A molecular phylogenetic hypothesis for the Asian agamid lizard genus Phrynocephalus reveals discrete biogeographic clades implicated by plate tectonics

Zootaxa ◽  
2018 ◽  
Vol 4467 (1) ◽  
pp. 1 ◽  
Author(s):  
J. ROBERT MACEY ◽  
JAMES A. II SCHULTE ◽  
NATALIA B. ANANJEVA ◽  
ERIK T. VAN DYKE ◽  
YUEZHAO WANG ◽  
...  
Keyword(s):  
Plate Tectonics ◽  
Arabian Plate ◽  
Current Status ◽  
Molecular Evidence ◽  
Caspian Basin ◽  
Agamid Lizard ◽  
Molecular Phylogenetic ◽  
Rag 1 ◽  
Phylogenetic Lineages ◽  
Allozyme Loci

Phylogenetic relationships of the agamid lizard genus Phrynocephalus are described in the context of plate tectonics. A near comprehensive taxon sampling reports three data sets: (1) mitochondrial DNA from ND1 to COI (3’ end of ND1, tRNAGln, tRNAIle, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and the 5’ end of COI) with 1761 aligned positional sites (1595 included, 839 informative), (2) nuclear RAG-1 DNA with 2760 aligned positional sites (342 informative), and (3) 25 informative allozyme loci with 213 alleles (107 informative when coded as presence/absence). It is hypothesized that Phrynocephalus phyletic patterns and speciation reflect fault lines of ancient plates now in Asia rejuvenated by the more recent Indian and Arabian plate collisions. Molecular estimates of lineage splits are highly congruent with geologic dates from the literature.  A southern origin for the genus in Southwest Asia is resolved in phylogenetic estimates and a northern origin is statistically rejected. On the basis of monophyly and molecular evidence several taxa previously recognized as subspecies are recognized as species: P. hongyuanensis, P. sogdianus, and P. strauchi as “Current Status”; Phrynocephalus bannikovi, Phrynocephalus longicaudatus, Phrynocephalus turcomanus, and Phrynocephalus vindumi are formally “New Status”. Phylogenetic evaluation indicates a soft substrate habitat of sand for the shared ancestor of modern Phrynocephalus. Size diversity maximally overlaps in the Caspian Basin and northwestern Iranian Plateau. The greatest species numbers of six in sympatry and regional allopatry are found in the southern Caspian Basin and southern Helmand Basin, both from numerous phylogenetic lineages in close proximity attributed to tectonic induced events. 

scholarly journals A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3354 ◽  
Author(s):  
Timur G. Simdyanov ◽  
Laure Guillou ◽  
Andrei Y. Diakin ◽  
Kirill V. Mikhailov ◽  
Joseph Schrével ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Wide Distribution ◽  
Phylogenetic Study ◽  
Molecular Evidence ◽  
Molecular Phylogenetic ◽  
Phylogenetic Lineages

Background Gregarines are a group of early branching Apicomplexa parasitizing invertebrate animals. Despite their wide distribution and relevance to the understanding the phylogenesis of apicomplexans, gregarines remain understudied: light microscopy data are insufficient for classification, and electron microscopy and molecular data are fragmentary and overlap only partially. Methods Scanning and transmission electron microscopy, PCR, DNA cloning and sequencing (Sanger and NGS), molecular phylogenetic analyses using ribosomal RNA genes (18S (SSU), 5.8S, and 28S (LSU) ribosomal DNAs (rDNAs)). Results and Discussion We present the results of an ultrastructural and molecular phylogenetic study on the marine gregarine Ancora sagittata from the polychaete Capitella capitata followed by evolutionary and taxonomic synthesis of the morphological and molecular phylogenetic evidence on eugregarines. The ultrastructure of Ancora sagittata generally corresponds to that of other eugregarines, but reveals some differences in epicytic folds (crests) and attachment apparatus to gregarines in the family Lecudinidae, where Ancora sagittata has been classified. Molecular phylogenetic trees based on SSU (18S) rDNA reveal several robust clades (superfamilies) of eugregarines, including Ancoroidea superfam. nov., which comprises two families (Ancoridae fam. nov. and Polyplicariidae) and branches separately from the Lecudinidae; thus, all representatives of Ancoroidea are here officially removed from the Lecudinidae. Analysis of sequence data also points to possible cryptic species within Ancora sagittata and the inclusion of numerous environmental sequences from anoxic habitats within the Ancoroidea. LSU (28S) rDNA phylogenies, unlike the analysis of SSU rDNA alone, recover a well-supported monophyly of the gregarines involved (eugregarines), although this conclusion is currently limited by sparse taxon sampling and the presence of fast-evolving sequences in some species. Comparative morphological analyses of gregarine teguments and attachment organelles lead us to revise their terminology. The terms “longitudinal folds” and “mucron” are restricted to archigregarines, whereas the terms “epicystic crests” and “epimerite” are proposed to describe the candidate synapomorphies of eugregarines, which, consequently, are considered as a monophyletic group. Abolishing the suborders Aseptata and Septata, incorporating neogregarines into the Eugregarinida, and treating the major molecular phylogenetic lineages of eugregarines as superfamilies appear as the best way of reconciling recent morphological and molecular evidence. Accordingly, the diagnosis of the order Eugregarinida Léger, 1900 is updated.

