1
|
Kotsakiozi P, Antoniou A, Psonis N, Sagonas Κ, Karameta E, Ilgaz Ç, Kumlutaş Y, Avcı A, Jablonski D, Darriba D, Stamatakis A, Lymberakis P, Poulakakis N. Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region. Mol Phylogenet Evol 2024; 197:108091. [PMID: 38719080 DOI: 10.1016/j.ympev.2024.108091] [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: 09/08/2023] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/20/2024]
Abstract
Cryptic diversity poses a great obstacle in our attempts to assess the current biodiversity crisis and may hamper conservation efforts. The gekkonid genus Mediodactylus, a well-known case of hidden species and genetic diversity, has been taxonomically reclassified several times during the last decade. Focusing on the Mediterranean populations, a recent study within the M. kotschyi species complex using classic mtDNA/nuDNA markers suggested the existence of five distinct species, some being endemic and some possibly threatened, yet their relationships have not been fully resolved. Here, we generated genome-wide SNPs (using ddRADseq) and applied molecular species delimitation approaches and population genomic analyses to further disentangle these relationships. Τhe most extensive nuclear dataset, so far, encompassing 2,360 loci and ∼ 699,000 bp from across the genome of Mediodactylus gecko, enabled us to resolve previously obscure phylogenetic relationships among the five, recently elevated, Mediodactylus species and to support the hypothesis that the taxon includes several new, undescribed species. Population genomic analyses within each of the proposed species showed strong genetic structure and high levels of genetic differentiation among populations.
Collapse
Affiliation(s)
- Panayiota Kotsakiozi
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece.
| | - Aglaia Antoniou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Heraklion 71003, P.O. Box 2214, Crete, Greece
| | - Nikolaos Psonis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Κostas Sagonas
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Emmanouela Karameta
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Çetin Ilgaz
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Yusuf Kumlutaş
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca/İzmir 35160, Türkiye
| | - Aziz Avcı
- Department of Biology, Faculty of Science, Aydın Adnan Menderes University, Aydın 09010, Türkiye
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Mlynská dolina, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Diego Darriba
- Computer Architecture Group, Centro de investigación CITIC, University of A Coruña, A Coruña, Spain
| | - Alexandros Stamatakis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Greece; Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76128, Germany
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion 71409, Greece; Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [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: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
Collapse
Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
| |
Collapse
|
4
|
Santos-Perdomo I, Suárez D, Moraza ML, Arribas P, Andújar C. Towards a Canary Islands barcode database for soil biodiversity: revealing cryptic and unrecorded mite species diversity within insular soils. Biodivers Data J 2024; 12:e113301. [PMID: 38314123 PMCID: PMC10838043 DOI: 10.3897/bdj.12.e113301] [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: 09/26/2023] [Accepted: 12/23/2023] [Indexed: 02/06/2024] Open
Abstract
Soil arthropod diversity contributes to a high proportion of the total biodiversity on Earth. However, most soil arthropods are still undescribed, hindering our understanding of soil functioning and global biodiversity estimations. Inventorying soil arthropods using conventional taxonomical approaches is particularly difficult and costly due to the great species richness, abundance and local-scale heterogeneity of mesofauna communities and the poor taxonomic background knowledge of most lineages. To alleviate this situation, we have designed and implemented a molecular barcoding framework adapted to soil fauna. This pipeline includes different steps, starting with a morphology-based selection of specimens which are imaged. Then, DNA is extracted non-destructively. Both images and voucher specimens are used to assign a taxonomic identification, based on morphology that is further checked for consistency with molecular information. Using this procedure, we studied 239 specimens of mites from the Canary Islands including representatives of Mesostigmata, Sarcoptiformes and Trombidiformes, of which we recovered barcode sequences for 168 specimens that were morphologically identified to 49 species, with nine specimens that could only be identified at the genus or family levels. Multiple species delimitation analyses were run to compare molecular delimitations with morphological identifications, including ASAP, mlPTP, BINs and 3% and 8% genetic distance thresholds. Additionally, a species-level search was carried out at the Biodiversity Databank of the Canary Islands (BIOTA) to evaluate the number of species in our dataset that were not previously recorded in the archipelago. In parallel, a sequence-level search of our sequences was performed against BOLD Systems. Our results reveal that multiple morphologically identified species correspond to different molecular lineages, which points to significant levels of unknown cryptic diversity within the archipelago. In addition, we evidenced that multiple species in our dataset constituted new records for the Canary Islands fauna and that the information for these lineages within online genetic repositories is very incomplete. Our study represents the first systematic effort to catalogue the soil arthropod mesofauna of the Canary Islands and establishes the basis for the Canary Islands Soil Biodiversity barcode database. This resource will constitute a step forward in the knowledge of these arthropods in a region of special interest.
