1
|
Hamilton CA, Hendrixson BE, Silvestre Bringas K. Discovery of a new tarantula species from the Madrean Sky Islands and the first documented instance of syntopy between two montane endemics (Araneae, Theraphosidae, Aphonopelma): a case of prior mistaken identity. Zookeys 2024; 1210:61-98. [PMID: 39185330 PMCID: PMC11344175 DOI: 10.3897/zookeys.1210.125318] [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: 04/25/2024] [Accepted: 07/11/2024] [Indexed: 08/27/2024] Open
Abstract
The Chiricahua Mountains in southeastern Arizona are renowned for their exceptional biodiversity and high levels of endemism. Morphological, genomic, behavioral, and distributional data were used to report the discovery of a remarkable new tarantula species from this range. Aphonopelmajacobii sp. nov. inhabits high-elevation mixed conifer forests in these mountains, but also co-occurs and shares its breeding period with A.chiricahua-a related member of the Marxi species group-in mid-elevation Madrean evergreen oak and pine-oak woodlands. This marks the first documented case of syntopy between two montane endemics in the Madrean Archipelago and adds to our knowledge of this threatened region's unmatched tarantula diversity in the United States. An emended diagnosis and redescription for A.chiricahua are also provided based on several newly acquired and accurately identified specimens. Phylogenetic analyses of mitochondrial and genomic-scale data reveal that A.jacobii sp. nov. is more closely related to A.marxi, a species primarily distributed on the Colorado Plateau, than to A.chiricahua or the other Madrean Sky Island taxa. These data provide the evolutionary framework for better understanding the region's complex biogeographic history (e.g., biotic assembly of the Chiricahua Mountains) and conservation of these spiders.
Collapse
Affiliation(s)
- Chris A. Hamilton
- Department of Entomology, Plant Pathology & Nematology, University of Idaho, Moscow, ID 83844, USAUniversity of IdahoMoscowUnited States of America
| | - Brent E. Hendrixson
- Department of Biology, Millsaps College, Jackson, MS 39210, USAMillsaps CollegeJacksonUnited States of America
| | - Karina Silvestre Bringas
- Department of Entomology, Plant Pathology & Nematology, University of Idaho, Moscow, ID 83844, USAUniversity of IdahoMoscowUnited States of America
| |
Collapse
|
2
|
Newton LG, Starrett J, Jochim EE, Bond JE. Phylogeography and cohesion species delimitation of California endemic trapdoor spiders within the Aptostichus icenoglei sibling species complex (Araneae: Mygalomorphae: Euctenizidae). Ecol Evol 2023; 13:e10025. [PMID: 37122769 PMCID: PMC10133383 DOI: 10.1002/ece3.10025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
Species delimitation is an imperative first step toward understanding Earth's biodiversity, yet what constitutes a species and the relative importance of the various processes by which new species arise continue to be debatable. Species delimitation in spiders has traditionally used morphological characters; however, certain mygalomorph spiders exhibit morphological homogeneity despite long periods of population-level isolation, absence of gene flow, and consequent high degrees of molecular divergence. Studies have shown strong geographic structuring and significant genetic divergence among several species complexes within the trapdoor spider genus Aptostichus, most of which are restricted to the California Floristic Province (CAFP) biodiversity hotspot. Specifically, the Aptostichus icenoglei complex, which comprises the three sibling species, A. barackobamai, A. isabella, and A. icenoglei, exhibits evidence of cryptic mitochondrial DNA diversity throughout their ranges in Northern, Central, and Southern California. Our study aimed to explicitly test species hypotheses within this assemblage by implementing a cohesion species-based approach. We used genomic-scale data (ultraconserved elements, UCEs) to first evaluate genetic exchangeability and then assessed ecological interchangeability of genetic lineages. Biogeographical analysis was used to assess the likelihood of dispersal versus vicariance events that may have influenced speciation pattern and process across the CAFP's complex geologic and topographic landscape. Considering the lack of congruence across data types and analyses, we take a more conservative approach by retaining species boundaries within A. icenoglei.
Collapse
Affiliation(s)
- Lacie G. Newton
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - James Starrett
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Emma E. Jochim
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Jason E. Bond
- Department of Entomology & NematologyUniversity of CaliforniaDavisCaliforniaUSA
| |
Collapse
|
3
|
Songsangchote C, Sippawat Z, Khaikaew W, Chomphuphuang N. A new genus of bamboo culm tarantula from Thailand (Araneae, Mygalomorphae, Theraphosidae). Zookeys 2022; 1080:1-19. [PMID: 35068962 PMCID: PMC8752575 DOI: 10.3897/zookeys.1080.76876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/13/2021] [Indexed: 11/28/2022] Open
Abstract
Bamboo plays an important role in the animal world, including providing a nutritious food source, shelter, and habitat. Inside of bamboo culm, we discovered a new genus of tarantula, which we describe here as Taksinusgen. nov. (♂♀). Specimens of this new tarantula were collected from Mae Tho, Mueang Tak district, Tak province, in Thailand, making it geographically distant from any other arboreal genera. Genital morphology was used to diagnose its genus, which is supported by distributional data, natural history, morphological characters, and photographic illustrations of the male and female. Diagnosis of the new genus was determined by distinguishing its different characters from those of other arboreal theraphosid spiders distributed throughout Southeast Asia. This tarantula’s specialization is that it lives in the stalks of the Asian bamboo Gigantochloa sp.
Collapse
|
4
|
Opatova V, Hamilton CA, Hedin M, De Oca LM, Král J, Bond JE. Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data. Syst Biol 2021; 69:671-707. [PMID: 31841157 DOI: 10.1093/sysbio/syz064] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here, we present a comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We sampled nearly all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing insights to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly proposed. Such a major rearrangement in classification, recognizing nine newly established family-level rank taxa, is the largest the group has seen in over three decades. [Biogeography; molecular clocks; phylogenomics; spider web foraging; taxonomy.].
Collapse
Affiliation(s)
- Vera Opatova
- Department of Entomology and Nematology, University of California, 1282 Academic Surge, One Shields Avenue, Davis, CA 95616, USA
| | - Chris A Hamilton
- Department of Entomology, Plant Pathology & Nematology, University of Idaho, 875 Perimeter Dr. MS 2329, Moscow ID 83844-2329, USA
| | - Marshal Hedin
- Department of Biology, LSN 204E, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-4614, USA
| | - Laura Montes De Oca
- Departamento de Ecología y Biología Evolutiva, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, Montevideo 11600, Uruguay
| | - Jiři Král
- Department of Genetics and Microbiology, Faculty of Sciences, Charles University, Viničná 5, Prague 2 128 44, Czech Republic
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, 1282 Academic Surge, One Shields Avenue, Davis, CA 95616, USA
| |
Collapse
|
5
|
Shivambu TC, Shivambu N, Lyle R, Jacobs A, Kumschick S, Foord SH, Robertson MP. Tarantulas (Araneae: Theraphosidae) in the pet trade in South Africa. AFRICAN ZOOLOGY 2020. [DOI: 10.1080/15627020.2020.1823879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Tinyiko C Shivambu
- Centre for Invasion Biology, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Centre for Invasion Biology, Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Ndivhuwo Shivambu
- Centre for Invasion Biology, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Centre for Invasion Biology, Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Robin Lyle
- Biosystematics Division, Agriculture Research Council-Plant Protection Health and Protection, Pretoria, South Africa
| | - Adriaana Jacobs
- Biosystematics Division, Agriculture Research Council-Plant Protection Health and Protection, Pretoria, South Africa
| | - Sabrina Kumschick
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Cape Town, South Africa
| | - Stefan H Foord
- Department of Zoology and Centre for Invasion Biology, University of Venda, Thohoyandou, South Africa
| | - Mark P Robertson
- Centre for Invasion Biology, Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
6
|
Ortiz D, Pekár S, Bilat J, Alvarez N. Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider. Mol Phylogenet Evol 2020; 154:106997. [PMID: 33164854 DOI: 10.1016/j.ympev.2020.106997] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 11/28/2022]
Abstract
Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data.
