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Xiao R, Zhao J, Zhao L, Derkarabetian S, Zhang F, Zhang C. Phylogeographic and genetic insights into Sinonychia martensi: an endemic cave-dwelling harvestman in Beijing. BMC Ecol Evol 2025; 25:5. [PMID: 39773162 PMCID: PMC11708087 DOI: 10.1186/s12862-024-02341-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Accepted: 12/18/2024] [Indexed: 01/11/2025] Open
Abstract
Caves are one of the most exciting environments on earth, often considered an evolutionary laboratory due to the suite of convergent adaptive traits (troglomorphisms) of organisms inhabiting them. Sinonychia martensi Zhang & Derkarabetian, 2021, is the first and only Travunioidea species recorded in China and is endemic to Beijing, being known from multiple caves. However, nothing is known regarding its phylogeographic or evolutionary history. In this study, we assessed the species boundaries of S. martensi from nine caves using morphological and molecular methods to elucidate its phylogenetic position and genealogical relationships. We also investigated the genetic diversity, population genetic structure and demographic history of S. martensi to clarify the population-level relationships and make inferences about historical phylogeography. The results indicate that the species from different caves all belonged to S. martensi but represent different populations. These populations exhibit strong population structure and low genetic diversity. Cave populations may share a common ancestor and multiple independent invasions to different caves. The diversification within S. martensi was likely driven by climate change and subtropical evergreen broadleaf forests associated with the middle Miocene. This study highlights the need for further conservation efforts and exploration in Beijing caves.
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Affiliation(s)
- Ruoyi Xiao
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, Hebei, 071002, China
| | - Jingjing Zhao
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, Hebei, 071002, China
| | - Likun Zhao
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, Hebei, 071002, China
| | - Shahan Derkarabetian
- Department of Entomology, San Diego Natural History Museum, San Diego, CA, 92101, USA
| | - Feng Zhang
- Hebei Basic Science Center for Biotic Interaction, Hebei University, Baoding, Hebei, 071002, China.
- Key Laboratory of Zoological Systematics and Application, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
| | - Chao Zhang
- Key Laboratory of Zoological Systematics and Application, Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding, Hebei, 071002, China.
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2
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Shanaida M, Lysiuk R, Mykhailenko O, Hudz N, Abdulsalam A, Gontova T, Oleshchuk O, Ivankiv Y, Shanaida V, Lytkin D, Bjørklund G. Alpha-lipoic Acid: An Antioxidant with Anti-aging Properties for Disease Therapy. Curr Med Chem 2025; 32:23-54. [PMID: 38644711 DOI: 10.2174/0109298673300496240416114827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/23/2024]
Abstract
The anti-aging effects of alpha-lipoic acid (αLA), a natural antioxidant synthesized in human tissues, have attracted a growing interest in recent years. αLA is a short- -chain sulfur-containing fatty acid occurring in the mitochondria of all kinds of eukaryotic cells. Both the oxidized disulfide of αLA and its reduced form (dihydrolipoic acid, DHLA) exhibit prominent antioxidant function. The amount of αLA inside the human body gradually decreases with age resulting in various health disorders. Its lack can be compensated by supplying from external sources such as dietary supplements or medicinal dosage forms. The primary objectives of this study were the analysis of updated information on the latest two-decade research regarding the use of αLA from an anti-aging perspective. The information was collected from PubMed, Wiley Online Library, Scopus, ScienceDirect, SpringerLink, Google Scholar, and clinicaltrials.gov. Numerous in silico, in vitro, in vivo, and clinical studies revealed that αLA shows a protective role in biological systems by direct or indirect reactive oxygen/nitrogen species quenching. αLA demonstrated beneficial properties in the prevention and treatment of many age-related disorders such as neurodegeneration, metabolic disorders, different cancers, nephropathy, infertility, and skin senescence. Its preventive effects in case of Alzheimer's and Parkinson's diseases are of particular interest. Further mechanistic and clinical studies are highly recommended to evaluate the wide spectrum of αLA therapeutic potential that could optimize its dietary intake for prevention and alleviation disorders related to aging.
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Affiliation(s)
- Mariia Shanaida
- I. Horbachevsky Ternopil National Medical University, 46001, Ternopil, Ukraine
- CONEM Ukraine Natural Drugs Research Group, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
| | - Roman Lysiuk
- Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
| | - Olha Mykhailenko
- Department of Research National University of Pharmacy, Kharkiv, 61168, Ukraine
- Pharmacognosy and Phytotherapy Group, UCL School of Pharmacy; 29-39 Brunswick Square, WC1N 1AX, London, United Kingdom
- CONEM Ukraine Bromatology and Medicinal Chemistry Group, National University of Pharmacy, Kharkiv, Ukraine
| | - Nataliia Hudz
- Danylo Halytsky Lviv National Medical University, Lviv, 79010, Ukraine
- Department of Pharmacy and Ecological Chemistry, University of Opole, 45-052, Opole, Poland
| | | | - Tetiana Gontova
- Department of Research National University of Pharmacy, Kharkiv, 61168, Ukraine
| | | | - Yana Ivankiv
- I. Horbachevsky Ternopil National Medical University, 46001, Ternopil, Ukraine
| | - Volodymyr Shanaida
- CONEM Ukraine Natural Drugs Research Group, I. Horbachevsky Ternopil National Medical University, Ternopil, Ukraine
- Department of Research Ternopil Ivan Puluj National Technical University, Ternopil, 46001, Ukraine
| | - Dmytro Lytkin
- Department of Research National University of Pharmacy, Kharkiv, 61168, Ukraine
| | - Geir Bjørklund
- Department of Research Council for Nutritional and Environmental Medicine, 8610 Mo i Rana, Norway
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3
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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 2025; 20:33-49. [PMID: 38263700 DOI: 10.1111/1749-4877.12809] [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] [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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4
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Palandačić A, Reier S, Diripasko OA, Jelić D, Stroj A, Wanka A, Marić D, Bogutskaya NG. Substygophily in Dinaric Karst: A Model Case of Locally Endemic Minnows Phoxinellus (Leuciscinae). Ecol Evol 2024; 14:e70648. [PMID: 39717638 PMCID: PMC11664320 DOI: 10.1002/ece3.70648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 10/09/2024] [Accepted: 11/14/2024] [Indexed: 12/25/2024] Open
Abstract
The Dinaric Karst extends along the Adriatic coast of the Western Balkan Peninsula and is home to a group of "karst minnows" of the genera Delminichthys, Phoxinellus, and Telestes, which have adapted to the highly variable water conditions in the karst by spending up to several months underground, but require surface habitats for spawning, defining them as substygophiles. The three species of the genus Phoxinellus, P. alepidotus, P. pseudalepidotus, and P. dalmaticus, are defined by restricted ranges, making them vulnerable to pollution and extended draughts caused by the climate change. In this study, the phylogeny of Leusciscinae was reconstructed using 15 Phoxinellus and one Delminichthys adspersus, one Pelasgus epiroticus, and one Telestes polylepis complete mitochondrial genomes and the position of the genus Phoxinellus within the subfamily as sister species to the Chondrostoma clade was confirmed. The inter- and intrapopulation structure of the genus Phoxinellus was inferred using molecular (nuclear and mitochondrial data) and morphological analyses. For the molecular analysis, more than 150 historical specimens were analyzed for a short fragment of the cytochrome oxidase I (COI) barcoding region and 15 Phoxinellus specimens were subjected to single nucleotide polymorphism analysis. For morphological analysis, 121 Phoxinellus specimens were analyzed for 51 measurements and 8 counts. All analyses confirmed the clear delimitation of the three Phoxinellus species, but were insufficient to fully resolve the intrapopulation structure within the species. This study also included data from field surveys of Phoxinellus collected over the past 20 years, which showed that abundance is declining and ranges are shrinking. Phoxinellus are also threatened by invasive/introduced species. Based on cave observations/occurrence and morphological analysis, P. dalmaticus was classified as an advanced substygophile and P. alepidotus and P. pseudalepidotus were classified as basic stygophiles.
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Affiliation(s)
- Anja Palandačić
- First Zoological DepartmentVienna Museum of Natural HistoryViennaAustria
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Susanne Reier
- First Zoological DepartmentVienna Museum of Natural HistoryViennaAustria
| | | | - Dušan Jelić
- Croatian Institute for BiodiversityZagrebCroatia
| | | | - Alexandra Wanka
- First Zoological DepartmentVienna Museum of Natural HistoryViennaAustria
| | - Dario Marić
- Dobrič b.b.Široki BrijegBosnia and Herzegovina
| | - Nina G. Bogutskaya
- First Zoological DepartmentVienna Museum of Natural HistoryViennaAustria
- BIOTA j d.o.o.Dolga GoraSlovenia
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5
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Harvey MS, Steinmann DB. A new troglomorphic species of Larca (Pseudoscorpiones, Larcidae) from Colorado. Zookeys 2024; 1198:279-294. [PMID: 38708379 PMCID: PMC11066502 DOI: 10.3897/zookeys.1198.120353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/26/2024] [Indexed: 05/07/2024] Open
Abstract
A new species of Larca is described from dry habitats in a cave in central Colorado. Like other cave-dwelling species of Larca, the new species Larcabouldericasp. nov., shows relatively modest morphological adaptations, such as pale colouration and slightly elongated appendages, compared with their epigean counterparts. This species is the sixth cave-dwelling species of Larca described from North America and, like other cave-dwelling Larca in North America and Europe, tends to be distributed in more southerly regions.
