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Weinell JL, Burbrink FT, Das S, Brown RM. Novel phylogenomic inference and 'Out of Asia' biogeography of cobras, coral snakes and their allies. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240064. [PMID: 39113776 PMCID: PMC11303032 DOI: 10.1098/rsos.240064] [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: 01/11/2024] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 08/10/2024]
Abstract
Estimation of evolutionary relationships among lineages that rapidly diversified can be challenging, and, in such instances, inaccurate or unresolved phylogenetic estimates can lead to erroneous conclusions regarding historical geographical ranges of lineages. One example underscoring this issue has been the historical challenge posed by untangling the biogeographic origin of elapoid snakes, which includes numerous dangerously venomous species as well as species not known to be dangerous to humans. The worldwide distribution of this lineage makes it an ideal group for testing hypotheses related to historical faunal exchanges among the many continents and other landmasses occupied by contemporary elapoid species. We developed a novel suite of genomic resources, included worldwide sampling, and inferred a robust estimate of evolutionary relationships, which we leveraged to quantitatively estimate geographical range evolution through the deep-time history of this remarkable radiation. Our phylogenetic and biogeographical estimates of historical ranges definitively reject a lingering former 'Out of Africa' hypothesis and support an 'Out of Asia' scenario involving multiple faunal exchanges between Asia, Africa, Australasia, the Americas and Europe.
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Affiliation(s)
- Jeffrey L. Weinell
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd, Lawrence, KS66045, USA
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY10024, USA
| | - Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY10024, USA
| | - Sunandan Das
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki00014, Finland
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd, Lawrence, KS66045, USA
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2
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Yan Y, da Fonseca RR, Rahbek C, Borregaard MK, Davis CC. A new nuclear phylogeny of the tea family (Theaceae) unravels rapid radiations in genus Camellia. Mol Phylogenet Evol 2024; 196:108089. [PMID: 38679302 DOI: 10.1016/j.ympev.2024.108089] [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: 04/23/2023] [Revised: 03/08/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Molecular analyses of rapidly radiating groups often reveal incongruence between gene trees. This mainly results from incomplete lineage sorting, introgression, and gene tree estimation error, which complicate the estimation of phylogenetic relationships. In this study, we reconstruct the phylogeny of Theaceae using 348 nuclear loci from 68 individuals and two outgroup taxa. Sequence data were obtained by target enrichment using the recently released Angiosperm 353 universal probe set applied to herbarium specimens. The robustness of the topologies to variation in data quality was established under a range of different filtering schemes, using both coalescent and concatenation approaches. Our results confirmed most of the previously hypothesized relationships among tribes and genera, while clarifying additional interspecific relationships within the rapidly radiating genus Camellia. We recovered a remarkably high degree of gene tree heterogeneity indicative of rapid radiation in the group and observed cytonuclear conflicts, especially within Camellia. This was especially pronounced around short branches, which we primarily associate with gene tree estimation error. Our analysis also indicates that incomplete lineage sorting (ILS) contributed to gene-tree conflicts and accounted for approximately 14 % of the explained variation, whereas inferred introgression levels were low. Our study advances the understanding of the evolution of this important plant family and provides guidance on the application of target capture methods and the evaluation of key processes that influence phylogenetic discordances.
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Affiliation(s)
- Yujing Yan
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA.
| | - Rute R da Fonseca
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Center for Global Mountain Biodiversity, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark; Department of Life Sciences, Imperial College London, Silkwood Park campus, Ascot SL5 7PY, UK; Danish Institute for Advanced Study, University of Southern Denmark, 5230 Odense M, Denmark
| | - Michael K Borregaard
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Ave, Cambridge, MA 02138, USA
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Guo ZQ, Gao YJ, Chen YX, Zhan LM, Storey KB, Yu DN, Zhang JY. Comparative Mitogenome of Phylogenetic Relationships and Divergence Time Analysis within Potamanthidae (Insecta: Ephemeroptera). INSECTS 2024; 15:357. [PMID: 38786913 PMCID: PMC11122660 DOI: 10.3390/insects15050357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Potamanthidae belongs to the superfamily Ephemeroidea but has no complete mt genome released in the NCBI (except for two unchecked and one partial mt genome). Since the sister clade to Potamanthidae has always been controversial, we sequenced seven mt genomes of Potamanthidae (two species from Rhoenanthus and five species from Potamanthus) in order to rebuild the phylogenetic relationships of Potamanthidae in this study. The divergence time of Potamanthidae was also investigated by utilizing five fossil calibration points because of the indeterminate origin time. In addition, because Rhoenanthus coreanus and Potamanthus luteus are always in low-temperature environments, we aimed to explore whether these two species were under positive selection at the mt genome level. Amongst the 13 PCGs, CGA was used as the start codon in COX1, whereas other genes conformed to initiating with an ATN start codon. From this analysis, UUA (L), AUU (I), and UUU (F) had the highest usage. Furthermore, the DHU arm was absent in the secondary structure of S1 in all species. By combining the 13 PCGs and 2 rRNAs, we reconstructed the phylogenetic relationship of Potamanthidae within Ephemeroptera. The monophyly of Potamanthidae and the monophyly of Rhoenanthus and Potamanthus were supported in the results. The phylogenetic relationship of Potamanthidae + (Ephemeridae + Polymitarcyidae) was also recovered with a high prior probability. The divergence times of Potamanthidae were traced to be 90.44 Mya (95% HPD, 62.80-121.74 Mya), and the divergence times of Rhoenanthus and Potamanthus originated at approximately 64.77 Mya (95% HPD, 43.82-88.68 Mya), thus belonging to the late Pliocene Epoch or early Miocene Epoch. In addition, the data indicated that R. coreanus was under negative selection and that ATP8 and ND2 in Potamanthidae had a high evolutionary rate.
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Affiliation(s)
- Zhi-Qiang Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ya-Jie Gao
- School of Bioengineering, Aksu Vocational Technical College, Aksu 843000, China
| | - Yu-Xin Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Le-Mei Zhan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Covnservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Covnservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Cole JA, Chatfield-Taylor W, Smeds EA, Cooley JR, Gonzalez VA, Wong C. Phylogeny of North Americas largest cicada radiation redefines Tibicinoides and Okanagana (Hemiptera: Auchenorrhyncha: Cicadidae: Tibicininae). Zootaxa 2023; 5346:501-531. [PMID: 38221325 DOI: 10.11646/zootaxa.5346.5.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Indexed: 01/16/2024]
Abstract
Tibicinoides, with three small endemic California cicada species, has a confusing, intertwined systematic history with Okanagana that we unravel here. An ingroup including all species of Tibicinoides and the majority (84.7%) of Okanagana species were sampled for six gene regions, polarized with Clidophleps, Okanagodes, Subpsaltria, and Tibicina outgroups, and subjected to Bayesian phylogenetic analysis. Although the ingroup was monophyletic from all outgroups including Tibicina, Tibicinoides rendered Okanagana paraphyletic among two major ingroup clades. To bring classification into agreement with phylogeny, we redescribe and redefine Tibicinoides to include all Okanagana species with a hooked uncus in the male genitalia, all of which grouped with the type T. cupreosparsa (Uhler, 1889) in the first of these clades: T. boweni (Chatfield-Taylor & Cole, 2020) comb. n., T. catalina (Davis, 1936) comb. n., T. hesperia (Uhler, 1876) comb. n., T. mercedita (Davis, 1915), T. minuta (Davis, 1915), T. pallidula (Davis, 1917a) comb. n., T. pernix (Bliven, 1964) comb. n., T. rubrovenosa (Davis, 1915) comb. n., T. simulata (Davis, 1921) comb. n., T. striatipes (Haldeman, 1852) comb. n., T. uncinata (Van Duzee, 1915) comb. n., T. utahensis (Davis, 1919) comb. n., and T. vanduzeei (Distant, 1914) comb. n. Okanagana is redescribed and restricted to the species of the second major clade which contained the type O. rimosa (Say, 1830). We describe two new genera for morphologically distinct orphan lineages: Chlorocanta gen. nov. for C. viridis (Davis, 1918) comb. n. and Hewlettia gen. nov. for H. nigriviridis (Davis, 1921) comb. n. We recognize O. rubrobasalis Davis, 1926 stat. rev. as a species and relegate two former species to junior subjective synonyms: O. noveboracensis (Emmons, 1854) = O. canadensis (Provancher, 1889) and O. occidentalis (Walker in Lord, 1866) = O. lurida Davis, 1919. Tibicinoides and Okanagana together represent a rapid radiation that presents challenges to phylogenetic analysis including suboptimal outgroups and short internodes.
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Affiliation(s)
- Jeffrey A Cole
- Entomology Section; Natural History Museum of Los Angeles County; 900 Exposition Boulevard; Los Angeles; CA 90007 USA; Division of Natural Sciences; Pasadena City College; 1570 East Colorado Boulevard; Pasadena; CA 91106 USA.
| | - Will Chatfield-Taylor
- Institute of Biology; Carleton University; 1125 Colonel By Drive; Ottawa; Canada; K1S 5B6.
| | - Elliott A Smeds
- Department of Entomology; California Academy of Sciences; 55 Music Concourse Drive; San Francisco; CA 94188 USA.
| | - John R Cooley
- Department of Ecology and Evolutionary Biology; University of Connecticut Hartford; 10 Prospect Street; Hartford; CT 06103 USA.
| | - Valorie A Gonzalez
- Department of Biochemistry; University of California San Diego; 9500 Gilman Drive; La Jolla; CA 92093 USA.
| | - Caressa Wong
- Division of Natural Sciences; Pasadena City College; 1570 East Colorado Boulevard; Pasadena; CA 91106 USA.
