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Corrêa de Barros R, Moreira da Rocha R. Genetic analyses reveal cryptic diversity in the widely distributed Styela canopus (Ascidiacea:Styelidae). INVERTEBR SYST 2021. [DOI: 10.1071/is20058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The routine use of DNA sequencing techniques and phylogenetic analysis has resulted in the discovery of many cryptic species, especially in the oceans. The common, globally introduced species Styela canopus is suspected to be a complex of cryptic species because of its widespread distribution and variable external morphology. We tested this possibility using COI and ANT marker sequences to uncover the phylogenetic relationship among 19 populations, and to examine genetic variability as well as gene flow. We obtained 271 COI and 67 ANT sequences and found surprising diversity among the 19 populations (COI: π = 0.18, hd = 0.99; ANT: π = 0.13, hd = 0.95). Corresponding topologies were found using Bayesian inference and maximum likelihood for both simple locus (COI) and multilocus (COI + ANT) analyses and so the clades received strong support. We used simple (ABGD, bPTP, GMYC) and multiple (BSD) locus methods to delimit species. The simple locus methods indicated that the current Styela canopus comprises at least 15 species. The BSD method for concatenated data supported 7 of the 15 species. We suggest that S. canopus should be treated as the Styela canopus complex. The large number of cryptic species found, often with more than one clade found in sympatry, creates opportunities for better understanding reproductive isolation, hybridisation or speciation. As several lineages have already been introduced widely around the world, we must quickly understand their diversity and invasive abilities.
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Wang T, Qi D, Sun S, Liu Z, Du Y, Guo S, Ma J. DNA barcodes and their characteristic diagnostic sites analysis of Schizothoracinae fishes in Qinghai province. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:592-601. [PMID: 30952197 DOI: 10.1080/24701394.2019.1580273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Qinghai-Tibetan Plateau (QTP), the source and upper reaches of many Asian rivers, are crisscrossed by rivers and dotted with lakes. Schizothoracinae fishes, species native to the QTP, are distributed widely through these rivers and lakes. Over the past decades, ecological protection has become increasingly intense. The rapid acquisition of the genetic information and accurate gene sequence database are assumed to play an important role in the conservation of species diversity and biodiversity. In this study, 153 COI sequences (648bp in length) covering 13 species in 8 genera of Schizothoracinae fishes in Qinghai Province were used to determine whether barcode could identify Schizothoracinae species accurately. The average Kimura two parameter (K2P) genetic distances within and among species were 0.35% and 8.83%, respectively. The maximum K2P distance within species was observed in Gymnocypris eckloni (1.36%) while minimum K2P distance among species was observed between Chuanchia labiosa and Schizopygopsis pylzovi (0.23%). Overlaps existed in K2P distance intra- and inter- species based on both the genes. Eleven groups with 9 single-species groups and 2 multi-species groups were identified through Automatic Barcode Gap Discovery System, which were consistent with the overlaps of K2P distance. 96.7% as the accurate ratio for COI barcode was calculated and high solution was observed in the phylogenetic trees based on COI gene and Cyt b gene. Except for the similar results based on two genes above, COI barcode was more economical than Cyt b gene. The SOM model successfully predicted characteristic-diagnostic sites at species level: 36 characteristic-diagnostic sites from eight species, in which 12 from Gmnodiptychus pachycgeilus, 2 from Platypharodon extremus, 7 from Ptychobarbus kaznakovi, 2 from Schizopygopsis anteroventris, 2 from Schizopygopsis malacanthus, 3 from Schizopygopsis malacanthus chengi, 3 from Schizothorax dolichonema and 5 from Schizothorax lantsangensis. Our results show that Schizothoracinae fishes can be identified validly by using COI DNA barcode. Thirty-six characteristic-diagnostic sites were proposed to be applied into works of species identification for the Schizothoracinae fishes in Qinghai Province.
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Affiliation(s)
- Ting Wang
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Desheng Qi
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Shihao Sun
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Zhonghao Liu
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Yurong Du
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
| | - Songchang Guo
- c College of Animal Science and Technology , Hunan Agricultural University , Changsha , China
| | - Jianbin Ma
- a College of Life Sciences , Qinghai Normal University , Xining , China.,b Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibetan Plateau in Qinghai Province , Xining , China
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Yang F, Ding F, Chen H, He M, Zhu S, Ma X, Jiang L, Li H. DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2018; 2018:5160254. [PMID: 29849709 PMCID: PMC5937547 DOI: 10.1155/2018/5160254] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/11/2018] [Indexed: 02/06/2023]
Abstract
Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.
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Affiliation(s)
- Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Fei Ding
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Hong Chen
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Mingqi He
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Shixin Zhu
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
| | - Xin Ma
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Li Jiang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China
- Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Beijing 100038, China
| | - Haifeng Li
- Center for Bioresources & Drug Discovery and School of Biosciences & Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, China
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Sharina SN, Chernyshev AV, Zaslavskaya NI. Genetic diversity and phylogeny of limpets of the genus Nipponacmea (Patellogastropoda: Lottiidae) based on mitochondrial DNA sequences. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:703-710. [PMID: 27159730 DOI: 10.3109/24701394.2016.1174224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Species of the genus Nipponacmea inhabit only the Pacific coast of Asia, including the Russian Far East. Their external morphological characters are highly variable and often lead to misidentifications of species. So far, little research has been conducted using molecular markers. We used sequences from three mitochondrial genes (fragments of cytochrome c oxidase subunit I gene (COI), 12S and 16S rDNA). For comparison, additional genetic and taxonomic data on other species belonging to this genus were derived from GenBank. The molecular phylogenetic trees suggest that the species N. fuscoviridis and N. nigrans are species complexes. N. fuscoviridis is divided into three subgroups with high support and relatively large distances between them (N. fuscoviridis A, B and C); N. nigrans fall into two subgroups and one of them (N. nigrans A) is more closely related to N. moskalevi than to the other subgroup of N. nigrans (B).
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Affiliation(s)
- Svetlana N Sharina
- a A.V. Zhirmunsky Institute of Marine Biology , Vladivostok , Russian Federation.,b School of Natural Sciences , Far Eastern Federal University , Vladivostok , Russian Federation
| | - Alexei V Chernyshev
- a A.V. Zhirmunsky Institute of Marine Biology , Vladivostok , Russian Federation.,b School of Natural Sciences , Far Eastern Federal University , Vladivostok , Russian Federation
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González-Castro M, Rosso JJ, Mabragaña E, Díaz de Astarloa JM. Surfing among species, populations and morphotypes: Inferring boundaries between two species of new world silversides (Atherinopsidae). C R Biol 2015; 339:10-23. [PMID: 26705969 DOI: 10.1016/j.crvi.2015.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 11/16/2022]
Abstract
Atherinopsidae are widespread freshwater and shallow marine fish with singular economic importance. Morphological, genetical and life cycles differences between marine and estuarine populations were already reported in this family, suggesting ongoing speciation. Also, coexistence and interbreeding between closely related species were documented. The aim of this study was to infer boundaries among: (A) Odontesthes bonariensis and O. argentinensis at species level, and intermediate morphs; (B) the population of O. argentinensis of Mar Chiquita Lagoon and its marine conspecifics. To achieve this, we integrated, meristic, Geometrics Morphometrics and DNA Barcode approaches. Four groups were discriminated and subsequently characterized according to their morphological traits, shape and meristic characters. No shared haplotypes between O. bonariensis and O. argentinensis were found. Significative-meristic and body shape differences between the Mar Chiquita and marine individuals of O. argentinensis were found, suggesting they behave as well differentiated populations, or even incipient ecological species. The fact that the Odontesthes morphotypes shared haplotypes with both, O. argentinensis and O. bonariensis, but also possess meristic and morphometric distinctive traits open new questions related to the origin of this morphogroup.
