Molecular systematics of the enigmatic 'phascolosoricine' marsupials of New Guinea

2004 ◽  
Vol 52 (4) ◽  
pp. 389 ◽  
Author(s):  
Carey Krajewski ◽  
Gregory R. Moyer ◽  
Justin T. Sipiorski ◽  
Matthew G. Fain ◽  
Michael Westerman
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Sampling Bias ◽  
Morphological Data ◽  
12S Rrna ◽  
Mitochondrial Cytochrome B ◽  
Exon 1 ◽  
Phylogenetic Estimation ◽  
Nuclear Loci ◽  
Or Gene

Previous analyses of DNA sequences for mitochondrial cytochrome-b and 12S rRNA, along with the nuclear protamine P1 genes, suggested that the New Guinean dasyurid genera Phascolosorex and Neophascogale (phascolosoricines) form the sister groups of quolls (Dasyurus) and Tasmanian devils (Sarcophilus). This runs counter to a common perception that phascolosoricines are anatomically primitive and only distantly related to other dasyurids. We report the DNA sequences of two additional mitochondrial loci (tRNAVal and 16S rRNA) and nuclear loci (interphotoreceptor binding protein exon 1, beta-fibrinogen intron 7) from Phascolosorex dorsalis, Neophascogale lorentzii, and all but three other dasyurid species. These sequences, along with those previously published, comprise a dataset of 7053 nucleotides. Phylogenetic analyses indicate that phascolosoricines form a clade that is highly resolved as sister to Dasyurus + Sarcophilus. This result is obtained independently by mitochondrial and nuclear genes, and cannot be attributed to taxon- or gene-sampling bias, compositional heterogeneity, or the use of overly simplistic phylogenetic estimation procedures. A re-evaluation of published morphological data bearing on the relationships of phascolosoricines demonstrates that, although the conflict with molecular results is significant, it is limited to a small number of correlated dental features that show considerable homoplasy in their evolution.

scholarly journals The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

2015 ◽  
Vol 46 (3) ◽  
pp. 269-290 ◽  
Author(s):  
Ian J. Kitching ◽  
C. Lorna Culverwell ◽  
Ralph E. Harbach
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Set ◽  
Generic Status ◽  
Strong Signal ◽  
Phylogenetic Studies ◽  
Data Support

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

Monophyly of Verbascum (Scrophularieae : Scrophulariaceae): evidence from nuclear and plastid phylogenetic analyses

2014 ◽  
Vol 62 (8) ◽  
pp. 638 ◽  
Author(s):  
Farrokh Ghahremaninejad ◽  
Mehrshid Riahi ◽  
Melina Babaei ◽  
Faride Attar ◽  
Lütfi Behçet ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nrdna Its ◽  
Starting Point ◽  
High Species Diversity ◽  
Phylogenetic Estimation

Verbascum is one of the main genera of Scrophulariaceae, but delimitation and phylogenetic relationships of this genus are unclear and have not yet been studied using DNA sequences. Here, using four selected molecular markers (nrDNA ITS and the plastid spacers trnS/G, psbA-trnH and trnY/T), we present a phylogeny of Verbascum and test previous infrageneric taxonomic hypotheses as well as its monophyly with respect to Scrophularia. We additionally discuss morphological variation and the utility of morphological characters as predictors of phylogenetic relationships. Our results show that while molecular data unambiguously support the circumscription of Verbascum inferred from morphology, they prove to be of limited utility in resolving infrageneric relationships, suggesting that Verbascum ‘s high species diversity is due to rapid and recent radiation. Our work provides phylogenetic estimation of the genus Verbascum using molecular data and can serve as a starting point for future investigations of Verbascum and relatives.

scholarly journals Three, two, one! Revision of the long-bodied sphaerodorids (Sphaerodoridae, Annelida) and synonymization ofEphesiella,EphesiopsisandSphaerodorum

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5783 ◽  
Author(s):  
María Capa ◽  
Torkild Bakken ◽  
Karin Meißner ◽  
Arne Nygren
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Intraspecific Variability ◽  
Morphological Data ◽  
Nominal Species ◽  
Type Specimens ◽  
Diagnostic Features ◽  
28S Rdna Sequence

