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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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Ji BY, Guo TY, Gu MC, Ren GD, Li XM. Description of five larvae of the genus Gnaptorina Reitter, 1887 from Xizang, China (Coleoptera, Tenebrionidae, Blaptinae), with molecular species delimitation and diagnoses. Zookeys 2024; 1209:295-314. [PMID: 39175828 PMCID: PMC11339538 DOI: 10.3897/zookeys.1209.124184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 07/09/2024] [Indexed: 08/24/2024] Open
Abstract
With 39 described species in three subgenera, the Gnaptorina is the second most species-rich genus in the subtribe Gnaptorinina (Tenebrionidae: Blaptinae). In this study, a phylogeny of Gnaptorina was reconstructed based on one nuclear (28S-D2) and three mitochondrial (COI, Cytb, and 16S) gene fragments; multiple molecular species delimitation approaches were also implemented to assess the taxonomic status of larval specimens based on COI gene fragment. Larvae of five known species of the subgenus Hesperoptorina are described and illustrated for the first time: Gnaptorinanigera Shi, Ren & Merkl, 2007, Gnaptorinatishkovi Medvedev, 1998, Gnaptorinabrucei Blair, 1923, Gnaptorinahimalaya Shi, Ren & Merkl, 2007, Gnaptorinakangmar Shi, Ren & Merkl, 2007. A key to larvae of four genera of the tribe Blaptini and a key to the known larvae of the genus Gnaptorina are provided. This study provides valuable morphological data for larval studies of the tribe Blaptini.
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Affiliation(s)
- Bao-Yue Ji
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, ChinaHebei UniversityBaodingChina
| | - Tong-Yang Guo
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, ChinaHebei UniversityBaodingChina
| | - Mei-Chang Gu
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, ChinaHebei UniversityBaodingChina
| | - Guo-Dong Ren
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, ChinaHebei UniversityBaodingChina
| | - Xiu-Min Li
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, ChinaHebei UniversityBaodingChina
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Blázquez M, Pérez-Vargas I, Garrido-Benavent I, Villar-dePablo M, Turégano Y, Frías-López C, Sánchez-Gracia A, de los Ríos A, Gasulla F, Pérez-Ortega S. Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group ( Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group. PERSOONIA 2024; 52:44-93. [PMID: 39161630 PMCID: PMC11319839 DOI: 10.3767/persoonia.2024.52.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/08/2023] [Accepted: 11/15/2023] [Indexed: 08/21/2024]
Abstract
Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi. Citation: Blázquez M, Pérez-Vargas I, Garrido-Benavent I, et al. 2024. Endless forms most frustrating: disentangling species boundaries in the Ramalina decipiens group (Lecanoromycetes, Ascomycota), with the description of six new species and a key to the group. Persoonia 52: 44-93. https://doi.org/10.3767/persoonia.2024.52.03 .
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Affiliation(s)
- M. Blázquez
- Department of Mycology, Real Jardín Botánico (CSIC), Madrid, Spain
| | - I. Pérez-Vargas
- Department of Botany, Ecology and Plant Physiology, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - I. Garrido-Benavent
- Departament de Botànica i Geologia, Facultat de Ciències Biològiques, Universitat de València (UV), València, Spain
| | - M. Villar-dePablo
- Department of Microbial Ecology and Geomicrobiology, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | - Y. Turégano
- Department of Mycology, Real Jardín Botánico (CSIC), Madrid, Spain
| | - C. Frías-López
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - A. Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - A. de los Ríos
- Department of Microbial Ecology and Geomicrobiology, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | - F. Gasulla
- Department of Life Sciences, Universidad de Alcalá, Alcalá de Henares, Spain
| | - S. Pérez-Ortega
- Department of Mycology, Real Jardín Botánico (CSIC), Madrid, Spain
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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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Xu WT, Lu XY, Wang Y, Li MH, Hu K, Shen ZJ, Sun XQ, Zhang YM. A Lateral Flow-Recombinase Polymerase Amplification Method for Colletotrichum gloeosporioides Detection. J Fungi (Basel) 2024; 10:315. [PMID: 38786670 PMCID: PMC11121841 DOI: 10.3390/jof10050315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
The greater yam (Dioscorea alata), a widely cultivated and nutritious food crop, suffers from widespread yield reduction due to anthracnose caused by Colletotrichum gloeosporioides. Latent infection often occurs before anthracnose phenotypes can be detected, making early prevention difficult and causing significant harm to agricultural production. Through comparative genomic analysis of 60 genomes of 38 species from the Colletotrichum genus, this study identified 17 orthologous gene groups (orthogroups) that were shared by all investigated C. gloeosporioides strains but absent from all other Colletotrichum species. Four of the 17 C. gloeosporioides-specific orthogroups were used as molecular markers for PCR primer designation and C. gloeosporioides detection. All of them can specifically detect C. gloeosporioides out of microbes within and beyond the Colletotrichum genus with different sensitivities. To establish a rapid, portable, and operable anthracnose diagnostic method suitable for field use, specific recombinase polymerase amplification (RPA) primer probe combinations were designed, and a lateral flow (LF)-RPA detection kit for C. gloeosporioides was developed, with the sensitivity reaching the picogram (pg) level. In conclusion, this study identified C. gloeosporioides-specific molecular markers and developed an efficient method for C. gloeosporioides detection, which can be applied to the prevention and control of yam anthracnose as well as anthracnose caused by C. gloeosporioides in other crops. The strategy adopted by this study also serves as a reference for the identification of molecular markers and diagnosis of other plant pathogens.
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Affiliation(s)
- Wei-Teng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (W.-T.X.); (X.-Y.L.); (Y.W.); (M.-H.L.); (K.H.); (Z.-J.S.); (X.-Q.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing 210014, China
| | - Xin-Yu Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (W.-T.X.); (X.-Y.L.); (Y.W.); (M.-H.L.); (K.H.); (Z.-J.S.); (X.-Q.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing 210014, China
| | - Yue Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (W.-T.X.); (X.-Y.L.); (Y.W.); (M.-H.L.); (K.H.); (Z.-J.S.); (X.-Q.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing 210014, China
| | - Ming-Han Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (W.-T.X.); (X.-Y.L.); (Y.W.); (M.-H.L.); (K.H.); (Z.-J.S.); (X.-Q.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing 210014, China
| | - Ke Hu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (W.-T.X.); (X.-Y.L.); (Y.W.); (M.-H.L.); (K.H.); (Z.-J.S.); (X.-Q.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing 210014, China
| | - Zi-Jie Shen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (W.-T.X.); (X.-Y.L.); (Y.W.); (M.-H.L.); (K.H.); (Z.-J.S.); (X.-Q.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing 210014, China
| | - Xiao-Qin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (W.-T.X.); (X.-Y.L.); (Y.W.); (M.-H.L.); (K.H.); (Z.-J.S.); (X.-Q.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing 210014, China
| | - Yan-Mei Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (W.-T.X.); (X.-Y.L.); (Y.W.); (M.-H.L.); (K.H.); (Z.-J.S.); (X.-Q.S.)
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China
- Jiangsu Provincial Science and Technology Resources Coordination Platform (Agricultural Germplasm Resources) Germplasm Resources Nursery of Medicinal Plants, Nanjing 210014, China
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Trewick SA, Koot EM, Morgan-Richards M. Ngāokeoke Aotearoa: The Peripatoides Onychophora of New Zealand. INSECTS 2024; 15:248. [PMID: 38667378 PMCID: PMC11050097 DOI: 10.3390/insects15040248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024]
Abstract
(1) Background: Originally described as a single taxon, Peripatoides novaezealandiae (Hutton, 1876) are distributed across both main islands of New Zealand; the existence of multiple distinct lineages of live-bearing Onychophora across this spatial range has gradually emerged. Morphological conservatism obscured the true endemic diversity, and the inclusion of molecular tools has been instrumental in revealing these cryptic taxa. (2) Methods: Here, we review the diversity of the ovoviviparous Onychophora of New Zealand through a re-analysis of allozyme genotype data, mitochondrial DNA cytochrome oxidase subunit I sequences, geographic information and morphology. (3) Results: New analysis of the multilocus biallelic nuclear data using methods that do not require a priori assumptions of population assignment support at least six lineages of ovoviviparous Peripatoides in northern New Zealand, and mtDNA sequence variation is consistent with these divisions. Expansion of mitochondrial DNA sequence data, including representation of all existing taxa and additional populations extends our knowledge of the scale of sympatry among taxa and shows that three other lineages from southern South Island can be added to the Peripatoides list, and names are proposed here. In total, 10 species of Peripatoides can be recognised with current data.
