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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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2
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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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3
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Brandt S, Sole C, Lyle R. The phylogenetic structure and coalescent species delimitation of an endemic trapdoor spider genus, Stasimopus (Araneae, Mygalomorphae, Stasimopidae) in the Karoo region of South Africa. Mol Phylogenet Evol 2023; 184:107798. [PMID: 37094612 DOI: 10.1016/j.ympev.2023.107798] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 04/26/2023]
Abstract
The Karoo region of South Africa is a unique and sensitive ecosystem which is facing pressure for development due to economic incentives such as mining, farming and shale gas exploration. The species diversity of many taxa in the area is largely unknown. A phylogenetic analysis of the cork-lid trapdoor spider genus, Stasimopus (Stasimopidae) was undertaken in order to gain insight into the relationships between the species that may be present in the area. The species within Stasimopus are challenging to identify and define using traditional morphological methods due to a high degree of morphological conservatism within the genus. For this reason, multiple coalescent based species delimitation methods were used to attempt to determine the species present for Stasimopus in the region which was tested against the morphological identifications and genetic clades (based on CO1, 16S and EF-1ɣ). We tested single-locus methods Automatic Barcode Gap Discovery (ABGD), Bayesian implementation of Poisson Tree Processes (bPTP) and General Mixed Yule- Coalescent (GMYC), as well as multi-locus Brownie. The phylogenetic analysis of Stasimopus in the Karoo showed that there is a high degree of genetic diversity within the genus. The species delimitation results proved unfruitful for the genus, as they appear to delimit population structure rather than species for most methods. Alternative methods should be investigated to aid in the identification of the species in order truly understand the species diversity of the genus.
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Affiliation(s)
- Shannon Brandt
- Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa.
| | - Catherine Sole
- Department of Zoology and Entomology, University of Pretoria, Hatfield, Pretoria, South Africa.
| | - Robin Lyle
- Agricultural Research Council - Plant Health and Protection, Biosystematics, Roodeplaat, Pretoria, South Africa
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4
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Deep mtDNA Sequence Divergences and Possible Species Radiation of Whip Spiders (Arachnida, Amblypygi, Phrynidae, Phrynus/Paraphrynus) among Caribbean Oceanic and Cave Islands. TAXONOMY 2023. [DOI: 10.3390/taxonomy3010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Islands—whether classic oceanic islands or habitat islands such as isolated thermal vents, mountain tops, or caves—often promote the diversification of lineages that colonize them. We examined CO1 mtDNA sequence divergences within the tailless whip spider genus Phrynus Lamarck, 1809 (Amblypygi: Phrynidae) among oceanic islands and among cave ’islands´ distributed across the Caribbean archipelago and on the continental mainland. The significance of this study lies in the extensive taxon sampling of a supposedly depauperate lineage (considering its age), over a large proportion of its geographical range, and the discovery of deep mtDNA sequence divergences. We sampled thousands of specimens—and sequenced 544, including six outgroup species—across 173 localities on 17 islands (135 localities) and five countries on the North to South American mainland (38 localities), including a total of 63 caves. Classical taxonomy identified ten named Phrynus and two Paraphrynus Moreno, 1940 species. Paraphrynus seems to be paraphyletic and nested in Phrynus. Uncorrected genetic distances within named species and among morphological species ranged up to 15% and 19%, respectively. Geographic distances explained a significant portion of genetic distances on islands (19%, among both subterranean and epigean specimens), and for epigean specimens on the mainland (27%). Species delimitation analyses indicated that the 12 named species harbored from 66 to well over 100 putative species. The highest number of species was indicated by the GMYC method (114 species) while the Bayesian Poisson tree processes (bPTP) and the BP&P relaying on the Markov chain Monte Carlo Bayesian Phylogenetic model estimated an upper level of 110 species. On the other hand, the recently recommended and relatively conservative distance-based (phylogeny free) ASAP model has the greatest support for 73 species. In either case, nearly all putative species are tightly limited to a single locality, often a small cave system, and sometimes to the surrounding epigean area. Caribbean Phrynus diversity has likely been vastly underestimated, likely due to both morphological crypsis and the ignorance of Caribbean cave fauna. Although mtDNA sequences can suggest species limits, nuclear DNA sequencing and detailed morphological research are necessary to corroborate them and explore whether this phenomenon constitutes species radiation or perhaps just mtDNA divergences as a consequence of, for example, stationary females and actively dispersing males.
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Chamberland L, Agnarsson I, Quayle IL, Ruddy T, Starrett J, Bond JE. Biogeography and eye size evolution of the ogre-faced spiders. Sci Rep 2022; 12:17769. [PMID: 36273015 PMCID: PMC9588044 DOI: 10.1038/s41598-022-22157-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 10/10/2022] [Indexed: 01/19/2023] Open
Abstract
Net-casting spiders (Deinopidae) comprise a charismatic family with an enigmatic evolutionary history. There are 67 described species of deinopids, placed among three genera, Deinopis, Menneus, and Asianopis, that are distributed globally throughout the tropics and subtropics. Deinopis and Asianopis, the ogre-faced spiders, are best known for their giant light-capturing posterior median eyes (PME), whereas Menneus does not have enlarged PMEs. Molecular phylogenetic studies have revealed discordance between morphology and molecular data. We employed a character-rich ultra-conserved element (UCE) dataset and a taxon-rich cytochrome-oxidase I (COI) dataset to reconstruct a genus-level phylogeny of Deinopidae, aiming to investigate the group's historical biogeography, and examine PME size evolution. Although the phylogenetic results support the monophyly of Menneus and the single reduction of PME size in deinopids, these data also show that Deinopis is not monophyletic. Consequently, we formally transfer 24 Deinopis species to Asianopis; the transfers comprise all of the African, Australian, South Pacific, and a subset of Central American and Mexican species. Following the divergence of Eastern and Western deinopids in the Cretaceous, Deinopis/Asianopis dispersed from Africa, through Asia and into Australia with its biogeographic history reflecting separation of Western Gondwana as well as long-distance dispersal events.
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Affiliation(s)
- Lisa Chamberland
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Ingi Agnarsson
- grid.14013.370000 0004 0640 0021Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102 Reykjavik, Iceland
| | - Iris L. Quayle
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Tess Ruddy
- grid.267778.b0000 0001 2290 5183Vassar College, Poughkeepsie, NY 12604 USA
| | - James Starrett
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Jason E. Bond
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
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6
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Ciaccio E, Debray A, Hedin M. Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with the description of a new species from montane California. Zookeys 2022; 1086:163-204. [PMID: 35221748 PMCID: PMC8873193 DOI: 10.3897/zookeys.1086.77190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/18/2022] [Indexed: 12/31/2022] Open
Abstract
Hypochilus is a relictual lineage of Nearctic spiders distributed disjunctly across the United States in three montane regions (California, southern Rocky Mountains, southern Appalachia). Phylogenetic resolution of species relationships in Hypochilus has been challenging, and conserved morphology coupled with extreme genetic divergence has led to uncertain species limits in some complexes. Here, Hypochilus interspecies relationships have been reconstructed and cryptic speciation more critically evaluated using a combination of ultraconserved elements, mitochondrial CO1 by-catch, and morphology. Phylogenomic data strongly support the monophyly of regional clades and support a ((California, Appalachia), southern Rocky Mountains) topology. In Appalachia, five species are resolved as four lineages (H.thorelli Marx, 1888 and H.coylei Platnick, 1987 are clearly sister taxa), but the interrelationships of these four lineages remain unresolved. The Appalachian species H.pococki Platnick, 1987 is recovered as monophyletic but is highly genetically structured at the nuclear level. While algorithmic analyses of nuclear data indicate many species (e.g., all H.pococki populations as species), male morphology instead reveals striking stasis. Within the California clade, nuclear and mitochondrial lineages of H.petrunkevitchi Gertsch, 1958 correspond directly to drainage basins of the southern Sierra Nevada, with H.bernardino Catley, 1994 nested within H.petrunkevitchi and sister to the southernmost basin populations. Combining nuclear, mitochondrial, geographical, and morphological evidence a new species from the Tule River and Cedar Creek drainages is described, Hypochilusxomotesp. nov. We also emphasize the conservation issues that face several microendemic, habitat-specialized species in this remarkable genus.
