Nuclear DNA Evolution and Phylogeny of the New World Nine-Primaried Oscines

The Auk ◽  
1988 ◽  
Vol 105 (3) ◽  
pp. 504-515 ◽  
Author(s):  
Anthony H. Bledsoe
Keyword(s):  
Dna Sequences ◽  
Goodness Of Fit ◽  
New World ◽  
Nuclear Dna ◽  
Thermal Dissociation ◽  
Branch Length ◽  
Sister Group ◽  
Single Copy ◽  
The North ◽  
Dissociation Curves

Abstract Estimates of phylogeny were derived from measures of dissimilarity of single-copy nuclear-DNA sequences for 13 species that represent the currently recognized major groups of New World nine-primaried oscines and an outgroup (Passer). The dissimilarity coefficients (delta mode and delta T50H) calculated from thermal dissociation curves of reassociated DNA sequences exhibited the properties of a metric. No statistically significant increase in goodness-of-fit of the raw data to a phylogeny estimated from a least-squares analysis of the 13 × 13 matrix of distances was achieved when the lengths of sister branches were allowed to vary. "Jackknife" and negative branch-length analyses identified unstable stems that resulted from non-additivity caused in part by measurement error. Such stems were collapsed to produce a more robust topology, which served as the basis for estimating the positions of taxa not included in the 13 × 13 matrix. The clade that subsumed several "typical" tanagers (e.g. Tachyphonus rufus) also included Sicalis luteola and Diuca diuca (usually allied with the North American emberizine sparrows); Cyanerpes cyaneus, two species of Diglossa, and Coereba flaveola (often split among several major groups); and Tersina viridis, Catamblyrhynchus diadema, and Nephelornis oneilli (whose affinities are often considered uncertain). This "tanager" clade and its sister group, the cardinals (represented by Cardinalis cardinalis), together formed one fork of a trichotomy. Several emberizine sparrows (e.g. Pooecetes gramineus) formed the second fork, and wood-warblers (e.g. Dendroica striata) and New World orioles (e.g. Psarocolius angustifrons) formed the third. The chaffinches (represented by Fringilla coelebs) and several cardueline finches (e.g. Carduelis pinus) together formed the sister group of the other New World nine-primaried oscines included in the study. This phylogeny implies that convergence in feeding specializations among lineages is more extensive than traditional arrangements of the assemblage would suggest.

Phylogeny and biogeography of Apiaceae tribe Oenantheae inferred from nuclear rDNA ITS and cpDNA psbI–5′trnK(UUU) sequences, with emphasis on the North American Endemics clade

Botany ◽  
2008 ◽  
Vol 86 (9) ◽  
pp. 1039-1064 ◽  
Author(s):  
Stephen R. Downie ◽  
Deborah S. Katz-Downie ◽  
Feng-Jie Sun ◽  
Chang-Shook Lee
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Maximum Parsimony ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Intergenic Spacers ◽  
Rdna Its ◽  
The North

Intergeneric phylogenetic relationships within Apiaceae tribe Oenantheae were investigated using sequence data from the chloroplast DNA psbI–5′trnK(UUU) and nuclear ribosomal DNA internal transcribed spacer regions. One hundred and thirty-one accessions were examined, representing all 17 genera of the tribe and approximately one-half of its species. The cpDNA region includes four intergenic spacers and the rps16 intron and these noncoding loci were analyzed separately to assess their relative utility for resolving relationships. Separate maximum parsimony analyses of the entire psbI–5′trnK(UUU) and ITS regions, each with and without scored indels, yielded concordant trees. Phylogenies derived from maximum parsimony, Bayesian, or maximum likelihood analyses of combined chloroplast and nuclear DNA sequences for 82 accessions were highly resolved, well supported, and consistent. Among the five noncoding loci examined, the trnQ(UUG)–5′rps16 and 3′rps16–5′trnK(UUU) intergenic spacers are the most variable, with the latter contributing the greatest total number of parsimony informative characters relative to its size. The North American genera Atrema , Cynosciadium , Daucosma , Limnosciadium , Neogoezia , Oxypolis , Ptilimnium , and Trepocarpus ally with the western hemispheric and Australasian genus Lilaeopsis in a strongly supported North American Endemics clade that is a sister group to a clade composed primarily of Old World taxa ( Berula sensu lato, Cryptotaenia , Helosciadium , and Sium ). Oxypolis and Ptilimnium are not monophyletic, with the rachis-leaved members of each comprising a clade separate from their compound-leaved congeners. Dispersal-vicariance analysis suggests that the ancestors of the North American Endemics clade probably originated in Canada and the USA or in a broader ancestral area including Mexico and South America.