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Affiliation(s)
- Steven A. Trewick
- Wildlife & Ecology, School of Natural Sciences, Massey University, Private Bag 11-222, Palmerston North 4410, New Zealand;
| | - Emily M. Koot
- New Zealand Institute for Plant and Food Research Ltd., Palmerston North 4410, New Zealand;
| | - Mary Morgan-Richards
- Wildlife & Ecology, School of Natural Sciences, Massey University, Private Bag 11-222, Palmerston North 4410, New Zealand;
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Martinet KM, Harmon LJ. Delimiting the rare, endangered and actively speciating. Mol Ecol Resour 2024; 24:e13938. [PMID: 38409662 DOI: 10.1111/1755-0998.13938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 02/28/2024]
Abstract
Species delimitation is a contentious topic. The genomics revolution initially brought hope that identifying and classifying species would be easier through better methods and more data, but genomics has also brought complexity and controversy to delimitation. One solution can be to collect a larger sample of individuals at a finer geographic scale. But what if taxa are rare and collecting more samples is difficult or detrimental to the organisms at hand? In this issue of Molecular Ecology Resources, Opatova et al. (2023) tackle the ambiguity of species delimitation in rare and endangered trapdoor spiders (genus Cyclocosmia). The authors propose a framework for delimiting species when samples are hard to come by, such as in these rare and cryptic spiders. The authors combine extensive genomic sampling with statistical approaches that consider both the genetic distinctiveness of each population of spiders and how much gene flow occurs between these populations. Their proposed taxonomy balances two opposing signals, structure and gene flow, to count eight lineages of Cyclocosmia, and to point the way for future taxonomic studies of the rare or difficult to obtain.
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Affiliation(s)
- Kristen M Martinet
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Luke J Harmon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
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Zhang P, Cai Y, Ma L, Chai J, Zhou Z. DNA barcoding of the genus Gampsocleis (Orthoptera, Tettigoniidae) from China. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22070. [PMID: 38288484 DOI: 10.1002/arch.22070] [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: 08/04/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 02/01/2024]
Abstract
DNA barcoding is a useful addition to the traditional morphology-based taxonomy. A ca. 650 bp fragment of the 5' end of mitochondrial cytochrome c oxidase subunit I (hereafter COI-5P) DNA barcoding was sued as a practical tool for Gampsocleis species identification. DNA barcodes from 889 specimens belonging to 8 putative Gampsocleis species was analyzed, including 687 newly generated DNA barcodes. These barcode sequences were clustered/grouped into Operational Taxonomic Units (OTUs) using the criteria of five algorithms, namely Barcode Index Number (BIN) System, Assemble Species by Automatic Partitioning (ASAP), a Java program uses an explicit, determinate algorithm to define Molecular Operational Taxonomic Unit (jMOTU), Generalized Mixed Yule Coalescent (GMYC), and Bayesian implementation of the Poisson Tree Processes model (bPTP). The Taxon ID Tree grouped sequences of morphospecies and almost all MOTUs in distinct nonoverlapping clusters. Both long- and short-winged Gampsocleis species are reciprocally monophyletic in the Taxon ID Tree. In BOLD, 889 barcode sequences are assigned to 17 BINs. The algorithms ASAP, jMOTU, bPTP and GMYC clustered the barcode sequences into 6, 13, 10, and 23 MOTUs, respectively. BIN, ASAP, and bPTP algorithm placed three long-winged species, G. sedakovii, G. sinensis and G. ussuriensis within the same MOTU. All species delimitation algorithms split two short-winged species,G. fletcheri and G. gratiosa into at least two MOTUs each, except for ASAP algorithm. More detailed molecular and morphological integrative studies are required to clarify the status of these MOTUs in the future.
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Affiliation(s)
- Pu Zhang
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Yuting Cai
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Lan Ma
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Jinyan Chai
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
| | - Zhijun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding, China
- Institute of Life Science and Green Development, Hebei University, Baoding, China
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9
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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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Alexander Pyron R. Unsupervised machine learning for species delimitation, integrative taxonomy, and biodiversity conservation. Mol Phylogenet Evol 2023; 189:107939. [PMID: 37804960 DOI: 10.1016/j.ympev.2023.107939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
Integrative taxonomy, combining data from multiple axes of biologically relevant variation, is a major goal of systematics. Ideally, such taxonomies will derive from similarly integrative species-delimitation analyses. Yet, most current methods rely solely or primarily on molecular data, with other layers often incorporated only in a post hoc qualitative or comparative manner. A major limitation is the difficulty of devising quantitative parametric models linking different datasets in a unified ecological and evolutionary framework. Machine Learning (ML) methods offer flexibility in this arena by easily learning high-dimensional associations between observations (e.g., individual specimens) across a wide array of input features (e.g., genetics, geography, environment, and phenotype) to delimit statistically meaningful clusters. Here, I implement an unsupervised method using Self-Organizing (or "Kohonen") Maps (SOMs) for such purposes. Recent extensions called "SuperSOMs" can integrate multiple layers, each of which exerts independent influence on a two-dimensional output grid via empirically estimated weights. The grid cells are then delimited into K distinct units that can be interpreted as species or other entities. I show empirical examples in salamanders (Desmognathus) and snakes (Storeria) with layers representing alleles, space, climate, and traits. Simulations reveal that the SuperSOM approach can detect K = 1, tends not to over-split, reflects contributions from all layers, and limits large layers (e.g., genetic matrices) from overwhelming other datasets, desirable properties addressing major concerns from previous studies. Finally, I suggest that these and similar methods could integrate conservation-relevant layers such as population trends and human encroachment to delimit management units from an explicitly quantitative framework grounded in the ecology and evolution of species limits and boundaries.
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Affiliation(s)
- R Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington, DC 20052 USA.
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11
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Jeena NS, Sajikumar KK, Rahuman S, Ragesh N, Koya KPS, Chinnadurai S, Sasikumar G, Mohamed KS. Insights into the divergent evolution of the oceanic squid Sthenoteuthis oualaniensis (Cephalopoda: Ommastrephidae) from the Indian Ocean. Integr Zool 2023; 18:924-948. [PMID: 36610009 DOI: 10.1111/1749-4877.12705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Sthenoteuthis oualaniensis is known for its complex population structure with three major transoceanic forms (viz. middle-sized, dwarf, and giant forms) whose taxonomic status has been disputed for decades. This integrated taxonomic study examines these prevenient morphotypes gathered on cruises in the Indian Ocean to ascertain their status in the evolutionary history of the species. Molecular analyses employing mitochondrial (COI, ND2) and nuclear (H3) markers revealed four genetically distinct and novel lineages of the species in the Indian Ocean, representing three morphotypes from the Arabian Sea and one from the Southern Indian Ocean. The mitochondrial-based phylograms revealed two distinct clades in the species: "dwarf forms + giant form" and "middle-sized forms," which further branch into geographically structured evolutionary units. Species delimitation analyses recovered five distinct clades, namely, the Arabian Sea giant and dwarf forms, Equatorial, Eastern Typical, and Other Middle-sized forms, representing the consensus molecular operational taxonomic units. H3 being heterozygous could not resolve the phylogeny. Haplotype network and AMOVA analysis of mtDNA genes indicated explicit phylogeographic structuring of haplotypes, whereas these outputs and PCA results were incongruent with the morphological grouping. Phenetic features distinguishing the morphotypes were sometimes plastic and mismatched with the genotypes. The giant form was genetically close to the dwarf forms, contradicting the earlier notion that it descended from the middle-sized form. It may be assumed that the dwarf form evolved following sympatric speciation and adaptation to warm equatorial waters, while the focal features of the Western Arabian Sea guide toward allopatric speciation of the giant form.
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Affiliation(s)
- Nikarthil S Jeena
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | | | - Summaya Rahuman
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - Nadakkal Ragesh
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - K P Said Koya
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
| | - Shunmugavel Chinnadurai
- Fishing Technology Division, Veraval Research Centre of ICAR-Central Institute of Fisheries Technology, Matsyabhavan, Bhidia, Veraval, Gujarat, India
| | - Geetha Sasikumar
- ICAR-Central Marine Fisheries Research Institute, Kochi, Kerala, India
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12
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Franco ADODR, Ashworth MP, Odebrecht C. Comparison between p-distance and single-locus species delimitation models for delineating reproductively tested strains of pennate diatoms (Bacillariophyceae) using cox1, rbcL and ITS. J Eukaryot Microbiol 2023; 70:e12986. [PMID: 37243408 DOI: 10.1111/jeu.12986] [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: 03/28/2022] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Several automated molecular methods have emerged for distinguishing eukaryote species based on DNA sequence data. However, there are knowledge gaps around which of these single-locus methods is more accurate for the identification of microalgal species, such as the highly diverse and ecologically relevant diatoms. We applied genetic divergence, Automatic Barcode Gap Discovery for primary species delimitation (ABGD), Assemble Species by Automatic Partitioning (ASAP), Statistical Parsimony Network Analysis (SPNA), Generalized Mixed Yule Coalescent (GMYC) and Poisson Tree Processes (PTP) using partial cox1, rbcL, 5.8S + ITS2, ITS1 + 5.8S + ITS2 markers to delineate species and compare to published polyphasic identification data (morphological features, phylogeny and sexual reproductive isolation) to test the resolution of these methods. ASAP, ABGD, SPNA and PTP models resolved species of Eunotia, Seminavis, Nitzschia, Sellaphora and Pseudo-nitzschia corresponding to previous polyphasic identification, including reproductive isolation studies. In most cases, these models identified diatom species in similar ways, regardless of sequence fragment length. GMYC model presented smallest number of results that agreed with previous published identification. Following the recommendations for proper use of each model presented in the present study, these models can be useful tools to identify cryptic or closely related species of diatoms, even when the datasets have relatively few sequences.