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Affiliation(s)
- Erik Ciaccio
- Department of Biology, San Diego State University, San Diego, California, USA San Diego State University San Diego United States of America.,Department of Entomology, Plant Pathology and Nematology, University of Idaho, Idaho, USA University of Idaho Idaho United States of America
| | - Andrew Debray
- Department of Biology, San Diego State University, San Diego, California, USA San Diego State University San Diego United States of America.,Nano PharmaSolutions Inc., San Diego, California, USA Nano PharmaSolutions Inc. San Diego United States of America
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California, USA San Diego State University San Diego United States of America
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7
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Derkarabetian S, Paquin P, Reddell J, Hedin M. Conservation genomics of federally endangered Texella harvester species (Arachnida, Opiliones, Phalangodidae) from cave and karst habitats of central Texas. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01427-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Isaia M, Arnedo MA, Mammola S. A multi-layered approach uncovers overlooked taxonomic and physiological diversity in Alpine subterranean spiders (Araneae: Linyphiidae: Troglohyphantes). INVERTEBR SYST 2022. [DOI: 10.1071/is21054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Improving Taxonomic Practices and Enhancing Its Extensibility—An Example from Araneology. DIVERSITY 2021. [DOI: 10.3390/d14010005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely available, whether an explicit species hypothesis was stated, what types of media were used, the sample sizes, and the degree to which species constructs were integrative. The findings we report reveal that taxonomy remains largely descriptive, not integrative, and provides no explicit conceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-third of all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies made data freely available, and only ~14% of all newly described species employed more than one line of evidence, with molecular data used in ~6% of the studies. These same trends have been discovered in other animal groups, and therefore we find it logical that taxonomists face an uphill challenge when justifying the scientific rigor of their field and securing the needed resources. To move taxonomy forward, we make recommendations that, if implemented, will enhance its rigor, repeatability, and scientific standards.
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Kallal RJ, Kulkarni SS, Dimitrov D, Benavides LR, Arnedo MA, Giribet G, Hormiga G. Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web. Cladistics 2021; 37:298-316. [PMID: 34478199 DOI: 10.1111/cla.12439] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2020] [Indexed: 12/20/2022] Open
Abstract
High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long-standing hypotheses. Likewise, the evolution of spider webs-perhaps their most emblematic attribute-is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages using a variety of orthology assessment methods, occupancy thresholds, tree inference methods and support metrics. Our analyses include families not previously sampled in transcriptomic analyses, such as Symphytognathidae, the only araneoid family absent in such prior works. We find support for the major established spider lineages, including Mygalomorphae, Araneomorphae, Synspermiata, Palpimanoidea, Araneoidea and the Retrolateral Tibial Apophysis Clade, as well as the uloborids, deinopids, oecobiids and hersiliids Grade. Resulting trees are evaluated using bootstrapping, Shimodaira-Hasegawa approximate likelihood ratio test, local posterior probabilities and concordance factors. Using structured Markov models to assess the evolution of spider webs while accounting for hierarchically nested traits, we find multiple convergent occurrences of the orb web across the spider tree-of-life. Overall, we provide the most comprehensive spider tree-of-life to date using transcriptomic data and use new methods to explore controversial issues of web evolution, including the origins and multiple losses of the orb web.
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Affiliation(s)
- Robert J Kallal
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Department of Entomology, National Museum of Natural History, 10th & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Siddharth S Kulkarni
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA.,Department of Entomology, National Museum of Natural History, 10th & Constitution Ave. NW, Washington, DC, 20560, USA
| | - Dimitar Dimitrov
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, Bergen, 5020, Norway
| | - Ligia R Benavides
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Miquel A Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Biodiversity Research Institute (IRBio), Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, Spain
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Gustavo Hormiga
- Department of Biological Sciences, The George Washington University, 2029 G St. NW, Washington, DC, 20052, USA
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11
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Sukumaran J, Holder MT, Knowles LL. Incorporating the speciation process into species delimitation. PLoS Comput Biol 2021; 17:e1008924. [PMID: 33983918 PMCID: PMC8118268 DOI: 10.1371/journal.pcbi.1008924] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/29/2021] [Indexed: 11/22/2022] Open
Abstract
The "multispecies" coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.
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Affiliation(s)
- Jeet Sukumaran
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Mark T. Holder
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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12
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Marshall TL, Chambers EA, Matz MV, Hillis DM. How mitonuclear discordance and geographic variation have confounded species boundaries in a widely studied snake. Mol Phylogenet Evol 2021; 162:107194. [PMID: 33940060 DOI: 10.1016/j.ympev.2021.107194] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/12/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
As DNA sequencing technologies and methods for delimiting species with genomic data become more accessible and numerous, researchers have more tools than ever to investigate questions in systematics and phylogeography. However, easy access to sophisticated computational tools is not without its drawbacks. Choosing the right approach for one's question can be challenging when presented with multitudinous options, some of which fail to distinguish between species and intraspecific population structure. Here, we employ a methodology that emphasizes intensive geographic sampling, particularly at contact zones between populations, with a focus on differentiating intraspecific genetic clusters from species in the Pantherophis guttatus complex, a group of North American ratsnakes. Using a mitochondrial marker as well as ddRADseq data, we find evidence of mitonuclear discordance which has contributed to historical confusion about the relationships within this group. Additionally, we identify geographically and genetically structured populations within the species Pantherophis emoryi that are congruent with previously described morphological variation. Importantly, we find that these structured populations within P. emoryi are highly admixed throughout the range of the species and show no evidence of any reproductive isolation. Our data support a revision of the taxonomy of this group, and we recognize two species within the complex and three subspecies within P. emoryi. This study illustrates the importance of thorough sampling of contact zones and consideration of gene flow when delimiting species in widespread complexes containing parapatric lineages.
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Affiliation(s)
- Thomas L Marshall
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA.
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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13
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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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14
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Baroni S, Damasceno RP, Almeida-Toledo LFD. Paraphyly and evolutionary independent lineages in Gymnotus pantherinus (Gymnotiformes: Gymnotidae) in the Brazilian Atlantic Forest Coastal Streams. Mol Phylogenet Evol 2021; 161:107159. [PMID: 33794394 DOI: 10.1016/j.ympev.2021.107159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/01/2021] [Accepted: 03/23/2021] [Indexed: 11/18/2022]
Abstract
In the Brazilian Atlantic Forest (AF), many terrestrial species with broad geographical distributions show high diversity and endemism of intraspecific lineages, as revealed by molecular genetic data. This pattern, however, is less explored in freshwater fishes. Gymnotus pantherinus is an electric fish endemic to the Brazilian coastal drainages that shows a wide distribution, ranging from the states of Bahia to Santa Catarina, an unusual pattern for AF fishes. It has been hypothesized that G. pantherinus is a species complex because distinct morphotypes were described for the species based on morphometric and meristic features. We used mitochondrial and nuclear data to test this hypothesis. Based on phylogenetic inference and multi-locus, multispecies coalescent methods, we identified six independent lineages, flagging them as candidate species. One such lineage is the recently described species G. refugio that is nested within G. pantherinus and renders it paraphyletic, showing it is a species complex. We named G. pantherinus stricto sensu the lineage that includes samples from the type locality (Santos, SP). Our results show that genetic lineages correspond only partially and far exceed the number of previously reported morphotypes. Genetic breaks in the group correspond to landscape features associated with the Serra do Mar mountain range and with riverine dynamics caused by sea level changes during the last glacial maximum. Moreover, we found evidence of river capture events affecting phylogeographic structure in the group. We uncovered an important dimension of diversity in the group and encourage further integration of genetic and phenotypic data. Such integration is a fruitful approach not only to reduce the gap between taxonomy and evolutionary history in Gymnotidae, but also to uncover the real AF biodiversity.
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Affiliation(s)
- Sabrina Baroni
- Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil.
