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Legeai F, Romain S, Capblancq T, Doniol-Valcroze P, Joron M, Lemaitre C, Després L. Chromosome-Level Assembly and Annotation of the Pearly Heath Coenonympha arcania Butterfly Genome. Genome Biol Evol 2024; 16:evae055. [PMID: 38491969 PMCID: PMC10980516 DOI: 10.1093/gbe/evae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
We present the first chromosome-level genome assembly and annotation of the pearly heath Coenonympha arcania, generated with a PacBio HiFi sequencing approach and complemented with Hi-C data. We additionally compare synteny, gene, and repeat content between C. arcania and other Lepidopteran genomes. This reference genome will enable future population genomics studies with Coenonympha butterflies, a species-rich genus that encompasses some of the most highly endangered butterfly taxa in Europe.
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Affiliation(s)
- Fabrice Legeai
- Inria, CNRS, IRISA, University of Rennes, 35000 Rennes, France
- IGEPP, INRAE, Institut Agro, University of Rennes, 35653 Le Rheu, France
| | - Sandra Romain
- Inria, CNRS, IRISA, University of Rennes, 35000 Rennes, France
| | - Thibaut Capblancq
- LECA, CNRS, Université Grenoble-Alpes, Université Savoie Mont Blanc, Grenoble, France
| | | | - Mathieu Joron
- CEFE, CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
| | - Claire Lemaitre
- Inria, CNRS, IRISA, University of Rennes, 35000 Rennes, France
| | - Laurence Després
- LECA, CNRS, Université Grenoble-Alpes, Université Savoie Mont Blanc, Grenoble, France
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2
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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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3
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Dubatolov VV, Korb SK, Yakovlev RV. A review of the genus Triphysa Zeller, 1858 (Lepidoptera, Satyridae)*. ECOLOGICA MONTENEGRINA 2023. [DOI: 10.37828/em.2023.61.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
A review of the genus Triphysa Zeller, 1858 is presented. One new species Triphysa issykkulica sp.n. (type locality: Kazakhstan, W of Almaty, 800 m) and 8 new subspecies are described: Triphysa phryne kasikoporana ssp. n. (type locality: Kasikoporan [NE Turkey, Agri prov.]), Triphysa striatula urumtchiensis ssp. n. (type locality: Urumtchi), Triphysa issykkulica pljustchi ssp. n. (type locality: W. Kirgiziya, Talasskii Mts., Manas), Triphysa nervosa tuvinica ssp. n. (type locality: N. Tuva, near Kyzyl, Tuge Mt.), Triphysa nervosa arturi ssp. n. (type locality: S. Tuva, 15 km WSW Erzin), Triphysa nervosa kobdoensis ssp. n. (type locality: W. Mongolia, Hovd aimak, 15 km S Khara-Us-Nuur lake, 1300 m), Triphysa nervosa mongolaltaica ssp. n. (type locality: Mongolia, Hovd aimak, Bulgan-Gol basin, middle stream of Ulyasutai-Gol river, 2500−3000 m) and Triphysa nervosa brinikhi ssp. n. (type locality: Russia, Chita Reg., Onon distr., 18 km WSW Nizhniy Zasuchey vill., Butyvken lake, Pinus forest, steppe) are described. New status for Triphysa striatula Elwes, 1899, stat. n. is established. The lectotypes of Triphysa nervosa gartoki O.Bang-Haas, 1927, Triphysa phryne kintschouensis O. Bang-Haas, 1939, Triphysa phryne biocellata Staudinger, 1901, Triphysa nervosa tscherski Grum-Grshimailo, 1889 [1890], Triphysa nervosa glacialis A. Bang-Haas, 1912 are designated, the neotype of T. dohrnii Zeller, 1850 (type locality: [Russia], Sarepta) is designated.
