Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution.

BACKGROUND: Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Gallus gallus (Red Junglefowl, the progenitor of the chicken), we know little about the genomes of closely related species. Gallus gallus is highly sexually dichromatic and polygynous, but its sister genus, Bambusicola, is smaller, sexually monomorphic, and monogamous with biparental care. We sequenced the genome of Bambusicola thoracicus (Chinese Bamboo Partridge) using a single insert library to test hypotheses about genome evolution in galliforms. Selection acting at the phenotypic level could result in more evidence of positive selection in the Gallus genome than in Bambusicola. However, the historical range size of Bambusicola was likely smaller than Gallus, and demographic effects could lead to higher rates of nonsynonymous substitution in Bambusicola than in Gallus. RESULTS: We generated a genome assembly suitable for evolutionary analyses. We examined the impact of selection on coding regions by examining shifts in the average nonsynonymous to synonymous rate ratio (dN/dS) and the proportion of sites subject to episodic positive selection. We observed elevated dN/dS in Bambusicola relative to Gallus, which is consistent with our hypothesis that demographic effects may be important drivers of genome evolution in Bambusicola. We also demonstrated that alignment error can greatly inflate estimates of the number of genes that experienced episodic positive selection and heterogeneity in dN/dS. However, overall patterns of molecular evolution were robust to alignment uncertainty. Bambusicola thoracicus has higher estimates of heterozygosity than Gallus gallus, possibly due to migration events over the past 100,000 years. CONCLUSIONS: Our results emphasized the importance of demographic processes in generating the patterns of variation between Bambusicola and Gallus. We also demonstrated that genome assemblies generated using a single library can provide valuable insights into avian evolutionary history and found that it is important to account for alignment uncertainty in evolutionary inferences from draft genomes.

Two-dimensional echocardiographic valve measurements in healthy children: gender-specific differences.

The goal of this study was to create nomograms of echocardiographic two-dimensional valve dimensions based on a large group of children without heart disease. Children aged 0-18 years underwent standard echocardiographic evaluation. Referring diagnoses were chest pain, heart murmur, or syncope. Only patients with a structurally normal heart and normal systolic and diastolic function were included. All four valves were measured at their maximal dimensions. A total of 748 children (314 girls and 434 boys) met the inclusion criteria. Mean values and standard deviations were calculated, and z value nomograms based on body surface area were developed. Surprisingly, the boys had larger valve dimensions at all ages. These valve dimension differences were statistically significant for three of four valves even after adjustment for the differences in body sizes. The difference may be due to higher circulating blood volume in boys compared to that in girls. Because the differences are subtle, they reach statistical significance only when evaluated in a large group of subjects. Presented normal value data will be helpful in following cardiology patients and evaluating intervention strategy in patients with valve hypoplasia.

Molecular and morphological reassessment of relationships within the Vittadinia group of Astereae (Asteraceae).

Morphological and ITS (internal transcribed spacer) sequence data for 40 species of the Austral-Pacific genera Camptacra, Kippistia, Minuria, Peripleura, Tetramolopium, and Vittadinia as well as one semiherbaceous species of Olearia were subjected to cladistic analysis, separately and together. Minuria, Peripleura, and Tetramolopium are paraphyletic as currently defined. Tetramolopium vagans from Australia appears to represent an undescribed genus. Both Kippistia suadefolia and Peripleura diffusa show close affinity to Minuria species, and Minuria macrorhiza appears to contain two distinct but closely related species. Vittadinia and the remaining species of Tetramolopium and Peripleura form a strong affinity group. The distribution of indels and the combined analysis each provide evidence that the Hawaiian and Cook Island species of Tetramolopium are descended from New Guinea species. The combined analysis also suggests that the Cook Island species T. mitiaroense is sister to the Hawaiian clade. Olearia arguta groups strongly with Camptacra and shows no close affinity with either of the arborescent species of Olearia used to root these analyses. Marked homoplasy among morphological characters indicates why generic delimitation in the group has been problematic.

