are poorly studied in the southern hemisphere. Here we assess the hypothesis of recent introduction for populations of the Chydorus sphaericus group (Crustacea: Cladocera) in Australia. We analyzed 254 sequences (63 original sequences) from the cytochrome oxidase I region of mitochondrial DNA of Chydorus sp., which included global representation. Three Australian populations were connected with separate clades in the northern hemisphere, suggesting multiple colonization events for Australia. The timescale of the divergences was consistent with recent (Quaternary) dispersal. As Australian populations are exposed to migrating birds from the northern hemisphere, both avian and anthropogenic sources are candidates for dispersal vectors. We concluded that recent cross-hemisphere dispersal in the Chydorus sphaericus group is more common than previously believed.
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Fassio G, Bouchet P, Oliverio M, Strong EE. Re-evaluating the case for poecilogony in the gastropod Planaxis sulcatus (Cerithioidea, Planaxidae). BMC Ecol Evol 2022; 22:13. [PMID: 35130841 PMCID: PMC8822645 DOI: 10.1186/s12862-022-01961-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022] Open
Abstract
Background Planaxis sulcatus has been touted as a textbook example of poecilogony, with members of this wide-ranging Indo-Pacific marine gastropod said to produce free-swimming veligers as well as brooded juveniles. A recent paper by Wiggering et al. (BMC Evol Biol 20:76, 2020) assessed a mitochondrial gene phylogeny based on partial COI and 16S rRNA sequences for 31 individuals supplemented by observations from the brood pouch of 64 mostly unsequenced individuals. ABGD and bGYMC supported three reciprocally monophyletic clades, with two distributed in the Indo-Pacific, and one restricted to the northern Indian Ocean and Red Sea. Given an apparent lack of correlation between clade membership and morphological differentiation or mode of development, the reported 3.08% maximum K2P model-corrected genetic divergence in COI among all specimens was concluded to represent population structuring. Hence, the hypothesis that phylogenetic structure is evidence of cryptic species was rejected and P. sulcatus was concluded to represent a case of geographic poecilogony. Results Our goal was to reassess the case for poecilogony in Planaxis sulcatus with a larger molecular dataset and expanded geographic coverage. We sequenced an additional 55 individuals and included published and unpublished sequence data from other sources, including from Wiggering et al. Our dataset comprised 108 individuals (88 COI, 81 16S rRNA) and included nine countries unrepresented in the previous study. The expanded molecular dataset yielded a maximum K2P model-corrected genetic divergence among all sequenced specimens of 12.09%. The value of 3.08% erroneously reported by Wiggering et al. is the prior maximal distance value that yields a single-species partition in ABGD, and not the maximum K2P intraspecific divergence that can be calculated for the dataset. The bGMYC analysis recognized between two and six subdivisions, while the best-scoring ASAP partitions recognized two, four, or five subdivisions, not all of which were robustly supported in Bayesian and maximum likelihood phylogenetic analyses of the concatenated and single gene datasets. These hypotheses yielded maximum intra-clade genetic distances in COI of 2.56–6.19%, which are more consistent with hypothesized species-level thresholds for marine caenogastropods. Conclusions Based on our analyses of a more comprehensive dataset, we conclude that the evidence marshalled by Wiggering et al. in support of Planaxis sulcatus comprising a single widespread, highly variable species with geographic poecilogony is unconvincing and requires further investigation in an integrative taxonomic framework. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-01961-7.
