A BARCODE-BASED PHYLOGENETIC SCAFFOLD FOR XYSTICUS AND ITS RELATIVES (ARANEAE: THOMISIDAE: CORIARACHNINI)

The phylogenetic relationships and taxonomy of the crab spider genus Xysticus and its closest relatives (i.e., the tribe Coriarachnini, also including, e.g., Ozyptila, Coriarachne and Bassaniana) have long been controversial, with several alternative classifications being proposed, none of which has gained universal acceptance. As Coriarachnini is largely confined to the Holarctic region, the main target area of recent DNA barcoding projects for spiders, a large amount of genetic data for the group is now publicly available. The results of a phylogenetic analysis of this sequence dataset are largely congruent with earlier morphology-based results regarding the evolutionary structure of the group. In particular, they highlight the fact that Xysticus s. lat. is a paraphyletic assembly and that several species groups need to be placed in separate genera to achieve monophyly of Xysticus s. str. Similarly, Coriarachne and Bassaniana appear as independent clades rather than a joined monophyletic Coriarachne s. lat. In contrast, further subdivision of Ozyptila is not supported by the genetic data. Importantly, the analysis also shows that anapophysate members of Xysticus s. lat. form two widely separated groups: a primarily anapophysate division, also including Coriarachne and Bassaniana, at the base of Xysticus s. lat., and a secondarily anapophysate clade deeply nested within Xysticus s. str. This might explain some of the earlier difficulties when trying to define generally accepted subgroups within Xysticus s. lat. The phylogenetic scaffold based on barcode sequences is sufficiently dense and well resolved to attempt the tentative and provisional placement of the majority of species in Xysticus s. lat. in the independent genera Xysticus s. str., Bassaniodes, Psammitis and Spiracme as a starting point for a future more formal revision of the group.

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Genetic variation in intraspecific populations of Rabdophaga rosaria (Diptera: Cecidomyiidae) indicating possible diversification scenarios into sibling species along with host range expansion on willows (Salicaceae: Salix)

Zoological Journal of the Linnean Society ◽

10.1093/zoolinnean/zlz179 ◽

2020 ◽

Vol 189 (4) ◽

pp. 1426-1437

Author(s):

Shinsuke Sato ◽

Keith M Harris ◽

Dominique M Collet ◽

Wanggyu Kim ◽

Junichi Yukawa

Keyword(s):

Sibling Species ◽

Genetic Data ◽

Coi Gene ◽

Salix Alba ◽

Host Range Expansion ◽

Maximum Likelihood Tree ◽

Holarctic Region ◽

Species Groups ◽

Clade 1 ◽

The Uk

Abstract We analysed the COI gene of mitochondrial DNA extracted from larvae of Rabdophaga (Diptera: Cecidomyiidae) that induce rosette galls on Salix in the Holarctic Region. Genetic data show that they belong to species groups of Rabdophaga rosaria and Rabdophaga strobiloides. A maximum likelihood tree indicates that R. rosaria and R. strobiloides populations are divided into clades 1 and 2, respectively. Clade 1 is divided into subclades 1 and 2, and the latter is further divided into subclades 2A and 2B. Subclade 1 consists of populations on several Salix species of section Cinerella in subgenus Vetrix in Georgia and the UK. Subclade 2A contains populations on Salix alba (section Salix, subgenus Salix) in The Netherlands and the UK. Subclade 2B consists of populations on section Helix in Poland, Phylicifoliae in Alaska and Salix species in the Eastern Palaearctic Region. The genetic differences between populations of subclades 1, 2A and 2B range from 1.06 to 3.46%. We propose a possible diversification scenario of R. rosaria into sibling species through the expansion of host plant ranges. Clade 2 consists of R. strobiloides populations on two Alaskan Salix species of the sections Hastatae and Sitchenses in subgenus Vetrix.

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Phylogenetic analysis of Gigantodax (Diptera: Simuliidae)

Insect Systematics & Evolution ◽

10.1163/187631205788838465 ◽

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.