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Affiliation(s)
- Mark S. Harvey
- Collections & Research, Western Australian Museum, 49 Kew Street, Welshpool, Western Australia 6106, AustraliaWestern Australian MuseumWelshpoolAustralia
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia 6009, AustraliaUniversity of Western AustraliaCrawleyAustralia
| | - David B. Steinmann
- Department of Zoology, Denver Museum of Nature & Science, 2001 Colorado Boulevard, Denver, Colorado 80205, USADenver Museum of Nature & ScienceDenverUnited States of America
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6
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Ito HC, Sasaki A. The Adaptation Front Equation Explains Innovation-Driven Taxonomic Turnovers and Living Fossilization. Am Nat 2023; 202:E163-E180. [PMID: 38033181 DOI: 10.1086/727046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
AbstractEvolutionary taxonomic turnovers are often associated with innovations beneficial in various ecological niches. Such innovations can repeatedly occur in species occupying optimum niches for a focal species group, resulting in their repeated diversifications and species flows from optimum to suboptimum niches, at the expense of less innovated ones. By combining species packing theory and adaptive dynamics theory, we develop an equation that allows analytical prediction for such innovation-driven species flows over a niche space of arbitrary dimension under a unimodal carrying capacity distribution. The developed equation and simulated evolution show that central niches (with the highest carrying capacities) tend to attain the fastest innovation speeds to become biodiversity sources. Species that diverge from the central niches outcompete the indigenous species in peripheral niches. The outcompeted species become extinct or evolve directionally toward far more peripheral niches. Because of this globally acting process over niches, species occupying the most peripheral niches are the least innovated and have deep divergence times from their closest relatives, and thus they correspond to living fossils. The extension of this analysis for multiple geographic regions shows that living fossils are also expected in geographically peripheral regions for the focal species group.
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7
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Balart-García P, Aristide L, Bradford TM, Beasley-Hall PG, Polak S, Cooper SJB, Fernández R. Parallel and convergent genomic changes underlie independent subterranean colonization across beetles. Nat Commun 2023; 14:3842. [PMID: 37386018 PMCID: PMC10310748 DOI: 10.1038/s41467-023-39603-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/21/2023] [Indexed: 07/01/2023] Open
Abstract
Adaptation to life in caves is often accompanied by dramatically convergent changes across distantly related taxa, epitomized by the loss or reduction of eyes and pigmentation. Nevertheless, the genomic underpinnings underlying cave-related phenotypes are largely unexplored from a macroevolutionary perspective. Here we investigate genome-wide gene evolutionary dynamics in three distantly related beetle tribes with at least six instances of independent colonization of subterranean habitats, inhabiting both aquatic and terrestrial underground systems. Our results indicate that remarkable gene repertoire changes mainly driven by gene family expansions occurred prior to underground colonization in the three tribes, suggesting that genomic exaptation may have facilitated a strict subterranean lifestyle parallelly across beetle lineages. The three tribes experienced both parallel and convergent changes in the evolutionary dynamics of their gene repertoires. These findings pave the way towards a deeper understanding of the evolution of the genomic toolkit in hypogean fauna.
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Affiliation(s)
- Pau Balart-García
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
| | - Leandro Aristide
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Tessa M Bradford
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, and Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Perry G Beasley-Hall
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, and Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Slavko Polak
- Notranjska Museum Postojna, Kolodvorska c. 3, 6230, Postojna, Slovenia
| | - Steven J B Cooper
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, and Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Museum, Adelaide, SA, 5000, Australia
| | - Rosa Fernández
- Metazoa Phylogenomics Lab, Biodiversity Program, Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
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8
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Liu S, Zhou C, Lin Y. New Insights into the Variation and Admixture of the Cave-Dwelling Spider Trogloneta yunnanensis in South China Karst. Animals (Basel) 2023; 13:ani13071244. [PMID: 37048500 PMCID: PMC10093053 DOI: 10.3390/ani13071244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/26/2023] [Accepted: 04/01/2023] [Indexed: 04/07/2023] Open
Abstract
Subterranean karst caves can contain unexpected biodiversity, but few studies related to spider population genetics have been conducted in the karst area of Southern China. In this study, we investigated the population genetic structure of Trogloneta yunnanensis (Song & Zhu, 1994) based on 73 spider samples from six underground populations in South China Karst. Population genetic structure analysis showed a clear divergence (FST > 0.9 and Nm < 0.05) among populations according to mitochondrial genes. The phylogenetic gene tree constructed by BI and ML methods recovered six geographic clades. Divergence time estimation indicated that the divergence of these six populations can be traced back to the late Pleistocene. We supposed that the geographic isolation led to the extreme population structure. According to this study and previous studies about troglobites living in this region, the subterranean habitats of the Yunnan-Guizhou Plateau may contain many organisms with similar genetic structures. The subterranean biodiversity in the karst area of Southern China needs to be re-evaluated and protected.
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Affiliation(s)
- Shiliang Liu
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Chuang Zhou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Sichuan University, Chengdu 610064, China
| | - Yucheng Lin
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, China
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9
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Aharon S, Ballesteros JA, Gainett G, Hawlena D, Sharma PP, Gavish-Regev E. In the land of the blind: Exceptional subterranean speciation of cryptic troglobitic spiders of the genus Tegenaria (Araneae: Agelenidae) in Israel. Mol Phylogenet Evol 2023; 183:107705. [PMID: 36707009 DOI: 10.1016/j.ympev.2023.107705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/14/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
Caves have long been recognized as a window into the mechanisms of diversification and convergent evolution, due to the unique conditions of isolation and life in the dark. These lead to adaptations and reduce dispersal and gene flow, resulting in high levels of speciation and endemism. The Israeli cave arachnofauna remains poorly known, but likely represents a rich assemblage. In a recent survey, we found troglophilic funnel-web spiders of the genus Tegenaria in 26 caves, present mostly at the cave entrance ecological zone. In addition, we identified at least 14 caves inhabited by troglobitic Tegenaria, which are present mostly in the twilight and dark ecological zones. Ten of the caves, located in the north and center of Israel, are inhabited by both troglophilic and troglobitic Tegenaria. These spiders bear superficial phenotypic similarities but differ in the levels of eye reduction and pigmentation. To test whether these taxa constitute separate species, as well as understand their relationships to epigean counterparts, we conducted a broad geographic sampling of cave-dwelling Tegenaria in Israel and Palestine, using morphological and molecular evidence. Counterintuitively, our results show that the troglobitic Tegenaria we studied are distantly related to the troglophilic Tegenaria found at each of the cave entrances we sampled. Moreover, seven new troglobitic species can be identified based on genetic differences, eye reduction level, and features of the female and male genitalia. Our COI analysis suggest that the Israeli troglobitic Tegenaria species are more closely related to eastern-Mediterranean congeners than to the local sympatric troglophile Tegenaria species, suggesting a complex biogeographic history.