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Affiliation(s)
- Mariano González-Castro
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Juan José Rosso
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ezequiel Mabragaña
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan Martín Díaz de Astarloa
- Grupo de Biotaxonomía Morfológica y molecular de peces, IIMyC-CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Lin J, Kong L, Li Q. DNA barcoding of true limpets (Order Patellogastropoda) along coast of China: a case study. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2310-4. [PMID: 25812056 DOI: 10.3109/19401736.2015.1022758] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, we applied a partial sequence of mitochondrial COI gene as DNA barcode to assess the viability of DNA barcoding for distinguishing Patellogastropoda. One-hundred thirty-five COI gene sequences were obtained from 13 species belonging to Nacellidae (Cellana) and Lottiidae (Lottia, Patelloida and Nipponacmea) along the coast of China. The alignment result of these sequences indicated the existence of insertions in mitochondrial COI gene of Patellogastropoda. The Kimura 2-parameter (K2P) distances within species and genera were 0.00-1.01% (average 0.07%) and 18.09-37.80% (average 24.07%), respectively, an obvious barcoding gap existed. All species in our study were clearly discriminated in all trees (neighbor-joining (NJ), Bayesian, and maximum likelihood (ML) tree) with a highly supported clade node. The character-based barcode method successfully identified 100% of the Patellogastropod species included, and performed well in discriminating Patellogastropod genera. The results of this study affirm that DNA barcoding based on the COI gene can identify species belonging to Patellogastropoda rapidly and accurately.
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Affiliation(s)
- Jiping Lin
- a Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
| | - Lingfeng Kong
- a Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
| | - Qi Li
- a Key Laboratory of Mariculture, Ministry of Education, Ocean University of China , Qingdao , China
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Benzaquem DC, Oliveira C, da Silva Batista J, Zuanon J, Porto JIR. DNA barcoding in pencilfishes (Lebiasinidae: Nannostomus) reveals cryptic diversity across the Brazilian Amazon. PLoS One 2015; 10:e0112217. [PMID: 25658694 PMCID: PMC4320009 DOI: 10.1371/journal.pone.0112217] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 10/11/2014] [Indexed: 11/24/2022] Open
Abstract
Nannostomus is comprised of 20 species. Popularly known as pencilfishes the vast majority of these species lives in the flooded forests of the Amazon basin and are popular in the ornamental trade. Among the lebiasinids, it is the only genus to have undergone more than one taxonomic revision. Even so, it still possesses poorly defined species. Here, we report the results of an application of DNA barcoding to the identification of pencilfishes and highlight the deeply divergent clades within four nominal species. We surveyed the sequence variation in the mtDNA cytochrome c oxidase subunit I gene among 110 individuals representing 14 nominal species that were collected from several rivers along the Amazon basin. The mean Kimura-2-parameter distances within species and genus were 2% and 19,0%, respectively. The deep lineage divergences detected in N. digrammus, N. trifasciatus, N. unifasciatus and N. eques suggest the existence of hidden diversity in Nannostomus species. For N. digrammus and N. trifasciatus, in particular, the estimated divergences in some lineages were so high that doubt about their conspecific status is raised.
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Affiliation(s)
- Denise Corrêa Benzaquem
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2.936, Petrópolis, CEP 69067-375, Manaus, AM, Brazil
| | - Claudio Oliveira
- Instituto de Biociências, Departamento de Morfologia, UNESP, CEP 18618-970 Botucatu, SP, Brazil
| | - Jaqueline da Silva Batista
- Laboratório de Fisiologia Comportamental e Evolução, Laboratório Temático de Biologia Molecular, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2.936, Petrópolis, CEP 69067-375, Manaus, AM, Brazil
| | - Jansen Zuanon
- Laboratório de Sistemática e Ecologia de Peixes, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2.936, Petrópolis, CEP 69067-375, Manaus, AM, Brazil
| | - Jorge Ivan Rebelo Porto
- Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia, Av. André Araújo, 2.936, Petrópolis, CEP 69067-375, Manaus, AM, Brazil
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Roxo FF, Ochoa LE, Costa-Silva GJ, Oliveira C. Species delimitation in Neoplecostomus (Siluriformes: Loricariidae) using morphologic and genetic approaches. ACTA ACUST UNITED AC 2015. [DOI: 10.1515/dna-2015-0014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractIn the present study, we compare the results of alpha taxonomy (based on morphology), DNA Barcoding method with a 2% genetic divergence threshold, and the GMYC (General Model Yule Coalescent) technique to identify species clusters in Neoplecostomus. We used partial sequences of mitochondrial COI (Cytochrome oxidase subunit I) for 59 specimens representing 13 valid species (Neoplecostomus bandeirante, N. jaguari, N. langeanii, N. paranensis, N. yapo, N. botucatu, N. selenae, N. doceensis, N. corumba, N. ribeirensis, N. microps, N. espiritosantensis and N. franciscoensis) of Neoplecostomus collected in all its distribution area. For the analysis we used Bayesian inference of phylogeny with relaxed clock methods on an arbitrary timescale, using BEAST. The ultrametrics genes trees obtained for each tree prior evaluated (Yule, Birth-death and coalescent Population Size) were used in the GMYC analysis to identify a time in the tree when the branching rate shifts (in forward time) from Yule and Birth-Death (species) to a coalescent (population) process. We found that the GMYC model using the Yule prior identified 11 groups, closer to the current taxonomy (13 species). GMYC analyses using other ultrametric gene trees estimated under alternative prior such as Birth-Death and Coalescent Population Size, identified 9 groups, results observed in the traditional 2% genetic distance threshold, resulting in a low number of species recognized compared to the number of species identified with current taxonomy. Based on these results we conclude that the molecular approaches are helpful to distinguish species of Neoplecostomus, nevertheless it is important to combine molecular methodologies with current taxonomy in order to identify correctly species that recently originated.