Collapse
Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Julia Bilat
- Geneva Natural History Museum, Geneva, Switzerland
| | - Nadir Alvarez
- Geneva Natural History Museum, Geneva, Switzerland; Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| |
Collapse
|
7
|
Candia-Ramírez DT, Francke OF. Another stripe on the tiger makes no difference? Unexpected diversity in the widespread tiger tarantula Davus pentaloris (Araneae: Theraphosidae: Theraphosinae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Abstract
Integrative taxonomy is relevant for the discovery and delimitation of cryptic species by incorporating different sources of evidence to construct rigorous species hypotheses. The genus Davus was recently revised and it was found that Davus pentaloris presents high morphological variation across its widespread distribution. However, tarantulas usually present low dispersal capabilities that occasionally result in local endemism. In order to evaluate species boundaries within this taxon, we examine the morphological variation and, additionally, employ four strategies based on mtDNA data (COI): two distance-based [automatic barcode gap discovery (ABGD) and Neighbor-Joining (NJ)] and two tree-based methods [general mixed Yule coalescent (GMYC) and Bayesian Poisson tree process (bPTP)]. Available morphological evidence recovers 13 putative morphospecies, but the different methods based on molecular data recover a variable number of candidate species (16–18). Based on the congruence across all analyses and the available morphological data, we recognize 13 clearly diagnosable species, 12 of them new to science. We conclude that the underestimation of the diversity in D. pentaloris was mainly caused by deficient practices in taxonomy, rather than by the presence of cryptic diversity. Although COI is a functional barcoding marker and it gives reliable results in our study, we recommend combining multiple sources of evidence and strategies to construct better species delimitation hypotheses.
Collapse
Affiliation(s)
- Daniela T Candia-Ramírez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Avenida Universidad 3000, 04510 Coyoacán, Mexico City, Mexico
- Colección Nacional de Arácnidos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
| | - Oscar F Francke
- Colección Nacional de Arácnidos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Mexico City, Mexico
| |
Collapse
|
8
|
Calatayud-Mascarell A, Sánchez-Vialas A. Ampliación del rango de distribución de <em>Harpactirella insidiosa</em> (Denis, 1960) (Araneae: Mygalomorphae: Theraphosidae): una araña endémica de Marruecos poco conocida. GRAELLSIA 2020. [DOI: 10.3989/graellsia.2020.v76.267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
En este trabajo presentamos una nueva cita de Harpactirella insidiosa (Denis, 1960), un terafósido escasamente estudiado de Marruecos, solamente conocido de la localidad tipo, situada en los alrededores de Ben Slimane. Este nuevo registro, basado en dos hembras adultas, amplía el área de distribución de la especie 210 km al suroeste de la localidad tipo. Ambos ejemplares fueron encontrados en la llanura de Doukkala, 14 km al sur de Oualidia, y comparados con topotipos de la especie. Esta nota se acompaña con las primeras imágenes de la especie in vivo y se discute, además, su situación taxonómica.
Collapse
|
9
|
Graham MR, Santibáñez‐López CE, Derkarabetian S, Hendrixson BE. Pleistocene persistence and expansion in tarantulas on the Colorado Plateau and the effects of missing data on phylogeographical inferences from RADseq. Mol Ecol 2020; 29:3684-3701. [DOI: 10.1111/mec.15588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Matthew R. Graham
- Department of Biology Eastern Connecticut State University Willimantic CT USA
| | | | - Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology Museum of Comparative Zoology Harvard University Cambridge MA USA
| | | |
Collapse
|
10
|
Huang W, Xie X, Huo L, Liang X, Wang X, Chen X. An integrative DNA barcoding framework of ladybird beetles (Coleoptera: Coccinellidae). Sci Rep 2020; 10:10063. [PMID: 32572078 PMCID: PMC7308296 DOI: 10.1038/s41598-020-66874-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/12/2020] [Indexed: 11/17/2022] Open
Abstract
Even though ladybirds are well known as economically important biological control agents, an integrative framework of DNA barcoding research was not available for the family so far. We designed and present a set of efficient mini-barcoding primers to recover full DNA barcoding sequences for Coccinellidae, even for specimens collected 40 years ago. Based on these mini-barcoding primers, we obtained 104 full DNA barcode sequences for 104 species of Coccinellidae, in which 101 barcodes were newly reported for the first time. We also downloaded 870 COI barcode sequences (658 bp) from GenBank and BOLD database, belonging to 108 species within 46 genera, to assess the optimum genetic distance threshold and compare four methods of species delimitation (GMYC, bPTP, BIN and ABGD) to determine the most accurate approach for the family. The results suggested the existence of a 'barcode gap' and that 3% is likely an appropriate genetic distance threshold to delimit species of Coccinellidae using DNA barcodes. Species delimitation analyses confirm ABGD as an accurate and efficient approach, more suitable than the other three methods. Our research provides an integrative framework for DNA barcoding and descriptions of new taxa in Coccinellidae. Our results enrich DNA barcoding public reference libraries, including data for Chinese coccinellids. This will facilitate taxonomic identification and biodiversity monitoring of ladybirds using metabarcoding.
Collapse
Affiliation(s)
- Weidong Huang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm; Department of Forest Protection, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province; Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province, Engineering Research Center of Biological Control, Ministry of Education, Guangzhou, 510640, China
| | - Xiufeng Xie
- Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, 510507, China
| | - Lizhi Huo
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, 510405, China
| | - Xinyue Liang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm; Department of Forest Protection, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510640, China
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province; Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province, Engineering Research Center of Biological Control, Ministry of Education, Guangzhou, 510640, China
| | - Xingmin Wang
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province; Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province, Engineering Research Center of Biological Control, Ministry of Education, Guangzhou, 510640, China
| | - Xiaosheng Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm; Department of Forest Protection, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510640, China.
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province; Engineering Technology Research Center of Agricultural Pest Biocontrol, Guangdong Province, Engineering Research Center of Biological Control, Ministry of Education, Guangzhou, 510640, China.
| |
Collapse
|
11
|
Newton LG, Starrett J, Hendrixson BE, Derkarabetian S, Bond JE. Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex. Mol Ecol 2020; 29:2269-2287. [PMID: 32452095 DOI: 10.1111/mec.15483] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/26/2022]
Abstract
Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution. A past study using two molecular markers, COI and 28S, revealed that A. unicolor is paraphyletic with respect to A. microunicolor. To better investigate species boundaries in the complex, we implement the cohesion species concept and use multiple lines of evidence for testing genetic exchangeability and ecological interchangeability. Our integrative approach includes extensively sampling homologous loci across the genome using a RADseq approach (3RAD), assessing population structure across their geographic range using multiple genetic clustering analyses that include structure, principal components analysis and a recently developed unsupervised machine learning approach (Variational Autoencoder). We evaluate ecological similarity by using large-scale ecological data for niche-based distribution modelling. Based on our analyses, we conclude that this complex has at least one additional species as well as confirm species delimitations based on previous less comprehensive approaches. Our study demonstrates the efficacy of genomic-scale data for recognizing cryptic species, suggesting that species delimitation with one data type, whether one mitochondrial gene or morphology, may underestimate true species diversity in morphologically homogenous taxa with low vagility.