Collapse
Affiliation(s)
- Irene Santos-Perdomo
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206, La Laguna, Spain Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 La Laguna Spain
- School of Doctoral and Postgraduate Studies, University of La Laguna, 38206, La Laguna, Spain School of Doctoral and Postgraduate Studies, University of La Laguna, 38206 La Laguna Spain
| | - Daniel Suárez
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206, La Laguna, Spain Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 La Laguna Spain
- School of Doctoral and Postgraduate Studies, University of La Laguna, 38206, La Laguna, Spain School of Doctoral and Postgraduate Studies, University of La Laguna, 38206 La Laguna Spain
| | - María L Moraza
- Universidad de Navarra, Instituto de Biodiversidad y Medioambiente BIOMA, Irunlarrea 1, 31008, Pamplona, Spain Universidad de Navarra, Instituto de Biodiversidad y Medioambiente BIOMA, Irunlarrea 1, 31008 Pamplona Spain
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206, La Laguna, Spain Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 La Laguna Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206, La Laguna, Spain Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), 38206 La Laguna Spain
| |
Collapse
|
5
|
Serrano M, Ortiz S. Species Delimitation in a Polyploid Group of Iberian Jasione (Campanulaceae) Unveils Coherence between Cryptic Speciation and Biogeographical Regionalization. PLANTS (BASEL, SWITZERLAND) 2023; 12:4176. [PMID: 38140501 PMCID: PMC10747609 DOI: 10.3390/plants12244176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Groups with morphological stasis are an interesting framework to address putative cryptic species that may be hidden behind traditional taxonomic treatments, particularly when distribution ranges suggest disjunct and environmentally heterogeneous biogeographic patterns. New hypotheses of delimitation of evolutionary independent units can lead to the identification of different biogeographic processes, laying the foundation to investigate their historical and ecological significance. Jasione is a plant genus with a distribution centered in the Mediterranean basin, characterized by significant morphological stasis. Within the western Mediterranean J. gr. crispa species complex, J. sessiliflora s.l. and allied taxa form a distinct group, occupying environmentally diverse regions. At least two ploidy levels, diploid and tetraploid, are known to occur in the group. The internal variability is assessed with phylogenetic tools, viz. GMYC and ASAP, for species delimitation. The results are compared with other lines of evidence, including morphology and cytology. The fitting of distribution patterns of the inferred entities to chorological subprovinces is also used as a biogeographical and environmental framework to test the species hypothesis. Despite the scarcity of diagnostic morphological characters in the group, phylogenetic delimitation supports the description of at least one cryptic species, a narrow endemic in the NE Iberian Peninsula. Moreover, the results support the segregation of a thermophilic group of populations in eastern Iberia from J. sessiliflora. Ploidy variation from a wide geographical survey supports the systematic rearrangement suggested by species delimitation. Taxonomic reorganization in J. sessiliflora s.l. would allow ecological interpretations of distribution patterns in great accordance with biogeographical regionalization at the subprovince level, supporting geobotanical boundaries as a framework to interpret species ecological coherence of cryptic lineages. These results suggest that species differentiation, together with geographic isolation and polyploidization, is associated with adaptation to different environments, shifting from more to less thermophilic conditions. Thus, the recognition of concealed evolutionary entities is essential to correctly interpret biogeographical patterns in regions with a complex geologic and evolutionary history, such as the Mediterranean basin, and biogeographical units emerge as biologically sound frameworks to test the species hypothesis.
