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Cheng R, Luo A, Orr M, Ge D, Hou Z, Qu Y, Guo B, Zhang F, Sha Z, Zhao Z, Wang M, Shi X, Han H, Zhou Q, Li Y, Liu X, Shao C, Zhang A, Zhou X, Zhu C. Cryptic diversity begets challenges and opportunities in biodiversity research. Integr Zool 2024. [PMID: 38263700 DOI: 10.1111/1749-4877.12809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.
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Affiliation(s)
- Rui Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Michael Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhong'e Hou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baocheng Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Zhongli Sha
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Zhe Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Mingqiang Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoyu Shi
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongxiang Han
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qingsong Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yuanning Li
- Institute of Oceanography, Shandong University, Qingdao, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chen Shao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Aibing Zhang
- College of Life Science, Capital Normal University, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences/International College, University of Chinese Academy of Sciences, Beijing, China
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Marsh JR, Milner SJ, Shaw M, Stempel AJ, Harvey MS, Rix MG. A Case for Below-Ground Dispersal? Insights into the Biology, Ecology and Conservation of Blind Cave Spiders in the Genus Troglodiplura (Mygalomorphae: Anamidae). INSECTS 2023; 14:insects14050449. [PMID: 37233077 DOI: 10.3390/insects14050449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/05/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023]
Abstract
Previously described from only fragments of exoskeleton and juvenile specimens, the cave spider genus Troglodiplura (Araneae: Anamidae), endemic to the Nullarbor Plain, is the only troglomorphic member of the infraorder Mygalomorphae recorded from Australia. We investigated the distribution of Troglodiplura in South Australia, collecting and observing the first (intact) mature specimens, widening the number of caves it has been recorded in, and documenting threats to conservation. Phylogenetic analyses support the placement of Troglodiplura as an independent lineage within the subfamily Anaminae (the 'Troglodiplura group') and provide unequivocal evidence that populations from apparently isolated cave systems are conspecifics of T. beirutpakbarai Harvey & Rix, 2020, with extremely low or negligible inter-population mitochondrial divergences. This is intriguing evidence for recent or contemporary subterranean dispersal of these large, troglomorphic spiders. Observations of adults and juvenile spiders taken in the natural cave environment, and supported by observations in captivity, revealed the use of crevices within caves as shelters, but no evidence of silk use for burrow construction, contrasting with the typical burrowing behaviours seen in other Anamidae. We identify a range of threats posed to the species and to the fragile cave ecosystem, and provide recommendations for further research to better define the distribution of vulnerable taxa within caves and identify actions needed to protect them.
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Affiliation(s)
- Jessica R Marsh
- Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
- Biological Sciences, South Australian Museum, GPO Box 234, Adelaide, SA 5001, Australia
- Invertebrates Australia, Osborne Park, WA 6017, Australia
| | - Steven J Milner
- School of Biological Sciences, Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, SA 5005, Australia
| | - Matthew Shaw
- Biological Sciences, South Australian Museum, GPO Box 234, Adelaide, SA 5001, Australia
| | | | - Mark S Harvey
- Collections & Research, Western Australian Museum, 49 Kew Street, Welshpool, WA 6106, Australia
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Michael G Rix
- Collections & Research, Western Australian Museum, 49 Kew Street, Welshpool, WA 6106, Australia
- Biodiversity and Geosciences Program, Queensland Museum Collections & Research Centre, Hendra, QLD 4011, Australia
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Liu S, Zhou C, Lin Y. New Insights into the Variation and Admixture of the Cave-Dwelling Spider Trogloneta yunnanensis in South China Karst. Animals (Basel) 2023; 13:ani13071244. [PMID: 37048500 PMCID: PMC10093053 DOI: 10.3390/ani13071244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/26/2023] [Accepted: 04/01/2023] [Indexed: 04/07/2023] Open
Abstract
Subterranean karst caves can contain unexpected biodiversity, but few studies related to spider population genetics have been conducted in the karst area of Southern China. In this study, we investigated the population genetic structure of Trogloneta yunnanensis (Song & Zhu, 1994) based on 73 spider samples from six underground populations in South China Karst. Population genetic structure analysis showed a clear divergence (FST > 0.9 and Nm < 0.05) among populations according to mitochondrial genes. The phylogenetic gene tree constructed by BI and ML methods recovered six geographic clades. Divergence time estimation indicated that the divergence of these six populations can be traced back to the late Pleistocene. We supposed that the geographic isolation led to the extreme population structure. According to this study and previous studies about troglobites living in this region, the subterranean habitats of the Yunnan-Guizhou Plateau may contain many organisms with similar genetic structures. The subterranean biodiversity in the karst area of Southern China needs to be re-evaluated and protected.
