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Vences M, Anslan S, Sabino-Pinto J, Bonilla-Flores M, Echeverría-Galindo P, John U, Nass B, Pérez L, Preick M, Zhu L, Schwalb A. Dataset from RNAseq analysis of differential gene expression among developmental stages of two non-marine ostracodes. Data Brief 2024; 53:110070. [PMID: 38317728 PMCID: PMC10838692 DOI: 10.1016/j.dib.2024.110070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/12/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
We contribute transcriptomic data for two species of Ostracoda, an early-diverged group of small-sized pancrustaceans. Data include new reference transcriptomes for two asexual non-marine species (Dolerocypris sinensis and Heterocypris aff. salina), as well as single-specimen transcriptomic data that served to analyse gene expression across four developmental stages in D. sinensis. Data are evaluated by computing gene expression profiles of the different developmental stages which consistently placed eggs and small larvae (at the stage of instar A-8) similar to each other, and apart from adults which were distinct from all other developmental stages but closest to large larvae (instar A-4). We further evaluated the transcriptomic data with two newly sequenced low-coverage genomes of the target species. The new data thus document the feasibility of obtaining reliable transcriptomic data from single specimens - even eggs - of these small metazoans.
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Affiliation(s)
- Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Juhan Liivi 2, 50409 Tartu, Estonia
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Joana Sabino-Pinto
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Mauricio Bonilla-Flores
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Langer Kamp 19c, 38106 Braunschweig, Germany
| | - Paula Echeverría-Galindo
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Langer Kamp 19c, 38106 Braunschweig, Germany
| | - Uwe John
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Benneth Nass
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany
| | - Liseth Pérez
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Langer Kamp 19c, 38106 Braunschweig, Germany
| | - Michaela Preick
- Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Liping Zhu
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 16 Lincui Road, Beijing 100101, China
| | - Antje Schwalb
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Langer Kamp 19c, 38106 Braunschweig, Germany
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2
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Wang W, Dong Z, Du Z, Wu P. Genome-scale approach to reconstructing the phylogenetic tree of psyllids (superfamily Psylloidea) with account of systematic bias. Mol Phylogenet Evol 2023; 189:107924. [PMID: 37699449 DOI: 10.1016/j.ympev.2023.107924] [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: 05/17/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 09/14/2023]
Abstract
Psyllids (class Insecta: order Hemiptera: superfamily Psylloidea) are a taxonomically and phylogenetically challenging clade. Recent studies have largely advanced the phylogeny of this group, yet the family-level relationships among Aphalaridae, Carsidaridae, and others remain unresolved. Genome-scale phylogenetic analysis is known to provide a finer resolution for problems like that. However, such phylogenomics also introduces new problems: incorrect trees with high confidence yielded due to systematic error (bias). Here we addressed these issues using hundreds of single-copy orthologous (SCO) genes in psyllid transcriptomes and genomes. Our analyses revealed conflicts between the nucleotide-based and amino-acid-based phylogenetic trees. While the nucleotide-based phylogeny strongly supported the (Aphalaridae + Carsidaridae) + Others relationship, the amino-acid-based one recovered Aphalaridae + (Carsidaridae + Others) with 100% support. Further inspection revealed significant compositional heterogeneity in nucleotide sequences for 67% of SCO genes, but not in the corresponding translated amino acid sequences. We then used different strategies to combat this compositional bias, and found that using the RY-coding strategy (coding the standard nucleotides as purines and pyrimidines) the nucleotide-based phylogeny became consistent with the amino-acid-based one. We further applied RY-coding to a published concatenated nucleotide dataset and recovered the Aphalaridae monophyly (which is refuted by the original literature on non-recoded sequences) at the base of psyllid tree. Moreover, it was found that variations in evolutionary rate could lead to errors in nucleotide-based phylogeny. The fast-evolving Heteropsylla cubana (Psyllidae: Ciriacreminae) was incorrectly placed within the subfamily Psyllinae. This bias can be avoided by using data removal or RY-coding strategies. Together, our results strongly support the family relationship of Aphalaridae + (Carsidaridae + Others), and show that the amino-acid-based concatenation analysis is more robust than nucleotide-based one. Future phylogenomic analysis of psyllid nucleotide sequences should take into account methods such as the RY-coding scheme to address potential systematic biases arising from composition and rate heterogeneities.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zequn Dong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengxiang Wu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Bernot JP, Owen CL, Wolfe JM, Meland K, Olesen J, Crandall KA. Major Revisions in Pancrustacean Phylogeny and Evidence of Sensitivity to Taxon Sampling. Mol Biol Evol 2023; 40:msad175. [PMID: 37552897 PMCID: PMC10414812 DOI: 10.1093/molbev/msad175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 08/10/2023] Open
Abstract
The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group of animals on earth, containing over 80% of animal species and half of animal biomass. It has been the subject of several recent phylogenomic analyses, yet relationships within Pancrustacea show a notable lack of stability. Here, the phylogeny is estimated with expanded taxon sampling, particularly of malacostracans. We show small changes in taxon sampling have large impacts on phylogenetic estimation. By analyzing identical orthologs between two slightly different taxon sets, we show that the differences in the resulting topologies are due primarily to the effects of taxon sampling on the phylogenetic reconstruction method. We compare trees resulting from our phylogenomic analyses with those from the literature to explore the large tree space of pancrustacean phylogenetic hypotheses and find that statistical topology tests reject the previously published trees in favor of the maximum likelihood trees produced here. Our results reject several clades including Caridoida, Eucarida, Multicrustacea, Vericrustacea, and Syncarida. Notably, we find Copepoda nested within Allotriocarida with high support and recover a novel relationship between decapods, euphausiids, and syncarids that we refer to as the Syneucarida. With denser taxon sampling, we find Stomatopoda sister to this latter clade, which we collectively name Stomatocarida, dividing Malacostraca into three clades: Leptostraca, Peracarida, and Stomatocarida. A new Bayesian divergence time estimation is conducted using 13 vetted fossils. We review our results in the context of other pancrustacean phylogenetic hypotheses and highlight 15 key taxa to sample in future studies.
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Affiliation(s)
- James P Bernot
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Christopher L Owen
- Systematic Entomology Laboratory, USDA-ARS, ℅ National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kenneth Meland
- Department of Biology, University of Bergen, Bergen, Norway
| | - Jørgen Olesen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Keith A Crandall
- Department of Invertebrate Zoology, US National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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4
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Zwick P, Zwick A. Revision of the African Neoperla Needham, 1905 (Plecoptera: Perlidae: Perlinae) based on morphological and molecular data. Zootaxa 2023; 5316:1-194. [PMID: 37518401 DOI: 10.11646/zootaxa.5316.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Adults of the African species of the genus Neoperla Needham, 1905 (Plecoptera: Perlidae: Perlinae) are revised, and 82 valid species are recognised. Of the original 29 named species, 14 valid ones are redescribed from types, nine lectotypes are designated, and nine new synonymies are proposed. Sixty-two new species are named, and several additional new species only known from material insufficient for formal description are listed. There are one unavailable nomen nudum and three doubtful names. Diagnostic morphological traits of the recognised species are described and illustrated in detail where available of males, females, and eggs. Dichotomous keys to all species are provided. Mitochondrial DNA-data of 71 species-group taxa are available, which permits reliable association of sexes and minimises the risk of synonymies between species known from only one sex. Importantly, this includes DNA sequences from 50 holotypes. The DNA-data will also permit future monitoring with eDNA sequencing and identification of nymphs, which are probably important but so far unidentifiable bioindicators in streams. The genus Neoperla occurs largely in the northern hemisphere and in Africa, where it is restricted to the Ethiopian region south of the Sahara but unknown from Madagascar. A single specimen not clearly distinct from a widespread mainland species was taken on Comoro Island. All African species are endemic, but one African species group has a few outlying members in Asia. The Asian N. montivaga-group is not known from Africa. The following new species are described and named: N. aethiopica n. sp., N. amoena n. sp., N. angolana n. sp., N. bareensis n. sp., N. bella n. sp., N. benti n. sp., N. beta n. sp., N. bipolaris n. sp., N. biserrata n. sp., N. brachyphallus n. sp., N. caeleps n. sp., N. cataractae n. sp., N. claviger n. sp., N. coffea n. sp., N. costata n. sp., N. crenulata n. sp., N. crustata n. sp., N. decorata n. sp., N. dianae n. sp., N. dolium n. sp., N. dundoana n. sp., N. duodeviginti n. sp., N. erinaceus n. sp., N. excavata n. sp., N. filamentosa n. sp., N. funiculata n. sp., N. gibbosa n. sp., N. gordius n. sp., N. heideae n. sp., N. ivanloebli n. sp., N. juxtadidita n. sp., N. kalengonis n. sp., N. larvata n. sp., N. lineata n. sp., N. luhohonis n. sp., N. massevensis n. sp., N. multiserrata n. sp., N. muyukae n. sp., N. nichollsi n. sp., N. occulta n. sp., N. orthonema n. sp., N. pallidogigas n. sp., N. panafricana n. sp., N. pickeri n. sp., N. pilulifera n. sp., N. pirus n. sp., N. planidorsum n. sp., N. plicata n. sp., N. proxima n. sp., N. pusilla n. sp., N. rostrata n. sp., N. sambarua n. sp., N. sassandrae n. sp., N. schuelei n. sp., N. serrula n. sp., N. simplex n. sp., N. socia n. sp., N. sorella n. sp., N. spaghetti n. sp., N. spectabilis n. sp., N. spironema n. sp., N. tangana n. sp., N. tansanica n. sp., N. usambara n. sp., and N. vicina n. sp..