A REVISED GENERIC SYNOPSIS OF HYACINTHACEAE IN SUB-SAHARAN AFRICA, BASED ON MOLECULAR EVIDENCE, INCLUDING NEW COMBINATIONS AND THE NEW TRIBE PSEUDOPROSPEREAE

2003 ◽  
Vol 60 (3) ◽  
pp. 533-568 ◽  
Author(s):  
J. C. MANNING ◽  
P. GOLDBLATT ◽  
M. F. FAY
Keyword(s):  
Phylogenetic Analysis ◽  
Sub Saharan Africa ◽  
Molecular Evidence ◽  
New Combinations ◽  
Generic Level ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Single Genus ◽  
New Tribe ◽  
Sub Saharan

A revised generic synopsis of sub-Saharan Hyacinthaceae is presented, based on a molecular phylogenetic analysis of the family. Generic rank is accorded only to reciprocally monophyletic clades that can be distinguished by recognizable morphological discontinuities, thereby permitting an appropriate generic assignment of species not included in the analysis. Three subfamilies are recognized within the region. Subfamily Ornithogaloideae, characterized by flattened or angular seeds with tightly adhering testa, is considered to include the single genus Ornithogalum, which is expanded to include the genera Albuca, Dipcadi, Galtonia, Neopatersonia and Pseudogaltonia. Recognizing any of these segregates at generic level renders the genus Ornithogalum polyphyletic, while subdivision of Ornithogalum into smaller, morphologically distinguishable segregates in order to preserve the monophyly of each is not possible. Subfamily Urgineoideae, characterized by flattened or winged seeds with brittle, loosely adhering testa, comprises the two mainland African genera Bowiea and Drimia. The latter is well circumscribed by its deciduous, short-lived perianth and includes the previously recognized genera Litanthus, Rhadamanthus, Schizobasis and Tenicroa. The monotypic Madagascan Igidia is provisionally included in the subfamily as a third genus on the basis of its seeds, pending molecular confirmation of its relationships. Subfamily Hyacinthoideae resolves into three clades, distinguished as tribes Hyacintheae (strictly northern hemisphere and not treated further), Massonieae and Pseudoprospereae tribus nov. Full descriptions and a key to their identification are provided for all genera. New combinations reflecting the generic circumscriptions adopted here are made for most African and all Indian and Madagascan species.

scholarly journals Crustal density structure of the northwestern Iranian Plateau

2019 ◽  
Vol 56 (12) ◽  
pp. 1347-1365 ◽  
Author(s):  
Vahid Teknik ◽  
Abdolreza Ghods ◽  
Hans Thybo ◽  
Irina M. Artemieva
Keyword(s):  
High Density ◽  
Central Iran ◽  
P Wave ◽  
Arabian Plate ◽  
Scale Model ◽  
Moho Depth ◽  
Caspian Basin ◽  
The South ◽  
South Caspian Basin ◽  
Iranian Plateau