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Phylogeny, biogeography, and character evolution of the genus Sophora s.l. (Fabaceae, Papilionoideae). Mol Phylogenet Evol 2023; 181:107713. [PMID: 36693532 DOI: 10.1016/j.ympev.2023.107713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
The papilionoid legume genus Sophora (Fabaceae) exhibits a worldwide distribution, but a phylogenetic framework to understand the evolution of this group is lacking to date. Previous studies have demonstrated that Sophora is not monophyletic and might include Ammodendron, Ammothamnus, and Echinosophora, but the relationships among these four genera (defined as Sophora s.l.) are unclear. Here we used a nuclear DNA dataset (ETS, ITS, SQD1) and a plastid DNA dataset (matK, rbcL, rpl32-trnL, trnL-F) of 654 accession sequences to reconstruct the phylogenetic relationships, estimate the divergence times and ancestral range of Sophora s.l., and infer the evolution of chromosome number and morphological characteristics. Our major aim was to reconstruct phylogenetic relationships to test monophyly and elucidate relationships within the genus. Our results indicated that Ammodendron, Ammothamnus, and Echinosophora are embedded within Sophora s.s. and that nine well-supported clades can be recognized within comprise Sophora s.l. Ancestral character state estimation revealed that the most recent common ancestor of Sophora s.l. was a deciduous shrub that lacks rhizome spines and has unwinged legumes. Divergence times estimation and ancestral area reconstruction showed that Sophora s.l. originated in Central Asia and/or adjacent Southeast China in the early Oligocene (ca. 31 Mya) and dispersed from these regions into East and South Asia's adjacent areas and North America via the Bering land bridge. The analyses also supported a South American origin for S. sect. Edwardsia, which experienced rapid radiation with its major lineages diversifying over a relatively narrow timescale (8 Mya).
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Das S, Greenbaum E, Meiri S, Bauer AM, Burbrink FT, Raxworthy CJ, Weinell JL, Brown RM, Brecko J, Pauwels OSG, Rabibisoa N, Raselimanana AP, Merilä J. Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family. Mol Phylogenet Evol 2023; 180:107700. [PMID: 36603697 DOI: 10.1016/j.ympev.2022.107700] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023]
Abstract
The highly diverse snake superfamily Elapoidea is considered to be a classic example of ancient, rapid radiation. Such radiations are challenging to fully resolve phylogenetically, with the highly diverse Elapoidea a case in point. Previous attempts at inferring a phylogeny of elapoids produced highly incongruent estimates of their evolutionary relationships, often with very low statistical support. We sought to resolve this situation by sequencing over 4,500 ultraconserved element loci from multiple representatives of every elapoid family/subfamily level taxon and inferring their phylogenetic relationships with multiple methods. Concatenation and multispecies coalescent based species trees yielded largely congruent and well-supported topologies. Hypotheses of a hard polytomy were not retained for any deep branches. Our phylogenies recovered Cyclocoridae and Elapidae as diverging early within Elapoidea. The Afro-Malagasy radiation of elapoid snakes, classified as multiple subfamilies of an inclusive Lamprophiidae by some earlier authors, was found to be monophyletic in all analyses. The genus Micrelaps was consistently recovered as sister to Lamprophiidae. We establish a new family, Micrelapidae fam. nov., for Micrelaps and assign Brachyophis to this family based on cranial osteological synapomorphy. We estimate that Elapoidea originated in the early Eocene and rapidly diversified into all the major lineages during this epoch. Ecological opportunities presented by the post-Cretaceous-Paleogene mass extinction event may have promoted the explosive radiation of elapoid snakes.
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Affiliation(s)
- Sunandan Das
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland.
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 W. University Avenue, El Paso, TX 79968, USA
| | - Shai Meiri
- School of Zoology, Tel Aviv University, Tel Aviv, Israel; The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Israel
| | - Aaron M Bauer
- Department of Biology and Center for Biodiversity and Ecosystem Stewardship, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5192, USA
| | - Christopher J Raxworthy
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5192, USA
| | - Jeffrey L Weinell
- Department of Herpetology, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5192, USA; Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Rafe M Brown
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
| | - Jonathan Brecko
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, B-1000 Brussels, Belgium; Royal Museum for Central Africa, Tervuren, Belgium
| | - Olivier S G Pauwels
- Royal Belgian Institute of Natural Sciences, Rue Vautier 29, B-1000 Brussels, Belgium
| | - Nirhy Rabibisoa
- Sciences de la Vie et de l'Environnement, Faculté des Sciences, de Technologies et de l'Environnement, Université de Mahajanga, Campus Universitaire d'Ambondrona, BP 652, Mahajanga 401, Madagascar
| | - Achille P Raselimanana
- Zoologie et Biodiversité Animale, Faculté des Sciences, Université d'Antananarivo, BP 906, Antananarivo 101, Madagascar
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FI-00014 University of Helsinki, Finland; Area of Ecology and Biodiversity, School of Biological Sciences, Kadoorie Biological Sciences Building, Pokfulam Road, The University of Hong Kong, Hong Kong Special Administrative Region
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Duan Y, Fu S, Ye Z, Bu W. Phylogeny of Urostylididae (Heteroptera: Pentatomoidea) reveals rapid radiation and challenges traditional classification. ZOOL SCR 2023. [DOI: 10.1111/zsc.12582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yujie Duan
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Siying Fu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences Nankai University Tianjin China
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Prokop J, Nel A, Engel MS. Diversity, Form, and Postembryonic Development of Paleozoic Insects. ANNUAL REVIEW OF ENTOMOLOGY 2023; 68:401-429. [PMID: 36689304 DOI: 10.1146/annurev-ento-120220-022637] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
While Mesozoic, Paleogene, and Neogene insect faunas greatly resemble the modern one, the Paleozoic fauna provides unique insights into key innovations in insect evolution, such as the origin of wings and modifications of postembryonic development including holometaboly. Deep-divergence estimates suggest that the majority of contemporary insect orders originated in the Late Paleozoic, but these estimates reflect divergences between stem groups of each lineage rather than the later appearance of the crown groups. The fossil record shows the initial radiations of the extant hyperdiverse clades during the Early Permian, as well as the specialized fauna present before the End Permian mass extinction. This review summarizes the recent discoveries related to the documented diversity of Paleozoic hexapods, as well as current knowledge about what has actually been verified from fossil evidence as it relates to postembryonic development and the morphology of different body parts.
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Affiliation(s)
- Jakub Prokop
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic;
| | - André Nel
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France;
| | - Michael S Engel
- Division of Entomology, University of Kansas Natural History Museum, Lawrence, Kansas, USA;
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, USA
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Chen YP, Turdimatovich TO, Nuraliev MS, Lazarević P, Drew BT, Xiang CL. Phylogeny and biogeography of the northern temperate genus Dracocephalum s.l. (Lamiaceae). Cladistics 2022; 38:429-451. [PMID: 35358338 DOI: 10.1111/cla.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 11/28/2022] Open
Abstract
The northern temperate genus Dracocephalum consists of approximately 70 species mainly distributed in the steppe-desert biomes of Central and West Asia and the alpine region of the Qinghai-Tibetan Plateau (QTP). Previous work has shown that Dracocephalum is not monophyletic and might include Hyssopus and Lallemantia. This study attempts to clarify the phylogenetic relationships, diversification patterns, and the biogeographical history of the three genera (defined as Dracocephalum s.l.). Based on a sampling of 66 taxa comprising more than 80% from extant species of Dracocephalum s.l., morphological, phylogenetic (maximum parsimony, likelihood, and Bayesian inference based on nuclear ITS and ETS, plastid rpl32-trnL, trnL-trnF, ycf1, and ycf1-rps15, and two low-copy nuclear markers AT3G09060 and AT1G09680), molecular dating, diversification, and ancestral range estimation analyses were carried out. Our results demonstrate that both Hyssopus and Lallemantia are embedded within Dracocephalum and nine well-supported clades can be recognized within Dracocephalum s.l. Analyses of divergence times suggest that the genus experienced an early rapid radiation during the middle to late Miocene with major lineages diversifying within a relatively narrow timescale. Ancestral area reconstruction analyses indicate that Dracocephalum s.l. originated in Central and West Asia and southern Siberia, and dispersed from Central and West Asia into the QTP and adjacent areas twice independently during the Pliocene. The aridification of the Asian interior possibly promoted the rapid radiation of Dracocephalum within this region, and the uplift of the QTP appears to have triggered the dispersal and recent rapid diversification of the genus in the QTP and adjacent regions. Combining molecular phylogenetic and morphological evidence, a revised infrageneric classification of Dracocephalum s.l. is proposed, which recognizes nine sections within the genus.
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Affiliation(s)
- Ya-Ping Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | - Maxim S Nuraliev
- Department of Higher Plants, Biological Faculty, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Predrag Lazarević
- Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade, Belgrade, 11000, Serbia
| | - Bryan T Drew
- Department of Biology, University of Nebraska-Kearney, Kearney, 68849, USA
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Kataoka K, Togawa Y, Sanno R, Asahi T, Yura K. Dissecting cricket genomes for the advancement of entomology and entomophagy. Biophys Rev 2022; 14:75-97. [PMID: 35340598 PMCID: PMC8921346 DOI: 10.1007/s12551-021-00924-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Significant advances in biophysical methods such as next-generation sequencing technologies have now opened the way to conduct evolutionary and applied research based on the genomic information of greatly diverse insects. Crickets belonging to Orthoptera (Insecta: Polyneoptera), one of the most flourishing groups of insects, have contributed to the development of multiple scientific fields including developmental biology and neuroscience and have been attractive targets in evolutionary ecology for their diverse ecological niches. In addition, crickets have recently gained recognition as food and feed. However, the genomic information underlying their biological basis and application research toward breeding is currently underrepresented. In this review, we summarize the progress of genomics of crickets. First, we outline the phylogenetic position of crickets in insects and then introduce recent studies on cricket genomics and transcriptomics in a variety of fields. Furthermore, we present findings from our analysis of polyneopteran genomes, with a particular focus on their large genome sizes, chromosome number, and repetitive sequences. Finally, how the cricket genome can be beneficial to the food industry is discussed. This review is expected to enhance greater recognition of how important the cricket genomes are to the multiple biological fields and how basic research based on cricket genome information can contribute to tackling global food security.