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Affiliation(s)
- Shlomi Aharon
- The National Natural History Collections, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; Department of Ecology, Evolution & Behavior, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
| | | | - Guilherme Gainett
- Department of Integrative Biology, University of Madison-Wisconsin, 441 Birge Hall, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Dror Hawlena
- Department of Ecology, Evolution & Behavior, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Prashant P Sharma
- Department of Integrative Biology, University of Madison-Wisconsin, 441 Birge Hall, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Efrat Gavish-Regev
- The National Natural History Collections, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
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10
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Mammola S, Meierhofer MB, Borges PA, Colado R, Culver DC, Deharveng L, Delić T, Di Lorenzo T, Dražina T, Ferreira RL, Fiasca B, Fišer C, Galassi DMP, Garzoli L, Gerovasileiou V, Griebler C, Halse S, Howarth FG, Isaia M, Johnson JS, Komerički A, Martínez A, Milano F, Moldovan OT, Nanni V, Nicolosi G, Niemiller ML, Pallarés S, Pavlek M, Piano E, Pipan T, Sanchez‐Fernandez D, Santangeli A, Schmidt SI, Wynne JJ, Zagmajster M, Zakšek V, Cardoso P. Towards evidence-based conservation of subterranean ecosystems. Biol Rev Camb Philos Soc 2022; 97:1476-1510. [PMID: 35315207 PMCID: PMC9545027 DOI: 10.1111/brv.12851] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 02/22/2022] [Accepted: 03/01/2022] [Indexed: 12/18/2022]
Abstract
Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems have traditionally been overlooked in global conservation agendas and multilateral agreements, a quantitative assessment of solution-based approaches to safeguard subterranean biota and associated habitats is timely. This assessment allows researchers and practitioners to understand the progress made and research needs in subterranean ecology and management. We conducted a systematic review of peer-reviewed and grey literature focused on subterranean ecosystems globally (terrestrial, freshwater, and saltwater systems), to quantify the available evidence-base for the effectiveness of conservation interventions. We selected 708 publications from the years 1964 to 2021 that discussed, recommended, or implemented 1,954 conservation interventions in subterranean ecosystems. We noted a steep increase in the number of studies from the 2000s while, surprisingly, the proportion of studies quantifying the impact of conservation interventions has steadily and significantly decreased in recent years. The effectiveness of 31% of conservation interventions has been tested statistically. We further highlight that 64% of the reported research occurred in the Palearctic and Nearctic biogeographic regions. Assessments of the effectiveness of conservation interventions were heavily biased towards indirect measures (monitoring and risk assessment), a limited sample of organisms (mostly arthropods and bats), and more accessible systems (terrestrial caves). Our results indicate that most conservation science in the field of subterranean biology does not apply a rigorous quantitative approach, resulting in sparse evidence for the effectiveness of interventions. This raises the important question of how to make conservation efforts more feasible to implement, cost-effective, and long-lasting. Although there is no single remedy, we propose a suite of potential solutions to focus our efforts better towards increasing statistical testing and stress the importance of standardising study reporting to facilitate meta-analytical exercises. We also provide a database summarising the available literature, which will help to build quantitative knowledge about interventions likely to yield the greatest impacts depending upon the subterranean species and habitats of interest. We view this as a starting point to shift away from the widespread tendency of recommending conservation interventions based on anecdotal and expert-based information rather than scientific evidence, without quantitatively testing their effectiveness.
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Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS), University of HelsinkiPohjoinen Rautatiekatu 13Helsinki00100Finland
- Molecular Ecology Group (dark‐MEG)Water Research Institute (IRSA), National Research Council (CNR)Largo Tonolli, 50Verbania‐Pallanza28922Italy
| | - Melissa B. Meierhofer
- BatLab Finland, Finnish Museum of Natural History Luomus (LUOMUS)University of HelsinkiPohjoinen Rautatiekatu 13Helsinki00100Finland
| | - Paulo A.V. Borges
- cE3c—Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group / CHANGE – Global Change and Sustainability InstituteUniversity of Azores, Faculty of Agrarian Sciences and Environment (FCAA), Rua Capitão João d'ÀvilaPico da Urze, 9700‐042 Angra do HeroísmoAzoresPortugal
| | - Raquel Colado
- Departament of Ecology and HidrologyUniversity of MurciaMurcia30100Spain
| | - David C. Culver
- Department of Environmental ScienceAmerican University4400 Massachusetts Avenue, N.WWashingtonDC20016U.S.A.
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS UMR 7205, MNHN, UPMC, EPHEMuseum National d'Histoire Naturelle, Sorbonne UniversitéParisFrance
| | - Teo Delić
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Tiziana Di Lorenzo
- Research Institute on Terrestrial Ecosystems (IRET‐CNR), National Research CouncilVia Madonna del Piano 10, 50019 Sesto FiorentinoFlorenceItaly
| | - Tvrtko Dražina
- Division of Zoology, Department of BiologyFaculty of Science, University of ZagrebRooseveltov Trg 6Zagreb10000Croatia
- Croatian Biospeleological SocietyRooseveltov Trg 6Zagreb10000Croatia
| | - Rodrigo L. Ferreira
- Center of Studies in Subterranean Biology, Biology Department, Federal University of LavrasCampus universitário s/n, Aquenta SolLavrasMG37200‐900Brazil
| | - Barbara Fiasca
- Department of Life, Health and Environmental SciencesUniversity of L'AquilaVia Vetoio 1, CoppitoL'Aquila67100Italy
| | - Cene Fišer
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Diana M. P. Galassi
- Department of Life, Health and Environmental SciencesUniversity of L'AquilaVia Vetoio 1, CoppitoL'Aquila67100Italy
| | - Laura Garzoli
- Molecular Ecology Group (dark‐MEG)Water Research Institute (IRSA), National Research Council (CNR)Largo Tonolli, 50Verbania‐Pallanza28922Italy
| | - Vasilis Gerovasileiou
- Department of Environment, Faculty of EnvironmentIonian University, M. Minotou‐Giannopoulou strPanagoulaZakynthos29100Greece
- Hellenic Centre for Marine Research (HCMR), Institute of Marine BiologyBiotechnology and Aquaculture (IMBBC)Thalassocosmos, GournesCrete71500Greece
| | - Christian Griebler
- Department of Functional and Evolutionary Ecology, Division of LimnologyUniversity of ViennaDjerassiplatz 1Vienna1030Austria
| | - Stuart Halse
- Bennelongia Environmental Consultants5 Bishop StreetJolimontWA6014Australia
| | | | - Marco Isaia
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Joseph S. Johnson
- Department of Biological SciencesOhio University57 Oxbow TrailAthensOH45701U.S.A.
| | - Ana Komerički
- Croatian Biospeleological SocietyRooseveltov Trg 6Zagreb10000Croatia
| | - Alejandro Martínez
- Molecular Ecology Group (dark‐MEG)Water Research Institute (IRSA), National Research Council (CNR)Largo Tonolli, 50Verbania‐Pallanza28922Italy
| | - Filippo Milano
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Oana T. Moldovan
- Emil Racovita Institute of SpeleologyClinicilor 5Cluj‐Napoca400006Romania
- Romanian Institute of Science and TechnologySaturn 24‐26Cluj‐Napoca400504Romania
| | - Veronica Nanni
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Giuseppe Nicolosi
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Matthew L. Niemiller
- Department of Biological SciencesThe University of Alabama in Huntsville301 Sparkman Drive NWHuntsvilleAL35899U.S.A.
| | - Susana Pallarés
- Departamento de Biogeografía y Cambio GlobalMuseo Nacional de Ciencias Naturales, CSICCalle de José Gutiérrez Abascal 2Madrid28006Spain
| | - Martina Pavlek
- Croatian Biospeleological SocietyRooseveltov Trg 6Zagreb10000Croatia
- Ruđer Bošković InstituteBijenička cesta 54Zagreb10000Croatia
| | - Elena Piano
- Department of Life Sciences and Systems BiologyUniversity of TurinVia Accademia Albertina, 13TorinoI‐10123Italy
| | - Tanja Pipan
- ZRC SAZUKarst Research InstituteNovi trg 2Ljubljana1000Slovenia
- UNESCO Chair on Karst EducationUniversity of Nova GoricaGlavni trg 8Vipava5271Slovenia
| | | | - Andrea Santangeli
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiViikinkaari 1Helsinki00014Finland
| | - Susanne I. Schmidt
- Institute of Hydrobiology, Biology Centre CASNa Sádkách 702/7České Budějovice370 05Czech Republic
- Department of Lake ResearchHelmholtz Centre for Environmental ResearchBrückstraße 3aMagdeburg39114Germany
| | - J. Judson Wynne
- Department of Biological SciencesCenter for Adaptable Western Landscapes, Box 5640, Northern Arizona UniversityFlagstaffAZ86011U.S.A.
