scholarly journals Mediterranean Ant Nest Beetles (Carabidae: Paussus): Out of Africa and Asia

2019 ◽  
Vol 2 ◽  
Author(s):  
Wendy Moore ◽  
James Robertson ◽  
Peter Nagel ◽  
Andrea Di Giulio
Keyword(s):  
Molecular Phylogenetics ◽  
Sequence Data ◽  
General Rule ◽  
Sampling Strategy ◽  
Species Group ◽  
Sub Saharan Africa ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Ant Nest ◽  
Sub Saharan

Endemic to the Palaeotropic and southern Palaearctic regions, ant nest beetles (Carabidae: Paussus) are specialized predators that depend on ants for their survival. This obligate relationship has driven extreme morphological adaptations that obscured our understanding of Paussus species relationships and subgeneric clades for centuries. Molecular phylogenetics has revealed patterns of relationship with high levels of convergence, and as a general rule, areas of endemism are better predictors of monophyly than overall morphology. For example, the species rich fauna of Madagascar is the product of one dispersal event from Africa approximately 2.6 million years ago, after which Malagasy ant nest beetles undertook one of the fastest species radiations ever documented within animals. With their center of diversity in sub-Saharan Africa, the Paussus fauna of the Mediterranean is relatively depauperate with only seven species described from north of the Sahara. Pre-molecular subgeneric classifications, which were based on overall morphology, suggest that these seven species represent five species group lineages. Here, we use molecular sequence data from five genes and a taxon-sampling strategy aimed at investigating the biogeographic origins of five Mediterranean species. We find that the present-day Mediterranean fauna, unlike that of Madagascar, is the result of five separate dispersal events, four from the Afrotropical Region and one from the Indomalayan Region. Implications of associated host ant shifts are also explored.

scholarly journals On the systematics and the phylogenetic position of the poorly known, montane dragon-lizard species Pseudocalotes austeniana (Annandale, 1908) (Squamata, Agamidae, Draconinae)

2021 ◽  
Vol 5 (1) ◽  
pp. 141-150
Author(s):  
Gaurang G. Gowande ◽  
Harshal S. Bhosale ◽  
Pushkar U. Phansalkar ◽  
Mandar Sawant ◽  
Zeeshan A. Mirza
Keyword(s):  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Systematic Position ◽  
Sensu Stricto ◽  
Evolutionary Significance ◽  
Phylogenetic Position ◽  
Gene Trees ◽  
Lizard Species ◽  
Molecular Sequence Data ◽  
Molecular Sequence

The montane agamid species Pseudocalotes austeniana has had a complicated taxonomic history, as the species was initially described as a member of the genus Salea Gray, 1845. Later, the species was placed in a monotypic genus Mictopholis Smith, 1935, which was erected only to include this species; however, the species was later on transferred to the genus Pseudocalotes Fitzinger, 1843, owing to the morphological similarities, and lack of strong characters to diagnose the genus Mictopholis. Nonetheless, its precise phylogenetic and systematic position has remained unresolved due to the lack of molecular sequence data. During a herpetological expedition to Arunachal Pradesh, specimens of P. austeniana were collected from the hills near the type locality. The mitochondrial 16S rRNA, ND2 and ND4, and the nuclear RAG1 regions were subjected to molecular phylogenetics. Maximum Likelihood and Bayesian Inference gene trees revealed that P. austeniana is a member of the subfamily Draconinae. The analyses showed that the genus Pseudocalotes is polyphyletic, and P. austeniana was embedded within the genus Japalura Gray, 1853 sensu stricto. We here, thus, propose to transfer the species P. austeniana to the genus Japlaura, as Japalura austenianacomb. nov. Biogeographic and evolutionary significance of the findings are discussed.