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Affiliation(s)
| | - Andreas Zwick
- Australian National Insect Collection; National Research Collections Australia; CSIRO; Canberra; ACT 2601; Australia.
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Wang T, Li TZ, Chen SS, Yang T, Shu JP, Mu YN, Wang KL, Chen JB, Xiang JY, Yan YH. Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:918155. [PMID: 36507421 PMCID: PMC9730426 DOI: 10.3389/fpls.2022.918155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/11/2022] [Indexed: 06/17/2023]
Abstract
Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.
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Affiliation(s)
- Ting Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ting-Zhang Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Si-Si Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Tuo Yang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jiang-Ping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Yu-Nong Mu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Kang-Lin Wang
- Green Development Institute, Southwest Forestry University, Kunming, China
| | - Jian-Bing Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jian-Ying Xiang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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6
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A Rearrangement of the Mitochondrial Genes of Centipedes (Arthropoda, Myriapoda) with a Phylogenetic Analysis. Genes (Basel) 2022; 13:genes13101787. [DOI: 10.3390/genes13101787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Due to the limitations of taxon sampling and differences in results from the available data, the phylogenetic relationships of the Myriapoda remain contentious. Therefore, we try to reconstruct and analyze the phylogenetic relationships within the Myriapoda by examining mitochondrial genomes (the mitogenome). In this study, typical circular mitogenomes of Mecistocephalus marmoratus and Scolopendra subspinipes were sequenced by Sanger sequencing; they were 15,279 bp and 14,637 bp in length, respectively, and a control region and 37 typical mitochondrial genes were annotated in the sequences. The results showed that all 13 PCGs started with ATN codons and ended with TAR codons or a single T; what is interesting is that the gene orders of M. marmoratus have been extensively rearranged compared with most Myriapoda. Thus, we propose a simple duplication/loss model to explain the extensively rearranged genes of M. marmoratus, hoping to provide insights into mitogenome rearrangement events in Myriapoda. In addition, our mitogenomic phylogenetic analyses showed that the main myriapod groups are monophyletic and supported the combination of the Pauropoda and Diplopoda to form the Dignatha. Within the Chilopoda, we suggest that Scutigeromorpha is a sister group to the Lithobiomorpha, Geophilomorpha, and Scolopendromorpha. We also identified a close relationship between the Lithobiomorpha and Geophilomorpha. The results also indicate that the mitogenome can be used as an effective mechanism to understand the phylogenetic relationships within Myriapoda.
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7
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlab125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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8
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Ballesteros JA, Hormiga G. Molecular phylogeny of the orb-weaving spider genus Leucauge and the intergeneric relationships of Leucauginae (Araneae, Tetragnathidae). INVERTEBR SYST 2021. [DOI: 10.1071/is21029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The tetragnathid genus Leucauge includes some of the most common orb-weaving spiders in the tropics. Although some species in this genus have attained relevance as model systems for several aspects of spider biology, our understanding of the generic diversity and evolutionary relationships among the species is poor. In this study we present the first attempt to determine the phylogenetic structure within Leucauge and the relationship of this genus with other genera of Leucauginae. This is based on DNA sequences from the five loci commonly used and Histone H4, used for the first time in spider phylogenetics. We also assess the informativeness of the standard markers and test for base composition biases in the dataset. Our results suggest that Leucauge is not monophyletic since species of the genera Opas, Opadometa, Mecynometa and Alcimosphenus are included within the current circumscription of the genus. Based on a phylogenetic re-circumscription of the genus to fulfil the requirement for monophyly of taxa, Leucauge White, 1841 is deemed to be a senior synonym of the genera Opas Pickard-Cambridge, 1896 revalidated synonymy, Mecynometa Simon, 1894 revalidated synonymy, Opadometa Archer, 1951 new synonymy and Alcimosphenus Simon, 1895 new synonymy. We identify groups of taxa critical for resolving relationships within Leucauginae and describe the limitations of the standard loci for accomplishing these resolutions.
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Szucsich NU, Bartel D, Blanke A, Böhm A, Donath A, Fukui M, Grove S, Liu S, Macek O, Machida R, Misof B, Nakagaki Y, Podsiadlowski L, Sekiya K, Tomizuka S, Von Reumont BM, Waterhouse RM, Walzl M, Meng G, Zhou X, Pass G, Meusemann K. Four myriapod relatives - but who are sisters? No end to debates on relationships among the four major myriapod subgroups. BMC Evol Biol 2020; 20:144. [PMID: 33148176 PMCID: PMC7640414 DOI: 10.1186/s12862-020-01699-0] [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: 05/16/2020] [Accepted: 09/30/2020] [Indexed: 11/20/2022] Open
Abstract
Background Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data. Results We generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda. Conclusions Our best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal.
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Affiliation(s)
- Nikolaus U Szucsich
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria. .,Central Research Laboratories, Natural History Museum of Vienna, A-1010, Vienna, Austria.
| | - Daniela Bartel
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Alexander Blanke
- Institute for Zoology, Biocenter, University of Cologne, D-50674, Cologne, Germany.,Institute of Evolutionary Biology and Animal Ecology, University of Bonn, D-53121, Bonn, Germany
| | - Alexander Böhm
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Alexander Donath
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Makiko Fukui
- Department of Biology, Graduate School of Science and Engineering, Ehime University, Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Simon Grove
- Invertebrate Zoology, Collections and Research Facility, Tasmanian Museum and Art Gallery, Rosny, Tasmania, 7018, Australia
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Oliver Macek
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria.,Central Research Laboratories, Natural History Museum of Vienna, A-1010, Vienna, Austria
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Yasutaka Nakagaki
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | - Lars Podsiadlowski
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Kaoru Sekiya
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda, Nagano, 386-2204, Japan
| | | | - Björn M Von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.,Animal Venomics, Institute for Insect Biotechnology, University of Giessen, Heinrich Buff Ring 26-32, D-35394, Giessen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Manfred Walzl
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Guanliang Meng
- Centre of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Günther Pass
- Department of Evolutionary Biology, University of Vienna, A-1090, Vienna, Austria
| | - Karen Meusemann
- Centre for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, D-53113, Bonn, Germany. .,Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), University of Freiburg, D-79104, Freiburg, Germany. .,Australian National Insect Collection, National Research Collections Australia, CSIRO, ACT, Canberra, 2601, Australia.
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10
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Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera). G3-GENES GENOMES GENETICS 2020; 10:3047-3060. [PMID: 32601059 PMCID: PMC7466995 DOI: 10.1534/g3.120.401028] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Measuring genome size across different species can yield important insights into evolution of the genome and allow for more informed decisions when designing next-generation genomic sequencing projects. New techniques for estimating genome size using shallow genomic sequence data have emerged which have the potential to augment our knowledge of genome sizes, yet these methods have only been used in a limited number of empirical studies. In this project, we compare estimation methods using next-generation sequencing (k-mer methods and average read depth of single-copy genes) to measurements from flow cytometry, a standard method for genome size measures, using ground beetles (Carabidae) and other members of the beetle suborder Adephaga as our test system. We also present a new protocol for using read-depth of single-copy genes to estimate genome size. Additionally, we report flow cytometry measurements for five previously unmeasured carabid species, as well as 21 new draft genomes and six new draft transcriptomes across eight species of adephagan beetles. No single sequence-based method performed well on all species, and all tended to underestimate the genome sizes, although only slightly in most samples. For one species, Bembidion sp. nr. transversale, most sequence-based methods yielded estimates half the size suggested by flow cytometry.
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Hu C, Wang S, Huang B, Liu H, Xu L, Zhigang Hu, Liu Y. The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes. Zookeys 2020; 925:73-88. [PMID: 32390741 PMCID: PMC7197263 DOI: 10.3897/zookeys.925.47820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Scolopendramutilans L. Koch, 1878 is an important Chinese animal with thousands of years of medicinal history. However, the genomic information of this species is limited, which hinders its further application. Here, the complete mitochondrial genome (mitogenome) of S.mutilans was sequenced and assembled by next-generation sequencing. The genome is 15,011 bp in length, consisting of 13 protein-coding genes (PCGs), 14 tRNA genes, and two rRNA genes. Most PCGs start with the ATN initiation codon, and all PCGs have the conventional stop codons TAA and TAG. The S.mutilans mitogenome revealed nine simple sequence repeats (SSRs), and an obviously lower GC content compared with other seven centipede mitogenomes previously sequenced. After analysis of homologous regions between the eight centipede mitogenomes, the S.mutilans mitogenome further showed clear genomic rearrangements. The phylogenetic analysis of eight centipedes using 13 conserved PCG genes was finally performed. The phylogenetic reconstructions showed Scutigeromorpha as a separate group, and Scolopendromorpha in a sister-group relationship with Lithobiomorpha and Geophilomorpha. Collectively, the S.mutilans mitogenome provided new genomic resources, which will improve its medicinal research and applications in the future.