| | - Maja Zagmajster
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Valerija Zakšek
- SubBio Lab, Department of Biology, Biotechnical FacultyUniversity of LjubljanaJamnikarjeva 101Ljubljana1000Slovenia
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe)Finnish Museum of Natural History (LUOMUS), University of HelsinkiPohjoinen Rautatiekatu 13Helsinki00100Finland
- cE3c—Centre for Ecology, Evolution and Environmental Changes / Azorean Biodiversity Group / CHANGE – Global Change and Sustainability InstituteUniversity of Azores, Faculty of Agrarian Sciences and Environment (FCAA), Rua Capitão João d'ÀvilaPico da Urze, 9700‐042 Angra do HeroísmoAzoresPortugal
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11
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Derkarabetian S, Starrett J, Hedin M. Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data. Front Zool 2022; 19:8. [PMID: 35193622 PMCID: PMC8862334 DOI: 10.1186/s12983-022-00453-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/27/2022] [Indexed: 12/28/2022] Open
Abstract
The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation. These taxa present a conundrum when delimiting species: analyses rely heavily, if not entirely, on genetic data which over split species, while other lines of evidence lump. We showcase this conundrum in the harvester Theromaster brunneus, a low dispersal taxon with a wide geographic distribution and high potential for cryptic species. Integrating morphology, mitochondrial, and sub-genomic (double-digest RADSeq and ultraconserved elements) data, we find high discordance across analyses and data types in the number of inferred species, with further evidence that multispecies coalescent approaches over split. We demonstrate the power of a supervised machine learning approach in effectively delimiting cryptic species by creating a "custom" training data set derived from a well-studied lineage with similar biological characteristics as Theromaster. This novel approach uses known taxa with particular biological characteristics to inform unknown taxa with similar characteristics, using modern computational tools ideally suited for species delimitation. The approach also considers the natural history of organisms to make more biologically informed species delimitation decisions, and in principle is broadly applicable for taxa across the tree of life.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
| | - James Starrett
- Department of Entomology and Nematology, University of California, Davis, Briggs Hall, Davis, CA, 95616-5270, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182-4614, USA
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12
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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: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Jugovic J, Šumer N. Differences in Troglomorphism and Sexual Dimorphism in Two Sympatric Subtroglophile Crickets of Genus Troglophilus (Insecta: Orthoptera). POLISH JOURNAL OF ECOLOGY 2021. [DOI: 10.3161/15052249pje2021.69.1.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jure Jugovic
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
| | - Nika Šumer
- Department of Biodiversity, Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia
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14
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Gainett G, Ballesteros JA, Kanzler CR, Zehms JT, Zern JM, Aharon S, Gavish-Regev E, Sharma PP. Systemic paralogy and function of retinal determination network homologs in arachnids. BMC Genomics 2020; 21:811. [PMID: 33225889 PMCID: PMC7681978 DOI: 10.1186/s12864-020-07149-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/13/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Arachnids are important components of cave ecosystems and display many examples of troglomorphisms, such as blindness, depigmentation, and elongate appendages. Little is known about how the eyes of arachnids are specified genetically, let alone the mechanisms for eye reduction and loss in troglomorphic arachnids. Additionally, duplication of Retinal Determination Gene Network (RDGN) homologs in spiders has convoluted functional inferences extrapolated from single-copy homologs in pancrustacean models. RESULTS We investigated a sister species pair of Israeli cave whip spiders, Charinus ioanniticus and C. israelensis (Arachnopulmonata, Amblypygi), of which one species has reduced eyes. We generated embryonic transcriptomes for both Amblypygi species, and discovered that several RDGN homologs exhibit duplications. We show that duplication of RDGN homologs is systemic across arachnopulmonates (arachnid orders that bear book lungs), rather than being a spider-specific phenomenon. A differential gene expression (DGE) analysis comparing the expression of RDGN genes in field-collected embryos of both species identified candidate RDGN genes involved in the formation and reduction of eyes in whip spiders. To ground bioinformatic inference of expression patterns with functional experiments, we interrogated the function of three candidate RDGN genes identified from DGE using RNAi in the spider Parasteatoda tepidariorum. We provide functional evidence that one of these paralogs, sine oculis/Six1 A (soA), is necessary for the development of all arachnid eye types. CONCLUSIONS Our work establishes a foundation to investigate the genetics of troglomorphic adaptations in cave arachnids, and links differential gene expression to an arthropod eye phenotype for the first time outside of Pancrustacea. Our results support the conservation of at least one RDGN component across Arthropoda and provide a framework for identifying the role of gene duplications in generating arachnid eye diversity.
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Affiliation(s)
- Guilherme Gainett
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Jesús A Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Charlotte R Kanzler
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jakob T Zehms
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John M Zern
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Shlomi Aharon
- National Natural History Collections, The Hebrew University of Jerusalem , Jerusalem, 9190401, Israel
| | - Efrat Gavish-Regev
- National Natural History Collections, The Hebrew University of Jerusalem , Jerusalem, 9190401, Israel
| | - Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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15
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Boyd OF, Philips TK, Johnson JR, Nixon JJ. Geographically structured genetic diversity in the cave beetle Darlingtonea kentuckensis Valentine, 1952 (Coleoptera, Carabidae, Trechini, Trechina). SUBTERRANEAN BIOLOGY 2020. [DOI: 10.3897/subtbiol.34.46348] [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] Open
Abstract
Cave beetles of the eastern USA are one of many poorly studied groups of insects and nearly all previous work delimiting species is based solely on morphology. This study assesses genetic diversity in the monotypic cave carabid beetle genus DarlingtoneaValentine 1952, to test the relationship between putative geographical barriers to subterranean dispersal and the boundaries of genetically distinct groups. Approximately 400bp of the mitochondrial cytochrome oxidase I (COI) gene was sequenced from up to four individuals from each of 27 populations, sampled from caves along the escarpments of the Mississippian and Cumberland plateaus in eastern Kentucky, USA. The 81 individuals sequenced yielded 28 unique haplotypes. Hierarchical analyses of molecular variance (AMOVA) within and among geographically defined groups tested two a priori hypotheses of structure based on major and minor river drainages, as well as genetic distance clusters defined a posteriori from an unrooted analysis. High genetic differentiation (FST) between populations was found across analyses. The influence of isolation by distance could potentially account for much but not all of the variation found among geographically defined groups at both levels. High variability among the three northernmost genetic clusters (FCT), low variability among populations within clusters (FSC), and low within-cluster Mantel correlations indicate the importance of unidentified likely intra-karst barriers to gene flow separating closely grouped cave populations. Overall phylogeographic patterns are consistent with previous evidence of population isolation among cave systems in the region, revealing geographically structured cryptic diversity in Darlingtonea over its distribution. The landscape features considered a priori in this study were not predictive of the genetic breaks among the three northern clusters, which are genetically distinct despite their close geographic proximity.
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16
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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: 3.6] [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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Acosta LE. A relictual troglomorphic harvestman discovered in a volcanic cave of western Argentina: Otilioleptes marcelae, new genus, new species, and Otilioleptidae, new family (Arachnida, Opiliones, Gonyleptoidea). PLoS One 2019; 14:e0223828. [PMID: 31644592 PMCID: PMC6808334 DOI: 10.1371/journal.pone.0223828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/27/2019] [Indexed: 02/06/2023] Open
Abstract
The troglomorphic harvestman Otilioleptes marcelae gen. nov., sp. nov. from the basaltic cave Doña Otilia, Payunia region, Mendoza Province, Argentina, is described. Its systematic affinities were studied through cladistic and Bayesian analyses that included representatives of Gonyleptoidea; it was determined to represent a new monotypic family, Otilioleptidae fam. nov., occupying a basal position within the clade Laminata. This species shows accentuated troglomorphic traits, typical for troglobitic harvestmen: elongated appendages, depigmentation, reduction of eyes and fading of scutal sulci. Additionally, it almost lacks sexual dimorphism, the distal portion of coxa IV is not completely fused to the stigmatic segment, and penis morphology is remarkably divergent with other Laminata; these features cannot be attributed to cave adaptation and may reflect early lineage divergence. Otilioleptes marcelae is the first troglobitic gonyleptoid known from a lava tube. The xeric environments around the cave (Patagonian ecoregion) and the paleoenvironmental history of the area suggest the relictual character of O. marcelae. Scattered evidence supports a long time evolutionary scenario and a presumable relationship with the Chilean opiliofauna (especially with genus Osornogyndes). A comparative overview of all known troglobitic gonyleptoids is provided. The urgent need to protect this new species and its unique cave environment is emphasized.
