scholarly journals Ten genes and two topologies: an exploration of higher relationships in skipper butterflies (Hesperiidae)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2653 ◽  
Author(s):  
Ranjit Kumar Sahoo ◽  
Andrew D. Warren ◽  
Niklas Wahlberg ◽  
Andrew V. Z. Brower ◽  
Vladimir A. Lukhtanov ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Nuclear Markers ◽  
Gene Markers ◽  
Mitochondrial Markers ◽  
Molecular Dataset

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.

Phylogenetic analysis of the subfamily Hylodinae (Anura, Leptodactylidae) based on morphological characters

2005 ◽  
Vol 26 (2) ◽  
pp. 139-147 ◽  
Author(s):  
Francisca do Val ◽  
Paulo Nuin
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
The Other ◽  
The Family

AbstractThe systematics and phylogenetic relationships of the family Leptodactylidae are controversial as is the intrafamilial phylogeny of the leptodactylids. Here we analyze the relationships of the leptodactylid subfamily Hylodinae. This subfamily has been considered to be monophyletic and composed of three genera, Hylodes, Crossodactylus and Megaelosia. In the present study 49 characters were used, based on different studies on Leptodactylidae phylogeny. Maximum parsimony methods with unweighted and successively weighted characters were used to estimate the phylogeny of the Hylodinae. Upon analysis, the data provided further evidence of the monophyletic status of the three genera, with Megaelosia being the basal genus and the other two genera being sister taxa. The analysis with successive weighting results in a more resolved topology of the species subgroups of the genus Hylodes and separates this genus from Crossodactylus and confirms that the hylodines are monophyletic.

scholarly journals Highly Resolved Phylogenetic Relationships within Order Acipenseriformes According to Novel Nuclear Markers

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 38 ◽  
Author(s):  
Dehuai Luo ◽  
Yanping Li ◽  
Qingyuan Zhao ◽  
Lianpeng Zhao ◽  
Arne Ludwig ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Single Copy ◽  
Species Trees ◽  
Degenerate Primers ◽  
Nuclear Markers ◽  
Gene Markers ◽  
Fossil Species ◽  
Living Fossil ◽  
Molecular Clock Model ◽  
Extant Species

Order Acipenseriformes contains 27 extant species distributed across the northern hemisphere, including so-called “living fossil” species of garfish and sturgeons. Previous studies have focused on their mitochondrial genetics and have rarely used nuclear genetic data, leaving questions as to their phylogenetic relationships. This study aimed to utilize a bioinformatics approach to screen for candidate single-copy nuclear genes, using transcriptomic data from sturgeon species and genomic data from the spotted gar, Lepisosteus oculatus. We utilized nested polymerase chain reaction (PCR) and degenerate primers to identify nuclear protein-coding (NPC) gene markers to determine phylogenetic relationships among the Acipenseriformes. We identified 193 nuclear single-copy genes, selected from 1850 candidate genes with at least one exon larger than 700 bp. Forty-three of these genes were used for primer design and development of 30 NPC markers, which were sequenced for at least 14 Acipenseriformes species. Twenty-seven NPC markers were found completely in 16 species. Gene trees according to Bayesian inference (BI) and maximum likelihood (ML) were calculated based on the 30 NPC markers (20,946 bp total). Both gene and species trees produced very similar topologies. A molecular clock model estimated the divergence time between sturgeon and paddlefish at 204.1 Mya, approximately 10% later than previous estimates based on cytochrome b data (184.4 Mya). The successful development and application of NPC markers provides a new perspective and insight for the phylogenetic relationships of Acipenseriformes. Furthermore, the newly developed nuclear markers may be useful in further studies on the conservation, evolution, and genomic biology of this group.

scholarly journals Cretaceous origin and repeated tertiary diversification of the redefined butterflies