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15
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Mammola S, Hesselberg T, Lunghi E. A trade‐off between latitude and elevation contributes to explain range segregation of broadly distributed cave‐dwelling spiders. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (LUOMUS) University of Helsinki Helsinki Finland
- Molecular Ecology Group (MEG) Water Research Institute (IRSA) National Research Council (CNR) Verbania Pallanza Italy
| | | | - Enrico Lunghi
- Key Laboratory of the Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences Beijing China
- Museo di Storia Naturale dell'Università degli Studi di Firenze Sezione di Zoologia "La Specola" Firenze Italy
- Natural Oasis Prato Italy
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16
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Mussmann SM, Douglas MR, Oakey DD, Douglas ME. Defining relictual biodiversity: Conservation units in speckled dace (Leuciscidae: Rhinichthys osculus) of the Greater Death Valley ecosystem. Ecol Evol 2020; 10:10798-10817. [PMID: 33072297 PMCID: PMC7548178 DOI: 10.1002/ece3.6736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/19/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species-population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates this approach in speckled dace (Leuciscidae: Rhinichthys osculus) endemic to two basins (Owens and Amargosa) in the Death Valley ecosystem. These fish persist in the Mojave Desert as isolated Plio-Pleistocene relicts and are of conservation concern, but lack formal taxonomic descriptions/designations. Double digest RAD (ddRAD) methods identified 14,355 SNP loci across 10 populations (N = 140). Species delimitation analyses [multispecies coalescent (MSC) and unsupervised machine learning (UML)] delineated four putative ESUs. F ST outlier loci (N = 106) were juxtaposed to uncover the potential for localized adaptations. We detected one hybrid population that resulted from upstream reconnection of habitat following contemporary pluvial periods, whereas remaining populations represent relics of ancient tectonism within geographically isolated springs and groundwater-fed streams. Our study offers three salient conclusions: a blueprint for a multifaceted delimitation of conservation units; a proposed mechanism by which criteria for intraspecific biodiversity can be potentially standardized; and a strong argument for the proactive management of critically endangered Death Valley ecosystem fishes.
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Affiliation(s)
- Steven M. Mussmann
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - David D. Oakey
- School of Life SciencesArizona State UniversityTempeAZUSA
- Present address:
Arizona State Veteran HomePhoenixAZUSA
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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17
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Mason NA, Fletcher NK, Gill BA, Funk WC, Zamudio KR. Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1730475] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Nicholas A. Mason
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Nicholas K. Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
| | - Brian A. Gill
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - W. Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, New York 14853, USA
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18
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Mammola S, Arnedo MA, Fišer C, Cardoso P, Dejanaz AJ, Isaia M. Environmental filtering and convergent evolution determine the ecological specialization of subterranean spiders. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13527] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Stefano Mammola
- Molecular Ecology Group (MEG) IRSA—Water Research Institute National Research Council Verbania Pallanza Italy
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (LUOMUS) University of Helsinki Helsinki Finland
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Miquel A. Arnedo
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute University of Barcelona Barcelona Spain
| | - Cene Fišer
- Department of Biology Biotechnical Faculty University of Ljubljana Ljubljana Slovenia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (LUOMUS) University of Helsinki Helsinki Finland
| | - Andrea J. Dejanaz
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Marco Isaia
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
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19
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Mammola S, Cardoso P, Angyal D, Balázs G, Blick T, Brustel H, Carter J, Ćurčić S, Danflous S, Dányi L, Déjean S, Deltshev C, Elverici M, Fernández J, Gasparo F, Komnenov M, Komposch C, Kováč L, Kunt KB, Mock A, Moldovan OT, Naumova M, Pavlek M, Prieto CE, Ribera C, Rozwałka R, Růžička V, Vargovitsh RS, Zaenker S, Isaia M. Local- versus broad-scale environmental drivers of continental β-diversity patterns in subterranean spider communities across Europe. Proc Biol Sci 2019; 286:20191579. [PMID: 31662080 DOI: 10.1098/rspb.2019.1579] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Macroecologists seek to identify drivers of community turnover (β-diversity) through broad spatial scales. However, the influence of local habitat features in driving broad-scale β-diversity patterns remains largely untested, owing to the objective challenges of associating local-scale variables to continental-framed datasets. We examined the relative contribution of local- versus broad-scale drivers of continental β-diversity patterns, using a uniquely suited dataset of cave-dwelling spider communities across Europe (35-70° latitude). Generalized dissimilarity modelling showed that geographical distance, mean annual temperature and size of the karst area in which caves occurred drove most of β-diversity, with differential contributions of each factor according to the level of subterranean specialization. Highly specialized communities were mostly influenced by geographical distance, while less specialized communities were mostly driven by mean annual temperature. Conversely, local-scale habitat features turned out to be meaningless predictors of community change, which emphasizes the idea of caves as the human accessible fraction of the extended network of fissures that more properly represents the elective habitat of the subterranean fauna. To the extent that the effect of local features turned to be inconspicuous, caves emerge as experimental model systems in which to study broad biological patterns without the confounding effect of local habitat features.
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Affiliation(s)
- Stefano Mammola
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy.,LIBRe-Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Pedro Cardoso
- LIBRe-Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Dorottya Angyal
- UMDI, Faculty of Sciences, UNAM National Autonomous University of Mexico, Sisal, Mexico.,Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Gergely Balázs
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, Hungary
| | - Theo Blick
- Independent Researcher, Hummeltal, Germany
| | | | | | - Srećko Ćurčić
- Institute of Zoology, University of Belgrade-Faculty of Biology, Belgrade, Serbia
| | - Samuel Danflous
- Conservatoire d'Espaces Naturels de Midi-Pyrénées, Toulouse, France
| | - László Dányi
- Department of Zoology, Hungarian Natural History Museum, Budapest, Hungary
| | - Sylvain Déjean
- Conservatoire d'Espaces Naturels de Midi-Pyrénées, Toulouse, France
| | - Christo Deltshev
- National Museum of Natural History, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Mert Elverici
- Department of Biology, Faculty of Science and Arts, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | | | - Fulvio Gasparo
- Commissione Grotte 'E. Boegan', Società Alpina delle Giulie, C.A.I., Trieste, Italy
| | - Marjan Komnenov
- Independent Researcher, Blwd Kuzman Josifovski Pitu, Skopje, Republic of North Macedonia
| | - Christian Komposch
- OEKOTEAM - Institute for Animal Ecology and Landscape Planning, Graz, Austria
| | | | - Kadir Boğaç Kunt
- Department of Biology, Faculty of Science, Eskişehir Technical University, Eskişehir, Turkey.,Zoological Collection of Cyprus Wildlife Research Institute, Taşkent, Kyrenia, Cyprus
| | - Andrej Mock
- Pavol Jozef Šafárik University, Košice, Slovakia
| | - Oana Teodora Moldovan
- Emil Racovitza Institute of Speleology, Cluj-Napoca, Romania.,Romanian Institute of Science and Technology, Cluj-Napoca, Romania
| | - Maria Naumova
- Institute of Biodiversity and Ecosystem Research, Sofia, Bulgaria
| | - Martina Pavlek
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute, University of Barcelona, Barcelona, Spain.,Croatian Biospeleological Society, Zagreb, Croatia
| | - Carlos E Prieto
- Department of Zoology & Animal Cell Biology, University of the Basque Country, Bilbao, Spain
| | - Carles Ribera
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
| | - Robert Rozwałka
- Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warszawa, Poland
| | - Vlastimil Růžička
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Robert S Vargovitsh
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Stefan Zaenker
- Verband der deutschen Höhlen- und Karstforscher e.V., Fulda, Germany
| | - Marco Isaia
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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20
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Hu GL, Gao K, Wang JS, Hebert PDN, Hua BZ. Molecular phylogeny and species delimitation of the genus Dicerapanorpa (Mecoptera: Panorpidae). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Given that species is the fundamental unit in systematic biology, rigorous species delimitation is crucial for taxonomic studies, yet routine species delimitation remains an ongoing challenge in the taxonomic practice of insects. The two-horned scorpionfly Dicerapanorpa is a small genus in Panorpidae (Mecoptera) endemic to the Qinling-Bashan and Hengduan mountains, a biodiversity hotspot. However, species of Dicerapanorpa are difficult to delineate owing to marked intraspecific variation and interspecific similarity. Here, we investigate the diversity and species boundaries of Dicerapanorpa using an integrative approach based on DNA barcoding, morphological, geometric morphometric and molecular phylogenetic analyses. This integrative analyses confirmed the 13 described species of Dicerapanorpa and revealed three new species: Dicerapanorpa lativalva sp. nov., Dicerapanorpa hualongshana sp. nov. and Dicerapanorpa minshana sp. nov. Most molecular operational taxonomic units are in congruence with morphological clusters. Possible reasons for several discordances in Dicerapanorpa are tentatively discussed.