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Irisarri I, Eernisse DJ, Zardoya R. Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics. J NAT HIST 2014. [DOI: 10.1080/00222933.2014.963721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Versteirt V, Nagy ZT, Roelants P, Denis L, Breman FC, Damiens D, Dekoninck W, Backeljau T, Coosemans M, Van Bortel W. Identification of Belgian mosquito species (Diptera: Culicidae) by DNA barcoding. Mol Ecol Resour 2014; 15:449-57. [PMID: 25143182 DOI: 10.1111/1755-0998.12318] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/07/2014] [Accepted: 08/11/2014] [Indexed: 11/30/2022]
Abstract
Since its introduction in 2003, DNA barcoding has proven to be a promising method for the identification of many taxa, including mosquitoes (Diptera: Culicidae). Many mosquito species are potential vectors of pathogens, and correct identification in all life stages is essential for effective mosquito monitoring and control. To use DNA barcoding for species identification, a reliable and comprehensive reference database of verified DNA sequences is required. Hence, DNA sequence diversity of mosquitoes in Belgium was assessed using a 658 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene, and a reference data set was established. Most species appeared as well-supported clusters. Intraspecific Kimura 2-parameter (K2P) distances averaged 0.7%, and the maximum observed K2P distance was 6.2% for Aedes koreicus. A small overlap between intra- and interspecific K2P distances for congeneric sequences was observed. Overall, the identification success using best match and the best close match criteria were high, that is above 98%. No clear genetic division was found between the closely related species Aedes annulipes and Aedes cantans, which can be confused using morphological identification only. The members of the Anopheles maculipennis complex, that is Anopheles maculipennis s.s. and An. messeae, were weakly supported as monophyletic taxa. This study showed that DNA barcoding offers a reliable framework for mosquito species identification in Belgium except for some closely related species.
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Affiliation(s)
- V Versteirt
- Department of Biomedical Science, Vector Biology Group, Medical Entomology Unit, Institute of Tropical Medicine, Nationalestraat 155, Antwerp, B-2000, Belgium; Avia-GIS, Risschotlei 33, Zoersel, B-2980, Belgium
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Zhang G, Chen J, Yang Y, Liu N, Jiang W, Gu S, Wang X, Wang Z. Utility of DNA barcoding in distinguishing species of the family Taeniidae. J Parasitol 2014; 100:542-6. [PMID: 24611571 DOI: 10.1645/13-224.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The family Taeniidae comprises many parasitic species, which cause serious zoonoses. However, effective identification of Taeniidae species is a long-standing problem, especially in samples from wild hosts with mixed infections of different Taeniidae species. DNA barcoding analysis of small fragments of the cytochrome c oxidase subunit I (COI) gene has been confirmed as an effective and useful method for identifying Taenia species. We therefore performed DNA barcoding analysis using a 351-bp region of the COI gene to identify 27 taeniid species including 9 in the genus Echinococcus, 2 in Hydatigera, 15 in Taenia, and 1 in Versteria. A total of 484 COI sequences were used to calculate genetic divergence expressed by the Kimura 2-parameter (K2P) distance. The mean intra-specific K2P distance in the family Taeniidae was 0.71 ± 0.17% (±SE), while inter-specific divergences were considerably higher. We found that, generally, a 2.0% optimal barcoding threshold could be set to distinguish taeniid species. Taenia polyacantha and Hydatigera taeniaeformis were the only 2 false-positive species identification cases in this study for their intra-specific divergences above the 2.0% optimal threshold. Their high intra-specific divergences coincided with fact that cryptic divergences exist in these 2 species, to which new taxa were recommended. On the other hand, sister species T. asiatica and T. saginata showed a 2.48 ± 0.83% inter-specific divergence, which was the smallest among all the taeniid species. Although fitting the 2.0% optimal species barcoding threshold, the close genetic relationship between T. asiatica and T. saginata implies that longer mitochondrial DNA sequences like the complete COI sequence are needed to strictly distinguish them. Therefore, we concluded that the barcoding technique based on a 351-bp region of the COI gene is able to distinguish taeniid species except for cryptic T. polyacantha and H. taeniaeformis and should be carefully used in distinguishing the closely related species T. asiatica and T. saginata .
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Affiliation(s)
- Gaotian Zhang
- School of Life Sciences, East China Normal University, 200062 Shanghai, China
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Krug PJ, Vendetti JE, Rodriguez AK, Retana JN, Hirano YM, Trowbridge CD. Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control. Mol Phylogenet Evol 2013; 69:1101-19. [PMID: 23876292 DOI: 10.1016/j.ympev.2013.07.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 07/10/2013] [Accepted: 07/11/2013] [Indexed: 11/30/2022]
Abstract
DNA barcoding can highlight taxa in which conventional taxonomy underestimates species richness, identifying mitochondrial lineages that may correspond to unrecognized species. However, key assumptions of barcoding remain untested for many groups of soft-bodied marine invertebrates with poorly resolved taxonomy. Here, we applied an integrative approach for species delimitation to herbivorous sea slugs in clade Sacoglossa, in which unrecognized diversity may complicate studies of drug discovery, plastid endosymbiosis, and biological control. Using the mitochondrial barcoding COI gene and the nuclear histone 3 gene, we tested the hypothesis that three widely distributed "species" each comprised a complex of independently evolving lineages. Morphological and reproductive characters were then used to evaluate whether each lineage was distinguishable as a candidate species. The "circumtropical" Elysia ornata comprised a Caribbean species and four Indo-Pacific candidate species that are potential sources of kahalalides, anti-cancer compounds. The "monotypic" and highly photosynthetic Plakobranchus ocellatus, used for over 60 years to study chloroplast symbiosis, comprised 10 candidate species. Finally, six candidate species were distinguished in the Elysia tomentosa complex, including potential biological control agents for invasive green algae (Caulerpa spp.). We show that a candidate species approach developed for vertebrates effectively categorizes cryptic diversity in marine invertebrates, and that integrating threshold COI distances with non-molecular character data can delimit species even when common assumptions of DNA barcoding are violated.
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Affiliation(s)
- Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA 90032-8201, USA.
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Wong EHK, Shivji MS, Hanner RH. Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach. Mol Ecol Resour 2013; 9 Suppl s1:243-56. [PMID: 21564984 DOI: 10.1111/j.1755-0998.2009.02653.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Shark fisheries worldwide are mostly unmanaged, but the burgeoning shark fin industry in the last few decades has made monitoring catch and trade of these animals critical. As a tool for molecular species identification, DNA barcoding offers significant potential. However, the genetic distance-based approach towards species identification employed by the Barcode of Life Data Systems may oftentimes lack the specificity needed for regulatory or legal applications that require unambiguous identification results. This is because such specificity is not typically realized by anything less than a 100% match of the query sequence to an entry in the reference database using genetic distance. Although various divergence thresholds have been proposed to define acceptable levels of intraspecific variation, enough exceptions exist to cast reasonable doubt on many less than exact matches using a distance-based approach for the identification of unknowns. An alternative approach relies on the identification of discrete molecular characters that can be used to unambiguously diagnose species. The objective of this study was to assess the performance differences between these competing approaches by examining more than 1000 DNA barcodes representing nearly 20% of all known elasmobranch species. Our results demonstrate that a character-based, nucleotide diagnostic (ND) approach to barcode identification is feasible and also provides novel insights into the structure of haplotype diversity among closely related species of sharks. Considerations for the use of NDs in applied fields are also explored.