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Affiliation(s)
- Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Yuki Togawa
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Ryuto Sanno
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
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11
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Esquerré D, Keogh JS, Demangel D, Morando M, Avila LJ, Sites JW, Ferri-Yáñez F, Leaché AD. Rapid radiation and rampant reticulation: Phylogenomics of South American Liolaemus lizards. Syst Biol 2021; 71:286-300. [PMID: 34259868 DOI: 10.1093/sysbio/syab058] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/09/2023] Open
Abstract
Understanding the factors that cause heterogeneity among gene trees can increase the accuracy of species trees. Discordant signals across the genome are commonly produced by incomplete lineage sorting (ILS) and introgression, which in turn can result in reticulate evolution. Species tree inference using the multispecies coalescent is designed to deal with ILS and is robust to low levels of introgression, but extensive introgression violates the fundamental assumption that relationships are strictly bifurcating. In this study, we explore the phylogenomics of the iconic Liolaemus subgenus of South American lizards, a group of over 100 species mostly distributed in and around the Andes mountains. Using mitochondrial DNA (mtDNA) and genome-wide restriction-site associated DNA sequencing (RADseq; nDNA hereafter), we inferred a time-calibrated mtDNA gene tree, nDNA species trees, and phylogenetic networks. We found high levels of discordance between mtDNA and nDNA, which we attribute in part to extensive ILS resulting from rapid diversification. These data also reveal extensive and deep introgression, which combined with rapid diversification, explain the high level of phylogenetic discordance. We discuss these findings in the context of Andean orogeny and glacial cycles that fragmented, expanded, and contracted species distributions. Finally, we use the new phylogeny to resolve long-standing taxonomic issues in one of the most studied lizard groups in the New World.
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Affiliation(s)
- Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | | | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Luciano J Avila
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC- CONICET), Puerto Madryn, Chubut, Argentina
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, Utah, USA
| | - Francisco Ferri-Yáñez
- Departamento de Biogeografía y Cambio Global, Museo Nacional de Ciencias Naturales, CSIC & Laboratorio Internacional en Cambio Global CSIC-PUC (LINCGlobal), Calle José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
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Yu DN, Yu PP, Zhang LP, Storey KB, Gao XY, Zhang JY. Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations. PeerJ 2021; 9:e11402. [PMID: 34221707 PMCID: PMC8231340 DOI: 10.7717/peerj.11402] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera. METHODS Mitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups. RESULTS Among these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata.
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Affiliation(s)
- Dan-Na Yu
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Pan-Pan Yu
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Le-Ping Zhang
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | | | - Xin-Yan Gao
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
| | - Jia-Yong Zhang
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang, China
- The Department of Biology, College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang, China
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13
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Arifin U, Chan KO, Smart U, Hertwig ST, Smith EN, Iskandar DT, Haas A. Revisiting the phylogenetic predicament of the genus Huia (Amphibia: Ranidae) using molecular data and tadpole morphology. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Despite a considerable amount of research, the systematics of the ranid genus Huia have remained unresolved, mostly owing to insufficient sampling and morphological similarities. As currently circumscribed, Huia consists of five species, but multiple studies have consistently demonstrated that it is not a monophyletic genus. However, no study has approached the problem with adequate data and provided a systematically sound solution, leaving the genus to languish in a classification that is phylogenetically incoherent. We generated the most comprehensive sampling of Huia to date, based on extensive fieldwork in Java and Sumatra. Using an integrative taxonomy framework, we analysed four mitochondrial and two nuclear markers and, in conjunction with tadpole morphology, investigated the phylogenetics of Huia and its congeners. Corroborating previous studies, Huia is recovered as a paraphyletic group. Huia cavitympanum emerges as the sister taxon to Meristogenys. The remaining members of Huia form a monophyletic group, sister to the H. cavitympanum + Meristogenys clade. Our extensive geographical sampling in Sumatra and Java reveals multiple highly divergent lineages that potentially represent undescribed species. Using our expanded molecular and morphological dataset, we resolve the paraphyly of Huia by restricting the genus to its type species and propose a new genus to accommodate the strongly supported clade of Sumatran and Javan populations previously belonging to Huia.
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Affiliation(s)
- Umilaela Arifin
- Centrum für Naturkunde-Zoologisches Museum, Universität Hamburg, Edmund-Siemers-Allee, Hamburg, Germany
| | - Kin Onn Chan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore
| | - Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA
- Amphibian & Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Stefan T Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse, Bern, Switzerland
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse, Bern, Switzerland
| | - Eric N Smith
- Amphibian & Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Djoko T Iskandar
- School of Life Sciences & Technology, Bandung Institute of Technology, Jalan Ganeca 10 Tamansari, Bandung, Indonesia
| | - Alexander Haas
- Centrum für Naturkunde-Zoologisches Museum, Universität Hamburg, Edmund-Siemers-Allee, Hamburg, Germany
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14
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Sharanowski BJ, Ridenbaugh RD, Piekarski PK, Broad GR, Burke GR, Deans AR, Lemmon AR, Moriarty Lemmon EC, Diehl GJ, Whitfield JB, Hines HM. Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization. Mol Phylogenet Evol 2020; 156:107023. [PMID: 33253830 DOI: 10.1016/j.ympev.2020.107023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/28/2020] [Accepted: 11/23/2020] [Indexed: 12/26/2022]
Abstract
Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.
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Affiliation(s)
| | - Ryan D Ridenbaugh
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - Patrick K Piekarski
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA; Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY 10065, USA
| | - Gavin R Broad
- Department of Life Sciences, the Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30606, USA
| | - Andrew R Deans
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | | | - Gloria J Diehl
- Department of Biology, University of Central Florida, Orlando, FL 32816, USA
| | - James B Whitfield
- Department of Entomology, University of Illinois, Urbana, IL 61801, USA
| | - Heather M Hines
- Department of Entomology, Pennsylvania State University, University Park, PA, 16802; Department of Biology, Pennsylvania State University, University Park, PA, 16802
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15
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Çıplak B, Yahyaoğlu Ö, Uluar O. Revisiting Pholidopterini (Orthoptera, Tettigoniidae): Rapid radiation causes homoplasy and phylogenetic instability. ZOOL SCR 2020. [DOI: 10.1111/zsc.12463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Battal Çıplak
- Department of Biology Faculty of Science Akdeniz University Antalya Turkey
| | - Özgül Yahyaoğlu
- Department of Biology Faculty of Science Akdeniz University Antalya Turkey
| | - Onur Uluar
- Department of Biology Faculty of Science Akdeniz University Antalya Turkey
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16
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Cai L, Xi Z, Lemmon EM, Lemmon AR, Mast A, Buddenhagen CE, Liu L, Davis CC. The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales. Syst Biol 2020; 70:491-507. [PMID: 33169797 DOI: 10.1093/sysbio/syaa083] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 10/20/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022] Open
Abstract
The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order includes 9 of the top 10 most unstable nodes in angiosperms, which have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 10.0$\%$, 34.8$\%$, and 21.4$\%$ of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution. [Coalescent; concatenation; flanking region; hybrid enrichment, introgression; phylogenomics; rapid radiation, triplet frequency.].
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Affiliation(s)
- Liming Cai
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhenxiang Xi
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Emily Moriarty Lemmon
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL 32306, USA
| | - Austin Mast
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher E Buddenhagen
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA
- AgResearch, 10 Bisley Road, Hamilton 3214, New Zealand
| | - Liang Liu
- Department of Statistics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA
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17
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Chan KO, Hutter CR, Wood PL, Grismer LL, Brown RM. Larger, unfiltered datasets are more effective at resolving phylogenetic conflict: Introns, exons, and UCEs resolve ambiguities in Golden-backed frogs (Anura: Ranidae; genus Hylarana). Mol Phylogenet Evol 2020; 151:106899. [PMID: 32590046 DOI: 10.1016/j.ympev.2020.106899] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/18/2020] [Accepted: 06/17/2020] [Indexed: 01/01/2023]
Abstract
Using FrogCap, a recently-developed sequence-capture protocol, we obtained >12,000 highly informative exons, introns, and ultraconserved elements (UCEs), which we used to illustrate variation in evolutionary histories of these classes of markers, and to resolve long-standing systematic problems in Southeast Asian Golden-backed frogs of the genus-complex Hylarana. We also performed a comprehensive suite of analyses to assess the relative performance of different genetic markers, data filtering strategies, tree inference methods, and different measures of branch support. To reduce gene tree estimation error, we filtered the data using different thresholds of taxon completeness (missing data) and parsimony informative sites (PIS). We then estimated species trees using concatenated datasets and Maximum Likelihood (IQ-TREE) in addition to summary (ASTRAL-III), distance-based (ASTRID), and site-based (SVDQuartets) multispecies coalescent methods. Topological congruence and branch support were examined using traditional bootstrap, local posterior probabilities, gene concordance factors, quartet frequencies, and quartet scores. Our results did not yield a single concordant topology. Instead, introns, exons, and UCEs clearly possessed different phylogenetic signals, resulting in conflicting, yet strongly-supported phylogenetic estimates. However, a combined analysis comprising the most informative introns, exons, and UCEs converged on a similar topology across all analyses, with the exception of SVDQuartets. Bootstrap values were consistently high despite high levels of incongruence and high proportions of gene trees supporting conflicting topologies. Although low bootstrap values did indicate low heuristic support, high bootstrap support did not necessarily reflect congruence or support for the correct topology. This study reiterates findings of some previous studies, which demonstrated that traditional bootstrap values can produce positively misleading measures of support in large phylogenomic datasets. We also showed a remarkably strong positive relationship between branch length and topological congruence across all datasets, implying that very short internodes remain a challenge to resolve, even with orders of magnitude more data than ever before. Overall, our results demonstrate that more data from unfiltered or combined datasets produced superior results. Although data filtering reduced gene tree incongruence, decreased amounts of data also biased phylogenetic estimation. A point of diminishing returns was evident, at which higher congruence (from more stringent filtering) at the expense of amount of data led to topological error as assessed by comparison to more complete datasets across different genomic markers. Additionally, we showed that applying a parameter-rich model to a partitioned analysis of concatenated data produces better results compared to unpartitioned, or even partitioned analysis using model selection. Despite some lingering uncertainties, a combined analysis of our genomic data and sequences supplemented from GenBank (on the basis of a few gene regions) revealed highly supported novel systematic arrangements. Based on these new findings, we transfer Amnirana nicobariensis into the genus Indosylvirana; and I. milleti and Hylarana celebensis to the genus Papurana. We also provisionally place H. attigua in the genus Papurana pending verification from positively identified (voucher substantiated) samples.