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Affiliation(s)
- Gui-Lin Hu
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Kai Gao
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Ji-Shen Wang
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Bao-Zhen Hua
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
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21
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Mammola S, Cardoso P, Angyal D, Balázs G, Blick T, Brustel H, Carter J, Ćurčić S, Danflous S, Dányi L, Déjean S, Deltshev C, Elverici M, Fernández J, Gasparo F, Komnenov M, Komposch C, Kováč L, Kunt KB, Mock A, Moldovan O, Naumova M, Pavlek M, Prieto CE, Ribera C, Rozwałka R, Růžička V, Vargovitsh RS, Zaenker S, Isaia M. Continental data on cave-dwelling spider communities across Europe (Arachnida: Araneae). Biodivers Data J 2019; 7:e38492. [PMID: 31636503 PMCID: PMC6794329 DOI: 10.3897/bdj.7.e38492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/07/2019] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Spiders (Arachnida: Araneae) are widespread in subterranean ecosystems worldwide and represent an important component of subterranean trophic webs. Yet, global-scale diversity patterns of subterranean spiders are still mostly unknown. In the frame of the CAWEB project, a European joint network of cave arachnologists, we collected data on cave-dwelling spider communities across Europe in order to explore their continental diversity patterns. Two main datasets were compiled: one listing all subterranean spider species recorded in numerous subterranean localities across Europe and another with high resolution data about the subterranean habitat in which they were collected. From these two datasets, we further generated a third dataset with individual geo-referenced occurrence records for all these species. NEW INFORMATION Data from 475 geo-referenced subterranean localities (caves, mines and other artificial subterranean sites, interstitial habitats) are herein made available. For each subterranean locality, information about the composition of the spider community is provided, along with local geomorphological and habitat features. Altogether, these communities account for > 300 unique taxonomic entities and 2,091 unique geo-referenced occurrence records, that are made available via the Global Biodiversity Information Facility (GBIF) (Mammola and Cardoso 2019). This dataset is unique in that it covers both a large geographic extent (from 35° south to 67° north) and contains high-resolution local data on geomorphological and habitat features. Given that this kind of high-resolution data are rarely associated with broad-scale datasets used in macroecology, this dataset has high potential for helping researchers in tackling a range of biogeographical and macroecological questions, not necessarily uniquely related to arachnology or subterranean biology.
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Affiliation(s)
- Stefano Mammola
- Department of Life Sciences and Systems Biology, University of Turin, Turin, ItalyDepartment of Life Sciences and Systems Biology, University of TurinTurinItaly
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, University of Helsinki, Helsinki, FinlandLaboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, University of HelsinkiHelsinkiFinland
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, University of Helsinki, Helsinki, FinlandLaboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History, University of HelsinkiHelsinkiFinland
| | - Dorottya Angyal
- Department of Zoology, Hungarian Natural History Museum, Budapest, HungaryDepartment of Zoology, Hungarian Natural History MuseumBudapestHungary
- UMDI, Faculty of Sciences, UNAM National Autonomous University of Mexico, Sisal, MexicoUMDI, Faculty of Sciences, UNAM National Autonomous University of MexicoSisalMexico
| | - Gergely Balázs
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, HungaryDepartment of Systematic Zoology and Ecology, Eötvös Loránd UniversityBudapestHungary
| | - Theo Blick
- Independent Researcher, Hummeltal, GermanyIndependent ResearcherHummeltalGermany
| | - Hervé Brustel
- Ecole d'Ingénieur de Purpan, Toulouse, FranceEcole d'Ingénieur de PurpanToulouseFrance
| | - Julian Carter
- Amgueddfa Cymru National Museum Wales, Cardiff, United KingdomAmgueddfa Cymru National Museum WalesCardiffUnited Kingdom
| | - Srećko Ćurčić
- Faculty of Biology, Institute of Zoology, University of Belgrade, Belgrade, SerbiaFaculty of Biology, Institute of Zoology, University of BelgradeBelgradeSerbia
| | - Samuel Danflous
- Conservatoire d'Espaces Naturels de Midi-Pyrénées, Toulouse, FranceConservatoire d'Espaces Naturels de Midi-PyrénéesToulouseFrance
| | - László Dányi
- Department of Zoology, Hungarian Natural History Museum, Budapest, HungaryDepartment of Zoology, Hungarian Natural History MuseumBudapestHungary
| | - Sylvain Déjean
- Conservatoire d'Espaces Naturels de Midi-Pyrénées, Tolouse, FranceConservatoire d'Espaces Naturels de Midi-PyrénéesTolouseFrance
| | - Christo Deltshev
- National Museum of Natural History, Bulgarian Academy of Sciences, Sofia, BulgariaNational Museum of Natural History, Bulgarian Academy of SciencesSofiaBulgaria
| | - Mert Elverici
- Department of Biology, Faculty of Science and Arts, Erzincan Binali Yıldırım University, Erzincan, TurkeyDepartment of Biology, Faculty of Science and Arts, Erzincan Binali Yıldırım UniversityErzincanTurkey
| | - Jon Fernández
- Independent researcher, Basque Country, SpainIndependent researcherBasque CountrySpain
| | - Fulvio Gasparo
- Commissione Grotte “E. Boegan”, Società Alpina delle Giulie, C.A.I., Trieste, ItalyCommissione Grotte “E. Boegan”, Società Alpina delle Giulie, C.A.I.TriesteItaly
| | - Marjan Komnenov
- Independent Researcher, Blwd Kuzman Josifovski Pitu, Skopje, MacedoniaIndependent Researcher, Blwd Kuzman Josifovski PituSkopjeMacedonia
| | - Christian Komposch
- OEKOTEAM - Institute for Animal Ecology and Landscape Planning, Graz, AustriaOEKOTEAM - Institute for Animal Ecology and Landscape PlanningGrazAustria
| | - L’ubomír Kováč
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Košice, SlovakiaInstitute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik UniversityKošiceSlovakia
| | - Kadir Boğaç Kunt
- Zoological Collection of Cyprus Wildlife Research Institute, Kyrenia, CyprusZoological Collection of Cyprus Wildlife Research InstituteKyreniaCyprus
- Department of Biology, Faculty of Science, Eskişehir Technical University, Eskişehir, TurkeyDepartment of Biology, Faculty of Science, Eskişehir Technical UniversityEskişehirTurkey
| | - Andrej Mock
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University, Košice, SlovakiaInstitute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik UniversityKošiceSlovakia
| | - Oana Moldovan
- Emil Racovitza Institute of Speleology, Cluj-Napoca, RomaniaEmil Racovitza Institute of SpeleologyCluj-NapocaRomania
| | - Maria Naumova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, BulgariaInstitute of Biodiversity and Ecosystem Research, Bulgarian Academy of SciencesSofiaBulgaria
| | - Martina Pavlek
- Ruđer Bošković Institute, Zagreb, CroatiaRuđer Bošković InstituteZagrebCroatia
- Croatian Biospeleological Society, Zagreb, CroatiaCroatian Biospeleological SocietyZagrebCroatia
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute, University of Barcelona, Barcelona, SpainDepartment of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute, University of BarcelonaBarcelonaSpain
| | - Carlos E. Prieto
- Department of Zoology & Animal Cell Biology, Faculty of Science and Technology, University of the Basque Country, Bilbao, SpainDepartment of Zoology & Animal Cell Biology, Faculty of Science and Technology, University of the Basque CountryBilbaoSpain
| | - Carles Ribera
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute, University of Barcelona, Barcelona, SpainDepartment of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute, University of BarcelonaBarcelonaSpain
| | - Robert Rozwałka
- Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, PolandFaculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński UniversityWarsawPoland
| | - Vlastimil Růžička
- Biology Centre, Institute of Entomology, České Budějovice, Czech RepublicBiology Centre, Institute of EntomologyČeské BudějoviceCzech Republic
| | - Robert S. Vargovitsh
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Kiev, UkraineSchmalhausen Institute of Zoology, National Academy of Sciences of UkraineKievUkraine
| | - Stefan Zaenker
- Verband der deutschen Höhlen- und Karstforscher e.V., Fulda, GermanyVerband der deutschen Höhlen- und Karstforscher e.V.FuldaGermany
| | - Marco Isaia
- Department of Life Sciences and Systems Biology, University of Turin, Turin, ItalyDepartment of Life Sciences and Systems Biology, University of TurinTurinItaly
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22
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Derkarabetian S, Castillo S, Koo PK, Ovchinnikov S, Hedin M. A demonstration of unsupervised machine learning in species delimitation. Mol Phylogenet Evol 2019; 139:106562. [PMID: 31323334 PMCID: PMC6880864 DOI: 10.1016/j.ympev.2019.106562] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 07/03/2019] [Accepted: 07/15/2019] [Indexed: 01/13/2023]
Abstract
One major challenge to delimiting species with genetic data is successfully differentiating population structure from species-level divergence, an issue exacerbated in taxa inhabiting naturally fragmented habitats. Many fields of science are now using machine learning, and in evolutionary biology supervised machine learning has recently been used to infer species boundaries. These supervised methods require training data with associated labels. Conversely, unsupervised machine learning (UML) uses inherent data structure and does not require user-specified training labels, potentially providing more objectivity in species delimitation. In the context of integrative taxonomy, we demonstrate the utility of three UML approaches (random forests, variational autoencoders, t-distributed stochastic neighbor embedding) for species delimitation in an arachnid taxon with high population genetic structure (Opiliones, Laniatores, Metanonychus). We find that UML approaches successfully cluster samples according to species-level divergences and not high levels of population structure, while model-based validation methods severely over-split putative species. UML offers intuitive data visualization in two-dimensional space, the ability to accommodate various data types, and has potential in many areas of systematic and evolutionary biology. We argue that machine learning methods are ideally suited for species delimitation and may perform well in many natural systems and across taxa with diverse biological characteristics.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, United States; Department of Biology, San Diego State University, San Diego, CA 92182, United States; Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, Riverside, CA 92521, United States.