Collapse
Affiliation(s)
- Lacie G Newton
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | - James Starrett
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | | | - Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| |
Collapse
|
12
|
Fabiano-Da-Silva W, Guadanucci JPL, Dasilva MAB. Taxonomy and phylogenetics of Tmesiphantes Simon, 1892 (Araneae, Theraphosidae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1685021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Willian Fabiano-Da-Silva
- Centro de Ciências Exatas e da Natureza, Campus I, Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Cidade Universitária, CEP 58050-970, João Pessoa, Paraíba, Brazil
| | - José Paulo Leite Guadanucci
- Departamento de Zoologia, Universidade Estadual Paulista, Rio Claro, Instituto de Biociências, Av. 24 A, 1515, Bairro Bela Vista, CEP 13.506-900, Rio Claro, São Paulo, Brazil
| | - MArcio Bernardino Dasilva
- Centro de Ciências Exatas e da Natureza, Campus I, Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, Cidade Universitária, CEP 58050-970, João Pessoa, Paraíba, Brazil
| |
Collapse
|
13
|
Mendoza J, Francke O. Systematic revision of Mexican threatened tarantulas Brachypelma (Araneae: Theraphosidae: Theraphosinae), with a description of a new genus, and implications on the conservation. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract
The tarantula genus Brachypelma includes colourful species that are highly sought after in the commercial pet trade. They are all included in CITES appendix II. We present phylogenetic analyses using molecular and morphological characters to revise Brachypelma, in which we include all currently known species. Our results agree with a previous study that shows the non-monophyly of Brachypelma. Both phylogenies strongly favour the division of Brachypelma into two smaller genera. The first clade (Brachypelma s.s.) is formed by B.albiceps, B. auratum, B. baumgarteni, B. boehmei, B. emilia, B. hamorii, B. klaasi and B. smithi. The species included in the second clade are transferred to the new genus Tliltocatl and is formed by T. albopilosum comb. nov., T. epicureanum comb. nov., T. kahlenbergi comb. nov., T. sabulosum comb. nov., T. schroederi comb. nov., T. vagans comb. nov. and T. verdezi comb. nov. Both genera can be differentiated by their coloration and the shape of the genitalia. We transfer to Tliltocatl: T. alvarezi, T. andrewi and T. aureoceps, but should be considered as nomina dubia. In addition, we transfer B. fossorium to Stichoplastoris. We discuss the implications of these taxonomical changes for CITES and for the Mexican Laws for wildlife protection.
Collapse
Affiliation(s)
- Jorge Mendoza
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de MEXICO, Coyoacán, Distrito Federal, MEXICO
- Colección Nacional de Arácnidos, Módulo D planta baja, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de MEXICO, Ciudad Universitaria, Coyoacán, Distrito Federal
| | - Oscar Francke
- Colección Nacional de Arácnidos, Módulo D planta baja, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de MEXICO, Ciudad Universitaria, Coyoacán, Distrito Federal
| |
Collapse
|
14
|
Ferretti NE, Soresi DS, González A, Arnedo M. An integrative approach unveils speciation within the threatened spider Calathotarsus simoni (Araneae: Mygalomorphae: Migidae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1643423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nelson E. Ferretti
- Instituto de Ciencias Biológicas y Biomédicas del Sur (INBIOSUR-CONICET-UNS), San Juan 670, Bahía Blanca, 8000, Buenos Aires, Argentina
| | - Daniela S. Soresi
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS-CONICET-UNS), Camino La Carrindanga Km 7, Bahía Blanca, 8000, Buenos Aires, Argentina
| | - Alda González
- Centro de Estudios Parasitológicos y de Vectores (CEPAVE-CCT-CONICET-La Plata), Boulevard 120 s/n (e/60-64), La Plata, 1900, Buenos Aires, Argentina
| | - Miquel Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 643, Barcelona, 08028, Spain
| |
Collapse
|
15
|
Jirapatrasilp P, Backeljau T, Prasankok P, Chanabun R, Panha S. Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus). Mol Phylogenet Evol 2019; 139:106531. [PMID: 31185298 DOI: 10.1016/j.ympev.2019.106531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/19/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022]
Abstract
Semi-aquatic freshwater earthworms in the genus Glyphidrilus from Southeast Asia are characterized by both an extreme morphological crypsis among divergent phylogenetic lineages and a high morphological variability within the same phylogenetic lineages. The present study provides a new taxonomic framework for this problematic genus in SE Asia by integrating DNA sequence and morphological data. When single-locus and multilocus multispecies coalescent-based (MSC) species delimitation methods were applied to DNA sequence data, they usually yielded highly incongruent results compared to morphology-based species identifications. This suggested the presence of several cryptic species and high levels of intraspecific morphological variation. Applying reciprocal monophyly to the cytochrome c oxidase subunit 1 (COI) gene tree allowed us to propose the existence of 33 monophyletic species. Yet, often substantially more molecular operational taxonomic units (MOTUs) were obtained when species delimitation was based on COI and 16S rRNA sequences. In contrast, the ITS1 and ITS2 sequences suggested fewer MOTUs and did not recover most of the monophyletic species from the Mekong basin. However, several of these latter taxa were better supported when MSC species delimitation methods were applied to the combined mtDNA and ITS datasets. The ITS2 secondary structure retrieved one unnamed Mekong basin species that was not uncovered by the other methods when applied to ITS2 sequences. In conclusion, based on an integrative taxonomic workflow, 26 Glyphidrilus candidate species were retained and two remained to be confirmed. As such, this study provides evidence to suggest nine species new to science and to synonymize 12 nominal morphospecies. It also illustrates that the uncritical use of COI as a universal DNA barcode may overestimate species diversity because COI may be unable to distinguish between divergent conspecific lineages and different candidate species.
Collapse
Affiliation(s)
- Parin Jirapatrasilp
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Pongpun Prasankok
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Ratmanee Chanabun
- Program in Animal Science, Faculty of Agriculture Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon 47000, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
| |
Collapse
|
16
|
Massó S, López-Pujol J, Vilatersana R. Reinterpretation of an endangered taxon based on integrative taxonomy: The case of Cynara baetica (Compositae). PLoS One 2018; 13:e0207094. [PMID: 30485285 PMCID: PMC6261557 DOI: 10.1371/journal.pone.0207094] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 10/24/2018] [Indexed: 11/18/2022] Open
Abstract
The Strait of Gibraltar, the gateway between the Atlantic Ocean and the Mediterranean Sea, has a convulsive geological history, with recurring closing and opening events since the late Miocene. As a consequence, this region has played a major role in the evolutionary history of many species. Cynara baetica (Compositae) is a diploid perennial herb distributed in both sides of this strait. It is currently subdivided into two subspecies: C. baetica subsp. baetica for the Spanish populations, and C. baetica subsp. maroccana for the Moroccan ones. Following three different approximations of species delimitation, including phylogenetic and population genetic analyses (based on three AFLP primer combinations and two intergenic spacers of cpDNA), ecological niche modeling (ENM) and morphological studies, this taxon is investigated and reinterpreted. The results obtained showed a clear genetic, morphological and ecological differentiation between the two taxa and the important role played by the Strait of Gibraltar as a geographical barrier. Based on this evidence, the current taxonomic treatment is modified (both taxa should recover their specific rank) and specific conservation guidelines are proposed for the newly delimited taxa.
Collapse
Affiliation(s)
- Sergi Massó
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
- BioC-GReB, Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- * E-mail:
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Barcelona, Catalonia, Spain
| |
Collapse
|
17
|
Ortiz D, Francke OF, Bond JE. A tangle of forms and phylogeny: Extensive morphological homoplasy and molecular clock heterogeneity in Bonnetina and related tarantulas. Mol Phylogenet Evol 2018; 127:55-73. [DOI: 10.1016/j.ympev.2018.05.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 04/25/2018] [Accepted: 05/13/2018] [Indexed: 12/13/2022]
|
18
|
Zhang L, Wang M, Ma T, Liu J. Taxonomic status of Populuswulianensis and P.ningshanica (Salicaceae). PHYTOKEYS 2018:117-129. [PMID: 30275735 PMCID: PMC6160800 DOI: 10.3897/phytokeys.108.25600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/26/2018] [Indexed: 05/03/2023]
Abstract
Species delimitation in the genus Populus is particularly challenging due to high levels of intraspecific polymorphism as well as frequent interspecific hybridisation and introgression. In this study, we aimed to examine the taxonomic status of Populusningshanica and P.wulianensis using an integrative taxonomy that considers multiple operational criteria. We carried out morphometric analyses of leaf traits and genetic examinations (including sequence variations at five barcoding DNAs and polymorphisms at 14 nuclear microsatellite SSR primers) at the population level between them and two closely related species P.adenopoda and P.davidiana. Results suggest that P.wulianensis belongs to the polymorphic species, P.adenopoda and should be considered as a synonym of the latter. P.ningshanica may have arisen as a result on the hybridisation between P.adenopoda and P.davidiana and therefore should be treated as P.×ningshanica. This study highlights the importance of the integrated evidence in taxonomic decisions of the disputed species.