BackgroundLong-bodied sphaerodorids (Annelida, Sphaerodoridae) is the common name for members of the three closely and morphologically homogenous currently accepted genera of benthic marine bristle worms:Ephesiella,EphesiopsisandSphaerodorum. Members of this group share the presence of two dorsal and longitudinal rows of macrotubercles with terminal papillae, and two longitudinal rows of microtubercles, features that are unique among sphaerodorids. Genera are distinguished by the chaetae morphology. Members ofEphesiellaare characterised by having compound chaetae (except, sometimes, simple chaetae in the first chaetigers),Sphaerodorumbear only simple chaetae, andEphesiopsishave both compound and simple chaetae in all parapodia.MethodsMitochondrial (partial COI and 16S rDNA) and nuclear (partial 18S rDNA and 28S rDNA) sequence data of long-bodied sphaerodorids with compound and simple chaetae, and an outgroup of additional seven sphaerodorid species were analysed separately and in combination using Bayesian inference (BA), and Maximum Likelihood (ML) methods. Long-bodied sphaerodorids from around the world (including type specimens) were examined under a range of optical equipment in order to evaluate putative generic and specific diagnostic features, in addition to intraspecific variability.ResultsPhylogenetic analyses of mitochondrial and nuclear DNA sequences of specimens identified asEphesiellaandSphaerodorum,based on chaeta morphology, were performed.SphaerodorumandEphesiellawere recovered as paraphyletic and nested within each other. Revision of current nominal species diagnostic features are performed and discussed.DiscussionResults contradict current generic definitions. Recovery of paraphyletic compound and simple chaetae clades urge the synonymization of these two genera of long-bodied sphaerodorids. Morphological data also suggest the synonymization ofEphesiopsis.

Discovery of two ‘chimeric’ Gastrotricha and their systematic placement based on an integrative approach

2020 ◽  
Author(s):  
Alexander Kieneke ◽  
M Antonio Todaro
Keyword(s):  
Dna Sequences ◽  
New Genus ◽  
Phylogenetic Analyses ◽  
Mouth Opening ◽  
Reproductive Organs ◽  
Morphological Data ◽  
Integrative Approach ◽  
New Taxon ◽  
Linear Distance ◽  
Molecular Phylogenetic

Abstract Sublittoral sand from the islands of Sardinia (Italy) and Flores (Azores) – separated by more than 3700 km linear distance and 8 years between two independent sampling campaigns – yielded conspicuous specimens of two bizarre, yet undescribed, species of the marine gastrotrich clade Macrodasyida. These gastrotrichs combine several character traits that were already known from two, non-related genera. Morphological data were carefully analysed and digitally documented, and nuclear and mitochondrial DNA sequences were used for phylogenetic inference. The results of these analyses claim for the erection of a new genus. Specimens of the new taxon have a body length of less than 400 µm and are characterized by a wide, funnel-shaped mouth opening shielded dorsally by an oral hood and possess a posterior peduncle that ends with a Y-shaped pair of appendages that carry the posterior adhesive tubes. Further tubes occur as anterior, ventrolateral and lateral series; the gonads are unpaired and there is a set of two accessory reproductive organs. Molecular phylogenetic analyses confirm the results of former studies and clearly place the new taxon in Thaumastodermatidae. We hereby propose the establishment of Chimaeradasys gen. nov. and describe C. oligotubulatus sp. nov. from the Azores and C. polytubulatus sp. nov. from Sardinia.

scholarly journals Molecular data indicate a cryptic species in Neotoma albigula (Cricetidae: Neotominae) from northwestern México

2015 ◽  
Vol 97 (1) ◽  
pp. 187-199
Author(s):  
Robert D. Bradley ◽  
Matthew R. Mauldin
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Genetic Distances ◽  
Dehydrogenase Gene ◽  
Mitochondrial Cytochrome B ◽  
Northwestern Mexico ◽  
Morphological Differences ◽  
Intron 2

Abstract DNA sequences from the mitochondrial cytochrome- b gene were obtained from 41 specimens of Neotoma albigula from the southwestern United States and northwestern México. Phylogenetic analyses depicted that samples of N. a. melanura from southern Sonora and northern Sinaloa formed a clade separate from representatives of the other sampled subspecies of N. albigula ( albigula , laplataensis , mearnsi , seri , sheldoni , and venusta ). Genetic distances detected between these clades (7.41%) approached divergence levels reported for other sister species of woodrats and indicated that N. a. melanura is presumably a cryptic and genetically differentiated species relative to N . albigula . Analyses of DNA sequences from a nuclear gene (intron 2 of the alcohol dehydrogenase gene, Adh 1-I2) indicated that samples of N. a. melanura formed a separate, monophyletic clade relative to the remainder of N. albigula . Further, habitat, geographic distinctions, and morphological differences were apparent between members of the 2 clades. Together, those data support the elevation of N. a. melanura to species status. Secuencias de ADN del gen mitocondrial citocromo- b se obtuvieron de 41 especímenes de Neotoma albigula provenientes del suroeste de los Estados Unidos y del noroeste de México. Análisis filogenéticos revelaron que las muestras de N. a. melanura del sureste de Sonora y del norte de Sinaloa formaron un clado separado de especímenes que representan a las otras subspecies de N. albigula (albigula, laplataensis, mearnsi, seri, sheldoni , y venusta ). Las distancias genéticas detectadas entre estos clados (7.41%) se aproximan a los valores de divergencia reportados para otras especies de ratas magueyeras, indicando que N. a. melanura es presumiblemente una especie críptica y relativamente diferenciada genéticamente de N. albigula . Los análisis de secuencias de ADN de un gen nuclear (intron 2 del gen alcohol deshidrogenasa, Adh -I2) indicaron que las muestras de N. a. melanura formaron un clado separado relativamente a especímenes de N. albigula . Adicionalmente, hábitat, distinciones geográficas, y diferencias morfológicas fueron aparentes entre miembros de los dos clados. Todos estos datos soportan la elevación de N. a. melanura al estatus de especie.