| | - Stephanie Castillo
- Department of Biology, San Diego State University, San Diego, CA 92182, United States; Department of Entomology, University of California, Riverside, Riverside, CA 92521, United States
| | - Peter K Koo
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, United States
| | - Sergey Ovchinnikov
- Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA 92182, United States
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23
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Wagner F, Ott T, Zimmer C, Reichhart V, Vogt R, Oberprieler C. 'At the crossroads towards polyploidy': genomic divergence and extent of homoploid hybridization are drivers for the formation of the ox-eye daisy polyploid complex (Leucanthemum, Compositae-Anthemideae). THE NEW PHYTOLOGIST 2019; 223:2039-2053. [PMID: 30851196 DOI: 10.1111/nph.15784] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/06/2019] [Indexed: 05/23/2023]
Abstract
Polyploidy plays a paramount role in phytodiversity, but the causes of this evolutionary pathway require further study. Here, we use phylogenetic methods to examine possible polyploidy-promoting factors by comparing diploid representatives of the comprehensive European polyploid complex Leucanthemum with members of its strictly diploid North African counterpart Rhodanthemum. We investigate genetic divergence and gene flow among all diploid lineages of both genera to evaluate the role of genomic differentiation and hybridization for polyploid speciation. To test whether hybridization in Leucanthemum has been triggered by the geological conditions during its diversification, we additionally generate a time-calibrated phylogeny of 46 species of the subtribe Leucantheminae. Leucanthemum shows a significantly higher genetic divergence and hybridization signal among diploid lineages compared with Rhodanthemum, in spite of a similar crown age and diversification pattern during the Quaternary. Our study demonstrates the importance of genetic differentiation among diploid progenitors and their concurrent affinity for natural hybridization for the formation of a polyploid complex. Furthermore, the role of climate-induced range overlaps on hybridization and polyploid speciation during the Quaternary is discussed.
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Affiliation(s)
- Florian Wagner
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Tankred Ott
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Claudia Zimmer
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Verena Reichhart
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Robert Vogt
- Botanic Garden & Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str. 6-8, D-14191, Berlin, Germany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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24
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Mammola S, Piano E, Malard F, Vernon P, Isaia M. Extending Janzen’s hypothesis to temperate regions: A test using subterranean ecosystems. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13382] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefano Mammola
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
- LIBRe – Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History University of Helsinki Helsinki Finland
| | - Elena Piano
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
| | - Florian Malard
- Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE Villeurbanne France
| | - Philippe Vernon
- Univ Rennes, Université Rennes 1, CNRS UMR 6553, ECOBIO Station Biologique de Paimpont Paimpont France
| | - Marco Isaia
- Department of Life Sciences and Systems Biology University of Turin Turin Italy
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25
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Sumner-Rooney L. The Kingdom of the Blind: Disentangling Fundamental Drivers in the Evolution of Eye Loss. Integr Comp Biol 2019; 58:372-385. [PMID: 29873729 DOI: 10.1093/icb/icy047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Light is a fundamentally important biological cue used by almost every animal on earth, to maintain daily rhythms, navigate, forage, find mates, or avoid predators. But an enormous number of species live in darkness: in subterranean caves, deep oceans, underground burrows, and within parasitic host bodies, and the loss of eyes appears consistently across these ecosystems. However, the evolutionary mechanisms that lead to the reduction of the visual system remain the subject of great interest and debate more than 150 years after Darwin tackled the issue. Studies of model taxa have discovered significant roles for natural selection, neutral evolution, and pleiotropy, but the interplay between them remains unclear. To nail down unifying concepts surrounding the evolution of eye loss, we must embrace the enormous range of affected animals and habitats. The fine developmental details of model systems such as the Mexican cave tetra Astyanax mexicanus have transformed and enriched the field, but these should be complemented by wider studies to identify truly overarching patterns that apply throughout animals. Here, the major evolutionary drivers are placed within a conceptual cost-benefit framework that incorporates the fundamental constraints and forces that influence evolution in the dark. Major physiological, ecological, and environmental factors are considered within the context of this framework, which appears faithful to observed patterns in deep-sea and cavernicolous animals. To test evolutionary hypotheses, a comparative phylogenetic approach is recommended, with the goal of studying large groups exhibiting repeated reduction, and then comparing these across habitats, taxa, and lifestyles. Currently, developmental and physiological methods cannot feasibly be used on such large scales, but penetrative imaging techniques could provide detailed morphological data non-invasively and economically for large numbers of species. Comprehensive structural datasets can then be contextualized phylogenetically to examine recurrent trends and associations, and to reconstruct character histories through multiple independent transitions into darkness. By assessing these evolutionary trajectories within an energetic cost-benefit framework, the relationships between fundamental influences can be inferred and compared across different biological and physical parameters. However, substantial numbers of biological and environmental factors affect the evolutionary trajectory of loss, and it is critical that researchers make fair and reasonable comparisons between objectively similar groups.
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26
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Different species or genetically divergent populations? Integrative species delimitation of the Primulina hochiensis complex from isolated karst habitats. Mol Phylogenet Evol 2019; 132:219-231. [DOI: 10.1016/j.ympev.2018.12.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 12/09/2018] [Accepted: 12/09/2018] [Indexed: 12/15/2022]
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27
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Devitt TJ, Wright AM, Cannatella DC, Hillis DM. Species delimitation in endangered groundwater salamanders: Implications for aquifer management and biodiversity conservation. Proc Natl Acad Sci U S A 2019; 116:2624-2633. [PMID: 30642970 PMCID: PMC6377464 DOI: 10.1073/pnas.1815014116] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Groundwater-dependent species are among the least-known components of global biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion at regional and global scales. The karstic Edwards-Trinity aquifer system of west-central Texas is one of the most species-rich groundwater systems in the world, represented by dozens of endemic groundwater-obligate species with narrow, naturally fragmented distributions. Here, we examine how geomorphological and hydrogeological processes have driven population divergence and speciation in a radiation of salamanders (Eurycea) endemic to the Edwards-Trinity system using phylogenetic and population genetic analysis of genome-wide DNA sequence data. Results revealed complex patterns of isolation and reconnection driven by surface and subsurface hydrology, resulting in both adaptive and nonadaptive population divergence and speciation. Our results uncover cryptic species diversity and refine the borders of several threatened and endangered species. The US Endangered Species Act has been used to bring state regulation to unrestricted groundwater withdrawals in the Edwards (Balcones Fault Zone) Aquifer, where listed species are found. However, the Trinity and Edwards-Trinity (Plateau) aquifers harbor additional species with similarly small ranges that currently receive no protection from regulatory programs designed to prevent groundwater depletion. Based on regional climate models that predict increased air temperature, together with hydrologic models that project decreased springflow, we conclude that Edwards-Trinity salamanders and other codistributed groundwater-dependent organisms are highly vulnerable to extinction within the next century.