Collapse
Affiliation(s)
- Lei Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P. R. ChinaSichuan UniversityChengduChina
| | - Mingcheng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P. R. ChinaSichuan UniversityChengduChina
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P. R. ChinaSichuan UniversityChengduChina
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, P. R. ChinaSichuan UniversityChengduChina
| |
Collapse
|
19
|
Gibbs J. DNA barcoding a nightmare taxon: assessing barcode index numbers and barcode gaps for sweat bees. Genome 2018; 61:21-31. [DOI: 10.1139/gen-2017-0096] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
There is an ongoing campaign to DNA barcode the world’s >20 000 bee species. Recent revisions of Lasioglossum (Dialictus) (Hymenoptera: Halictidae) for Canada and the eastern United States were completed using integrative taxonomy. DNA barcode data from 110 species of L. (Dialictus) are examined for their value in identification and discovering additional taxonomic diversity. Specimen identification success was estimated using the best close match method. Error rates were 20% relative to current taxonomic understanding. Barcode Index Numbers (BINs) assigned using Refined Single Linkage Analysis (RESL) and barcode gaps using the Automatic Barcode Gap Discovery (ABGD) method were also assessed. RESL was incongruent for 44.5% of species, although some cryptic diversity may exist. Forty-three of 110 species were part of merged BINs with multiple species. The barcode gap is non-existent for the data set as a whole and ABGD showed levels of discordance similar to the RESL. The viridatum species-group is particularly problematic, so that DNA barcodes alone would be misleading for species delimitation and specimen identification. Character-based methods using fixed nucleotide substitutions could improve specimen identification success in some cases. The use of DNA barcoding for species discovery for standard taxonomic practice in the absence of a well-defined barcode gap is discussed.
Collapse
Affiliation(s)
- Jason Gibbs
- University of Manitoba, Department of Entomology, 12 Dafoe Rd., Winnipeg, MB R3T 2N2, Canada
- University of Manitoba, Department of Entomology, 12 Dafoe Rd., Winnipeg, MB R3T 2N2, Canada
| |
Collapse
|
20
|
Turner SP, Longhorn SJ, Hamilton CA, Gabriel R, PÉrez-Miles F, Vogler AP. Re-evaluating conservation priorities of New World tarantulas (Araneae: Theraphosidae) in a molecular framework indicates non-monophyly of the genera, Aphonopelma and Brachypelma. SYST BIODIVERS 2017. [DOI: 10.1080/14772000.2017.1346719] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Steven P. Turner
- The Natural History Museum (NHM), Cromwell Road, South Kensington, London, UK
- Beneficial Insect Laboratory, North Carolina Department of Agriculture and Consumer Services, Cary, North Carolina, USA
| | | | - Chris A. Hamilton
- Auburn University Museum of Natural History (AUMNH), and Dept. Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Ray Gabriel
- Oxford Museum of Natural History (OUMNH), Parks Road, Oxford, UK
| | | | - Alfried P. Vogler
- The Natural History Museum (NHM), Cromwell Road, South Kensington, London, UK
- Imperial College London, South Kensington, London, UK
| |
Collapse
|
21
|
Hao G, Zhang C, AL-Shehbaz IA, Guo X, Bi H, Wang J, Liu J. Eutrema giganteum (Brassicaceae), a new species from Sichuan, southwest China. PHYTOKEYS 2017; 82:15-26. [PMID: 28794679 PMCID: PMC5546392 DOI: 10.3897/phytokeys.82.12329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/05/2017] [Indexed: 06/07/2023]
Abstract
Eutrema giganteum (Brassicaceae), a new species from Hengduan Mountains in Sichuan Province, southwest China, is described, and its relationships to the closely related E. yunnanense is discussed based on morphological, cytological, and molecular data. It is similar morphologically to E. yunnanense but is readily distinguished by having robust (vs. slender), erect (vs. decumbent), and branched (vs. mostly simple), and rather tall stems (60-110 cm vs. 20-60 cm); curved (vs. straight), smooth (vs. torulose), and shorter fruit (5-8 mm vs. 8-15 mm); and fewer ovules per ovary (1-4 vs. 6-10). All examined individuals from different populations of E. giganteum clustered into a single clade sister to E. yunnanense in phylogenetic analyses using the combined nuclear ITS and plastid DNA datasets. Our cytological studies revealed that the chromosome number of E. giganteum is 2n = 44, with a genome size of 1160 (±8) Mb, while that of E. yunnanense is 2n = 28, with a genome size of 718 (±15) Mb. Multiple lines of evidence support the recognition of E. giganteum as a distinct species well differentiated from E. yunnanense.
Collapse
Affiliation(s)
- Guoqian Hao
- Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, Leshan 614000, P. R. China
| | - Changbing Zhang
- Sichuan Academy of Grassland Sciences, Chengdu 610065, P. R. China
| | | | - Xinyi Guo
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610065, P. R. China
| | - Hao Bi
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610065, P. R. China
| | - Junyin Wang
- Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, Leshan 614000, P. R. China
| | - Jianquan Liu
- MOE Key Laboratory for Bio-Resources and Eco-Environment, College of Life Science, Sichuan University, Chengdu 610065, P. R. China
| |
Collapse
|
22
|
Ortiz D, Francke OF. Reconciling morphological and molecular systematics in tarantulas (Araneae: Theraphosidae): revision of the Mexican endemic genus Bonnetina. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlw013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
23
|
Zheng H, Fan L, Milne RI, Zhang L, Wang Y, Mao K. Species Delimitation and Lineage Separation History of a Species Complex of Aspens in China. FRONTIERS IN PLANT SCIENCE 2017; 8:375. [PMID: 28377782 PMCID: PMC5359289 DOI: 10.3389/fpls.2017.00375] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/06/2017] [Indexed: 05/13/2023]
Abstract
Species delimitation in tree species is notoriously challenging due to shared polymorphisms among species. An integrative survey that considers multiple operational criteria is a possible solution, and we aimed to test it in a species complex of aspens in China. Genetic [four chloroplast DNA (cpDNA) fragments and 14 nuclear microsatellite loci (nSSR)] and morphological variations were collected for 76 populations and 53 populations, respectively, covering the major geographic distribution of the Populus davidiana-rotundifolia complex. Bayesian clustering, analysis of molecular variance (AMOVA), Principle Coordinate Analysis (PCoA), ecological niche modeling (ENM), and gene flow (migrants per generation), were employed to detect and test genetic clustering, morphological and habitat differentiation, and gene flow between/among putative species. The nSSR data and ENM suggested that there are two separately evolving meta-population lineages that correspond to P. davidiana (pd) and P. rotundifolia (pr). Furthermore, several lines of evidence supported a subdivision of P. davidiana into Northeastern (NEC) and Central-North (CNC) groups, yet they are still functioning as one species. CpDNA data revealed that five haplotype clades formed a pattern of [pdNEC, ((pdCNC, pr), (pdCNC, pr))], but most haplotypes are species-specific. Meanwhile, PCA based on morphology suggested a closer relationship between the CNC group (P. davidiana) and P. rontundifolia. Discrepancy of nSSR and ENM vs. cpDNA and morphology could have reflected a complex lineage divergence and convergence history. P. davidiana and P. rotundifolia can be regarded as a recently diverged species pair that experienced parapatric speciation due to ecological differentiation in the face of gene flow. Our findings highlight the importance of integrative surveys at population level, as we have undertaken, is an important approach to detect the boundary of a group of species that have experienced complex evolutionary history.