Collapse
Affiliation(s)
- Miguel Serrano
- Department of Botany, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | | |
Collapse
|
6
|
Zurita-Artaloitia JM, Rivera J, Vinuesa P. Extensive Cryptic Diversity and Ecological Associations Uncovered among Mexican and Global Collections of Naegleria and Vermamoeba Species by 18S Ribosomal DNA, Internal Transcribed Spacer, and Cytochrome Oxidase Subunit I Sequence Analysis. Microbiol Spectr 2023; 11:e0379522. [PMID: 36943092 PMCID: PMC10100766 DOI: 10.1128/spectrum.03795-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/26/2023] [Indexed: 03/23/2023] Open
Abstract
Free-living amoebae (FLA) are phagocytic protists that play crucial roles in microbial communities as significant microbial grazers. However, our current knowledge of their diversity, ecology, and population genetic structures is marginal due to the shallow and biased sampling of ecosystems and the use of few, poorly resolving molecular markers. Thirty-two FLA were isolated from soil and water samples collected across representative ecosystems of the State of Morelos in Central Mexico, including the drinking water distribution system (DWDS) from the state capital. We classified our isolates as members of Acanthamoeba, Vermamoeba, Naegleria, and Tetramitus by 18S ribosomal DNA (rDNA) sequencing. Vermamoeba isolates were recovered exclusively from the DWDS samples. In contrast, Naegleria strains displayed a broad distribution in soil and water samples across the natural ecosystems. We used a combination of phylogenetic and population genetic analyses of internal transcribed spacer (ITS) and cytochrome oxidase subunit I (COI) sequences from our isolates and a comprehensive set of reference sequences to analyze the currently known diversity of Naegleria spp. Significant associations were uncovered between the most prevalent lineages of Naegleria and Vermamoeba and broad ecological and geographical variables at regional and global levels. The population structure and cryptic diversity within the Naegleria galeacystis-Naegleria americana and Vermamoeba vermiformis species complexes were thoroughly analyzed. Our results prove that the genus Vermamoeba, which was previously thought to consist of only one species, actually encompasses at least seven widely distributed species, as indicated by consistent evidence from Bayesian phylogenetics, two species-delimitation programs, and population genetics analyses. IMPORTANCE Our study sheds new light on the population genetic structure of V. vermiformis and diverse Naegleria species. Using improved molecular markers and advanced analytical approaches, we discovered that N. americana, previously considered a single species, actually contains multiple distinct lineages, as revealed by COI sequencing. These lineages are highly differentiated, with little gene flow between them. Our findings demonstrate that the genus Vermamoeba holds multiple cryptic species, requiring a significant taxonomic revision in light of multilocus sequence analyses. These results advance our understanding of the ecology, molecular systematics, and biogeography of these genera and species complexes at both regional and global scales. This study has significant implications for diagnosing amoebal infections and evaluating health risks associated with FLA in domestic and recreational waters.
Collapse
Affiliation(s)
| | - Javier Rivera
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| |
Collapse
|
7
|
Kayastha P, Stec D, Sługocki Ł, Gawlak M, Mioduchowska M, Kaczmarek Ł. Integrative taxonomy reveals new, widely distributed tardigrade species of the genus Paramacrobiotus (Eutardigrada: Macrobiotidae). Sci Rep 2023; 13:2196. [PMID: 36750641 PMCID: PMC9905614 DOI: 10.1038/s41598-023-28714-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/23/2023] [Indexed: 02/09/2023] Open
Abstract
In a moss sample collected in Ribeiro Frio, Madeira, Paramacrobiotus gadabouti sp. nov. was found and described using the integrative taxonomy approach. The new species is described based on morphological and morphometric data from both phase-contrast light microscopy (PCM), as well as scanning electron microscopy (SEM). Moreover, four DNA markers, three nuclear (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial (COI) markers, were used to elucidate the phylogenetic position of the new species within the family Macrobiotidae. The new species has a microplacoid that placed it within Parmacrobiotus richtersi group and exhibit richtersi-type eggs having processes terminated with cap-like structures. Paramacrobiotus gadabouti sp. nov. is most similar to Pam. alekseevi, Pam. filipi and Pam. garynahi, but differs from them mainly in details of egg morphology and morphometrics. Unlike other species from this group, which were confirmed as bisexual and showed limited distribution, Paramacrobiotus gadabouti sp. nov. is yet another parthenogenetic species with a wide distribution, demonstrating that at least some tardigrades confirm to the hypothesis of 'everything is everywhere'.