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Aduse-Poku K, van Bergen E, Sáfián S, Collins SC, Etienne RS, Herrera-Alsina L, Brakefield PM, Brattström O, Lohman DJ, Wahlberg N. Miocene Climate and Habitat Change Drove Diversification in Bicyclus, Africa's Largest Radiation of Satyrine Butterflies. Syst Biol 2021; 71:570-588. [PMID: 34363477 PMCID: PMC9016770 DOI: 10.1093/sysbio/syab066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/14/2022] Open
Abstract
Compared to other regions, the drivers of diversification in Africa are poorly understood. We studied a radiation of insects with over 100 species occurring in a wide range of habitats across the Afrotropics to investigate the fundamental evolutionary processes and geological events that generate and maintain patterns of species richness on the continent. By investigating the evolutionary history of Bicyclus butterflies within a phylogenetic framework, we inferred the group's origin at the Oligo-Miocene boundary from ancestors in the Congolian rainforests of central Africa. Abrupt climatic fluctuations during the Miocene (ca. 19-17 Ma) likely fragmented ancestral populations, resulting in at least eight early-divergent lineages. Only one of these lineages appears to have diversified during the drastic climate and biome changes of the early Miocene, radiating into the largest group of extant species. The other seven lineages diversified in forest ecosystems during the late Miocene and Pleistocene when climatic conditions were more favourable-warmer and wetter. Our results suggest changing Neogene climate, uplift of eastern African orogens, and biotic interactions might have had different effects on the various subclades of Bicyclus, producing one of the most spectacular butterfly radiations in Africa.
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Affiliation(s)
- Kwaku Aduse-Poku
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.,Biology Department, University of Richmond, Richmond, 138 UR Drive, USA.,Department of Life and Earth Sciences, Perimeter College, Georgia State University, USA
| | - Erik van Bergen
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.,Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland
| | - Szabolcs Sáfián
- Institute of Silviculture and Forest Protection, University of Sopron, Sopron, Hungary
| | - Steve C Collins
- African Butterfly Research Institute, P.O. Box 14308, 0800 Westlands, Nairobi, Kenya
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, 9700 CC Groningen, The Netherlands
| | | | - Paul M Brakefield
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK
| | - Oskar Brattström
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, UK.,African Butterfly Research Institute, P.O. Box 14308, 0800 Westlands, Nairobi, Kenya.,University of Glasgow, School of Life Sciences, Glasgow, Scotland, UK.,University of Glasgow, Institute of Biodiversity, Animal Health and Comparative Medicine, Glasgow, Scotland, UK
| | - David J Lohman
- Biology Department, City College of New York, City University of New York, USA.,Ph.D. Program in Biology, Graduate Center, City University of New York, NY, USA.,Entomology Section, National Museum of Natural History, Manila, 1000, Philippines
| | - Niklas Wahlberg
- Department of Biology, Lund University, Sölvegatan35, SE-223, 62 Lund, Sweden
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Le Kim T, Le Sy V. mPartition: A Model-Based Method for Partitioning Alignments. J Mol Evol 2020; 88:641-652. [PMID: 32864711 DOI: 10.1007/s00239-020-09963-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 08/08/2020] [Indexed: 10/23/2022]
Abstract
Maximum likelihood (ML) analysis of nucleotide or amino-acid alignments is widely used to infer evolutionary relationships among species. Computing the likelihood of a phylogenetic tree from such alignments is a complicated task because the evolutionary processes typically vary across sites. A number of studies have shown that partitioning alignments into sub-alignments of sites, where each sub-alignment is analyzed using a different model of evolution (e.g., GTR + I + G), is a sensible strategy. Current partitioning methods group sites into subsets based on the inferred rates of evolution at the sites. However, these do not provide sufficient information to adequately reflect the substitution processes of characters at the sites. Moreover, the site rate-based methods group all invariant sites into one subset, potentially resulting in wrong phylogenetic trees. In this study, we propose a partitioning method, called mPartition, that combines not only the evolutionary rates but also substitution models at sites to partition alignments. Analyses of different partitioning methods on both real and simulated datasets showed that mPartition was better than the other partitioning methods tested. Notably, mPartition overcame the pitfall of grouping all invariant sites into one subset. Using mPartition may lead to increased accuracy of ML-based phylogenetic inference, especially for multiple loci or whole genome datasets.