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Affiliation(s)
| | | | | | | | | | - Zhigang Hu
- College of Pharmacy.,Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan, China
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Noah KE, Hao J, Li L, Sun X, Foley B, Yang Q, Xia X. Major Revisions in Arthropod Phylogeny Through Improved Supermatrix, With Support for Two Possible Waves of Land Invasion by Chelicerates. Evol Bioinform Online 2020; 16:1176934320903735. [PMID: 32076367 PMCID: PMC7003163 DOI: 10.1177/1176934320903735] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/02/2020] [Indexed: 01/04/2023] Open
Abstract
Deep phylogeny involving arthropod lineages is difficult to recover because the erosion of phylogenetic signals over time leads to unreliable multiple sequence alignment (MSA) and subsequent phylogenetic reconstruction. One way to alleviate the problem is to assemble a large number of gene sequences to compensate for the weakness in each individual gene. Such an approach has led to many robustly supported but contradictory phylogenies. A close examination shows that the supermatrix approach often suffers from two shortcomings. The first is that MSA is rarely checked for reliability and, as will be illustrated, can be poor. The second is that, to alleviate the problem of homoplasy at the third codon position of protein-coding genes due to convergent evolution of nucleotide frequencies, phylogeneticists may remove or degenerate the third codon position but may do it improperly and introduce new biases. We performed extensive reanalysis of one of such "big data" sets to highlight these two problems, and demonstrated the power and benefits of correcting or alleviating these problems. Our results support a new group with Xiphosura and Arachnopulmonata (Tetrapulmonata + Scorpiones) as sister taxa. This favors a new hypothesis in which the ancestor of Xiphosura and the extinct Eurypterida (sea scorpions, of which many later forms lived in brackish or freshwater) returned to the sea after the initial chelicerate invasion of land. Our phylogeny is supported even with the original data but processed with a new "principled" codon degeneration. We also show that removing the 1673 codon sites with both AGN and UCN codons (encoding serine) in our alignment can partially reconcile discrepancies between nucleotide-based and AA-based tree, partly because two sequences, one with AGN and the other with UCN, would be identical at the amino acid level but quite different at the nucleotide level.
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Affiliation(s)
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Luyan Li
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaoyan Sun
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Brian Foley
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Qun Yang
- Nanjing Institute of Geology and Paleontology, Chinese Academy of Sciences, Nanjing, China
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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Fu CN, Mo ZQ, Yang JB, Ge XJ, Li DZ, Xiang QY(J, Gao LM. Plastid phylogenomics and biogeographic analysis support a trans-Tethyan origin and rapid early radiation of Cornales in the Mid-Cretaceous. Mol Phylogenet Evol 2019; 140:106601. [DOI: 10.1016/j.ympev.2019.106601] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/17/2019] [Accepted: 08/20/2019] [Indexed: 12/14/2022]
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Parker E, Dornburg A, Domínguez-Domínguez O, Piller KR. Assessing phylogenetic information to reveal uncertainty in historical data: An example using Goodeinae (Teleostei: Cyprinodontiformes: Goodeidae). Mol Phylogenet Evol 2019; 134:282-290. [DOI: 10.1016/j.ympev.2019.01.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/17/2019] [Accepted: 01/30/2019] [Indexed: 01/18/2023]
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15
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Arthropod venoms: Biochemistry, ecology and evolution. Toxicon 2018; 158:84-103. [PMID: 30529476 DOI: 10.1016/j.toxicon.2018.11.433] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 12/17/2022]
Abstract
Comprising of over a million described species of highly diverse invertebrates, Arthropoda is amongst the most successful animal lineages to have colonized aerial, terrestrial, and aquatic domains. Venom, one of the many fascinating traits to have evolved in various members of this phylum, has underpinned their adaptation to diverse habitats. Over millions of years of evolution, arthropods have evolved ingenious ways of delivering venom in their targets for self-defence and predation. The morphological diversity of venom delivery apparatus in arthropods is astounding, and includes extensively modified pedipalps, tail (telson), mouth parts (hypostome), fangs, appendages (maxillulae), proboscis, ovipositor (stinger), and hair (urticating bristles). Recent investigations have also unravelled an astonishing venom biocomplexity with molecular scaffolds being recruited from a multitude of protein families. Venoms are a remarkable bioresource for discovering lead compounds in targeted therapeutics. Several components with prospective applications in the development of advanced lifesaving drugs and environment friendly bio-insecticides have been discovered from arthropod venoms. Despite these fascinating features, the composition, bioactivity, and molecular evolution of venom in several arthropod lineages remains largely understudied. This review highlights the prevalence of venom, its mode of toxic action, and the evolutionary dynamics of venom in Arthropoda, the most speciose phylum in the animal kingdom.
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Boudinot BE. A general theory of genital homologies for the Hexapoda (Pancrustacea) derived from skeletomuscular correspondences, with emphasis on the Endopterygota. ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:563-613. [PMID: 30419291 DOI: 10.1016/j.asd.2018.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 10/16/2018] [Accepted: 11/03/2018] [Indexed: 06/09/2023]
Abstract
No consensus exists for the homology and terminology of the male genitalia of the Hexapoda despite over a century of debate. Based on dissections and the literature, genital skeletomusculature was compared across the Hexapoda and contrasted with the Remipedia, the closest pancrustacean outgroup. The pattern of origin and insertion for extrinsic and intrinsic genitalic musculature was found to be consistent among the Ectognatha, Protura, and the Remipedia, allowing for the inference of homologies given recent phylogenomic studies. The penis of the Hexapoda is inferred to be derived from medially-fused primary gonopods (gonopore-bearing limbs), while the genitalia of the Ectognatha are inferred to include both the tenth-segmental penis and the ninth-segmental secondary gonopods, similar to the genitalia of female insects which comprise gonopods of the eighth and ninth segments. A new nomenclatural system for hexapodan genitalic musculature is presented and applied, and a general list of anatomical concepts is provided. Novel and refined homologies are proposed for all hexapodan orders, and a series of groundplans are postulated. Emphasis is placed on the Endopterygota, for which fine-grained transition series are hypothesized given observed skeletomuscular correspondences.
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Affiliation(s)
- Brendon E Boudinot
- Department of Entomology & Nematology, University of California, Davis, One Shields Ave., Davis, CA 95616, USA.
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Camp LE, Radke MR, Shihabi DM, Pagan C, Yang G, Nadler SA. Molecular phylogenetics and species-level systematics of Baylisascaris. INTERNATIONAL JOURNAL FOR PARASITOLOGY-PARASITES AND WILDLIFE 2018; 7:450-462. [PMID: 30568876 PMCID: PMC6275171 DOI: 10.1016/j.ijppaw.2018.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/16/2018] [Accepted: 09/30/2018] [Indexed: 02/07/2023]
Abstract
Nucleotide sequences representing nine genes and five presumptive genetic loci were used to infer phylogenetic relationships among seven Baylisascaris species, including one species with no previously available molecular data. These genes were used to test the species status of B. procyonis and B. columnaris using a coalescent approach. Phylogenetic analysis based on combined analysis of sequence data strongly supported monophyly of the genus and separated the species into two main clades. Clade 1 included B. procyonis, B. columnaris, and B. devosi, species hosted by musteloid carnivores. Clade 2 included B. transfuga and B. schroederi from ursids, B. ailuri, a species from the red panda (a musteloid), and B. tasmaniensis from a marsupial. Within clade 2, geographic isolates of B. transfuga, B. schroederi (from giant panda), and B. ailuri formed a strongly supported clade. In certain analyses (e.g., some single genes), B. tasmaniensis was sister to all other Baylisascaris species rather than sister to the species from ursids and red panda. Using one combination of priors corresponding to moderate population size and shallow genetic divergence, the multispecies coalescent analysis of B. procyonis and B. columnaris yielded moderate support (posterior probability 0.91) for these taxa as separate species. However, other prior combinations yielded weak or no support for delimiting these taxa as separate species. Similarly, tree topologies constrained to represent reciprocal monophyly of B. columnaris and B. procyonis individuals (topologies consistent with separate species) were significantly worse in some cases, but not others, depending on the dataset analyzed. An expanded analysis of SNPs and other genetic markers that were previously suggested to distinguish between individuals of B. procyonis and B. columnaris was made by characterization of additional individual nematodes. The results suggest that many of these SNPs do not represent fixed differences between nematodes derived from raccoon and skunk hosts. A phylogenetic hypothesis for Baylisascaris species was produced using nine genes. Genetic data was generated for two new species- B. devosi and B. tasmaniensis. Baylisascaris devosi and B. tasmaniensis were part of a monophyletic Baylisascaris. B. procyonis (raccoon) and B. columnaris (skunk) could not be reliably distinguished. Established SNPs may not be diagnostic for Baylisascaris from raccoons and skunks.
