scholarly journals Chromosomal Signatures Corroborate the Phylogenetic Relationships within Akodontini (Rodentia, Sigmodontinae)

2020 ◽  
Vol 21 (7) ◽  
pp. 2415 ◽  
Author(s):  
Willam Oliveira da Silva ◽  
Stella Miranda Malcher ◽  
Adenilson Leão Pereira ◽  
Julio Cesar Pieczarka ◽  
Malcolm Andrew Ferguson-Smith ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Chromosome Painting ◽  
Species Complex ◽  
Taxonomic Status ◽  
Molecular Topology ◽  
Comparative Chromosome Painting ◽  
Clade B ◽  
Karyotypic Variability ◽  
Painting Analysis ◽  
Molecular Relationships

Comparative chromosome-painting analysis among highly rearranged karyotypes of Sigmodontinae rodents (Rodentia, Cricetidae) detects conserved syntenic blocks, which are proposed as chromosomal signatures and can be used as phylogenetic markers. In the Akodontini tribe, the molecular topology (Cytb and/or IRBP) shows five low-supported clades (divisions: “Akodon”, “Bibimys”, “Blarinomys”, “Oxymycterus”, and “Scapteromys”) within two high-supported major clades (clade A: “Akodon”, “Bibimys”, and “Oxymycterus”; clade B: “Blarinomys” and “Scapteromys”). Here, we examine the chromosomal signatures of the Akodontini tribe by using Hylaeamys megacephalus (HME) probes to study the karyotypes of Oxymycterus amazonicus (2n = 54, FN = 64) and Blarinomys breviceps (2n = 28, FN = 50), and compare these data with those from other taxa investigated using the same set of probes. We strategically employ the chromosomal signatures to elucidate phylogenetic relationships among the Akodontini. When we follow the evolution of chromosomal signature states, we find that the cytogenetic data corroborate the current molecular relationships in clade A nodes. We discuss the distinct events that caused karyotypic variability in the Oxymycterus and Blarinomys genera. In addition, we propose that Blarinomys may constitute a species complex, and that the taxonomy should be revised to better delimit the geographical boundaries and their taxonomic status.

scholarly journals Chromosomal phylogeny and comparative chromosome painting among Neacomys species (Rodentia, Sigmodontinae) from eastern Amazonia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Willam Oliveira da Silva ◽  
Julio Cesar Pieczarka ◽  
Marlyson Jeremias Rodrigues da Costa ◽  
Malcolm Andrew Ferguson-Smith ◽  
Patricia Caroline Mary O’Brien ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Chromosome Painting ◽  
Chromosomal Evolution ◽  
Distribution Area ◽  
Comparative Chromosome Painting ◽  
Candidate Species ◽  
Character Matrix ◽  
Coi Sequences ◽  
Molecular Relationships ◽  
Chromosomal Phylogeny

Abstract Background The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and chromosome painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by chromosome painting with Hylaeamys megacephalus (HME) whole-chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. Results The comparative chromosome painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by chromosome painting among the karyotypes. Conclusions Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.

scholarly journals Resolving the Taxonomic Status of Potential Biocontrol Agents Belonging to the Neglected Genus Lipolexis Förster (Hymenoptera, Braconidae, Aphidiinae) with Descriptions of Six New Species

Insects ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 667
Author(s):  
Korana Kocić ◽  
Andjeljko Petrović ◽  
Jelisaveta Čkrkić ◽  
Nickolas G. Kavallieratos ◽  
Ehsan Rakhshani ◽  
...  
Keyword(s):  
Biological Control ◽  
New Species ◽  
Molecular Analysis ◽  
Phylogenetic Relationships ◽  
Morphological Study ◽  
Species Complex ◽  
Taxonomic Status ◽  
Integrative Approach ◽  
Control Programs ◽  
Small Genus

Lipolexis is a small genus in the subfamily Aphidiinae represented by one species in Europe (Lipolexis gracilis Förster) and by four in Asia (Lipolexis wuyiensis Chen, L. oregmae Gahan, L. myzakkaiae Pramanik and Raychaudhuri and L. pseudoscutellaris Pramanik and Raychaudhuri). Although L. oregmae is employed in biological control programs against pest aphids, the last morphological study on the genus was completed over 50 years ago. This study employs an integrative approach (morphology and molecular analysis (COI barcode region)), to examine Lipolexis specimens that were sampled worldwide, including specimens from BOLD database. These results establish that two currently recognized species of Lipolexis (L. gracilis, L. oregmae) are actually a species complex and also reveal phylogenetic relationships within the genus. Six new species are described and a global key for the identification of Lipolexis species is provided.

scholarly journals Phylogenetic relationships among subclades within the Trinity bristle snail species complex, riverine barriers, and re-classification

2021 ◽  
pp. 107-145
Author(s):  
Robert M. Sullivan
Keyword(s):  
Genetic Variation ◽  
Phylogenetic Relationships ◽  
Species Complex ◽  
Phylogenetic Signal ◽  
Taxonomic Status ◽  
Molecular Evidence ◽  
Snail Species ◽  
Character State ◽  
Reconstruction Methods ◽  
The Trinity