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Affiliation(s)
| | - Matt P Ashworth
- Department of Molecular Biosciences, UTEX Culture Collection of Algae, University of Texas at Austin, Austin, Texas, USA
| | - Clarisse Odebrecht
- Institute of Oceanography, Federal University of Rio Grande - FURG, Rio Grande, Brazil
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13
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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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Hernández-Díaz YQ, Solis F, Beltrán-López RG, Benítez HA, Díaz-Jaimes P, Paulay G. Integrative species delimitation in the common ophiuroid Ophiothrix angulata (Echinodermata: Ophiuroidea): insights from COI, ITS2, arm coloration, and geometric morphometrics. PeerJ 2023; 11:e15655. [PMID: 37483979 PMCID: PMC10358340 DOI: 10.7717/peerj.15655] [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: 02/02/2023] [Accepted: 06/07/2023] [Indexed: 07/25/2023] Open
Abstract
Ophiothrix angulata (Say, 1825) is one of the most common and well-known ophiuroids in the Western Atlantic, with a wide geographic and bathymetric range. The taxonomy of this species has been controversial for a century because of its high morphological variability. Here we integrate information from DNA sequence data, color patterns, and geometric morphometrics to assess species delimitation and geographic differentiation in O. angulata. We found three deeply divergent mtDNA-COI clades (K2P 17.0-27.9%). ITS2 nuclear gene and geometric morphometrics of dorsal and ventral arm plates differentiate one of these lineages, as do integrative species delineation analyses, making this a confirmed candidate species.
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Affiliation(s)
- Yoalli Quetzalli Hernández-Díaz
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
- Unidad Multidisciplinaria de Docencia e Investigación - Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Yucatán, México
| | - Francisco Solis
- Laboratorio de Sistemática y Ecología de Equinodermos, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rosa G. Beltrán-López
- Laboratorio de Ictiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Hugo A. Benítez
- Laboratorio de Ecología y Morfometría Evolutiva, Centro de Investigación de Estudios Avanzados del Maule, Instituto Milenio Biodiversidad de Ecosistemas Antárticos y Subantárticos (BASE), Universidad Católica del Maule, Talca, Chile
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Píndaro Díaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Gustav Paulay
- Florida Natural History Museum, University of Florida, Gainesville, FL, United States of America
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Kerr M, Leavitt SD. A Custom Regional DNA Barcode Reference Library for Lichen-Forming Fungi of the Intermountain West, USA, Increases Successful Specimen Identification. J Fungi (Basel) 2023; 9:741. [PMID: 37504730 PMCID: PMC10381598 DOI: 10.3390/jof9070741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/27/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023] Open
Abstract
DNA barcoding approaches provide powerful tools for characterizing fungal diversity. However, DNA barcoding is limited by poor representation of species-level diversity in fungal sequence databases. Can the development of custom, regionally focused DNA reference libraries improve species-level identification rates for lichen-forming fungi? To explore this question, we created a regional ITS database for lichen-forming fungi (LFF) in the Intermountain West of the United States. The custom database comprised over 4800 sequences and represented over 600 formally described and provisional species. Lichen communities were sampled at 11 sites throughout the Intermountain West, and LFF diversity was characterized using high-throughput ITS2 amplicon sequencing. We compared the species-level identification success rates from our bulk community samples using our regional ITS database and the widely used UNITE database. The custom regional database resulted in significantly higher species-level assignments (72.3%) of candidate species than the UNITE database (28.3-34.2%). Within each site, identification of candidate species ranged from 72.3-82.1% using the custom database; and 31.5-55.4% using the UNITE database. These results highlight that developing regional databases may accelerate a wide range of LFF research by improving our ability to characterize species-level diversity using DNA barcoding.
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Affiliation(s)
- Michael Kerr
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Steven D Leavitt
- M.L. Bean Life Science Museum and Department of Biology, Brigham Young University, Provo, UT 84602, USA
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Dong X, Zhang H, Zhu X, Wang K, Xue H, Ye Z, Zheng C, Bu W. Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae). Mol Phylogenet Evol 2023; 184:107802. [PMID: 37221926 DOI: 10.1016/j.ympev.2023.107802] [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: 11/08/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.
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Affiliation(s)
- Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haiguang Zhang
- College of Life Science, Linyi University, Linyi 276000, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kaibin Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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Pérez-Rodríguez R, Domínguez-Domínguez O, Pedraza-Lara C, Rosas-Valdez R, Pérez-Ponce de León G, García-Andrade AB, Doadrio I. Multi-locus phylogeny of the catfish genus Ictalurus Rafinesque, 1820 (Actinopterygii, Siluriformes) and its systematic and evolutionary implications. BMC Ecol Evol 2023; 23:27. [PMID: 37370016 PMCID: PMC10304232 DOI: 10.1186/s12862-023-02134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Ictalurus is one of the most representative groups of North American freshwater fishes. Although this group has a well-studied fossil record and has been the subject of several morphological and molecular phylogenetic studies, incomplete taxonomic sampling and insufficient taxonomic studies have produced a rather complex classification, along with intricate patterns of evolutionary history in the genus that are considered unresolved and remain under debate. RESULTS Based on four loci and the most comprehensive taxonomic sampling analyzed to date, including currently recognized species, previously synonymized species, undescribed taxa, and poorly studied populations, this study produced a resolved phylogenetic framework that provided plausible species delimitation and an evolutionary time framework for the genus Ictalurus. CONCLUSIONS Our phylogenetic hypothesis revealed that Ictalurus comprises at least 13 evolutionary units, partially corroborating the current classification and identifying populations that emerge as putative undescribed taxa. The divergence times of the species indicate that the diversification of Ictalurus dates to the early Oligocene, confirming its status as one of the oldest genera within the family Ictaluridae.
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Affiliation(s)
- Rodolfo Pérez-Rodríguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
| | - Carlos Pedraza-Lara
- Forensic Science, Medicine School, National Autonomous University of Mexico, Circuito de la investigación científica s/n, Ciudad Universitaria, Coyoacan, 04510, CdMx, Mexico
| | - Rogelio Rosas-Valdez
- Laboratorio de Colecciones Biológicas y Sistemática Molecular, Unidad Académica de Ciencias Biológicas, Universidad Autónoma de Zacatecas, Av. Preparatoria S/N, Campus Universitario II, Col. Agronómica, Zacatecas, C. P. 98066, México
| | - Gerardo Pérez-Ponce de León
- Instituto de Biología, UNAM, Circuito exterior s/n, Ciudad Universitaria, Coyoacán, C.P. 04510, D.F, México
- Escuela Nacional de Estudios Superiores Unidad Mérida, Universidad Nacional Autónoma de México, Km 4.5 Carretera Mérida-Tetiz, Ucú, Yucatán, México
| | - Ana Berenice García-Andrade
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, 58000, Michoacán, México
- Laboratorio de Macroecología Evolutiva, Red de Biología Evolutiva, Instituto de Ecología, A.C. Carretera antigua a Coatepec 351, El Haya, Xalapa, 91070, Veracruz, México
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, c/José Gutiérrez Abascal 2, Madrid, E-28006, España.
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Bukin YS, Mikhailov IS, Petrova DP, Galachyants YP, Zakharova YR, Likhoshway YV. The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton. World J Microbiol Biotechnol 2023; 39:229. [PMID: 37341802 DOI: 10.1007/s11274-023-03678-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/13/2023] [Indexed: 06/22/2023]
Abstract
Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.
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Affiliation(s)
- Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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19
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Arantes ÍC, Vasconcellos MM, Smith ML, Garrick RC, Colli GR, Noonan BP. Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas. Mol Phylogenet Evol 2023:107843. [PMID: 37286064 DOI: 10.1016/j.ympev.2023.107843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/09/2023]
Abstract
Understanding the processes that generate and maintain biodiversity at and below the species level is a central goal of evolutionary biology. Here we explore the spatial and temporal drivers of diversification of the treefrog subgroup Dendropsophus rubicundulus, a subgroup of the D. microcephalus species group, over periods of pronounced geological and climatic changes in the Neotropical savannas that they inhabit. This subgroup currently comprises 11 recognized species distributed across the Brazilian and Bolivian savannas, but the taxonomy has been in a state of flux, necessitating reexamination. Using newly generated single nucleotide polymorphism (SNP) data from restriction-site associated DNA sequencing (RADseq) and mitochondrial 16S sequence data for ∼150 specimens, we inferred phylogenetic relationships, tested species limits using a model-based approach, and estimated divergence times to gain insights into the geographic and climatic events that affected the diversification of this subgroup. Our results recognized at least nine species: D. anataliasiasi, D. araguaya, D. cerradensis, D. elianeae, D. jimi, D. rubicundulus, D. tritaeniatus, D. rozenmani, and D. sanborni. Although we did not collect SNP data for the latter two species, they are likely distinct based on mitochondrial data. In addition, we found genetic structure within the widespread species D. rubicundulus, which comprises three allopatric lineages connected by gene flow upon secondary contact. We also found evidence of population structure and perhaps undescribed diversity in D. elianeae, which warrants further study. The D. rubicundulus subgroup is estimated to have originated in the Late Miocene (∼5.45 million years ago), with diversification continuing through the Pliocene and Early Pleistocene, followed by the most recent divergence of D. rubicundulus lineages in the Middle Pleistocene. The epeirogenic uplift followed by erosion and denudation of the central Brazilian plateau throughout the Pliocene and Pleistocene, in combination with the increasing frequency and amplitude of climatic fluctuations during the Pleistocene, was important for generating and structuring diversity at or below the species level in the D. rubicundulus subgroup.