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Affiliation(s)
- Shiliang Liu
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Chuang Zhou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Sichuan University, Chengdu 610064, China
| | - Yucheng Lin
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
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Ortiz D, Pekár S, Bryjová A. Gene flow assessment helps to distinguish strong genomic structure from speciation in an Iberian ant-eating spider. Mol Phylogenet Evol 2023; 180:107682. [PMID: 36574825 DOI: 10.1016/j.ympev.2022.107682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022]
Abstract
Although genomic data is boosting our understanding of evolution, we still lack a solid framework to perform reliable genome-based species delineation. This problem is especially critical in the case of phylogeographically structured organisms, with allopatric populations showing similar divergence patterns as species. Here, we assess the species limits and phylogeography of Zodarion alacre, an ant-eating spider widely distributed across the Iberian Peninsula. We first performed species delimitation based on genome-wide data and then validated these results using additional evidence. A commonly employed species delimitation strategy detected four distinct lineages with almost no admixture, which present allopatric distributions. These lineages showed ecological differentiation but no clear morphological differentiation, and evidence of introgression in a mitochondrial barcode. Phylogenomic networks found evidence of substantial gene flow between lineages. Finally, phylogeographic methods highlighted remarkable isolation by distance and detected evidence of range expansion from south-central Portugal to central-north Spain. We conclude that despite their deep genomic differentiation, the lineages of Z. alacre do not show evidence of complete speciation. Our results likely shed light on why Zodarion is among the most diversified spider genera despite its limited distribution and support the use of gene flow evidence to inform species boundaries.
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Affiliation(s)
- David Ortiz
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia.
| | - Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czechia
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Nolasco S, Valdez-Mondragón A. To be or not to be… Integrative taxonomy and species delimitation in the daddy long-legs spiders of the genus Physocyclus (Araneae, Pholcidae) using DNA barcoding and morphology. Zookeys 2022; 1135:93-118. [PMID: 36761795 PMCID: PMC9836410 DOI: 10.3897/zookeys.1135.94628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
Integrative taxonomy is crucial for discovery, recognition, and species delimitation, especially in underestimated species complex or cryptic species, by incorporating different sources of evidence to construct rigorous species hypotheses. The spider genus Physocyclus Simon, 1893 (Pholcidae, Arteminae) is composed of 37 species, mainly from North America. In this study, traditional morphology was compared with three DNA barcoding markers regarding their utility in species delimitation within the genus: 1) Cytochrome c Oxidase subunit 1 (CO1), 2) Internal Transcribed Spacer 2 (ITS2), and 3) Ribosomal large subunit (28S). The molecular species delimitation analyses were carried out using four methods under the corrected p-distances Neighbor-Joining (NJ) criteria: 1) Automatic Barcode Gap Discovery (ABGD), 2) Assemble Species by Automatic Partitioning (ASAP), 3) General Mixed Yule Coalescent model (GMYC), and 4) Bayesian Poisson Tree Processes (bPTP). The analyses incorporated 75 terminals from 22 putative species of Physocyclus. The average intraspecific genetic distance (p-distance) was found to be < 2%, whereas the average interspecific genetic distance was 20.6%. The ABGD, ASAP, and GMYC methods were the most congruent, delimiting 26 or 27 species, while the bPTP method delimited 33 species. The use of traditional morphology for species delimitation was congruent with most molecular methods, with the male palp, male chelicerae, and female genitalia shown to be robust characters that support species-level identification. The barcoding with CO1 and 28S had better resolution for species delimitation in comparison with ITS2. The concatenated matrix and traditional morphology were found to be more robust and informative for species delimitation within Physocyclus.