The Trinity bristle snail (Monadenia setosa) is listed as a threatened species under the California Endangered Species Act (CESA). In northern California, populations of this endemic terrestrial gastropod occur in rare, isolated, and highly fragmented locations within the greater Trinity Basin. Since 1952 when it was originally described, the taxonomic status of the Trinity bristle snail has been questioned based on unpublished information limited in geographic scope and sample size, which resulted in the taxon being reduced from species status (M. setosa) to subspecific status (M. i. setosa) within the Redwood sideband (M. infumata) species complex. Primary objectives of the present study were to: 1) use DNA extraction and PCR sequencing to gain insight into patterns of genetic variation and phylogenetic relationships among a larger sample of endemic populations of the Trinity bristle snail; 2) re-evaluate the systematic and taxonomic status of the species using outgroup analysis and references samples from sympatric ecologically co-occurring taxa within the genus Monadenia; and 3) evaluate the potential biogeographic effects of major riverine systems on genetic differentiation among relic and disjunct populations within the Trinity Basin. Results of the DNA sequence analysis using several different tree reconstruction methods revealed that subspecies of the Redwood sideband (M. i. subcarinata), Yellow-based sideband (M. i. ochromphalus), and the Trinity bristle (M. i. setosa) exhibited a phylogenetic signal at > 95% species probability. Except for the Yellow-based sideband, molecular evidence detected the presence of several morphologically cryptic subclades within each species clade formerly undescribed by the scientific community. Syntopic1 ecological relationships between subclades of the Trinity bristle snail and the Redwood sideband occurred in several areas within the geographic range of the Trinity bristle snail, which indicated that these subclades were conservatively differentiated at the subspecific level. A Bayesian coalescent tree showed that genetic variation 1 Syntopy refers to the joint occurrence of two species in the same habitat at the same time, which may result in hybridization between closely related taxa or sister species. In contrast, sympatric species occur together in the same region, but do not necessarily share the same localities as syntopic species do (Futuma 2009). among allopatric subclades of the Trinity bristle snail and the Redwood sideband were congruent with hydrological discontinuities associated with site-specific riparian stream corridors and the primary river systems within the Trinity Basin. Correlation analysis revealed a pattern of area effects, wherein sparsely bristled Trinity bristle snails were generally found to the northwest and more abundantly bristled individuals to the southeast in relation to primary river corridors that bisect the central Trinity Basin. A similar but opposite trend was observed in the directional pattern of banding. Here the most conspicuously banded individuals were found in samples distributed to the northwest while individuals with less conspicuous banding patterns occurred in a more southeasterly direction in relation to primary riverine corridors. These geographic patterns of bristles and bands appeared to reflect shallow clines that were evident in samples of both the Trinity bristle snail and the Redwood sideband. Parsimony character state reconstructions revealed that the presence of bristles and conspicuousness of bands was widespread among genetic samples, but these attributes did not provide a definitive morphological character that could be used to distinguish among co-occurring taxa.

Phylogenetic relationships of Pakistan Gelidium (Gelidiales, Rhodophyta) species with recognition of Gelidium pakistanicum stat. nov.

2019 ◽  
Vol 62 (2) ◽  
pp. 141-147 ◽  
Author(s):  
D. Wilson Freshwater ◽  
Laila Shahnaz
Keyword(s):  
Data Analysis ◽  
Phylogenetic Relationships ◽  
Species Complex ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Molecular Data ◽  
Gelidium Pusillum

Abstract Two species of Gelidium, Gelidium usmanghanii and Gelidium pusillum var. pakistanicum are reported only from Pakistan, but their taxonomic status, phylogenetic relationships, and distributions have not been assessed with molecular data. Analysis of rbcL sequences revealed that G. usmanghanii was a distinct species with a distribution extending at least to the coast of Oman. This analysis also resolved G. pusillum var. pakistanicum within a Gelidium millariana species complex that was distantly related to G. pusillum. Further analyses of rbcL and COI-5P sequences showed that G. pusillum var. pakistanicum was a distinct species in this complex, and based on these molecular, and previous morphological results, this variety is elevated to the rank of species as Gelidium pakistanicum stat. nov.