Collapse
Affiliation(s)
- Pushpalata Kayastha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Daniel Stec
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016, Kraków, Poland
| | - Łukasz Sługocki
- Department of Hydrobiology, Institute of Biology, University of Szczecin, Szczecin, Poland
| | - Magdalena Gawlak
- The Institute of Plant Protection-National Research Institute, Węgorka 20, 60-318, Poznań, Poland
| | - Monika Mioduchowska
- Department of Evolutionary Genetics and Biosystematics, Faculty of Biology, University of Gdańsk, Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Łukasz Kaczmarek
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| |
Collapse
|
8
|
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.
Collapse
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:
| |
Collapse
|
9
|
Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson R, Visagie C, Yilmaz N, Gené J, Cano J, Chen A, Nováková A, Yaguchi T, Kolařík M, Hubka V. Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Stud Mycol 2022; 102:53-93. [PMID: 36760461 PMCID: PMC9903908 DOI: 10.3114/sim.2022.102.02] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022] Open
Abstract
Aspergillus series Versicolores members occur in a wide range of environments and substrates such as indoor environments, food, clinical materials, soil, caves, marine or hypersaline ecosystems. The taxonomy of the series has undergone numerous re-arrangements including a drastic reduction in the number of species and subsequent recovery to 17 species in the last decade. The identification to species level is however problematic or impossible in some isolates even using DNA sequencing or MALDI-TOF mass spectrometry indicating a problem in the definition of species boundaries. To revise the species limits, we assembled a large dataset of 518 strains. From these, a total of 213 strains were selected for the final analysis according to their calmodulin (CaM) genotype, substrate and geography. This set was used for phylogenetic analysis based on five loci (benA, CaM, RPB2, Mcm7, Tsr1). Apart from the classical phylogenetic methods, we used multispecies coalescence (MSC) model-based methods, including one multilocus method (STACEY) and five single-locus methods (GMYC, bGMYC, PTP, bPTP, ABGD). Almost all species delimitation methods suggested a broad species concept with only four species consistently supported. We also demonstrated that the currently applied concept of species is not sustainable as there are incongruences between single-gene phylogenies resulting in different species identifications when using different gene regions. Morphological and physiological data showed overall lack of good, taxonomically informative characters, which could be used for identification of such a large number of existing species. The characters expressed either low variability across species or significant intraspecific variability exceeding interspecific variability. Based on the above-mentioned results, we reduce series Versicolores to four species, namely A. versicolor, A. creber, A. sydowii and A. subversicolor, and the remaining species are synonymized with either A. versicolor or A. creber. The revised descriptions of the four accepted species are provided. They can all be identified by any of the five genes used in this study. Despite the large reduction in species number, identification based on phenotypic characters remains challenging, because the variation in phenotypic characters is high and overlapping among species, especially between A. versicolor and A. creber. Similar to the 17 narrowly defined species, the four broadly defined species do not have a specific ecology and are distributed worldwide. We expect that the application of comparable methodology with extensive sampling could lead to a similar reduction in the number of cryptic species in other extensively studied Aspergillus species complexes and other fungal genera. Citation: Sklenář F, Glässnerová K, Jurjević Ž, Houbraken J, Samson RA, Visagie CM, Yilmaz N, Gené J, Cano J, Chen AJ, Nováková A, Yaguchi T, Kolařík M, Hubka V (2022). Taxonomy of Aspergillus series Versicolores: species reduction and lessons learned about intraspecific variability. Studies in Mycology 102 : 53-93. doi: 10.3114/sim.2022.102.02.