We present a new 2D crustal-scale model of the northwestern Iranian plateau based on gravity–magnetic modeling along the 500 km long China–Iran Geological and Geophysical Survey in the Iranian plateau (CIGSIP) seismic profile across major tectonic provinces of Iran from the Arabian plate into the South Caspian Basin (SCB). The seismic P-wave receiver function (RF) model along the profile is used to constrain major crustal boundaries in the density model. Our 2D crustal model shows significant variation in the sedimentary thickness, Moho depth, and the depth and extent of intra-crustal interfaces. The Main Recent Fault (MRF) between the Arabian crust and the overriding central Iran crust dips at approximately 13° towards the northeast to a depth of about 40 km. The geometry of the MRF suggests about 150 km of underthrusting of the Arabian plate beneath central Iran. Our results indicate the presence of a high-density lower crustal layer beneath Zagros. We identify a new crustal-scale suture beneath the Tarom valley between the South Caspian Basin crust and Central Iran and the Alborz. This suture is associated with sharp variation in Moho depth, topography, and magnetic anomalies, and is underlain by a 20 km thick high-density crustal root at 35–55 km depth. The high-density lower crust in Alborz and Zagros may be related to partial eclogitization of crustal roots below about 40 km depth. The gravity and magnetic models indicate a highly extended continental crust for the SCB crust along the profile. Low observed magnetic susceptibility of the Kermanshah ophiolites likely indicates that the ophiolite rocks only form a thin layer that has been thrust over the sedimentary cover.

DNA barcodes provide evidence for the independent origin of the cultivated silkworms Samia ricini and Samia cynthia

2021 ◽  
pp. 1-8
Author(s):  
J.-C. Huang ◽  
X.-Y. Li ◽  
Y.-P. Li ◽  
R.-S. Zhang ◽  
D.-B. Chen ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Phylogenetic Relationship ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Dna Barcodes ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework

Samia ricini (Wm. Jones) and Samia cynthia (Drury) (Lepidoptera: Saturniidae) have been used as traditional sources of food as well as silk-producing insects. However, the phylogenetic relationship between the two silkworms remains to be addressed. In this study, the mitochondrial cytochrome c oxidase subunit 1 (COI) gene sequences corresponding to DNA barcodes from 13 Samia species were analysed, and a DNA barcode-based phylogenetic framework for these Samia species was provided. Phylogenetic analysis showed that multiple individuals of a species could be clustered together. Our analysis revealed a close relationship among Samia yayukae Paukstadt, Peigler and Paukstadt, Samia abrerai Naumann and Peigler, Samia kohlli Naumann and Peigler, Samia naessigi Naumann and Peigler, Samia naumanni Paukstadt, Peigler and Paukstadt, and Samia kalimantanensis Paukstadt and Paukstadt. The mixed clustering relationship and low Kimura-2-parameter (K2P) genetic distance (0.006) between individuals of S. ricini and Samia canningi (Hutton) indicated that the cultivated silkworm S. ricini was derived from the non-cultivated silkworm S. canningi. The remote phylogenetic relationship and high K2P genetic distance (0.039) indicated that S. ricini and S. cynthia are distinct species, thus providing solid molecular evidence that they had entirely independent origins. The relationships between S. kalimantanensis and S. naumanni and between S. cynthia and Samia wangi Naumann and Peigler, as well as the potential cryptic species within S. abrerai were also discussed. This is the first study to assess the DNA barcodes of the genus Samia, which supplements the knowledge of species identification and provides the first molecular phylogenetic framework for Samia species.

scholarly journals Molecular epidemiology of Rabbit haemorrhagic disease virus

2002 ◽  
Vol 83 (10) ◽  
pp. 2461-2467 ◽  
Author(s):  
S. R. Moss ◽  
S. L. Turner ◽  
R. C. Trout ◽  
P. J. White ◽  
P. J. Hudson ◽  
...  
Keyword(s):  
Disease Virus ◽  
Nucleotide Sequencing ◽  
Molecular Evidence ◽  
Rabbit Haemorrhagic Disease Virus ◽  
Rabbit Haemorrhagic Disease ◽  
Molecular Phylogenetic ◽  
Virulent Virus ◽  
Rabbit Bone ◽  
European Rabbits ◽  
Haemorrhagic Disease

Millions of domestic and wild European rabbits (Oryctolagus cuniculus) have died in Europe, Asia, Australia and New Zealand during the past 17 years following infection by Rabbit haemorrhagic disease virus (RHDV). This highly contagious and deadly disease was first identified in China in 1984. Epidemics of RHDV then radiated across Europe until the virus apparently appeared in Britain in 1992. However, this concept of radiation of a new and virulent virus from China is not entirely consistent with serological and molecular evidence. This study shows, using RT–PCR and nucleotide sequencing of RNA obtained from the serum of healthy rabbits stored at 4 °C for nearly 50 years, that, contrary to previous opinions, RHDV circulated as an apparently avirulent virus throughout Britain more than 50 years ago and more than 30 years before the disease itself was identified. Based on molecular phylogenetic analysis of British and European RHDV sequences, it is concluded that RHDV has almost certainly circulated harmlessly in Britain and Europe for centuries rather than decades. Moreover, analysis of partial capsid sequences did not reveal significant differences between RHDV isolates that came from either healthy rabbits or animals that had died with typical haemorrhagic disease. The high stability of RHDV RNA is also demonstrated by showing that it can be amplified and sequenced from rabbit bone marrow samples collected at least 7 weeks after the animal has died.