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Affiliation(s)
- Eugene H-K Wong
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2W1, Guy Harvey Research Institute and Save Our Seas Shark Center, Nova Southeastern University, 8000 North Ocean Drive, Dania Beach, FL 33004, USA
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Pereira LHG, Hanner R, Foresti F, Oliveira C. Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna? BMC Genet 2013; 14:20. [PMID: 23497346 PMCID: PMC3608943 DOI: 10.1186/1471-2156-14-20] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 03/05/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. RESULTS Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species. CONCLUSIONS Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.
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Affiliation(s)
- Luiz H G Pereira
- Laboratory of Biology and Genetic of Fish, Department of Morphology, Biosciences Institute, State University of São Paulo, São Paulo, Brazil.
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Sigwart JD, Stoeger I, Knebelsberger T, Schwabe E. Chiton phylogeny (Mollusca : Polyplacophora) and the placement of the enigmatic species Choriplax grayi (H. Adams & Angas). INVERTEBR SYST 2013. [DOI: 10.1071/is13013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Shallow marine chitons (Mollusca : Polyplacophora : Chitonida) are widespread and well described from established morphoanatomical characters, yet key aspects of polyplacophoran phylogeny have remained unresolved. Several species, including Hemiarthrum setulosum Carpenter in Dall, 1876, and especially the rare and enigmatic Choriplax grayi (Adams & Angas, 1864), defy systematic placement. Choriplax is known from only a handful of specimens and its morphology is a mosaic of key taxonomic features from two different clades. Here, new molecular evidence provides robust support for its correct association with a third different clade: Choriplax is placed in the superfamily Mopalioidea. Hemiarthrum is included in Cryptoplacoidea, as predicted from morphological evidence. Our multigene analysis of standard nuclear and mitochondrial markers demonstrates that the topology of the order Chitonida is divided into four clades, which have also been recovered in previous studies: Mopalioidea is sister to Cryptoplacoidea, forming a clade Acanthochitonina. The family Callochitonidae is sister to Acanthochitonina. Chitonoidea is resolved as the earliest diverging group within Chitonida. Consideration of this unexpected result for Choriplax and our well-supported phylogeny has revealed differing patterns of shell reduction separating the two superfamilies within Acanthochitonina. As in many molluscs, shell reduction as well as the de novo development of key shell features has occurred using different mechanisms, in multiple lineages of chitons.
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Abstract
Invertebrates comprise approximately 34 phyla, while vertebrates represent one subphylum and insects a (very large) class. Thus, the clades excepting vertebrates and insects encompass almost all of animal diversity. Consequently, the barcoding challenge in invertebrates is that of barcoding animals in general. While standard extraction, cleaning, PCR methods, and universal primers work for many taxa, taxon-specific challenges arise because of the shear genetic and biochemical diversity present across the kingdom, and because problems arising as a result of this diversity, and solutions to them, are still poorly characterized for many metazoan clades. The objective of this chapter is to emphasize general approaches, and give practical advice for overcoming the diverse challenges that may be encountered across animal taxa, but we stop short of providing an exhaustive inventory. Rather, we encourage researchers, especially those working on poorly studied taxa, to carefully consider methodological issues presented below, when standard approaches perform poorly.
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Affiliation(s)
- Nathaniel Evans
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
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Reid NM, Carstens BC. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evol Biol 2012; 12:196. [PMID: 23031350 PMCID: PMC3503838 DOI: 10.1186/1471-2148-12-196] [Citation(s) in RCA: 329] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 09/19/2012] [Indexed: 11/10/2022] Open
Abstract
Background Species are considered the fundamental unit in many ecological and evolutionary analyses, yet accurate, complete, accessible taxonomic frameworks with which to identify them are often unavailable to researchers. In such cases DNA sequence-based species delimitation has been proposed as a means of estimating species boundaries for further analysis. Several methods have been proposed to accomplish this. Here we present a Bayesian implementation of an evolutionary model-based method, the general mixed Yule-coalescent model (GMYC). Our implementation integrates over the parameters of the model and uncertainty in phylogenetic relationships using the output of widely available phylogenetic models and Markov-Chain Monte Carlo (MCMC) simulation in order to produce marginal probabilities of species identities. Results We conducted simulations testing the effects of species evolutionary history, levels of intraspecific sampling and number of nucleotides sequenced. We also re-analyze the dataset used to introduce the original GMYC model. We found that the model results are improved with addition of DNA sequence and increased sampling, although these improvements have limits. The most important factor in the success of the model is the underlying phylogenetic history of the species under consideration. Recent and rapid divergences result in higher amounts of uncertainty in the model and eventually cause the model to fail to accurately assess uncertainty in species limits. Conclusion Our results suggest that the GMYC model can be useful under a wide variety of circumstances, particularly in cases where divergences are deeper, or taxon sampling is incomplete, as in many studies of ecological communities, but that, in accordance with expectations from coalescent theory, rapid, recent radiations may yield inaccurate results. Our implementation differs from existing ones in two ways: it allows for the accounting for important sources of uncertainty in the model (phylogenetic and in parameters specific to the model) and in the specification of informative prior distributions that can increase the precision of the model. We have incorporated this model into a user-friendly R package available on the authors’ websites.
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Affiliation(s)
- Noah M Reid
- Department of Biological Science, Louisiana State University, Baton Rouge, LA 70803, USA.
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Taylor HR, Harris WE. An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding. Mol Ecol Resour 2012; 12:377-88. [PMID: 22356472 DOI: 10.1111/j.1755-0998.2012.03119.x] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA barcoding has become a well-funded, global enterprise since its proposition as a technique for species identification, delimitation and discovery in 2003. However, the rapid development of next generation sequencing (NGS) has the potential to render DNA barcoding irrelevant because of the speed with which it generates large volumes of genomic data. To avoid obsolescence, the DNA barcoding movement must adapt to use this new technology. This review examines the DNA barcoding enterprise, its continued resistance to improvement and the implications of this on the future of the discipline. We present the consistent failure of DNA barcoding to recognize its limitations and evolve its methodologies, reducing the usefulness of the data produced by the movement and throwing into doubt its ability to embrace NGS.
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Affiliation(s)
- H R Taylor
- Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Kelburn, PO Box 600 Wellington, New Zealand.
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Elmeer K, Almalki A, Mohran K, AL-Qahtani K, Almarri M. DNA barcoding of Oryx leucoryx using the mitochondrial cytochrome C oxidase gene. GENETICS AND MOLECULAR RESEARCH 2012; 11:539-47. [DOI: 10.4238/2012.march.8.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Clare EL, Lim BK, Fenton MB, Hebert PDN. Neotropical bats: estimating species diversity with DNA barcodes. PLoS One 2011; 6:e22648. [PMID: 21818359 PMCID: PMC3144236 DOI: 10.1371/journal.pone.0022648] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 06/27/2011] [Indexed: 11/18/2022] Open
Abstract
DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI) is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera). This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0-11.79%) with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.