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Martínez-Borrego D, Arellano E, González-Cózatl FX, Castro-Arellano I, León-Paniagua L, Rogers DS. Molecular systematics of the Reithrodontomys tenuirostris group (Rodentia: Cricetidae) highlighting the Reithrodontomys microdon species complex. J Mammal 2022; 103:29-44. [PMID: 35087329 PMCID: PMC8789765 DOI: 10.1093/jmammal/gyab133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 10/23/2021] [Indexed: 11/13/2022] Open
Abstract
The Reithrodontomys tenuirostris species group is considered "the most specialized" within the genus Reithrodontomys from morphological and ecological perspectives. Previous studies based on molecular data recommended changes in the taxonomy of the group. In particular, R. microdon has been the most taxonomically questioned, with the suggestion that it constitutes a complex of cryptic species. We analyzed the phylogenetic relationships of the R. tenuirostris species group using DNA sequences from the mitochondrial Cytochrome b gene and Intron 7 of the nuclear beta fibrinogen gene. In addition, divergence times were estimated, and possible new taxa delimited with three widely used species delimitation methods. Finally, possible connectivity routes based on shared haplotypes were tested among the R. microdon populations. All species were recovered as monophyletic with the exception of R. microdon, whose individuals were grouped into four different haplogroups, one of which included specimens of R. bakeri. Diversification within the R. tenuirostris species group began about 3 Ma, in the Pleistocene. The bGMYC and STACEY delimitation methods were congruent with each other, delimiting at the species-level each haplogroup within R. microdon, while the mPTP suggested a greater number of species. Moreover, none of the haplogroups showed potential connectivity routes between them, evidencing lack of gene flow. Our results suggest the existence of a higher number of species in the R. tenuirostris group, because we show that there are four species within what is currently recognized as R. microdon.
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Affiliation(s)
- Daily Martínez-Borrego
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad, Chamilpa, Cuernavaca, Morelos, México
| | - Elizabeth Arellano
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad, Chamilpa, Cuernavaca, Morelos, México
| | - Francisco X González-Cózatl
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Avenida Universidad, Chamilpa, Cuernavaca, Morelos, México
| | | | - Livia León-Paniagua
- Colección de Mamíferos – Museo de Zoología “Alfonso L. Herrera”, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
| | - Duke S Rogers
- Department of Biology and Monte L Bean Life Science Museum, Brigham Young University, Provo, UT, USA
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Barbo FE, Booker WW, Duarte MR, Chaluppe B, Portes-Junior JA, Franco FL, Grazziotin FG. Speciation process on Brazilian continental islands, with the description of a new insular lancehead of the genus Bothrops (Serpentes, Viperidae). SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2021.2017059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Fausto E. Barbo
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - William W. Booker
- Department of Biological Sciences, Florida State University, 319 Stadium Drive, Tallahassee, 32306 FL, USA
| | - Marcelo R. Duarte
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - Betina Chaluppe
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - José A. Portes-Junior
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - Francisco L. Franco
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
| | - Felipe G. Grazziotin
- Laboratório de Coleções Zoológicas – LCZ, Instituto Butantan, Avenida Vital Brazil, 1500, São Paulo, 05503-900 SP, Brazil
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45
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Quiroga-Carmona M, Abud C, Lessa EP, D’Elía G. The Mitochondrial Genetic Diversity of the Olive Field Mouse Abrothrix olivacea (Cricetidae; Abrotrichini) is Latitudinally Structured Across Its Geographic Distribution. J MAMM EVOL 2022. [DOI: 10.1007/s10914-021-09582-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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47
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Ximenes AM, Bittencourt PS, Machado VN, Hrbek T, Farias IP. Mapping the hidden diversity of the Geophagus sensu stricto species group (Cichlidae: Geophagini) from the Amazon basin. PeerJ 2021; 9:e12443. [PMID: 34909270 PMCID: PMC8641480 DOI: 10.7717/peerj.12443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/15/2021] [Indexed: 11/20/2022] Open
Abstract
South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and from DNA-based inventories which consistently identify large numbers of divergent lineages within even well-studied species groups. In the present study, we investigated lineage diversity within the Geophagus sensu stricto species group. To achieve these objectives, we analyzed 337 individuals sampled from 77 locations within and outside the Amazon basin representing 10 nominal and six morphologically distinct but undescribed species. We sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and delimited lineages using four different single-locus species discovery methods (mPTP-15 lineages; LocMin-14 lineages; bGMYC-18 lineages; and GMYC-30 lineages). The six morphologically distinct but undescribed species were also delimited by the majority of the species discovery methods. Five of these lineages are restricted to a single collection site or a watershed and their habitats are threatened by human activities such as deforestation, agricultural activities and construction of hydroelectric plants. Our results also highlight the importance of combining DNA and morphological data in biodiversity assessment studies especially in taxonomically diverse tropical biotas.
