c-mos variation in songbirds: molecular evolution, phylogenetic implications, and comparisons with mitochondrial differentiation

Nucleotide sequences from the c-mos proto-oncogene have previously been used to reconstruct the phylogenetic relationships between distantly related vertebrate taxa. To explore c-mos variation at shallower levels of avian divergence, we compared c-mos sequences from representative passerine taxa that span a range of evolutionary differentiation, from basal passerine lineages to closely allied genera. Phylogenetic reconstructions based on these c-mos sequences recovered topologies congruent with previous DNA-DNA hybridization-based reconstructions, with many nodes receiving high support, as indicated by bootstrap and reliability values. One exception was the relationship of Acanthisitta to the remaining passerines, where the c-mos-based searches indicated a three-way polytomy involving the Acanthisitta lineage and the suboscine and oscine passerine clades. We also compared levels of c-mos and mitochondrial differentiation across eight oscine passerine taxa and found that c-mos nucleotide substitutions accumulate at a rate similar to that of transversion substitutions in mitochondrial protein-coding genes. These comparisons suggest that nuclear-encoded loci such as c-mos provide a temporal window of phylogenetic resolution that overlaps the temporal range where mitochondrial protein-coding sequences have their greatest utility and that c-mos substitutions and mtDNA transversions can serve as complementary, informative, and independent phylogenetic markers for the study of avian relationships.     

Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing

There has been a growing interest in using next-generation sequencing (NGS) to profile extracellular small RNAs from the blood and cerebrospinal fluid (CSF) of patients with neurological diseases, CNS tumors, or traumatic brain injury for biomarker discovery. Small sample volumes and samples with low RNA abundance create challenges for downstream small RNA sequencing assays. Plasma, serum, and CSF contain low amounts of total RNA, of which small RNAs make up a fraction. The purpose of this study was to maximize RNA isolation from RNA-limited samples and apply these methods to profile the miRNA in human CSF by small RNA deep sequencing. We systematically tested RNA isolation efficiency using ten commercially available kits and compared their performance on human plasma samples. We used RiboGreen to quantify total RNA yield and custom TaqMan assays to determine the efficiency of small RNA isolation for each of the kits. We significantly increased the recovery of small RNA by repeating the aqueous extraction during the phenol-chloroform purification in the top performing kits. We subsequently used the methods with the highest small RNA yield to purify RNA from CSF and serum samples from the same individual. We then prepared small RNA sequencing libraries using Illumina’s TruSeq sample preparation kit and sequenced the samples on the HiSeq 2000. Not surprisingly, we found that the miRNA expression profile of CSF is substantially different from that of serum. To our knowledge, this is the first time that the small RNA fraction from CSF has been profiled using next-generation sequencing.     

THE INFLUENCE OF SAMPLING DESIGN ON SPECIES TREE INFERENCE: A NEW RELATIONSHIP FOR THE NEW WORLD CHICKADEES (AVES: POECILE)

In this study, we explore the long‐standing issue of how many loci are needed to infer accurate phylogenetic relationships, and whether loci with particular attributes (e.g., parsimony informativeness, variability, gene tree resolution) outperform others. To do so, we use an empirical data set consisting of the seven species of chickadees (Aves: Paridae), an analytically tractable, recently diverged group, and well‐studied ecologically but lacking a nuclear phylogeny. We estimate relationships using 40 nuclear loci and mitochondrial DNA using four coalescent‐based species tree inference methods (BEST, *BEAST, STEM, STELLS). Collectively, our analyses contrast with previous studies and support a sister relationship between the Black‐capped and Carolina Chickadee, two superficially similar species that hybridize along a long zone of contact. Gene flow is a potential source of conflict between nuclear and mitochondrial gene trees, yet we find a significant, albeit low, signal of gene flow. Our results suggest that relatively few loci with high information content may be sufficient for estimating an accurate species tree, but that substantially more loci are necessary for accurate parameter estimation. We provide an empirical reference point for researchers designing sampling protocols with the purpose of inferring phylogenies and population parameters of closely related taxa.     

Inherited nuclear cataracts in the Morgan horse

Congenital cataracts affecting the fetal and embryonal lens nucleus were found in 12 Morgan horses. Ten of the 12 affected animals were sired by the same stallion and the condition also affected his female half sibling. Although females were almost three times more likely to be affected than males (9 vs 3), the difference was not significant. The ratio of 11 normal to 10 affected offspring by the affected stallion is compatible with an autosomal dominant mode of inheritance.     