scholarly journals Discovery of a new family of amphibians from northeast India with ancient links to Africa

2012 ◽  
Vol 279 (1737) ◽  
pp. 2396-2401 ◽  
Author(s):  
Rachunliu G. Kamei ◽  
Diego San Mauro ◽  
David J. Gower ◽  
Ines Van Bocxlaer ◽  
Emma Sherratt ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Northeast India ◽  
Sister Group Relationship ◽  
New Family ◽  
Ancient Lineage ◽  
Molecular Phylogenetic ◽  
Threatened Habitats

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

Phylogeny, diversity, and species delimitation of the North American Round-Nosed Minnows (Teleostei: Dionda), as inferred from mitochondrial and nuclear DNA sequences

2012 ◽  
Vol 62 (1) ◽  
pp. 427-446 ◽  
Author(s):  
Susana Schönhuth ◽  
David M. Hillis ◽  
David A. Neely ◽  
Lourdes Lozano-Vilano ◽  
Anabel Perdices ◽  
...  
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Species Delimitation ◽  
Nuclear Dna ◽  
The North

Phylogeny and higher classification of the scale insects (Hemiptera: Sternorrhyncha: Coccoidea)*

Zootaxa ◽  
2007 ◽  
Vol 1668 (1) ◽  
pp. 413-425 ◽  
Author(s):  
P. J. GULLAN ◽  
L. G. COOK
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nuclear Dna ◽  
Sister Group ◽  
Scale Insect ◽  
Scale Insects ◽  
Morphological Data ◽  
Adult Males ◽  
Plant Feeding ◽  
Phylogenetic Studies

The superfamily Coccoidea contains nearly 8000 species of plant-feeding hemipterans comprising up to 32 families divided traditionally into two informal groups, the archaeococcoids and the neococcoids. The neococcoids form a monophyletic group supported by both morphological and genetic data. In contrast, the monophyly of the archaeococcoids is uncertain and the higher level ranks within it have been controversial, particularly since the late Professor Jan Koteja introduced his multi-family classification for scale insects in 1974. Recent phylogenetic studies using molecular and morphological data support the recognition of up to 15 extant families of archaeococcoids, including 11 families for the former Margarodidae sensu lato, vindicating Koteja’s views. Archaeococcoids are represented better in the fossil record than neococcoids, and have an adequate record through the Tertiary and Cretaceous but almost no putative coccoid fossils are known from earlier. In contrast, the sister group of the scale insects (Aphidoidea) has a more informative Jurassic and Triassic record. Relationships among most scale insect families are unresolved in phylogenetic trees based on nuclear DNA sequences, and most nodes in trees based on morphological data, including those from adult males, are poorly supported. Within the neococcoids, the Eriococcidae is not monophyletic and the monophyly of the Coccidae and Diaspididae may be compromised by the current family-level recognition of a few species-poor autapomorphic groups.

Phylogeny in the genus Hordeum based on nucleotide sequences closely linked to the vrs1 locus (row number of spikelets)

Genome ◽  
1999 ◽  
Vol 42 (5) ◽  
pp. 973-981 ◽  
Author(s):  
Takao Komatsuda ◽  
Ken-ichi Tanno ◽  
Björn Salomon ◽  
Tomas Bryngelsson ◽  
Roland von Bothmer
Keyword(s):  
Nuclear Dna ◽  
Sister Group ◽  
Single Copy ◽  
Nucleotide Sequences ◽  
Restriction Maps ◽  
Deletion Event ◽  
Single Base ◽  
Genome Group ◽  
The Difference ◽  
Hordeum Species