Collapse
Affiliation(s)
- Honglei Zheng
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Liqiang Fan
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Richard I. Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Lei Zhang
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
| | - Yaling Wang
- Life Science and Engineering College, Northwest University for NationalitiesLanzhou, China
| | - Kangshan Mao
- MOE Key Laboratory of Bio-Resources and Eco-Environment, College of Life Science, Sichuan UniversityChengdu, China
- *Correspondence: Kangshan Mao ;
| |
Collapse
|
24
|
Mendoza J, Francke O. Systematic revision of Brachypelma red-kneed tarantulas (Araneae : Theraphosidae), and the use of DNA barcodes to assist in the identification and conservation of CITES-listed species. INVERTEBR SYST 2017. [DOI: 10.1071/is16023] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mexican red-kneed tarantulas of the genus Brachypelma are regarded as some of the most desirable invertebrate pets, and although bred in captivity, they continue to be smuggled out of the wild in large numbers. Species are often difficult to identify based solely on morphology, therefore prompt and accurate identification is required for adequate protection. Thus, we explored the applicability of using COI-based DNA barcoding as a complementary identification tool. Brachypelma smithi (F. O. Pickard-Cambridge, 1897) and Brachypelma hamorii Tesmongt, Cleton & Verdez, 1997 are redescribed, and their morphological differences defined. Brachypelma annitha is proposed as a new synonym of B. smithi. The current distribution of red-kneed tarantulas shows that the Balsas River basin may act as a geographical barrier. Morphological and molecular evidence are concordant and together provide robust hypotheses for delimiting Mexican red-kneed tarantula species. DNA barcoding of these tarantulas is further shown to be useful for species-level identification and for potentially preventing black market trade in these spiders. As a Convention on International Trade in Endangered Species (CITES) listing does not protect habitat, or control wildlife management or human interactions with organisms, it is important to support environmental conservation activities to provide an alternative income for local communities and to avoid damage to wildlife populations.
Collapse
|
25
|
Cao X, Liu J, Chen J, Zheng G, Kuntner M, Agnarsson I. Rapid dissemination of taxonomic discoveries based on DNA barcoding and morphology. Sci Rep 2016; 6:37066. [PMID: 27991489 PMCID: PMC5171852 DOI: 10.1038/srep37066] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 10/25/2016] [Indexed: 01/12/2023] Open
Abstract
The taxonomic impediment is characterized by dwindling classical taxonomic expertise, and slow pace of revisionary work, thus more rapid taxonomic assessments are needed. Here we pair rapid DNA barcoding methods with swift assessment of morphology in an effort to gauge diversity, establish species limits, and rapidly disseminate taxonomic information prior to completion of formal taxonomic revisions. We focus on a poorly studied, but diverse spider genus, Pseudopoda, from East Asia. We augmented the standard barcoding locus (COI) with nuclear DNA sequence data (ITS2) and analyzed congruence among datasets and species delimitation methods for a total of 572 individuals representing 23 described species and many potentially new species. Our results suggest that a combination of CO1 + ITS2 fragments identify and diagnose species better than the mitochondrial barcodes alone, and that certain tree based methods yield considerably higher diversity estimates than the distance-based approaches and morphology. Combined, through an extensive field survey, we detect a twofold increase in species diversity in the surveyed area, at 42–45, with most species representing short range endemics. Our study demonstrates the power of biodiversity assessments and swift dissemination of taxonomic data through rapid inventory, and through a combination of morphological and multi-locus DNA barcoding diagnoses of diverse arthropod lineages.
Collapse
Affiliation(s)
- Xiaowei Cao
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Centre for Behavioural Ecology and Evolution, College of Life Sciences, Hubei University, Wuhan 430062, Hubei, China
| | - Jie Liu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Centre for Behavioural Ecology and Evolution, College of Life Sciences, Hubei University, Wuhan 430062, Hubei, China
| | - Jian Chen
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Centre for Behavioural Ecology and Evolution, College of Life Sciences, Hubei University, Wuhan 430062, Hubei, China
| | - Guo Zheng
- College of Life Sciences, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Matjaž Kuntner
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Centre for Behavioural Ecology and Evolution, College of Life Sciences, Hubei University, Wuhan 430062, Hubei, China.,Institute of Biology, Scientific Research Centre of the Slovenian Academy of Sciences and Arts, Novi Trg 2, 1000 Ljubljana, Slovenia.,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Ingi Agnarsson
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Biology, University of Vermont, Burlington, VT, USA
| |
Collapse
|
26
|
Reed Z, Doering C, Barrett PM. Tarantula Hair Keratoconjunctivitis with Concurrent Fungal Infection in a Rat Terrier. J Am Anim Hosp Assoc 2016; 52:392-397. [DOI: 10.5326/jaaha-ms-6380] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ABSTRACT
A 9 yr old rat terrier presented with corneal ulceration and conjunctivitis that developed acutely after digging among dry leaves in wooded northern Arizona. Ophthalmic examination revealed multiple linear foreign bodies throughout the adnexal tissue and cornea of the left eye. Manual removal of material was unsuccessful. The palpebral conjunctiva required excision with tenotomy scissors to remove structures and allow corneal healing. Microscopic examination revealed structures believed to be setae from a Theraphosidae tarantula. This was confirmed morphologically by an entomologist and by comparison with hairs from a captive spider of the suspected species. The excised tissue also contained fruiting bodies, hyphae, and microconidia consistent with Aspergillus spp. The captive spider hairs also cultured positive for Aspergillus, suggesting a relationship between this fungus and tarantulas in captivity and in their native habitat. This is the first report in the veterinary literature to confirm tarantula hair as the causative agent in keratoconjunctivitis and corneal ulceration, adding it to the list of differential diagnoses for ocular foreign body. This is also the first report to suggest a relationship between Aspergillus and tarantulas of the Theraphosidae family, which should be considered in the diagnostics and treatment of patients with suspected tarantula hair keratoconjunctivitis.
Collapse
Affiliation(s)
- Zoe Reed
- From Eye Care for Animals, Phoenix, Arizona
| | | | | |
Collapse
|
27
|
Ortiz D, Francke OF. Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae). Mol Phylogenet Evol 2016; 101:176-193. [DOI: 10.1016/j.ympev.2016.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 04/07/2016] [Accepted: 05/01/2016] [Indexed: 12/13/2022]
|
28
|
Kornilios P, Thanou E, Kapli P, Parmakelis A, Chatzaki M. Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae. Mol Phylogenet Evol 2016; 98:300-13. [DOI: 10.1016/j.ympev.2016.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/23/2015] [Accepted: 01/31/2016] [Indexed: 10/22/2022]
|
29
|
Ritchie AM, Lo N, Ho SYW. Examining the sensitivity of molecular species delimitations to the choice of mitochondrial marker. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0275-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
30
|
Feng X, Liu J, Gong X. Species Delimitation of the Cycas segmentifida Complex (Cycadaceae) Resolved by Phylogenetic and Distance Analyses of Molecular Data. FRONTIERS IN PLANT SCIENCE 2016; 7:134. [PMID: 26913044 PMCID: PMC4753401 DOI: 10.3389/fpls.2016.00134] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/25/2016] [Indexed: 06/02/2023]
Abstract
The Cycas segmentifida complex consists of eight species whose distributions overlap in a narrow region in Southwest China. These eight taxa are also morphologically similar and are difficult to be distinguished. Consequently, their taxonomic status has been a matter of discussion in recent years. To study this species complex, we sequenced four plastid intergenic spacers (cpDNA), three nuclear genes and genotyped 12 microsatellites for the eight taxa from 19 different localities. DNA sequences were analyzed using Maximum Likelihood (ML) method and Bayesian Inference (BI), and microsatellites were analyzed using the Neighbor-joining (NJ) and structure inference methods. Results of cpDNA, nuclear gene GTP and microsatellites all rejected the hypotheses that this complex consisted of eight taxa or one distinct lineage (species) but two previously described species were adopted: Cycas guizhouensis K. M. Lan et R. F. Zou and Cycas segmentifida D. Y. Wang et C. Y. Deng. Cycas longlinensis H. T. Chang et Y. C. Zhong was included in C. guizhouensis and the other five taxa were included in C. segmentifida. Our species delimitation inferred from molecular data largely corresponds to morphological differentiation. However, the other two nuclear genes were unable to resolve species boundaries for this complex independently. This study offered evidences from different genomes for dealing with the species boundaries and taxonomical treatment of the C. segmentifida complex in an integrated perspective.