A new mouse of the Peromyscus maniculatus species complex (Cricetidae) from the highlands of central Mexico

2020 ◽  
Vol 101 (4) ◽  
pp. 1117-1132
Author(s):  
M Ángel Léon-Tapia ◽  
Jesús A Fernández ◽  
Yessica Rico ◽  
F A Cervantes ◽  
Alejandro Espinosa de los Monteros
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Species Complex ◽  
Peromyscus Maniculatus ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Volcanic Belt ◽  
Genetic Distances ◽  
Central Mexico ◽  
Molecular Phylogenetic

Abstract The Peromyscus maniculatus species complex is one of the most widespread group of small mammals in North America. However, the taxonomy and phylogenetic relationships among its constituent taxa remain unclear. As part of a revision of Peromyscus specimens from the highlands of the Trans-Mexican Volcanic Belt in central Mexico, we identified five individuals collected in 1968 that differed externally from other Peromyscus specimens, although morphologically similar to P. labecula and P. melanotis, both latter in the P. maniculatus species complex. Based on cranial measurements and mitochondrial DNA sequences, we aimed to more accurately determine the phylogenetic relationships and the taxonomic status of these individuals. Molecular phylogenetic analyses showed that the specimens formed a monophyletic clade sister to the P. maniculatus species complex. Pairwise genetic distances between those specimens and other species within the P. maniculatus species complex were greater than 7.91%. In addition, morphological analyses clearly distinguished the test specimens from P. melanotis and P. labecula. Based on the results of our molecular and morphological analyses, we conclude that these specimens represent an undescribed species of the P. maniculatus species complex, which we describe herein.

scholarly journals Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 668
Author(s):  
Tinghao Yu ◽  
Yalin Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Strong Support ◽  
Intergenic Spacer ◽  
Taxonomic Status ◽  
Start Codon ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

scholarly journals Comparative chromosome painting discloses homologous segments in distantly related mammals

1994 ◽  
Vol 6 (4) ◽  
pp. 342-347 ◽  
Author(s):  
Harry Scherthan ◽  
Thomas Cremer ◽  
Ulfur Arnason ◽  
Heinz-Ulrich Weier ◽  
Antonio Lima-de-Faria ◽  
...  
Keyword(s):  
Chromosome Painting ◽  
Comparative Chromosome Painting

Molecular phylogenetic relationships within the Phrynocephalus maculatus‐arabicus species complex (Sauria: Agamidae) in Iran

2021 ◽  
Vol 59 (7) ◽  
pp. 1583-1588
Author(s):  
Farnaz Ebrahimipour ◽  
Nasrullah Rastegar‐Pouyani ◽  
Eskandar Rastegar‐Pouyani ◽  
Seyyed Saeed Hosseinian Yousefkhani ◽  
Kamran Kamali
Keyword(s):  
Phylogenetic Relationships ◽  
Species Complex ◽  
Molecular Phylogenetic

scholarly journals ORBITOLINA DAVIESI HOFKER, 1966: A FORGOTTEN ORBITOLINIDAE FROM THE THANETIAN OF PAKISTAN AND ITS TAXONOMIC STATUS

2020 ◽  
pp. 41-48
Author(s):  
FELIX SCHLAGINTWEIT
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Taxonomic Status ◽  
Original Description ◽  
Junior Synonym ◽  
New Combination ◽  
Linear Arrangement ◽  
Radial Zone

Orbitolina daviesi Hofker, 1966 (family Orbitolinidae) was validly described and thoroughly illustrated from Thanetian limestones of Pakistan. Although its attribution to the genus Orbitolina d’Orbigny and any phylogenetic relationships with the Cretaceous taxa have been refuted shortly afterwards, the species has not been taxonomically revised since then. Karsella hottingeri Sirel, 1999 was established as new genus and new species from the Thanetian of Turkey, without taking into account J. Hofker’s publication. The original description and genus diagnosis of Karsella has meanwhile been emended to include the occurrence of a radial zone with septula that follow a zig-zag pattern and associated linear arrangement of the foramina, as well as a complex embryo. Orbitolina daviesi clearly displays these features and is here considered a species of the genus Karsella Sirel. Karsella hottingeri is regarded as a subjective junior synonym of O. daviesi Hofker and therefore, the only species of the genus is given as a new combination: Karsella daviesi (Hofker). From a suprageneric viewpoint, the two Paleogene genera Karsella Sirel and Cushmania Silvestri display a complex embryo and might belong to a new subfamily of the Orbitolinidae, phylogenetically different and unrelated to the lower-mid Cretaceous Orbitolininae.

scholarly journals Taxonomic notes on Scutellaria taipeiensis (Lamiaceae) from morphological and molecular data

PhytoKeys ◽  
2020 ◽  
Vol 140 ◽  
pp. 33-45
Author(s):  
Chien-Ti Chao ◽  
Bing-Hong Huang ◽  
Jui-Tse Chang ◽  
Pei-Chun Liao
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Taxonomic Status ◽  
Plastid Dna ◽  
Single Species ◽  
Molecular Data ◽  
Sequence Information ◽  
Related Literature ◽  
Morphological And Molecular Data ◽  
Comprehensive Study

The genus Scutellaria comprises eight species distributed from 50 to 2000 m in Taiwan. Amongst them, S. barbata and S. taipeiensis are very similar on the basis of morphological and plastid DNA sequence information. Therefore, a comprehensive study of the taxonomic status of S. taipeiensis is necessary. We reviewed the herbarium sheets, related literature and protologues and compared morphologies of these two species, as well as their phylogenetic relationships. All evidence, including the diagnostic characters between S. taipeiensis and S. barbata, suggest that they belonged to a single species rather than two. As a result, S. taipeiensis is treated as a synonym of S. barbata.

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