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Affiliation(s)
- Thomas J Devitt
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712;
- Biodiversity Center, The University of Texas at Austin, Austin, TX 78712
| | - April M Wright
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
- Biodiversity Center, The University of Texas at Austin, Austin, TX 78712
| | - David C Cannatella
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
- Biodiversity Center, The University of Texas at Austin, Austin, TX 78712
| | - David M Hillis
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712;
- Biodiversity Center, The University of Texas at Austin, Austin, TX 78712
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28
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Leray VL, Caravas J, Friedrich M, Zigler KS. Mitochondrial sequence data indicate “Vicariance by Erosion” as a mechanism of species diversification in North American Ptomaphagus (Coleoptera, Leiodidae, Cholevinae) cave beetles. SUBTERRANEAN BIOLOGY 2019. [DOI: 10.3897/subtbiol.29.31377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Small carrion beetles (Coleoptera: Leiodidae: Cholevinae) are members of cave communities around the world and important models for understanding the colonization of caves, adaptation to cave life, and the diversification of cave-adapted lineages. We developed a molecular phylogeny to examine the diversification of the hirtus-group of the small carrion beetle genus Ptomaphagus. The hirtus-group has no surface-dwelling members; it consists of 19 short-range endemic cave- and soil-dwelling species in the central and southeastern United States of America. Taxonomic, phylogenetic and biogeographic data were previously interpreted to suggest the hirtus-group diversified within the past 350,000 years through a series of cave colonization and speciation events related to Pleistocene climate fluctuations. However, our time-calibrated molecular phylogeny resulting from the analysis of 2,300 nucleotides from five genes across three mitochondrial regions (cox1, cytb, rrnL-trnL-nad1) for all members of the clade paints a different picture. We identify three stages of diversification in the hirtus-group: (1) ~10 million years ago (mya), the lineage that develops into P.shapardi, a soil-dwelling species from the Ozarks, diverged from the lineage that gives rise to the 18 cave-obligate members of the group; (2) between 8.5 mya and 6 mya, seven geographically distinct lineages diverged across Kentucky, Tennessee, Alabama and Georgia; six of these lineages represent a single species today, whereas (3) the ‘South Cumberlands’ lineage in Tennessee and Alabama diversified into 12 species over the past ~6 my. While the events triggering diversification during the first two stages remain to be determined, the distributions, phylogenetic relationships and divergence times in the South Cumberlands lineage are consistent with populations being isolated by vicariant events as the southern Cumberland Plateau eroded and fragmented over millions of years.
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29
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Johnson NA, Smith CH, Pfeiffer JM, Randklev CR, Williams JD, Austin JD. Integrative taxonomy resolves taxonomic uncertainty for freshwater mussels being considered for protection under the U.S. Endangered Species Act. Sci Rep 2018; 8:15892. [PMID: 30367102 PMCID: PMC6203750 DOI: 10.1038/s41598-018-33806-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/07/2018] [Indexed: 11/30/2022] Open
Abstract
Objectively delimiting species boundaries remains an important challenge in systematics and becomes urgent when unresolved taxonomy complicates conservation and recovery efforts. We examined species boundaries in the imperiled freshwater mussel genus Cyclonaias (Bivalvia: Unionidae) using morphometrics, molecular phylogenetics, and multispecies coalescent models to help guide pending conservation assessments and legislative decisions. Congruence across multiple lines of evidence indicated that current taxonomy overestimates diversity in the C. pustulosa species complex. The only genetically and morphologically diagnosable species in the C. pustulosa species complex were C. pustulosa and C. succissa and we consider C. aurea, C. houstonensis, C. mortoni, and C. refulgens to be synonyms of C. pustulosa. In contrast, all three species in the C. nodulata complex (C. necki, C. nodulata, and C. petrina) were genetically, geographically, and morphologically diagnosable. Our findings have important conservation and management implications, as three nominal species (C. aurea, C. houstonensis, and C. petrina) are being considered for protection under the Endangered Species Act.
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Affiliation(s)
- Nathan A Johnson
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA.
| | - Chase H Smith
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA.,Baylor University, Biology Department, Waco, TX, 76798, USA
| | - John M Pfeiffer
- University of Florida, Florida Museum, Gainesville, FL, 32611, USA
| | - Charles R Randklev
- Texas A&M Natural Resources Institute and AgriLife Research Center, Dallas, TX, 75252, USA
| | - James D Williams
- University of Florida, Florida Museum, Gainesville, FL, 32611, USA
| | - James D Austin
- Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32601, USA
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30
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Speciation patterns in complex subterranean environments: a case study using short-tailed whipscorpions (Schizomida: Hubbardiidae). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Hedin M, Derkarabetian S, Blair J, Paquin P. Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae). Zookeys 2018; 769:49-76. [PMID: 29988790 PMCID: PMC6030207 DOI: 10.3897/zookeys.769.25814] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/27/2018] [Indexed: 01/21/2023] Open
Abstract
Morphological, mitochondrial, and nuclear phylogenomic data were combined to address phylogenetic and species delimitation questions in cave-limited Cicurina spiders from central Texas. Special effort was focused on specimens and cave locations in the San Antonio region (Bexar County), home to four eyeless species listed as US Federally Endangered. Sequence capture experiments resulted in the recovery of ~200-400 homologous ultra-conserved element (UCE) nuclear loci across taxa, and nearly complete COI mitochondrial DNA sequences from the same set of individuals. Some of these nuclear and mitochondrial sequences were recovered from "standard" museum specimens without special preservation of DNA material, including museum specimens preserved in the 1990s. Multiple phylogenetic analyses of the UCE data agree in the recovery of two major lineages of eyeless Cicurina in Texas. These lineages also differ in mitochondrial clade membership, female genitalic morphology, degree of troglomorphy (as measured by relative leg length), and are mostly allopatric across much of Texas. Rare sympatry was confirmed in Bexar County, where members of the two major clades sometimes co-exist in the same karst feature. Both nuclear phylogenomic and mitochondrial data indicate the existence of undescribed species from the San Antonio region, although further sampling and collection of adult specimens is needed to explicitly test these hypotheses. Our data support the two following species synonymies (Cicurina venii Gertsch, 1992 = Cicurina madla Gertsch, 1992; Cicurina loftini Cokendolpher, 2004 = Cicurina vespera Gertsch, 1992), formally proposed here. Overall, our taxonomy-focused research has many important conservation implications, and again highlights the fundamental importance of robust taxonomy in conservation research.