Evolution of species diversity in the genus Chamaecostus (Costaceae): molecular phylogenetics and morphometric approaches

Phytotaxa ◽  
2015 ◽  
Vol 204 (4) ◽  
pp. 265 ◽  
Author(s):  
Thiago Jose de Carvalho Andre ◽  
CHELSEA SPECHT ◽  
SHAYLA SALZMAN ◽  
CLARISSE PALMA-SILVA ◽  
TÂNIA WENDT
Keyword(s):  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Geographic Range ◽  
New Combination ◽  
Herbarium Specimens ◽  
Geographic Proximity ◽  
Morphometric Measurements ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Phylogenetic Lineages

While most species within the genus Chamaecostus (Costaceae) are well defined, the broad geographic range and long list of synonyms associated with Chamaecostus subsessilis led us to believe there may be some cryptic species within the complex. We thus investigate the phylogenetic relationships of species in the Chamaecostus lineage and specifically test the monophyly and diversity of the Chamaecostus subsessilis species complex from a population perspective by analyzing molecular sequence data and leaf morphometrics. We interpret evolutionary trends across the entire genus based on a molecular character-based phylogenetic hypothesis that includes all currently described species of Chamaecostus. Our results show that while Chamaecostus is strongly monophyletic, C. cuspidatus is found to be sister to a clade of some but not all samples of C. subsessilis, making it necessary to acknowledge more than one species in the C. subsessilis complex. Herbarium specimens of the C. subsessilis complex could be assigned based on geographic proximity to one of the major three clades recovered in the phylogenetic analysis. Leaf morphometric measurements were performed on each of these lineages and traits were tested to detect differences among phylogenetic lineages. We conclude by proposing the recognition of a new combination, Chamaecostus acaulis, which we describe.

Molecular phylogenetics of snailfishes (Cottoidei: Liparidae) based on MtDNA and RADseq genomic analyses, with comments on selected morphological characters

Zootaxa ◽  
2019 ◽  
Vol 4642 (1) ◽  
pp. 1-79 ◽  
Author(s):  
JAMES WILDER ORR ◽  
INGRID SPIES ◽  
DUANE E. STEVENSON ◽  
GARY C. LONGO ◽  
YOSHIAKI KAI ◽  
...  
Keyword(s):  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Morphological Characters ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Genome Wide ◽  
The Pacific ◽  
The Family ◽  
Genomic Analyses ◽  
Gene Coi

Phylogenetic relationships of snailfishes of the family Liparidae were analyzed on the basis of two sets of molecular sequence data: one from the mitochondrial DNA cytochrome c oxidase subunit one gene (COI) and another from restriction-site associated genome-wide sequences (RADseq). The analysis of COI sequence data from at least 122 species of 18 genera from the Pacific, Atlantic, and Southern oceans resulted in a moderately well-resolved phylogeny among the major clades, albeit with significant polytomy among central clades. Nectoliparis was the sister of all other members of the family, followed by Liparis. Liparis, Careproctus, and Paraliparis were paraphyletic. Liparis was recovered in two closely related clades, with L. fucensis sister of all other liparids except Nectoliparis, and both Careproctus and Paraliparis were each recovered among at least three widely separated clades. The RADseq analysis of 26 species of 11 genera from the eastern North Pacific strongly confirmed the overall results of the COI analysis, with the exception of the paraphyly of Liparis due to the absence of L. fucensis. Our results show that the pelvic disc has been independently lost multiple times and the pectoral-fin girdle has been independently reduced in multiple lineages. 

Rediscovery of Mus nitidulus Blyth (Rodentia: Muridae), an endemic murine rodent of the central basin of Myanmar

Zootaxa ◽  
2007 ◽  
Vol 1498 (1) ◽  
pp. 45-68 ◽  
Author(s):  
TOMOFUMI SHIMADA ◽  
KENNETH P. APLIN ◽  
PAULINA JENKINS ◽  
HITOSHI SUZUKI
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Species Group ◽  
Central Basin ◽  
Mammal Species ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rainfed Rice ◽  
South Central ◽  
Murine Rodent