Pigmentation Genes Show Evidence of Repeated Divergence and Multiple Bouts of Introgression in Setophaga Warblers

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Phylogeography and conservation of the endemic Hispaniolan Palm-Tanagers (Aves: <Emphasis Type="Italic">Phaenicophilus</Emphasis>)

The Gray-crowned Palm-Tanager (Phaenicophilus poliocephalus), sometimes considered conspecific with its more widespread congener P. palmarum, is restricted to Haiti’s Tiburon Peninsula, a biodiversity hotspot threatened by extensive habitat loss. We used a multilocus phylogeographic approach to identify evolutionarily distinct populations of Phaenicophilus. Mitochondrial haplotypes formed two reciprocally monophyletic groups separated by 5% uncorrected divergence. Genealogical patterns of differentiation at nuclear intron alleles were congruent with those of mtDNA, and the two species also differed in body size and shape. An ancient sea channel between the Tiburon Peninsula and mainland Haiti was likely a dispersal barrier that led to allopatric divergence, a hypothesis supported by our estimates of divergence times. Our results support the recognition of two Palm-Tanager species, confirming P. poliocephalus as Haiti’s only endemic bird species and underscoring the need to protect the Tiburon Peninsula’s single primary forest reserve.     

Extra‐pair paternity in a population of Chilean Swallows breeding at 54 degrees south

Geographic patterns of variation in life‐history traits have puzzled researchers for decades. However, the widely accepted idea that mating systems exhibit a tropical–temperate latitudinal trend, with extra‐pair mating systems being the norm among temperate species and genetic monogamy the norm among tropical species, is supported by sparse data, particularly for birds breeding in the tropics and even more so for birds that breed in the southern hemisphere temperate zone. Our objective was to examine the genetic mating system of Chilean Swallows (Tachycineta meyeni) breeding at 54°S in Tierra del Fuego, Argentina. From 2006 to 2009, we examined the paternity of young in 52 broods. Contrary to predictions based on their congeners that breed at equivalent latitudes in the northern hemisphere, Chilean Swallows in our study had low rates of extra‐pair paternity (EPP), with 13.5% of nests (N = 52) having at least one extra‐pair young and 6.8% of all nestlings (N = 161) fathered by extra‐pair males. These rates are also lower than those reported for species of Tachycineta swallows that breed at tropical latitudes. We found no support for a tropical–south temperate latitudinal cline in EPP rates. The highly unpredictable weather of the island of Tierra del Fuego might be influencing parental investment at this site; small clutch sizes and low EPP rates are expected if biparental attention is crucial for chick survival and reproductive success for these aerial insectivores. We argue that the sparse sampling of mating systems in birds worldwide may have contributed to a misapprehension of a global pattern. More studies of tropical and south‐temperate systems are needed to build on theories based on a wider set of taxa.     

Comparative metabolic diversity in two solar salterns

The purpose of this study was to compare the metabolic diversity of the whole microbial community in an oligotrophic saltern (Eilat, Israel) and in a saltern with a more enriched source water (Newark, California). Between 1993 and 1998 water samples were taken from selected locations within the solar salterns of the Cargill Solar Salt Plant, Newark, California, and the Israel Salt Co. in Eilat, Israel. To examine the whole community metabolic diversity, we used the 96-well BIOLOG GN^{{ TM}} plates which contain 95 different carbon sources and a control well. Plates from samples containing greater than 15% salt were excluded from the final analyses because of a lack of reproducibility when multiple plates were inoculated with the same sample. The data were analyzed by simple matching coefficient and principal component analysis. Both methods gave similar results. Two major clusters were formed. These could be subdivided into 10 sub-clusters with only three samples from the Newark saltern in December 1997 joining at the 95% similarity level. Most of the inlet and lower salinity samples from the Cargill samples comprised one large subcluster. Several carbon sources were used by 85% of the microbial community from the California samples, while 85% of the Eilat samples had no commonly used carbon sources. These results suggest that ponds in different geographic locations may have communities with different microbial populations despite the similarities in salt content and processing for salt production.     

The Assembly of an Island Fauna by Natural Invasion: Sources and Temporal Patterns in the Avian Colonization of Barbados

By virtue of their isolation and depauperate faunas, oceanic islands offer unique opportunities to characterize the historical development of ecological communities derived from both natural and anthropogenic invasions. Barbados, an outlying island in the Lesser Antilles, was formed approximately 700,000 YBP by tectonic uplift and was then colonized by birds via natural invasion from the much older volcanic islands in the main Lesser Antillean arc. We investigated the timing and sources of the avian invasion of Barbados by determining levels of mitochondrial DNA (mtDNA) divergence between populations of eight bird species from Barbados and those on the nearby putative source islands of St. Lucia and St. Vincent. Although all Barbados populations appeared to be young relative to the geological age of the island, we found differences among species in their inferred times of colonization and we identified at least two sources of immigrants to Barbados. In contrast to these historical differences across species and populations, our characterization of the mitochondrial genotypes of 231 individual birds suggests that each island population represents the descendants of a single founding maternal lineage. Considered in concert, the results of this molecular survey indicate that the Barbados bird community is composed of species with different invasion histories, which in turn suggests that the island's community composition has changed repeatedly over its 700,000 year history.