scholarly journals Nuclear and mitochondrial DNA sequences from two Denisovan individuals

2015 ◽  
Vol 112 (51) ◽  
pp. 15696-15700 ◽  
Author(s):  
Susanna Sawyer ◽  
Gabriel Renaud ◽  
Bence Viola ◽  
Jean-Jacques Hublin ◽  
Marie-Theres Gansauge ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Nuclear Genome ◽  
Extended Period ◽  
Sister Group ◽  
Morphological Description ◽  
Dna Sequence Data ◽  
Mtdna Sequence

Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.

scholarly journals Characterization of an unusually conserved AluI highly reiterated DNA sequence family from the honeybee, Apis mellifera.

Genetics ◽  
1993 ◽  
Vol 134 (4) ◽  
pp. 1195-1204
Author(s):  
S Tarès ◽  
J M Cornuet ◽  
P Abad
Keyword(s):  
Apis Mellifera ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Repeated Sequence ◽  
Consensus Sequences ◽  
Dna Sequence Data ◽  
Repeat Class ◽  
Honeybee Subspecies

Abstract An AluI family of highly reiterated nontranscribed sequences has been found in the genome of the honeybee Apis mellifera. This repeated sequence is shown to be present at approximately 23,000 copies per haploid genome constituting about 2% of the total genomic DNA. The nucleotide sequence of 10 monomers was determined. The consensus sequences is 176 nucleotides long and has an A + T content of 58%. There are clusters of both direct and inverted repeats. Internal subrepeating units ranging from 11 to 17 nucleotides are observed, suggesting that it could have evolved from a shorter sequence. DNA sequence data reveal that this repeat class is unusually homogeneous compared to the other class of invertebrate highly reiterated DNA sequences. The average pairwise sequence divergence between the repeats is 2.5%. In spite of this unusual homogeneity, divergence has been found in the repeated sequence hybridization ladder between four different honeybee subspecies. Therefore, the AluI highly reiterated sequences provide a new probe for fingerprinting in A. m. mellifera.

Phylogeny, taxonomy, and zoogeography of the genus Gekko Laurenti, 1768 with the revalidation of G. reevesii Gray, 1831 (Sauria: Gekkonidae)

Zootaxa ◽  
2011 ◽  
Vol 2989 (1) ◽  
pp. 1 ◽  
Author(s):  
HERBERT RÖSLER ◽  
AARON M. BAUER ◽  
MATTHEW P. HEINICKE ◽  
ELI GREENBAUM ◽  
TODD JACKMAN ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Identification Key ◽  
Dna Sequence Data ◽  
Preliminary Identification ◽  
Specific Rank ◽  
Species Groups

A review of the taxonomy, phylogeny, and zoogeography of all currently recognized Gekko species is provided based on morphology (including size, scalation, color, and pattern) and mitochondrial and nuclear DNA sequence data. We distinguish six morphological (phenotypic) species groups within the gekkonid genus Gekko: the G. gecko, G. japonicus, G. monarchus, G. petricolus, G. porosus, and G. vittatus groups, all of which receive support from molecular phylogenetics. The taxon G. reevesii, formerly evaluated as a synonym of G. gekko, is revalidated herein at specific rank. Furthermore, a preliminary identification key of all currently recognized Gekko taxa is provided.

Validation of three sympatric Thoracophelia species (Annelida: Opheliidae) from Dillon Beach, California using mitochondrial and nuclear DNA sequence data

Zootaxa ◽  
2013 ◽  
Vol 3608 (1) ◽  
pp. 67-74 ◽  
Author(s):  
Chris J. LAW ◽  
KELLY M. DORGAN ◽  
GREG W. ROUSE
Keyword(s):  
Dna Sequence ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Hemoglobin Concentration ◽  
Sympatric Species ◽  
Sandy Beaches ◽  
Additional Species ◽  
Dna Sequence Data ◽  
C Subunit ◽  
Coi Sequences

Thoracophelia (Annelida, Opheliidae) are burrowing deposit feeders generally found in the mid- to upper intertidal areas of sandy beaches. Thoracophelia mucronata (Treadwell, 1914) is found along the west coast of North America, including at Dillon Beach, CA. Two additional species, Thoracophelia dillonensis (Hartman, 1938) and T. williamsi (Hartman, 1938) were also described from this beach. These three sympatric species have been primarily distinguished by branchial morphology, and efforts to determine the validity of the species have been based on morphological, reproductive and ecological studies. Here we demonstrate using mitochondrial and nuclear DNA sequence data that these three species are valid. Mitochondrial Cytochrome c subunit 1 (COI) sequences show uncorrected interspecific distances of ~9–13%. We found no inter—specific differences in body color or in hemoglobin concentration, but found that reproductive males were pinkish-red in color and had lower hemoglobin concentrations than purplish—red reproductive females.