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Affiliation(s)
- Samuel Nolasco
- Posgrado en Ciencias Biológicas (Doctorado), Centro Tlaxcala de Biología de la Conducta (CTBC), Universidad Autónoma de Tlaxcala (UATx), Carretera Federal Tlaxcala-Puebla, Km. 1.5, C. P. 90062, Tlaxcala, Mexico,Laboratory of Arachnology (LATLAX), Laboratorio Regional de Biodiversidad y Cultivo de Tejidos Vegetales (LBCTV), Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), sede Tlaxcala, Ex-Fábrica San Manuel, San Miguel Contla, 90640 Santa Cruz Tlaxcala, Tlaxcala, Mexico
| | - Alejandro Valdez-Mondragón
- Laboratory of Arachnology (LATLAX), Laboratorio Regional de Biodiversidad y Cultivo de Tejidos Vegetales (LBCTV), Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), sede Tlaxcala, Ex-Fábrica San Manuel, San Miguel Contla, 90640 Santa Cruz Tlaxcala, Tlaxcala, Mexico
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Oh JH, Kim S, Lee S. DNA barcodes reveal population-dependent cryptic diversity and various cases of sympatry of Korean leptonetid spiders (Araneae: Leptonetidae). Sci Rep 2022; 12:15528. [PMID: 36109541 PMCID: PMC9478141 DOI: 10.1038/s41598-022-18666-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
Leptonetidae are tiny, rarely encountered spiders that mainly inhabit moist environments, such as caves, leaf litter, and rock piles. Because they are microhabitat specialists, most leptonetid species have short-range endemism, and rarely occur in sympatry. Their small size, relatively simple habitus features and reproductive organ structure increase the difficulty of identification. The identification of leptonetids and other spiders may also be time-consuming due to their sexual dimorphism, polymorphism, and lack of diagnostic characteristics in juveniles. DNA barcoding has been used as an effective tool for species identification to overcome these obstacles. Herein, we conducted a test of DNA barcoding based on 424 specimens of Korean Leptonetidae representing 76 morphospecies. A threshold of 4.2% based on maximum intraspecific genetic divergence was estimated to efficiently differentiate the morphospecies. The species assignments tested by five species delimitation methods (ABGD, ASAP, GMYC, PTP, and bPTP) were consistent with the morphological identifications for only 47 morphospecies (61.8%), indicating many cases of cryptic diversity among the remaining morphospecies. Furthermore, sympatry in leptonetids, which are known to be rare, was revealed to be common in South Korea, especially in epigean species. Our results showed that sympatries within families, congeners, and intraclades potentially occur throughout the entire region of Korea.
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Macharoenboon K, Siriwut W, Jeratthitikul E. A review of the taxonomy of spiny-backed orb-weaving spiders of the subfamily Gasteracanthinae (Araneae, Araneidae) in Thailand. Zookeys 2021; 1032:17-62. [PMID: 33958915 PMCID: PMC8065025 DOI: 10.3897/zookeys.1032.62001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/17/2021] [Indexed: 11/12/2022] Open
Abstract
Spiny-backed orb-weaving spiders of the subfamily Gasteracanthinae are broadly distributed in the Old World. Despite their use as a model species in biology, evolution, and behavior because of their extraordinary characteristics, the systematics of this group of spiders are still poorly understood. This study elucidates the systematics of Gasteracanthinae in Thailand based on morphological and molecular-based analyses. In total, seven species from three genera, namely Gasteracantha, Macracantha, and Thelacantha, were recorded in Thailand. Shape of abdominal spines, pattern of sigilla, and female genitalia are significant characters for species identification. In contrast, coloration shows highly intraspecific variation in most species within Gasteracanthinae. A phylogenetic tree based on partial sequences of COI, 16S, and H3 genes recovered Gasteracanthinae as a monophyletic group and supports the existence of three clades. Gasteracantha hasselti is placed as a sister taxon to Macracantha arcuata. Hence, we propose to transfer G. hasselti to Macracantha. Moreover, molecular species delimitation analyses (ABGD, bPTP, and GMYC) using 675 bp of COI gene support all nominal species, with evidence of possible additional cryptic species.