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Affiliation(s)
- Thu Le Kim
- University of Engineering and Technology, Vietnam National University Hanoi, 144 Xuan Thuy, Cau Giay, Hanoi, 10000, Vietnam.,Hanoi University of Science and Technology, 1st Dai Co Viet, Hai Ba Trung, Hanoi, 10000, Vietnam
| | - Vinh Le Sy
- University of Engineering and Technology, Vietnam National University Hanoi, 144 Xuan Thuy, Cau Giay, Hanoi, 10000, Vietnam.
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6
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Mitochondrial genomes of four satyrine butterflies and phylogenetic relationships of the family Nymphalidae (Lepidoptera: Papilionoidea). Int J Biol Macromol 2020; 145:272-281. [DOI: 10.1016/j.ijbiomac.2019.12.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/01/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023]
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Rota J, Malm T, Chazot N, Peña C, Wahlberg N. A simple method for data partitioning based on relative evolutionary rates. PeerJ 2018; 6:e5498. [PMID: 30186687 PMCID: PMC6118207 DOI: 10.7717/peerj.5498] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 08/01/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns. METHODS We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k-means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder. RESULTS Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset. DISCUSSION We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.
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Affiliation(s)
- Jadranka Rota
- Department of Biology, Lund University, Lund, Sweden
| | - Tobias Malm
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Carlos Peña
- HipLead, San Francisco, CA, United States of America
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8
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Cyriac VP, Kodandaramaiah U. Paleoclimate determines diversification patterns in the fossorial snake family Uropeltidae Cuvier, 1829. Mol Phylogenet Evol 2017; 116:97-107. [PMID: 28867076 DOI: 10.1016/j.ympev.2017.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/17/2017] [Accepted: 08/24/2017] [Indexed: 11/15/2022]
Abstract
Understanding how and why diversification rates vary across evolutionary time is central to understanding how biodiversity is generated and maintained. Recent mathematical models that allow estimation of diversification rates across time from reconstructed phylogenies have enabled us to make inferences on how biodiversity copes with environmental change. Here, we explore patterns of temporal diversification in Uropeltidae, a diverse fossorial snake family. We generate a time-calibrated phylogenetic hypothesis for Uropeltidae and show a significant correlation between diversification rate and paleotemperature during the Cenozoic. We show that the temporal diversification pattern of this group is punctuated by one rate shift event with a decrease in diversification and turnover rate between ca. 11Ma to present, but there is no strong support for mass extinction events. The analysis indicates higher turnover during periods of drastic climatic fluctuations and reduced diversification rates associated with contraction and fragmentation of forest habitats during the late Miocene. Our study highlights the influence of environmental fluctuations on diversification rates in fossorial taxa such as uropeltids, and raises conservation concerns related to present rate of climate change.
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Affiliation(s)
- Vivek Philip Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Thiruvananthapuram, Kerala 695551, India.
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Thiruvananthapuram, Kerala 695551, India
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Sahoo RK, Warren AD, Wahlberg N, Brower AVZ, Lukhtanov VA, Kodandaramaiah U. Ten genes and two topologies: an exploration of higher relationships in skipper butterflies (Hesperiidae). PeerJ 2016; 4:e2653. [PMID: 27957386 PMCID: PMC5144725 DOI: 10.7717/peerj.2653] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/04/2016] [Indexed: 11/20/2022] Open
Abstract
Despite multiple attempts to infer the higher-level phylogenetic relationships of skipper butterflies (Family Hesperiidae), uncertainties in the deep clade relationships persist. The most recent phylogenetic analysis included fewer than 30% of known genera and data from three gene markers. Here we reconstruct the higher-level relationships with a rich sampling of ten nuclear and mitochondrial markers (7,726 bp) from 270 genera and find two distinct but equally plausible topologies among subfamilies at the base of the tree. In one set of analyses, the nuclear markers suggest two contrasting topologies, one of which is supported by the mitochondrial dataset. However, another set of analyses suggests mito-nuclear conflict as the reason for topological incongruence. Neither topology is strongly supported, and we conclude that there is insufficient phylogenetic evidence in the molecular dataset to resolve these relationships. Nevertheless, taking morphological characters into consideration, we suggest that one of the topologies is more likely.