2011 ◽  
Vol 279 (1731) ◽  
pp. 1093-1099 ◽  
Author(s):  
Maria Heikkilä ◽  
Lauri Kaila ◽  
Marko Mutanen ◽  
Carlos Peña ◽  
Niklas Wahlberg
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Sister Group ◽  
Morphological Characters ◽  
Molecular Data ◽  
Bayesian Approaches ◽  
The Family ◽  
Family Level ◽  
Morphological And Molecular Data

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous–Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis , a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

scholarly journals Restructuring the Ancorabolidae Sars (Copepoda, Harpacticoida) and Cletodidae T. Scott, with a new phylogenetic hypothesis regarding the relationships of the Laophontoidea T. Scott, Ancorabolidae and Cletodidae

2020 ◽  
Vol 96 (2) ◽  
pp. 455-498
Author(s):  
Kai Horst George
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Characteristics ◽  
Sister Group ◽  
Morphological Characters ◽  
Sister Group Relationship ◽  
Phylogenetic Hypothesis ◽  
The Family ◽  
Swimming Leg

Uncovering the systematics of CopepodaHarpacticoida, the second-most abundant component of the meiobenthos after Nematoda, is of major importance for any further research dedicated especially to ecological and biogeographical approaches. Based on the evolution of the podogennontan first swimming leg, a new phylogenetic concept of the Ancorabolidae Sars and Cletodidae T. Scott sensu Por (Copepoda, Harpacticoida) is presented, using morphological characteristics. It confirms the polyphyletic status of the Ancorabolidae and its subfamily Ancorabolinae Sars and the paraphyletic status of the subfamily Laophontodinae Lang. Moreover, it clarifies the phylogenetic relationships of the so far assigned members of the family. An exhaustive phylogenetic analysis was undertaken using 150 morphological characters, resulting in the establishment of a now well-justified monophylum Ancorabolidae. In that context, the Ancorabolus-lineage sensu Conroy-Dalton and Huys is elevated to sub-family rank. Furthermore, the membership of Ancorabolina George in a rearranged monophylum Laophontodinae is confirmed. Conversely, the Ceratonotus-group sensu Conroy-Dalton is transferred from the hitherto Ancorabolinae to the Cletodidae. Within these, the Ceratonotus-group and its hypothesised sister-group Cletodes Brady are combined to form a monophyletic subfamily Cletodinae T. Scott, subfam. nov. Consequently, it was necessary to restructure the Ancorabolidae, Ancorabolinae and Laophontodinae and extend the Cletodidae to include the displacement and exclusion of certain taxa. Moreover, comparison of the Ancorabolidae, Cletodidae, Laophontoidea and other Podogennonta shows that the Ancorabolidae and Cletodidae form sister-groups in a monophylum Cletodoidea Bowman and Abele, which similarly has a sister-group-relationship with the Laophontoidea T. Scott. According to the present study, both taxa constitute a derived monophylum within the Podogennonta Lang.

Revisited phylogeny of Bethylinae (Hymenoptera, Bethylidae) solves basal polytomy

2020 ◽  
Vol 51 (3) ◽  
pp. 296-346
Author(s):  
Magno S. Ramos ◽  
Celso O. Azevedo
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Female Characters ◽  
Wing Morphology ◽  
Male And Female ◽  
Strongly Convex ◽  
The Family ◽  
Males And Females ◽  
First Time

Bethylinae are a morphologically well-defined subfamily of Bethylidae, with remarkable characters, such as strongly convex clypeal carina and bifid and angled tarsal claws. However, there is no consensus about the phylogenetic relationships among the genera within the family, regarding mainly Eupsenella and Lytopsenella. To resolve this problem, a phylogeny of the Bethylinae is inferred based on parsimony analyses separately of 43 and 44 morphological characters for males and females, respectively. We performed combined analyses of both sexes with 49 morphological characters, including genitalia. We present a phylogenetic analysis, including a total 118 species of Bethylinae. Male and female characters were included in these analyses. We discuss wing morphology and deformability of forewings for the first time. In summary, the basal polytomy was solved for the first time. Seven of the eight genera were recovered as monophyletic groups. The unique exception is Goniozus, which was retrieved as paraphyletic in all topologies.