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Affiliation(s)
- Lauren E. Camp
- Department of Entomology and Nematology, University of California, One Shields Avenue, Davis, CA 95616, USA
- Corresponding author.
| | - Marc R. Radke
- Department of Entomology and Nematology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Danny M. Shihabi
- Department of Entomology and Nematology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Christopher Pagan
- Department of Entomology and Nematology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Steven A. Nadler
- Department of Entomology and Nematology, University of California, One Shields Avenue, Davis, CA 95616, USA
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Mclean BS, Bell KC, Allen JM, Helgen KM, Cook JA. Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini). Syst Biol 2018; 68:298-316. [DOI: 10.1093/sysbio/syy064] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/12/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Bryan S Mclean
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
- Department of Invertebrate Zoology, Smithsonian Institution National Museum of Natural History, P.O. Box 37012, MRC 163, Washington, DC 20013-7012, USA
| | - Julie M Allen
- Department of Biology, University of Nevada, 1664 N. Virginia Street, Reno, NV 89557, USA
| | - Kristofer M Helgen
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, 1 University of New Mexico, MSC03-2020, Albuquerque, NM 87131, USA
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Torres-Gutierrez C, de Oliveira TMP, Emerson KJ, Sterlino Bergo E, Mureb Sallum MA. Molecular phylogeny of Culex subgenus Melanoconion (Diptera: Culicidae) based on nuclear and mitochondrial protein-coding genes. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171900. [PMID: 29892381 PMCID: PMC5990733 DOI: 10.1098/rsos.171900] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
The subgenus Melanoconion of the mosquito genus Culex is taxonomically diverse and is widely distributed in the Neotropical Region, with 10 species occurring in the Nearctic Region. Species of this subgenus pose a taxonomical challenge because morphological identification is based largely on anatomical characters of the male genitalia. We addressed the monophyly of the Spissipes and Melanoconion Sections of the subgenus Melanoconion and some of the informal groups in each section. Our sample taxa included 97 specimens representing 43 species, from which we analysed fragments of two single-copy nuclear genes (CAD, HB) and one mitochondrial gene (COI). Phylogenetic relationships within the subgenus are presented based on results of maximum-likelihood and Bayesian analyses using a multi-locus matrix of DNA sequences. We show a molecular phylogeny of Melanoconion in which both sections were recovered as monophyletic groups. The monophyly of the Atratus and Pilosus groups was confirmed. Within each section, other monophyletic groups were recovered highlighting the potential need for future nomenclature rearrangement. The phylogenetic signal contained in nuclear genes, when analysed together, was more informative than each gene analysed separately, corroborating monophyly of Melanoconion relative to Culex (Culex) species included in the analyses, the Melanoconion and Spissipes Sections and some species groups. Our results provide new information for the classification of the subgenus and additional data that can be used to improve species identification when a more representative taxon sampling is available.
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Affiliation(s)
- Carolina Torres-Gutierrez
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Avenida Doutor Arnaldo 715, CEP 01246-904, São Paulo, Brazil
- Research Associate, Programa de Estudio y Control de Enfermedades Tropicales, PECET, Facultad de Medicina, Universidad de Antioquia. Calle 67 No. 53-108, Medellin, Colombia
| | - Tatiane M. P. de Oliveira
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Avenida Doutor Arnaldo 715, CEP 01246-904, São Paulo, Brazil
| | - Kevin J. Emerson
- Biology Department, St. Mary's College of Maryland, St. Mary's City, MD, USA
| | - Eduardo Sterlino Bergo
- Superintendência de Controle de Endemias, Secretaria de Estado da Saúde de São Paulo, Araraquara, São Paulo, Brazil
| | - Maria Anice Mureb Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, Avenida Doutor Arnaldo 715, CEP 01246-904, São Paulo, Brazil
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21
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Lin XL, Stur E, Ekrem T. Exploring species boundaries with multiple genetic loci using empirical data from non-biting midges. ZOOL SCR 2018. [DOI: 10.1111/zsc.12280] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Xiao-Long Lin
- Department of Natural History; NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
| | - Elisabeth Stur
- Department of Natural History; NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
| | - Torbjørn Ekrem
- Department of Natural History; NTNU University Museum; Norwegian University of Science and Technology; Trondheim Norway
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22
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Barrales-Alcalá D, Francke OF, Prendini L. Systematic Revision of the Giant Vinegaroons of theMastigoproctus giganteusComplex (Thelyphonida: Thelyphonidae) of North America. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2018. [DOI: 10.1206/0003-0090-418.1.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Diego Barrales-Alcalá
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México; Colección Nacional de Arácnidos, Departamento de Zoologia, Instituto de Biología, Universidad Nacional Autónoma de México
| | - Oscar F. Francke
- Colección Nacional de Arácnidos, Departamento de Zoologia, Instituto de Biología, Universidad Nacional Autónoma de México
| | - Lorenzo Prendini
- Division of Invertebrate Zoology, American Museum of Natural History
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Klopfstein S, Massingham T, Goldman N. More on the Best Evolutionary Rate for Phylogenetic Analysis. Syst Biol 2018; 66:769-785. [PMID: 28595363 PMCID: PMC5790136 DOI: 10.1093/sysbio/syx051] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 05/24/2017] [Indexed: 11/13/2022] Open
Abstract
The accumulation of genome-scale molecular data sets for nonmodel taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data available, a number of studies that each used thousands of genes have reported conflicting results. The focus of phylogenomic projects must thus shift to more careful experimental design. Even though we still have a limited understanding of what are the best predictors of the phylogenetic informativeness of a gene, there is wide agreement that one key factor is its evolutionary rate; but there is no consensus as to whether the rates derived as optimal in various analytical, empirical, and simulation approaches have any general applicability. We here use simulations to infer optimal rates in a set of realistic phylogenetic scenarios with varying tree sizes, numbers of terminals, and tree shapes. Furthermore, we study the relationship between the optimal rate and rate variation among sites and among lineages. Finally, we examine how well the predictions made by a range of experimental design methods correlate with the observed performance in our simulations.We find that the optimal level of divergence is surprisingly robust to differences in taxon sampling and even to among-site and among-lineage rate variation as often encountered in empirical data sets. This finding encourages the use of methods that rely on a single optimal rate to predict a gene's utility. Focusing on correct recovery either of the most basal node in the phylogeny or of the entire topology, the optimal rate is about 0.45 substitutions from root to tip in average Yule trees and about 0.2 in difficult trees with short basal and long-apical branches, but all rates leading to divergence levels between about 0.1 and 0.5 perform reasonably well.Testing the performance of six methods that can be used to predict a gene's utility against our simulation results, we find that the probability of resolution, signal-noise analysis, and Fisher information are good predictors of phylogenetic informativeness, but they require specification of at least part of a model tree. Likelihood quartet mapping also shows very good performance but only requires sequence alignments and is thus applicable without making assumptions about the phylogeny. Despite them being the most commonly used methods for experimental design, geometric quartet mapping and the integration of phylogenetic informativeness curves perform rather poorly in our comparison. Instead of derived predictors of phylogenetic informativeness, we suggest that the number of sites in a gene that evolve at near-optimal rates (as inferred here) could be used directly to prioritize genes for phylogenetic inference. In combination with measures of model fit, especially with respect to compositional biases and among-site and among-lineage rate variation, such an approach has the potential to greatly improve marker choice and should be tested on empirical data.