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Affiliation(s)
- Kin Onn Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, 2 Conservatory Drive, 117377, Singapore.
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA; Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Perry L Wood
- Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA; Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - L Lee Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA 92505, USA
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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18
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Song N, Geng Y, Li X. The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes. Front Microbiol 2020; 11:863. [PMID: 32457727 PMCID: PMC7225605 DOI: 10.3389/fmicb.2020.00863] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/09/2020] [Indexed: 12/01/2022] Open
Abstract
A number of species in Bipolaris are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of Bipolaris based solely on morphology. In this study, we sequenced the complete mitochondrial genome of Bipolaris sorokiniana, and presented the detailed annotation of the genome. The B. sorokiniana mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core protein-coding genes, 38 tRNA genes. In addition, two ribosomal protein genes (rps3 gene and rps5 gene) and the fungal mitochondrial RNase P gene (rnpB) are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core protein-coding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of Capnodiales, Botryosphaeriales and Pleosporales are consistently supported in all analyses. The Venturiaceae forms an independent lineage, with a distant phylogenetic relationship to Pleosporales. At the family level, the Mycosphaerellaceae, Botryosphaeriaceae. Phaeosphaeriaceae, and Pleosporaceae are recognized in the majority of trees.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuehua Geng
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
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19
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Li Z, Li X, Song N, Tang H, Yin X. The Mitochondrial Genome of Amara aulica (Coleoptera, Carabidae, Harpalinae) and Insights into the Phylogeny of Ground Beetles. Genes (Basel) 2020; 11:E181. [PMID: 32050506 PMCID: PMC7074353 DOI: 10.3390/genes11020181] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 11/16/2022] Open
Abstract
Carabidae are one of the most species-rich families of beetles, comprising more than 40,000 described species worldwide. Forty-three complete or partial mitochondrial genomes (mitogenomes) from this family have been published in GenBank to date. In this study, we sequenced a nearly complete mitogenome of Amara aulica (Carabidae), using a next-generation sequencing method. This mitogenome was 16,646 bp in length, which encoded the typical 13 mitochondrial protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Combining with the published mitogenomes of Carabidae and five outgroup species from Trachypachidae, Gyrinidae and Dytiscidae, we performed phylogenetic estimates under maximum likelihood and Bayesian inference criteria to investigate the phylogenetic relationships of carabid beetles. The results showed that the family Carabidae was a non-monophyletic assemblage. The subfamilies Cicindelinae, Elaphrinae, Carabinae, Trechinae and Harpalinae were recovered as monophyletic groups. Moreover, the clade (Trechinae + (Brachininae + Harpalinae)) was consistently recovered in all analyses.
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Affiliation(s)
- Zhenya Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (Z.L.); (X.L.); (X.Y.)
| | - Xinxin Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (Z.L.); (X.L.); (X.Y.)
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (Z.L.); (X.L.); (X.Y.)
| | - Huiji Tang
- Technical Center, Zhengzhou Customs District, Zhengzhou 450002, China;
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (Z.L.); (X.L.); (X.Y.)
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20
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Gadelha SDS, Zaldívar-Riverón A, de Oliveira ML. Molecular phylogenetics disentangles the limits of a group of related Neotropical doryctine parasitoid wasp genera (Hymenoptera : Braconidae). INVERTEBR SYST 2020. [DOI: 10.1071/is20030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Doryctinae is one of the most specious subfamilies of the mainly parasitoid wasp family Braconidae. Members of this subfamily are characterised by having a very heterogeneous external morphology, which has made establishing the limits of several of its genera extremely difficult. The Neotropical Callihormius Ashmead, Platydoryctes Barbalho & Penteado-Dias, and Aphelopsia Marsh are prime examples of this, since they show extensive interspecific morphological variation but lack consistent diagnostic features among them. We carried out a comprehensive phylogenetic study among several representative species belonging to the above genera as well as other morphologically similar doryctine taxa based on three nuclear and two mitochondrial (mt)DNA sequence markers. Based on the relationships recovered, we assessed the generic limits among the examined taxa and investigated the times of origin and diversification in this group. Our best estimate of phylogeny did not recover Callihormius as monophyletic, and thus we propose a taxonomic arrangement where we elevate the status of Ca. (Dmitriohormius) Belokobylskij, Zaldívar-Riverón & Coronado-Blanco to genus level, stat. nov., and also describe four new genera: Macrometasoma, gen. nov., Caputlenis, gen. nov., Platyhormius, gen. nov. and Caputrugosus, gen. nov. Platydoryctes is delimited morphologically, and the body flatness is proposed to have independently evolved more than once within the group of genera examined. Aphelopsia was not recovered as monophyletic, though the relationships involved were weakly supported and therefore we maintain its species composition. Panama Marsh, stat. rev., which was considered a junior synonym of Leluthia Cameron, is resurrected. Basal relationships in the phylogeny had very short branch lengths, which could be due to ancient rapid radiation events that occurred during the early evolution of the group. The estimated times of divergence showed that the clade containing Callihormius and its related genera originated between the late Oligocene and middle Miocene, whereas its early diversification events probably occurred between the middle to late Miocene.
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21
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Martín-Hernanz S, Aparicio A, Fernández-Mazuecos M, Rubio E, Reyes-Betancort JA, Santos-Guerra A, Olangua-Corral M, Albaladejo RG. Maximize Resolution or Minimize Error? Using Genotyping-By-Sequencing to Investigate the Recent Diversification of Helianthemum (Cistaceae). FRONTIERS IN PLANT SCIENCE 2019; 10:1416. [PMID: 31781140 PMCID: PMC6859804 DOI: 10.3389/fpls.2019.01416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/11/2019] [Indexed: 05/27/2023]
Abstract
A robust phylogenetic framework, in terms of extensive geographical and taxonomic sampling, well-resolved species relationships and high certainty of tree topologies and branch length estimations, is critical in the study of macroevolutionary patterns. Whereas Sanger sequencing-based methods usually recover insufficient phylogenetic signal, especially in recently diversified lineages, reduced-representation sequencing methods tend to provide well-supported phylogenetic relationships, but usually entail remarkable bioinformatic challenges due to the inherent trade-off between the number of SNPs and the magnitude of associated error rates. The genus Helianthemum (Cistaceae) is a species-rich and taxonomically complex Palearctic group of plants that diversified mainly since the Upper Miocene. It is a challenging case study since previous attempts using Sanger sequencing were unable to resolve the intrageneric phylogenetic relationships. Aiming to obtain a robust phylogenetic reconstruction based on genotyping-by-sequencing (GBS), we established a rigorous methodological workflow in which we i) explored how variable settings during dataset assembly have an impact on error rates and on the degree of resolution under concatenation and coalescent approaches, ii) assessed the effect of two extreme parameter configurations (minimizing error rates vs. maximizing phylogenetic resolution) on tree topology and branch lengths, and iii) evaluated the effects of these two configurations on estimates of divergence times and diversification rates. Our analyses produced highly supported topologically congruent phylogenetic trees for both configurations. However, minimizing error rates did produce more reliable branch lengths, critically affecting the accuracy of downstream analyses (i.e. divergence times and diversification rates). In addition to recommending a revision of intrageneric systematics, our results enabled us to identify three highly diversified lineages in Helianthemum in contrasting geographical areas and ecological conditions, which started radiating in the Upper Miocene.