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Affiliation(s)
- Ranjit Kumar Sahoo
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, India
| | - Andrew D. Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, UF Cultural Plaza, Gainesville, FL, USA
| | - Niklas Wahlberg
- Department of Biology, Lund University, Lund, Sweden
- Department of Biology, University of Turku, Turku, Finland
| | - Andrew V. Z. Brower
- Evolution and Ecology Group, Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Vladimir A. Lukhtanov
- Department of Insect Systematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia
- Department of Entomology, St. Petersburg State University, St. Petersburg, Russia
| | - Ullasa Kodandaramaiah
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, India
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10
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Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Mol Phylogenet Evol 2016; 97:32-42. [DOI: 10.1016/j.ympev.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/04/2015] [Accepted: 12/23/2015] [Indexed: 02/02/2023]
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11
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Sobral G, Sues HD, Müller J. Anatomy of the Enigmatic Reptile Elachistosuchus huenei Janensch, 1949 (Reptilia: Diapsida) from the Upper Triassic of Germany and Its Relevance for the Origin of Sauria. PLoS One 2015; 10:e0135114. [PMID: 26352985 PMCID: PMC4564268 DOI: 10.1371/journal.pone.0135114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/19/2015] [Indexed: 12/03/2022] Open
Abstract
The holotype and only known specimen of the enigmatic small reptile Elachistosuchus huenei Janensch, 1949 from the Upper Triassic (Norian) Arnstadt Formation of Saxony-Anhalt (Germany) is redescribed using μCT scans of the material. This re-examination revealed new information on the morphology of this taxon, including previously unknown parts of the skeleton such as the palate, braincase, and shoulder girdle. Elachistosuchus is diagnosed especially by the presence of the posterolateral process of the frontal, the extension of the maxillary tooth row to the posterior margin of the orbit, the free posterior process of the jugal, and the notched anterior margin of the interclavicle. Phylogenetic analyses using two recently published character-taxon matrices recovered conflicting results for the phylogenetic position of Elachistosuchus-either as an archosauromorph, as a lepidosauromorph or as a more basal, non-saurian diapsid. These different placements highlight the need of a thorough revision of critical taxa and new character sets used for inferring neodiapsid relationships.
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Affiliation(s)
- Gabriela Sobral
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
| | - Hans-Dieter Sues
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, MRC 121, Washington, DC, United States of America
| | - Johannes Müller
- Museum für Naturkunde Berlin, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
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12
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Peña C, Espeland M. Diversity dynamics in Nymphalidae butterflies: effect of phylogenetic uncertainty on diversification rate shift estimates. PLoS One 2015; 10:e0120928. [PMID: 25830910 PMCID: PMC4382342 DOI: 10.1371/journal.pone.0120928] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 02/09/2015] [Indexed: 01/27/2023] Open
Abstract
The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution.
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Affiliation(s)
- Carlos Peña
- Laboratory of Genetics, Department of Biology, University of Turku, Turku, Finland
| | - Marianne Espeland
- Museum of Comparative Zoology, Harvard University, Cambridge, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
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13
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Nylin S, Slove J, Janz N. Host plant utilization, host range oscillations and diversification in nymphalid butterflies: a phylogenetic investigation. Evolution 2014; 68:105-24. [PMID: 24372598 PMCID: PMC3912913 DOI: 10.1111/evo.12227] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 07/26/2013] [Indexed: 11/26/2022]
Abstract
It has been suggested that phenotypic plasticity is a major factor in the diversification of life, and that variation in host range in phytophagous insects is a good model for investigating this claim. We explore the use of angiosperm plants as hosts for nymphalid butterflies, and in particular the evidence for past oscillations in host range and how they are linked to host shifts and to diversification. At the level of orders of plants, a relatively simple pattern of host use and host shifts emerges, despite the 100 million years of history of the family Nymphalidae. We review the evidence that these host shifts and the accompanying diversifications were associated with transient polyphagous stages, as suggested by the "oscillation hypothesis." In addition, we investigate all currently polyphagous nymphalid species and demonstrate that the state of polyphagy is rare, has a weak phylogenetic signal, and a very apical distribution in the phylogeny; we argue that these are signs of its transient nature. We contrast our results with data from the bark beetles Dendroctonus, in which a more specialized host use is instead the apical state. We conclude that plasticity in host use is likely to have contributed to diversification in nymphalid butterflies.