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Affiliation(s)
- Aline Mourão Ximenes
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil.,Programa de Pós-Graduação em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Pedro Senna Bittencourt
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Valéria Nogueira Machado
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | - Tomas Hrbek
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil.,Biology Department, Trinity University, San Antonio, Texas, USA
| | - Izeni Pires Farias
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
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48
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Anjos MDS, Jardim de Queiroz L, Penido IDS, Bitencourt JDA, Barreto SB, Sarmento‐Soares LM, Batalha‐Filho H, Affonso PRADM. A taxonomically complex catfish group from an underrepresented geographic area: Systematics and species limits in
Hypostomus
Lacépède, 1803 (Siluriformes, Loricariidae) from Eastern South America. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Luiz Jardim de Queiroz
- Department of Fish Ecology and Evolution Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf Switzerland
| | - Iago de Souza Penido
- Programa de Pós‐Graduação em Biologia Comparada Universidade Estadual de Maringá Maringá Brazil
| | | | - Silvia Britto Barreto
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT INTREE) Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
| | | | - Henrique Batalha‐Filho
- Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT INTREE) Instituto de Biologia Universidade Federal da Bahia Salvador Brazil
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49
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Tolley KA, Telford NS, Taft JM, Bates MF, Conradie W, Makhubo BG, Alexander GJ. Taxonomic inflation due to inadequate sampling: are girdled lizards (Cordylus minor species complex) from the Great Karoo one and the same? Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The Great Karoo and Namaqualand of South Africa are home to a species complex of morphologically conserved lizards that occur in allopatry (Karoo: Cordylus aridus, Cordylus cloetei, Cordylus minor; Namaqualand: Cordylus imkeae). However, there are negligible morphological differences and a lack of obvious physical or climatic barriers, particularly among the three Karoo species. We hypothesized that poor geographic coverage in previous studies and lack of an explicit species concept has caused taxonomic inflation. We therefore tested species boundaries by examining multiple criteria: multi-gene phylogenetics, niche distribution modelling and re-examination of diagnostic morphological features with a larger sample size. We found that C. aridus, C. cloetei and C. minor lack diagnosable differences for both genetics and morphology. Distribution modelling, ranging from present day to the last interglacial period, show connectivity has been maintained especially during cooler periods. Conversely, C. imkeae is morphologically diagnosable, genetically distinct and lacks connectivity with the other taxa. By evaluating multiple operational criteria, we conclude that the C. minor species complex comprises only two species, C. minor (with C. aridus and C. cloetei as junior synonyms) and C. imkeae, demonstrating that species defined from inadequate data and lack of an explicit species concept can lead to taxonomic inflation.
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Affiliation(s)
- Krystal A Tolley
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicolas S Telford
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa
| | - Jody M Taft
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont 7735, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michael F Bates
- Division of Herpetology, Department of Animal and Plant Systematics, National Museum, Bloemfontein, South Africa
- Department of Zoology & Entomology, University of the Free State, Bloemfontein, South Africa
| | - Werner Conradie
- Port Elizabeth Museum (Bayworld), Gqeberha, South Africa
- Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Buyisile G Makhubo
- Division of Herpetology, Department of Animal and Plant Systematics, National Museum, Bloemfontein, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Graham J Alexander
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
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50
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Paulus E, Brix S, Siebert A, Martínez Arbizu P, Rossel S, Peters J, Svavarsson J, Schwentner M. Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics. Mol Ecol 2021; 31:313-330. [PMID: 34676606 DOI: 10.1111/mec.16234] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 02/06/2023]
Abstract
The crustacean marine isopod species Haploniscus bicuspis (Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using confocal laser scanning microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the GIF Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably instead refer to different male developmental stages.
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Affiliation(s)
- Eva Paulus
- University of Groningen, Groningen, The Netherlands.,Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Hamburg, Germany
| | - Saskia Brix
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Hamburg, Germany
| | - Annabelle Siebert
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Hamburg, Germany.,Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Sven Rossel
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Janna Peters
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Jörundur Svavarsson
- Department of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Martin Schwentner
- Center of Natural History (CeNak), Universität Hamburg, Hamburg, Germany.,Naturhistorisches Museum Wien, Vienna, Austria
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