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Affiliation(s)
- Luis E. Acosta
- Universidad Nacional de Córdoba, Facultad de Ciencias Exactas, Físicas y Naturales, Cátedra de Diversidad Biológica II, Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Diversidad y Ecología Animal (IDEA), Córdoba, Argentina
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18
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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: 1.0] [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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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: 51] [Impact Index Per Article: 8.5] [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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20
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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: 0.7] [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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21
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22
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Derkarabetian S, Starrett J, Tsurusaki N, Ubick D, Castillo S, Hedin M. A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements. Zookeys 2018; 760:1-36. [PMID: 29872361 PMCID: PMC5986891 DOI: 10.3897/zookeys.760.24937] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 04/26/2018] [Indexed: 01/09/2023] Open
Abstract
Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe. This clade has had a challenging taxonomic history, but the current classification consists of ~77 species in three families, the Travuniidae, Paranonychidae, and Nippononychidae. Travunioidea classification has traditionally been based on structure of the tarsal claws of the hind legs. However, it is now clear that tarsal claw structure is a poor taxonomic character due to homoplasy at all taxonomic levels. Here, we utilize DNA sequences derived from capture of ultraconserved elements (UCEs) to reconstruct travunioid relationships. Data matrices consisting of 317-677 loci were used in maximum likelihood, Bayesian, and species tree analyses. Resulting phylogenies recover four consistent and highly supported clades; the phylogenetic position and taxonomic status of the enigmatic genus Yuria is less certain. Based on the resulting phylogenies, a revision of Travunioidea is proposed, now consisting of the Travuniidae, Cladonychiidae, Paranonychidae (Nippononychidae is synonymized), and the new family Cryptomastridae Derkarabetian & Hedin, fam. n., diagnosed here. The phylogenetic utility and diagnostic features of the intestinal complex and male genitalia are discussed in light of phylogenomic results, and the inappropriateness of the tarsal claw in diagnosing higher-level taxa is further corroborated.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Biology, San Diego State University, San Diego, California 92182-4614, USA
- Department of Biology, University of California, Riverside, Riverside, California 92521, USA
- Present address: Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - James Starrett
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Nobuo Tsurusaki
- Laboratory of Zoological Systematics, Faculty of Agriculture, in Faculty of Regional Sciences Building, Tottori University, Tottori, 680-8551, Japan
| | - Darrell Ubick
- Department of Entomology, California Academy of Sciences, San Francisco, California 94118, USA
| | - Stephanie Castillo
- Department of Entomology, University of California, Riverside, Riverside, California 92521, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California 92182-4614, USA
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Deharveng L, Bedos A. Diversity of Terrestrial Invertebrates in Subterranean Habitats. CAVE ECOLOGY 2018. [DOI: 10.1007/978-3-319-98852-8_7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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25
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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: 4.1] [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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26
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Conde-Vela VM. The troglomorphic adaptations of Namanereidinae (Annelida, Nereididae) revisited, including a redescription of Namanereis cavernicola (Solís-Weiss & Espinasa, 1991), and a new Caribbean species of Namanereis Chamberlin, 1919. SUBTERRANEAN BIOLOGY 2017. [DOI: 10.3897/subtbiol.23.13701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Liu W, Golovatch S, Wesener T, Tian M. Convergent Evolution of Unique Morphological Adaptations to a Subterranean Environment in Cave Millipedes (Diplopoda). PLoS One 2017; 12:e0170717. [PMID: 28178274 PMCID: PMC5298257 DOI: 10.1371/journal.pone.0170717] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/09/2017] [Indexed: 01/29/2023] Open
Abstract
Animal life in caves has fascinated researchers and the public alike because of the unusual and sometimes bizarre morphological adaptations observed in numerous troglobitic species. Despite their worldwide diversity, the adaptations of cave millipedes (Diplopoda) to a troglobitic lifestyle have rarely been examined. In this study, morphological characters were analyzed in species belonging to four different orders (Glomerida, Polydesmida, Chordeumatida, and Spirostreptida) and six different families (Glomeridae, Paradoxosomatidae, Polydesmidae, Haplodesmidae, Megalotylidae, and Cambalopsidae) that represent the taxonomic diversity of class Diplopoda. We focused on the recently discovered millipede fauna of caves in southern China. Thirty different characters were used to compare cave troglobites and epigean species within the same genera. A character matrix was created to analyze convergent evolution of cave adaptations. Males and females were analyzed independently to examine sex differences in cave adaptations. While 10 characters only occurred in a few phylogenetic groups, 20 characters were scored for in all families. Of these, four characters were discovered to have evolved convergently in all troglobitic millipedes. The characters that represented potential morphological cave adaptations in troglobitic species were: (1) a longer body; (2) a lighter body color; (3) elongation of the femora; and (4) elongation of the tarsi of walking legs. Surprisingly, female, but not male, antennae were more elongated in troglobites than in epigean species. Our study clearly shows that morphological adaptations have evolved convergently in different, unrelated millipede orders and families, most likely as a direct adaptation to cave life.
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Affiliation(s)
- Weixin Liu
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Zoological Research Museum A. Koenig, Leibniz Institute for Terrestrial Biodiversity, Bonn, Germany
| | - Sergei Golovatch
- Institute for Problems of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Thomas Wesener
- Zoological Research Museum A. Koenig, Leibniz Institute for Terrestrial Biodiversity, Bonn, Germany
| | - Mingyi Tian
- Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
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Mammola S, Giachino PM, Piano E, Jones A, Barberis M, Badino G, Isaia M. Ecology and sampling techniques of an understudied subterranean habitat: the Milieu Souterrain Superficiel (MSS). Naturwissenschaften 2016; 103:88. [DOI: 10.1007/s00114-016-1413-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/14/2016] [Accepted: 09/18/2016] [Indexed: 11/30/2022]
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Derkarabetian S, Burns M, Starrett J, Hedin M. Population genomic evidence for multiple Pliocene refugia in a montane‐restricted harvestman (Arachnida, Opiliones,
Sclerobunus robustus
) from the southwestern United States. Mol Ecol 2016; 25:4611-31. [DOI: 10.1111/mec.13789] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 07/11/2016] [Accepted: 07/19/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Shahan Derkarabetian
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
- Department of Biology University of California Riverside Riverside CA 92521 USA
| | - Mercedes Burns
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
| | - James Starrett
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
| | - Marshal Hedin
- Department of Biology San Diego State University 5500 Campanile Dr. San Diego CA 92182‐4614 USA
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Sumner-Rooney L, Sigwart JD, McAfee J, Smith L, Williams ST. Repeated eye reduction events reveal multiple pathways to degeneration in a family of marine snails. Evolution 2016; 70:2268-2295. [PMID: 27488448 DOI: 10.1111/evo.13022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 07/08/2016] [Accepted: 07/24/2016] [Indexed: 02/02/2023]
Abstract
Eye reduction occurs in many troglobitic, fossorial, and deep-sea animals but there is no clear consensus on its evolutionary mechanism. Given the highly conserved and pleiotropic nature of many genes instrumental to eye development, degeneration might be expected to follow consistent evolutionary trajectories in closely related animals. We tested this in a comparative study of ocular anatomy in solariellid snails from deep and shallow marine habitats using morphological, histological, and tomographic techniques, contextualized phylogenetically. Of 67 species studied, 15 lack retinal pigmentation and at least seven have eyes enveloped by surrounding epithelium. Independent instances of reduction follow numerous different morphological trajectories. We estimate eye loss has evolved at least seven times within Solariellidae, in at least three different ways: characters such as pigmentation loss, obstruction of eye aperture, and "lens" degeneration can occur in any order. In one instance, two morphologically distinct reduction pathways appear within a single genus, Bathymophila. Even amongst closely related animals living at similar depths and presumably with similar selective pressures, the processes leading to eye loss have more evolutionary plasticity than previously realized. Although there is selective pressure driving eye reduction, it is clearly not morphologically or developmentally constrained as has been suggested by previous studies.
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Affiliation(s)
- Lauren Sumner-Rooney
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland. .,Queen's University Marine Laboratory, Queen's University Belfast, Portaferry, Co. Down, BT22 1PF, Northern Ireland.
| | - Julia D Sigwart
- School of Biological Sciences, Queen's University Belfast, Belfast, BT9 7BL, Northern Ireland.,Queen's University Marine Laboratory, Queen's University Belfast, Portaferry, Co. Down, BT22 1PF, Northern Ireland
| | - Jenny McAfee
- Queen's University Marine Laboratory, Queen's University Belfast, Portaferry, Co. Down, BT22 1PF, Northern Ireland
| | - Lisa Smith
- Core Research Facility, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Suzanne T Williams
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
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31
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Burns M, Starrett J, Derkarabetian S, Richart CH, Cabrero A, Hedin M. Comparative performance of double‐digest
RAD
sequencing across divergent arachnid lineages. Mol Ecol Resour 2016; 17:418-430. [DOI: 10.1111/1755-0998.12575] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/23/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Mercedes Burns
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
| | - James Starrett
- 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 Biology University of California 900 University Avenue Riverside CA 92521 USA
| | - Casey H. Richart
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
- Department of Biology University of California 900 University Avenue Riverside CA 92521 USA
| | - Allan Cabrero
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
| | - Marshal Hedin
- Department of Biology San Diego State University 5500 Campanile Drive San Diego CA 92182 USA
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DiDomenico A, Hedin M. New species in the Sitalcina sura species group (Opiliones, Laniatores, Phalangodidae), with evidence for a biogeographic link between California desert canyons and Arizona sky islands. Zookeys 2016:1-36. [PMID: 27199607 PMCID: PMC4857029 DOI: 10.3897/zookeys.586.7832] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/23/2016] [Indexed: 11/12/2022] Open
Abstract
The western United States is home to numerous narrowly endemic harvestman taxa (Arachnida, Opiliones), including members of the genus Sitalcina Banks, 1911. Sitalcina is comprised of three species groups, including the monospecific Sitalcina californica and Sitalcina lobata groups, and the Sitalcina sura group with eight described species. All species in the Sitalcina sura group have very small geographic distributions, with group members distributed like disjunct "beads on a string" from Monterey south to southern California and southeast to the sky-island mountain ranges of southern Arizona. Here, molecular phylogenetic and species delimitation analyses were conducted for all described species in the Sitalcina sura group, plus several newly discovered populations. Species trees were reconstructed using multispecies coalescent methods implemented in *BEAST, and species delimitation was accomplished using Bayes Factor Delimitation (BFD). Based on quantitative species delimitation results supported by consideration of morphological characters, two new species (Sitalcina oasiensis sp. n., Sitalcina ubicki sp. n.) are described. We also provide a description of the previously unknown male of Sitalcina borregoensis Briggs, 1968. Molecular phylogenetic evidence strongly supports distinctive desert versus coastal clades, with desert canyon taxa from southern California more closely related to Arizona taxa than to geographically proximate California coastal taxa. We hypothesize that southern ancestry and plate tectonics have played a role in the diversification history of this animal lineage, similar to sclerophyllous plant taxa of the Madro-Tertiary Geoflora. Molecular clock analyses for the Sitalcina sura group are generally consistent with these hypotheses. We also propose that additional Sitalcina species await discovery in the desert canyons of southern California and northern Baja, and the mountains of northwestern mainland Mexico.