Collapse
Affiliation(s)
- Xiuyan Feng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jian Liu
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Xun Gong
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| |
Collapse
|
31
|
Hamilton CA, Hendrixson BE, Bond JE. Taxonomic revision of the tarantula genus Aphonopelma Pocock, 1901 (Araneae, Mygalomorphae, Theraphosidae) within the United States. Zookeys 2016; 560:1-340. [PMID: 27006611 PMCID: PMC4768370 DOI: 10.3897/zookeys.560.6264] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/24/2015] [Indexed: 11/12/2022] Open
Abstract
This systematic study documents the taxonomy, diversity, and distribution of the tarantula spider genus Aphonopelma Pocock, 1901 within the United States. By employing phylogenomic, morphological, and geospatial data, we evaluated all 55 nominal species in the United States to examine the evolutionary history of Aphonopelma and the group's taxonomy by implementing an integrative approach to species delimitation. Based on our analyses, we now recognize only 29 distinct species in the United States. We propose 33 new synonymies (Aphonopelma apacheum, Aphonopelma minchi, Aphonopelma rothi, Aphonopelma schmidti, Aphonopelma stahnkei = Aphonopelma chalcodes; Aphonopelma arnoldi = Aphonopelma armada; Aphonopelma behlei, Aphonopelma vogelae = Aphonopelma marxi; Aphonopelma breenei = Aphonopelma anax; Aphonopelma chambersi, Aphonopelma clarum, Aphonopelma cryptethum, Aphonopelma sandersoni, Aphonopelma sullivani = Aphonopelma eutylenum; Aphonopelma clarki, Aphonopelma coloradanum, Aphonopelma echinum, Aphonopelma gurleyi, Aphonopelma harlingenum, Aphonopelma odelli, Aphonopelma waconum, Aphonopelma wichitanum = Aphonopelma hentzi; Aphonopelma heterops = Aphonopelma moderatum; Aphonopelma jungi, Aphonopelma punzoi = Aphonopelma vorhiesi; Aphonopelma brunnius, Aphonopelma chamberlini, Aphonopelma iviei, Aphonopelma lithodomum, Aphonopelma smithi, Aphonopelma zionis = Aphonopelma iodius; Aphonopelma phanum, Aphonopelma reversum = Aphonopelma steindachneri), 14 new species (Aphonopelma atomicum sp. n., Aphonopelma catalina sp. n., Aphonopelma chiricahua sp. n., Aphonopelma icenoglei sp. n., Aphonopelma johnnycashi sp. n., Aphonopelma madera sp. n., Aphonopelma mareki sp. n., Aphonopelma moellendorfi sp. n., Aphonopelma parvum sp. n., Aphonopelma peloncillo sp. n., Aphonopelma prenticei sp. n., Aphonopelma saguaro sp. n., Aphonopelma superstitionense sp. n., and Aphonopelma xwalxwal sp. n.), and seven nomina dubia (Aphonopelma baergi, Aphonopelma cratium, Aphonopelma hollyi, Aphonopelma mordax, Aphonopelma radinum, Aphonopelma rusticum, Aphonopelma texense). Our proposed species tree based on Anchored Enrichment data delimits five major lineages: a monotypic group confined to California, a western group, an eastern group, a group primarily distributed in high-elevation areas, and a group that comprises several miniaturized species. Multiple species are distributed throughout two biodiversity hotspots in the United States (i.e., California Floristic Province and Madrean Pine-Oak Woodlands). Keys are provided for identification of both males and females. By conducting the most comprehensive sampling of a single theraphosid genus to date, this research significantly broadens the scope of prior molecular and morphological investigations, finally bringing a modern understanding of species delimitation in this dynamic and charismatic group of spiders.
Collapse
Affiliation(s)
- Chris A. Hamilton
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | | | - Jason E. Bond
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| |
Collapse
|
32
|
Ahrens D, Fujisawa T, Krammer HJ, Eberle J, Fabrizi S, Vogler AP. Rarity and Incomplete Sampling in DNA-Based Species Delimitation. Syst Biol 2016; 65:478-94. [PMID: 26797695 DOI: 10.1093/sysbio/syw002] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 01/13/2016] [Indexed: 11/14/2022] Open
Abstract
DNA-based species delimitation may be compromised by limited sampling effort and species rarity, including "singleton" representatives of species, which hampers estimates of intra- versus interspecies evolutionary processes. In a case study of southern African chafers (beetles in the family Scarabaeidae), many species and subclades were poorly represented and 48.5% of species were singletons. Using cox1 sequences from >500 specimens and ∼100 species, the Generalized Mixed Yule Coalescent (GMYC) analysis as well as various other approaches for DNA-based species delimitation (Automatic Barcode Gap Discovery (ABGD), Poisson tree processes (PTP), Species Identifier, Statistical Parsimony), frequently produced poor results if analyzing a narrow target group only, but the performance improved when several subclades were combined. Hence, low sampling may be compensated for by "clade addition" of lineages outside of the focal group. Similar findings were obtained in reanalysis of published data sets of taxonomically poorly known species assemblages of insects from Madagascar. The low performance of undersampled trees is not due to high proportions of singletons per se, as shown in simulations (with 13%, 40% and 52% singletons). However, the GMYC method was highly sensitive to variable effective population size ([Formula: see text]), which was exacerbated by variable species abundances in the simulations. Hence, low sampling success and rarity of species affect the power of the GMYC method only if they reflect great differences in [Formula: see text] among species. Potential negative effects of skewed species abundances and prevalence of singletons are ultimately an issue about the variation in [Formula: see text] and the degree to which this is correlated with the census population size and sampling success. Clade addition beyond a limited study group can overcome poor sampling for the GMYC method in particular under variable [Formula: see text] This effect was less pronounced for methods of species delimitation not based on coalescent models.