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Affiliation(s)
- Kongkit Macharoenboon
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, ThailandAnimal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol UniversityBangkokThailand
| | - Warut Siriwut
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, ThailandAnimal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol UniversityBangkokThailand
| | - Ekgachai Jeratthitikul
- Animal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, ThailandAnimal Systematics and Molecular Ecology Laboratory, Department of Biology, Faculty of Science, Mahidol UniversityBangkokThailand
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Wang CX, Li SQ, Zhu WH. Taxonomic notes on Leptonetidae (Arachnida, Araneae) from China, with descriptions of one new genus and eight new species. Zool Res 2020; 41:684-704. [PMID: 33058572 PMCID: PMC7671919 DOI: 10.24272/j.issn.2095-8137.2020.214] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/10/2020] [Indexed: 11/07/2022] Open
Abstract
Species of the spider family Leptonetidae Simon, 1890 from China are revised based on molecular and morphological data analyses. A new genus, Jingneta Wang & Li gen. nov., is erected, with Leptoneta cornea Tong & Li, 2008 as the type species. Twenty-two Chinese species previously assigned to the genus Leptoneta Simon, 1872 are revised, with eight transferred to Falcileptoneta Komatsu, 1970, seven transferred to Jingneta gen. nov., five transferred to Leptonetela Kratochvíl, 1978, and one species each transferred to Longileptoneta Seo, 2015 and Masirana Kishida, 1942. Eight new species are described: i.e., Falcileptoneta shuanglong Wang & Li sp. nov. (♂), Jingneta caoxian Wang & Li sp. nov. (♂♀), J. jingdong Wang & Li sp. nov. (♂♀), Longileptoneta gutan Wang & Li sp. nov. (♂♀), L. huangshan Wang & Li sp. nov. (♂♀), L. shenxian Wang & Li sp. nov. (♂♀), L. yeren Wang & Li sp. nov. (♂), and L. zhuxian Wang & Li sp. nov. (♂♀). In total, 127 leptonetid species from six genera are documented from China: nine species of Falcileptoneta, nine species of Jingneta gen. nov., 101 species of Leptonetela, six species of Longileptoneta, one species of Masirana, and one species of Rhyssoleptoneta Tong & Li, 2007.
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Affiliation(s)
- Chun-Xia Wang
- Hebei Key Laboratory of Animal Diversity, College of Life Science, Langfang Normal University, Langfang, Hebei 065000, China
| | - Shu-Qiang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China. E-mail:
| | - Wen-Hui Zhu
- Life Science College, Shenyang Normal University, Shenyang, Liaoning 110034, China
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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.
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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
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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.
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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
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Ashfaq M, Blagoev G, Tahir HM, Khan AM, Mukhtar MK, Akhtar S, Butt A, Mansoor S, Hebert PDN. Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan. PLoS One 2019; 14:e0217086. [PMID: 31116764 PMCID: PMC6530854 DOI: 10.1371/journal.pone.0217086] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/04/2019] [Indexed: 01/16/2023] Open
Abstract
Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0-5.3% while congeneric distances varied from 2.8-23.2%. Excepting one species pair (Oxyopes azhari-Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.
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Affiliation(s)
- Muhammad Ashfaq
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Gergin Blagoev
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Arif M. Khan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | | | - Saleem Akhtar
- Directorate of Entomology, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Abida Butt
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
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Mammola S, Cardoso P, Ribera C, Pavlek M, Isaia M. A synthesis on cave-dwelling spiders in Europe. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12201] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefano Mammola
- Department of Life Sciences and Systems Biology; University of Torino; Turin Italy
| | - Pedro Cardoso
- Finnish Museum of Natural History; University of Helsinki; Helsinki Finland
| | - Carles Ribera
- Biodiversity Research Institute and Department of Animal Biology; University of Barcelona; Barcelona Spain
| | - Martina Pavlek
- Biodiversity Research Institute and Department of Animal Biology; University of Barcelona; Barcelona Spain
- Ruđer Bošković Institute; Zagreb Croatia
- Croatian Biospeleological Society; Zagreb Croatia
| | - Marco Isaia
- Department of Life Sciences and Systems Biology; University of Torino; Turin Italy
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15
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Abstract
World experts of different disciplines, from molecular biology to macro-ecology, recognize the value of cave ecosystems as ideal ecological and evolutionary laboratories. Among other subterranean taxa, spiders stand out as intriguing model organisms for their ecological role of top predators, their unique adaptations to the hypogean medium and their sensitivity to anthropogenic disturbance. As the description of the first eyeless spider (Stalita taenaria), an array of papers on subterranean spider biology, ecology and evolution has been published, but a comprehensive review on these topics is still lacking. We provide a general overview of the spider families recorded in hypogean habitats worldwide, we review the different adaptations of hypogean spiders to subterranean life, and we summarize the information gathered so far about their origin, population structure, ecology and conservation status. Finally, we point out the limits of the knowledge we currently have regarding hypogean spiders, aiming to stimulate future research.