scholarly journals Morphological and molecular evidence for the occurrence of Itajahya galericulata (Basidiomycota, Phallales) in India

2018 ◽  
Vol 63 (2) ◽  
pp. 39-44
Author(s):  
Ravi S. Patel ◽  
Ajit M. Vasava ◽  
Kishore S. Rajput
Keyword(s):  
South America ◽  
Phylogenetic Analyses ◽  
Its Sequences ◽  
Molecular Evidence ◽  
Nuclear Rdna ◽  
Gujarat State ◽  
Rdna Its ◽  
Molecular Phylogenetic ◽  
Rdna Its Sequences ◽  
The City

AbstractItajahya galericulata (Phallales, Phallaceae) was previously reported from several countries in South America and Africa. Recently we found I. galericulata in the city of Vadodara, Gujarat State, India. To verify its identity we studied its morphology and performed molecular phylogenetic analyses using nuclear rDNA LSU and mitochondrial ATP6 loci. Here we also provide nuclear rDNA ITS sequences for the Indian collection, since up to now no sequences of this region have been available for I. galericulata in GenBank. This study furnishes the first evidence for the occurrence of I. galericulata in India and in Asia as a whole.

The Phylogenetic Position of Crenea in the Lythraceae Based on Molecular Evidence, and the Transfer of Its Two Species to Ammannia

2021 ◽  
Vol 106 ◽  
pp. 325-339
Author(s):  
Shirley A. Graham ◽  
Peter W. Inglis ◽  
Taciana B. Cavalcanti
Keyword(s):  
Morphological Character ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Phylogenetic Position ◽  
Molecular Evidence ◽  
Monophyletic Lineage ◽  
The Family ◽  
Mangrove Vegetation ◽  
Molecular Phylogenetic ◽  
Globally Distributed

Crenea Aubl. (Lythraceae) is a ditypic genus of subshrubs occurring in mangrove vegetation on the coasts of northern South America. Phylogenetic analyses based on morphology have offered unresolved and conflicting phylogenetic positions for the genus in the family. This study presents the first molecular sequences for Crenea, from nrITS, rbcL, trnL, trnL-F, and matK regions. Molecular phylogenetic analyses find full support for Crenea within Ammannia L., a relationship not previously recognized. Ammannia is a globally distributed genus of terrestrial to amphibious herbs mostly occurring in freshwater marshes and wetlands. It was recently reconfigured based on phylogenetic evidence to include the genera Nesaea Comm. ex Kunth and Hionanthera A. Fern. & Diniz. The transfer of Crenea to Ammannia further extends the morphological, ecological, and biogeographical diversity of Ammannia and provides the final evidence defining Ammannia as a monophyletic lineage of the Lythraceae. A revised circumscription of Ammannia s.l. adds several new morphological character states and the first species in the genus restricted to mangrove vegetation. Two changes in taxonomic status are made: Ammannia maritima (Aubl.) S. A. Graham, P. W. Inglis, & T. B. Cavalc., comb. nov., and Ammannia patentinervius (Koehne) S. A. Graham, P. W. Inglis, & T. B. Cavalc., comb. nov. The new combinations are described, a list of exsiccatae examined is provided, and the effects of the reconfiguration to the morphology and biogeography of the genus are detailed.

Phylogenetics of the mycoheterotrophic genus Thismia (Thismiaceae: Dioscoreales) with a focus on the Old World taxa: delineation of novel natural groups and insights into the evolution of morphological traits

2020 ◽  
Vol 193 (3) ◽  
pp. 287-315 ◽  
Author(s):  
Ekaterina A Shepeleva ◽  
Mikhail I Schelkunov ◽  
Michal Hroneš ◽  
Michal Sochor ◽  
Martin Dančák ◽  
...  
Keyword(s):  
Significant Proportion ◽  
Morphological Diversity ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Morphological Description ◽  
Molecular Evidence ◽  
Ancestral State ◽  
Old World ◽  
Molecular Phylogenetic ◽  
Floral Characters

