scholarly journals The Bushlike Radiation of Muroid Rodents Is Exemplified by the Molecular Phylogeny of the LCAT Nuclear Gene

2000 ◽  
Vol 17 (2) ◽  
pp. 280-293 ◽  
Author(s):  
Johan Michaux ◽  
François Catzeflis
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Gene ◽  
Muroid Rodents

Molecular phylogeny and taxonomic evaluation of the genus Asaccus Dixon and Anderson, 1973 (Reptilia: Phyllodactylidae) in Iran

2020 ◽  
pp. 207-214
Author(s):  
Akbar Fattahi
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Gene ◽  
Genetic Distances ◽  
Genetic Lineage ◽  
New Taxon ◽  
Zagros Mountains ◽  
Relict Species ◽  
Taxonomical Revision ◽  
Two Populations ◽  
Taxonomic Evaluation

The Iranian species of the phyllodactylid geckos of the genus Asaccus are found only in the valleys of the Zagros Mountains, a region which represents an important area of endemism in western Iran. Recently, many relict species have been described from the central and southern parts of the Zagros Mountains, which were previously known as A. elisae. The recent descriptions of species within this complex suggest that diversity within the genus may be higher than expected and that its taxonomy and systematics should be revised. In the present study, phylogenetic relationships within the genus Asaccus were evaluated using two mitochondrial and one nuclear gene. Genetically, the genus shows high levels of variability. The molecular phylogeny of the genus suggests the presence of three main clades along the Zagros Mountains with the southern population (from the Hormozgan province) and one clade (A. sp8 and A. sp9) being sister taxon to A. montanus from UAE. The remaining samples are separated into two reciprocally monophyletic groups: the northern (Kurdistan, Kermanshah and Ilam provinces) and the central (Lorestan, Khuzestan, Kohgilouye-Bouyer Ahmad and Fars provinces) Zagros groups. The results of the present study suggest that populations attributed to A. elisae in Iran correspond to distinct lineages with high genetic distances. In brief, our results suggest that the genus needs a major taxonomical revision The Arabian origin of the genus has not been confirmed, because two populations from Zagros were located within the A. montanus, A. gallagheri and A. platyrhynchus clade. Further morphological analyses are needed to systematically define each genetic lineage as a new taxon.

Molecular phylogeny of Pemphiginae (Hemiptera: Aphididae) inferred from nuclear gene EF-1α sequences

2008 ◽  
Vol 98 (5) ◽  
pp. 499-507 ◽  
Author(s):  
H.C. Zhang ◽  
G.X. Qiao
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogeny ◽  
Host Specificity ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Molecular Phylogenetic Analysis ◽  
Phylogenetic Study ◽  
Primary Host ◽  
Molecular Phylogenetic Study ◽  
Molecular Phylogenetic

AbstractThree traditional tribes of Fordini, Pemphigini and Eriosomatini comprise Pemphiginae, and there are two subtribes in Fordini and Pemphigini, respectively. Most of the species in this subfamily live heteroecious holocyclic lives with distinct primary host specificity. The three tribes of Pemphigini (except Prociphilina), Eriosomatini and Fordini use three families of plants, Salicaceae (Populus), Ulmaceae (Ulums) and Anacardiaceae (Pistacia and Rhus), as primary hosts, respectively, and form galls on them. Therefore, the Pemphigids are well known as gall makers, and their galls can be divided into true galls and pseudo-galls in type. We performed the first molecular phylogenetic study of Pemphiginae based on molecular data (EF-1α sequences). Results show that Pemphiginae is probably not a monophylum, but the monophyly of Fordini is supported robustly. The monophyly of Pemphigini is not supported, and two subtribes in it, Pemphigina and Prociphilina, are suggested to be raised to tribal level, equal with Fordini and Eriosomatini. The molecular phylogenetic analysis does not show definite relationships among the four tribes of Pemphiginae, as in the previous phylogenetic study based on morphology. It seems that the four tribes radiated at nearly the same time and then evolved independently. Based on this, we can speculate that galls originated independently four times in the four tribes, and there is no evidence to support that true galls are preceded by pseudo-galls, as in the case of thrips and willow sawflies.

scholarly journals Molecular evidence and marine snake origins

2005 ◽  
Vol 1 (2) ◽  
pp. 227-230 ◽  
Author(s):  
Michael S.Y Lee
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Morphological Data ◽  
Molecular Evidence ◽  
Gene Sequences ◽  
Molecular Analyses ◽  
Marine Origin ◽  
Molecular Tree