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Affiliation(s)
- Ísis C Arantes
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA.
| | - Mariana M Vasconcellos
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Megan L Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
| | - Guarino R Colli
- Departamento de Zoologia, Universidade de Brasília, 70910-900 Brasília, Distrito Federal, Brazil
| | - Brice P Noonan
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA
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Korshunova T, Grøtan VV, Johnson KB, Bakken T, Picton BE, Martynov A. Similar Ones Are Not Related and Vice Versa—New Dendronotus Taxa (Nudibranchia: Dendronotidae) from the North Atlantic Ocean Provide a Platform for Discussion of Global Marine Biodiversity Patterns. DIVERSITY 2023. [DOI: 10.3390/d15040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
One new species of the genus Dendronotus (Nudibranchia: Dendronotidae) is described from Norway and Northern Ireland, as well as from the adjacent North Sea, and one new subspecies of Dendronotus arcticus is described from Norway by applying a combination of fine-scale morphological and molecular phylogenetic data. The present case demonstrates multilevel morphological and molecular similarities and differences considering on the one hand a grouping of three similar looking sympatric taxa (D. yrjargul, D. arcticus gartensis n. subsp. and D. keatleyae n. sp.), and on the other hand two different looking apparently allopatric subspecies (D. arcticus arcticus and D. arcticus gartensis n. subsp.). The type species of the genus, D. frondosus, which is the commonest dendronotid in Norway and the United Kingdom, consistently demonstrates substantial molecular and fine-scale morphological differences from D. keatleyae n. sp. The present study, apart from providing purely taxonomic information, also provides new data for a broad discussion of global biodiversity patterns.
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Affiliation(s)
| | | | | | - Torkild Bakken
- NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Bernard E. Picton
- National Museums Northern Ireland, Holywood BT18 0EU, UK
- Marine Laboratory, Queen’s University Belfast, Belfast BT22 1PF, Northern Ireland, UK
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21
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Wu YH, Hou SB, Yuan ZY, Jiang K, Huang RY, Wang K, Liu Q, Yu ZB, Zhao HP, Zhang BL, Chen JM, Wang LJ, Stuart BL, Chambers EA, Wang YF, Gao W, Zou DH, Yan F, Zhao GG, Fu ZX, Wang SN, Jiang M, Zhang L, Ren JL, Wu YY, Zhang LY, Yang DC, Jin JQ, Yin TT, Li JT, Zhao WG, Murphy RW, Huang S, Guo P, Zhang YP, Che J. DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs. Mol Ecol Resour 2023. [PMID: 36924341 DOI: 10.1111/1755-0998.13784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023]
Abstract
DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes.
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Affiliation(s)
- Yun-He Wu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Shao-Bing Hou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Zhi-Yong Yuan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ke Jiang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ru-Yi Huang
- Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kai Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Zhong-Bin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Hai-Peng Zhao
- School of Life Science, Henan University, Kaifeng, Henan, 475001, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jin-Min Chen
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Li-Jun Wang
- School of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158, China
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601, USA
| | - E Anne Chambers
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720, USA
| | - Yu-Fan Wang
- Zhejiang Forest Resource Monitoring Center, Hangzhou, Zhejiang, 310020, China
| | - Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Da-Hu Zou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- College of Science, Tibet University, Lhasa, Tibet, 850000, China
| | - Fang Yan
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Gui-Gang Zhao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Zhong-Xiong Fu
- Yunnan Senye Biotechnology Co., Ltd, Xishuangbanna, Yunnan, 666100, China
| | - Shao-Neng Wang
- Bureau of Guangxi Mao'er Mountain Nature Reserve, Guilin, Guangxi, 541316, China
| | - Ming Jiang
- Gongshan Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan, 650224, China
| | - Liang Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260, China
| | - Jin-Long Ren
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Ya-Yong Wu
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Lu-Yang Zhang
- Beijing Mountains & Seas Eco Technology Co. Ltd, Beijing, 101100, China
| | - Dian-Cheng Yang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jia-Tang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041, China
| | - Wen-Ge Zhao
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada
| | - Song Huang
- Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000, China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
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22
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Uluar O, Yahyaoğlu Ö, Başıbüyük HH, Çıplak B. Taxonomy of the rear-edge populations: the case of genus Anterastes (Orthoptera, Tettigoniidae). ORG DIVERS EVOL 2023. [DOI: 10.1007/s13127-023-00602-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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23
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Bachmann L, Beermann J, Brey T, de Boer HJ, Dannheim J, Edvardsen B, Ericson PGP, Holston KC, Johansson VA, Kloss P, Konijnenberg R, Osborn KJ, Pappalardo P, Pehlke H, Piepenburg D, Struck TH, Sundberg P, Markussen SS, Teschke K, Vanhove MPM. The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022. ZOOL SCR 2023. [DOI: 10.1111/zsc.12593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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24
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Freire-Rallo S, Wedin M, Diederich P, Millanes AM. To explore strange new worlds - The diversification in Tremella caloplacae was linked to the adaptive radiation of the Teloschistaceae. Mol Phylogenet Evol 2023; 180:107680. [PMID: 36572164 DOI: 10.1016/j.ympev.2022.107680] [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: 12/13/2021] [Revised: 09/12/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Lichenicolous fungi are a heterogeneous group of organisms that grow exclusively on lichens, forming obligate associations with them. It has often been assumed that cospeciation has occurred between lichens and lichenicolous fungi, but this has been seldom analysed from a macroevolutionary perspective. Many lichenicolous species are rare or are rarely observed, which results in frequent and large gaps in the knowledge of the diversity of many groups. This, in turn, hampers evolutionary studies that necessarily are based on a reasonable knowledge of this diversity. Tremella caloplacae is a heterobasidiomycete growing on various hosts from the lichen-forming family Teloschistaceae, and evidence suggests that it may represent a species complex. We combine an exhaustive sampling with molecular and ecological data to study species delimitation, cophylogenetic events and temporal concordance of this association. Tremella caloplacae is here shown to include at least six distinct host-specific lineages (=putative species). Host switch is the dominant and most plausible event influencing diversification and explaining the coupled evolutionary history in this system, although cospeciation cannot be discarded. Speciation in T. caloplacae would therefore have occurred coinciding with the rapid diversification - by an adaptive radiation starting in the late Cretaceous - of their hosts. New species in T. caloplacae would have developed as a result of specialization on diversifying lichen hosts that suddenly offered abundant new ecological niches to explore or adapt to.
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Affiliation(s)
- Sandra Freire-Rallo
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
| | - Mats Wedin
- Swedish Museum of Natural History/Botany Dept., PO Box 50007, SE-10405 Stockholm, Sweden.
| | - Paul Diederich
- Musée national d'histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg
| | - Ana M Millanes
- Rey Juan Carlos University/Departamento de Biología y Geología, Física y Química Inorgánica, E-28933 Móstoles, Spain
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25
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Csősz S, Báthori F, Rádai Z, Herczeg G, Fisher BL. Comparing ant morphology measurements from microscope and online AntWeb.org 2D z-stacked images. Ecol Evol 2023; 13:e9897. [PMID: 36950369 PMCID: PMC10025076 DOI: 10.1002/ece3.9897] [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: 12/22/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/22/2023] Open
Abstract
Unprecedented technological advances in digitization and the steadily expanding open-access digital repositories are yielding new opportunities to quickly and efficiently measure morphological traits without transportation and advanced/expensive microscope machinery. A prime example is the AntWeb.org database, which allows researchers from all over the world to study taxonomic, ecological, or evolutionary questions on the same ant specimens with ease. However, the reproducibility and reliability of morphometric data deduced from AntWeb compared to traditional microscope measurements has not yet been tested. Here, we compared 12 morphological traits of 46 Temnothorax ant specimens measured either directly by stereomicroscope on physical specimens or via the widely used open-access software tpsDig utilizing AntWeb digital images. We employed a complex statistical framework to test several aspects of reproducibility and reliability between the methods. We estimated (i) the agreement between the measurement methods and (ii) the trait value dependence of the agreement, then (iii) compared the coefficients of variation produced by the different methods, and finally, (iv) tested for systematic bias between the methods in a mixed modeling-based statistical framework. The stereomicroscope measurements were extremely precise. Our comparisons showed that agreement between the two methods was exceptionally high, without trait value dependence. Furthermore, the coefficients of variation did not differ between the methods. However, we found systematic bias in eight traits: apart from one trait where software measurements overestimated the microscopic measurements, the former underestimated the latter. Our results shed light on the fact that relying solely on the level of agreement between methods can be highly misleading. In our case, even though the software measurements predicted microscope measurements very well, replacing traditional microscope measurements with software measurements, and especially mixing data collected by the different methods, might result in erroneous conclusions. We provide guidance on the best way to utilize virtual specimens (2D z-stacked images) as a source of morphometric data, emphasizing the method's limitations in certain fields and applications.