The genus Iare Barbalho and Penteado-Dias (Hymenoptera: Braconidae: Doryctinae) in Mexico, with the description of two new species

Zootaxa ◽  
2010 ◽  
Vol 2685 (1) ◽  
pp. 30 ◽  
Author(s):  
JUAN JOSÉ MARTÍNEZ ◽  
FADIA SARA CECCARELLI ◽  
ALEJANDRO ZALDÍVAR-RIVERÓN
Keyword(s):  
New Species ◽  
Bayesian Analysis ◽  
Dna Sequence ◽  
Sequence Data ◽  
Tropical Dry Forest ◽  
Sister Group ◽  
Dry Forest ◽  
Dna Sequence Data ◽  
Single Clade ◽  
Two New Species

Two new species of the doryctine genus Iare, I. mexicanus sp. nov. and I. cheguevarai sp. nov., are genetically and morphologically described from a tropical dry forest in Jalisco, Mexico. Iare belokobylskiji Marsh is also reported for the latter region. These species represent the northernmost distribution records for the genus. A simultaneous Bayesian analysis with COI and 28S DNA sequence data recovered the three examined species of Iare within a single clade, though with low support. This genus appears nested within a large doryctine Neotropical clade as sister group of a cluster containing species of Callihormius Ashmead, Leluthia Cameron, Histeromeroides Marsh and Panama Marsh.

Association of larvae and adults of Mexican species of Macrelmis (Coleoptera: Elmidae): a preliminary analysis using DNA sequences

Zootaxa ◽  
2012 ◽  
Vol 3361 (1) ◽  
pp. 56-62 ◽  
Author(s):  
JOSEFINA CURIEL ◽  
JUAN J. MORRONE
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Preliminary Analysis ◽  
Sequence Data ◽  
Strong Association ◽  
Life Stages ◽  
Adult Morphology ◽  
Dna Sequence Data ◽  
Mexican Species ◽  
Major Impediment

Insect life stages are known imperfectly in many cases, and classifications are usually based on adult morphology. This isunfortunate as information on other life stages may be useful for biomonitoring. The major impediment to using elmid(Coleoptera) larvae for freshwater biomonitoring is the lack of larval descriptions and illustrations. Reliable molecular proto-cols may be used to associate larvae and adults. After adults of seven species of Mexican Macrelmis were identified morpho-logically, seven larval specimens were associated to them based on two gene fragments: Cox1 and Cob. The phylogeneticanalysis allowed identifying the larval specimens as Macrelmis leonilae, M. scutellaris, M. species 7, M. species 10, and M.species 11. Two species based on adults associated uncertainly with one larva, and one larva did not match with any adult. Adult/larval association in elmids using DNA sequence data seems to be promising in terms of speed and reliability.

The evolution of Dianthus polylepis complex (Caryophyllaceae) inferred from morphological and nuclear DNA sequence data: one or two species?

2013 ◽  
Vol 299 (8) ◽  
pp. 1419-1431 ◽  
Author(s):  
Mohammad Farsi ◽  
Maryam Behroozian ◽  
Jamil Vaezi ◽  
Mohammad Reza Joharchi ◽  
Farshid Memariani
Keyword(s):  
Dna Sequence ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Dna Sequence Data

scholarly journals Toward a Natural Classification of Botryosphaeriaceae: A Study of the Type Specimens of Botryosphaeria sensu lato

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Zhang ◽  
Yupei Zhou ◽  
Wei Sun ◽  
Lili Zhao ◽  
D. Pavlic-Zupanc ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Type Specimens ◽  
Natural Classification ◽  
Dna Sequence Data

The genus Botryosphaeria includes more than 200 epithets, but only the type species, Botryosphaeria dothidea and a dozen or more other species have been identified based on DNA sequence data. The taxonomic status of the other species remains unconfirmed because they lack either morphological information or DNA sequence data. In this study, types or authentic specimens of 16 “Botryosphaeria” species are reassessed to clarify their identity and phylogenetic position. nuDNA sequences of four regions, ITS, LSU, tef1-α and tub2, are analyzed and considered in combination with morphological characteristics. Based on the multigene phylogeny and morphological characters, Botryosphaeria cruenta and Botryosphaeria hamamelidis are transferred to Neofusicoccum. The generic status of Botryosphaeria aterrima and Botryosphaeria mirabile is confirmed in Botryosphaeria. Botryosphaeria berengeriana var. weigeliae and B. berengeriana var. acerina are treated synonyms of B. dothidea. Botryosphaeria mucosa is transferred to Neodeightonia as Neodeightonia mucosa, and Botryosphaeria ferruginea to Nothophoma as Nothophoma ferruginea. Botryosphaeria foliicola is reduced to synonymy with Phyllachorella micheliae. Botryosphaeria abuensis, Botryosphaeria aesculi, Botryosphaeria dasylirii, and Botryosphaeria wisteriae are tentatively kept in Botryosphaeria sensu stricto until further phylogenetic analysis is carried out on verified specimens. The ordinal status of Botryosphaeria apocyni, Botryosphaeria gaubae, and Botryosphaeria smilacinina cannot be determined, and tentatively accommodate these species in Dothideomycetes incertae sedis. The study demonstrates the significance of a polyphasic approach in characterizing type specimens, including the importance of using of DNA sequence data.

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