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Phylogenetic analysis and reclassification of the genus Priochirus Sharp (Coleoptera:Staphylinidae:Osoriinae)

Invertebrate Systematics ◽

10.1071/is06010 ◽

2007 ◽

Vol 21 (1) ◽

pp. 73 ◽

Cited By ~ 6

Author(s):

Jie Wu ◽

Hong-Zhang Zhou

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Phylogenetic Relationships ◽

Cladistic Analysis ◽

Phylogenetic Inference ◽

Sister Group ◽

Rove Beetle ◽

New Subgenus ◽

Species Groups ◽

Sister Relationships

The genus Priochirus Sharp (Coleoptera : Staphylinidae) is a rove beetle group with great variation in cephalic structures, especially the teeth on the frontal margin of head. In this paper, phylogenetic relationships among ten subgenera of the genus Priochirus sensu lato, and of Priochirus and other genera of the tribe Leptochirini are analysed. A cladistic analysis was conducted based on 62 characters of adult morphology. Results indicate that the genus Priochirus is not a monophyletic group and is divided into two lineages (called here Lineages I and II respectively). The subgenus Euleptarthrus Jakobson, which included three species-groups (japonicus, longicornis and malayanus), is shown to be polyphyletic. Lineage I corresponds with the Leiochirus + (Exochirus + Syncampsochirus) + (Eutriacanthus + (Plastus + (japonicus-group of Euleptarthrus + (Barychirus + Stigmatochirus)))) clade and forms a sister group to the genus Thoracochirus Bernhauer. Lineage II corresponds with the Priochirus, s. str. + (Cephalomerus + (longicornis- and malayanus-group of the Euleptarthrus)) clade. In addition, the analysis reveals sister relationships between representatives of Lineage I and the genus Thoracochirus. On the basis of phylogenetic inference, the genus Plastus Bernhauer, stat. nov. is proposed to include the subgenera of Lineage I and a new subgenus Sinumandibulus, subgen. nov., which is erected for the japonicus-group of the former subgenus Euleptarthrus. The genus Priochirus Sharp sensu novo is redefined to include the subgenera of Lineage II. Seven new species are described from China: Plastus (Sinumandibulus) curvaticornis, sp. nov. from Sichuan; Plastus (Sinumandibulus) recticornis, sp. nov. from Hubei; Priochirus (Euleptarthrus) amblyodontus, sp. nov. from Hunan; Priochirus (Euleptarthrus) baoxingensis, sp. nov. from Sichuan, Priochirus (Euleptarthrus) elongates, sp. nov. from Guizhou, Priochirus (Euleptarthrus) parvicornis, sp. nov. from Fujian and Priochirus (Euleptarthrus) oxygonus, sp. nov. from Hainan.

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The Phylogenetic Study of the White-Bellied Sea Eagle [Haliaeetus leucogaster (Gmelin, 1788)] Based on DNA Barcoding Cytochrome-c Oxidase Subunit I (COI)

KnE Life Sciences ◽

10.18502/kls.v3i4.706 ◽

2017 ◽

Vol 3 (4) ◽

pp. 208

Author(s):

Riri Wiyanti Retnaningtyas ◽

Windri Hermadhiyanti ◽

Dwi Listyorini

Keyword(s):

Phylogenetic Analysis ◽

Dna Barcoding ◽

Gene Sequence ◽

Genetic Data ◽

Coi Gene ◽

Phylogenetic Study ◽

Haliaeetus Leucocephalus ◽

Coastal Regions ◽

Illegal Hunting ◽

Global Population

Even though not yet considered as endangered, White-bellied Sea Eagle’s global population is decreasing due to illegal hunting, bird trading, and deforestation. So far, there hasn’t been any report regarding the phylogenetic study of the White-bellied Sea Eagle inhabiting the coastal regions of Java. Moreover, there hasn’t been any report on the genetic data, especially COI gene, of the White-bellied Sea Eagle living in coastal area of Java. Thus, in this research, two individuals of Heliaeetus leucogaster (<a title="Johann Friedrich Gmelin" href="https://en.wikipedia.org/wiki/Johann_Friedrich_Gmelin">Gmelin</a>, 1788); are compared based on its COI gene sequence to the member of genus Haliaeetus to determine their position in the phylogenetic tree of genus Haliaeetus. COI gene amplification is performed using Forward primer BirdF1 5’- TTC TCC AAC CAC AAA GAC ATT GGC AC-3’ and Reverse primer BirdR2 5’ ACT ACA TGT GAG ATG ATT CCG AAT-3’. The phylogenetic analysis using MEGA6 with Maximum Likelihood method shows that Haliaeetus leucogaster in this study is related to Haliaeetus leucocephalus (Linnaeus, 1766), Haliaeetus pelagicus (Pallas, 1811), and Haliaeetus albicilla (Linnaeus, 1758). <div>Keywords: phylogenetic study; Heliaeetus leucogaster (<a title="Johann Friedrich Gmelin" href="https://en.wikipedia.org/wiki/Johann_Friedrich_Gmelin">Gmelin</a>, 1788); DNA barcoding, Cytochrome-c Oxidase Subunit I (COI).</div>

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Monophyly and phylogenetic relationships of Thereva and therevine genus-groups (Insecta:Diptera:Therevidae) based on EF-1α, 28S rDNA and mitochondrial 16S rDNA sequences