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Affiliation(s)
- Sándor Csősz
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
| | - Ferenc Báthori
- Department of Systematic Zoology and EcologyInstitute of Biology, ELTE‐Eötvös Loránd UniversityBudapestHungary
| | - Zoltán Rádai
- Lendület Seed Ecology Research GroupInstitute of Ecology and Botany, Centre for Ecological ResearchVácrátótHungary
| | - Gábor Herczeg
- ELKH‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
- Department of Systematic Zoology and EcologyInstitute of Biology, ELTE‐Eötvös Loránd UniversityBudapestHungary
| | - Brian L. Fisher
- EntomologyCalifornia Academy of SciencesSan FranciscoCaliforniaUSA
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26
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Molecular phylogeny reveals distinct evolutionary lineages of the banded krait, Bungarus fasciatus (Squamata, Elapidae) in Asia. Sci Rep 2023; 13:2061. [PMID: 36739450 PMCID: PMC9899266 DOI: 10.1038/s41598-023-28241-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/16/2023] [Indexed: 02/06/2023] Open
Abstract
The banded krait, Bungarus fasciatus is a widespread elapid snake, likely to comprise several distinct species in different geographic regions of Asia. Therefore, based on molecular phylogenetics and comparative morphology data, we present an overview of the systematic composition of the species to delimit potential biogeographic boundaries. Our phylogenetic analyses, based on four mitochondrial genes, reveal the existence of at least three evolutionary lineages within B. fasciatus, corresponding to Indo-Myanmar, Sundaic and eastern Asian lineages. We are convinced that there are at least three taxonomic entities within the nomen B. fasciatus and restrict the distribution of B. fasciatus sensu stricto to the Indo-Myanmar region. We also provide additional natural history data of the taxon from eastern India. Finally, we advocate further studies to establish the degree of reproductive isolation among these diverging evolutionary lineages and to reassess the systematic status of this species complex especially the Sundaic and eastern Asian lineages.
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27
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Han W, Tang H, Wei L, Zhang E. The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases. Ecol Evol 2023; 13:e9849. [PMID: 36861023 PMCID: PMC9969238 DOI: 10.1002/ece3.9849] [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: 12/11/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.
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Affiliation(s)
- Wu Han
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
- University of Chinese Academy of SciencesBeijing100039China
| | - Hongqu Tang
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Lili Wei
- Life Science and Technology CollegeJinan UniversityGuangzhouChina
| | - Enlou Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and LimnologyChinese Academy of ScienceNanjingChina
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28
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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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29
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Vieira JPS, Selbach-Schnadelbach A, Braz M, Ribeiro PL, van den Berg C, Oliveira RP. Coalescent-Based Species Delimitation in Herbaceous Bamboos (Bambusoideae, Olyreae) from Eastern Brazil: Implications for Taxonomy and Conservation in a Group with Weak Morphological Divergence Coupled with Low Genetic Diversity. PLANTS (BASEL, SWITZERLAND) 2022; 12:107. [PMID: 36616235 PMCID: PMC9824829 DOI: 10.3390/plants12010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Species delimitation in herbaceous bamboos has been complex and, in some genera, a great part of its diversity has been confirmed only based on genetic information, as is the case of the genus Raddia. It includes nine species, all occurring in Brazil, but only R. portoi predominates in dry forests of the Northeast associated with the Caatinga phytogeographic domain. This species is morphologically close to R. angustifolia, which is known for a single location in the Atlantic Forest in Southern Bahia, and is considered to be threatened by extinction. Besides problems with taxonomic focus, actions for its conservation are complicated because it is not certain if it must be considered an independent species or included in the more widespread R. portoi. In this study, we used coalescent multispecies (MSC) theory approaches combined with genetic structure analyses in an attempt to delimit these two species. Different analyses were congruent and the species delimitation using MSC inferred distinct lineages supporting their recognition as two species. These results solved the taxonomic doubts and also showed the power of these approaches to delimit species as lineages, even in groups with weak morphological divergence and low genetic variability, and also impacting our knowledge for conservation purposes.
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Affiliation(s)
- João Paulo S. Vieira
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana 44031-460, Bahia, Brazil
| | - Alessandra Selbach-Schnadelbach
- Instituto de Biologia, Universidade Federal da Bahia, Av. Barão de Jeremoabo s.n., Ondina, Salvador 40150-170, Bahia, Brazil
| | - Marcos Braz
- Instituto de Biologia, Universidade Federal da Bahia, Av. Barão de Jeremoabo s.n., Ondina, Salvador 40150-170, Bahia, Brazil
| | - Patrícia L. Ribeiro
- Centro de Ciências Agrárias, Ambientais e Biológicas, Universidade Federal do Recôncavo da Bahia, Cruz das Almas 44380-000, Bahia, Brazil
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana 44031-460, Bahia, Brazil
| | - Reyjane P. Oliveira
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, Feira de Santana 44031-460, Bahia, Brazil
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30
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Nolasco S, Valdez-Mondragón A. To be or not to be… Integrative taxonomy and species delimitation in the daddy long-legs spiders of the genus Physocyclus (Araneae, Pholcidae) using DNA barcoding and morphology. Zookeys 2022; 1135:93-118. [PMID: 36761795 PMCID: PMC9836410 DOI: 10.3897/zookeys.1135.94628] [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: 09/08/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
Integrative taxonomy is crucial for discovery, recognition, and species delimitation, especially in underestimated species complex or cryptic species, by incorporating different sources of evidence to construct rigorous species hypotheses. The spider genus Physocyclus Simon, 1893 (Pholcidae, Arteminae) is composed of 37 species, mainly from North America. In this study, traditional morphology was compared with three DNA barcoding markers regarding their utility in species delimitation within the genus: 1) Cytochrome c Oxidase subunit 1 (CO1), 2) Internal Transcribed Spacer 2 (ITS2), and 3) Ribosomal large subunit (28S). The molecular species delimitation analyses were carried out using four methods under the corrected p-distances Neighbor-Joining (NJ) criteria: 1) Automatic Barcode Gap Discovery (ABGD), 2) Assemble Species by Automatic Partitioning (ASAP), 3) General Mixed Yule Coalescent model (GMYC), and 4) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 75 terminals from 22 putative species of Physocyclus. The average intraspecific genetic distance (p-distance) was found to be < 2%, whereas the average interspecific genetic distance was 20.6%. The ABGD, ASAP, and GMYC methods were the most congruent, delimiting 26 or 27 species, while the bPTP method delimited 33 species. The use of traditional morphology for species delimitation was congruent with most molecular methods, with the male palp, male chelicerae, and female genitalia shown to be robust characters that support species-level identification. The barcoding with CO1 and 28S had better resolution for species delimitation in comparison with ITS2. The concatenated matrix and traditional morphology were found to be more robust and informative for species delimitation within Physocyclus.
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Affiliation(s)
- Samuel Nolasco
- Posgrado en Ciencias Biológicas (Doctorado), Centro Tlaxcala de Biología de la Conducta (CTBC), Universidad Autónoma de Tlaxcala (UATx), Carretera Federal Tlaxcala-Puebla, Km. 1.5, C. P. 90062, Tlaxcala, Mexico,Laboratory of Arachnology (LATLAX), Laboratorio Regional de Biodiversidad y Cultivo de Tejidos Vegetales (LBCTV), Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), sede Tlaxcala, Ex-Fábrica San Manuel, San Miguel Contla, 90640 Santa Cruz Tlaxcala, Tlaxcala, Mexico
| | - Alejandro Valdez-Mondragón
- Laboratory of Arachnology (LATLAX), Laboratorio Regional de Biodiversidad y Cultivo de Tejidos Vegetales (LBCTV), Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), sede Tlaxcala, Ex-Fábrica San Manuel, San Miguel Contla, 90640 Santa Cruz Tlaxcala, Tlaxcala, Mexico
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31
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Conjectures and refutations: Species diversity and phylogeny of Australoheros from coastal rivers of southern South America (Teleostei: Cichlidae). PLoS One 2022; 17:e0261027. [PMID: 36490238 PMCID: PMC9733902 DOI: 10.1371/journal.pone.0261027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/22/2021] [Indexed: 12/13/2022] Open
Abstract
Morphological and genetic analyses of species of Australoheros focusing on those distributed in coastal rivers from the Rio de La Plata north to the Rio Buranhém, support recognition of 17 valid species in the genus. Eight species are represented in coastal rivers: A acaroides, A. facetus, A. ipatinguensis, A. oblongus, A. ribeirae, and A. sanguineus are validated from earlier descriptions. Australoheros mboapari is a new species from the Rio Taquari in the Rio Jacuí drainage. Australoheros ricani is a new species from the upper Rio Jacuí. Specimens from the Rio Yaguarón and Rio Tacuary, affluents of Laguna Merín, and tributaries of the Rio Negro, tributary of the Rio Uruguay are assigned to A. minuano pending critical data on specimens from the type locality of A. minuano. Australoheros taura is a junior synonym of A. acaroides. Australoheros autrani, A. saquarema, A. capixaba, A. macaensis, A. perdi, and A. muriae are junior synonyms of A. ipatinguensis. Heros autochthon, A. mattosi, A. macacuensis, A. montanus, A. tavaresi, A. paraibae, and A. barbosae, are junior synonyms of A. oblongus. Heros jenynsii is a junior synonym of A. facetus.