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Affiliation(s)
- Sara Martín-Hernanz
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Abelardo Aparicio
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | | | - Encarnación Rubio
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - J. Alfredo Reyes-Betancort
- Jardín de Aclimatación de la Orotava, Instituto Canario de Investigaciones Agrarias (ICIA), Santa Cruz de Tenerife, Spain
| | - Arnoldo Santos-Guerra
- Jardín de Aclimatación de la Orotava, Instituto Canario de Investigaciones Agrarias (ICIA), Santa Cruz de Tenerife, Spain
| | - María Olangua-Corral
- Departamento de Biología Reproductiva y Micro-morfología, Jardín Botánico Canario ‘Viera y Clavijo’—Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Rafael G. Albaladejo
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
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22
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Vasilikopoulos A, Balke M, Beutel RG, Donath A, Podsiadlowski L, Pflug JM, Waterhouse RM, Meusemann K, Peters RS, Escalona HE, Mayer C, Liu S, Hendrich L, Alarie Y, Bilton DT, Jia F, Zhou X, Maddison DR, Niehuis O, Misof B. Phylogenomics of the superfamily Dytiscoidea (Coleoptera: Adephaga) with an evaluation of phylogenetic conflict and systematic error. Mol Phylogenet Evol 2019; 135:270-285. [DOI: 10.1016/j.ympev.2019.02.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
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23
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Wipfler B, Letsch H, Frandsen PB, Kapli P, Mayer C, Bartel D, Buckley TR, Donath A, Edgerly-Rooks JS, Fujita M, Liu S, Machida R, Mashimo Y, Misof B, Niehuis O, Peters RS, Petersen M, Podsiadlowski L, Schütte K, Shimizu S, Uchifune T, Wilbrandt J, Yan E, Zhou X, Simon S. Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects. Proc Natl Acad Sci U S A 2019; 116:3024-3029. [PMID: 30642969 PMCID: PMC6386694 DOI: 10.1073/pnas.1817794116] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyneoptera represents one of the major lineages of winged insects, comprising around 40,000 extant species in 10 traditional orders, including grasshoppers, roaches, and stoneflies. Many important aspects of polyneopteran evolution, such as their phylogenetic relationships, changes in their external appearance, their habitat preferences, and social behavior, are unresolved and are a major enigma in entomology. These ambiguities also have direct consequences for our understanding of the evolution of winged insects in general; for example, with respect to the ancestral habitats of adults and juveniles. We addressed these issues with a large-scale phylogenomic analysis and used the reconstructed phylogenetic relationships to trace the evolution of 112 characters associated with the external appearance and the lifestyle of winged insects. Our inferences suggest that the last common ancestors of Polyneoptera and of the winged insects were terrestrial throughout their lives, implying that wings did not evolve in an aquatic environment. The appearance of the first polyneopteran insect was mainly characterized by ancestral traits such as long segmented abdominal appendages and biting mouthparts held below the head capsule. This ancestor lived in association with the ground, which led to various specializations including hardened forewings and unique tarsal attachment structures. However, within Polyneoptera, several groups switched separately to a life on plants. In contrast to a previous hypothesis, we found that social behavior was not part of the polyneopteran ground plan. In other traits, such as the biting mouthparts, Polyneoptera shows a high degree of evolutionary conservatism unique among the major lineages of winged insects.
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Affiliation(s)
- Benjamin Wipfler
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany;
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Harald Letsch
- Department für Botanik und Biodiversitätsforschung, Universität Wien, 1030 Vienna, Austria
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84604
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002
| | - Paschalia Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Daniela Bartel
- Department of Integrative Zoology, Universität Wien, 1090 Vienna, Austria
| | - Thomas R Buckley
- New Zealand Arthropod Collection, Manaaki Whenua - Landcare Research, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Janice S Edgerly-Rooks
- Department of Biology, College of Arts and Sciences, Santa Clara University, Santa Clara, CA 95053
| | - Mari Fujita
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Shanlin Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Ryuichiro Machida
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Yuta Mashimo
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Oliver Niehuis
- Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, 79104 Freiburg, Germany
| | - Ralph S Peters
- Center of Taxonomy and Evolutionary Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Kai Schütte
- Tierökologie und Naturschutz, Universität Hamburg, 20146 Hamburg, Germany
| | - Shota Shimizu
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Toshiki Uchifune
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
- Yokosuka City Museum, Fukadadai, Kanagawa 238-0016, Japan
| | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany
| | - Evgeny Yan
- Institut für Spezielle Zoologie und Evolutionsbiologie, Friedrich-Schiller-University Jena, 07743 Jena, Germany
- Borissiak Palaeontological Institute, Russian Academy of Sciences, 123 Moscow, Russia
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100083, China
| | - Sabrina Simon
- Biosystematics Group, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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Mongiardino Koch N, Gauthier JA. Noise and biases in genomic data may underlie radically different hypotheses for the position of Iguania within Squamata. PLoS One 2018; 13:e0202729. [PMID: 30133514 PMCID: PMC6105018 DOI: 10.1371/journal.pone.0202729] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/08/2018] [Indexed: 12/23/2022] Open
Abstract
Squamate reptiles are a major component of vertebrate biodiversity whose crown-clade traces its origin to a narrow window of time in the Mesozoic during which the main subclades diverged in rapid succession. Deciphering phylogenetic relationships among these lineages has proven challenging given the conflicting signals provided by genomic and phenomic data. Most notably, the placement of Iguania has routinely differed between data sources, with morphological evidence supporting a sister relationship to the remaining squamates (Scleroglossa hypothesis) and molecular data favoring a highly nested position alongside snakes and anguimorphs (Toxicofera hypothesis). We provide novel insights by generating an expanded morphological dataset and exploring the presence of phylogenetic signal, noise, and biases in molecular data. Our analyses confirm the presence of strong conflicting signals for the position of Iguania between morphological and molecular datasets. However, we also find that molecular data behave highly erratically when inferring the deepest branches of the squamate tree, a consequence of limited phylogenetic signal to resolve this ancient radiation with confidence. This, in turn, seems to result from a rate of evolution that is too high for historical signals to survive to the present. Finally, we detect significant systematic biases, with iguanians and snakes sharing faster rates of molecular evolution and a similarly biased nucleotide composition. A combination of scant phylogenetic signal, high levels of noise, and the presence of systematic biases could result in the misplacement of Iguania. We regard this explanation to be at least as plausible as the complex scenario of convergence and reversals required for morphological data to be misleading. We further evaluate and discuss the utility of morphological data to resolve ancient radiations, as well as its impact in combined-evidence phylogenomic analyses, with results relevant for the assessment of evidence and conflict across the Tree of Life.
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Affiliation(s)
- Nicolás Mongiardino Koch
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
| | - Jacques A. Gauthier
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut, United States of America
- Yale Peabody Museum of Natural History, New Haven, Connecticut, United States of America
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25
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Freitas L, Mello B, Schrago CG. Multispecies coalescent analysis confirms standing phylogenetic instability in Hexapoda. J Evol Biol 2018; 31:1623-1631. [PMID: 30058265 DOI: 10.1111/jeb.13355] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/28/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
The multispecies coalescent (MSC) has been increasingly used in phylogenomic analyses due to the accommodation of gene tree topological heterogeneity by taking into account population-level processes, such as incomplete lineage sorting. In this sense, the phylogeny of insect species, which are characterized by their large effective population sizes, is suitable for a coalescent-based analysis. Furthermore, studies so far recovered short internal branches at early divergences of the insect tree of life, indicating fast evolutionary radiations that increase the probability of incomplete lineage sorting in deep time. Here, we investigated the performance of the MSC for a phylogenomic data set of hexapods compiled by Misof et al. (2014, Science 346:763). Our analysis recovered the monophyly of most insect orders, and major phylogenetic relationships were in agreement with current insect systematics. We identified, however, some evolutionary associations that were consistently problematic. Most noticeable, Hexapod monophyly was disrupted by the sister group relationship between the remiped crustacean and Insecta. Additionally, the interordinal relationships within Polyneoptera and Neuropteroidea were found to be phylogenetically unstable. We show that these controversial phylogenetic arrangements were also poorly supported by previous analyses, and therefore, we evaluated their robustness to stochastic errors from sampling sites and terminals, confirming standing problems in hexapod phylogeny in the genomics age.
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Affiliation(s)
- Lucas Freitas
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Beatriz Mello
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos G Schrago
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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26
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Carneiro LS, Teixeira SAMV, Gonçalves WG, Fernandes KM, Zanuncio JC, Serrão JE. Histochemistry, immunohistochemistry and cytochemistry of the anterior midgut region of the stingless bee Melipona quadrifasciata and honey bee Apis mellifera (Hymenoptera: Apidae). Micron 2018; 113:41-47. [PMID: 30007857 DOI: 10.1016/j.micron.2018.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 06/11/2018] [Accepted: 06/26/2018] [Indexed: 11/29/2022]
Abstract
The anterior midgut region of stingless bees is anatomically differentiated with tall and narrow cells, whereas in other social and solitary bees this anatomical gut region is lacking. The objective of the present study was to describe the histochemistry, immunohistochemistry and cytochemistry of the anterior midgut region of the stingless bee Melipona quadrifasciata in comparison with the honey bee Apis mellifera. The anterior midgut region of both species was evaluated for identification of the enzymes β- galactosidase, glucose-6-phosphatase, acid phosphatase, and alkaline phosphatase, the membrane transporter aquaporin, the hormone FMRF-amide, and lysosomes. Histology of the anterior midgut region showed that this region in M. quadrifasciata workers did not present external folds of the wall, whereas the following midgut wall presented many. In A. mellifera, folds in the midgut wall occur starting from the fore- midgut transition region. Despite these morphological differences, the tests evaluated were similar in both species. β-galactosidase was not found in the anterior midgut cells. Glucose-6-phosphatase and acid phosphatase occurred in the apical region of the gut epithelium. Alkaline phosphatase occurred in vesicles in apical cytoplasm and in the basal plasma membrane infoldings of the epithelial cells. Aquaporin was found in the basal region of the midgut epithelium and in the associated visceral muscles. FMRF-amide was found only in nerve endings in the anterior midgut region. All cells in the anterior midgut region were rich in lysosomes. These results suggest that in both bee species, although they have anatomically different anterior midgut regions, these regions present high metabolic activity and function in cellular homeostasis, lipid absorption and are under neurohormone control.