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Affiliation(s)
- Seraina Klopfstein
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastr. 15, CH-3005 Bern, Switzerland.,University of Bern, Institute of Ecology and Evolution, Baltzerstr. 6, CH-3012 Bern, Switzerland
| | - Tim Massingham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK
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Wang YH, Wu HY, Rédei D, Xie Q, Chen Y, Chen PP, Dong ZE, Dang K, Damgaard J, Štys P, Wu YZ, Luo JY, Sun XY, Hartung V, Kuechler SM, Liu Y, Liu HX, Bu WJ. When did the ancestor of true bugs become stinky? Disentangling the phylogenomics of Hemiptera-Heteroptera. Cladistics 2017; 35:42-66. [DOI: 10.1111/cla.12232] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2017] [Indexed: 01/27/2023] Open
Affiliation(s)
- Yan-Hui Wang
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hao-Yang Wu
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Dávid Rédei
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Qiang Xie
- Department of Ecology and Evolution; College of Life Sciences; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- State Key Laboratory of Biocontrol; Sun Yat-sen University; 135 Xingangxi Road Guangzhou 510275 Guangdong China
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Yan Chen
- Chinese Academy of Inspection and Quarantine; No. A3, Gaobeidian Bei Lu Chaoyang District Beijing 100123 China
| | - Ping-Ping Chen
- Netherlands Centre of Biodiversity Naturalis; 2300 RA Leiden Netherlands
| | - Zhuo-Er Dong
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Kai Dang
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jakob Damgaard
- Natural History Museum of Denmark; Universitetsparken 15 2100 Copenhagen Ø Denmark
| | - Pavel Štys
- Department of Zoology; Faculty of Science; Charles University in Prague; Viničná 7 CZ-128 44 Praha 2 Czech Republic
| | - Yan-Zhuo Wu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Jiu-Yang Luo
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Xiao-Ya Sun
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Viktor Hartung
- Staatliches Museum für Naturkunde Karslruhe; Erbprinzenstrasse 13 76133 Karlsruhe Germany
- Museum für Naturkunde - Leibniz-Institute for Research on Evolution and Biodiversity; Invalidenstrasse 43 10115 Berlin Germany
| | - Stefan M. Kuechler
- Department of Animal Ecology II; University of Bayreuth; Universitaetsstrasse 30 95440 Bayreuth Germany
| | - Yang Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Hua-Xi Liu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
| | - Wen-Jun Bu
- Institute of Entomology; College of Life Sciences; Nankai University; 94 Weijin Road 300071 Tianjin China
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Sproul JS, Maddison DR. Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- John S Sproul
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
| | - David R Maddison
- Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
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Khodami S, McArthur JV, Blanco-Bercial L, Martinez Arbizu P. Molecular Phylogeny and Revision of Copepod Orders (Crustacea: Copepoda). Sci Rep 2017; 7:9164. [PMID: 28831035 PMCID: PMC5567239 DOI: 10.1038/s41598-017-06656-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 06/16/2017] [Indexed: 11/10/2022] Open
Abstract
For the first time, the phylogenetic relationships between representatives of all 10 copepod orders have been investigated using 28S and 18S rRNA, Histone H3 protein and COI mtDNA. The monophyly of Copepoda (including Platycopioida Fosshagen, 1985) is demonstrated for the first time using molecular data. Maxillopoda is rejected, as it is a polyphyletic group. The monophyly of the major subgroups of Copepoda, including Progymnoplea Lang, 1948 (=Platycopioida); Neocopepoda Huys and Boxshall, 1991; Gymnoplea Giesbrecht, 1892 (=Calanoida Sars, 1903); and Podoplea Giesbrecht, 1892, are supported in this study. Seven copepod orders are monophyletic, including Platycopioida, Calanoida, Misophrioida Gurney, 1933; Monstrilloida Sars, 1901; Siphonostomatoida Burmeister, 1834; Gelyelloida Huys, 1988; and Mormonilloida Boxshall, 1979. Misophrioida (=Propodoplea Lang, 1948) is the most basal Podoplean order. The order Cyclopoida Burmeister, 1835, is paraphyletic and now encompasses Poecilostomatoida Thorell, 1859, as a sister to the family Schminkepinellidae Martinez Arbizu, 2006. Within Harpacticoida Sars, 1903, both sections, Polyarthra Lang, 1948, and Oligoarthra Lang, 1948, are monophyletic, but not sister groups. The order Canuelloida is proposed while maintaining the order Harpacticoida s. str. (Oligoarthra). Cyclopoida, Harpacticoida and Cyclopinidae are redefined, while Canuelloida ordo. nov., Smirnovipinidae fam. nov. and Cyclopicinidae fam. nov are proposed as new taxa.
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Affiliation(s)
- Sahar Khodami
- Senckenberg am Meer, German Center for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany.
| | | | | | - Pedro Martinez Arbizu
- Senckenberg am Meer, German Center for Marine Biodiversity Research, Südstrand 44, 26382, Wilhelmshaven, Germany
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Escalona HE, Zwick A, Li HS, Li J, Wang X, Pang H, Hartley D, Jermiin LS, Nedvěd O, Misof B, Niehuis O, Ślipiński A, Tomaszewska W. Molecular phylogeny reveals food plasticity in the evolution of true ladybird beetles (Coleoptera: Coccinellidae: Coccinellini). BMC Evol Biol 2017. [PMID: 28651535 PMCID: PMC5485688 DOI: 10.1186/s12862-017-1002-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tribe Coccinellini is a group of relatively large ladybird beetles that exhibits remarkable morphological and biological diversity. Many species are aphidophagous, feeding as larvae and adults on aphids, but some species also feed on other hemipterous insects (i.e., heteropterans, psyllids, whiteflies), beetle and moth larvae, pollen, fungal spores, and even plant tissue. Several species are biological control agents or widespread invasive species (e.g., Harmonia axyridis (Pallas)). Despite the ecological importance of this tribe, relatively little is known about the phylogenetic relationships within it. The generic concepts within the tribe Coccinellini are unstable and do not reflect a natural classification, being largely based on regional revisions. This impedes the phylogenetic study of important traits of Coccinellidae at a global scale (e.g. the evolution of food preferences and biogeography). RESULTS We present the most comprehensive phylogenetic analysis of Coccinellini to date, based on three nuclear and one mitochondrial gene sequences of 38 taxa, which represent all major Coccinellini lineages. The phylogenetic reconstruction supports the monophyly of Coccinellini and its sister group relationship to Chilocorini. Within Coccinellini, three major clades were recovered that do not correspond to any previously recognised divisions, questioning the traditional differentiation between Halyziini, Discotomini, Tytthaspidini, and Singhikaliini. Ancestral state reconstructions of food preferences and morphological characters support the idea of aphidophagy being the ancestral state in Coccinellini. This indicates a transition from putative obligate scale feeders, as seen in the closely related Chilocorini, to more agile general predators. CONCLUSIONS Our results suggest that the classification of Coccinellini has been misled by convergence in morphological traits. The evolutionary history of Coccinellini has been very dynamic in respect to changes in host preferences, involving multiple independent host switches from different insect orders to fungal spores and plants tissues. General predation on ephemeral aphids might have created an opportunity to easily adapt to mixed or specialised diets (e.g. obligate mycophagy, herbivory, predation on various hemipteroids or larvae of leaf beetles (Chrysomelidae)). The generally long-lived adults of Coccinellini can consume pollen and floral nectars, thereby surviving periods of low prey frequency. This capacity might have played a central role in the diversification history of Coccinellini.
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Affiliation(s)
- Hermes E Escalona
- Centre for Molecular Biodiversity Research (ZMB), Museum Alexander Koenig, Adenauerallee, 53113, Bonn, Germany.,Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Hao-Sen Li
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institute, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jiahui Li
- College of Environment and Plant Protection, Hainan University, No. 58 Renmin Avenue, Haikou, 570228, China
| | - Xingmin Wang
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province, Guangzhou, China
| | - Hong Pang
- State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institute, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Diana Hartley
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Lars S Jermiin
- Centre for Biodiversity Analysis, Australian National University, ACT, Acton, 2601, Australia
| | - Oldřich Nedvěd
- Institute of Entomology, Biology Centre, Branišovská 31, -37005, České Budějovice, CZ, Czech Republic.,University of South Bohemia, Branišovská, 31, České Budějovice, Czech Republic
| | - Bernhard Misof
- Centre for Molecular Biodiversity Research (ZMB), Museum Alexander Koenig, Adenauerallee, 53113, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology) Albert Ludwig University of Freiburg, Hauptstr. 1, 79104, Freiburg, Germany
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Wioletta Tomaszewska
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warszawa, Poland.
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Sproul JS, Maddison DR. Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded
DNA. Mol Ecol Resour 2017; 17:1183-1201. [DOI: 10.1111/1755-0998.12660] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 11/28/2022]
Affiliation(s)
- John S. Sproul
- Department of Integrative Biology Oregon State University 3029 Cordley Hall Corvallis OR 97331 USA
| | - David R. Maddison
- Department of Integrative Biology Oregon State University 3029 Cordley Hall Corvallis OR 97331 USA
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Lopez-Osorio F, Pickett KM, Carpenter JM, Ballif BA, Agnarsson I. Phylogenomic analysis of yellowjackets and hornets (Hymenoptera: Vespidae, Vespinae). Mol Phylogenet Evol 2017; 107:10-15. [DOI: 10.1016/j.ympev.2016.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/24/2016] [Accepted: 10/10/2016] [Indexed: 11/28/2022]
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Dong Y, Zhu L, Bai Y, Ou Y, Wang C. Complete mitochondrial genomes of two flat-backed millipedes by next-generation sequencing (Diplopoda, Polydesmida). Zookeys 2017:1-20. [PMID: 28138271 PMCID: PMC5240118 DOI: 10.3897/zookeys.637.9909] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 11/17/2016] [Indexed: 11/30/2022] Open
Abstract
A lack of mitochondrial genome data from myriapods is hampering progress across genetic, systematic, phylogenetic and evolutionary studies. Here, the complete mitochondrial genomes of two millipedes, Asiomorphacoarctata Saussure, 1860 (Diplopoda: Polydesmida: Paradoxosomatidae) and Xystodesmus sp. (Diplopoda: Polydesmida: Xystodesmidae) were assembled with high coverage using Illumina sequencing data. The mitochondrial genomes of the two newly sequenced species are circular molecules of 15,644 bp and 15,791 bp, within which the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs and two ribosomal RNA genes could be identified. The mitochondrial genome of Asiomorphacoarctata is the first complete sequence in the family Paradoxosomatidae (Diplopoda: Polydesmida) and the gene order of the two flat-backed millipedes is novel among known myriapod mitochondrial genomes. Unique translocations have occurred, including inversion of one half of the two genomes with respect to other millipede genomes. Inversion of the entire side of a genome (trnF-nad5-trnH-nad4-nad4L, trnP, nad1-trnL2-trnL1-rrnL-trnV-rrnS, trnQ, trnC and trnY) could constitute a common event in the order Polydesmida. Last, our phylogenetic analyses recovered the monophyletic Progoneata, subphylum Myriapoda and four internal classes.