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Affiliation(s)
- Sören Nylin
- Department of Zoology, Stockholm University, Stockholm, 10691, Sweden.
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14
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Sessa EB, Zimmer EA, Givnish TJ. Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae). BMC Evol Biol 2012; 12:104. [PMID: 22748145 PMCID: PMC3509404 DOI: 10.1186/1471-2148-12-104] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/14/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The thirteen species of Dryopteris in North America have long been suspected of having undergone a complicated history of reticulate evolution via allopolyploid hybridization. Various explanations for the origins of the allopolyploid taxa have been suggested, and though most lines of evidence have supported the so-called "semicristata" hypothesis, contention over the group's history has continued in several recent, conflicting studies. RESULTS Sequence data from nine plastid and two nuclear markers were collected from 73 accessions representing 35 species of Dryopteris. Sequences from each of the allopolyploids are most closely related to their progenitor species as predicted by the "semicristata" hypothesis. Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D. expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D. carthusiana and D. cristata, from diploid "D. semicristata" x D. intermedia and D. ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D. cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma. We found no evidence for recurrent formation of any of the allopolyploids. The sexual allopolyploid taxa are derived from crosses between parents that show intermediate levels of genetic divergence relative to all pairs of potential progenitors. In addition, the four allotetraploids are transgressive with respect to geographic range relative to one or both of their parents (their ranges extend beyond those of the parents), suggesting that ecological advantages in novel habitats or regions may promote long-term regional coexistence of the hybrid taxa with their progenitors. CONCLUSIONS This study provides the first thorough evaluation of the North American complex of woodferns using extensive sampling of taxa and genetic markers. Phylogenies produced from each of three datasets (one plastid and two nuclear) support the "semicristata" hypothesis, including the existence of a missing diploid progenitor, and allow us to reject all competing hypotheses. This study demonstrates the value of using multiple, biparentally inherited markers to evaluate reticulate complexes, assess the frequency of recurrent polyploidization, and determine the relative importance of introgression vs. hybridization in shaping the histories of such groups.
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Affiliation(s)
- Emily B Sessa
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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Rooting phylogenies using gene duplications: An empirical example from the bees (Apoidea). Mol Phylogenet Evol 2011; 60:295-304. [DOI: 10.1016/j.ympev.2011.05.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 04/26/2011] [Accepted: 05/03/2011] [Indexed: 12/23/2022]
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KODANDARAMAIAH U, WEINGARTNER E, JANZ N, DALÉN L, NYLIN S. Population structure in relation to host-plant ecology and Wolbachia infestation in the comma butterfly. J Evol Biol 2011; 24:2173-85. [DOI: 10.1111/j.1420-9101.2011.02352.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Thomson MM, Fernández-García A. Phylogenetic structure in African HIV-1 subtype C revealed by selective sequential pruning. Virology 2011; 415:30-8. [PMID: 21507449 DOI: 10.1016/j.virol.2011.03.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 03/11/2011] [Accepted: 03/17/2011] [Indexed: 10/18/2022]
Abstract
Subtype C is the most prevalent clade in the HIV-1 pandemic. Previous studies suggested that African HIV-1 subtype C lacks a well-defined phylogenetic structure. Here we show that, by sequential pruning of ambiguously positioned taxa, a well-defined intrasubtype C phylogenetic structure becomes apparent, with 52% African HIV-1 subtype C isolates analyzed in envelope sequences branching within 11 clusters, also supported in a tree of full-length genomes, and all with geographical associations. Among 46 viruses recently transmitted in South Africa, 70% branched within 7 clusters (41% in the largest one) and 15% additional isolates were intercluster recombinants. Choice of the outgroup sequence and inclusion of intrasubtype recombinant viruses in the analyses could greatly affect support of clusters. The identification of clusters comprising a large proportion of African HIV-1 subtype C viruses may have implications for the design of vaccines intended for use in areas where subtype C is prevalent.