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Affiliation(s)
- Angela DiDomenico
- Department of Biology, 5500 Campanile Drive, San Diego State University, San Diego, CA 92182-4614, USA
| | - Marshal Hedin
- Department of Biology, 5500 Campanile Drive, San Diego State University, San Diego, CA 92182-4614, USA
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Emata K, Hedin M. From the mountains to the coast and back again: Ancient biogeography in a radiation of short-range endemic harvestmen from California. Mol Phylogenet Evol 2016; 98:233-43. [DOI: 10.1016/j.ympev.2016.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 12/16/2015] [Accepted: 02/01/2016] [Indexed: 10/22/2022]
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34
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Delić T, Trontelj P, Zakšek V, Fišer C. Biotic and abiotic determinants of appendage length evolution in a cave amphipod. J Zool (1987) 2016. [DOI: 10.1111/jzo.12318] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- T. Delić
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - P. Trontelj
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
- Museum für Naturkunde; Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin; Berlin Germany
| | - V. Zakšek
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - C. Fišer
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
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35
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Starrett J, Derkarabetian S, Richart CH, Cabrero A, Hedin M. A new monster from southwest Oregon forests: Cryptomaster behemoth sp. n. (Opiliones, Laniatores, Travunioidea). Zookeys 2016:11-35. [PMID: 26877685 PMCID: PMC4740820 DOI: 10.3897/zookeys.555.6274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/15/2015] [Indexed: 12/03/2022] Open
Abstract
The monotypic genus Cryptomaster Briggs, 1969 was described based on individuals from a single locality in southwestern Oregon. The described species Cryptomasterleviathan Briggs, 1969 was named for its large body size compared to most travunioid Laniatores. However, as the generic name suggests, Cryptomaster are notoriously difficult to find, and few subsequent collections have been recorded for this genus. Here, we increase sampling of Cryptomaster to 15 localities, extending their known range from the Coast Range northeast to the western Cascade Mountains of southern Oregon. Phylogenetic analyses of mitochondrial and nuclear DNA sequence data reveal deep phylogenetic breaks consistent with independently evolving lineages. We use discovery and validation species delimitation approaches to generate and test species hypotheses, including a coalescent species delimitation method to test multi-species hypotheses. For delimited species, we use light microscopy and SEM to discover diagnostic morphological characters. Although Cryptomaster has a small geographic distribution, this taxon is consistent with other short-range endemics in having deep phylogenetic breaks indicative of species level divergences. Herein we describe Cryptomasterbehemothsp. n., and provide morphological diagnostic characters for identifying Cryptomasterleviathan and Cryptomasterbehemoth.
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Affiliation(s)
- James Starrett
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA
| | - Shahan Derkarabetian
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA; Department of Biology, 900 University Avenue, University of California, Riverside, Riverside, CA 92521, USA
| | - Casey H Richart
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA; Department of Biology, 900 University Avenue, University of California, Riverside, Riverside, CA 92521, USA
| | - Allan Cabrero
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA
| | - Marshal Hedin
- Department of Biology, 5500 Campanile Drive San Diego State University, San Diego, CA 92182, USA
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36
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Cimmaruta R, Lucente D, Nascetti G. Persistence, isolation and diversification of a naturally fragmented species in local refugia: the case of Hydromantes strinatii. PLoS One 2015; 10:e0131298. [PMID: 26107249 PMCID: PMC4479377 DOI: 10.1371/journal.pone.0131298] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 06/01/2015] [Indexed: 11/19/2022] Open
Abstract
The study of the European plethodontid salamander Hydromantes strinatii using allozyme and mitochondrial markers showed a strong geographical genetic structure. This was likely the outcome of different evolutionary mechanisms leaving their signature despite the effects of the genetic drift due to the low population size typical of this species. Two highly divergent clades were identified in the eastern and central-western part of the range, with further geographic sub-structure. Nuclear and mitochondrial markers substantially recovered the same population groups but were conflicting in reconstructing their relationships. This apparent incongruence highlighted the action of different mechanisms such as secondary contacts and incomplete lineage sorting in originating the observed genetic variation. The troglophilic habit of this species provided the opportunity to show the importance of caves as local refugia in maintaining the genetic diversity through the persistence of local populations. Accordingly, high nucleotide and haplotype diversity, strong geographic genetic structuring and lack of expansion were evidenced. This signature was found in the populations from the Ligurian and Maritime Alps, in agreement with the complex orography and paleoclimatic history of this Mediterranean hotspot.
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Affiliation(s)
- Roberta Cimmaruta
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
- * E-mail:
| | - Daniela Lucente
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
| | - Giuseppe Nascetti
- Dipartimento di Scienze Ecologiche e Biologiche, Università della Tuscia, Viterbo, Italy
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Vaschetto LM, González-Ittig RE, Vergara J, Acosta LE. High genetic diversity in the harvestman Geraeocormobius sylvarum
(Arachnida, Opiliones, Gonyleptidae) from subtropical forests in north-eastern Argentina revealed by mitochondrial DNA sequences. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luis M. Vaschetto
- Instituto de Diversidad y Ecología Animal (IDEA); CONICET-Universidad Nacional de Córdoba; Facultad de Ciencias Exactas; Físicas y Naturales; U. N. C Córdoba Argentina
- Cátedra de Diversidad Animal I; Facultad de Ciencias Exactas; Físicas y Naturales; U.N.C Córdoba Argentina
| | - Raúl E. González-Ittig
- Instituto de Diversidad y Ecología Animal (IDEA); CONICET-Universidad Nacional de Córdoba; Facultad de Ciencias Exactas; Físicas y Naturales; U. N. C Córdoba Argentina
- Cátedra de Genética de Poblaciones y Evolución; Facultad de Ciencias Exactas; Físicas y Naturales; U.N.C Córdoba Argentina
| | - Julia Vergara
- Instituto de Diversidad y Ecología Animal (IDEA); CONICET-Universidad Nacional de Córdoba; Facultad de Ciencias Exactas; Físicas y Naturales; U. N. C Córdoba Argentina
- Cátedra de Diversidad Animal I; Facultad de Ciencias Exactas; Físicas y Naturales; U.N.C Córdoba Argentina
| | - Luis E. Acosta
- Instituto de Diversidad y Ecología Animal (IDEA); CONICET-Universidad Nacional de Córdoba; Facultad de Ciencias Exactas; Físicas y Naturales; U. N. C Córdoba Argentina
- Cátedra de Diversidad Animal I; Facultad de Ciencias Exactas; Físicas y Naturales; U.N.C Córdoba Argentina
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Hedin M. High-stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas. Mol Ecol 2015; 24:346-61. [PMID: 25492722 DOI: 10.1111/mec.13036] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 01/26/2023]
Abstract
A remarkable radiation of completely eyeless, cave-obligate spider species (Cicurina) has been described from limestone caves of Texas. This radiation includes over 50 described species, with a large number of hypothesized single-cave endemics, and four species listed as US Federally Endangered. Because of this conservation importance, species delimitation in the group is 'high-stakes'- it is imperative that species hypotheses are data rich, objective, and robust. This study focuses on a complex of four cave-dwelling Cicurina distributed on the northwestern edge of Austin, Texas. Several of the existing species hypotheses in this complex are weak, based on morphological comparisons of small samples of adult female specimens; one species description (for C. wartoni) is based on a single adult specimen. Species limits in this group were newly assessed using morphological, mitochondrial and nuclear DNA sequence data evidence, analysed using a variety of approaches. All data support a clear lineage separation between C. buwata versus the C. travisae complex (including C. travisae, C. wartoni and C. reddelli). Observed congruence across multiple analyses indicate that the C. travisae complex represents a single species, and the formal species synonymy presented here has important conservation implications. The integrative framework utilized in this study serves as a potential model for other Texas cave Cicurina, including US Federally Endangered species. More generally, this study illustrates how and why taxon-focused conservation efforts must prioritize modern species delimitation research (if the existing taxonomy is weak), before devoting precious downstream resources to conservation efforts. The study also highlights the issue of taxonomic type II error that diversity biologists increasingly face as species delimitation moves into the genomics era.