Collapse
Affiliation(s)
- Dirk Ahrens
- Centre of Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany; Department of Life Sciences, Natural History Museum, London SW7 5BD, UK;
| | - Tomochika Fujisawa
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606 8502, Japan; Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot SL7 5PY, UK
| | - Hans-Joachim Krammer
- Centre of Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany
| | - Jonas Eberle
- Centre of Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany
| | - Silvia Fabrizi
- Centre of Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany; Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK; Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot SL7 5PY, UK
| |
Collapse
|
33
|
Montes de Oca L, D'Elía G, Pérez-Miles F. An integrative approach for species delimitation in the spider genusGrammostola(Theraphosidae, Mygalomorphae). ZOOL SCR 2015. [DOI: 10.1111/zsc.12152] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Laura Montes de Oca
- Laboratorio de Etología, Ecología y Evolución; Instituto de Investigaciones Biológicas Clemente Estable; Av. Italia 3318 CP 11600 Montevideo Uruguay
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Campus Isla Teja s/n casilla 567 Valdivia Chile
| | - Fernando Pérez-Miles
- Sección Entomología; Facultad de Ciencias; Universidad de la República; Igua 4225 CP 11600 Montevideo Uruguay
| |
Collapse
|
34
|
Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae). Mol Phylogenet Evol 2015; 91:56-67. [DOI: 10.1016/j.ympev.2015.05.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/11/2015] [Accepted: 05/19/2015] [Indexed: 11/20/2022]
|
35
|
Xu X, Liu F, Chen J, Li D, Kuntner M. Integrative taxonomy of the primitively segmented spider genusGanthela(Araneae: Mesothelae: Liphistiidae): DNA barcoding gap agrees with morphology. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12280] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Xin Xu
- Centre for Behavioural Ecology and Evolution; College of Life Sciences; Hubei University; Wuhan China
| | - Fengxiang Liu
- Centre for Behavioural Ecology and Evolution; College of Life Sciences; Hubei University; Wuhan China
| | - Jian Chen
- Centre for Behavioural Ecology and Evolution; College of Life Sciences; Hubei University; Wuhan China
| | - Daiqin Li
- Centre for Behavioural Ecology and Evolution; College of Life Sciences; Hubei University; Wuhan China
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 117543 Singapore
| | - Matjaž Kuntner
- Centre for Behavioural Ecology and Evolution; College of Life Sciences; Hubei University; Wuhan China
- Evolutionary Zoology Laboratory; Biological Institute ZRC SAZU; Novi trg 2 P. O. Box 306 SI-1001 Ljubljana Slovenia
- Department of Entomology; National Museum of Natural History; Smithsonian Institution; Washington, DC USA
| |
Collapse
|
36
|
Valdez-Mondragón A, Francke OF. Phylogeny of the spider genusIxchela Huber, 2000 (Araneae: Pholcidae) based on morphological and molecular evidence (CO1 and 16S), with a hypothesized diversification in the Pleistocene. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alejandro Valdez-Mondragón
- Colección Nacional de Arácnidos (CNAN); Instituto de Biología; Universidad Nacional Autónoma de México (UNAM); Apartado Postal 70-153 C. P. 04510 Ciudad Universitaria Coyoacán, DF Mexico City Mexico
- Alexander Koenig Research Museum of Zoology; Adenauerallee 160 53113 Bonn Germany
| | - Oscar F. Francke
- Colección Nacional de Arácnidos (CNAN); Instituto de Biología; Universidad Nacional Autónoma de México (UNAM); Apartado Postal 70-153 C. P. 04510 Ciudad Universitaria Coyoacán, DF Mexico City Mexico
| |
Collapse
|
37
|
Schwarzfeld MD, Sperling FAH. Comparison of five methods for delimitating species in Ophion Fabricius, a diverse genus of parasitoid wasps (Hymenoptera, Ichneumonidae). Mol Phylogenet Evol 2015; 93:234-48. [PMID: 26265257 DOI: 10.1016/j.ympev.2015.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 07/31/2015] [Accepted: 08/04/2015] [Indexed: 10/23/2022]
Abstract
DNA taxonomy has been proposed as a method to quickly assess diversity and species limits in highly diverse, understudied taxa. Here we use five methods for species delimitation and two genetic markers (COI and ITS2) to assess species diversity within the parasitoid genus, Ophion. We searched for compensatory base changes (CBC's) in ITS2, and determined that they are too rare to be of practical use in delimiting species in this genus. The other four methods used both COI and ITS2, and included distance-based (threshold analysis and ABGD) and tree-based (GMYC and PTP) models. We compared the results of these analyses to each other under various parameters and tested their performance with respect to 11 Nearctic species/morphospecies and 15 described Palearctic species. We also computed barcode accumulation curves of COI sequences to assess the completeness of sampling. The species count was highly variable depending on the method and parameters used, ranging from 47 to 168 species, with more conservative estimates of 89-121 species. Despite this range, many of the Nearctic test species were fairly robust with respect to method. We concluded that while there was often good congruence between methods, GMYC and PTP were less reliant on arbitrary parameters than the other two methods and more easily applied to genetic markers other than COI. However, PTP was less successful at delimiting test species than was GMYC. All methods, as well as the barcode accumulation curves, indicate that several Palearctic species remain undescribed and that we have scarcely begun to appreciate the Nearctic diversity within this genus.
Collapse
Affiliation(s)
- Marla D Schwarzfeld
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
| | - Felix A H Sperling
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| |
Collapse
|
38
|
Su X, Wu G, Li L, Liu J. Species delimitation in plants using the Qinghai-Tibet Plateau endemic Orinus (Poaceae: Tridentinae) as an example. ANNALS OF BOTANY 2015; 116:35-48. [PMID: 25987712 PMCID: PMC4479750 DOI: 10.1093/aob/mcv062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 11/27/2014] [Accepted: 03/31/2015] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Accurate identification of species is essential for the majority of biological studies. However, defining species objectively and consistently remains a challenge, especially for plants distributed in remote regions where there is often a lack of sufficient previous specimens. In this study, multiple approaches and lines of evidence were used to determine species boundaries for plants occurring in the Qinghai-Tibet Plateau, using the genus Orinus (Poaceae) as a model system for an integrative approach to delimiting species. METHODS A total of 786 individuals from 102 populations of six previously recognized species were collected for niche, morphological and genetic analyses. Three plastid DNA regions (matK, rbcL and trnH-psbA) and one nuclear DNA region [internal transcribed space (ITS)] were sequenced. KEY RESULTS Whereas six species had been previously recognized, statistical analyses based on character variation, molecular data and niche differentiation identified only two well-delimited clusters, together with a third possibly originating from relatively recent hybridization between, or historical introgression from, the other two. CONCLUSIONS Based on a principle of integrative species delimitation to reconcile different sources of data, the results provide compelling evidence that the six previously recognized species of the genus Orinus that were examined should be reduced to two, with new circumscriptions, and a third, identified in this study, should be described as a new species. This empirical study highlights the value of applying genetic differentiation, morphometric statistics and ecological niche modelling in an integrative approach to re-circumscribing species boundaries. The results produce relatively objective, operational and unbiased taxonomic classifications of plants occurring in remote regions.
Collapse
Affiliation(s)
- Xu Su
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Guili Wu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Lili Li
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Science, Lanzhou University, Lanzhou 730000, PR China and Key Laboratory of Education Ministry of Environments and Resources in the Qinghai-Tibet Plateau, School of Geography and Life Science, Qinghai Normal University, Xining 810008, PR China
| |
Collapse
|
39
|
Planas E, Ribera C. Description of six new species ofLoxosceles(Araneae: Sicariidae) endemic to the Canary Islands and the utility of DNA barcoding for their fast and accurate identification. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12226] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Enric Planas
- Institut de Recerca de la Biodiversitat (IRBio); Departament de Biologia Animal; Facultat de Biologia; Universitat de Barcelona; Avinguda Diagonal 643 08028 Barcelona Spain
| | - Carles Ribera
- Institut de Recerca de la Biodiversitat (IRBio); Departament de Biologia Animal; Facultat de Biologia; Universitat de Barcelona; Avinguda Diagonal 643 08028 Barcelona Spain
| |
Collapse
|
40
|
Kekkonen M, Mutanen M, Kaila L, Nieminen M, Hebert PDN. Delineating species with DNA barcodes: a case of taxon dependent method performance in moths. PLoS One 2015; 10:e0122481. [PMID: 25849083 PMCID: PMC4406103 DOI: 10.1371/journal.pone.0122481] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/22/2015] [Indexed: 11/26/2022] Open
Abstract
The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.
Collapse
Affiliation(s)
- Mari Kekkonen
- Finnish Museum of Natural History, University of Helsinki, Zoology Unit, University of Helsinki, Helsinki, Finland
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, Oulu, Finland
| | - Lauri Kaila
- Finnish Museum of Natural History, University of Helsinki, Zoology Unit, University of Helsinki, Helsinki, Finland
| | - Marko Nieminen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paul D. N. Hebert
- Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
41
|
Harvey MS, Main BY, Rix MG, Cooper SJB. Refugia within refugia: in situ speciation and conservation of threatened Bertmainius (Araneae : Migidae), a new genus of relictual trapdoor spiders endemic to the mesic zone of south-western Australia. INVERTEBR SYST 2015. [DOI: 10.1071/is15024] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The trapdoor spider family Migidae has a classical Gondwanan distribution and is found on all southern continents except the Indian region. The Australian fauna consists of three genera including Moggridgea O. P. Cambridge from south-western Australia and Kangaroo Island, South Australia; Moggridgea is otherwise widespread throughout Africa. The sole named species of Moggridgea from Western Australia, M. tingle Main, and its unnamed relatives are the subject of the present paper, which was stimulated by concern for the long-term persistence of populations, and the discovery of deep genetic divergences between populations. A phylogeny of the Western Australian species relative to African and South Australian Moggridgea was generated using molecular COI and ITS rDNA data, and based on both molecular and morphological criteria we conclude that the Western Australian taxa should be removed from Moggridgea and transferred to a new genus, Bertmainius. The seven species are delimited using both morphological and molecular criteria: B. tingle (Main) (the type species), and six new species, B. colonus, B. monachus, B. mysticus, B. opimus, B. pandus and B. tumidus. All seven species are considered to be threatened using IUCN criteria, with the major threatening processes being inappropriate fire regimes and climate change.