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Affiliation(s)
- Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego CA, 92182, USA
| | - Shahan Derkarabetian
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego CA, 92182, USA
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge MA, 02138, USA
| | - Jennifer Blair
- Blair Wildlife Consulting, 3815 Dacy Lane, Kyle TX, 78640, USA
| | - Pierre Paquin
- Scienceinfuse Inc, 12 Saxby Sud, Shefford, QC, J2M 1S2, Canada
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32
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Liu Z, Chen G, Zhu T, Zeng Z, Lyu Z, Wang J, Messenger K, Greenberg AJ, Guo Z, Yang Z, Shi S, Wang Y. Prevalence of cryptic species in morphologically uniform taxa - Fast speciation and evolutionary radiation in Asian frogs. Mol Phylogenet Evol 2018; 127:723-731. [PMID: 29920336 DOI: 10.1016/j.ympev.2018.06.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 02/08/2023]
Abstract
Diversity and distributions of cryptic species have long been a vexing issue. Identification of species boundaries is made difficult by the lack of obvious morphological differences. Here, we investigate the cryptic diversity and evolutionary history of an underappreciated group of Asian frog species (Megophrys) to explore the pattern and dynamic of amphibian cryptic species. We sequenced four mitochondrial genes and five nuclear genes and delineated species using multiple approaches, combining DNA and mating-call data. A Bayesian species tree was generated to estimate divergence times and to reconstruct ancestral ranges. Macroevolutionary analyses and hybridization tests were conducted to explore the evolutionary dynamics of this cryptic group. Our phylogenies support the current subgenera. We revealed 43 cryptic species, 158% higher than previously thought. The species-delimitation results were further confirmed by mating-call data and morphological divergence. We found that these Asian frogs entered China from the Sunda Shelf 48 Mya, followed by an ancient radiation event during middle Miocene. We confirmed the efficiency of the multispecies coalescent model for delimitation of species with low morphological diversity. Species diversity of Megophrys is severely underappreciated, and species distributions have been misestimated as a result.
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Affiliation(s)
- Zuyao Liu
- The Museum of Biology, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China; State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong, China
| | - Guoling Chen
- The Museum of Biology, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Tianqi Zhu
- Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China; Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhaochi Zeng
- The Museum of Biology, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Zhitong Lyu
- The Museum of Biology, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Jian Wang
- The Museum of Biology, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China
| | - Kevin Messenger
- Department of Zoology, Nanjing Forestry University, 210037 Jiangsu, China
| | | | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong, China
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, Guangdong, China.
| | - Yingyong Wang
- The Museum of Biology, School of Life Sciences, Sun Yat-sen University, 510275 Guangzhou, China.
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33
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Singhal S, Hoskin CJ, Couper P, Potter S, Moritz C. A Framework for Resolving Cryptic Species: A Case Study from the Lizards of the Australian Wet Tropics. Syst Biol 2018; 67:1061-1075. [DOI: 10.1093/sysbio/syy026] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/27/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sonal Singhal
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biology, California State University—Dominguez Hills, Carson, CA 90747, USA
| | - Conrad J Hoskin
- College of Science & Engineering, James Cook University, Townsville, Queensland 4811, Australia
| | - Patrick Couper
- Biodiversity Program, Queensland Museum, South Brisbane, Queensland 4101, Australia
| | - Sally Potter
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology and Centre for Biodiversity Analysis, Australian National University, Acton, ACT 2601, Australia
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34
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35
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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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36
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Dupuis JR, Mcdonald CM, Acorn JH, Sperling FAH. Genomics-informed species delimitation to support morphological identification of anglewing butterflies (Lepidoptera: Nymphalidae: Polygonia). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Julian R Dupuis
- Department of Plant and Environmental Protection Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - Christianne M Mcdonald
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
| | - John H Acorn
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, CW 405 Biosciences Centre, University of Alberta, Edmonton, AB, Canada
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37
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Smith CH, Johnson NA, Pfeiffer JM, Gangloff MM. Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus). Mol Phylogenet Evol 2017; 119:50-62. [PMID: 29074460 DOI: 10.1016/j.ympev.2017.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 10/20/2017] [Accepted: 10/22/2017] [Indexed: 11/19/2022]
Abstract
Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent 'Strophitus' connasaugaensis and 'Strophitus' subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize the potential for a third putative species (Strophitus sp. cf. pascagoulaensis). Our findings aid stakeholders in establishing conservation and management strategies for the members of Anodontoides, Strophitus, and Pseudodontoideus.
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Affiliation(s)
- Chase H Smith
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL 32653, USA
| | - Nathan A Johnson
- US Geological Survey, Wetland and Aquatic Research Center, 7920 NW 71st Street, Gainesville, FL 32653, USA.
| | - John M Pfeiffer
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Michael M Gangloff
- Biology Department, Appalachian State University, Boone, NC 28608-2027, USA
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38
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Xu X, Liu F, Ono H, Chen J, Kuntner M, Li D. Targeted sampling in Ryukyus facilitates species delimitation of the primitively segmented spider genus Ryuthela (Araneae: Mesothelae: Liphistiidae). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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39
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Wagner F, Härtl S, Vogt R, Oberprieler C. "Fix Me Another Marguerite!": Species delimitation in a group of intensively hybridizing lineages of ox-eye daisies (Leucanthemum Mill., Compositae-Anthemideae). Mol Ecol 2017; 26:4260-4283. [PMID: 28502098 DOI: 10.1111/mec.14180] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/28/2017] [Accepted: 05/05/2017] [Indexed: 01/26/2023]
Abstract
Delineating species boundaries in the framework of the multi-species coalescent (MSC) proves to be a reliable, objective, and reproducible method in an increasing number of studies. However, the underlying model assumes the lack of gene flow after speciation; an assumption which may be frequently violated in plant evolution. This study evaluates the robustness of currently available species delimitation methods implemented in beast (BFD, BFD*, and dissect) in the closely-knit ox-eye daisy group around Leucanthemum ageratifolium Pau. Comprising five taxa being allopatrically distributed between northern Spain and southern Italy this study group shows signs of hybridization with the widespread and codistributed species Leucanthemum vulgare (Vaill.) Lam. to various extent. As expected, our empirical analyses based on both AFLP fingerprinting and sequence data demonstrate that the robustness of species delimitation results is considerably influenced by the intensity of hybridization among species and the number of hybrid individuals included. Therefore, we set up a methodological pipeline with a first step of identification and subsequent removal of individuals showing admixed genetic patterns caused by actual interbreeding using AFLP-fingerprint and morphometric data, followed by application of different Bayesian MSC species delimitation methods based on the remnant individuals using both AFLP-fingerprint and sequence data (four nuclear markers, five concatenated intergenic spacer regions of the plastid genome). The results argue for acknowledgement of Leucanthemum laciniatum, L. legraeanum, and L. ligusticum as independent species, show the close relationship of L. ageratifolium, L. monspeliense, and L. vulgare, and give rise to the description of three nothospecies new to science.
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Affiliation(s)
- Florian Wagner
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
| | - Sabine Härtl
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
| | - Robert Vogt
- Botanic Garden & Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
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40
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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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41
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Carlson DE, Hedin M. Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes. PLoS One 2017; 12:e0174102. [PMID: 28379977 PMCID: PMC5381867 DOI: 10.1371/journal.pone.0174102] [Citation(s) in RCA: 7] [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: 10/15/2016] [Accepted: 03/04/2017] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.
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Affiliation(s)
- David E. Carlson
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California, United States of America
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42
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Li YM, Shivas RG, Cai L. Cryptic diversity in Tranzscheliella spp. (Ustilaginales) is driven by host switches. Sci Rep 2017; 7:43549. [PMID: 28256543 PMCID: PMC5335255 DOI: 10.1038/srep43549] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/25/2017] [Indexed: 01/19/2023] Open
Abstract
Species of Tranzscheliella have been reported as pathogens of more than 30 genera of grasses (Poaceae). In this study, a combined morphological and molecular phylogenetic approach was used to examine 33 specimens provisionally identified as belonging to the T. hypodytes species complex. The phylogenetic analysis resolved several well-supported clades that corresponded to known and novel species of Tranzscheliella. Four new species are described and illustrated. In addition, a new combination in Tranzscheliella is proposed for Sorosporium reverdattoanum. Cophylogenetic analyses assessed by distance-based and event-cost based methods, indicated host switches are likely the prominent force driving speciation in Tranzscheliella.
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Affiliation(s)
- Ying-Ming Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Roger G Shivas
- Plant Pathology Herbarium, Department of Agriculture and Forestry, Dutton Park, Queensland, 4102, Australia
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
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43
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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.