Description of a new endemic species of mountain lizard from Northwestern Spain: Iberolacerta galani sp. nov. (Squamata : Lacertidae)

Zootaxa ◽  
2006 ◽  
Vol 1240 (1) ◽  
pp. 1 ◽  
Author(s):  
OSCAR ARRIBAS ◽  
SALVADOR CARRANZA ◽  
GAETANO ODIERNA
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Posterior Part ◽  
Rrna Genes ◽  
12S Rrna ◽  
Strongly Correlated ◽  
Large Size ◽  
Lacertid Lizards ◽  
Northwestern Spain

A new species of Iberolacerta is described from the Montes de León (northwest Iberia). This new species, Iberolacerta galani sp. nov., is characterized by its relatively large size, high number of blue ocelli on the shoulders and the relatively frequent contact or near-contact between the supranasal and the first loreal scale, the fairly straight squamosal bone (only curved on its posterior part), a unique karyotype in Iberolacerta combining 2n=36 chromosomes, an L-type NOR and differentiated W and Z sex chromosomes, and unique mitochondrial DNA sequences for the cytochrome b and 12S rRNA genes. The correlation analyses show that morphology in general, but especially scalation, is strongly correlated with the amount of precipitation during the months of lizard activity, which suggests that these are not good taxonomic characters, and that other characters apparently independent of the climate like for instance osteological, karyological and DNA features are much more reliable in delimiting species boundaries in Iberolacerta. According to our phylogenetic analyses, I. galani nov. is part of a very well supported clade that originated around 2.5 mya and also includes I. monticola and I. martinezricai. Phylogeny suggests I.martinezricai might be the sister taxon to I. galani nov. from which it split approximately 2 mya, at the beginning of the Pleistocene. The clade containing I. galani nov., I. martinezricai and I. monticola was probably widely distributed across western Iberia during moderately cool and moist phases of the Pleistocene, but it was probably restricted to its present range as a result of the general temperature increase during the Holocene and competition with other lacertid lizards. Iberolacerta galani nov. is endemic to the Montes de León, where it is isolated from the other species of the “monticola-group” by the Duero and Miño-Sil Rivers, but particularly by the Bibei river valley.

Taxonomy and phylogeny of Nitella (Charophyceae, Characeae) from Brazil with emphasis on the midwest and southeast regions

Phytotaxa ◽  
2018 ◽  
Vol 356 (3) ◽  
pp. 181
Author(s):  
FABIO RENATO BORGES ◽  
ORLANDO NECCHI JR
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Evidence ◽  
Type Specimens ◽  
Brazilian Studies ◽  
Two Populations ◽  
Section Level

The genus Nitella is the most species-rich within the Charales. Brazilian studies on the genus are relatively scarce and consist of floristic surveys, lacking modern and more precise information. This investigation applied scanning electron microscopy to analyze the oospore wall and molecular data associated with traditional morphological characters to analyze forty-two populations of Nitella from the midwest and southeast regions of Brazil. Forty-two new sequences of rbcL, twelve of ITS1 and twenty-three of ITS2 were generated for the five species recognized in this study: Nitella acuminata A. Braun ex Wallman, Nitella axillaris A. Braun, Nitella elegans B. P. Pal, Nitella flagellifera J. Groves & G. O. Allen and Nitella microcarpa A. Braun.. Phylogenetic analyses of sequences of these three markers were congruent in that they grouped our species with others from different countries to form five clades. Our results on ultrastrucure of the oospore wall were consistent with previous studies for the same species from other regions of the world. The data reinforced the conclusion that the use of ornamentation of oospore wall may be extremely useful for the construction of a natural system for Characeae at section level. Molecular evidence, reinforced by morphological data, for the Brazilian material analyzed suggests that Nitella subglomerata A. Braun and Nitella gollmeriana A. Braun could be synonymys of Nitella acuminata; and Nitella axilliformis K. Imahori appears to be the same as Nitella axillaris. However, no formal proposition was made considering that type specimens were not analyzed and these observations were based on a relatively small number of samples strictly from Brazil. We showed that even among geographically distant populations, such as from other continents, of some Nitella species, the degree of identity among DNA sequences was high.