Collapse
|
42
|
Opatova V, Arnedo MA. Spiders on a Hot Volcanic Roof: Colonisation Pathways and Phylogeography of the Canary Islands Endemic Trap-Door Spider Titanidiops canariensis (Araneae, Idiopidae). PLoS One 2014; 9:e115078. [PMID: 25494329 PMCID: PMC4262472 DOI: 10.1371/journal.pone.0115078] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 11/03/2014] [Indexed: 11/19/2022] Open
Abstract
Studies conducted on volcanic islands have greatly contributed to our current understanding of how organisms diversify. The Canary Islands archipelago, located northwest of the coast of northern Africa, harbours a large number of endemic taxa. Because of their low vagility, mygalomorph spiders are usually absent from oceanic islands. The spider Titanidiops canariensis, which inhabits the easternmost islands of the archipelago, constitutes an exception to this rule. Here, we use a multi-locus approach that combines three mitochondrial and four nuclear genes to investigate the origins and phylogeography of this remarkable trap-door spider. We provide a timeframe for the colonisation of the Canary Islands using two alternative approaches: concatenation and species tree inference in a Bayesian relaxed clock framework. Additionally, we investigate the existence of cryptic species on the islands by means of a Bayesian multi-locus species delimitation method. Our results indicate that T. canariensis colonised the Canary Islands once, most likely during the Miocene, although discrepancies between the timeframes from different approaches make the exact timing uncertain. A complex evolutionary history for the species in the archipelago is revealed, which involves two independent colonisations of Fuerteventura from the ancestral range of T. canariensis in northern Lanzarote and a possible back colonisation of southern Lanzarote. The data further corroborate a previously proposed volcanic refugium, highlighting the impact of the dynamic volcanic history of the island on the phylogeographic patterns of the endemic taxa. T. canariensis includes at least two different species, one inhabiting the Jandia peninsula and central Fuerteventura and one spanning from central Fuerteventura to Lanzarote. Our data suggest that the extant northern African Titanidiops lineages may have expanded to the region after the islands were colonised and, hence, are not the source of colonisation. In addition, T. maroccanus may harbour several cryptic species.
Collapse
Affiliation(s)
- Vera Opatova
- Institut de Recerca de la Biodiversitat & Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
- * E-mail:
| | - Miquel A. Arnedo
- Institut de Recerca de la Biodiversitat & Departament de Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
43
|
Čandek K, Kuntner M. DNA barcoding gap: reliable species identification over morphological and geographical scales. Mol Ecol Resour 2014; 15:268-77. [DOI: 10.1111/1755-0998.12304] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/06/2014] [Accepted: 07/16/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Klemen Čandek
- Institute of Biology; Scientific Research Centre of the Slovenian Academy of Sciences and Arts; Novi Trg 2 1000 Ljubljana Slovenia
| | - Matjaž Kuntner
- Institute of Biology; Scientific Research Centre of the Slovenian Academy of Sciences and Arts; Novi Trg 2 1000 Ljubljana Slovenia
- Centre for Behavioural Ecology and Evolution; College of Life Sciences; Hubei University; 368 Youyi Road 430062 Wuhan China
- Department of Entomology; National Museum of Natural History; Smithsonian Institution; PO Box 37012 Washington DC 20013-7012 USA
| |
Collapse
|
44
|
Kekkonen M, Hebert PDN. DNA barcode-based delineation of putative species: efficient start for taxonomic workflows. Mol Ecol Resour 2014; 14:706-15. [PMID: 24479435 PMCID: PMC4264940 DOI: 10.1111/1755-0998.12233] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/02/2014] [Accepted: 01/18/2014] [Indexed: 11/29/2022]
Abstract
The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies.
Collapse
Affiliation(s)
- Mari Kekkonen
- Zoology Unit, Finnish Museum of Natural History, University of HelsinkiP.O. Box 17, FI-00014, Helsinki, Finland
| | - Paul D N Hebert
- Biodiversity Institute of Ontario, University of GuelphGuelph, ON, N1G 2W1, Canada
| |
Collapse
|
45
|
Ortiz D, Francke OF. Two new species ofBonnetinatarantulas (Theraphosidae: Theraphosinae) from Mexico: contributions to morphological nomenclature and molecular characterization of types. J NAT HIST 2014. [DOI: 10.1080/00222933.2014.924770] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
46
|
Hamilton CA, Hendrixson BE, Brewer MS, Bond JE. An evaluation of sampling effects on multiple DNA barcoding methods leads to an integrative approach for delimiting species: A case study of the North American tarantula genus Aphonopelma (Araneae, Mygalomorphae, Theraphosidae). Mol Phylogenet Evol 2014; 71:79-93. [DOI: 10.1016/j.ympev.2013.11.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/29/2013] [Accepted: 11/11/2013] [Indexed: 10/26/2022]
|
47
|
Lopardo L, Uhl G. Testing mitochondrial marker efficacy for DNA barcoding in spiders: a test case using the dwarf spider genus Oedothorax (Araneae : Linyphiidae : Erigoninae). INVERTEBR SYST 2014. [DOI: 10.1071/is14017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The present study focusses on comparatively assessing the efficacy for DNA barcoding of the two most commonly used mitochondrial markers (cox1 and 16S) in a genus of erigonine spiders. In total, 53 specimens representing five species, including four multi-sampled species, were sampled from several European localities. Initial evaluation of species monophyly was performed through parsimony and Bayesian phylogenetic analyses. Efficacy of mitochondrial markers was tested using operational (including distance-, tree-based measures and Barcode Gap) and evolutionary criteria (using the General Mixed Yule-coalescent Model) for species delimitation. We propose that the cox1 marker can potentially overestimate analyses of biodiversity and thus might not be the preferred marker for DNA species identification and delimitation methods in Oedothorax. Instead, our results suggest that the 16S marker appears to be a promising candidate for such endeavour. Evaluating the contribution and suitability of markers to the re-identification of species, measured by their recovery of well established morphological species, is critical for future studies and for reliable results in species identification in spiders.
Collapse
|
48
|
Parmakelis A, Kotsakiozi P, Stathi I, Poulikarakou S, Fet V. Hidden diversity ofEuscorpius(Scorpiones: Euscorpiidae) in Greece revealed by multilocus species-delimitation approaches. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12170] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Aristeidis Parmakelis
- Department of Ecology and Taxonomy; Faculty of Biology; University of Athens; Panepistimioupoli Zografou GR-15784 Athens Greece
| | - Panayiota Kotsakiozi
- Department of Human and Animal Physiology; Faculty of Biology; University of Athens; Panepistimioupoli Zografou GR-15784 Athens Greece
| | - Iasmi Stathi
- Natural History Museum of Crete; University of Crete; GR-71409 Heraklion Crete Greece
| | - Stavroula Poulikarakou
- Department of Ecology and Taxonomy; Faculty of Biology; University of Athens; Panepistimioupoli Zografou GR-15784 Athens Greece
| | - Victor Fet
- Department of Biological Sciences; Marshall University; Huntington WV 25755 USA
| |
Collapse
|
49
|
Satler JD, Carstens BC, Hedin M. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus). Syst Biol 2013; 62:805-23. [PMID: 23771888 DOI: 10.1093/sysbio/syt041] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.
Collapse
Affiliation(s)
- Jordan D Satler
- Department of Evolution, Ecology and Organismal Biology, The Ohio University, Columbus, OH 43210, USA and Department of Biology, San Diego University, San Diego, CA 92182, USA
| | | | | |
Collapse
|