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Affiliation(s)
- Yan Dong
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Lixin Zhu
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Yu Bai
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Yongyue Ou
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
| | - Changbao Wang
- College of Biology and Food Engineering, Chuzhou University, Chuzhou 239000, China
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31
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Eyun SI. Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies. BMC Evol Biol 2017; 17:23. [PMID: 28103796 PMCID: PMC5244711 DOI: 10.1186/s12862-017-0883-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 01/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level. RESULTS This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of Copepoda among five other crustacean groups (Anostraca, Cladocera, Sessilia, Amphipoda, and Decapoda) using 24 nuclear protein-coding genes. Phylogenomics has confirmed the monophyly of Copepoda and Podoplea. However, this study reveals surprising differences with the majority of the copepod phylogenies and unexpected similarities with postembryonic characters and earlier proposed morphological phylogenies; More precisely, Cyclopoida is more closely related to Siphonostomatoida than to Harpacticoida which is likely the most basally-branching group of Podoplea. Divergence time estimation suggests that the origin of Harpacticoida can be traced back to the Devonian, corresponding well with recently discovered fossil evidence. Copepoda has a close affinity to the clade of Malacostraca and Thecostraca but not to Branchiopoda. This result supports the hypothesis of the newly proposed clades, Communostraca, Multicrustacea, and Allotriocarida but further challenges the validity of Hexanauplia and Vericrustacea. CONCLUSIONS The first phylogenomic study of Copepoda provides new insights into taxonomic relationships and represents a valuable resource that improves our understanding of copepod evolution and their wide range of ecological adaptations.
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Affiliation(s)
- Seong-Il Eyun
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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32
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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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33
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Shen XX, Salichos L, Rokas A. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference. Genome Biol Evol 2016; 8:2565-80. [PMID: 27492233 PMCID: PMC5010910 DOI: 10.1093/gbe/evw179] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2016] [Indexed: 12/13/2022] Open
Abstract
Molecular phylogenetic inference is inherently dependent on choices in both methodology and data. Many insightful studies have shown how choices in methodology, such as the model of sequence evolution or optimality criterion used, can strongly influence inference. In contrast, much less is known about the impact of choices in the properties of the data, typically genes, on phylogenetic inference. We investigated the relationships between 52 gene properties (24 sequence-based, 19 function-based, and 9 tree-based) with each other and with three measures of phylogenetic signal in two assembled data sets of 2,832 yeast and 2,002 mammalian genes. We found that most gene properties, such as evolutionary rate (measured through the percent average of pairwise identity across taxa) and total tree length, were highly correlated with each other. Similarly, several gene properties, such as gene alignment length, Guanine-Cytosine content, and the proportion of tree distance on internal branches divided by relative composition variability (treeness/RCV), were strongly correlated with phylogenetic signal. Analysis of partial correlations between gene properties and phylogenetic signal in which gene evolutionary rate and alignment length were simultaneously controlled, showed similar patterns of correlations, albeit weaker in strength. Examination of the relative importance of each gene property on phylogenetic signal identified gene alignment length, alongside with number of parsimony-informative sites and variable sites, as the most important predictors. Interestingly, the subsets of gene properties that optimally predicted phylogenetic signal differed considerably across our three phylogenetic measures and two data sets; however, gene alignment length and RCV were consistently included as predictors of all three phylogenetic measures in both yeasts and mammals. These results suggest that a handful of sequence-based gene properties are reliable predictors of phylogenetic signal and could be useful in guiding the choice of phylogenetic markers.
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Affiliation(s)
- Xing-Xing Shen
- Department of Biological Sciences, Vanderbilt University
| | - Leonidas Salichos
- Department of Biological Sciences, Vanderbilt University Department of Molecular Biophysics and Biochemistry, Yale University
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University
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34
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Fernández R, Edgecombe GD, Giribet G. Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction. Syst Biol 2016; 65:871-89. [PMID: 27162151 PMCID: PMC4997009 DOI: 10.1093/sysbio/syw041] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 04/28/2016] [Indexed: 11/14/2022] Open
Abstract
Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.
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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
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - 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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35
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Lozano-Fernandez J, Carton R, Tanner AR, Puttick MN, Blaxter M, Vinther J, Olesen J, Giribet G, Edgecombe GD, Pisani D. A molecular palaeobiological exploration of arthropod terrestrialization. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150133. [PMID: 27325830 PMCID: PMC4920334 DOI: 10.1098/rstb.2015.0133] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/29/2016] [Indexed: 12/28/2022] Open
Abstract
Understanding animal terrestrialization, the process through which animals colonized the land, is crucial to clarify extant biodiversity and biological adaptation. Arthropoda (insects, spiders, centipedes and their allies) represent the largest majority of terrestrial biodiversity. Here we implemented a molecular palaeobiological approach, merging molecular and fossil evidence, to elucidate the deepest history of the terrestrial arthropods. We focused on the three independent, Palaeozoic arthropod terrestrialization events (those of Myriapoda, Hexapoda and Arachnida) and showed that a marine route to the colonization of land is the most likely scenario. Molecular clock analyses confirmed an origin for the three terrestrial lineages bracketed between the Cambrian and the Silurian. While molecular divergence times for Arachnida are consistent with the fossil record, Myriapoda are inferred to have colonized land earlier, substantially predating trace or body fossil evidence. An estimated origin of myriapods by the Early Cambrian precedes the appearance of embryophytes and perhaps even terrestrial fungi, raising the possibility that terrestrialization had independent origins in crown-group myriapod lineages, consistent with morphological arguments for convergence in tracheal systems.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.
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Affiliation(s)
- Jesus Lozano-Fernandez
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Robert Carton
- Department of Biology, The National University of Ireland Maynooth, Maynooth, Kildare, Ireland
| | - Alastair R Tanner
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mark N Puttick
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3TF, UK
| | - Jakob Vinther
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jørgen Olesen
- Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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36
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Schön I, Martens K. Ostracod (Ostracoda, Crustacea) genomics - Promises and challenges. Mar Genomics 2016; 29:19-25. [PMID: 27020380 DOI: 10.1016/j.margen.2016.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 01/18/2023]
Abstract
Ostracods are well-suited model organisms for evolutionary research. Classic genetic techniques have mostly been used for phylogenetic studies on Ostracoda and were somewhat affected by the lack of large numbers of suitable markers. Genomic methods with their huge potential have so far rarely been applied to this group of crustaceans. We provide relevant examples of genomic studies on other organisms to propose future avenues of genomic ostracod research. At the same time, we suggest solutions to the potential problems in ostracods that the application of genomic techniques might present.
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Affiliation(s)
- Isa Schön
- Royal Belgian Institute of Natural Sciences, OD Nature, ATECO, Freshwater Biology, Vautierstraat 29, B-1000 Brussels, Belgium; University of Hasselt, Research Group Zoology, Agoralaan Building D, B-3590 Diepenbeek, Belgium.
| | - Koen Martens
- Royal Belgian Institute of Natural Sciences, OD Nature, ATECO, Freshwater Biology, Vautierstraat 29, B-1000 Brussels, Belgium; University of Ghent, Department of Biology, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
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37
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Yeates DK, Meusemann K, Trautwein M, Wiegmann B, Zwick A. Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution. CURRENT OPINION IN INSECT SCIENCE 2016; 13:16-23. [PMID: 27436549 DOI: 10.1016/j.cois.2015.10.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/08/2015] [Accepted: 10/18/2015] [Indexed: 06/06/2023]
Abstract
Our understanding on the phylogenetic relationships of insects has been revolutionised in the last decade by the proliferation of next generation sequencing technologies (NGS). NGS has allowed insect systematists to assemble very large molecular datasets that include both model and non-model organisms. Such datasets often include a large proportion of the total number of protein coding sequences available for phylogenetic comparison. We review some early entomological phylogenomic studies that employ a range of different data sampling protocols and analyses strategies, illustrating a fundamental renaissance in our understanding of insect evolution all driven by the genomic revolution. The analysis of phylogenomic datasets is challenging because of their size and complexity, and it is obvious that the increasing size alone does not ensure that phylogenetic signal overcomes systematic biases in the data. Biases can be due to various factors such as the method of data generation and assembly, or intrinsic biological feature of the data per se, such as similarities due to saturation or compositional heterogeneity. Such biases often cause violations in the underlying assumptions of phylogenetic models. We review some of the bioinformatics tools available and being developed to detect and minimise systematic biases in phylogenomic datasets. Phylogenomic-scale data coupled with sophisticated analyses will revolutionise our understanding of insect functional genomics. This will illuminate the relationship between the vast range of insect phenotypic diversity and underlying genetic diversity. In combination with rapidly developing methods to estimate divergence times, these analyses will also provide a compelling view of the rates and patterns of lineagenesis (birth of lineages) over the half billion years of insect evolution.