A genetically distinct population of mice from south central Myanmar is identified as Mus nitidulus Blyth, a taxon described in 1859 but subsequently treated as a synonym of a more widely distributed Asian mouse—Mus cervicolor Hodgson, 1845. We present molecular sequence data from mitochondrial and nuclear genes which demonstrate that M. nitidulus is distinct from M. cervicolor and from all other species of Mus currently recognized in the Asian region. The molecular data further show that M. nitidulus is a member of the Mus booduga Species Group within subgenus Mus, and thus phylogenetically remote from M. cervicolor. We stabilize the nomenclature of M. nitidulus by designating a lectotype with associated molecular sequence data. We review and illustrate the morphology of M. nitidulus and reassess all previously referred material. Mus nitidulus appears to be confined to the central basin of Myanmar, an area that formerly supported a mosaic of evergreen and deciduous monsoon forests. Today, this region is largely cleared and employed for rainfed rice cultivation. Mus nitidulus is only the second mammal species recorded as endemic to Myanmar. It can be locally abundant in ricefield habitat and is regarded locally as an agricultural pest.

scholarly journals Phylogeny of the supertribe Nebriitae (Coleoptera: Carabidae) based on analyses of molecular sequence data--some surprises. 

2019 ◽  
Vol 2 ◽  
Author(s):  
David Kavanaugh ◽  
David Maddison ◽  
Brian Simison ◽  
Sean Schoville ◽  
Joachim Schmidt ◽  
...  
Keyword(s):  
Posterior Probability ◽  
Nuclear Protein ◽  
Sequence Data ◽  
Group Identification ◽  
Species Group ◽  
Molecular Sequence Data ◽  
Protein Coding ◽  
Individual Gene ◽  
Molecular Sequence ◽  
High Bootstrap

To explore phylogenetic relationships among members of the carabid supertribe Nebriitae, we sampled DNA fragments extracted from adults of 244 nebriite species-group taxa, representing about 25% of known species-group taxa and 93% (38 of 41) of the currently accepted nebriite genus-group taxa. Sequence data were recorded for eight gene fragments (a total of 5654 bases) from nuclear ribosomal, mitochondrial, and nuclear protein coding genes. The resulting phylogeny is based on both individual gene and concatenated gene analyses using Maximum Likelihood and Bayesian methods, which produced nearly identical results. Most nodes are well supported by both high bootstrap and high posterior probability values, and many of them also by unique (autapomorphic) bases. Many of the previously recognized genus-group taxa are supported as monophyletic, but others are not. Alternative reclassifications that reflect monophyletic groups are still being considered, based on the molecular analyses along with considerations of ease of group identification and geographical distribution. Of the two alternative reclassifications being considered, one requires the designation of 16 new subgeneric synonymies and the other only nine new subgeneric synonymies plus the recognition of three new subgenera. However, under both schemes, Nippononebria Uéno (along with its subgenus, Vancouveria Kavanaugh) is re-established as a genus separate from Nebria and sister to Leistus Frölich; and Archastes is embedded within a monophyletic genus Nebria and closely related to subgenera Oreonebria Daniel and Orientonebria Shilenkov. Additional details will be reported in the presentation.

The status of Myriangiaceae (Dothideomycetes)

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 219 ◽  
Author(s):  
ASHA J. DISSANAYAKE ◽  
RUVISHIKA S. JAYAWARDENA ◽  
SARANYAPHAT BOONMEE ◽  
KASUN M. THAMBUGALA ◽  
QING TIAN ◽  
...  
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
The Status ◽  
Sexual State ◽  
Morphological And Molecular Data ◽  
Asexual State ◽  
Molecular Characters

The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, “Sphaceloma”-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

Apertochrysa (Neuroptera: Chrysopidae): A heterogeneric phantom? 