Phylogenetic analysis of the rumen ciliate family Ophryoscolecidae based on 18S ribosomal RNA sequences, with new sequences fromDiplodinium,Eudiplodinium, andOphryoscolex

1997 ◽  
Vol 75 (6) ◽  
pp. 963-970 ◽  
Author(s):  
André-Denis G. Wright ◽  
Denis H. Lynn
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Small Subunit ◽  
Base Pairs ◽  
Rna Sequences ◽  
Ribosomal Rna Sequences ◽  
The Family

Phylogenetic relationships within the largest family of entodiniomorphid rumen ciliates, the Ophryoscolecidae, were inferred from comparisons of small-subunit ribosomal RNA gene sequences. These included three new sequences from Diplodinium dentatum (1638 base pairs (bp)), Eudiplodinium maggii (1637 bp), and Ophryoscolex purkynjei (1636 bp). Using morphological characters, Lubinsky constructed a cladogram of the Ophryoscolecidae, and on the basis of his analysis, he divided the family into three subfamilies (Entodiniinae, Diplodiniinae, Ophryoscolecinae) to reflect his "natural" groupings (G. Lubinsky. 1957. Can. J. Zool. 35: 141 – 159). Our cladistic analysis, based on the limited morphological and ultrastructural data available, indicates that there are no synapomorphies supporting the Diplodiniinae sensu Lubinsky. However, based upon the six 18S sequences for the Ophryoscolecidae, the rumen ciliates are monophyletic and fall into three distinct groups corresponding to Lubinsky's subfamilial division of the family. Our molecular analysis shows Entodinium to be the earliest branching rumen ciliate (subfamily Entodiniinae) and Eudiplodinium, not Diplodiium, branching first among the diplodiniines.

Phylogenetic analysis of Gigantodax (Diptera: Simuliidae)

2005 ◽  
Vol 36 (2) ◽  
pp. 219-239
Author(s):  
Paulina Muñoz De Hoyos ◽  
Daniel Rafael Miranda-Esquivel ◽  
Nelsy Rocío Pinto-Sánchez
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Characters ◽  
Frequency Index ◽  
Species Groups

AbstractA study of the monophyly and phylogenetic relationships among the Gigantodax species-groups was conducted using all Gigantodax species and six outgroups. This analysis was conducted using 71 characters, 58 of them morphological characters derived from 66 species, and 13 of them cytological characters from 11 species. We conducted two analyses under linear parsimony and implied weights. To define the best concavity value we used the frequency index. The value that recovered the most of the groups was linear parsimony search. We obtained 2037 equally parsimonious trees of 277 steps (CI=0.37 RI=0.65). The second value to recover most of the groups was implied weight search with the concavity value of one. Only the igniculus and minor groups were recovered by both analyses (linear parsimony and implied weights K=1). Under linear parsimony the phylogenetic analysis recovered two species groups (igniculus and cormonsi). The remaining four groups (“brophyi”, “cilicinus”, “minor”, and “wrighti”) are non-monophyletic. Based on the cladogram we suggest the following species groups: igniculus (igniculus group), cormonsi (cormonsi group), minor (containing “minor” + “multifilis”), brophyi (G. antarcticus, G. brophyi, G. femineus, G. rufidulus, and G. trifidus), shannoni (containing G. bettyae, G. incomitatus, G. mariobordai, G. pennipunctus, G. septenarius, and G. shannoni), and rufescens (containing G. aquamarensis, G. arrarteorum, G. basinflatus, G. cervicornis, G. cilicinus, G. clandestinus, G. corniculatus, G. cypellus, G. dryadicaudicis, G. herreri, G. horcotiani, G. impossibilis, G. incapucara, G. nasutus, G. rufescens, and G. wrighti). Some species, previously assigned to “cilicinus”, “wrighti”, and “brophyi” groups are kept as inquerandae.