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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
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44
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Postaire B, Magalon H, Bourmaud CAF, Bruggemann JH. Molecular species delimitation methods and population genetics data reveal extensive lineage diversity and cryptic species in Aglaopheniidae (Hydrozoa). Mol Phylogenet Evol 2016; 105:36-49. [DOI: 10.1016/j.ympev.2016.08.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/16/2016] [Accepted: 08/21/2016] [Indexed: 01/04/2023]
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45
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Castelin M, Van Steenkiste N, Pante E, Harbo R, Lowe G, Gilmore SR, Therriault TW, Abbott CL. A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada. Mol Ecol Resour 2016; 16:1322-1339. [DOI: 10.1111/1755-0998.12534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/18/2016] [Accepted: 03/18/2016] [Indexed: 11/27/2022]
Affiliation(s)
- M. Castelin
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - N. Van Steenkiste
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - E. Pante
- LIENSs Laboratory; UMR 7266 CNRS-Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - R. Harbo
- Invertebrate Zoology; Royal BC Museum; 675 Belleville Street Victoria BC Canada V8W 9W2
| | - G. Lowe
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - S. R. Gilmore
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - T. W. Therriault
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
| | - C. L. Abbott
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC Canada V9T 6N7
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46
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Abstract
This catalogue lists 1,084 species of spiders (three identified to genus only) in 311 genera from 53 families currently recorded from Texas and is based on the "Bibliography of Texas Spiders" published by Bea Vogel in 1970. The online list of species can be found at http://pecanspiders.tamu.edu/spidersoftexas.htm. Many taxonomic revisions have since been published, particularly in the families Araneidae, Gnaphosidae and Leptonetidae. Many genera in other families have been revised. The Anyphaenidae, Ctenidae, Hahniidae, Nesticidae, Sicariidae and Tetragnathidae were also revised. Several families have been added and others split up. Several genera of Corinnidae were transferred to Phrurolithidae and Trachelidae. Two genera from Miturgidae were transferred to Eutichuridae. Zoridae was synonymized under Miturgidae. A single species formerly in Amaurobiidae is now in the Family Amphinectidae. Some trapdoor spiders in the family Ctenizidae have been transferred to Euctenizidae. Gertsch and Mulaik started a list of Texas spiders in 1940. In a letter from Willis J. Gertsch dated October 20, 1982, he stated "Years ago a first listing of the Texas fauna was published by me based largely on Stanley Mulaik material, but it had to be abandoned because of other tasks." This paper is a compendium of the spiders of Texas with distribution, habitat, collecting method and other data available from revisions and collections. This includes many records and unpublished data (including data from three unpublished studies). One of these studies included 16,000 adult spiders belonging to 177 species in 29 families. All specimens in that study were measured and results are in the appendix. Hidalgo County has 340 species recorded with Brazos County at 323 and Travis County at 314 species. These reflect the amount of collecting in the area.
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Affiliation(s)
- David Allen Dean
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
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47
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Dejaco T, Gassner M, Arthofer W, Schlick-Steiner BC, Steiner FM. Taxonomist's Nightmare … Evolutionist's Delight : An Integrative Approach Resolves Species Limits in Jumping Bristletails Despite Widespread Hybridization and Parthenogenesis. Syst Biol 2016; 65:947-974. [PMID: 26869489 PMCID: PMC5066060 DOI: 10.1093/sysbio/syw003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/26/2015] [Accepted: 01/14/2016] [Indexed: 11/13/2022] Open
Abstract
Accurate species delimitation is fundamental to biology. Traditionally, species were delimited based on morphological characters, sometimes leading to taxonomic uncertainty in morphologically conserved taxa. Recently, multiple taxonomically challenging cases have benefited from integrative taxonomy-an approach that highlights congruence among different disciplines and invokes evolutionary explanations for incongruence, acknowledging that different methods can mirror different stages of the speciation continuum. Here, we used a cohesive protocol for integrative taxonomy to revise species limits in 20 nominal species and 4 morphospecies of an ancestrally wingless insect group, the jumping bristletail genus Machilis from the European Eastern Alps. Even though morphologically conserved, several small-scale endemic species have been described from the Eastern Alps based on variation in hypodermal pigmentation patterns-a highly questionable character. As valuable as these endemics are for conservation, they have never been verified by alternative methods. Using traditional morphometrics, mitochondrial DNA, ribosomal DNA, and amplified fragment-length polymorphism markers, we identify six nominal species as taxonomic junior synonyms (Machilis alpicola Janetschek, 1953 syn. n. under M. vagans Wygodzinsky, 1941; M. ladensis Janetschek, 1950 syn. n., M. robusta Wygodzinsky, 1941 syn. n., and M. vicina Wygodzinsky, 1941 syn. n. under M. inermis Wygodzinsky, 1941; M. aleamaculata Wygodzinsky, 1941 syn. n. under M. montana Wygodzinsky, 1941; M. pulchra Janetschek, 1950 syn. n. under M. helleri Verhoeff, 1910) and describe two new species (Machilis cryptoglacialis sp. n. and Machilis albida sp. n.), one uncovered from morphological crypsis and one never sampled before. Building on numerous cases of incongruence among data sources, we further shed light on complex evolutionary histories including hybrid speciation, historical and recent hybridization, and ongoing speciation. We hypothesize that an inherent affinity to hybridization, combined with parallel switches to parthenogenesis and repeated postglacial colonization events may have boosted endemicity in Eastern Alpine Machilis We thus emphasize the importance of integrative taxonomy for rigorous species delimitation and its implication for evolutionary research and conservation in taxonomically challenging taxa.
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Affiliation(s)
- Thomas Dejaco
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria .,Museum of Nature South Tyrol, Bindergasse 1, 39100 Bozen/Bolzano, Italy
| | - Melitta Gassner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Wolfgang Arthofer
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Birgit C Schlick-Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Florian M Steiner
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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48
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Burgess MB, Cushman KR, Doucette ET, Frye CT, Campbell CS. Understanding diploid diversity: A first step in unraveling polyploid, apomictic complexity in Amelanchier. AMERICAN JOURNAL OF BOTANY 2015; 102:2041-2057. [PMID: 26643889 DOI: 10.3732/ajb.1500330] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Delimitation of Amelanchier species is difficult because of polyploidy and gametophytic apomixis. A first step in unraveling this species problem is understanding the diversity of the diploids that contributed genomes to polyploid apomicts. This research helps clarify challenging species-delimitation problems attending polyploid, apomictic complexity. METHODS We sampled 431 diploid accessions from 13 species, of which 10 are North American and three are Old World. Quantitative morphological analyses tested the null hypothesis of no discrete groups. Using three to nine diploid accessions per species, we constructed phylogenies with DNA sequences from ETS, ITS, the second intron of LEAFY, and chloroplast regions rpoB-trnC, rpl16, trnD-trnT, and ycf6-psbM. KEY RESULTS Most Amelanchier diploid taxa are morphologically and ecogeographically distinct and genetically exclusive lineages. They rarely hybridize with one another. Nuclear and chloroplast DNA sequences almost completely resolve the Amelanchier phylogeny. The backbone is the mostly western North American clade A, eastern North American clade B, and Old World clade O. DNA sequences and morphology support clades A and O as sister taxa. Despite extensive paralogy, our LEAFY data are phylogenetically informative and identify a clade (T) of three arborescent taxa within clade B. CONCLUSIONS Amelanchier diploids differ strikingly from polyploid apomicts, in that hybridization among them is rare, and they form taxa that would qualify as species by most species concepts. Knowledge of diploid morphology, phylogeny, and ecogeography provides a foundation for understanding the evolutionary history of polyploid apomicts, their patterns of diversification, and their species status.
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Affiliation(s)
- Michael B Burgess
- Department of Biological Sciences, State University of New York Plattsburgh, Plattsburgh, New York 12901, USA
| | - Kevin R Cushman
- School of Biology and Ecology, University of Maine, Orono, Maine 04469, USA
| | - Eric T Doucette
- School of Biology and Ecology, University of Maine, Orono, Maine 04469, USA
| | - Christopher T Frye
- Maryland Department of Natural Resources, Natural Heritage Program, 909 Wye Mills Road, Wye Mills, Maryland 21679, USA
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49
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Esposito LA, Bloom T, Caicedo-Quiroga L, Alicea-Serrano AM, Sánchez-Ruíz JA, May-Collado LJ, Binford GJ, Agnarsson I. Islands within islands: Diversification of tailless whip spiders (Amblypygi, Phrynus) in Caribbean caves. Mol Phylogenet Evol 2015. [DOI: 10.1016/j.ympev.2015.07.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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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]
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