The phylogenetic relationship between four basic genomes designated H, I, Xa, and Xu in the genus Hordeum was studied using a nuclear DNA sequence. The sequence, cMWG699, is single copy in the H. vulgare genome, and tightly linked to the vrs1 locus which controls two- and six-rowed spikes. DNA fragments homologous to cMWG699 were amplified from diploid Hordeum species and the nucleotide sequences were determined. A phylogeny based on both base substitutions and an insertion-deletion event showed that the H- and Xa-genome groups are positioned in one monophyletic group indicating that the Xa-genome taxa should be included in the H-genome group. The large H-genome group is highly homogeneous. The I and Xu genomes are distinctly separated from H and Xa, and form sister groups. Another phylogeny pattern based on data excluding the insertion-deletion gave a result that the Xa genome forms a sister group to the H-genome group. The difference between the H and Xa genomes was affected only by a single base insertion-deletion event, thus the H and Xa genomes are likely to be closely related. The I and Xu genomes were again distinctly separated from the H and Xa genomes.Key words: genome DNA, molecular markers, restriction maps, barley, Psathyrostachys.

Phylogenetic relationships in the tribes Schizopetaleae and Thelypodieae (Brassicaceae) based on nuclear ribosomal ITS region and plastid ndhF DNA sequences

Botany ◽  
2009 ◽  
Vol 87 (10) ◽  
pp. 961-985 ◽  
Author(s):  
Suzanne I. Warwick ◽  
Connie A. Sauder ◽  
Michael S. Mayer ◽  
Ihsan A. Al-Shehbaz
Keyword(s):  
Dna Sequences ◽  
New World ◽  
Sequence Data ◽  
Its Region ◽  
South American ◽  
Plastid Gene ◽  
The North ◽  
Cytological Data ◽  
Closed Tube ◽  
Data Elements

Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region and plastid gene ndhF of 95 species, represented by 147 accessions, were used to determine the tribal limits, monophyly status, and phylogenetic intra-tribal relationships of genera within the New World tribe Schizopetaleae (formerly Thelypodieae; Brassicaceae). Maximum parsimony, Bayesian, and maximum-likelihood analyses all support the separate recognition of three distinct and generally well-supported clades. The largest corresponds to the North–South American Thelypodieae (27 genera: Catadysia , Caulanthus , Chaunanthus , Chilocardamum , Chlorocrambe , Coelophragmus , Dictyophragmus , Dryopetalon , Englerocharis , Hesperidanthus , Mostacillastrum , Neuontobotrys , Polypsecadium , Pringlea , Pterygiosperma , Romanschulzia , Sibara , Sibaropsis , Stanleya , Streptanthella , Streptanthus , Thelypodiopsis , Thelypodium , Thysanocarpus , Warea , Weberbauera , and Werdermannia ). The remaining six South American Schizopetaleae genera were divided into two clades: SCHIZ I of four genera ( Aschersoniodoxa , Brayopsis , Eudema , and Onuris ) and SCHIZ II Schizopetaleae s. str.: Mathewsia , and Schizopetalon ). Resolution within the Thelypodieae clade was limited in both the ITS- and ndhF-based phylogenies. Based on ITS sequence data, elements of the Old World tribe Brassiceae were sister to the Thelypodieae, whereas the ndhF data strongly supported the Sisymbrieae as sister to the Thelypodieae, and the Brassiceae as sister to both tribes. Sister groups to the Schizopetaleae clades I and II were not clearly resolved. Morphological and cytological data support the separation of these three clades. In SCHIZ II, the sepals are always erect to form a closed tube, and the trichomes are mostly dendritic, although other types also occur. In both the Thelypodieae and SCHIZ I clades, the sepals are variously oriented but never form a closed tube, whereas the trichomes are either absent, or simple, forked, or rarely dendritic. The latter clade differs from both SCHIZ II and Thelypodieae by lacking trichomes or rarely having forked ones and by having exclusively basal, entire leaves. Thelypodieae circumscription should be restricted in future to the Thelypodieae clade, Schizopetaleae circumscription to the SCHIZ II clade, while a new tribe is needed for the SCHIZ I clade.

