Plastome and Nuclear Phylogenies of Dwarf Mistletoes (Arceuthobium: Viscaceae)

2021 ◽  
Vol 46 (2) ◽  
pp. 389-402
Author(s):  
Adam C. Schneider ◽  
Kate M. Sanders ◽  
Jacob H. Idec ◽  
Yun Jee Lee ◽  
Shawn C. Kenaley ◽  
...  
Keyword(s):  
New World ◽  
Sequence Data ◽  
Strong Support ◽  
Species Level ◽  
Species Relationships ◽  
Plastome Evolution ◽  
Subspecies Level ◽  
Infraspecific Taxa ◽  
Ribosomal Cistron ◽  
Number Of Individuals

Abstract— Dwarf mistletoes are a lineage of morphologically-reduced stem parasites inhabiting Pinaceae and Cupressaceae throughout the northern hemisphere and equatorial East Africa. Though diagnosable by a suite of morphological traits, phylogenetic knowledge of species relationships has been limited to studies employing either comprehensive taxonomic sampling of one or two genes, or more sequence data from a limited number of individuals. We used data from genome skimming to assemble 3kb of the nuclear ribosomal cistron and up to 45kb of the plastome to clarify the phylogenetic root of the genus, monophyly of species, and relationships among infraspecific taxa. Genomic differentiation among terminal taxa was variable; however, we found strong support for reciprocally monophyletic New World and Old World lineages, congruent nrDNA and plastome topologies at the species level and below, and monophyly of most taxonomic sections and species. Plastome gene content was stable across the genus with minimal pseudogenization or loss, as in other hemiparasites, with the notable exception of cemA. These findings form the basis of our re-evaluation of historical biogeographical hypotheses, species- and subspecies-level taxonomy, and plastome evolution in Arceuthobium. More broadly, this work provides a foundation for future clade-focused comparative and biosystematics studies of Arceuthobium.

scholarly journals Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
Author(s):  
W. Andrew Cox ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
New World ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Strong Support ◽  
Nuclear Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Mitochondrial Data ◽  
Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

scholarly journals Rhapsody in emerald: phylogenetic framework for Lestidae with reference to the systematic position of Chalcolestes Kennedy

2022 ◽  
Vol 25 ◽  
pp. 16-21
Author(s):  
Thomas J. Simonsen ◽  
Marcus Glahder ◽  
Thomas Pape ◽  
Kent Olsen ◽  
Marie Djernæs
Keyword(s):  
New World ◽  
Sequence Data ◽  
Strong Support ◽  
Systematic Position ◽  
The Other ◽  
Valid Genus ◽  
The Family ◽  
Statistical Support ◽  
Phylogenetic Framework ◽  
Molecular Dataset

We reconstruct a phylogenetic framework for the zygopteran family Lestidae based on a molecular dataset comprised of sequence data from the genes COI, 16S, 18S, 28S, and ITS1+2 from 41 ingroup taxa and 8 outgroup taxa with emphasis on the systematic position of the genus Chalcolestes Kennedy. We recover Lestidae as monophyletic with good statistical support. The family falls into two subequal clades. One, comprising the genus Sympecma Burmeister and Lestes Leach sensu lato (including the genus Archi­lestes Selys) is poorly to moderately supported. While the other, comprising the genera Austrolestes Tillyard, Indolestes Fraser, Orolestes McLachlan, and Chalcolestes is strongly supported. Chalcolestes is recovered as sister to the Oriental genus Orolestes with strong support. Our results thus support that Chalcolestes is a valid genus not closely related to Lestes. Monophyly of Lestes requires inclusion of the New World genus Archilestes, and our results support the need for a thorough revision of Lestes.

scholarly journals Historical specimens and the limits of subspecies phylogenomics in the New World quails (Odontophoridae)

2021 ◽  
Author(s):  
Jessie F Salter ◽  
Peter A Hosner ◽  
Edward L Braun ◽  
Rebecca T Kimball ◽  
Robb T Brumfield ◽  
...  
Keyword(s):  
New World ◽  
Phylogenetic Analyses ◽  
Species Level ◽  
Phylogenetic Structure ◽  
Northern Bobwhites ◽  
Geographic Structure ◽  
Subspecies Level ◽  
History Of ◽  
Diverse Groups ◽  
Historical Samples

As phylogenomics focuses on comprehensive taxon sampling at the species and population/subspecies levels, incorporating genomic data from historical specimens has become increasingly common. While historical samples can fill critical gaps in our understanding of the evolutionary history of diverse groups, they also introduce additional sources of phylogenomic uncertainty, making it difficult to discern novel evolutionary relationships from artifacts caused by sample quality issues. These problems highlight the need for improved strategies to disentangle artifactual patterns from true biological signal as historical specimens become more prevalent in phylogenomic datasets. Here, we tested the limits of historical specimen-driven phylogenomics to resolve subspecies-level relationships within a highly polytypic family, the New World quails (Odontophoridae), using thousands of ultraconserved elements (UCEs). We found that relationships at and above the species-level were well-resolved and highly supported across all analyses, with the exception of discordant relationships within the two most polytypic genera which included many historical specimens. We examined the causes of discordance and found that inferring phylogenies from subsets of taxa resolved the disagreements, suggesting that analyzing subclades can help remove artifactual causes of discordance in datasets that include historical samples. At the subspecies-level, we found well-resolved geographic structure within the two most polytypic genera, including the most polytypic species in this family, Northern Bobwhites (Colinus virginianus), demonstrating that variable sites within UCEs are capable of resolving phylogenetic structure below the species level. Our results highlight the importance of complete taxonomic sampling for resolving relationships among polytypic species, often through the inclusion of historical specimens, and we propose an integrative strategy for understanding and addressing the uncertainty that historical samples sometimes introduce to phylogenetic analyses.