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32
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Super-Mitobarcoding in Plant Species Identification? It Can Work! The Case of Leafy Liverworts Belonging to the Genus Calypogeia. Int J Mol Sci 2022; 23:ijms232415570. [PMID: 36555212 PMCID: PMC9779425 DOI: 10.3390/ijms232415570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Molecular identification of species is especially important where traditional taxonomic methods fail. The genus Calypogeia belongs to one of the tricky taxons. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. The finding of the universal single-locus DNA barcode in plants seems to be 'the Holy Grail'; therefore, researchers are increasingly looking for multiloci DNA barcodes or super-barcoding. Since the mitochondrial genome has low sequence variation in plants, species delimitation is usually based on the chloroplast genome. Unexpectedly, our research shows that super-mitobarcoding can also work! However, our outcomes showed that a single method of molecular species delimitation should be avoided. Moreover, it is recommended to interpret the results of molecular species delimitation alongside other types of evidence, such as ecology, population genetics or comparative morphology. Here, we also presented genetic data supporting the view that C. suecica is not a homogeneous species.
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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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Zhu X, Zheng C, Dong X, Zhang H, Ye Z, Xue H, Bu W. Species boundary and phylogeographical pattern provide new insights into the management efforts of Megacopta cribraria (Hemiptera: Plataspidae), a bean bug invading North America. PEST MANAGEMENT SCIENCE 2022; 78:4871-4881. [PMID: 36181419 DOI: 10.1002/ps.7108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Correct identification together with information on distribution range, geographical origin and evolutionary history are the necessary basis for the management and control of invasive species. The bean bug Megacopta cribraria is a crucial agricultural pest of soybean. Recently, M. cribraria has invaded the United States and spread rapidly, causing severe reductions in soybean yields. However, the species boundary and phylogeographical pattern of this invasive bean bug are still unclear. RESULTS The results of different species delimitation methods (Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Bayesian Poisson Tree Processes and Bayesian Phylogenetics and Phylogeography) strongly demonstrated that M. cribraria and Megacopta punctatissima represent the same species. M. punctatissima should not be considered a distinct species but rather a variety of M. cribraria. Phylogenetic analyses revealed three well-supported clades (Southeast Asia [SEA], East Asia continent [EAC] and Japan [JA]) with distinct geographical structures in the M. cribraria-M. punctatissima complex. The SEA clade was at the base of the phylogenetic tree, and the sister relationship between the EAC clade and JA clade was strongly supported. The split between the EAC clade and JA clade occurred at approximately 0.71 Ma, corresponding to the submergence period of the East China Sea land bridge. CONCLUSION This study clarified the species boundary between M. cribraria and its closely related species and revealed the phylogeographical pattern and evolutionary history of M. cribraria. The species delimitation and phylogeography results achieved in this study could provide new insights into the monitoring and management of this agricultural pest. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | | | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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Nacif CL, Bastos DL, Mello B, Lazar A, Hingst-Zaher E, Geise L, Bonvicino CR. Hidden diversity of the genus Trinomys (Rodentia: Echimyidae): phylogenetic and populational structure analyses uncover putative new lineages. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Trinomys, one of the most species-rich spiny rat genera in Brazil, is widely distributed in Caatinga, Cerrado and Atlantic Forest biomes, and currently includes ten recognized species, three of which are polytypic. Although some studies employing molecular data have been conducted to better characterize phylogenetic relationships among species, 19 nominal taxa have been suggested, implying considerable incongruence regarding species boundaries. We addressed this incongruence by intensively sampling all species across the geographic distribution of the genus. In addition to publicly available data, we generated 182 mt-Cytb gene sequences, and employed phylogenetic and computational species delimitation methods to obtain a clearer picture of the genus diversity. Moreover, we evaluated populational diversity within each accepted species, considering their geographical distribution and a timescale for the evolution of the genus. Beyond confirming the general patterns described for the evolution of the group, this new analysis suggests that Trinomys is comprised of at least 16 evolutionary lineages, 13 of them recognized as species or subspecies, and three never before characterized. This study highlights the importance of increased sample sizes and computational species delimitation methods in uncovering hidden diversity in Trinomys.
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Affiliation(s)
- Camila Leitão Nacif
- Graduate Genetics Program, Institute of Biology, Department of Genetics, Universidade Federal do Rio de Janeiro (UFRJ) , 21941-617, Rio de Janeiro, RJ , Brazil
| | - Diogo Lisbôa Bastos
- Graduate Program in Pathology, School of Medicine, Universidade Federal Fluminense (UFF) , Niterói, RJ , Brazil
| | - Beatriz Mello
- Department of Genetics, Federal University of Rio de Janeiro , Brazil
| | - Ana Lazar
- National Museum, Department of Vertebrates, Sector of Mastozoology, Universidade Federal do Rio de Janeiro (UFRJ) , 20940-040, Rio de Janeiro, RJ , Brazil
| | - Erika Hingst-Zaher
- Museu Biológico, Instituto Butantan , Avenida Vital Brazil, 1500, São Paulo , Brazil
| | - Lena Geise
- Laboratory of Mastozoology, Department of Zoology, Institute of Biology, Universidade do Estado do Rio de Janeiro (UERJ) , Rua São Francisco Xavier 524, 220559-900, Rio de Janeiro, RJ , Brazil
| | - Cibele Rodrigues Bonvicino
- Division of Genetics, National Cancer Institute (INCA) , Rua André Cavalcanti , 37, 4° andar, 20231-050, Rio de Janeiro, RJ , Brazil
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OTU Delimitation with Earthworm DNA Barcodes: A Comparison of Methods. DIVERSITY 2022. [DOI: 10.3390/d14100866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although DNA barcodes-based operational taxonomic units (OTUs) are increasingly used in earthworm research, the relative efficiency of the different methods available to delimit them has not yet been tested on a comprehensive dataset. For this study, we used three datasets containing 651, 2304 and 4773 COI barcodes of earthworms from French Guiana, respectively, to compare five of these methods: two phylogenetic methods—namely Poisson Tree Processes (PTP) and General Mixed Yule Coalescence (GMYC)—and three distance matrix methods—namely Refined Single Linkage (RESL, used for assigning Barcode Index Numbers in the Barcode of Life Data systems), Automatic Barcode Gap Discovery (ABGD), and Assemble Species by Automatic Partitioning (ASAP). We found that phylogenetic approaches are less suitable for delineating OTUs from DNA barcodes in earthworms, especially for large sets of sequences. The computation times are unreasonable, they often fail to converge, and they also show a strong tendency to oversplit species. Among distance-based methods, RESL also has a clear tendency to oversplitting, while ABGD and ASAP are less prone to mismatches and have short computation times. ASAP requires less a priori knowledge for model parameterisation than AGBD, provides efficient graphical outputs, and has a much lower tendency to generate mismatches.
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Forni G, Cussigh A, Brock PD, Jones BR, Nicolini F, Martelossi J, Luchetti A, Mantovani B. Taxonomic revision of the Australian stick insect genus Candovia (Phasmida: Necrosciinae): insight from molecular systematics and species-delimitation approaches. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The Phasmida genus Candovia comprises nine traditionally recognized species, all endemic to Australia. In this study, Candovia diversity is explored through molecular species-delimitation analyses using the COIFol gene fragment and phylogenetic inferences leveraging seven additional mitochondrial and nuclear loci. Molecular results were integrated with morphological observations, leading us to confirm the already described species and to the delineation of several new taxa and of the new genus Paracandovia. New Candovia species from various parts of Queensland and New South Wales are described and illustrated (C. alata sp. nov., C. byfieldensis sp. nov., C. dalgleishae sp. nov., C. eungellensis sp. nov., C. karasi sp. nov., C. koensi sp. nov. andC. wollumbinensis sp. nov.). New combinations are proposed and species removed from synonymy with the erection of the new genus Paracandovia (P. cercata stat. rev., comb. nov., P. longipes stat. rev., comb. nov., P. pallida comb. nov., P. peridromes comb. nov., P. tenera stat. rev., comb. nov.). Phylogenetic analyses suggest that the egg capitulum may have independently evolved multiple times throughout the evolutionary history of these insects. Furthermore, two newly described species represent the first taxa with fully developed wings in this previously considered apterous clade.
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Affiliation(s)
- Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
- Department of Agricultural and Environmental Sciences, University of Milan , Milano , Italy
| | - Alex Cussigh
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
- Department of Agricultural and Environmental Sciences, University of Milan , Milano , Italy
| | - Paul D Brock
- The Natural History Museum , Cromwell Road, London , UK
| | - Braxton R Jones
- School of Life and Environmental Sciences, The University of Sydney , Sydney NSW 2006 , Australia
| | - Filippo Nicolini
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
| | - Jacopo Martelossi
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna , Bologna , Italy
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38
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Bonvicino CR, Lazar A, Povill C, Caramaschi FP, de Freitas TPT, Crisóstomo CF, Botelho ALM, D’Andrea PS. Phylogeny of Didelphid marsupials (Didelphimorphia) from Acre, western Amazonia. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
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39
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Zink RM, Klicka LB. The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.971280] [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
More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.