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Affiliation(s)
- David K Yeates
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia.
| | - Karen Meusemann
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
| | - Michelle Trautwein
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Brian Wiegmann
- Department of Entomology, North Carolina State University, Raleigh, NC 27695-7613, USA
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
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Zhang L, Wu W, Yan HF, Ge XJ. Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales. Evol Bioinform Online 2016; 11:81-91. [PMID: 26819541 PMCID: PMC4718149 DOI: 10.4137/ebo.s22448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 12/19/2022] Open
Abstract
Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Wu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Hai-Fei Yan
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing. PLoS One 2015; 10:e0143929. [PMID: 26716693 PMCID: PMC4696846 DOI: 10.1371/journal.pone.0143929] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 10/12/2015] [Indexed: 01/30/2023] Open
Abstract
In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.
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Richart CH, Hayashi CY, Hedin M. Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies. Mol Phylogenet Evol 2015; 95:171-82. [PMID: 26691642 DOI: 10.1016/j.ympev.2015.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/16/2015] [Accepted: 11/13/2015] [Indexed: 11/19/2022]
Abstract
Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea.
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Affiliation(s)
- Casey H Richart
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA; Department of Biology, University of California, Riverside, CA 92521, USA.
| | - Cheryl Y Hayashi
- Department of Biology, University of California, Riverside, CA 92521, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
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Gäde G, Marco HG. The decapod red pigment-concentrating hormone (Panbo-RPCH) is the first identified neuropeptide of the order Plecoptera and is interpreted as homoplastic character state. Gen Comp Endocrinol 2015; 221:228-35. [PMID: 25733206 DOI: 10.1016/j.ygcen.2015.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 02/07/2015] [Accepted: 02/14/2015] [Indexed: 11/16/2022]
Abstract
This paper presents the first neuropeptide structure, identified by mass spectrometry, in two species of Plectoptera (stoneflies) and in one species of the coleopteran family Lycidae. In all three species, the octapeptide Panbo-RPCH (first identified in Pandalus borealis as a red pigment-concentrating hormone: pGlu-Leu-Asn-Phe-Ser-Pro-Gly-Trp amide) is present. A review of the literature available on invertebrate neuropeptides that are identified or predicted from expressed sequence tags, transcriptome shotgun assemblies, and from fully sequenced genomes, show that Panbo-RPCH is found in Malacostraca (Crustacea) and certain hemipteran Heteroptera (Insecta). To date, Panbo-RPCH has not been shown present in non-Malacostracan crustaceans, nor in basal taxa of the Insecta (Archaeognatha, Zygentoma, Ephemeroptera, Odonata). The present data adds to knowledge on the distribution of Panbo-RPCH, and when taking into account the most accepted, current phylogenetics of the Crustacea-Hexapoda relationship, this distribution of Panbo-RPCH in Malacostraca, Plecoptera, some hemipteran Heteroptera and in Coleoptera (Lycidae) can best be explained by homoplasy, implying parallel evolution.
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Affiliation(s)
- Gerd Gäde
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa.
| | - Heather G Marco
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
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Olfactory pathway in Xibalbanus tulumensis: remipedian hemiellipsoid body as homologue of hexapod mushroom body. Cell Tissue Res 2015; 363:635-48. [PMID: 26358175 DOI: 10.1007/s00441-015-2275-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/04/2015] [Indexed: 01/01/2023]
Abstract
The Remipedia have been proposed to be the crustacean sister group of the Hexapoda. These blind cave animals heavily rely on their chemical sense and are thus rewarding subjects for the analysis of olfactory pathways. The evolution of these pathways as a character for arthropod phylogeny has recently received increasing attention. Here, we investigate the situation in Xibalbanus tulumensis by focal dye injections and immunolabelling of the catalytic subunit of the cAMP-dependent protein kinase (DC0), an enzyme particularly enriched in insect mushroom bodies. DC0 labelling of the hemiellipsoid body suggests its subdivision into a cap-like and a core neuropil. Immunofluorescence of the enzyme glutamic acid decarboxylase (GAD), which synthesizes γ-aminobutyric acid (GABA), has revealed a cluster of GABAergic interneurons in the hemiellipsoid body, reminiscent of the characteristic feedback neurons of the mushroom body. Thus, the hemiellipsoid body of Xibalbanus shares many of the characteristics of insect mushroom bodies. Nevertheless, the general neuroanatomy of the olfactory pathway in the Remipedia strongly corresponds to the malacostracan ground pattern. Given that the Remipedia are probably the sister group of the Hexapoda, the phylogenetic appearance of the typical neuropilar compartments in the insect mushroom body has to be assigned to the origins of the Hexapoda.
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Chen MY, Liang D, Zhang P. Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny. Syst Biol 2015; 64:1104-20. [PMID: 26276158 DOI: 10.1093/sysbio/syv059] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 08/10/2015] [Indexed: 11/13/2022] Open
Abstract
Incongruence between different phylogenomic analyses is the main challenge faced by phylogeneticists in the genomic era. To reduce incongruence, phylogenomic studies normally adopt some data filtering approaches, such as reducing missing data or using slowly evolving genes, to improve the signal quality of data. Here, we assembled a phylogenomic data set of 58 jawed vertebrate taxa and 4682 genes to investigate the backbone phylogeny of jawed vertebrates under both concatenation and coalescent-based frameworks. To evaluate the efficiency of extracting phylogenetic signals among different data filtering methods, we chose six highly intractable internodes within the backbone phylogeny of jawed vertebrates as our test questions. We found that our phylogenomic data set exhibits substantial conflicting signal among genes for these questions. Our analyses showed that non-specific data sets that are generated without bias toward specific questions are not sufficient to produce consistent results when there are several difficult nodes within a phylogeny. Moreover, phylogenetic accuracy based on non-specific data is considerably influenced by the size of data and the choice of tree inference methods. To address such incongruences, we selected genes that resolve a given internode but not the entire phylogeny. Notably, not only can this strategy yield correct relationships for the question, but it also reduces inconsistency associated with data sizes and inference methods. Our study highlights the importance of gene selection in phylogenomic analyses, suggesting that simply using a large amount of data cannot guarantee correct results. Constructing question-specific data sets may be more powerful for resolving problematic nodes.
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Affiliation(s)
- Meng-Yun Chen
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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Saadaoui M, Litim-Mecheri I, Macchi M, Graba Y, Maurel-Zaffran C. A survey of conservation of sea spider and Drosophila Hox protein activities. Mech Dev 2015; 138 Pt 2:73-86. [PMID: 26238019 DOI: 10.1016/j.mod.2015.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/24/2015] [Accepted: 07/25/2015] [Indexed: 01/29/2023]
Abstract
Hox proteins have well-established functions in development and evolution, controlling the final morphology of bilaterian animals. The common phylogenetic origin of Hox proteins and the associated evolutionary diversification of protein sequences provide a unique framework to explore the relationship between changes in protein sequence and function. In this study, we aimed at questioning how sequence variation within arthropod Hox proteins influences function. This was achieved by exploring the functional impact of sequence conservation/divergence of the Hox genes, labial, Sex comb reduced, Deformed, Ultrabithorax and abdominalA from two distant arthropods, the sea spider and the well-studied Drosophila. Results highlight a correlation between sequence conservation within the homeodomain and the degree of functional conservation, and identify a novel functional domain in the Labial protein.
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Affiliation(s)
- Mehdi Saadaoui
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France; Institut de Biologie de l'ENS, 46, rue d'Ulm, 75005 Paris, France
| | - Isma Litim-Mecheri
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France; IGBMC, INSERM U964, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Meiggie Macchi
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
| | - Yacine Graba
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
| | - Corinne Maurel-Zaffran
- Aix Marseille Université, CNRS, IBDM, UMR 7288, Campus de Luminy, Marseille, cedex 09 13288, France
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Eytan RI, Evans BR, Dornburg A, Lemmon AR, Lemmon EM, Wainwright PC, Near TJ. Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment. BMC Evol Biol 2015; 15:113. [PMID: 26071950 PMCID: PMC4465735 DOI: 10.1186/s12862-015-0415-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 06/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be. RESULTS After using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree. CONCLUSIONS Although it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.
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Affiliation(s)
- Ron I Eytan
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, 77553, TX, USA.
| | - Benjamin R Evans
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
| | - Alex Dornburg
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, 32306, FL, USA.
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, 32306, FL, USA.
| | - Peter C Wainwright
- Department of Evolution & Ecology, University of California, One Shields Avenue, Davis, 95616, CA, USA.
| | - Thomas J Near
- Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, 06520, CT, USA.