An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships

2012 ◽  
Vol 25 (1) ◽  
pp. 1 ◽  
Author(s):  
Anna E. Syme ◽  
Daniel J. Murphy ◽  
Gareth D. Holmes ◽  
Stuart Gardner ◽  
Rachael Fowler ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Strong Support ◽  
Molecular Data ◽  
Species Level ◽  
Internal Transcribed Spacer Region ◽  
Deep Coalescence ◽  
History Of ◽  
Levels Of Support

Although the Australasian grass genus Austrostipa is species rich, abundant and ecologically significant, the subgeneric classification of its 62 species has not been comprehensively tested with molecular data. We used three molecular markers from 51 species to determine a phylogeny of the genus and found strong support for the following seven of the existing subgenera: Falcatae, Austrostipa, Aulax, Lobatae, Bambusina, Lancea and Longiaristatae. The molecular data do not support Tuberculatae and Eremophilae, which could be combined with subgenus Austrostipa. The data are equivocal or insufficient regarding monophyly of Ceres, Arbuscula, Petaurista and Lanterna. Data from the nuclear internal transcribed spacer region appear to be suitable for phylogenetic analysis of this group, and the degree of sequence variability resolves species-level relationships with good levels of support. In contrast, chloroplast sequence data from the matK and rbcL genes do not resolve most relationships at the species level, and the inferred phylogeny hints at gene duplication, chloroplast capture, or deep coalescence in the evolutionary history of Austrostipa.

scholarly journals The genus Amegilla (Hymenoptera, Apidae, Anthophorini) in Australia: a revision of the subgenus Asaropoda

ZooKeys ◽  
2020 ◽  
Vol 908 ◽  
pp. 45-122
Author(s):  
Remko Leijs ◽  
James Dorey ◽  
Katja Hogendoorn
Keyword(s):  
Sequence Data ◽  
Strong Support ◽  
Morphological Characters ◽  
Species Level ◽  
Mitochondrial Cytochrome ◽  
Species Delineation ◽  
Distribution Maps ◽  
Australian Species ◽  
Flower Visitation ◽  
Mitochondrial Cytochrome Oxidase

The species in the subgenus Amegilla (Asaropoda) are revised. Species delineation was decided based on diagnostic morphological characters as well as an incomplete phylogeny based on mitochondrial cytochrome oxidase 1 sequence data. Strong support was obtained for separating the Australian species of Amegilla into the three subgenera previously proposed on the basis of morphology. The subgenus Asaropoda was found to comprise 21 species, including ten new species: A. albiclypeata Leijs, sp. nov., A. aurantia Leijs, sp. nov., A. batleyi Leijs, sp. nov., A. crenata Leijs, sp. nov., A. griseocincta Leijs, sp. nov., A. incognita Leijs, sp. nov., A. nitidiventris Leijs, sp. nov., A. scoparia Leijs, sp. nov., A. xylocopoides Leijs, sp. nov., and A. youngi Leijs, sp. nov. The subspecies A. preissi frogatti is raised to species level, and 16 new synonymies are proposed. Keys to the species of both sexes and descriptions or redescriptions are provided. Distribution maps, data on flower visitation and phenology are given.

scholarly journals A Robust Phylogeny of the Oropendolas: Polyphyly Revealed by Mitochondrial Sequence Data

The Auk ◽  
2002 ◽  
Vol 119 (2) ◽  
pp. 335-348 ◽  
Author(s):  
J. Jordan Price ◽  
Scott M. Lanyon
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Species Level ◽  
Species Relationships ◽  
Base Pairs ◽  
Phylogenetic Information ◽  
Multiple Exemplars ◽  
Reconstruction Methods ◽  
Mitochondrial Cytochrome B ◽  
Wide Range

Abstract We present a robust, fully resolved phylogeny for the oropendolas that will serve as a basis for comparative studies in this group. We sequenced 2,011 base pairs (bp) of the mitochondrial cytochrome-b and ND2 genes from 22 individuals to reconstruct relationships between recognized species and subspecies and to assess variation within polytypic taxa. A single phylogenetic tree was produced despite the use of a wide range of weighting schemes and phylogenetic reconstruction methods. Our data provide strong evidence that oropendolas are polyphyletic, with two distinct groups within a larger clade of oropendolas and caciques. We confirm the monophyly of recognized species, but indicate that some within-species relationships do not conform to recognized subspecies limits. Our findings thus demonstrate the importance of including multiple exemplars from each taxon of interest. The two genes provided complimentary and equally effective phylogenetic information for comparisons within the oropendolas, but exhibited lower resolution in comparisons above the species level.