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40
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Herrera ND, Bell KC, Callahan CM, Nordquist E, Sarver BAJ, Sullivan J, Demboski JR, Good JM. Genomic resolution of cryptic species diversity in chipmunks. Evolution 2022; 76:2004-2019. [PMID: 35778920 DOI: 10.1111/evo.14546] [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: 03/07/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 01/22/2023]
Abstract
Discovery of cryptic species is essential to understand the process of speciation and assessing the impacts of anthropogenic stressors. Here, we used genomic data to test for cryptic species diversity within an ecologically well-known radiation of North American rodents, western chipmunks (Tamias). We assembled a de novo reference genome for a single species (Tamias minimus) combined with new and published targeted sequence-capture data for 21,551 autosomal and 493 X-linked loci sampled from 121 individuals spanning 22 species. We identified at least two cryptic lineages corresponding with an isolated subspecies of least chipmunk (T. minimus grisescens) and with a restricted subspecies of the yellow-pine chipmunk (Tamias amoenus cratericus) known only from around the extensive Craters of the Moon lava flow. Additional population-level sequence data revealed that the so-called Crater chipmunk is a distinct species that is abundant throughout the coniferous forests of southern Idaho. This cryptic lineage does not appear to be most closely related to the ecologically and phenotypically similar yellow-pine chipmunk but does show evidence for recurrent hybridization with this and other species.
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Affiliation(s)
- Nathanael D Herrera
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Kayce C Bell
- Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Colin M Callahan
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Erin Nordquist
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brice A J Sarver
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow, Idaho, USA
| | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Sciences, Denver, Colorado, USA
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA.,Wildlife Biology Program, University of Montana, Missoula, Montana, USA
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Hévin NM, Hansen S, Addison P, Benoit L, Kergoat GJ, Haran J. Late Cenozoic environmental changes drove the diversification of a weevil genus endemic to the Cape Floristic Region. ZOOL SCR 2022. [DOI: 10.1111/zsc.12563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noémie M.‐C. Hévin
- CBGP INRAE, CIRAD, IRD, Institut Agro, Univ. Montpellier Montpellier France
- Université de Poitiers Poitiers France
| | | | | | - Laure Benoit
- CBGP CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier Montpellier France
| | - Gael J. Kergoat
- CBGP INRAE, CIRAD, IRD, Institut Agro, Univ. Montpellier Montpellier France
| | - Julien Haran
- CBGP CIRAD, INRAE, IRD, Institut Agro, Univ. Montpellier Montpellier France
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42
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Novaes-e-Fagundes G, Lyra ML, Loredam VSA, Carvalho TR, Haddad CFB, Rodrigues MT, Baldo D, Barrasso DA, Loebmann D, Ávila RW, Brusquetti F, Prudente ALC, Wheeler WC, Goyannes Dill Orrico V, Peloso P. A tale of two bellies: systematics of the oval frogs (Anura: Microhylidae: Elachistocleis Parker, 1927). Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Oval frogs (Elachistocleis) have a broad geographic distribution covering nearly all of South America and parts of Central America. They also have a large inter- and intraspecific variation of the few morphological characters commonly used as diagnostic traits among species of the genus. Based on molecular data, we provide the most complete phylogeny of Elachistocleis to date, and explore its genetic diversity using distance-based and tree-based methods for putative species delimitation. Our results show that at least two of the most relevant traditional characters used in the taxonomy of this group (belly pattern and dorsal median white line) carry less phylogenetic information than previously thought. Based on our results, we propose some synonymizations and some candidate new species. This study is a first major step in disentangling the current systematics of Elachistocleis. Yet, a comprehensive review of morphological data is needed before any new species descriptions can be properly made.
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Affiliation(s)
- Gabriel Novaes-e-Fagundes
- Tropical Herpetology Laboratory, PPG Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz , Ilhéus, Bahia , Brazil
| | - Mariana L Lyra
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Vinicius S A Loredam
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Thiago R Carvalho
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Célio F B Haddad
- Instituto de Biociências, Departamento de Biodiversidade e Centro de Aquicultura (CAUNESP), Universidade Estadual Paulista , Rio Claro, São Paulo , Brazil
| | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo , São Paulo , Brazil
| | - Diego Baldo
- Laboratorio de Genética Evolutiva, Instituto de Biología Subtropical `Claudio Juan Bidau’ (CONICET-UNaM), Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones , Posadas, Misiones , Argentina
| | - Diego A Barrasso
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET) , Puerto Madryn, Chubut , Argentina
- Facultad de Ciencias Naturales y Ciencias de la Salud, Universidad Nacional de la Patagonia `San Juan Bosco’ , Puerto Madryn, Chubut , Argentina
| | - Daniel Loebmann
- Laboratório de Vertebrados, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande , Rio Grande, Rio Grande do Sul , Brazil
| | - Robson W Ávila
- Departamento de Biologia, Núcleo Regional de Ofiologia da UFC, Universidade Federal do Ceará , Fortaleza, Ceará , Brazil
| | - Francisco Brusquetti
- Instituto de Investigación Biológica del Paraguay , Del Escudo, Asunción , Paraguay
| | - Ana L C Prudente
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém, Pará , Brazil
| | - Ward C Wheeler
- Division of Invertebrate Zoology, American Museum of Natural History , New York, NY , USA
| | - Victor Goyannes Dill Orrico
- Tropical Herpetology Laboratory, PPG Zoologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz , Ilhéus, Bahia , Brazil
| | - Pedro Peloso
- Laboratório de Herpetologia, Coordenação de Zoologia, Museu Paraense Emílio Goeldi , Belém, Pará , Brazil
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Babb-Biernacki SJ, Esselstyn JA, Doyle VP. Predicting Species Boundaries and Assessing Undescribed Diversity in Pneumocystis, an Obligate Lung Symbiont. J Fungi (Basel) 2022; 8:jof8080799. [PMID: 36012788 PMCID: PMC9409666 DOI: 10.3390/jof8080799] [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: 05/23/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Far more biodiversity exists in Fungi than has been described, or could be described in several lifetimes, given current rates of species discovery. Although this problem is widespread taxonomically, our knowledge of animal-associated fungi is especially lacking. Fungi in the genus Pneumocystis are obligate inhabitants of mammal lungs, and they have been detected in a phylogenetically diverse array of species representing many major mammal lineages. The hypothesis that Pneumocystis cospeciate with their mammalian hosts suggests that thousands of Pneumocystis species may exist, potentially equal to the number of mammal species. However, only six species have been described, and the true correspondence of Pneumocystis diversity to host species boundaries is unclear. Here, we use molecular species delimitation to estimate the boundaries of Pneumocystis species sampled from 55 mammal species representing eight orders. Our results suggest that Pneumocystis species often colonize several closely related mammals, especially those in the same genus. Using the newly estimated ratio of fungal to host diversity, we estimate ≈4600 to 6250 Pneumocystis species inhabit the 6495 currently recognized extant mammal species. Additionally, we review the literature and find that only 240 (~3.7%) mammal species have been screened for Pneumocystis, and many detected Pneumocystis lineages are not represented by any genetic data. Although crude, our findings challenge the dominant perspective of strict specificity of Pneumocystis to their mammal hosts and highlight an abundance of undescribed diversity.
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Affiliation(s)
- Spenser J. Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
- Correspondence:
| | - Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Vinson P. Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, LA 70809, USA;
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Zhu Q, Wang H, Zhou Z, Shi F. Phylogeny and Integrative Taxonomy of the Genera Gymnaetoides and Pseudotachycines (Orthoptera: Rhaphidophoridae). INSECTS 2022; 13:insects13070628. [PMID: 35886804 PMCID: PMC9322046 DOI: 10.3390/insects13070628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/29/2022]
Abstract
The genera Gymnaetoides and Pseudotachycines are endemic to China and are morphologically homogeneous. The few available diagnostic characters make species identification particularly challenging. Species cannot be classified according to the given generic diagnosis, and phylogenetic analyses have not been reported. Here, we reconstruct the phylogeny using Bayesian inference and maximum likelihood and employ four approaches to delimit species. The results suggest that both Gymnaetoides and Pseudotachycines are paraphyletic. Therefore, we revise their taxonomy based on the combination of morphological characters and molecular data. A new genus Homotachycines Zhu & Shi gen. nov. is erected, and six new combinations are proposed. Species delimitation identifies 15 new species and one new subspecies: Gymnaetoides huangshanensis, G. petalus, G. yangmingensis, G. lushanensis, Pseudotachycines procerus, P. procerus guizhouensis, P. zhengi, P. nephrus, P. sagittus, P. fengyangshanensis, Homotachycines triangulus, H. quadratus, H. baokangensis, H. fusus, H. concavus, and H. qinlingensis sp. nov. Moreover, we find that the shapes of the dorsal lateral lobes and the dorsal median lobe of the male genitalia are also important characters for identifying these genera and that the shapes of the dorsal and lateral sclerites of the male genitalia are suitable for the classifications of species.