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Affiliation(s)
- Elizabeth L Clare
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
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Markolf M, Brameier M, Kappeler PM. On species delimitation: yet another lemur species or just genetic variation? BMC Evol Biol 2011; 11:216. [PMID: 21777472 PMCID: PMC3225081 DOI: 10.1186/1471-2148-11-216] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 07/21/2011] [Indexed: 12/28/2022] Open
Abstract
Background Although most taxonomists agree that species are independently evolving metapopulation lineages that should be delimited with several kinds of data, the taxonomic practice in Malagasy primates (Lemuriformes) looks quite different. Several recently described lemur species are based solely on evidence of genetic distance and diagnostic characters of mitochondrial DNA sequences sampled from a few individuals per location. Here we explore the validity of this procedure for species delimitation in lemurs using published sequence data. Results We show that genetic distance estimates and Population Aggregation Analysis (PAA) are inappropriate for species delimitation in this group of primates. Intra- and interspecific genetic distances overlapped in 14 of 17 cases independent of the genetic marker used. A simulation of a fictive taxonomic study indicated that for the mitochondrial D-loop the minimum required number of individuals sampled per location is 10 in order to avoid false positives via PAA. Conclusions Genetic distances estimates and PAA alone should not be used for species delimitation in lemurs. Instead, several nuclear and sex-specific loci should be considered and combined with other data sets from morphology, ecology or behavior. Independent of the data source, sampling should be done in a way to ensure a quantitative comparison of intra- and interspecific variation of the taxa in question. The results of our study also indicate that several of the recently described lemur species should be reevaluated with additional data and that the number of good species among the currently known taxa is probably lower than currently assumed.
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Affiliation(s)
- Matthias Markolf
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany.
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22
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Pereira LHG, Pazian MF, Hanner R, Foresti F, Oliveira C. DNA barcoding reveals hidden diversity in the Neotropical freshwater fishPiabina argentea(Characiformes: Characidae) from the Upper Paraná Basin of Brazil. ACTA ACUST UNITED AC 2011; 22 Suppl 1:87-96. [DOI: 10.3109/19401736.2011.588213] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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23
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Reid BN, LE M, McCord WP, Iverson JB, Georges A, Bergmann T, Amato G, Desalle R, Naro-Maciel E. Comparing and combining distance-based and character-based approaches for barcoding turtles. Mol Ecol Resour 2011; 11:956-67. [PMID: 21635698 DOI: 10.1111/j.1755-0998.2011.03032.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Molecular barcoding can serve as a powerful tool in wildlife forensics and may prove to be a vital aid in conserving organisms that are threatened by illegal wildlife trade, such as turtles (Order Testudines). We produced cytochrome oxidase subunit one (COI) sequences (650 bp) for 174 turtle species and combined these with publicly available sequences for 50 species to produce a data set representative of the breadth of the order. Variability within the barcode region was assessed, and the utility of both distance-based and character-based methods for species identification was evaluated. For species in which genetic material from more than one individual was available (n = 69), intraspecific divergences were 1.3% on average, although divergences greater than the customary 2% barcode threshold occurred within 15 species. High intraspecific divergences could indicate species with a high degree of internal genetic structure or possibly even cryptic species, although introgression is also probable in some of these taxa. Divergences between species of the same genus were 6.4% on average; however, 49 species were <2% divergent from congeners. Low levels of interspecific divergence could be caused by recent evolutionary radiations coupled with the low rates of mtDNA evolution previously observed in turtles. Complementing distance-based barcoding with character-based methods for identifying diagnostic sets of nucleotides provided better resolution in several cases where distance-based methods failed to distinguish species. An online identification engine was created to provide character-based identifications. This study constitutes the first comprehensive barcoding effort for this seriously threatened order.
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Affiliation(s)
- B N Reid
- Department of Forest and Wildlife Ecology, University of Wisconsin, 1630 Linden Drive, Madison, WI 53706, USA.
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Nicolalde-Morejón F, Vergara-Silva F, González-Astorga J, Stevenson DW, Vovides AP, Sosa V. A character-based approach in the Mexican cycads supports diverse multigene combinations for DNA barcoding. Cladistics 2011; 27:150-164. [DOI: 10.1111/j.1096-0031.2010.00321.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Abstract
New insights in the speciation process and the nature of "species" that accumulated in the past decade demand adjustments of the species concept. The standing of some of the most broadly accepted or most innovative species concepts in the light of the growing evidence that reproductive barriers are semipermeable to gene flow, that species can differentiate despite ongoing interbreeding, that a single species can originate polyphyletically by parallel evolution, and that uniparental organisms are organised in units that resemble species of biparental organisms is discussed. As a synthesis of ideas in existing concepts and the new insights, a generalization of the genic concept is proposed that defines species as groups of individuals that are reciprocally characterized by features that would have negative fitness effects in other groups and that cannot be regularly exchanged between groups upon contact. The benefits of this differential fitness species concept are that it classifies groups that keep differentiated and keep on differentiating despite interbreeding as species, that it is not restricted to specific mutations or mechanisms causing speciation, and that it can be applied to the whole spectrum of organisms from uni- to biparentals.
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Affiliation(s)
- Bernhard Hausdorf
- Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany.
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Luo A, Zhang A, Ho SY, Xu W, Zhang Y, Shi W, Cameron SL, Zhu C. Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals. BMC Genomics 2011; 12:84. [PMID: 21276253 PMCID: PMC3042414 DOI: 10.1186/1471-2164-12-84] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 01/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagnose and delimit species. However, there is no compelling a priori reason for the exclusive focus on this region, and it has been shown that it performs poorly for certain animal groups. To explore alternative mitochondrial barcoding regions, we compared the efficacy of the universal CO1 barcoding region with the other mitochondrial protein-coding genes in eutherian mammals. Four criteria were used for this comparison: the number of recovered species, sequence variability within and between species, resolution to taxonomic levels above that of species, and the degree of mutational saturation. RESULTS Based on 1,179 mitochondrial genomes of eutherians, we found that the universal CO1 barcoding region is a good representative of mitochondrial genes as a whole because the high species-recovery rate (> 90%) was similar to that of other mitochondrial genes, and there were no significant differences in intra- or interspecific variability among genes. However, an overlap between intra- and interspecific variability was still problematic for all mitochondrial genes. Our results also demonstrated that any choice of mitochondrial gene for DNA barcoding failed to offer significant resolution at higher taxonomic levels. CONCLUSIONS We suggest that the CO1 barcoding region, the universal DNA barcode, is preferred among the mitochondrial protein-coding genes as a molecular diagnostic at least for eutherian species identification. Nevertheless, DNA barcoding with this marker may still be problematic for certain eutherian taxa and our approach can be used to test potential barcoding loci for such groups.
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Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
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Abstract
More than 230,000 known species representing 31 metazoan phyla populate the world's oceans. Perhaps another 1,000,000 or more species remain to be discovered. There is reason for concern that species extinctions may out-pace discovery, especially in diverse and endangered marine habitats such as coral reefs. DNA barcodes (i.e., short DNA sequences for species recognition and discrimination) are useful tools to accelerate species-level analysis of marine biodiversity and to facilitate conservation efforts. This review focuses on the usual barcode region for metazoans: a approximately 648 base-pair region of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Barcodes have also been used for population genetic and phylogeographic analysis, identification of prey in gut contents, detection of invasive species, forensics, and seafood safety. More controversially, barcodes have been used to delimit species boundaries, reveal cryptic species, and discover new species. Emerging frontiers are the use of barcodes for rapid and increasingly automated biodiversity assessment by high-throughput sequencing, including environmental barcoding and the use of barcodes to detect species for which formal identification or scientific naming may never be possible.