The types of skippers described by Shu-Iti Murayama (Lepidoptera: Hesperiidae)

Zootaxa ◽  
2020 ◽  
Vol 4801 (2) ◽  
pp. 280-290
Author(s):  
HIDEYUKI CHIBA ◽  
HIROSHI TSUKIYAMA ◽  
JIA-YUAN LIANG ◽  
SHOU-MING WANG ◽  
ZONG-YU SHEN ◽  
...  
Keyword(s):  
Taxonomic Status ◽  
Species Level ◽  
Valid Species ◽  
Subspecies Level ◽  
Subjective Synonym

Fifteen holotypes of Asian Hesperiidae taxa described by Shu-iti Murayama were examined, and their taxonomic status is discussed. We confirm that five are valid names while the rest are synonyms as indicated partially by previous authors. Valid species-level names are Aeromachus matudai (Murayama), Aeromachus bandaishanus Murayama & Shimonoya, Coladenia pinsbukana (Shimonoya & Murayama), and Sebastonyma suthepiana Murayama & Kimura. Valid subspecies-level name is Ochlodes yuchingkina Murayama & Shimonoya. In order to settle the taxonomic status of Pedesta masuriensis cuneomaculata Murayama, masuriensis and tali were studied morphologically and molecularly. As a result, we consider that masuriensis and tali are two different species and treat cuneomaculata as a junior subjective synonym of tali. 

scholarly journals Identification of Ciprofloxacin-ResistantCampylobacter jejuni by Use of a Fluorogenic PCR Assay

2000 ◽  
Vol 38 (11) ◽  
pp. 3971-3978 ◽  
Author(s):  
David L. Wilson ◽  
Sheila R. Abner ◽  
Thomas C. Newman ◽  
Linda S. Mansfield ◽  
John E. Linz
Keyword(s):  
Antimicrobial Agents ◽  
Sequence Data ◽  
Dna Gyrase ◽  
Species Level ◽  
Primary Target ◽  
Pcr Assay ◽  
Nucleotide Sequence Data ◽  
Rapid Pcr ◽  
Fluoroquinolone Antibiotics ◽  
Ciprofloxacin Resistance

Fluoroquinolones are one class of antimicrobial agents commonly used to treat severe Campylobacter jejuni infection.C. jejuni strains resistant to high levels of the fluoroquinolone ciprofloxacin (MIC ≥16 μg/ml) have been predominantly characterized with a C→T transition in codon 86 ofgyrA. The gyrA gene encodes one subunit of DNA gyrase, which is a primary target for fluoroquinolone antibiotics. This study establishes a rapid PCR-based TaqMan method for identifying ciprofloxacin-resistant C. jejuni strains that carry the C→T transition in codon 86 of gyrA. The assay uses real-time detection, eliminating the need for gel electrophoresis. Optimization of the assay parameters using purified Campylobacter DNA resulted in the ability to detect femtogram levels of DNA. The method should be useful for monitoring the development of ciprofloxacin resistance in C. jejuni. Compiled nucleotide sequence data on the quinolone resistance-determining region of gyrA inCampylobacter indicate that sequence comparison of this region is a useful method for tentative identification ofCampylobacter isolates at the species level.

Descriptions of two new species of Philodina (Rotifera, Bdelloidea), with notes on seven rare bdelloids from Korea

Zootaxa ◽  
2020 ◽  
Vol 4772 (2) ◽  
pp. 253-276
Author(s):  
MIN OK SONG ◽  
CHANG-HO LEE
Keyword(s):  
New Species ◽  
Species Level ◽  
Taxonomic Study ◽  
Mitochondrial Cytochrome ◽  
Bdelloid Rotifers ◽  
Subspecies Level ◽  
Two New Species ◽  
Terrestrial Habitats ◽  
I Gene ◽  
Rotifera Bdelloidea

A taxonomic study on bdelloid rotifers collected from various terrestrial habitats at five different locations in Korea resulted in eight new Korean records and two new species-level taxa, Philodina clypeata  n. sp. and P. verrucosa  n. sp. Among the eight new Korean records, two species- and three subspecies-level taxa are new to Asia as well. These new Korean records also include seven rare species/subspecies-level taxa with poorly known distributions. Habrotrocha gracilis quadridens Schulte and Macrotrachela zickendrahti seda Donner were rediscovered in Korea 64 and 53 years, respectively, after the original descriptions. Habrotrocha ligula aligula Burger, Macrotrachela insulana Donner, M. petulans Milne, M. pinnigera (Murray), and Philodina parvicalcar De Koning have been reported from two to three countries only including their type localities before the present study. In addition, a partial sequence of mitochondrial cytochrome c oxidase subunit I gene (mtCOX1) for P. verrucosa  n. sp. as well as a taxonomic key for the Philodina species recorded from Korea to date are also provided here. 

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