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Affiliation(s)
- Lenise Silva Carneiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil.
| | | | - Wagner Gonzaga Gonçalves
- Departamento de Biologia Geral, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil.
| | - Kenner Morais Fernandes
- Departamento de Biologia Geral, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil.
| | - José Cola Zanuncio
- Departamento de Entomologia/BIOGRO, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
| | - José Eduardo Serrão
- Departamento de Biologia Geral, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil.
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27
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Simon S, Blanke A, Meusemann K. Reanalyzing the Palaeoptera problem - The origin of insect flight remains obscure. ARTHROPOD STRUCTURE & DEVELOPMENT 2018; 47:328-338. [PMID: 29763650 DOI: 10.1016/j.asd.2018.05.002] [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: 12/19/2017] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
The phylogenetic relationships of the winged insect lineages - mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera) - are still controversial with three hypotheses supported by different datasets: Palaeoptera, Metapterygota and Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus on detecting confounding and alternative signal. In this context, we provide a framework to quantitatively evaluate and assess incongruent molecular phylogenetic signal inherent in phylogenomic datasets. Despite overall support for the Palaeoptera hypothesis, we also found considerable signal for Chiastomyaria, which is not easily detectable by standardized tree inference approaches. Analyses of the accumulation of signal across gene partitions showed that signal accumulates gradually. However, even in case signal only slightly supported one over the other hypothesis, topologies inferred from large datasets switch from statistically strongly supported Palaeoptera to strongly supported Chiastomyaria. From a morphological point of view, Palaeoptera currently appears to be the best-supported hypothesis; however, recent analyses were restricted to head characters. Phylogenetic approaches covering all organ systems including analyses of potential functional or developmental convergence are still pending so that the Palaeoptera problem has to be considered an open question in insect systematics.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
| | - Alexander Blanke
- Institute of Zoology, Biocenter Cologne, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany; Medical and Biological Engineering Research Group, School of Engineering and Computer Science, University of Hull, Cottingham Road, HU6 7RX, Hull, UK
| | - Karen Meusemann
- Evolutionary Biology & Ecology, Institute for Biology, University of Freiburg, Hauptstr. 1, D-79104 Freiburg (Brsg.), Germany; Center of Molecular Biodiversity Research (ZMB), Zoological Research Museum A. Koenig (ZFMK), Adenauerallee 160, D-53113 Bonn, Germany.
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28
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Whitfield JB, Austin AD, Fernandez-Triana JL. Systematics, Biology, and Evolution of Microgastrine Parasitoid Wasps. ANNUAL REVIEW OF ENTOMOLOGY 2018; 63:389-406. [PMID: 29058979 DOI: 10.1146/annurev-ento-020117-043405] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The braconid parasitoid wasp subfamily Microgastrinae is perhaps the most species-rich subfamily of animals on Earth. Despite their small size, they are familiar to agriculturalists and field ecologists alike as one of the principal groups of natural enemies of caterpillars feeding on plants. Their abundance and nearly ubiquitous terrestrial distribution, their intricate interactions with host insects, and their historical association with mutualistic polydnaviruses have all contributed to Microgastrinae becoming a key group of organisms for studying parasitism, parasitoid genomics, and mating biology. However, these rich sources of data have not yet led to a robust genus-level classification of the group, and some taxonomic confusion persists as a result. We present the current status of understanding of the general biology, taxonomic history, diversity, geographical patterns, host relationships, and phylogeny of Microgastrinae as a stimulus and foundation for further study. Current progress in elucidating the biology and taxonomy of this important group is rapid and promises a revolution in the classification of these wasps in the near future.
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Affiliation(s)
- James B Whitfield
- Department of Entomology, University of Illinois, Urbana, Illinois 61801, USA;
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia;
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29
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Expansion of Arthropod Herbivory in Late Triassic South Africa: The Molteno Biota, Aasvoëlberg 411 Site and Developmental Biology of a Gall. TOPICS IN GEOBIOLOGY 2018. [DOI: 10.1007/978-3-319-68009-5_14] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Du C, Zhang L, Lu T, Ma J, Zeng C, Yue B, Zhang X. Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera. BMC Genomics 2017; 18:698. [PMID: 28874137 PMCID: PMC5585954 DOI: 10.1186/s12864-017-4102-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very little is known about mitogenomes of Meloidae. RESULTS We determined complete or nearly complete mitogenomes of seven meloid species. The circular genomes encode 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) and two ribosomal RNAs (rRNAs), and contain a control region, with gene arrangement identical to the ancestral type for insects. The evolutionary rates of all PCGs indicate that their evolution is based on purifying selection. The comparison of tRNA secondary structures indicates diverse substitution patterns in Meloidae. Remarkably, all mitogenomes of the three studied Hycleus species contain two large intergenic spacers (IGSs). IGS1 is located between trnW and trnC, including a 9 bp consensus motif. IGS2 is located between trnS2 (UCN) and nad1, containing discontinuous repeats of a pentanucleotide motif and two 18-bp repeat units in both ends. To date, IGS2 is found only in genera Hycleus across all published Coleopteran mitogenomes. The duplication/random loss model and slipped-strand mispairing are proposed as evolutionary mechanisms for the two IGSs (IGS1, IGS2). The phylogenetic analyses using MrBayes, RAxML, and PhyloBayes methods based on nucleotide and amino acid datasets of 13 PCGs from all published mitogenomes of Tenebrionoids, consistently recover the monophylies of Meloidae and Tenebrionidae. Within Meloidae, the genus Lytta clusters with Epicauta rather than with Mylabris. Although data collected thus far could not resolve the phylogenetic relationships within Meloidae, this study will assist in future mapping of the Meloidae phylogeny. CONCLUSIONS This study presents mitogenomes of seven meloid beetles. New mitogenomes retain the genomic architecture of the Coleopteran ancestor, but contain two IGSs in the three studied Hycleus species. Comparative analyses of two IGSs suggest that their evolutionary mechanisms are duplication/random loss model and slipped-strand mispairing.
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Affiliation(s)
- Chao Du
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.,Nanchong Vocational and Technical College, Nanchong, 637131, Sichuan, People's Republic of China
| | - Lifang Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Ting Lu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jingnan Ma
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Chenjuan Zeng
- Sichuan Key Laboratory of Medicinal American Cockroach, Chengdu, 610041, People's Republic of China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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31
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Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N. Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study. Mol Phylogenet Evol 2017. [DOI: 10.1016/j.ympev.2017.06.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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32
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Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements. Mol Phylogenet Evol 2017; 113:33-48. [PMID: 28487262 DOI: 10.1016/j.ympev.2017.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/23/2022]
Abstract
Phylogenetics is undergoing a revolution as large-scale molecular datasets reveal unexpected but repeatable rearrangements of clades that were previously thought to be disparate lineages. One of the most unusual clades of fishes that has been found using large-scale molecular datasets is an expanded Syngnathiformes including traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), as well as a diverse set of largely benthic-associated fishes (Callionymoidei, Dactylopteridae, Mullidae, Pegasidae) that were previously dispersed across three orders. The monophyly of this surprising clade of fishes has been upheld by recent studies utilizing both nuclear and mitogenomic data, but the relationships among major lineages within Syngnathiformes remain ambiguous; previous analyses have inconsistent topologies and are plagued by low support at deep divergences between the major lineages. In this study, we use a dataset of ultraconserved elements (UCEs) to conduct the first phylogenomic study of Syngnathiformes. UCEs have been effective markers for resolving deep phylogenetic relationships in fishes and, combined with increased taxon sampling, we expected UCEs to resolve problematic syngnathiform relationships. Overall, UCEs were effective at resolving relationships within Syngnathiformes at a range of evolutionary timescales. We find consistent support for the monophyly of traditional long-snouted syngnathiform lineages (Aulostomidae, Centriscidae, Fistulariidae, Solenostomidae, Syngnathidae), which better agrees with morphological hypotheses than previously published topologies from molecular data. This result was supported by all Bayesian and maximum likelihood analyses, was robust to differences in matrix completeness and potential sources of bias, and was highly supported in coalescent-based analyses in ASTRAL when matrices were filtered to contain the most phylogenetically informative loci. While Bayesian and maximum likelihood analyses found support for a benthic-associated clade (Callionymidae, Dactylopteridae, Mullidae, and Pegasidae) as sister to the long-snouted clade, this result was not replicated in the ASTRAL analyses. The base of our phylogeny is characterized by short internodes separating major syngnathiform lineages and is consistent with the hypothesis of an ancient rapid radiation at the base of Syngnathiformes. Syngnathiformes therefore present an exciting opportunity to study patterns of morphological variation and functional innovation arising from rapid but ancient radiation.