A molecular phylogeny was used to refute the marine scenario for snake origins. Nuclear gene sequences suggested that snakes are not closely related to living varanid lizards, thus also apparently contradicting proposed relationships between snakes and marine mosasaurs (usually considered to be varanoids). However, mosasaurs share derived similarities with both snakes and living varanids. A reanalysis of the morphological data suggests that, if the relationships between living taxa are constrained to the proposed molecular tree, with fossil forms allowed to insert in their optimal positions within this framework, mosasaurs cluster with snakes rather than with varanids. Combined morphological and molecular analyses also still unite marine lizards with snakes. Thus, the molecular data do not refute the phylogenetic evidence for a marine origin of snakes.

Molecular Phylogeny of Rodents, with Special Emphasis on Murids: Evidence from Nuclear Gene LCAT

1997 ◽  
Vol 8 (3) ◽  
pp. 423-434 ◽  
Author(s):  
Marc Robinson ◽  
François Catzeflis ◽  
Jérôme Briolay ◽  
Dominique Mouchiroud
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Gene

Systematics and molecular phylogenetics of Asian snail-eating snakes (Pareatidae)

Zootaxa ◽  
2011 ◽  
Vol 3001 (1) ◽  
pp. 57 ◽  
Author(s):  
YUHONG GUO ◽  
YUNKE WU ◽  
SHUNPING HE ◽  
HAITAO Shi ◽  
ERMI ZHAO
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Molecular Phylogenetics ◽  
Nuclear Gene ◽  
Morphological Characters ◽  
Cyt B ◽  
Ongoing Controversy ◽  
Distinct Genus ◽  
Molecular Studies

The taxonomy of the Asian snail-eating snakes (Pareatidae) is an ongoing controversy, partly because morphological characters do not yield consistent results across studies. We infer phylogenetic relationships within Pareatidae using ~ 2 kilobases of DNA sequences including two mitochondrial (cyt b and ND4) and one nuclear gene (c-mos). Results reveal four major lineages: Aplopeltura, Asthenodipsas, a clade formed by Pareas carinatus and P. nuchalis, and a clade comprising all other species of Pareas sampled in this study. Our data do not have enough signal to either support or reject a monophyletic Pareas. However, large molecular divergence (16.5%) is observed between the two major clades of Pareas, a level that is comparable to that between Pareas and Aplopeltura. Scale characters also suggest that P. carinatus and P. nuchalis are distinct from congeners, and future morphological and/or molecular studies might assess whether a distinct genus should be recognized. The molecular phylogeny further suggests a distant relationship between P. chinensis and P. formosensis and supports the validity of the former species.

scholarly journals Phylogeography and ecology of an endemic radiation of Hawaiian aquatic case-bearing moths ( Hyposmocoma : Cosmopterigidae)

2008 ◽  
Vol 363 (1508) ◽  
pp. 3459-3465 ◽  
Author(s):  
Daniel Rubinoff
Keyword(s):  
Maximum Likelihood ◽  
Molecular Phylogeny ◽  
Mitochondrial Gene ◽  
Hawaiian Islands ◽  
Elongation Factor ◽  
Nuclear Gene ◽  
Base Pairs ◽  
Island Endemic ◽  
Northwestern Hawaiian Islands ◽  
Elongation Factor 1

The endemic moth genus Hyposmocoma (Lepidoptera: Cosmopterigidae) may be one of the most speciose and ecologically diverse genera in Hawaii. Among this diversity is the Hyposmocoma saccophora clade with previously unrecorded aquatic larvae. I present a molecular phylogeny based on 773 base pairs (bp) of the mitochondrial gene cytochrome c oxidase subunit I and 762 bp of the nuclear gene elongation factor 1-α. Topologies were constructed from data using maximum-parsimony, maximum-likelihood and Bayesian search criteria. Results strongly support the monophyly of the H. saccophora clade and the monophyly of the genus Hyposmocoma . The H. saccophora clade has single-island endemic species on Oahu, Molokai and West Maui. By contrast, there are three species endemic to Kauai, two being sympatric. The H. saccophora clade appears to follow the progression rule, with more basal species on older islands, including the most basal species on 11 Myr-old Necker Island, one of the Northwestern Hawaiian Islands. Aquatic behaviour either evolved recently in the species on the main Hawaiian Islands or was secondarily lost on the arid northwestern Necker Island. The phylogeny suggests that Hyposmocoma is older than any of the current main islands, which may, in part, explain Hyposmocoma 's remarkable diversity.

