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Ban XC, Shao ZK, Wu LJ, Sun JT, Xue XF. Highly diversified mitochondrial genomes provide new evidence for interordinal relationships in the Arachnida. Cladistics 2022; 38:452-464. [PMID: 35349189 DOI: 10.1111/cla.12504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2022] [Indexed: 12/11/2022] Open
Abstract
Arachnida is an exceptionally diverse class in the Arthropoda, consisting of 20 orders and playing crucial roles in the terrestrial ecosystems. However, their interordinal relationships have been debated for over a century. Rearranged or highly rearranged mitochondrial genomes (mitogenomes) were consistently found in this class, but their various extent in different lineages and efficiency for resolving arachnid phylogenies are unclear. Here, we reconstructed phylogenetic trees using mitogenome sequences of 290 arachnid species to decipher interordinal relationships as well as diversification through time. Our results recovered monophyly of ten orders (i.e. Amblypygi, Araneae, Ixodida, Mesostigmata, Opiliones, Pseudoscorpiones, Ricinulei, Sarcoptiformes, Scorpiones and Solifugae), while rejecting monophyly of the Trombidiformes due to the unstable position of the Eriophyoidea. The monophyly of Acari (subclass) was rejected, possibly due to the long-branch attraction of the Pseudoscorpiones. The monophyly of Arachnida was further rejected because the Xiphosura nested within arachnid orders with unstable positions. Mitogenomes that are highly rearranged in mites but less rearranged or conserved in the remaining lineages point to their exceptional diversification in mite orders; however, shared derived mitochondrial (mt) gene clusters were found within superfamilies rather than interorders, confusing phylogenetic signals in arachnid interordinal relationships. Molecular dating results show that arachnid orders have ancient origins, ranging from the Ordovician to the Carboniferous, yet have significantly diversified since the Cretaceous in orders Araneae, Mesostigmata, Sarcoptiformes, and Trombidiformes. By summarizing previously resolved key positions of some orders, we propose a plausible arachnid tree of life. Our results underline a more precise framework for interordinal phylogeny in the Arachnida and provide new insights into their ancient evolution.
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Affiliation(s)
- Xin-Chao Ban
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zi-Kai Shao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Li-Jun Wu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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2
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Duchêne DA, Mather N, Van Der Wal C, Ho SYW. Excluding loci with substitution saturation improves inferences from phylogenomic data. Syst Biol 2021; 71:676-689. [PMID: 34508605 PMCID: PMC9016599 DOI: 10.1093/sysbio/syab075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/07/2021] [Indexed: 11/21/2022] Open
Abstract
The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences. [Phylogenetic model performance; phylogenomics; substitution model; substitution saturation; test statistics.]
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Affiliation(s)
- David A Duchêne
- Centre for Evolutionary Hologenomics, University of Copenhagen, 1352 Copenhagen, Denmark
| | - Niklas Mather
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Cara Van Der Wal
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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3
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Vankan M, Ho SYW, Duchêne DA. Evolutionary Rate Variation Among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference. Syst Biol 2021; 71:490-500. [PMID: 34255084 PMCID: PMC8830059 DOI: 10.1093/sysbio/syab051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/18/2021] [Indexed: 11/12/2022] Open
Abstract
Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help to inform the choice of data for phylogenomic analysis. We investigated this in an analysis of 30 phylogenomic data sets. For each data set, we examined the association between several branch-length characteristics of gene trees and the distance between these gene trees and the corresponding species trees. We found that the distance of each gene tree to the species tree inferred from the full data set was positively associated with variation in root-to-tip distances and negatively associated with mean branch support. However, no such associations were found for gene-tree length, a measure of the overall substitution rate at each locus. We further explored the usefulness of the best-performing branch-based characteristics for selecting loci for phylogenomic analyses. We found that loci that yield gene trees with high variation in root-to-tip distances have a disproportionately distant signal of tree topology compared with the complete data sets. These results suggest that rate variation across lineages should be taken into consideration when exploring and even selecting loci for phylogenomic analysis.[Branch support; data filtering; nucleotide substitution model; phylogenomics; substitution rate; summary coalescent methods.]
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Affiliation(s)
- Mezzalina Vankan
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia.,Research School of Biology, Australian National University, ACT 2601, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - David A Duchêne
- Research School of Biology, Australian National University, ACT 2601, Australia.,Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen 1352, Denmark
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Chen S, Qing J, Liu Z, Liu Y, Tang M, Murphy RW, Pu Y, Wang X, Tang K, Guo K, Jiang X, Liu S. Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China. BMC Evol Biol 2020; 20:29. [PMID: 32059644 PMCID: PMC7023792 DOI: 10.1186/s12862-020-1588-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/27/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.
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Affiliation(s)
- Shunde Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jiao Qing
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157011, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Mingkun Tang
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Robert W Murphy
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, M5S 2C6, Canada
| | - Yingting Pu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Xuming Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Keji Guo
- Central South Forest Inventory and Planning Institute of State Forestry Administration, Changsha, 410014, China
| | - Xuelong Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China.