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Smart U, Sarker GC, Arifin U, Harvey MB, Sidik I, Hamidy A, Kurniawan N, Smith EN. A New Genus and Two New Species of Arboreal Toads from the Highlands of Sumatra with a Phylogeny of Sundaland Toad Genera. HERPETOLOGICA 2017. [DOI: 10.1655/herpetologica-d-16-00041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Utpal Smart
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Goutam C. Sarker
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Umilaela Arifin
- Centrum für Naturkunde - Zoologisches Museum, Universität Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Michael B. Harvey
- Department of Biological Sciences, Broward College, 3501 S.W. Davie Road, Davie, FL 33314, USA
| | - Irvan Sidik
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences–LIPI, Widyasatwa Loka Jl. Raya Jakarta Bogor km 46, Cibinong, West Java, Indonesia
| | - Amir Hamidy
- Laboratory of Herpetology, Museum Zoologicum Bogoriense, Research Center for Biology, Indonesian Institute of Sciences–LIPI, Widyasatwa Loka Jl. Raya Jakarta Bogor km 46, Cibinong, West Java, Indonesia
| | - Nia Kurniawan
- Department of Biology, Universitas Brawijaya, Jl. Veteran, Malang, East Java, Indonesia
| | - Eric N. Smith
- Amphibian and Reptile Diversity Research Center and Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
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Chen B, Shao J, Zhuang H, Wen J. Evolutionary dynamics of triosephosphate isomerase gene intron location pattern in Metazoa: A new perspective on intron evolution in animals. Gene 2017; 602:24-32. [PMID: 27864009 DOI: 10.1016/j.gene.2016.11.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/13/2016] [Accepted: 11/14/2016] [Indexed: 11/17/2022]
Abstract
Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated. From 133 representative species of ten phyla, 30 types of ILPs were identified. A most common one, which harbors the maximum six intron positions, is deduced to be the common ancestral tim ILP of Metazoa, which almost had formed in their protozoan ancestor and was surprisingly retained and passed down till to each ancestors of metazoan phyla. In the subsequent animal diversification, it underwent different evolutionary trajectories: within Deuterostomia, it was almost completely retained only with changes in a few species with relatively recently fast-evolving histories, while within the rapidly radiating Protostomia, besides few but remarkable retention, it usually displayed extensive intron losses and a few gains. Therefore, a common ancestral exon-intron arrangement pattern of an animal gene is definitely discovered; besides the 'intron-rich view' of early animal genes being confirmed, the novel insight that high exon-intron re-arrangements of genes seem to be associated with the relatively recently rapid evolution of lineages/species/genomes but have no correlation with the ancient major evolutionary transitions in animal evolution, is revealed.
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Affiliation(s)
- Bing Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Jingru Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Huifu Zhuang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Jianfan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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Blanke A, Watson PJ, Holbrey R, Fagan MJ. Computational biomechanics changes our view on insect head evolution. Proc Biol Sci 2017; 284:20162412. [PMID: 28179518 PMCID: PMC5310608 DOI: 10.1098/rspb.2016.2412] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/09/2017] [Indexed: 12/25/2022] Open
Abstract
Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, to objectively identify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
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Affiliation(s)
- Alexander Blanke
- Medical and Biological Engineering Research Group, School of Engineering, University of Hull, Hull HU6 7RX, UK
| | - Peter J Watson
- Medical and Biological Engineering Research Group, School of Engineering, University of Hull, Hull HU6 7RX, UK
| | - Richard Holbrey
- Medical and Biological Engineering Research Group, School of Engineering, University of Hull, Hull HU6 7RX, UK
| | - Michael J Fagan
- Medical and Biological Engineering Research Group, School of Engineering, University of Hull, Hull HU6 7RX, UK
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36
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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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Dunlop JA, Apanaskevich DA, Lehmann J, Hoffmann R, Fusseis F, Ehlke M, Zachow S, Xiao X. Microtomography of the Baltic amber tick Ixodes succineus reveals affinities with the modern Asian disease vector Ixodes ovatus. BMC Evol Biol 2016; 16:203. [PMID: 27724841 PMCID: PMC5057450 DOI: 10.1186/s12862-016-0777-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/29/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Fossil ticks are extremely rare and Ixodes succineus Weidner, 1964 from Eocene (ca. 44-49 Ma) Baltic amber is one of the oldest examples of a living hard tick genus (Ixodida: Ixodidae). Previous work suggested it was most closely related to the modern and widespread European sheep tick Ixodes ricinus (Linneaus, 1758). RESULTS Restudy using phase contrast synchrotron x-ray tomography yielded images of exceptional quality. These confirm the fossil's referral to Ixodes Latreille, 1795, but the characters resolved here suggest instead affinities with the Asian subgenus Partipalpiger Hoogstraal et al., 1973 and its single living (and medically significant) species Ixodes ovatus Neumann, 1899. We redescribe the amber fossil here as Ixodes (Partipalpiger) succineus. CONCLUSIONS Our data suggest that Ixodes ricinus is unlikely to be directly derived from Weidner's amber species, but instead reveals that the Partipalpiger lineage was originally more widely distributed across the northern hemisphere. The closeness of Ixodes (P.) succineus to a living vector of a wide range of pathogens offers the potential to correlate its spatial and temporal position (northern Europe, nearly 50 million years ago) with the estimated origination dates of various tick-borne diseases.
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Affiliation(s)
- Jason A. Dunlop
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, Invalidenstrasse 43, D-10115 Berlin, Germany
| | - Dmitry A. Apanaskevich
- United States National Tick Collection, The James H. Oliver, Jr. Institute for Coastal Plain Science, Georgia Southern University, Statesboro, GA 30460-8056 USA
| | - Jens Lehmann
- Faculty of Geosciences, University of Bremen, D-28357 Bremen, Germany
| | - René Hoffmann
- Department of Earth Sciences, Ruhr-Universität Bochum, Institute of Geology, Mineralogy, and Geophysics, D-44801 Bochum, Germany
| | - Florian Fusseis
- School of Geosciences, The University of Edinburgh, Grant Institute, King’s Buildings, West Mains Road, Edinburgh, EH9 3JW UK
| | - Moritz Ehlke
- Medical Planning Group, Zuse Institute Berlin, Department Visualization and Data Analysis, D-14195 Berlin, Germany
| | - Stefan Zachow
- Medical Planning Group, Zuse Institute Berlin, Department Visualization and Data Analysis, D-14195 Berlin, Germany
| | - Xianghui Xiao
- Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave, Lemont, IL 60439 USA
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Kjer KM, Simon C, Yavorskaya M, Beutel RG. Progress, pitfalls and parallel universes: a history of insect phylogenetics. J R Soc Interface 2016; 13:20160363. [PMID: 27558853 PMCID: PMC5014063 DOI: 10.1098/rsif.2016.0363] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/19/2016] [Indexed: 11/12/2022] Open
Abstract
The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.
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Affiliation(s)
- Karl M Kjer
- Department of Entomology and Nematology, University of California-Davis, 1282 Academic Surge, Davis, CA 95616, USA
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
| | - Margarita Yavorskaya
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
| | - Rolf G Beutel
- Institut für Spezielle Zoologie und Evolutionsbiologie, FSU Jena, 07743 Jena, Germany
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39
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Porto DS, Almeida EAB, Vilhelmsen L. Comparative morphology of internal structures of the mesosoma of bees with an emphasis on the corbiculate clade (Apidae: Apini). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Diego S. Porto
- Laboratório de Biologia Comparada e Abelhas (LBCA); Departamento de Biologia; Faculdade de Filosofia; Ciências e Letras de Ribeirão Preto (FFCLRP); Universidade de São Paulo; Avenida Bandeirantes, 3900 Ribeirão Preto SP 14040-901 Brazil
| | - Eduardo A. B. Almeida
- Laboratório de Biologia Comparada e Abelhas (LBCA); Departamento de Biologia; Faculdade de Filosofia; Ciências e Letras de Ribeirão Preto (FFCLRP); Universidade de São Paulo; Avenida Bandeirantes, 3900 Ribeirão Preto SP 14040-901 Brazil
| | - Lars Vilhelmsen
- Biosystematics; Natural History Museum of Denmark; Faculty of Science; University of Copenhagen; Universitetsparken 15 Copenhagen DK-2100 Denmark
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40
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Du C, He S, Song X, Liao Q, Zhang X, Yue B. The complete mitochondrial genome of Epicauta chinensis (Coleoptera: Meloidae) and phylogenetic analysis among Coleopteran insects. Gene 2016; 578:274-80. [DOI: 10.1016/j.gene.2015.12.036] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/07/2015] [Accepted: 12/16/2015] [Indexed: 11/15/2022]
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Sass C, Iles WJD, Barrett CF, Smith SY, Specht CD. Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage. PeerJ 2016; 4:e1584. [PMID: 26819846 PMCID: PMC4727956 DOI: 10.7717/peerj.1584] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022] Open
Abstract
The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order, Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.
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Affiliation(s)
- Chodon Sass
- Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley , Berkeley, CA , United States
| | - William J D Iles
- Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley , Berkeley, CA , United States
| | - Craig F Barrett
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States; Department of Biology, California State University, Los Angeles, Los Angeles, CA, United States
| | - Selena Y Smith
- Department of Earth & Environmental Sciences and the Museum of Paleontology, University of Michigan , Ann Arbor, MI , United States
| | - Chelsea D Specht
- Department of Plant and Microbial Biology, Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley , Berkeley, CA , United States
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Blaimer BB, Brady SG, Schultz TR, Lloyd MW, Fisher BL, Ward PS. Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants. BMC Evol Biol 2015; 15:271. [PMID: 26637372 PMCID: PMC4670518 DOI: 10.1186/s12862-015-0552-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/26/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Ultraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has yet to be extensively compared with that of traditional Sanger sequencing data sets. Moreover, UCE data on invertebrates, including insects, are sparse. We compared the phylogenetic informativeness of 959 UCE loci with a multi-locus data set of ten nuclear markers obtained via Sanger sequencing, testing the ability of these two types of data to resolve and date the evolutionary history of the second most species-rich subfamily of ants in the world, the Formicinae. RESULTS Phylogenetic analyses show that UCEs are superior in resolving ancient and shallow relationships in formicine ants, demonstrated by increased node support and a more resolved phylogeny. Phylogenetic informativeness metrics indicate a twofold improvement relative to the 10-gene data matrix generated from the identical set of taxa. We were able to significantly improve formicine classification based on our comprehensive UCE phylogeny. Our divergence age estimations, using both UCE and Sanger data, indicate that crown-group Formicinae are older (104-117 Ma) than previously suggested. Biogeographic analyses infer that the diversification of the subfamily has occurred on all continents with no particular hub of cladogenesis. CONCLUSIONS We found UCEs to be far superior to the multi-locus data set in estimating formicine relationships. The early history of the clade remains uncertain due to ancient rapid divergence events that are unresolvable even with our genomic-scale data, although this might be largely an effect of several problematic taxa subtended by long branches. Our comparison of divergence ages from both Sanger and UCE data demonstrates the effectiveness of UCEs for dating analyses. This comparative study highlights both the promise and limitations of UCEs for insect phylogenomics, and will prove useful to the growing number of evolutionary biologists considering the transition from Sanger to next-generation sequencing approaches.