Invertebrate Systematics ◽

10.1071/is06005 ◽

2007 ◽

Vol 21 (3) ◽

pp. 279 ◽

Cited By ~ 4

Author(s):

Kevin C. Holston ◽

Michael E. Irwin ◽

Brian M. Wiegmann

Keyword(s):

16S Rdna ◽

Phylogenetic Relationships ◽

Phylogenetic Signal ◽

Phylogenetic Analyses ◽

28S Rdna ◽

Partial Recovery ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Holarctic Region ◽

Species Groups

Phylogenetic analyses using 28S rDNA, elongation factor (EF)-1α, and mt 16S rDNA sequences were performed to test the monophyly of Thereva Latreille. Two of the three Afrotropical Thereva species groups lack the genitalia characters that unambiguously diagnose Thereva in the Holarctic Region, but phylogenetic relationships among Thereva species groups and therevine genera are poorly understood. Using an extensive taxonomic sample (39 of the 62 therevine genera) and Thereva, sensu lato (15 spp.), simultaneous analyses of all three gene partitions recovered Nearctic and Palaearctic Thereva species in a well supported clade that includes the Afrotropical seminitida-group but excludes the Afrotropical analis- and turneri-groups. Stronger phylogenetic signal from the EF-1α partition, measured by the skewness statistic and proportion of total parsimony informative characters, dominated conflicting signal from the 16S partition and weaker, but more congruent, signal from 28S. Reducing the taxonomic sample in analyses of Therevinae reduced homoplasy, increased phylogenetic structure and partitioned Bremer support values and reduced incongruence with 28S for the 16S partition. Although molecular analyses yielded partial recovery of informal therevine genus-groups, morphological diagnoses of higher-level groups are poorly supported with the exception of Cyclotelini. The ‘Holarctic radiation’ refers to a diverse clade of genera closely related to Pandivirilia Irwin & Lyneborg and Acrosathe Irwin & Lyneborg widely distributed throughout the Holarctic Region that is the sister-group to Thereva, sensu stricto. Results from these analyses underscore the importance of male and female genitalia characters in recognising monophyletic groups and regional endemism in therevine diversification.

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Molecular Evolution and the Phylogenetic Relationships of the African Toad, Bufo danielae PERRET, 1977 (Salientia : Bufonidae)

Amphibia-Reptilia ◽

10.1163/156853880x00169 ◽

1980 ◽

Vol 1 (2) ◽

pp. 173-183 ◽

Cited By ~ 2

Author(s):

A. Konrad ◽

H. Hemmer ◽

L.R. Maxson ◽

K. Bachmann

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Plasma Proteins ◽

Species Complex ◽

Nuclear Dna ◽

Nuclear Dna Content ◽

Species Groups ◽

Microcomplement Fixation ◽

Cellogel Electrophoresis ◽

Toad Bufo

AbstractPhylogenetic relationships of the African toad Bufo danielae are investigated using a variety of biochemical approaches. Nuclear DNA content was assayed and compared to representatives of three species groups of African Bufo. Cellogel electrophoresis of plasma proteins was performed and patterns of B. danielae compared with those of representatives of the African B. regularis species complex. Finally microcomplement fixation analyses of albumin relationships of B. danielae and African Bufo were carried out. The strengths of the varied approaches for phylogenetic analysis are discussed. B. danielae appears most closely related to B. maculatus and B. pusillus, it being some 5-6 million years since these species last shared a common gene pool.

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Phylogenetic analysis and preliminary classification of the Parathalassiinae (Diptera: Empidoidea: Dolichopodidae sensu lato)

Zootaxa ◽

10.11646/zootaxa.4648.1.5 ◽

2019 ◽

Vol 4648 (1) ◽

pp. 111-129

Author(s):

JEFFREY M. CUMMING ◽

SCOTT E. BROOKS

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Cladistic Analysis ◽

Species Group ◽

Group Level ◽

Present Concept ◽

Species Groups ◽

Preliminary Classification ◽

Generic Relationships

Phylogenetic relationships of the subgroups of Parathalassiinae are presented, based on a morphological cladistic analysis. Worldwide, all known extant genera, species groups and newly discovered undescribed lineages are represented in the analysis. Some previously proposed generic relationships are supported by the analysis, but recognition of many current genera renders the present concept of Microphorella Becker as both paraphyletic and polyphyletic. Microphorella merzi Gatt is here classified in Eothalassius Shamshev & Grootaert, as Eothalassius merzi (Gatt) comb. nov. A preliminary classification with all included extant lineages within the Parathalassiinae (at the genus and species group level) is outlined. The ranking of these lineages is discussed and several species groups of Microphorella may need to be elevated to generic or subgeneric level, whereas some currently recognized genera may need to be relegated to subgenera.