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Gatesy J, Sloan DB, Warren JM, Baker RH, Simmons MP, Springer MS. Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts. Mol Phylogenet Evol 2019; 139:106539. [DOI: 10.1016/j.ympev.2019.106539] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 06/10/2019] [Accepted: 06/17/2019] [Indexed: 12/26/2022]
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Benavides LR, Cosgrove JG, Harvey MS, Giribet G. Phylogenomic interrogation resolves the backbone of the Pseudoscorpiones tree of life. Mol Phylogenet Evol 2019; 139:106509. [DOI: 10.1016/j.ympev.2019.05.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 05/18/2019] [Accepted: 05/21/2019] [Indexed: 01/03/2023]
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Forthman M, Miller CW, Kimball RT. Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic. ZOOL SCR 2019. [DOI: 10.1111/zsc.12353] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Michael Forthman
- Entomology & Nematology Department University of Florida Gainesville Florida
| | - Christine W. Miller
- Entomology & Nematology Department University of Florida Gainesville Florida
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Aharon S, Ballesteros JA, Crawford AR, Friske K, Gainett G, Langford B, Santibáñez-López CE, Ya'aran S, Gavish-Regev E, Sharma PP. The anatomy of an unstable node: a Levantine relict precipitates phylogenomic dissolution of higher-level relationships of the armoured harvestmen (Arachnida: Opiliones: Laniatores). INVERTEBR SYST 2019. [DOI: 10.1071/is19002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
After tumultuous revisions to the family-level systematics of Laniatores (the armored harvestmen), the basally branching family Phalangodidae presently bears a disjunct and irregular distribution, attributed to the fragmentation of Pangea. One of the curious lineages assigned to Phalangodidae is the monotypic Israeli genus Haasus, the only Laniatores species that occurs in Israel, and whose presence in the Levant has been inferred to result from biogeographic connectivity with Eurasia. Recent surveys of Israeli caves have also yielded a new troglobitic morphospecies of Haasus. Here, we describe this new species as Haasus naasane sp. nov. So as to test the biogeographic affinity of Haasus, we sequenced DNA from both species and RNA from Haasus naasane sp. nov., to assess their phylogenetic placement. Our results showed that the new species is clearly closely related to Haasus judaeus, but Haasus itself is unambiguously nested within the largely Afrotropical family Pyramidopidae. In addition, the Japanese ‘phalangodid’ Proscotolemon sauteri was recovered as nested within the Southeast Asian family Petrobunidae. Phylogenomic placement of Haasus naasane sp. nov. in a 1550-locus matrix indicates that Pyramidopidae has an unstable position in the tree of Laniatores, with alternative partitioning of the matrix recovering high nodal support for mutually exclusive tree topologies. Exploration of phylogenetic signal showed the cause of this instability to be a considerable conflict between partitions, suggesting that the basal phylogeny of Laniatores may not yet be stable to addition of taxa. We transfer Haasus to Pyramidopidae (new familial assignment). Additionally, we transfer Proscotolemon to the family Petrobunidae (new familial assignment). Future studies on basal Laniatores phylogeny should emphasise the investigation of small-bodied and obscure groups that superficially resemble Phalangodidae.
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Fernández R, Sharma PP, Tourinho AL, Giribet G. The Opiliones tree of life: shedding light on harvestmen relationships through transcriptomics. Proc Biol Sci 2017; 284:20162340. [PMID: 28228511 PMCID: PMC5326524 DOI: 10.1098/rspb.2016.2340] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/27/2017] [Indexed: 12/12/2022] Open
Abstract
Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here, we analysed a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing approximately 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families and higher taxa are precisely placed. Our dating analyses using alternative calibration points, methods and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as an overview of the general biogeographic patterns of this ancient arthropod group.
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Affiliation(s)
- Rosa Fernández
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Prashant P Sharma
- Department of Zoology, University of Wisconsin-Madison, 352 Birge Hall, 430 Lincoln Drive, Madison, WI 53706, USA
| | - Ana Lúcia Tourinho
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade (CBIO), Avenida André Araújo, 2936, Aleixo, CEP 69011-970, Manaus, Amazonas, Brazil
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
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Sahoo RK, Warren AD, Wahlberg N, Brower AVZ, Lukhtanov VA, Kodandaramaiah U. Ten genes and two topologies: an exploration of higher relationships in skipper butterflies (Hesperiidae). PeerJ 2016; 4:e2653. [PMID: 27957386 PMCID: PMC5144725 DOI: 10.7717/peerj.2653] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/04/2016] [Indexed: 11/20/2022] Open
Abstract
Despite multiple attempts to infer the higher-level phylogenetic relationships of skipper butterflies (Family Hesperiidae), uncertainties in the deep clade relationships persist. The most recent phylogenetic analysis included fewer than 30% of known genera and data from three gene markers. Here we reconstruct the higher-level relationships with a rich sampling of ten nuclear and mitochondrial markers (7,726 bp) from 270 genera and find two distinct but equally plausible topologies among subfamilies at the base of the tree. In one set of analyses, the nuclear markers suggest two contrasting topologies, one of which is supported by the mitochondrial dataset. However, another set of analyses suggests mito-nuclear conflict as the reason for topological incongruence. Neither topology is strongly supported, and we conclude that there is insufficient phylogenetic evidence in the molecular dataset to resolve these relationships. Nevertheless, taking morphological characters into consideration, we suggest that one of the topologies is more likely.
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Affiliation(s)
- Ranjit Kumar Sahoo
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, India
| | - Andrew D. Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, UF Cultural Plaza, Gainesville, FL, USA
| | - Niklas Wahlberg
- Department of Biology, Lund University, Lund, Sweden
- Department of Biology, University of Turku, Turku, Finland
| | - Andrew V. Z. Brower
- Evolution and Ecology Group, Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Vladimir A. Lukhtanov
- Department of Insect Systematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia
| | - Ullasa Kodandaramaiah
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, India
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Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology Harvard University Cambridge MA 02138 USA
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