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Affiliation(s)
- Stefano Mammola
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- IUCN SSC Spider & Scorpion Specialist Group, Torino, Italy
| | - Marco Isaia
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
- IUCN SSC Spider & Scorpion Specialist Group, Torino, Italy
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16
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High endemism at cave entrances: a case study of spiders of the genus Uthina. Sci Rep 2016; 6:35757. [PMID: 27775081 PMCID: PMC5075877 DOI: 10.1038/srep35757] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/03/2016] [Indexed: 11/23/2022] Open
Abstract
Endemism, which is typically high on islands and in caves, has rarely been studied in the cave entrance ecotone. We investigated the endemism of the spider genus Uthina at cave entrances. Totally 212 spiders were sampled from 46 localities, from Seychelles across Southeast Asia to Fiji. They mostly occur at cave entrances but occasionally appear at various epigean environments. Phylogenetic analysis of DNA sequence data from COI and 28S genes suggested that Uthina was grouped into 13 well-supported clades. We used three methods, the Bayesian Poisson Tree Processes (bPTP) model, the Bayesian Phylogenetics and Phylogeography (BPP) method, and the general mixed Yule coalescent (GMYC) model, to investigate species boundaries. Both bPTP and BPP identified the 13 clades as 13 separate species, while GMYC identified 19 species. Furthermore, our results revealed high endemism at cave entrances. Of the 13 provisional species, twelve (one known and eleven new) are endemic to one or a cluster of caves, and all of them occurred only at cave entrances except for one population of one species. The only widely distributed species, U. luzonica, mostly occurred in epigean environments while three populations were found at cave entrances. Additionally, eleven new species of the genus are described.
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17
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Hurtado LA, Mateos M, Mattos G, Liu S, Haye PA, Paiva PC. Multiple transisthmian divergences, extensive cryptic diversity, occasional long-distance dispersal, and biogeographic patterns in a marine coastal isopod with an amphi-American distribution. Ecol Evol 2016; 6:7794-7808. [PMID: 30128130 PMCID: PMC6093162 DOI: 10.1002/ece3.2397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/21/2016] [Accepted: 08/01/2016] [Indexed: 12/12/2022] Open
Abstract
Excirolana braziliensis is a coastal intertidal isopod with a broad distribution spanning the Atlantic and Pacific tropical and temperate coasts of the American continent. Two separate regional studies (one in Panama and one in Chile) revealed the presence of highly genetically divergent lineages, implying that this taxon constitutes a cryptic species complex. The relationships among the lineages found in these two different regions and in the rest of the distribution, however, remain unknown. To better understand the phylogeographic patterns of E. braziliensis, we conducted phylogenetic analyses of specimens from much of its entire range. We obtained DNA sequences for fragments of four mitochondrial genes (16S rDNA, 12S rDNA, COI, and Cytb) and also used publicly available sequences. We conducted maximum likelihood and Bayesian phylogenetic reconstruction methods. Phylogeographic patterns revealed the following: (1) new highly divergent lineages of E. braziliensis; (2) three instances of Atlantic–Pacific divergences, some of which appear to predate the closure of the Isthmus of Panama; (3) the distributional limit of highly divergent lineages found in Brazil coincides with the boundary between two major marine coastal provinces; (4) evidence of recent long‐distance dispersal in the Caribbean; and (5) populations in the Gulf of California have closer affinities with lineages further south in the Pacific, which contrasts with the closer affinity with the Caribbean reported for other intertidal organisms. The high levels of cryptic diversity detected also bring about challenges for the conservation of this isopod and its fragile environment, the sandy shores. Our findings underscore the importance of comprehensive geographic sampling for phylogeographic and taxonomical studies of broadly distributed putative species harboring extensive cryptic diversity.