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Affiliation(s)
- Qidi Zhu
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China;
- Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Haijian Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China;
| | - Zhijun Zhou
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China;
- Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
- Correspondence: (Z.Z.); (F.S.)
| | - Fuming Shi
- Key Laboratory of Zoological Systematics and Application of Hebei Province, College of Life Sciences, Hebei University, Baoding 071002, China;
- Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
- Correspondence: (Z.Z.); (F.S.)
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45
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Deng Z, Yao Y, Blair D, Hu W, Yin M. Ceriodaphnia (Cladocera: Daphniidae) in China: Lineage diversity, phylogeography and possible interspecific hybridization. Mol Phylogenet Evol 2022; 175:107586. [PMID: 35810974 DOI: 10.1016/j.ympev.2022.107586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/29/2022]
Abstract
The distribution and species/lineage diversity of freshwater invertebrate zooplankton remains understudied in China. Here, we explored the species/lineage diversity and phylogeography of Ceriodaphnia species across China. The taxonomy of this genus is under-explored. Seven morphospecies of Ceriodaphnia (C. cornuta, C. laticaudata, C. megops, C. pulchella, C. quadrangula, C. rotunda and C. spinata) were identified across 45 of 422 water bodies examined. Rather little morphological variation was observed within any single morphospecies regardless of country of origin. Nevertheless, we recognized that some or all of these morphospecies might represent species complexes. To investigate this, phylogenetic relationships within and among these morphospecies were investigated based on mitochondrial (partial cytochrome c oxidase subunit I gene) and nuclear (partial 28S rRNA gene) markers. The mitochondrial marker placed these populations in nine lineages corresponding to the morphospecies: C. laticaudata and C. pulchella were each represented by two lineages, suggesting that both are species complexes. The remaining five morphospecies were each represented by a single mtDNA lineage. Three of the nine mitochondrial lineages (belonging to C. pulchella, C. rotunda and C. megops) are newly reported and exhibited a restricted distribution within China. The nuclear-DNA phylogeny also recognized seven Ceriodaphnia taxa within China. We detected occasional mito-nuclear discordances in Ceriodaphnia taxa across China, suggesting interspecific introgression and hybridization. Our study contributes to an understanding of the species/lineage diversity of Ceriodaphnia, a genus with understudied taxonomy.
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Affiliation(s)
- Zhixiong Deng
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - Yiyang Yao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China
| | - David Blair
- College of Science and Engineering, James Cook University, Townsville, Qld 4811, Australia
| | - Wei Hu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China; Department of Microbiology and Bioengineering, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Mingbo Yin
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Science, Fudan University, Songhu Road 2005, Shanghai, China.
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Systematic Review of the Genus Nalepa Reitter, 1887 (Coleoptera, Tenebrionidae, Blaptinae, Blaptini) from the Tibetan Plateau, with Description of Six New Species and Two Larvae. INSECTS 2022; 13:insects13070598. [PMID: 35886774 PMCID: PMC9316563 DOI: 10.3390/insects13070598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 01/27/2023]
Abstract
Simple Summary The Tibetan Plateau is the largest and highest plateau in the world. The Tibetan Plateau is widely considered as a large natural experimental area for speciation; its uplift has facilitated allopatric speciation and diversification since the Miocene. In general, the Tibetan Plateau is known for its large number of endemic species. In this study, we revise the systematics of the endemic Tibetan genus Nalepa Reitter, 1887 (Blaptini tribe) and describe six new species based on larval and adult morphology and molecular data. We also provide a diagnostic key to the members of the genus Nalepa. Larvae were associated with the adults using a combined molecular species delimitation, and adult males and females are described and illustrated. Phylogenetic relationships of the members of the genus Nalepa are provided and discussed based on fragments of the mitochondrial and nuclear markers. Further, we applied molecular species delimitation methods to verify the taxonomic status of the new species. Lastly, the status of the genus Nalepa from the Tibetan Plateau is briefly discussed. Abstract Nalepa Reitter, 1887 is a monotypic genus of the tenebrionid tribe Blaptini and is endemic to the Tibetan Plateau. In this study, the genus Nalepa was reviewed using a combination of molecular and morphological datasets. Based on the results, six new species were described: N.acuminatasp. n., N. ovalifoliasp. n., N.politasp. n., N. quadratasp. n.,N.xinlongensissp. n., and N.yushuensissp. n. In addition, the larvae of N. cylindracea Reitter, 1887 and N. quadratasp. n. were described and associated with related adults using molecular approaches. This study provides valuable molecular and morphological data for phylogenetic studies.
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Zhang YM, Sheikh SI, Ward AKG, Forbes AA, Prior KM, Stone GN, Gates MW, Egan SP, Zhang L, Davis C, Weinersmith KL, Melika G, Lucky A. Delimiting the cryptic diversity and host preferences of Sycophila parasitoid wasps associated with oak galls using phylogenomic data. Mol Ecol 2022; 31:4417-4433. [PMID: 35762844 DOI: 10.1111/mec.16582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/06/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022]
Abstract
Cryptic species diversity is a major challenge for the species-rich community of parasitoids attacking oak gall wasps due to a high degree of sexual dimorphism, morphological plasticity, small size, and poorly known biology. As such, we know very little about the number of species present, nor the evolutionary forces responsible for generating this diversity. One hypothesis is that trait diversity in the gall wasps, including the morphology of the galls they induce, has evolved in response to selection imposed by the parasitoid community, with reciprocal selection driving diversification of the parasitoids. Using a rare, continental-scale data set of Sycophila parasitoid wasps reared from 44 species of cynipid galls from 18 species of oak across the US, we combined mitochondrial DNA barcodes, Ultraconserved Elements (UCEs), morphological, and natural history data to delimit putative species. Using these results, we generate the first large-scale assessment of ecological specialization and host association in this species-rich group, with implications for evolutionary ecology and biocontrol. We find most Sycophila target specific subsets of available cynipid host galls with similar morphologies, and generally attack larger galls. Our results suggest that parasitoid wasps such as Sycophila have adaptations allowing them to exploit particular host trait combinations, while hosts with contrasting traits are resistant to attack. These findings support the tritrophic niche concept for the structuring of plant-herbivore-parasitoid communities.
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Affiliation(s)
- Y Miles Zhang
- Systematic Entomology Laboratory, USDA-ARS, c/o National Museum of Natural History, Washington, DC, USA.,Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
| | - Sofia I Sheikh
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Anna K G Ward
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Kirsten M Prior
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Graham N Stone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Michael W Gates
- Systematic Entomology Laboratory, USDA-ARS, c/o National Museum of Natural History, Washington, DC, USA
| | - Scott P Egan
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Linyi Zhang
- Department of BioSciences, Rice University, Houston, TX, USA.,Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Charles Davis
- Department of BioSciences, Rice University, Houston, TX, USA.,Department of Entomology, Pennsylvania State University, University Park, PA, USA
| | | | - George Melika
- Plant Health and Molecular Biology Laboratory, Directorate of Plant Protection, Budapest, Hungary
| | - Andrea Lucky
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
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Abstract
Acari harbor numerous minute species of agricultural economic importance, mainly Tetranychidae and Phytoseiidae. Great efforts have been established by means of recovering morphological, molecular, and phylogenetic traits for species identification. Traditional identification still relies on external diagnostic characters, which are limited and usually exhibit large phenotypic plasticity within the species, rendering them useless for species delimitation and identification. We decided to increase the number of sequences of the Acari mitochondrial COI (Cytochrome C oxidase I) marker and ITS nuclear ribosomal DNA region for species identification in Tetranychidae and Phytoseiidae. The molecular data allow us to establish species boundaries and phylogenetic relationships among several clades of Acari, mainly Tetranychidae and Phytoseiidae. Sequence comparisons between complete COI and the Acari mitochondrial COI, ITS1-5,8S-ITS2, and ITS2 among all Acari sequences have demonstrated that the selected regions, even small, gave enough informative positions for both species’ identification and phylogenetic studies. Analyses of both DNA regions have unveiled their use as species identification characters, with special emphasis on Acari mitochondrial COI for Tetranychidae and Phytoseiidae species in comparison with the Folmer fragment, which has been universally used as a barcode marker. We demonstrated that the Acari mitochondrial COI region is also a suitable marker to establish a barcode dataset for Acari identification. Our phylogenetic analyses are congruent with other recent works, showing that Acari is a monophyletic group, of which Astigmata, Ixodida, Mesostigmata, Oribatida, and Prostigmata are also monophyletic.
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49
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Ranasinghe UGSL, Eberle J, Thormann J, Bohacz C, Benjamin SP, Ahrens D. Multiple species delimitation approaches with
COI
barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae). Ecol Evol 2022; 12:e8942. [PMID: 35600695 PMCID: PMC9120212 DOI: 10.1002/ece3.8942] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/14/2022] [Accepted: 05/04/2022] [Indexed: 11/07/2022] Open
Abstract
DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species‐rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology‐based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over‐splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio‐based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.
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Affiliation(s)
| | - Jonas Eberle
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- University of Salzburg Salzburg Austria
| | - Jana Thormann
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Claudia Bohacz
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
| | - Suresh P. Benjamin
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
- National Institute of Fundamental Studies Kandy Sri Lanka
| | - Dirk Ahrens
- Zoological Research Museum A. Koenig Leibniz Institute for the Analysis of Biodiversity Change (LIB) Bonn Germany
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50
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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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