Phylogenetic analysis of the small fungivorous family Merothripidae (Thysanoptera)

2011 ◽  
Vol 42 (4) ◽  
pp. 385-409
Author(s):  
Veronica Pereyra
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Sister Group ◽  
Morphological Characters ◽  
First Approximation ◽  
Close Relatives

AbstractA phylogenetic analysis of the fungivorous Terebrantia family Merothripidae is performed based on 73 morphological characters and 24 taxa representing the three genera of Merothripidae and outgroups. Heterothrips mexicanus Watson, Heterothripidae; Dorythrips Hood, Melanthripidae; and two genera of Aeolothripidae,Gelothrips Bhatti and Orothrips Moulton represent the outgroup. The Melanthripidae and Aeolothripidae genera are included in order to have a first approximation of the phylogenetic relationships between Merothripidae and these two families (previously suggested to be close relatives). According to the results, the monophyly of Merothripidae is recovered; within Merothripidae, Erotidothrips is the sister group of Damerothrips+Merothrips. Dorythrips is supported as the sister group of Merothripidae, and Aeolothripidae are the sister group to that clade. Additionally, Merothripidae genera are diagnosed and illustrated.

Molecular phylogenetics and taxonomic reanalysis of the family Mithracidae MacLeay (Decapoda : Brachyura : Majoidea)

2014 ◽  
Vol 28 (2) ◽  
pp. 145 ◽  
Author(s):  
Amanda M. Windsor ◽  
Darryl L. Felder
Keyword(s):  
Molecular Phylogeny ◽  
Phylogenetic Relationships ◽  
Molecular Phylogenetics ◽  
Morphological Characters ◽  
Mitochondrial Genes ◽  
Hard Substrate ◽  
The Family ◽  
Molecular Dataset

Mithracid crabs comprise a primarily subtidal reef- and rubble-dwelling group inhabiting both tropical and subtropical seas. Despite their relative ubiquity in many hard-substrate environments, there has been little consensus about their phylogenetic relationships or whether their group rank should be that of subfamily or family. We have used a combined molecular dataset of two nuclear (18S, H3) and three mitochondrial (12S, 16S, COI) genes to build a preliminary molecular phylogeny of Majoidea in order to examine the membership of Mithracidae. We then built a second molecular phylogeny based on three mitochondrial genes to assess the internal composition of the family, and conducted comparative morphological examinations of genera and species that resolved in unexpected positions on the phylogram. Four genera are designated under new or resurrected names on the basis of molecular and morphological characters, while memberships of several other existing genera are modified. Following review of molecular and morphological characters, the genera Coelocerus, Cyclocoeloma, Cyphocarcinus, Leptopisa, Micippa, Picrocerodes, Stenocionops and Tiarinia are provisionally excluded from Mithracidae s.s., while Hemus and Pitho are included in it. A key to genera of Mithracidae is provided.

A revision of the wasp genus Paniscomima (Hymenoptera:Rhopalosomatidae) and a proposal of phylogenetic relationships among species

2007 ◽  
Vol 21 (4) ◽  
pp. 297 ◽  
Author(s):  
Antonia Elena Guidotti
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Phylogenetic Relationships ◽  
East Asian ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Nominal Species ◽  
Asian Clade ◽  
Malaise Traps ◽  
First Descriptions

Species of the wasp family Rhopalosomatidae are parasitoids of crickets. The last revision of this family was completed 30 years ago. Since then, with many more specimens collected by Malaise traps, an update of existing descriptions and keys has been made possible. New generic characters have been added to the description for Paniscomima Enderlein. Four new species of Paniscomima are described: P. angelae, sp. nov., P. darlingi, sp. nov., P. lottacontinua, sp. nov., and P. paropposita, sp. nov. The first descriptions of male P. seyrigi (Berland) and female P. opposita Townes and a key to the species of Paniscomima are provided. A cladistic analysis was performed to determine the relationships among the 11 nominal species of Paniscomima. Sixteen morphological characters were used in the analysis and exemplars from the genus Rhopalosoma were used as outgroup taxa. The phylogenetic analysis supports a South-east Asian clade with a sister species from Madagascar and a basal polytomy of species occurring in Africa (including Madagascar).

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