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Affiliation(s)
- Ann Bucklin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut 06340, USA.
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Hendrich L, Pons J, Ribera I, Balke M. Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates. PLoS One 2010; 5:e14448. [PMID: 21203427 PMCID: PMC3010977 DOI: 10.1371/journal.pone.0014448] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 12/06/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The demand for scientific biodiversity data is increasing, but taxonomic expertise is often limited or not available. DNA sequencing is a potential remedy to overcome this taxonomic impediment. Mitochondrial DNA is most commonly used, e.g., for species identification ("DNA barcoding"). Here, we present the first study in arthropods based on a near-complete species sampling of a family-level taxon from the entire Australian region. We aimed to assess how reliably mtDNA data can capture species diversity when many sister species pairs are included. Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured. METHODOLOGY/PRINCIPAL FINDINGS We sequenced 800 bp cox1 for 1,439 individuals including 260 Australian species (78% species coverage). We used clustering with thresholds of 1 to 10% and general mixed Yule Coalescent (GMYC) analysis for the estimation of species richness. The performance metrics used were taxonomic accuracy and agreement between the morphological and molecular species richness estimation. Clustering (at the 3% level) and GMYC reliably estimated species diversity for single or multiple geographic regions, with an error for larger clades of lower than 10%, thus outperforming parataxonomy. However, the rates of error were higher for some individual genera, with values of up to 45% when very recent species formed nonmonophyletic clusters. Taxonomic accuracy was always lower, with error rates above 20% and a larger variation at the genus level (0 to 70%). Sørensen similarity indices calculated for morphospecies, 3% clusters and GMYC entities for different pairs of localities was consistent among methods and showed expected decrease over distance. CONCLUSION/SIGNIFICANCE Cox1 sequence data are a powerful tool for large-scale species richness estimation, with a great potential for use in ecology and β-diversity studies and for setting conservation priorities. However, error rates can be high in individual lineages.
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Affiliation(s)
- Lars Hendrich
- Department of Entomology, Zoological State Collection, Munich, Germany
- GeoBioCenter, Ludwig-Maximilians-University, Munich, Germany
| | - Joan Pons
- Departament de Biodiversitat i Conservació, Institut Mediterrani d'Estudis Avançats, Esporles, Spain
| | | | - Michael Balke
- Department of Entomology, Zoological State Collection, Munich, Germany
- GeoBioCenter, Ludwig-Maximilians-University, Munich, Germany
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WEIGAND ALEXANDERM, JOCHUM ADRIENNE, PFENNINGER MARKUS, STEINKE DIRK, KLUSSMANN-KOLB ANNETTE. A new approach to an old conundrum-DNA barcoding sheds new light on phenotypic plasticity and morphological stasis in microsnails (Gastropoda, Pulmonata, Carychiidae). Mol Ecol Resour 2010; 11:255-65. [DOI: 10.1111/j.1755-0998.2010.02937.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Universal plant DNA barcode loci may not work in complex groups: a case study with Indian berberis species. PLoS One 2010; 5:e13674. [PMID: 21060687 PMCID: PMC2965122 DOI: 10.1371/journal.pone.0013674] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 10/06/2010] [Indexed: 11/25/2022] Open
Abstract
Background The concept of DNA barcoding for species identification has gained considerable momentum in animals because of fairly successful species identification using cytochrome oxidase I (COI). In plants, matK and rbcL have been proposed as standard barcodes. However, barcoding in complex genera is a challenging task. Methodology and Principal Findings We investigated the species discriminatory power of four reportedly most promising plant DNA barcoding loci (one from nuclear genome- ITS, and three from plastid genome- trnH-psbA, rbcL and matK) in species of Indian Berberis L. (Berberidaceae) and two other genera, Ficus L. (Moraceae) and Gossypium L. (Malvaceae). Berberis species were delineated using morphological characters. These characters resulted in a well resolved species tree. Applying both nucleotide distance and nucleotide character-based approaches, we found that none of the loci, either singly or in combinations, could discriminate the species of Berberis. ITS resolved all the tested species of Ficus and Gossypium and trnH-psbA resolved 82% of the tested species in Ficus. The highly regarded matK and rbcL could not resolve all the species. Finally, we employed amplified fragment length polymorphism test in species of Berberis to determine their relationships. Using ten primer pair combinations in AFLP, the data demonstrated incomplete species resolution. Further, AFLP analysis showed that there was a tendency of the Berberis accessions to cluster according to their geographic origin rather than species affiliation. Conclusions/Significance We reconfirm the earlier reports that the concept of universal barcode in plants may not work in a number of genera. Our results also suggest that the matK and rbcL, recommended as universal barcode loci for plants, may not work in all the genera of land plants. Morphological, geographical and molecular data analyses of Indian species of Berberis suggest probable reticulate evolution and thus barcode markers may not work in this case.
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UTHICKE SVEN, BYRNE MARIA, CONAND CHANTAL. Genetic barcoding of commercial Bêche‐de‐mer species (Echinodermata: Holothuroidea). Mol Ecol Resour 2010; 10:634-46. [DOI: 10.1111/j.1755-0998.2009.02826.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- SVEN UTHICKE
- Australian Institute of Marine Science, PMB No 3, Townsville, Qld 4810, Australia
| | - MARIA BYRNE
- Department of Anatomy and Histology, F13, University of Sydney, Sydney, NSW 2006, Australia
| | - CHANTAL CONAND
- Ecomar Laboratory, Universite de La Reunion, Saint Denis 97715, Reunion, France
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Jennings RM, Bucklin A, Pierrot-Bults A. Barcoding of arrow worms (Phylum Chaetognatha) from three oceans: genetic diversity and evolution within an enigmatic phylum. PLoS One 2010; 5:e9949. [PMID: 20376348 PMCID: PMC2848590 DOI: 10.1371/journal.pone.0009949] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 12/03/2009] [Indexed: 11/19/2022] Open
Abstract
Arrow worms (Phylum Chaetognatha) are abundant planktonic organisms and important predators in many food webs; yet, the classification and evolutionary relationships among chaetognath species remain poorly understood. A seemingly simple body plan is underlain by subtle variation in morphological details, obscuring the affinities of species within the phylum. Many species achieve near global distributions, spanning the same latitudinal bands in all ocean basins, while others present disjunct ranges, in some cases with the same species apparently found at both poles. To better understand how these complex evolutionary and geographic variables are reflected in the species makeup of chaetognaths, we analyze DNA barcodes of the mitochondrial cytochrome oxidase c subunit I (COI) gene, from 52 specimens of 14 species of chaetognaths collected mainly from the Atlantic Ocean. Barcoding analysis was highly successful at discriminating described species of chaetognaths across the phylum, and revealed little geographical structure. This barcode analysis reveals hitherto unseen genetic variation among species of arrow worms, and provides insight into some species relationships of this enigmatic group.