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Affiliation(s)
- Michael M Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. Majadahonda-Pozuelo Km. 2, Majadahonda, Madrid, Spain.
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Nazari V, Larsen TB, Lees DC, Brattström O, Bouyer T, Van de Poel G, Hebert PDN. Phylogenetic systematics of Colotis and associated genera (Lepidoptera: Pieridae): evolutionary and taxonomic implications. J ZOOL SYST EVOL RES 2011. [DOI: 10.1111/j.1439-0469.2011.00620.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Between a rock and a hard polytomy: Rapid radiation in the rupicolous girdled lizards (Squamata: Cordylidae). Mol Phylogenet Evol 2011; 58:53-70. [DOI: 10.1016/j.ympev.2010.08.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 08/21/2010] [Accepted: 08/24/2010] [Indexed: 11/22/2022]
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Zahiri R, Kitching IJ, Lafontaine JD, Mutanen M, Kaila L, Holloway JD, Wahlberg N. A new molecular phylogeny offers hope for a stable family level classification of the Noctuoidea (Lepidoptera). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00459.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Müller C, Beheregaray L. Palaeo island-affinities revisited – Biogeography and systematics of the Indo-Pacific genus Cethosia Fabricius (Lepidoptera: Nymphalidae). Mol Phylogenet Evol 2010; 57:314-26. [DOI: 10.1016/j.ympev.2010.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 05/23/2010] [Accepted: 07/01/2010] [Indexed: 11/25/2022]
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Kodandaramaiah U, Lees DC, Müller CJ, Torres E, Karanth KP, Wahlberg N. Phylogenetics and biogeography of a spectacular Old World radiation of butterflies: the subtribe Mycalesina (Lepidoptera: Nymphalidae: Satyrini). BMC Evol Biol 2010; 10:172. [PMID: 20537168 PMCID: PMC2898688 DOI: 10.1186/1471-2148-10-172] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Accepted: 06/10/2010] [Indexed: 02/07/2023] Open
Abstract
Background Butterflies of the subtribe Mycalesina (Nymphalidae: Satyrinae) are important model organisms in ecology and evolution. This group has radiated spectacularly in the Old World tropics and presents an exciting opportunity to better understand processes of invertebrate rapid radiations. However, the generic-level taxonomy of the subtribe has been in a constant state of flux, and relationships among genera are unknown. There are six currently recognized genera in the group. Mycalesis, Lohora and Nirvanopsis are found in the Oriental region, the first of which is the most speciose genus among mycalesines, and extends into the Australasian region. Hallelesis and Bicyclus are found in mainland Africa, while Heteropsis is primarily Madagascan, with a few species in Africa. We infer the phylogeny of the group with data from three genes (total of 3139 bp) and use these data to reconstruct events in the biogeographic history of the group. Results The results indicate that the group Mycalesina radiated rapidly around the Oligocene-Miocene boundary. Basal relationships are unresolved, but we recover six well-supported clades. Some species of Mycalesis are nested within a primarily Madagascan clade of Heteropsis, while Nirvanopsis is nested within Lohora. The phylogeny suggests that the group had its origin either in Asia or Africa, and diversified through dispersals between the two regions, during the late Oligocene and early Miocene. The current dataset tentatively suggests that the Madagascan fauna comprises two independent radiations. The Australasian radiation shares a common ancestor derived from Asia. We discuss factors that are likely to have played a key role in the diversification of the group. Conclusions We propose a significantly revised classification scheme for Mycalesina. We conclude that the group originated and radiated from an ancestor that was found either in Asia or Africa, with dispersals between the two regions and to Australasia. Our phylogeny paves the way for further comparative studies on this group that will help us understand the processes underlying diversification in rapid radiations of invertebrates.
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Peña C, Nylin S, Freitas AVL, Wahlberg N. Biogeographic history of the butterfly subtribe Euptychiina (Lepidoptera, Nymphalidae, Satyrinae). ZOOL SCR 2010. [DOI: 10.1111/j.1463-6409.2010.00421.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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