Abstract Thismia is a genus of > 80 mycoheterotrophic species characterized by a peculiar appearance and complex floral morphology. A significant proportion of the species and morphological diversity of Thismia has only been uncovered in the past two decades, and new discoveries continue to be made. Given that many new data have recently become available, and the most comprehensive taxonomic revision of the genus from 1938 addresses less than half of the currently known species, previous hypotheses for species relationships and infrageneric taxonomic classification in Thismia was in need of review. Extensive molecular phylogenetic studies of Thismia at the genus level have never been presented. We investigate the phylogenetic relationships of 41 species (and one variety) of Thismia from the Old World. Our study comprises 68 specimens (for 28 of which the data were newly generated), including outgroup taxa broadly representing Thismiaceae (= Burmanniaceae p.p. sensuAPG IV, 2016), and is based on two nuclear and one mitochondrial marker. We use maximum likelihood and Bayesian inference to infer relationships among the taxa. We also constructed a morphological dataset of 12 mostly floral characters, comparing these characters to hypotheses based on molecular evidence to identify putative synapomorphies for major clades and to discuss hypotheses regarding the evolution of structural traits in the genus. Our analyses indicate that the majority of currently accepted infrageneric taxa of Thismia are polyphyletic. We find support for the monophyly of the Old World group, in which we recognize five well-supported lineages (clades); the only New World species studied appears to be related to the Neotropical genus Tiputinia. Ancestral state reconstructions demonstrate that the evolution of most morphological characters was homoplastic, but we identify characters that provide each of the five clades of Old World Thismia with a unique morphological description. The geographical distribution of the species under study is also shown to be consistent with the major clades. Our investigation provides a phylogenetic basis for the development of a novel sectional classification of Thismia reflecting morphological and geographical traits.

Morphological and molecular evidence for a new species of the genus Panolis Hübner, [1821] (Lepidoptera: Noctuidae)

Zootaxa ◽  
2019 ◽  
Vol 4565 (4) ◽  
pp. 523
Author(s):  
XUAN AN ◽  
MAMORU OWADA ◽  
MIN WANG ◽  
HOU-SHUAI WANG
Keyword(s):  
New Species ◽  
Cytochrome C Oxidase ◽  
Phylogenetic Analyses ◽  
Species Group ◽  
Molecular Evidence ◽  
Mitochondrial Cytochrome ◽  
Molecular Phylogenetic ◽  
Lepidoptera Noctuidae ◽  
A New Species ◽  
I Gene

A new species of the genus Panolis Hübner, [1821], P. xundian sp. nov., is described and illustrated from southwestern China. It is well-defined morphologically by the male genitalia, with a well-developed pollex at the distal terminal of the sacculus and a broad, ventrally concave cucullus, the female corpus bursae with four long signum-stripes. Based on a 658 bp segment of the mitochondrial cytochrome c oxidase subunit I gene, we report the pairwise genetic distance of 2.5% from its allied species P. exquisita Draudt, 1950. Molecular phylogenetic analyses using three genes (2189 bp in total length) indicate that the new species belongs to the P. exquisita species group. 

Begonia yizhouensis, a new species in Begonia sect. Coelocentrum (Begoniaceae) from Guangxi, China

Phytotaxa ◽  
2019 ◽  
Vol 407 (1) ◽  
pp. 59-70 ◽  
Author(s):  
YI TONG ◽  
DAI-KE TIAN ◽  
JIANG-PING SHU ◽  
YAN XIAO ◽  
BING-MOU WANG ◽  
...  
Keyword(s):  
New Species ◽  
Iucn Red List ◽  
Molecular Evidence ◽  
Similar Species ◽  
Iucn Red List Categories ◽  
Monophyletic Lineage ◽  
Molecular Phylogenetic ◽  
Relationship Of ◽  
The Relationship ◽  
A New Species

Begonia yizhouensis, a new species in Begonia sect. Coelocentrum (Begoniaceae) from Guangxi of China, is described and illustrated. Morphologically, it is similar to the adjacently distributed B. luochengensis, but clearly separated by its waxy leaves with glabrous or sometimes sparsely puberulous surfaces, larger variation in leaf color and maculation along the main veins, white to pinkish-white flowers and late flowering. Furthermore, molecular phylogenetic analysis indicated B. yizhouensis was a monophyletic lineage and was sister with B. luochengensis. The relationship of the new species and other similar species is also discussed. This new species is endemic to limestone hills in Guangxi and is assessed as “Endangered” (EN) according to the IUCN Red List Categories and Criteria. Additionally, morphological and molecular evidence for B. yishanensis not being synonymous with B. porteri is presented.

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