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Cabrera AR, Shirk PD, Evans JD, Hung K, Sims J, Alborn H, Teal PEA. Three Halloween genes from the Varroa mite, Varroa destructor (Anderson & Trueman) and their expression during reproduction. INSECT MOLECULAR BIOLOGY 2015; 24:277-92. [PMID: 25488435 DOI: 10.1111/imb.12155] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The ecdysteroid biosynthetic pathway involves sequential enzymatic hydroxylations by a group of enzymes collectively known as Halloween gene proteins. Complete sequences for three Halloween genes, spook (Vdspo), disembodied (Vddib) and shade (Vdshd), were identified in varroa mites and sequenced. Phylogenetic analyses of predicted amino acid sequences for Halloween orthologues showed that the acarine orthologues were distantly associated with insect and crustacean clades indicating that acarine genes had more ancestral characters. The lack of orthologues or pseudogenes for remaining genes suggests these pathway elements had not evolved in ancestral arthropods. Vdspo transcript levels were highest in gut tissues, while Vddib transcript levels were highest in ovary-lyrate organs. In contrast, Vdshd transcript levels were lower overall but present in both gut and ovary-lyrate organs. All three transcripts were present in eggs removed from gravid female mites. A brood cell invasion assay was developed for acquiring synchronously staged mites. Mites within 4 h of entering a brood cell had transcript levels of all three that were not significantly different from mites on adult bees. These analyses suggest that varroa mites may be capable of modifying 7-dehydro-cholesterol precursor and hydroxylations of other steroid precursors, but whether the mites directly produce ecdysteroid precursors and products remains undetermined.
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Affiliation(s)
- A R Cabrera
- Entomology and Nematology Department, University of Florida, Gainesville, FL, 32611, USA
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Whelan NV, Kocot KM, Halanych KM. Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians. Integr Comp Biol 2015; 55:1084-95. [PMID: 25972566 DOI: 10.1093/icb/icv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite an explosion in the amount of sequence data, phylogenomics has failed to settle controversy regarding some critical nodes on the animal tree of life. Understanding relationships among Bilateria, Ctenophora, Cnidaria, Placozoa, and Porifera is essential for studying how complex traits such as neurons, muscles, and gastrulation have evolved. Recent studies have cast doubt on the historical viewpoint that sponges are sister to all other animal lineages with recent studies recovering ctenophores as sister. However, the ctenophore-sister hypothesis has been criticized as unrealistic and caused by systematic error. We review past phylogenomic studies and potential causes of systematic error in an effort to identify areas that can be improved in future studies. Increased sampling of taxa, less missing data, and a priori removal of sequences and taxa that may cause systematic error in phylogenomic inference will likely be the most fruitful areas of focus when assembling future datasets. Ultimately, we foresee metazoan relationships being resolved with higher support in the near future, and we caution against dismissing novel hypotheses merely because they conflict with historical viewpoints of animal evolution.
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Affiliation(s)
- Nathan V Whelan
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA;
| | - Kevin M Kocot
- School of Biological Sciences, The University of Queensland, 325 Goddard Building, St Lucia, QLD 4101, Australia
| | - Kenneth M Halanych
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
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Say goodbye to tribes in the new house fly classification: A new molecular phylogenetic analysis and an updated biogeographical narrative for the Muscidae (Diptera). Mol Phylogenet Evol 2015; 89:1-12. [PMID: 25869937 DOI: 10.1016/j.ympev.2015.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/02/2015] [Accepted: 04/07/2015] [Indexed: 02/03/2023]
Abstract
House flies are one of the best known groups of flies and comprise about 5000 species worldwide. Despite over a century of intensive taxonomic research on these flies, classification of the Muscidae is still poorly resolved. Here we brought together the most diverse molecular dataset ever examined for the Muscidae, with 142 species in 67 genera representing all tribes and all biogeographic regions. Four protein coding genes were analyzed: mitochondrial CO1 and nuclear AATS, CAD (region 4) and EF1-α. Maximum likelihood and Bayesian approaches were used to analyze five different partitioning schemes for the alignment. We also used Bayes factors to test monophyly of the traditionally accepted tribes and subfamilies. Most subfamilial taxa were not recovered in our analyses, and accordingly monophyly was rejected by Bayes factor tests. Our analysis consistently found three main clades of Muscidae and so we propose a new classification with only three subfamilies without tribes. Additionally, we provide the first timeframe for the diversification of all major lineages of house flies and examine contemporary biogeographic hypotheses in light of this timeframe. We conclude that the muscid radiation began in the Paleocene to Eocene and is congruent with the final stages of the breakup of Gondwana, which resulted in the complete separation of Antarctica, Australia, and South America. With this newly proposed classification and better understanding of the timing of evolutionary events, we provide new perspectives for integrating morphological and ecological evolutionary understanding of house flies, their taxonomy, phylogeny, and biogeography.
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Winkler IS, Blaschke JD, Davis DJ, Stireman JO, O'Hara JE, Cerretti P, Moulton JK. Explosive radiation or uninformative genes? Origin and early diversification of tachinid flies (Diptera: Tachinidae). Mol Phylogenet Evol 2015; 88:38-54. [PMID: 25841383 DOI: 10.1016/j.ympev.2015.03.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 12/01/2022]
Abstract
Molecular phylogenetic studies at all taxonomic levels often infer rapid radiation events based on short, poorly resolved internodes. While such rapid episodes of diversification are an important and widespread evolutionary phenomenon, much of this poor phylogenetic resolution may be attributed to the continuing widespread use of "traditional" markers (mitochondrial, ribosomal, and some nuclear protein-coding genes) that are often poorly suited to resolve difficult, higher-level phylogenetic problems. Here we reconstruct phylogenetic relationships among a representative set of taxa of the parasitoid fly family Tachinidae and related outgroups of the superfamily Oestroidea. The Tachinidae are one of the most species rich, yet evolutionarily recent families of Diptera, providing an ideal case study for examining the differential performance of loci in resolving phylogenetic relationships and the benefits of adding more loci to phylogenetic analyses. We assess the phylogenetic utility of nine genes including both traditional genes (e.g., CO1 mtDNA, 28S rDNA) and nuclear protein-coding genes newly developed for phylogenetic analysis. Our phylogenetic findings, based on a limited set of taxa, include: a close relationship between Tachinidae and the calliphorid subfamily Polleninae, monophyly of Tachinidae and the subfamilies Exoristinae and Dexiinae, subfamily groupings of Dexiinae+Phasiinae and Tachininae+Exoristinae, and robust phylogenetic placement of the somewhat enigmatic genera Strongygaster, Euthera, and Ceracia. In contrast to poor resolution and phylogenetic incongruence of "traditional genes," we find that a more selective set of highly informative genes is able to more precisely identify regions of the phylogeny that experienced rapid radiation of lineages, while more accurately depicting their phylogenetic context. Although much expanded taxon sampling is necessary to effectively assess the monophyly of and relationships among major tachinid lineages and their relatives, we show that a small number of well-chosen nuclear protein-coding genes can successfully resolve even difficult phylogenetic problems.
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Affiliation(s)
- Isaac S Winkler
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA; Department of Biology, Linfield College, McMinnville, OR 97128, USA
| | - Jeremy D Blaschke
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniel J Davis
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA
| | - John O Stireman
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
| | - James E O'Hara
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Pierfilippo Cerretti
- DAFNAE-Entomology, Università degli Studi di Padova, Viale dell'Università 16, 35020 Legnaro (Padova), Italy; Dipartimento di Biologia e Biotecnologie 'Charles Darwin', 'Sapienza' Università di Roma, Piazzale A. Moro 5, 00185 Rome, Italy
| | - John K Moulton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
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Robertson HE, Lapraz F, Rhodes AC, Telford MJ. The complete mitochondrial genome of the geophilomorph centipede Strigamia maritima. PLoS One 2015; 10:e0121369. [PMID: 25794168 PMCID: PMC4368715 DOI: 10.1371/journal.pone.0121369] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/31/2015] [Indexed: 12/05/2022] Open
Abstract
Strigamia maritima (Myriapoda; Chilopoda) is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of Strigamia maritima that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of Strigamia, the first from any geophilomorph centipede. The mitochondrial genome of S. maritima is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard ‘cloverleaf’ secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of S. maritima and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: Strigamia was resolved as the sister group of the scolopendromorph Scolopocryptos sp. and these two (Geophilomorpha and Scolopendromorpha), along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the S. maritima mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of Strigamia maritima is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or results from a more recent reorganisation in the lineage leading to Strigamia.
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Affiliation(s)
- Helen E. Robertson
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, United Kingdom
| | - François Lapraz
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, United Kingdom
| | - Adelaide C. Rhodes
- Center for Genome Research and Biocomputing, 2750 SW Campus Way, Oregon State University, Corvallis, Oregon, United States of America
| | - Maximilian J. Telford
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, United Kingdom
- * E-mail:
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