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Electrophoretic analysis of Phylogenetic relationships among Australian Carcharhinid Sharks

Marine and Freshwater Research ◽

10.1071/mf9920097 ◽

1992 ◽

Vol 43 (1) ◽

pp. 97 ◽

Cited By ~ 11

Author(s):

S Lavery

Keyword(s):

Phylogenetic Relationships ◽

Genetic Data ◽

Electrophoretic Analysis ◽

Phylogeny Reconstruction ◽

Allozyme Electrophoresis ◽

Closely Related Species ◽

The Family ◽

Distinct Lineage ◽

Species Groups ◽

Morphological Species

The phylogenetic relationships of 17 species of carcharhinid sharks and four other closely related species were examined by allozyme electrophoresis. Genetic data from 38 loci were used in three different techniques of phylogeny reconstruction (including both phenetic and cladistic methods). The two most instructive trees were produced by using maximum parsimony (PAUP) and Distance Wagner procedures. There was evidence that both the genus Carcharhinus and the family Carcharhinidae may actually comprise paraphyletic groups. A number of proposed morphological species groups were shown to also be closely related genetically. These included C. limbatus/C. tilstoni/C. amblyrhynchoides, C. melanopterus/C. cautus, and C. amblyrhynchos/C. albimarginatus. There appears to be a distinct lineage within the Carcharhinidae that may be characterized by the absence of the interdorsal ridge.

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Nothotrichocera Alexander (Diptera : Trichoceridae): new species, redescriptions and phylogenetic relationships within the genus

Invertebrate Systematics ◽

10.1071/it96033 ◽

2001 ◽

Vol 15 (2) ◽

pp. 205 ◽

Cited By ~ 4

Author(s):

Ewa Krzeminska

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Phylogenetic Relationships ◽

Species Groups ◽

A New Species ◽

Eleven Species ◽

Geographically Isolated

Nothotrichocera antarctica (Edwards), Nothotrichocera tonnoiri Alexander and Nothotrichocera tasmanica Alexander are redescribed and a new species of the cingulata-group, N. collessi, sp. nov., is described. The eleven species of Nothotrichocera belong in four well-defined groups of species, which have evolved in geographically isolated, circum-Antarctic regions. The unique positions of N. tonnoiri and N. tasmanica are stressed. A key to the species-groups is given and a phylogenetic analysis of the genus is presented.

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Phylogenetic relationships of Echeveria (Crassulaceae) and related genera from Mexico, based on three DNA barcoding loci

Phytotaxa ◽

10.11646/phytotaxa.422.1.3 ◽

2019 ◽

Vol 422 (1) ◽

pp. 33-57 ◽

Cited By ~ 1

Author(s):

LUIS E. DE LA CRUZ-LÓPEZ ◽

FRANCISCO VERGARA-SILVA ◽

JERÓNIMO REYES SANTIAGO ◽

GABRIELA ESPINO ORTEGA ◽

PABLO CARRILLO-REYES ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Maximum Likelihood ◽

Dna Barcoding ◽

Phylogenetic Relationships ◽

Consensus Trees ◽

As Species ◽

Tree Inference ◽

Selection Of

Mexico is considered as diversification and endemism center of the genus Echeveria. Previous tree inference studies have shown the genus to be non-monophyletic in relation to other genera, but sampling for Echeveria has been poor, and has not allowed to understand the relationships within the genus. In this work, Bayesian and maximum likelihood phylogenetic analysis were performed, using a combined standard DNA barcoding loci matrix (rbcL, matK and ITS2) and GenBank ITS2 accessions for Graptopetalum, some Sedum and few Echeveria taxa. The selection of taxa encompasses all current infrageneric categories of the genus Echeveria, as well as species from genera previously associated with it. The inferred consensus trees suggested that Echeveria is paraphyletic. Instead, four main clades were retrieved within the “Echeveria group”: Clade I includes exclusively Pachyphytum species. Clade II is formed by the majority of series Urbiniae; Clade III encompasses series Chloranthae, Ciliatae, Echeveria, Mucronatae, Nudae, Racemosae, Thyrsiflorae, Pachyphytum cuicatecananum and Thompsonella; Clade IV contains series Angulatae, Gibbiflorae, Occidentales, Pruinosae, Secundae, some Urbiniae species, Valvatae. genera Cremnophila, Graptopetalum and Reidmorania. Pachyphytum and Thompsonella were retrieved as monophyletic groups, but the first outside Echeveria while the latter inside. Results of our study suggest that Echeveria and the Echeveria Group require a redefinition.

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