Evolution of the mitochondrial DNA control region and cytochrome b genes and the inference of phylogenetic relationships in the avian genus Lophura (Galliformes).

The entire mitochondrial DNA control region (mtDNA CR) and cytochrome b (cyt b) genes were sequenced in 10 of the 11 extant species of gallopheasants (Lophura). The cyt b from L. diardi and L. ignita showed unusual leucine-coding codons at the expected terminal 3' end of the gene. Presence of conserved functional motifs in the inferred amino acid sequences, conserved secondary structures of the flanking tRNA(Pro) and tRNA(Thr), and Southern hybridization concordantly suggest that these cyt b represent functional mitochondrial genes and not nuclear transpositions. Functional stop codons can be generated by RNA editing of the primary transcripts from these sequences. Despite strong site and domain substitution rate heterogeneity, CR and cyt b diverged at similar rates, on average, and expressed congruent phylogenetic signals. Phylogenetic analyses of the concatenated sequences split Lophura into five clades including (1) L. bulweri, (2) L. diardi-L. ignita, (3) L. erythrophthalma-L. inornata, (4) L. leucomelanos-L. nycthemera, and (5) L. swinhoii-L. edwardsi-L. hatinhensis. Basal relationships among these clades, which include species distributed in continental South East Asia and the Sundaland archipelago, were weakly resolved, suggesting the occurrence of rapid cladogenic events in the early evolutionary history of Lophura. A conventional calibration of mtDNA sequence divergence indicates a mid to late Pliocene evolution of the main clades in Lophura, which could have diversified in allopatry in continental South East Asia. Sundaland could have been colonized lately and independently by the different clades. Consequently, cyclic changes in late Pleistocene climate and landscape might not have increased rates of speciation in genus Lophura in Sundaland.

A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic.

Cytochrome b and D-loop nucleotide sequences were used to study patterns of molecular evolution and phylogenetic relationships between the pheasants and the partridges, which are thought to form two closely related monophyletic galliform lineages. Our analyses used 34 complete cytochrome b and 22 partial D-loop sequences from the hypervariable domain I of the D-loop, representing 20 pheasant species (15 genera) and 12 partridge species (5 genera). We performed parsimony, maximum likelihood, and distance analyses to resolve these phylogenetic relationships. In this data set, transversion analyses gave results similar to those of global analyses. All of our molecular phylogenetic analyses indicated that the pheasants and partridges arose through a rapid radiation, making it difficult to establish higher level relationships. However, we were able to establish six major lineages containing pheasant and partridge taxa, including one lineage containing both pheasants and partridges (Gallus, Bambusicola and Francolinus). This result, supported by maximum likelihood tests, indicated that the pheasants and partridges do not form independent monophyletic lineages.

Resolution of the phylogenetic position of the Congo peafowl, Afropavo congensis: a biogeographic and evolutionary enigma.

Afropavo congensis, the Congo peafowl, has long fascinated ornithologists because of its uncertain phylogenetic position and unusual geographic distribution. While some researchers have placed Afropavo as a sister taxon to the true peafowl, Pavo species, others have suggested relationships with the guineafowl or an Old World partridge, Francolinus. These divergent opinions are due, at least in part, to (i) the unique morphological characteristics, lack of elaborate ornamentation, and monogamous mating system in Afropavo which differentiates it from Pavo; and (ii) the restricted distribution of Afropavo in Zaire, which is far removed from the Asian distribution of all other pheasant species. We obtained complete cytochrome b and partial D-loop sequences of Afropavo and compared them to Pavo, guineafowl, Francolinus and other galliform taxa. Our results strongly support a close relationship between Afropavo and Pavo, and we were able to reject alternative phylogenetic hypotheses. Molecular clock estimates of the divergence time place the separation of Afropavo and Pavo in the late Miocene. We also discuss other relatives of Afropavo and Pavo and use this information to propose hypotheses regarding the evolution of ornamentation and sexual dimorphism within this group of pheasants.