Single-copy nuclear DNA sequences obtained from noninvasively collected primate feces

2002 ◽  
Vol 56 (3) ◽  
pp. 185-190 ◽  
Author(s):  
Alison K. Surridge ◽  
Andrew C. Smith ◽  
Hannah M. Buchanan-Smith ◽  
Nicholas I. Mundy
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Single Copy

scholarly journals Molecular systematics of western North American cyprinids (Cypriniformes: Cyprinidae)

Zootaxa ◽  
2012 ◽  
Vol 3586 (1) ◽  
pp. 281 ◽  
Author(s):  
SUSANA SCHÖNHUTH ◽  
DENNIS K. SHIOZAWA ◽  
THOMAS E. DOWLING ◽  
RICHARD L. MAYDEN
Keyword(s):  
Dna Sequences ◽  
North American ◽  
Nuclear Dna ◽  
Modern Science ◽  
Sister Group ◽  
Molecular Data ◽  
Generic Level ◽  
Natural Classification ◽  
Extant Species ◽  
Group Relationships

The phylogenetic or evolutionary relationships of species of Cypriniformes, as well as their classification, is in a era offlux. For the first time ever, the Order, and constituent Families are being examined for relationships within aphylogenetic context. Relevant findings as to sister-group relationships are largely being inferred from analyses of bothmitochondrial and nuclear DNA sequences. Like the vast majority of Cypriniformes, due to an overall lack of anyphylogenetic investigation of these fishes since Hennig’s transformation of the discipline, changes in hypotheses ofrelationships and a natural classification of the species should not be of surprise to anyone. Basically, for most taxa noproperly supported phylogenetic hypothesis has ever been done; and this includes relationships with reasonable taxonand character sampling of even families and subfamilies. As such, like others, many western North American cyprinidgenera have had a controversial taxonomic and systematic history.Our effort to better understand the evolutionary history of this artificial geographic grouping of species (Western)surveyed taxa and characters broadly. We analyzed 127 taxa (71 species) from 36 genera, including representative taxafrom all 22 western genera hypothesized to form the Western Clade sensu Coburn and Cavender (1992). Our evaluationalso included additional sampling from a heterogeneous array of species from the western genera Algansea, Gila,Lepidomeda, Ptychocheilus and Siphateles. Resulting phylogenetic inferences, based on one mitochondrial and threenuclear genes (mtDNA: cytb; nDNA: Rag1, Rhod, S7), consistently resolved a well-supported Western Clade, but oneinclusive of Chrosomus erythrogaster. This taxon, always formed the sister group to the extant species of Gila plus 10other western genera. Our Western Clade is qualitatively different from that of prior studies and does not include thegenera Agosia, Algansea, Iotichthys, Lepidomeda, Meda, Mylocheilus, Plagopterus, Pogonichthys, Rhinichthys, Tiarogaor Yuriria. All of these taxa were, however, included in Coburn and Cavender´s (1992) Western Clade. Our broader-scalesurvey and increased character sampling were always resolved these latter taxa within one of two different major clades:the OPM Clade (sensu Mayden 1989) and the Creek Chub—Plagopterin Clade (sensu Simons et al. 2003). Ourhypothesized Western Clade places Orthodon sister to a Western Chub-Pikeminnow Clade also inclusive of Acrocheilus,Eremichthys, Gila, Hesperoleucus, Lavinia, Moapa, Mylopharodon, Ptychocheilus, Relictus and Siphateles. The lattertaxa have traditionally been recognized at the generic level, simply on the basis of their morphological distinctivenessand not on the basis of a phylogenetic evaluation of relationships. Composition of our Western Chub-Pikeminnow Cladealso reveals genetic divergences between species of some genera (Gila, Ptychocheilus, Siphateles) comparable to geneticdivergences documented between genera within the Western Clade. Relationships for these 10 genera also highlighttaxonomic inconsistencies relative to recent phylogenetic analysis and, in some cases, are in need of focused attentionusing morphology or additional molecular data to test relationships that will eventually establish a stable classification.Some of these genera are clearly unnatural relative to other genera and their classification or ranking is an obligatory change in modern science of phylogenetics.

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