Collapse
Affiliation(s)
- F. Sklenář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic;,*Corresponding author: V. Hubka, ; F. Sklenář,
| | - K. Glässnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ž. Jurjević
- EMSL Analytical, Cinnaminson, New Jersey, USA
| | - J. Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - R.A. Samson
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - C.M. Visagie
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - N. Yilmaz
- Department of Biochemistry, Genetics, and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - J. Gené
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - J. Cano
- Unitat de Micologia, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - A.J. Chen
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd., Guangzhou, China
| | - A. Nováková
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - T. Yaguchi
- Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan
| | - M. Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - V. Hubka
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic;, Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic;, Medical Mycology Research Center, Chiba University, Chuo-ku, Chiba, Japan,*Corresponding author: V. Hubka, ; F. Sklenář,
| |
Collapse
|
10
|
Massimino Cocuzza GE, Magoga G, Montagna M, Nieto Nafría JM, Barbagallo S. European and Mediterranean Myzocallidini Aphid Species: DNA Barcoding and Remarks on Ecology with Taxonomic Modifications in An Integrated Framework. INSECTS 2022; 13:1006. [PMID: 36354832 PMCID: PMC9693350 DOI: 10.3390/insects13111006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
The genus Myzocallis Passerini (Hemiptera, Aphididae, Calaphidinae, Myzocallidini) is a rather primitive group of aphids currently comprising 45 species and 3 subspecies, subdivided into ten subgenera, three of them having a West Palaearctic distribution. The majority of the species inhabit Fagales plants and some of them are considered pests. Despite their ecological interest and the presence of some taxonomic controversies, there are only a few molecular studies on the group. Here, the main aims were to develop a DNA barcodes library for the molecular identification of West Palaearctic Myzocallis species, to evaluate the congruence among their morphological, ecological and DNA-based delimitation, and verify the congruence of the subgeneric subdivision presently adopted by comparing the results with those obtained for other Panaphidini species. These study findings indicate that Myzocallis (Agrioaphis) leclanti, originally described as a subspecies of M. (A.) castanicola and M. (M.) schreiberi, considered as a subspecies of M. (M.) boerneri, should be regarded at a rank of full species, and the subgenera Agrioaphis, Lineomyzocallis, Neomyzocallis, Pasekia were elevated to the rank of genus, while Myzocallis remain as such.
Collapse
Affiliation(s)
| | - Giulia Magoga
- Dipartimento di Scienze Agrarie ed Ambientali (DISAA), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Matteo Montagna
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Via Università 100, 80055 Portici, Italy
- BAT Center–Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, Via Università 100, 80055 Portici, Italy
| | | | - Sebastiano Barbagallo
- Dipartimento di Agricoltura, Alimentazione e Ambiente, University of Catania, 95123 Catania, Italy
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Stec D, Cancellario T, Fontaneto D. Diversification rates in Tardigrada indicate a decreasing tempo of lineage splitting regardless of reproductive mode. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00578-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractUnderstanding the dynamics of speciation and extinction events is one of the most interesting subjects in evolutionary biology that relates to all life forms, even the smallest ones. Tardigrades are microscopic invertebrates that attracted public and scientific attention mostly due to their ability to enter into the diapause stage called cryptobiosis and in such stage resist extremely harsh environmental conditions. However, although recent research solved a considerable number of phylogenetic uncertainties and further uncovered physiological mechanisms of cryptobiosis, not much attention is given to the evolutionary forces shaping tardigrade diversity. Here, we investigated the effect of reproductive mode on diversification rates in tardigrades using three groups: macrobiotids, echiniscids and milnesids, which represent low, moderate and high levels of parthenogenesis, respectively. Our results showed a decreasing tempo of diversification events for each of the studied groups without any differences that could be ascribed to reproductive mode. We discussed the observed lack of effect in tardigrades acknowledging deficiencies in available data sets and encouraging further studies to understand whether our results can be considered reliable.