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Affiliation(s)
- Luis A Hurtado
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Mariana Mateos
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Gustavo Mattos
- Programa de Pós-Graduação em Ecologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
| | - Shuang Liu
- Department of Wildlife and Fisheries Sciences Texas A&M University College Station Texas
| | - Pilar A Haye
- Departamento de Biología Marina Universidad Católica del Norte Coquimbo Chile.,Centro de Estudios Avanzados en Zonas Áridas (CEAZA) Coquimbo Chile.,Interdisciplinary Center for Aquaculture Research (INCAR) Universidad de Concepción Casilla 160-C Concepción Chile
| | - Paulo C Paiva
- Programa de Pós-Graduação em Ecologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil.,Departamento de Zoologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil
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18
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Liu F, Wang M, Damm U, Crous PW, Cai L. Species boundaries in plant pathogenic fungi: a Colletotrichum case study. BMC Evol Biol 2016; 16:81. [PMID: 27080690 PMCID: PMC4832473 DOI: 10.1186/s12862-016-0649-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/31/2016] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Accurate delimitation of plant pathogenic fungi is critical for the establishment of quarantine regulations, screening for genetic resistance to plant pathogens, and the study of ecosystem function. Concatenation analysis of multi-locus DNA sequence data represents a powerful and commonly used approach to recognizing evolutionary independent lineages in fungi. It is however possible to mask the discordance between individual gene trees, thus the speciation events might be erroneously estimated if one simply recognizes well supported clades as distinct species without implementing a careful examination of species boundary. To investigate this phenomenon, we studied Colletotrichum siamense s. lat., which is a cosmopolitan pathogen causing serious diseases on many economically important plant hosts. Presently there are significant disagreements among mycologists as to what constitutes a species in C. siamense s. lat., with the number of accepted species ranging from one to seven. RESULTS In this study, multiple approaches were used to test the null hypothesis "C. siamense is a species complex", using a global strain collection. Results of molecular analyses based on the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and coalescent methods (e.g. Generalized Mixed Yule-coalescent and Poisson Tree Processes) do not support the recognition of any independent evolutionary lineages within C. siamense s. lat. as distinct species, thus rejecting the null hypothesis. This conclusion is reinforced by the recognition of genetic recombination, cross fertility, and the comparison of ecological and morphological characters. Our results indicate that reproductive isolation, geographic and host plant barriers to gene flow are absent in C. siamense s. lat. CONCLUSIONS This discovery emphasized the importance of a polyphasic approach when describing novel species in morphologically conserved genera of plant pathogenic fungi.
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Affiliation(s)
- Fang Liu
- />State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- />Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mei Wang
- />State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ulrike Damm
- />Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany
| | - Pedro W. Crous
- />Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- />CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- />Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Lei Cai
- />State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
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Wang GH, Jia LY, Xiao JH, Huang DW. Discovery of a new Wolbachia supergroup in cave spider species and the lateral transfer of phage WO among distant hosts. INFECTION GENETICS AND EVOLUTION 2016; 41:1-7. [PMID: 26997548 DOI: 10.1016/j.meegid.2016.03.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 12/21/2022]
Abstract
Wolbachia are widespread intracellular bacteria infecting the major classes of arthropods and some filarial nematodes. In arthropods, Wolbachia have evolved various intriguing reproductive manipulations, including cytoplasmic incompatibility, parthenogenesis, feminization, and male killing. Sixteen supergroups of Wolbachia have been identified, named A-Q (except G). Though Wolbachia present great diversity in arthropods, spiders, especially cave spiders, are still a poorly surveyed group of Wolbachia hosts. Here, we report a novel Wolbachia supergroup from nine Telema cave spiders (Araneae: Telemidae) based on five molecular markers (16S rRNA, ftsZ, gltA, groEL, and coxA). In addition, phage WO, which was previously reported only in Wolbachia supergroups A, B, and F, infects this new Wolbachia supergroup. We detected a 100% infection rate for phage WO and Wolbachia in Telema species. The phylogenetic trees of phage WO and Wolbachia are not congruent, which suggests that horizontal transfer of phage WO has occurred in these secluded species. Additionally, these data indicate Telema-Wolbachia-phage WO may be a good model for exploring the horizontal transfer history of WO among different host species.
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Affiliation(s)
- Guan-Hong Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ling-Yi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jin-Hua Xiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Da-Wei Huang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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