scholarly journals Land snails ofLeptopomaPfeiffer, 1847 in Sabah, Northern Borneo (Caenogastropoda: Cyclophoridae): an analysis of molecular phylogeny and geographical variations in shell form

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3981 ◽  
Author(s):  
Chee-Chean Phung ◽  
Pooi-San Heng ◽  
Thor-Seng Liew
Keyword(s):  
Molecular Phylogeny ◽  
Geographical Variation ◽  
Species Differences ◽  
Shell Height ◽  
Nuclear Gene ◽  
Small Sample ◽  
Land Snails ◽  
Shell Form ◽  
Geographical Variations ◽  
Starting Point

Leptopomais a species rich genus with approximately 100 species documented. Species-level identification in this group has been based on shell morphology and colouration, as well as some anatomical features based on small sample sizes. However, the implications of the inter- and intra-species variations in shell form to the taxonomy ofLeptopomaspecies and the congruency of its current shell based taxonomy with its molecular phylogeny are still unclear. There are fourLeptopomaspecies found in Sabah, Borneo, and their taxonomy status remains uncertain due to substantial variation in shell forms. This study focuses on the phylogenetic relationships and geographical variation in shell form of threeLeptopomaspecies from Sabah. The phylogenetic relationship of these species was first estimated by performing Maximum Likelihood and Bayesian analysis based on mitochondrial genes (16S rDNA and COI) and nuclear gene (ITS-1). Then, a total of six quantitative shell characters (i.e., shell height, shell width, aperture height, aperture width, shell spire height, and ratio of shell height to width) and three qualitative shell characters (i.e., shell colour patterns, spiral ridges, and dark apertural band) of the specimens were mapped across the phylogenetic tree and tested for phylogenetic signals. Data on shell characters ofLeptopoma sericatumandLeptopoma pellucidumfrom two different locations (i.e., Balambangan Island and Kinabatangan) where both species occurred sympatrically were then obtained to examine the geographical variations in shell form. The molecular phylogenetic analyses suggested that each of the threeLeptopomaspecies was monophyletic and indicated congruence with only one of the shell characters (i.e., shell spiral ridges) in the current morphological-based classification. Although the geographical variation analyses suggested some of the shell characters indicating inter-species differences between the twoLeptopomaspecies, these also pointed to intra-species differences between populations from different locations. This study onLeptopomaspecies is based on small sample size and the findings appear only applicable toLeptopomaspecies in Sabah. Nevertheless, we anticipate this study to be a starting point for more detailed investigations to include the other still little-known (ca. 100)Leptopomaspecies and highlights a need to assess variations in shell characters before they could be used in species classification.

Reconstruction of intrageneric relationships within the Indo-West Pacific littoral crab genus Metopograpsus (Decapoda, Brachyura, Grapsidae): an alternative speciation order according to a 28S rDNA molecular phylogeny

Crustaceana ◽  
2021 ◽  
Vol 94 (11-12) ◽  
pp. 1313-1325
Author(s):  
Elisabeth Mock ◽  
Christoph D. Schubart
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Gene ◽  
28S Rrna ◽  
Widespread Species ◽  
West Pacific ◽  
Phylogenetic Reconstructions ◽  
Geographic Coverage ◽  
Morphological Differences ◽  
First Time ◽  
Basal Position

Abstract The genus Metopograpsus H. Milne Edwards, 1853 is widespread throughout the Indo-West Pacific and currently consists of seven species that can only be separated by minor morphological differences. Therefore, it represents a good example for the usefulness of genetic analyses for identification and classification. In order to obtain phylogenetic information at both lower and higher evolutionary levels, it is best to use a combination of mitochondrial and nuclear molecular markers. Here we present for the first time a molecular phylogeny based on a relative long fragment of the 28S rRNA nuclear gene for the genus Metopograpsus, after application of newly developed primers. Our data suggest an alternative intrageneric speciation order, with M. thukuhar and M. cannicci holding a basal position and a monophyletic grouping of M. frontalis, M. oceanicus and M. quadridentatus, which differs from prior phylogenetic reconstructions. Previously recognized intraspecific phylogeographic patterns in M. latifrons and M. quadridentatus could not be confirmed, due to limited variability of this conserved nuclear gene and due to an incomplete geographic coverage of the corresponding species. In contrast, the previously indicated phylogenetic subdivision within the formerly widespread species M. thukuhar, which led to the recent description of M. cannicci, is here supported.

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