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Affiliation(s)
- Marshal Hedin
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
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Derkarabetian S, Hedin M. Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea). PLoS One 2014; 9:e104982. [PMID: 25144370 PMCID: PMC4140732 DOI: 10.1371/journal.pone.0104982] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/16/2014] [Indexed: 11/18/2022] Open
Abstract
Alpha taxonomy, and specifically the delimitation of species, is becoming increasingly objective and integrative. The use of coalescent-based methods applied to genetic data is providing new tools for the discovery and delimitation of species. Here, we use an integrative approach via a combination of discovery-based multivariate morphological analyses to detect potential new species. These potential species are then used as a priori species in hypothesis-driven validation analyses with genetic data. This research focuses on the harvestmen genus Sclerobunus found throughout the mountainous regions of western North America. Based on our analyses, we conduct a revision of Sclerobunus resulting in synonymy of Cyptobunus with Sclerobunus including transfer of S. cavicolens comb. nov. and elevation of both subspecies of S. ungulatus: S. ungulatus comb. nov. and S. madhousensis comb. nov., stat. nov. The three subspecies of S. robustus are elevated, S. robustus, S. glorietus stat. nov., and S. idahoensis stat. nov. Additionally, five new species of Sclerobunus are described from New Mexico and Colorado, including S. jemez sp. nov., S. klomax sp. nov., S. skywalkeri sp. nov., S. speoventus sp. nov., and S. steinmanni sp. nov. Several of the newly described species are single-cave endemics, and our findings suggest that further exploration of western North American cave habitats will likely yield additional new species.
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Affiliation(s)
- Shahan Derkarabetian
- Department of Biology, San Diego State University, San Diego, California, United States of America
- Department of Biology, University of California Riverside, Riverside, California, United States of America
| | - Marshal Hedin
- Department of Biology, San Diego State University, San Diego, California, United States of America
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Bryson RW, Prendini L, Savary WE, Pearman PB. Caves as microrefugia: Pleistocene phylogeography of the troglophilic North American scorpion Pseudouroctonus reddelli. BMC Evol Biol 2014; 14:9. [PMID: 24428910 PMCID: PMC3902065 DOI: 10.1186/1471-2148-14-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 01/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Survival in microrefugia represents an important paradigm in phylogeography for explaining rapid postglacial re-colonization by species in temperate regions. Microrefugia may allow populations to persist in areas where the climatic conditions on the surface have become unfavourable. Caves generally contain stable microclimates and may represent microrefugia for species capable of exploiting both cave and surface habitats (troglophiles). We examine the phylogeography of the troglophilic North American vaejovid scorpion Pseudouroctonus reddelli using 1,993 base pairs of mitochondrial and nuclear DNA sequence data generated from 12 populations. We use (i) descriptive measures of genetic diversity and population genetics statistics, (ii) reconstructions of phylogeographical structure, spatial diffusion during diversification, and population sizes through time, and (iii) species distribution modelling to test predictions of the hypothesis that caves serve as microrefugia. We compare phylogeographical patterns in P. reddelli with other troglophilic species across the Edwards Plateau karst region of Texas. RESULTS Results revealed high haplotype and nucleotide diversity and substantial phylogeographical structure, probably generated during the Pleistocene. Spatial diffusion occurred along the southern edge of the Edwards Plateau from multiple refugia along the Balcones Escarpment. There was little evidence for population and geographical expansion. Species distribution models predicted substantial reductions in suitable epigean habitat for P. reddelli at the Last Glacial Maximum (LGM). CONCLUSIONS High genetic diversity, strong phylogeographical structure, diffusion from multiple refugia, and unfavourable climatic conditions at the LGM collectively support the hypothesis that caves served as microrefugia for P. reddelli. Similar patterns of genetic structure in P. reddelli and other troglophilic species across the Edwards Plateau karst region of Texas suggest that caves serving as microrefugia are important for the formation, maintenance, and future survival of troglophilic species in temperate karst regions.
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Affiliation(s)
- Robert W Bryson
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Lorenzo Prendini
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024-5192, USA
| | - Warren E Savary
- Department of Entomology, California Academy of Sciences, 55 Music Concourse Drive, Golden Gate Park, San Francisco, CA 94118, USA
| | - Peter B Pearman
- Landscape Dynamics Unit, Swiss Federal Research Institute WSL, Zuercherstrasse 111, Birmensdorf CH-8903, Switzerland
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Bendik NF, Meik JM, Gluesenkamp AG, Roelke CE, Chippindale PT. Biogeography, phylogeny, and morphological evolution of central Texas cave and spring salamanders. BMC Evol Biol 2013; 13:201. [PMID: 24044519 PMCID: PMC3848792 DOI: 10.1186/1471-2148-13-201] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 09/12/2013] [Indexed: 11/23/2022] Open
Abstract
Background Subterranean faunal radiations can result in complex patterns of morphological divergence involving both convergent or parallel phenotypic evolution and cryptic species diversity. Salamanders of the genus Eurycea in central Texas provide a particularly challenging example with respect to phylogeny reconstruction, biogeography and taxonomy. These predominantly aquatic species inhabit karst limestone aquifers and spring outflows, and exhibit a wide range of morphological and genetic variation. We extensively sampled spring and cave populations of six Eurycea species within this group (eastern Blepsimolge clade), to reconstruct their phylogenetic and biogeographic history using mtDNA and examine patterns and origins of cave- and surface-associated morphological variation. Results Genetic divergence is generally low, and many populations share ancestral haplotypes and/or show evidence of introgression. This pattern likely indicates a recent radiation coupled with a complex history of intermittent connections within the aquatic karst system. Cave populations that exhibit the most extreme troglobitic morphologies show no or very low divergence from surface populations and are geographically interspersed among them, suggesting multiple instances of rapid, parallel phenotypic evolution. Morphological variation is diffuse among cave populations; this is in contrast to surface populations, which form a tight cluster in morphospace. Unexpectedly, our analyses reveal two distinct and previously unrecognized morphological groups encompassing multiple species that are not correlated with spring or cave habitat, phylogeny or geography, and may be due to developmental plasticity. Conclusions The evolutionary history of this group of spring- and cave-dwelling salamanders reflects patterns of intermittent isolation and gene flow influenced by complex hydrogeologic dynamics that are characteristic of karst regions. Shallow genetic divergences among several species, evidence of genetic exchange, and nested relationships across morphologically disparate cave and spring forms suggests that cave invasion was recent and many troglobitic morphologies arose independently. These patterns are consistent with an adaptive-shift hypothesis of divergence, which has been proposed to explain diversification in other karst fauna. While cave and surface forms often do not appear to be genetically isolated, morphological diversity within and among populations may be maintained by developmental plasticity, selection, or a combination thereof.
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Affiliation(s)
- Nathan F Bendik
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA.
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Barley AJ, White J, Diesmos AC, Brown RM. THE CHALLENGE OF SPECIES DELIMITATION AT THE EXTREMES: DIVERSIFICATION WITHOUT MORPHOLOGICAL CHANGE IN PHILIPPINE SUN SKINKS. Evolution 2013; 67:3556-72. [DOI: 10.1111/evo.12219] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/08/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Anthony J. Barley
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| | - Jordan White
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
| | | | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence Kansas 66045
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Soto-Adames FN, Taylor SJ. The dorsal chaetotaxy of Trogolaphysa (Collembola, Paronellidae), with descriptions of two new species from caves in Belize. Zookeys 2013:35-74. [PMID: 24003314 PMCID: PMC3760292 DOI: 10.3897/zookeys.323.4950] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 08/01/2013] [Indexed: 11/12/2022] Open
Abstract
Species diagnosis in Trogolaphysa has been based, until now, almost exclusively on number of eyes and shape of claws and mucro. Chaetotaxy, a character system important to diagnose species in other genera of scaled Entomobryoidea, has been described only for a few Trogolaphysa species. Here the complete dorsal chaetotaxy of six species of Trogolaphysa is described using the AMS and Szeptycki’s systems for head and body, respectively. A morphology-based parsimony analysis was performed to evaluate whether chaetotaxic characters overcome the influence of putatively cave adaptive convergent characters to resolve species level relationships, and to evaluate the evolution of the dorsal macrochaetae of the head. Phylogenetic analysis using only putative cave-adaptive characters support clades of unrelated taxa, but the addition of chaetotaxy overcomes the influence of convergent characters. A phylogeny based on all characters supports a trend towards reduced head macrochaetae number. Head macrochaetae are lost beginning with A3 and followed, in order, by S5, S3 and M3. In addition, a checklist of New World Trogolaphysa is provided and two new species, Trogolaphysa giordanoaesp. n. and Trogolaphysa jacobyisp. n., are described on the basis of material collected in six caves in southern Belize.