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Affiliation(s)
- Bonnie B Blaimer
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
| | - Seán G Brady
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
| | - Ted R Schultz
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
| | - Michael W Lloyd
- Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560, USA.
| | - Brian L Fisher
- Department of Entomology, California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - Philip S Ward
- Department of Entomology and Nematology, University of California-Davis, Davis, CA, 95616, USA.
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Heikkilä M, Mutanen M, Wahlberg N, Sihvonen P, Kaila L. Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera). BMC Evol Biol 2015; 15:260. [PMID: 26589618 PMCID: PMC4654798 DOI: 10.1186/s12862-015-0520-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/26/2015] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only. RESULTS Morphological characters are found phylogenetically informative in resolving apical nodes (superfamilies and families), but characters serving as evidence of relatedness of larger assemblages are few. Results include the recovery of a monophyletic Tineoidea, Sesioidea and Cossoidea, and a stable position for some unstable taxa (e.g. Epipyropidae, Cyclotornidae, Urodoidea + Schreckensteinioidea). Several such taxa, however, remain unstable even though morphological characters indicate a position in the tree (e.g. Immidae). Evidence supporting affinities between clades are suggested, e.g. a novel larval synapomorphy for Tineidae. We also propose the synonymy of Tineodidae with Alucitidae, syn. nov. CONCLUSIONS The large morphological dataset provides information on the diversity and distribution of morphological traits in Ditrysia, and can be used in future research on the evolution of these traits, in identification keys and in identification of fossil Lepidoptera. The "backbone" of the phylogeny for Ditrysia remains largely unresolved. As previously proposed as an explanation for the scarcity of molecular signal in resolving the deeper nodes, this may be due to the rapid radiation of Ditrysia in the Cretaceous.
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Affiliation(s)
- Maria Heikkilä
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, PO Box 3000, Oulu, 90014, Finland.
| | - Niklas Wahlberg
- Laboratory of Genetics, Department of Biology, University of Turku, Turku, 20014, Finland.
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Pasi Sihvonen
- University of Helsinki, Research Affairs, PO Box 33, Helsinki, 00014, Finland.
| | - Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
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44
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Xi Z, Liu L, Davis CC. The Impact of Missing Data on Species Tree Estimation. Mol Biol Evol 2015; 33:838-60. [DOI: 10.1093/molbev/msv266] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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45
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Dénes AL, Kolcsár LP, Török E, Keresztes L. Phylogeography of the micro-endemicPedicia staryigroup (Insecta: Diptera): evidence of relict biodiversity in the Carpathians. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Avar-Lehel Dénes
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
- Interdisciplinary Research Institute on Bio-Nano-Sciences of Babeş-Bolyai University; Treboniu Laurian 42 400271 Cluj-Napoca Romania
| | - Levente-Péter Kolcsár
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
| | - Edina Török
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
- Romanian Academy, Institute of Biology; Splaiul Independenţei 296 060031 Bucureşti Romania
| | - Lujza Keresztes
- Hungarian Department of Biology and Ecology; Faculty of Biology and Geology; Babeș-Bolyai University; Clinicilor 5-7 400006 Cluj-Napoca Romania
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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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Hamm CA, Fordyce JA. Patterns of host plant utilization and diversification in the brush-footed butterflies. Evolution 2015; 69:589-601. [PMID: 25546268 DOI: 10.1111/evo.12593] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 12/11/2014] [Indexed: 11/28/2022]
Abstract
Herbivorous insects represent one of the most successful animal radiations known. They occupy a wide range of niches, feed on a great variety of plants, and are species rich; yet the factors that influence their diversification are poorly understood. Host breadth is often cited as a major factor influencing diversification, and, according to the Oscillation Hypothesis, shifts from generalist to specialist feeding states increase the diversification rate for a clade. We explored the relationship between host breadth and diversification within the Nymphalidae (Lepidoptera) and explicitly tested predictions of the Oscillation Hypothesis. We found strong evidence of diversification rate heterogeneity, but no difference in host breadth between clades with a higher diversification rate compared to their sisters. We also found some clades exhibited phylogenetic nonindependence in host breadth and these clades had lower host plant turnover than expected by chance, suggesting host breadth is evolutionarily constrained. Finally, we found that transitions among host breadth categories varied, but the likelihood of reductions in host breadth was greater than that of increases. Our results indicate host breadth is decoupled from diversification rate within the Nymphalidae, and that constraints on diet breadth might play an important role in the evolution of herbivorous insects.
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Affiliation(s)
- Christopher A Hamm
- Department of Ecology and Evolutionary Biology, University of Kansas, 5032 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045.
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Ma C, Wang Y, Wu C, Kang L, Liu C. The compact mitochondrial genome of Zorotypus medoensis provides insights into phylogenetic position of Zoraptera. BMC Genomics 2014; 15:1156. [PMID: 25529234 PMCID: PMC4367826 DOI: 10.1186/1471-2164-15-1156] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 12/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Zoraptera, generally regarded as a member of Polyneoptera, represents one of the most enigmatic insect orders. Although phylogenetic analyses based on a wide array of morphological and/or nuclear data have been performed, the position of Zoraptera is still under debate. Mitochondrial genome (mitogenome) information is commonly considered to be preferable to reconstruct phylogenetic relationships, but no efforts have been made to incorporate it in Zorapteran phylogeny. To characterize Zoraptera mitogenome features and provide insights into its phylogenetic placement, here we sequenced, for the first time, one complete mitogenome of Zoraptera and reconstructed the phylogeny of Polyneoptera. RESULTS The mitogenome of Zorotypus medoensis with an A+T content of 72.50% is composed of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a noncoding A+T-rich region. The gene content and arrangement are identical to those considered ancestral for insects. This mitogenome shows a number of very unusual features. First, it is very compact, comprising 14,572 bp, and is the smallest among all known polyneopteran mitogenomes. Second, both noncoding sequences and coding genes exhibit a significant decrease in size compared with those of other polyneopterans. Third, Z. medoensis mitogenome has experienced an accelerated substitution rate. Fourth, truncated secondary structures of tRNA genes occur with loss of dihydrouridine (DHU) arm in trnC, trnR, and trnS(AGN) and loss of TΨC arm in trnH and trnT. The phylogenetic analyses based on the mitogenome sequence information indicate that Zoraptera, represented by Z. medoensis, is recovered as sister to Embioptera. However, both Zoraptera and Embioptera exhibit very long branches in phylogenetic trees. CONCLUSIONS Characterization of Z. medoensis mitogenome contributes to our understanding of the enigmatic Zoraptera. Mitogenome data demonstrate an overall strong resolution of deep-level phylogenies of Polyneoptera but not Insecta. It is preferable to expand taxon sampling of Zoraptera and other poorly represented orders in future to break up long branches.
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Affiliation(s)
- Chuan Ma
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yeying Wang
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chao Wu
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Le Kang
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101 China
| | - Chunxiang Liu
- />State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
- />Laboratory of Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
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Liu L, Xi Z, Davis CC. Coalescent Methods Are Robust to the Simultaneous Effects of Long Branches and Incomplete Lineage Sorting. Mol Biol Evol 2014; 32:791-805. [DOI: 10.1093/molbev/msu331] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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50
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Garwood RJ, Dunlop J. Three-dimensional reconstruction and the phylogeny of extinct chelicerate orders. PeerJ 2014; 2:e641. [PMID: 25405073 PMCID: PMC4232842 DOI: 10.7717/peerj.641] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/08/2014] [Indexed: 12/12/2022] Open
Abstract
Arachnids are an important group of arthropods. They are: diverse and abundant; a major constituent of many terrestrial ecosystems; and possess a deep and extensive fossil record. In recent years a number of exceptionally preserved arachnid fossils have been investigated using tomography and associated techniques, providing valuable insights into their morphology. Here we use X-ray microtomography to reconstruct members of two extinct arachnid orders. In the Haptopoda, we demonstrate the presence of 'clasp-knife' chelicerae, and our novel redescription of a member of the Phalangiotarbida highlights leg details, but fails to resolve chelicerae in the group due to their small size. As a result of these reconstructions, tomographic studies of three-dimensionally preserved fossils now exist for three of the four extinct orders, and for fossil representatives of several extant ones. Such studies constitute a valuable source of high fidelity data for constructing phylogenies. To illustrate this, here we present a cladistic analysis of the chelicerates to accompany these reconstructions. This is based on a previously published matrix, expanded to include fossil taxa and relevant characters, and allows us to: cladistically place the extinct arachnid orders; explicitly test some earlier hypotheses from the literature; and demonstrate that the addition of fossils to phylogenetic analyses can have broad implications. Phylogenies based on chelicerate morphology-in contrast to molecular studies-have achieved elements of consensus in recent years. Our work suggests that these results are not robust to the addition of novel characters or fossil taxa. Hypotheses surrounding chelicerate phylogeny remain in a state of flux.
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Affiliation(s)
- Russell J. Garwood
- School of Earth, Atmospheric and Environmental Sciences and The Manchester X-ray Imaging Facility, School of Materials, The University of Manchester, Manchester, UK
| | - Jason Dunlop
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity at the Humboldt University Berlin, Berlin, Germany
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