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Affiliation(s)
- Robert M Jennings
- Biology Department, University of Massachusetts at Boston, Boston, Massachusetts, United States of America.
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Casiraghi M, Labra M, Ferri E, Galimberti A, De Mattia F. DNA barcoding: a six-question tour to improve users' awareness about the method. Brief Bioinform 2010; 11:440-53. [PMID: 20156987 DOI: 10.1093/bib/bbq003] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding is a recent and widely used molecular-based identification system that aims to identify biological specimens, and to assign them to a given species. However, DNA barcoding is even more than this, and besides many practical uses, it can be considered the core of an integrated taxonomic system, where bioinformatics plays a key role. DNA barcoding data could be interpreted in different ways depending on the examined taxa but the technique relies on standardized approaches, methods and analyses. The existing reference towards a common way to treat DNA barcoding data, analyses and results is the Barcode of Life Data Systems. However, the scientific community has produced in the recent years a number of alternative methods to manage barcoding data. The present work starts from this point, because users should be aware of the consequences their choices produce on the results. Despite the fact that a strict standardization is the essence of DNA barcoding, we propose a tour of six questions to improve the users' awareness about the method, the correct use of concepts and alternative tools provided by scientific community.
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Affiliation(s)
- Maurizio Casiraghi
- ZooPlantLab, Dipartimento di Biotecnologie e Bioscienze, Università degli Studi di Milano Bicocca, Piazza della Scienza 2 - 20126, Milan, Italy.
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Lowenstein JH, Amato G, Kolokotronis SO. The real maccoyii: identifying tuna sushi with DNA barcodes--contrasting characteristic attributes and genetic distances. PLoS One 2009; 4:e7866. [PMID: 19924239 PMCID: PMC2773415 DOI: 10.1371/journal.pone.0007866] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 10/13/2009] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The use of DNA barcodes for the identification of described species is one of the least controversial and most promising applications of barcoding. There is no consensus, however, as to what constitutes an appropriate identification standard and most barcoding efforts simply attempt to pair a query sequence with reference sequences and deem identification successful if it falls within the bounds of some pre-established cutoffs using genetic distance. Since the Renaissance, however, most biological classification schemes have relied on the use of diagnostic characters to identify and place species. METHODOLOGY/PRINCIPAL FINDINGS Here we developed a cytochrome c oxidase subunit I character-based key for the identification of all tuna species of the genus Thunnus, and compared its performance with distance-based measures for identification of 68 samples of tuna sushi purchased from 31 restaurants in Manhattan (New York City) and Denver, Colorado. Both the character-based key and GenBank BLAST successfully identified 100% of the tuna samples, while the Barcode of Life Database (BOLD) as well as genetic distance thresholds, and neighbor-joining phylogenetic tree building performed poorly in terms of species identification. A piece of tuna sushi has the potential to be an endangered species, a fraud, or a health hazard. All three of these cases were uncovered in this study. Nineteen restaurant establishments were unable to clarify or misrepresented what species they sold. Five out of nine samples sold as a variant of "white tuna" were not albacore (T. alalunga), but escolar (Lepidocybium flavorunneum), a gempylid species banned for sale in Italy and Japan due to health concerns. Nineteen samples were northern bluefin tuna (T. thynnus) or the critically endangered southern bluefin tuna (T. maccoyii), though nine restaurants that sold these species did not state these species on their menus. CONCLUSIONS/SIGNIFICANCE The Convention on International Trade Endangered Species (CITES) requires that listed species must be identifiable in trade. This research fulfills this requirement for tuna, and supports the nomination of northern bluefin tuna for CITES listing in 2010.
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Affiliation(s)
- Jacob H. Lowenstein
- Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, United States of America
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Sergios-Orestis Kolokotronis
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
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Austerlitz F, David O, Schaeffer B, Bleakley K, Olteanu M, Leblois R, Veuille M, Laredo C. DNA barcode analysis: a comparison of phylogenetic and statistical classification methods. BMC Bioinformatics 2009; 10 Suppl 14:S10. [PMID: 19900297 PMCID: PMC2775147 DOI: 10.1186/1471-2105-10-s14-s10] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background DNA barcoding aims to assign individuals to given species according to their sequence at a small locus, generally part of the CO1 mitochondrial gene. Amongst other issues, this raises the question of how to deal with within-species genetic variability and potential transpecific polymorphism. In this context, we examine several assignation methods belonging to two main categories: (i) phylogenetic methods (neighbour-joining and PhyML) that attempt to account for the genealogical framework of DNA evolution and (ii) supervised classification methods (k-nearest neighbour, CART, random forest and kernel methods). These methods range from basic to elaborate. We investigated the ability of each method to correctly classify query sequences drawn from samples of related species using both simulated and real data. Simulated data sets were generated using coalescent simulations in which we varied the genealogical history, mutation parameter, sample size and number of species. Results No method was found to be the best in all cases. The simplest method of all, "one nearest neighbour", was found to be the most reliable with respect to changes in the parameters of the data sets. The parameter most influencing the performance of the various methods was molecular diversity of the data. Addition of genetically independent loci - nuclear genes - improved the predictive performance of most methods. Conclusion The study implies that taxonomists can influence the quality of their analyses either by choosing a method best-adapted to the configuration of their sample, or, given a certain method, increasing the sample size or altering the amount of molecular diversity. This can be achieved either by sequencing more mtDNA or by sequencing additional nuclear genes. In the latter case, they may also have to modify their data analysis method.
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Affiliation(s)
- Frederic Austerlitz
- CNRS, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Orsay, F-91405, France.
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DAVISON ANGUS, BLACKIE ROSELE, SCOTHERN GARYP. DNA barcoding of stylommatophoran land snails: a test of existing sequences. Mol Ecol Resour 2009; 9:1092-101. [DOI: 10.1111/j.1755-0998.2009.02559.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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RIVERA JULIO, CURRIE DOUGLASC. Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae). Mol Ecol Resour 2009; 9 Suppl s1:224-36. [DOI: 10.1111/j.1755-0998.2009.02648.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ward RD, Hanner R, Hebert PDN. The campaign to DNA barcode all fishes, FISH-BOL. JOURNAL OF FISH BIOLOGY 2009; 74:329-56. [PMID: 20735564 DOI: 10.1111/j.1095-8649.2008.02080.x] [Citation(s) in RCA: 439] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
FISH-BOL, the Fish Barcode of Life campaign, is an international research collaboration that is assembling a standardized reference DNA sequence library for all fishes. Analysis is targeting a 648 base pair region of the mitochondrial cytochrome c oxidase I (COI) gene. More than 5000 species have already been DNA barcoded, with an average of five specimens per species, typically vouchers with authoritative identifications. The barcode sequence from any fish, fillet, fin, egg or larva can be matched against these reference sequences using BOLD; the Barcode of Life Data System (http://www.barcodinglife.org). The benefits of barcoding fishes include facilitating species identification, highlighting cases of range expansion for known species, flagging previously overlooked species and enabling identifications where traditional methods cannot be applied. Results thus far indicate that barcodes separate c. 98 and 93% of already described marine and freshwater fish species, respectively. Several specimens with divergent barcode sequences have been confirmed by integrative taxonomic analysis as new species. Past concerns in relation to the use of fish barcoding for species discrimination are discussed. These include hybridization, recent radiations, regional differentiation in barcode sequences and nuclear copies of the barcode region. However, current results indicate these issues are of little concern for the great majority of specimens.
