scholarly journals A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 819
Author(s):  
Olivier C. G. Heylen ◽  
Nicolas Debortoli ◽  
Jonathan Marescaux ◽  
Jill K. Olofsson
Keyword(s):  
Real Number ◽  
Cryptic Species ◽  
Phylogenetic Relationships ◽  
Taxonomic Status ◽  
Hybrid Origin ◽  
Mentha Spicata ◽  
Phenotypic Information ◽  
Cryptic Taxa ◽  
Taxonomic Groups ◽  
Straightforward Interpretation

The genus Mentha is taxonomically and phylogenetically challenging due to complex genomes, polyploidization and an extensive historical nomenclature, potentially hiding cryptic taxa. A straightforward interpretation of phylogenetic relationships within the section Mentha is further hindered by dominant but outdated concepts on historically identified hybrid taxa. Mentha spicata is traditionally considered to be of hybrid origin, but the evidence for this is weak. Here, we aim to understand the phylogenetic relationships within the section Mentha using large sample sizes and to revisit the hybrid status and identity of M. spicata. We show that two of three traditional species in the subsection Spicatae are polyphyletic, as is the subsection as a whole, while the real number of cryptic species was underestimated. Compared to previous studies we present a fundamentally different phylogeny, with a basal split between M. spicata s.s. and M. longifolia s.s. Cluster analyses of morphological and genotypic data demonstrate that there is a dissociation between morphologically and genotypically defined groups of samples. We did not find any evidence that M. spicata is of hybrid origin, and we conclude its taxonomic status should be revised. The combination of genetic and phenotypic information is essential when evaluating hyperdiverse taxonomic groups.

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 Benchmarking DNA barcodes: an assessment using available primate sequences

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 851-854 ◽  
Author(s):  
Mehrdad Hajibabaei ◽  
Gregory AC Singer ◽  
Donal A Hickey
Keyword(s):  
New Species ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Primate Species ◽  
Dna Barcodes ◽  
Global Biodiversity ◽  
Efficient Sequence

DNA barcoding has been recently promoted as a method for both assigning specimens to known species and for discovering new and cryptic species. Here we test both the potential and the limitations of DNA barcodes by analysing a group of well-studied organisms—the primates. Our results show that DNA barcodes provide enough information to efficiently identify and delineate primate species, but that they cannot reliably uncover many of the deeper phylogenetic relationships. Our conclusion is that these short DNA sequences do not contain enough information to build reliable molecular phylogenies or define new species, but that they can provide efficient sequence tags for assigning unknown specimens to known species. As such, DNA barcoding provides enormous potential for use in global biodiversity studies.Key words: DNA barcoding, species identification, primate, biodiversity.

scholarly journals Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda)

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2982 ◽  
Author(s):  
Mun Hua Tan ◽  
Han Ming Gan ◽  
Yin Peng Lee ◽  
Gary C.B. Poore ◽  
Christopher M. Austin
Keyword(s):  
Codon Usage ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Decapod Crustacean ◽  
Illumina Miseq ◽  
Comparative Genomic ◽  
Decapod Crustaceans ◽  
Phylogenetic Studies ◽  
Significant Gene ◽  
Taxonomic Groups

BackgroundWhole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information.MethodsSequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements.ResultsWe present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps,Callianassa ceramicaandTrypaea australiensis, along with three caridean shrimps,Macrobrachium bullatum,Alpheus lobidens, andCaridinacf.nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders.DiscussionOur findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

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.

scholarly journals Early diversification and permeable species boundaries in the Mediterranean firs

2019 ◽  
Vol 125 (3) ◽  
pp. 495-507 ◽  
Author(s):  
Francisco Balao ◽  
María Teresa Lorenzo ◽  
José Manuel Sánchez-Robles ◽  
Ovidiu Paun ◽  
Juan Luis García-Castaño ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Taxonomic Status ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Early Diversification ◽  
Genome Wide ◽  
History Of ◽  
The Mediterranean ◽  
Independent Species

Abstract Background and Aims Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. Methods We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. Key Results Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene–Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. Conclusions Our phylogenomic results contribute to shed light on conifers’ diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.

Phylogenetic relationships of Mesoamerican species of the genus Sciurus (Rodentia: Sciuridae)

Zootaxa ◽  
2007 ◽  
Vol 1525 (1) ◽  
pp. 31-40 ◽  
Author(s):  
FEDERICO VILLALOBOS ◽  
FERNANDO CERVANTES-REZA
Keyword(s):  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Morphological Analysis ◽  
Taxonomic Status ◽  
The Other

The phylogenetic relationships of Sciurus species present in Mesoamerica are addressed using a morphological analysis under Maximum Parsimony. Our results recovered the existence of two clades: one comprising S. aureogaster, S. colliaei, S. variegatoides and Syntheosciurus brochus and the other clade composed by S. richmondi, S. granatensis, S. deppei, S. yucatanensis and Microsciurus alfari. The taxonomic status of the genera Microsciurus and Syntheosciurus is discussed as well the biogeographic implications of these findings.

scholarly journals Uniform Manifold Approximation and Projection for Clustering Taxa through Vocalizations in a Neotropical Passerine (Rough-Legged Tyrannulet, Phyllomyias burmeisteri)

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1406
Author(s):  
Ronald M. Parra-Hernández ◽  
Jorge I. Posada-Quintero ◽  
Orlando Acevedo-Charry ◽  
Hugo F. Posada-Quintero
Keyword(s):  
Principal Component Analysis ◽  
Bird Species ◽  
Principal Component ◽  
Taxonomic Status ◽  
Behavioral Traits ◽  
Reduction Techniques ◽  
Dimensionality Reduction Techniques ◽  
Taxonomic Groups ◽  
Source Of Information

Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sensitive techniques are required. In this study, we have evaluated the sensitivity of the Uniform Manifold Approximation and Projection (UMAP) technique for grouping the vocalizations of individuals of the Rough-legged Tyrannulet Phyllomyias burmeisteri complex. Although the existence of two taxonomic groups has been suggested by some studies, the species has presented taxonomic difficulties in classification in previous studies. UMAP exhibited a clearer separation of groups than previously used dimensionality-reduction techniques (i.e., principal component analysis), as it was able to effectively identify the two taxa groups. The results achieved with UMAP in this study suggest that the technique can be useful in the analysis of species with complex in taxonomy through vocalizations data as a complementary tool including behavioral traits such as acoustic communication.

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