scholarly journals A newly recognised species of Cryptes Maskell 1892 (Hemiptera: Coccidae) from Western Australia

Zootaxa ◽  
2018 ◽  
Vol 4508 (1) ◽  
pp. 101 ◽  
Author(s):  
YEN-PO LIN ◽  
TAKUMASA KONDO ◽  
TAKUMASA KONDO ◽  
PENNY J. GULLAN ◽  
LYN G. COOK
Keyword(s):  
Adult Female ◽  
Western Australia ◽  
Dna Sequences ◽  
Species Complex ◽  
Phylogenetic Analyses ◽  
Australian Species ◽  
Adult Females ◽  
Nuclear Loci ◽  
Acacia Aneura ◽  
Western Australian

Cryptes utzoni Lin, Kondo & Cook sp. n. (Hemiptera: Coccidae) is described based on adult female morphology and DNA sequences from mitochondrial and nuclear loci. This Australian endemic species was found on the stem of Acacia aneura (Fabaceae) in Western Australia. All phylogenetic analyses of three independent DNA loci show that C. utzoni is closely related to C. baccatus (Maskell), the type and only species of Cryptes Maskell, 1892. The adult female of C. utzoni is described and illustrated and a table is provided of the characters that differ among adult females of the two species of Cryptes now recognised (C. baccatus and C. utzoni) and a morphologically similar Western Australian species, Austrolichtensia hakearum (Fuller). There is deep genetic divergence in COI among samples of C. baccatus, suggesting the possibility of a species complex in this taxon. 

scholarly journals First records and three new species of the family Symphytognathidae (Arachnida, Araneae) from Thailand, and the circumscription of the genus Crassignatha Wunderlich, 1995

ZooKeys ◽  
2021 ◽  
Vol 1012 ◽  
pp. 21-53
Author(s):  
Francisco Andres Rivera-Quiroz ◽  
Booppa Petcharad ◽  
Jeremy A. Miller
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Coastal Region ◽  
3D Models ◽  
Morphological Data ◽  
The North ◽  
The Family ◽  
Ct Analysis ◽  
Three New Species

The family Symphytognathidae is reported from Thailand for the first time. Three new species: Anapistula choojaiaesp. nov., Crassignatha seeliamsp. nov., and Crassignatha seedamsp. nov. are described and illustrated. Distribution is expanded and additional morphological data are reported for Patu shiluensis Lin & Li, 2009. Specimens were collected in Thailand between July and August 2018. The newly described species were found in the north mountainous region of Chiang Mai, and Patu shiluensis was collected in the coastal region of Phuket. DNA sequences are provided for all the species here studied. The relations of these symphytognathid species were tested using previously published phylogenetic analyses on micro orb-weavers. Also, we used micro CT analysis to build 3D models of the male genitalia and somatic characters of two species of Crassignatha Wunderlich, 1995. The molecular phylogeny and 3D models were used to discuss the taxonomy and circumscription of the currently valid symphytognathid genera, with focus on Crassignatha and Patu Marples, 1951. Based on this, three new combinations are suggested: Crassignatha bicorniventris (Lin & Li, 2009), comb. nov., Crassignatha quadriventris (Lin & Li, 2009), comb. nov., and Crassignatha spinathoraxi (Lin & Li, 2009), comb. nov. A new record of Crassignatha danaugirangensisMiller et al. 2014 is reported from Brunei.

Evidence for the presence of a second species of mongoose in the Fiji Islands

2007 ◽  
Vol 13 (1) ◽  
pp. 29 ◽  
Author(s):  
Craig G. Morley ◽  
Patricia A. McLenachan ◽  
Peter J. Lockhart
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
The Body ◽  
Body Measurements ◽  
Fiji Islands ◽  
Asian Clade ◽  
Mitochondrial Cytochrome B ◽  
Hind Foot ◽  
Late Nineteenth ◽  
Small Indian Mongoose

The small Indian Mongoose Herpestes javanicus was introduced in the late nineteenth centure into Fiji and is now found throughout the two main islands of Fiji (Viti Levu and Vanua Levu) and on another 11 small outsr islands. When trapping mongoose as part of an investigation into the spread of leptospirosis around Suva, six large red-coloured mongoose were also captured. The body measurements (weight, length and hind-foot size) of these red-coloured mongoose were significantly larger than a random sample of the grey-coloured mongoose H. javanicus normally seen. To clarify whether the red-coloured mongoose was a different species or just a different colour morph of H. javanicus, mitochondrial cytochrome B cytb DNA sequences were determined from muscle tissue of four red-coloured Individuals. Phylogenetic analyses using cytb sequences show that while the red-coloured mongoose belongs to an Asian clade, it is not H. javanicus or H. edwardsi. Further research is needed to determine the identity and origin of the red-coloured mongoose and to ascertain its prevalence in Fiji.

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