Zootaxa ◽  
2017 ◽  
Vol 4238 (1) ◽  
pp. 58 ◽  
Author(s):  
ATSUSHI MOCHIZUKI ◽  
CHARLES S. HENRY ◽  
PETER DUELLI
Keyword(s):  
Type Species ◽  
Morphological Traits ◽  
New Genus ◽  
Sequence Data ◽  
New Combination ◽  
Wing Venation ◽  
Monophyletic Clade ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Group Relationships

The small lacewing genus Apertochrysa comprises species from Africa, Asia and Australia. All lack a tignum, but otherwise resemble distantly related genera. We show that Apertochrysa does not form a monophyletic clade, based on analyses of molecular sequence data and morphological traits such as the presence and shape of the male gonapsis, wing venation, and larval setae. Apertochrysa kichijoi forms a clade with Eremochrysa, Suarius and Chrysemosa, whereas A. albolineatoides belongs to a clade that includes Cunctochrysa. Apertochrysa albolineatoides should become a new combination as Cunctochrysa albolineatoides, while A. kichijoi will have to be transferred to a new genus. The Australian A. edwardsi, the African A. eurydera and the type species of the genus Apertochrysa, A. umbrosa, join the large Pseudomallada group. Relationships of A. umbrosa are less certain, because for it we could amplify only one of the three nuclear genes used in the overall analysis. However, in all morphological traits tested, that species strongly resembles A. edwardsi and A. eurydera and thus is very likely just another exceptional Pseudomallada lacking a tignum. The fate of the genus name Apertochrysa depends on additional molecular and morphological analyses of A. umbrosa. 

scholarly journals The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

2009 ◽  
Vol 364 (1527) ◽  
pp. 2197-2207 ◽  
Author(s):  
Peter G. Foster ◽  
Cymon J. Cox ◽  
T. Martin Embley
Keyword(s):  
Sequence Data ◽  
Phylogenetic Signal ◽  
Amino Acid Sequences ◽  
Rate Variation ◽  
Molecular Sequence Data ◽  
Protein Coding ◽  
Molecular Sequence ◽  
Heterogeneous Models ◽  
Matrix Heterogeneity ◽  
Rna Genes

The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the ‘eocyte hypothesis’, where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.

Revealing the endophytic mycoflora in tea (Camellia sinensis) leaves in Sri Lanka: the first comprehensive study

Phytotaxa ◽  
2021 ◽  
Vol 514 (3) ◽  
pp. 247-260
Author(s):  
KASUN THAMBUGALA ◽  
DINUSHANI DARANAGAMA ◽  
SAGARIKA KANNANGARA ◽  
THENUKA KODITUWAKKU
Keyword(s):  
Sri Lanka ◽  
Camellia Sinensis ◽  
Endophytic Fungi ◽  
Sequence Data ◽  
Fungal Endophytes ◽  
Fungal Endophyte ◽  
Tea Leaves ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rdna Sequence Data

Endophytic fungi are a diverse group of microorganisms that live asymptomatically in healthy tissues of host and they have been reported from all kinds of plant tissues such as leaves, stems, roots, flowers, and fruits. In this study, fungal endophytes associated with tea leaves (Camellia sinensis) were collected from Kandy, Kegalle, and Nuwara Eliya districts in Sri Lanka and were isolated, characterized, and identified. A total of twenty endophytic fungal isolates belonging to five genera were recovered and ITS-rDNA sequence data were used to identify them. All isolated endophytic fungal strains belong to the phylum Ascomycota and the majority of these isolates were identified as Colletotrichum species. Phyllosticta capitalensis was the most commonly found fungal endophyte in tea leaves and was recorded in all three districts where the samples were collected. This is the very first investigation on fungal endophytes associated with C. sinensis in Sri Lanka based on molecular sequence data. In addition, a comprehensive account of known endophytic fungi reported worldwide on Camellia sinensis is provided.

scholarly journals Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽  
2019 ◽  
Vol 83 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Adam W. Ferguson ◽  
Houssein R. Roble ◽  
Molly M. McDonough
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Molecular Phylogenetic ◽  
Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

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