Collapse
|
13
|
Magoga G, Forni G, Brunetti M, Meral A, Spada A, De Biase A, Montagna M. Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins. Database (Oxford) 2022; 2022:6633260. [PMID: 35796594 PMCID: PMC9261288 DOI: 10.1093/database/baac055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/15/2022]
Abstract
DNA metabarcoding is a widespread approach for the molecular identification of organisms. While the associated wet-lab and data processing procedures are well established and highly efficient, the reference databases for taxonomic assignment can be implemented to improve the accuracy of identifications. Insects are among the organisms for which DNA-based identification is most commonly used; yet, a DNA-metabarcoding reference database specifically curated for their species identification using software requiring local databases is lacking. Here, we present COins, a database of 5’ region cytochrome c oxidase subunit I sequences (COI-5P) of insects that includes over 532 000 representative sequences of >106 000 species specifically formatted for the QIIME2 software platform. Through a combination of automated and manually curated steps, we developed this database starting from all COI sequences available in the Barcode of Life Data System for insects, focusing on sequences that comply with several standards, including a species-level identification. COins was validated on previously published DNA-metabarcoding sequences data (bulk samples from Malaise traps) and its efficiency compared with other publicly available reference databases (not specific for insects). COins can allow an increase of up to 30% of species-level identifications and thus can represent a valuable resource for the taxonomic assignment of insects’ DNA-metabarcoding data, especially when species-level identification is needed https://doi.org/10.6084/m9.figshare.19130465.v1.
Collapse
Affiliation(s)
- Giulia Magoga
- Department of Agricultural and Environmental Sciences, University of Milan , Via Celoria 2, Milano 20133, Italy
| | - Giobbe Forni
- Department of Agricultural and Environmental Sciences, University of Milan , Via Celoria 2, Milano 20133, Italy
| | - Matteo Brunetti
- Department of Agricultural and Environmental Sciences, University of Milan , Via Celoria 2, Milano 20133, Italy
| | - Aycan Meral
- Department of Agricultural and Environmental Sciences, University of Milan , Via Celoria 2, Milano 20133, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences, University of Milan , Via Celoria 2, Milano 20133, Italy
| | - Alessio De Biase
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome , Viale dell’Università 32, Rome 00185, Italy
| | - Matteo Montagna
- Department of Agricultural Sciences, University of Naples Federico II , Via Università 100, Portici 80055, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II , Via Università 100, Naples 80055, Italy
| |
Collapse
|
14
|
Bellin N, Calzolari M, Magoga G, Callegari E, Bonilauri P, Lelli D, Dottori M, Montagna M, Rossi V. Unsupervised machine learning and geometric morphometrics as tools for the identification of inter and intraspecific variations in the Anopheles Maculipennis complex. Acta Trop 2022; 233:106585. [PMID: 35787418 DOI: 10.1016/j.actatropica.2022.106585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/08/2022] [Accepted: 06/30/2022] [Indexed: 11/01/2022]
Abstract
Geometric morphometric analysis was combined with two different unsupervised machine learning algorithms, UMAP and HDBSCAN, to visualize morphological differences in wing shape among and within four Anopheles sibling species (An. atroparvus, An. melanoon, An. maculipennis s.s. and An. daciae sp. inq.) of the Maculipennis complex in Northern Italy. Specifically, we evaluated: 1) wing shape variation among and within species; 2) the consistencies between groups of An. maculipennis s.s. and An. daciae sp. inq. identified based on COI sequences and wing shape variability; and 3) the spatial and temporal distribution of different morphotypes. UMAP detected at least 13 main patterns of variation in wing shape among the four analyzed species and mapped intraspecific morphological variations. The relationship between the most abundant COI haplotypes of An. daciae sp. inq. and shape ordination/variation was not significant. However, morphological variation within haplotypes was reported. HDBSCAN also recognized different clusters of morphotypes within An. daciae sp. inq. (12) and An. maculipennis s.s. (4). All morphotypes shared a similar pattern of variation in the subcostal vein, in the anal vein and in the radio-medial cross-vein of the wing. On the contrary, the marginal part of the wings remained unchanged in all clusters of both species. Any spatial-temporal significant difference was observed in the frequency of the identified morphotypes. Our study demonstrated that machine learning algorithms are a useful tool combined with geometric morphometrics and suggest to deepen the analysis of inter and intra specific shape variability to evaluate evolutionary constrains related to wing functionality.