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Affiliation(s)
- Felipe N Soto-Adames
- Illinois Natural History Survey, University of Illinois, 1816 S Oak St, Champaign IL 61820 USA
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Richart CH, Hedin M. Three new species in the harvestmen genus Acuclavella (Opiliones, Dyspnoi, Ischyropsalidoidea), including description of male Acuclavella quattuor Shear, 1986. Zookeys 2013; 311:19-68. [PMID: 23825441 PMCID: PMC3698555 DOI: 10.3897/zookeys.311.2920] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 06/06/2013] [Indexed: 11/12/2022] Open
Abstract
In Shear's (1986) cladistic analysis of the Ischyropsalidoidea, he described the new genus Acuclavella including four new species from the Pacific Northwest states of Washington and Idaho. Several of these species descriptions were based on very limited sample sizes. Our recent field work has increased by more than an order of magnitude both the number of specimens and known localities for Acuclavella. We use this new material to interpret species limits in Acuclavella using morphometric analyses and DNA sequence data from four gene regions. We sequence for the first time the protein-coding homolog of the Wnt2 gene for phylogenetic reconstruction in Opiliones. Our multi-locus phylogeny corroborates a sister relationship between Acuclavella and Ceratolasma, as hypothesized using morphology by Shear (1986). Within Acuclavella, morphometric clusters and reciprocal allelic monophyly allows recognition of three additional species: Acuclavella leonardi sp. n., Acuclavella sheari sp. n., and Acuclavella makah sp. n. This work also describes the previously unknown male of Acuclavella quattuor, from specimens collected at the type locality. Our research identifies a number of novel morphologies for Acuclavella, including females with four pairs of spines, individuals with three pairs of spines on scute areas I-III, and a population with two pairs of spines disjunct from Acuclavella quattuor, which was diagnosed with this spination character. We were unable to assign these populations to existing species, and conservatively do not yet recognize them as new. Intrageneric morphometrics and phylogenetic inference in Acuclavella were often concordant. However, we demonstrate that species delimitation signal would not be detected if only a single line of evidence were utilized.
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Affiliation(s)
- Casey H. Richart
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California, 92182, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California, 92182, USA
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Gainett G, Sharma PP, Pinto-da-Rocha R, Giribet G, Willemart RH. Walk it off: predictive power of appendicular characters toward inference of higher-level relationships in Laniatores (Arachnida: Opiliones). Cladistics 2013; 30:120-138. [DOI: 10.1111/cla.12029] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Guilherme Gainett
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Caixa Postal 11461 05422-970 São Paulo SP Brazil
| | - Prashant P. Sharma
- Division of Invertebrate Zoology; American Museum of Natural History; 200 Central Park West New York NY 10024 USA
| | - Ricardo Pinto-da-Rocha
- Departamento de Zoologia; Instituto de Biociências; Universidade de São Paulo; Caixa Postal 11461 05422-970 São Paulo SP Brazil
| | - Gonzalo Giribet
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| | - Rodrigo H. Willemart
- Escola de Artes Ciências e Humanidades; Universidade de São Paulo; Rua Arlindo Béttio, 1000-Ermelino Matarazzo CEP: 03828-000 São Paulo SP Brazil
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Clouse RM, Sharma PP, Giribet G, Wheeler WC. Elongation factor-1α, a putative single-copy nuclear gene, has divergent sets of paralogs in an arachnid. Mol Phylogenet Evol 2013; 68:471-81. [PMID: 23669012 DOI: 10.1016/j.ympev.2013.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 03/21/2013] [Accepted: 04/22/2013] [Indexed: 11/17/2022]
Abstract
Identification of paralogy in candidate nuclear loci is an important prerequisite in phylogenetics and statistical phylogeography, but one that is often overlooked. One marker commonly assumed to be a single-copy gene and claimed to harbor great utility for inferring recent divergences is elongation factor-1α (EF-1α). To test this hypothesis, we systematically cloned EF-1α in three disjunct populations of the harvestman Metasiro americanus. Here we show that EF-1α has a large number of paralogs in this species. The paralogs do not evolve in a concerted manner, and the paralogs diverged prior to the population divergence. Moreover, the paralogs of M. americanus are not comparable to the highly divergent EF-1α paralogs found in bees and spiders, which are easily recognized and separated through the use of specific primers. We demonstrate statistically that our detection of paralogs cannot be attributed to amplification error. The presence of EF-1α paralogs in M. americanus prevents its use in statistical phylogeography, and the presence of out-paralogs argues against its use in phylogenetic inference among recently diverged clades. These data contradict the common assumption that EF-1α is for most or all taxa a single-copy gene, or that it has a small number of paralogs that are homogenized through gene conversion, unequal crossing over, or other processes.
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Affiliation(s)
- Ronald M Clouse
- American Museum of Natural History, Division of Invertebrate Zoology, Central Park West at 79th St., New York City, NY 10024, USA.
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Schönhofer AL, McCormack M, Tsurusaki N, Martens J, Hedin M. Molecular phylogeny of the harvestmen genus Sabacon (Arachnida: Opiliones: Dyspnoi) reveals multiple Eocene-Oligocene intercontinental dispersal events in the Holarctic. Mol Phylogenet Evol 2012; 66:303-15. [PMID: 23085535 DOI: 10.1016/j.ympev.2012.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 09/06/2012] [Accepted: 10/03/2012] [Indexed: 11/18/2022]
Abstract
We investigated the phylogeny and biogeographic history of the Holarctic harvestmen genus Sabacon, which shows an intercontinental disjunct distribution and is presumed to be a relatively old taxon. Molecular phylogenetic relationships of Sabacon were estimated using multiple gene regions and Bayesian inference for a comprehensive Sabacon sample. Molecular clock analyses, using relaxed clock models implemented in BEAST, are applied to date divergence events. Biogeographic scenarios utilizing S-DIVA and Lagrange C++ are reconstructed over sets of Bayesian trees, allowing for the incorporation of phylogenetic uncertainty and quantification of alternative reconstructions over time. Four primary well-supported subclades are recovered within Sabacon: (1) restricted to western North America; (2) eastern North American S. mitchelli and sampled Japanese taxa; (3) a second western North American group and taxa from Nepal and China; and (4) eastern North American S. cavicolens with sampled European Sabacon species. Three of four regional faunas (wNA, eNA, East Asia) are thereby non-monophyletic, and three clades include intercontinental disjuncts. Molecular clock analyses and biogeographic reconstructions support nearly simultaneous intercontinental dispersal coincident with the Eocene-Oligocene transition. We hypothesize that biogeographic exchange in the mid-Tertiary is likely correlated with the onset of global cooling, allowing cryophilic Sabacon taxa to disperse within and among continents. Morphological variation supports the divergent genetic clades observed in Sabacon, and suggests that a taxonomic revision (e.g., splitting Sabacon into multiple genera) may be warranted.
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Affiliation(s)
- Axel L Schönhofer
- Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA.
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Breinholt JW, Porter ML, Crandall KA. Testing phylogenetic hypotheses of the subgenera of the freshwater crayfish genus Cambarus (Decapoda: Cambaridae). PLoS One 2012; 7:e46105. [PMID: 23049950 PMCID: PMC3458831 DOI: 10.1371/journal.pone.0046105] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 08/29/2012] [Indexed: 11/19/2022] Open
Abstract
Background The genus Cambarus is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using Cambarus we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression. Methodology/Principal Findings We use three mitochondrial and one nuclear gene regions to estimate the phylogenetic relationships for species within the genus Cambarus and test evolutionary hypotheses of relationships and associated morphological and biogeographical hypotheses. Our resulting phylogeny indicates that the genus Cambarus is polyphyletic, however we fail to reject the monophyly of Cambarus with a topology test. The majority of the Cambarus subgenera are rejected as monophyletic, suggesting the morphological characters used to define those taxa are subject to convergent evolution. While we found incongruence between taxonomy and estimated phylogenetic relationships, a multiple model regression analysis indicates that taxonomy had more explanatory power of genetic relationships than either habitat or geographic distance. Conclusions We find convergent evolution has impacted the morphological features used to delimit Cambarus subgenera. Studies of the crayfish genus Orconectes have shown gonopod morphology used to delimit subgenera is also affected by convergent evolution. This suggests that morphological diagnoses based on traditional crayfish taxonomy might be confounded by convergent evolution across the cambarids and has little utility in diagnosing relationships or defining natural groups. We further suggest that convergent morphological evolution appears to be a common occurrence in invertebrates suggesting the need for careful phylogenetically based interpretations of morphological evolution in invertebrate systematics.
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Fišer C, Zagmajster M, Zakšek V. Coevolution of life history traits and morphology in female subterranean amphipods. OIKOS 2012. [DOI: 10.1111/j.1600-0706.2012.20644.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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