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Affiliation(s)
- R D Ward
- CSIRO Wealth from Oceans Flagship, CSIRO Marine and Atmospheric Research, GPO Box 1538, Hobart, Tasmania 7001, Australia.
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Four years of DNA barcoding: Current advances and prospects. INFECTION GENETICS AND EVOLUTION 2008; 8:727-36. [DOI: 10.1016/j.meegid.2008.05.005] [Citation(s) in RCA: 240] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 05/23/2008] [Accepted: 05/27/2008] [Indexed: 11/21/2022]
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Abstract
The success of character-based DNA barcoding depends on the efficient identification of diagnostic character states from molecular sequences that have been organized hierarchically (e.g. according to phylogenetic methods). Similarly, the reliability of these identified diagnostic character states must be assessed according to their ability to diagnose new sequences. Here, a set of software tools is presented that implement the previously described Characteristic Attribute Organization System for both diagnostic identification and diagnostic-based classification. The software is publicly available from http://sarkarlab.mbl.edu/CAOS.
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Affiliation(s)
- Indra Neil Sarkar
- MBLWHOI Library, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA, Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street at CPW, New York, NY 10024, USA
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Drew J, Allen GR, Kaufman L, Barber PH. Endemism and regional color and genetic differences in five putatively cosmopolitan reef fishes. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2008; 22:965-975. [PMID: 18786099 DOI: 10.1111/j.1523-1739.2008.01011.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Endemism is thought to be relatively rare in marine systems due to the lack of allopatric barriers and the potential for long-distance colonization via pelagic larval dispersal. Although many species of coral reef fishes exhibit regionally restricted color variants that are suggestive of regional endemism, such variation is typically ascribed to intraspecific variation. We examined the genetic structure in 5 putatively monospecific fishes from the Indo-West Pacific (Amphiprion melanopus, Chrysiptera talboti, and Pomacentrus moluccensis [Pomacentridae] and Cirrhilabrus punctatus, and Labroides dimidiatus [Labridae]) that express regional color variation unique to this area. Mitochondrial-control-region sequence analysis showed shallow to deep genetic divergence in all 5 species (sequence divergence 2-17%), with clades concordant with regional color variation. These results were partially supported by nuclear RAG2 data. An analysis of molecular variation (AMOVA) mirrored the phylogenetic results; Phi(ST) values ranged from 0.91 to 0.7, indicating high levels of geographic partitioning of genetic variation. Concordance of genetics and phenotype demonstrate the genetic uniqueness of southwestern Pacific color variants, indicating that these populations are at a minimum distinct evolutionarily significant units and perhaps distinct regionally endemic species. Our results indicate that the alpha biodiversity of the southwestern Pacific is likely underestimated even in well-studied groups, such as reef fishes, and that regional endemism may be more common in tropical marine systems than previously thought.
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Affiliation(s)
- Joshua Drew
- Boston University Marine Program, Boston University, 5 Cummington Street, Boston, MA 02215, USA.
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CAMPBELL DAVIDC, JOHNSON PAULD, WILLIAMS JAMESD, RINDSBERG ANDREWK, SERB JEANNEM, SMALL KORYK, LYDEARD CHARLES. Identification of ‘extinct’ freshwater mussel species using DNA barcoding. Mol Ecol Resour 2008; 8:711-24. [DOI: 10.1111/j.1755-0998.2008.02108.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Elias M, Hill RI, Willmott KR, Dasmahapatra KK, Brower AVZ, Mallet J, Jiggins CD. Limited performance of DNA barcoding in a diverse community of tropical butterflies. Proc Biol Sci 2008; 274:2881-9. [PMID: 17785265 PMCID: PMC3227132 DOI: 10.1098/rspb.2007.1035] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DNA 'barcoding' relies on a short fragment of mitochondrial DNA to infer identification of specimens. The method depends on genetic diversity being markedly lower within than between species. Closely related species are most likely to share genetic variation in communities where speciation rates are rapid and effective population sizes are large, such that coalescence times are long. We assessed the applicability of DNA barcoding (here the 5' half of the cytochrome c oxidase I) to a diverse community of butterflies from the upper Amazon, using a group with a well-established morphological taxonomy to serve as a reference. Only 77% of species could be accurately identified using the barcode data, a figure that dropped to 68% in species represented in the analyses by more than one geographical race and at least one congener. The use of additional mitochondrial sequence data hardly improved species identification, while a fragment of a nuclear gene resolved issues in some of the problematic species. We acknowledge the utility of barcodes when morphological characters are ambiguous or unknown, but we also recommend the addition of nuclear sequence data, and caution that species-level identification rates might be lower in the most diverse habitats of our planet.
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Affiliation(s)
- Marianne Elias
- Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, UK.
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Kelly RP, Eernisse DJ. Reconstructing a radiation: the chiton genus Mopalia in the north Pacific. INVERTEBR SYST 2008. [DOI: 10.1071/is06021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The chiton genus Mopalia Gray, 1847 is highly speciose despite showing little morphological differentiation. Many of the 24 extant species are conspicuous, large-bodied and ecologically important today, but pre-Pleistocene fossils for the genus are rare. Here, we use a combined analysis of four gene regions (16S and COI mtDNA, 18S and 28S rDNA) to estimate the phylogenetic relationships for Mopalia species and use the inferred phylogeny to analyse the group’s biogeography and patterns of speciation. We then use these molecular data to distinguish between two alternative interpretations of the fossil record, as there is a large temporal gap between the oldest fossils tentatively identified as Mopalia and the next oldest fossils (Miocene versus Plio-Pleistocene). Based on the estimated substitution rates from a wide variety of other marine animals, we conclude that the observed rates in Mopalia are consistent with a Miocene origin for the genus. Given this age for the group and assuming a molecular clock, most speciation events in Mopalia are inferred to have occurred on average ~5 Mya. The phylogenetic results indicate that most of the speciation events leading to extant species must have occurred along the western North American coast, though there appear to have been multiple spreading events across the Pacific. When considered along with results for the many other near-shore taxa that have similar distributions to Mopalia, our findings suggest the emergence of a coherent historical biogeography of the northern Pacific.
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BOYER SARAHL, BAKER JESSICAM, GIRIBET GONZALO. Deep genetic divergences in Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi): a widespread ‘mite harvestman’ defies DNA taxonomy. Mol Ecol 2007; 16:4999-5016. [DOI: 10.1111/j.1365-294x.2007.03555.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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