Collapse
Affiliation(s)
- Nicolò Bellin
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze, 11/A 43124 Parma, Italy.
| | - Mattia Calzolari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna ''B. Ubertini'' (IZSLER), Brescia, Italy
| | - Giulia Magoga
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali, Via Celoria 2, 20133 Milan, Italy
| | - Emanuele Callegari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna ''B. Ubertini'' (IZSLER), Brescia, Italy
| | - Paolo Bonilauri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna ''B. Ubertini'' (IZSLER), Brescia, Italy
| | - Davide Lelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna ''B. Ubertini'' (IZSLER), Brescia, Italy
| | - Michele Dottori
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna ''B. Ubertini'' (IZSLER), Brescia, Italy
| | - Matteo Montagna
- Università degli Studi di Milano, Dipartimento di Scienze Agrarie e Ambientali, Via Celoria 2, 20133 Milan, Italy
| | - Valeria Rossi
- University of Parma, Department of Chemistry, Life Sciences and Environmental Sustainability, Parco Area delle Scienze, 11/A 43124 Parma, Italy
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Bhaskar R, Das MK, Sharon EA, Kumar RR, R. G. C. Genetic identification of marine eels (Anguilliformes: Congroidei) through DNA barcoding from Kasimedu fishing harbour. Mitochondrial DNA B Resour 2021; 6:3354-3361. [PMID: 34790868 PMCID: PMC8592592 DOI: 10.1080/23802359.2021.1996291] [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] [Indexed: 11/03/2022] Open
Abstract
Along with the mysteries of their body's shape like snakes, marine eels have fascinated biologists for centuries. Information on the molecular taxonomy of marine eels is scarce from the Southeast Indian region and hence, the present study aimed to barcode marine eels collected from Kasimedu fishing harbor, Chennai, Tamil Nadu. A total of 44 specimens were collected and DNA barcoding was done with a COI marker. The evolutionary history was inferred using the BA method. We observed 17 species, 10 genera, 4 families from the suborder Congroidei of which the genus Ariosoma and Conger were found to be predominant. The species of the family Muraenesocidae and Congridae are highly variable. The average Kimura two-parameter (K2P) distances within species, genera, and families were 3.08%, 6.80%, 13.80%, respectively. Maximum genetic distance (0.307) was observed between the species Muraenesox cinereus and Ariosoma sp.1. BA tree topology revealed distinct clusters in concurrence with the taxonomic status of the species. A deeper split was observed in Uroconger lepturus. We sequenced for the first-time barcode of Sauromuraenesox vorax and a new species Ophichthus chennaiensis is the gap-filling in identifying this taxon in the Indian context. We found a correct match between morphological and genetic identification of the species analyzed, depending on the cluster analysis performed (BINs and ASAP). This demonstrates that the COI gene sequence is suitable for phylogenetic analysis and species identification.
Collapse
Affiliation(s)
- Ranjana Bhaskar
- Zoological Survey of India, Southern Regional Centre, Chennai, India
| | - Mrinal Kumar Das
- Zoological Survey of India, Marine Biology Regional Centre, Chennai, India
| | - E. Agnita Sharon
- Zoological Survey of India, Southern Regional Centre, Chennai, India
| | | | - Chandika R. G.
- Zoological Survey of India, Southern Regional Centre, Chennai, India
| |
Collapse
|