Ecological factors drive the divergence of morphological, colour and behavioural traits in cactus wrens (Aves, Troglodytidae).

The study of ecological mechanisms influencing organisms' phenotypic variation is a central subject of evolutionary biology. In this study, we characterized morphological, plumage colour and acoustic variation in cactus wrens Campylorhynchus brunneicapillus throughout its distribution. We assessed whether Gloger's, Allen's and Bergmann's ecogeographical rules, and the acoustic adaptation hypothesis relate to geographical trait variation. We analysed specimen coloration in belly and crown plumage, beak shape and structural song characteristics. We tested whether the subspecific classification or the peninsular/mainland groups mirrored the geographical variation in phenotypes and whether ecological factors were associated with patterns of trait variation. Our results suggest that colour, beak shape and acoustic traits varied across the range, in agreement with two lineages described by genetics. The simple versions of Gloger's and Allen's rules are related to variations in colour traits and morphology. Conversely, patterns of phenotypic variation did not support Bergmann's rule. The acoustic adaptation hypothesis supported song divergence for frequency-related traits. Phenotypic variation supports the hypothesis of two taxa: C. affinis in the Baja California peninsula and C. brunneicapillus in the mainland. The ecological factors are associated with phenotypic trait adaptations, suggesting that divergence between lineages could result from ecological divergence.

Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence.

Comparative phylogeography explores the historical congruence of co-distributed species to understand the factors that led to their current genetic and phenotypic structures. Even species that span the same biogeographic barrier can exhibit different phylogeographic structures owing to differences in effective population sizes, genetic marker bias, and dispersal abilities. The Baja California peninsula and adjacent desert regions include several biogeographic barriers, including the Vizcaíno Desert and Sierra de la Laguna (Cape District), that have left phylogeographic patterns in some but not all species. We used genome-wide SNP data to test the hypothesis that the diverse phylogeographic patterns inferred from prior studies were supported. We found that mitochondrial DNA, single nuclear gene, and genome-wide SNP data show that the cactus wren and LeConte's thrasher have a concordant historical division at or near the Vizcaíno Desert in north-central Baja California, the Gila woodpecker is at an intermediate stage of divergence, and the California gnatcatcher lacks phylogeographic structure. None of these four species are classified taxonomically in a way that captures their evolutionary history with the exception of the LeConte's thrasher. We also analyzed mtDNA data on samples of nine other species that span the Vizcaíno Desert, with four showing no apparent division, and six additional species from the Sierra de la Laguna, all but one of which are differentiated. Reasons for contrasting phylogeographic patterns among these species should be explored further with genomic data to test the extent of concordant phylogeographic patterns. The evolutionary division at the Vizcaíno desert is well known in other vertebrate species, and our study further corroborates the extent, profound effect, and importance of this biogeographic boundary. The areas north and south of the Vizcaíno Desert, which contains considerable diversity, should be recognized as historically significant areas for conservation.

Autosomal, sex-linked and mitochondrial loci resolve evolutionary relationships among wrens in the genus Campylorhynchus.

Although there is general consensus that sampling of multiple genetic loci is critical in accurate reconstruction of species trees, the exact numbers and the best types of molecular markers remain an open question. In particular, the phylogenetic utility of sex-linked loci is underexplored. Here, we sample all species and 70% of the named diversity of the New World wren genus Campylorhynchus using sequences from 23 loci, to evaluate the effects of linkage on efficiency in recovering a well-supported tree for the group. At a tree-wide level, we found that most loci supported fewer than half the possible clades and that sex-linked loci produced similar resolution to slower-coalescing autosomal markers, controlling for locus length. By contrast, we did find evidence that linkage affected the efficiency of recovery of individual relationships; as few as two sex-linked loci were necessary to resolve a selection of clades with long to medium subtending branches, whereas 4-6 autosomal loci were necessary to achieve comparable results. These results support an expanded role for sampling of the avian Z chromosome in phylogenetic studies, including target enrichment approaches. Our concatenated and species tree analyses represent significant improvements in our understanding of diversification in Campylorhynchus, and suggest a relatively complex scenario for its radiation across the Miocene/Pliocene boundary, with multiple invasions of South America.

Geographic variation in the PRNP gene and its promoter, and their relationship to chronic wasting disease in North American deer.

PRNP genotypes, number of octarepeats (PHGGGWGQ) and indels in the PRNP promoter can influence the progression of prion disease in mammals. We found no relationship between presence of promoter indels in white-tailed deer and mule deer from Nebraska and CWD presence. White-tailed deer with the 95 H allele and G20D mule deer were more likely to be CWD-free, but unlike other studies white-tailed deer with the 96S allele(s) were equally likely to be CWD-free. We provide the first information on PRNP genotypes and indels in the promoter for Key deer (all homozygous 96SS) and Coues deer (lacked 95 H and 96S alleles, but possessed a uniquely high frequency of 103 T). All deer surveyed were homozygous for three tandem octarepeats.

Species Limits and Phylogenomic Relationships of Darwin's Finches Remain Unresolved: Potential Consequences of a Volatile Ecological Setting.

Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin's finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin's finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies of prior data and analytic methods explained different proposed classifications, we were surprised to observe that three new phylogenetic hypotheses derived mostly from the same genomics data were topologically inconsistent. We found that the differences between some of these genomics trees were as great as one would expect between two random trees with the same number of taxa. Thus, the phylogeny of Darwin's finches remains unresolved, as it has for more than a century. A component of phylogenetic uncertainty comes from unclear species limits, under any species concept, in the ground finches (Geospiza) and tree finches (Camarhynchus). We suggest that past authors should have tested the species limits of Lack, rather than uncritically accepting them. In fact, the impressive amount of genomics data do not provide unambiguous hypotheses of the number of species of Geospiza or Camarhynchus, although they imply greater species diversity than Lack's taxonomy. We suggest that insufficient sampling of species populations across islands (35.6% for morphometrics and 20.4% for genomics) prevents accurate diagnoses of species limits. However, it is unknown whether samples from a greater number of islands might result in bridging differences between species, or reveal many new ones. We conclude that attempts to interpret patterns of variation among the finches under standard evolutionary paradigms have obscured some major messages, most specifically the ongoing reciprocal interactions between geographic isolation and lineage divergence, and dispersal and gene flow caused by the volatile ecological conditions in the islands. Although the finches provide textbook examples of natural selection, better understanding of species limits and a robust phylogenetic hypothesis are required to corroborate past hypotheses of speciation and adaptive radiation in the finches of the Galapagos.

RNA profile diversity across arthropoda: guidelines, methodological artifacts, and expected outcomes.

High-quality RNA is an important precursor for high-throughput RNA sequencing (RNAseq) and subsequent analyses. However, the primary metric used to assess RNA quality, the RNA Integrity Number (RIN), was developed based on model bacterial and vertebrate organisms. Though the phenomenon is not widely recognized, invertebrate 28S ribosomal RNA (rRNA) is highly prone to a form of denaturation known as gap deletion, in which the subunit collapses into two smaller fragments. In many nonmodel invertebrates, this collapse of the 28S subunit appears as a single band similar in size to the 18S rRNA subunit. This phenomenon is hypothesized to be commonplace among arthropods and is often misinterpreted as a "degraded" rRNA profile. The limited characterization of gap deletion in arthropods, a highly diverse group, as well as other nonmodel invertebrates, often biases RNA quality assessments. To test whether the collapse of 28S is a general pattern or a methodological artifact, we sampled more than half of the major lineages within Arthropoda. We found that the 28S collapse is present in ∼90% of the species sampled. Nevertheless, RNA profiles exhibit considerable diversity with a range of banding patterns. High-throughput RNAseq and subsequent assembly of high-quality transcriptomes from select arthropod species exhibiting collapsed 28S subunits further illustrates the limitations of current RIN proxies in accurately characterizing RNA quality in nonmodel organisms. Furthermore, we show that this form of 28S denaturation, which is often mistaken for true "degradation," can occur at relatively low temperatures.

Complex biogeographic scenarios revealed in the diversification of the largest woodpecker radiation in the New World.

Phylogenetic relationships and patterns of evolution within Melanerpes, one of the most diverse groups of New World woodpeckers (22-23 lineages), have been complicated due to complex plumages and morphological adaptations. In an attempt to resolve these issues, we obtained sequence data from four nuclear introns and two mitochondrial protein-coding genes for 22 of the 24 currently recognized species in the genus. We performed phylogenetic analyses involving Maximum Likelihood and Bayesian Inference, species-tree divergence dating, and biogeographic reconstructions. Tree topologies from the concatenated and species-tree analyses of the mtDNA and nDNA showed broadly similar patterns, with three relatively well-supported groups apparent: (a) the Sphyrapicus clade (four species); (b) the typical Melanerpes clade, which includes temperate and subtropical dry forest black-backed species; and (c) the mostly barred-backed species, here referred to as the "Centurus" clade. The phylogenetic position of Melanerpes superciliaris regarding the rest of Melanerpes is ambiguous as it is recovered as sister to the rest of Melanerpes or as sister to a group including Sphyrapicus+Melanerpes. Our species tree estimations recovered the same well-delimited highly-supported clades. Geographic range evolution (estimated in BioGeoBEARS) was best explained by a DIVALIKE+j model, which includes vicariance, founder effect speciation, and anagenetic dispersal (range expansion) as important processes involved in the diversification of the largest radiation of woodpeckers in the New World.

Fluctuating fire regimes and their historical effects on genetic variation in an endangered shrubland specialist.

The Pleistocene was characterized by worldwide shifts in community compositions. Some of these shifts were a result of changes in fire regimes, which influenced the distribution of species belonging to fire-dependent communities. We studied an endangered juniper-oak shrubland specialist, the black-capped vireo (Vireo atricapilla). This species was locally extirpated in parts of Texas and Oklahoma by the end of the 1980s as a result of habitat change and loss, predation, brood parasitism, and anthropogenic fire suppression. We sequenced multiple nuclear loci and used coalescence methods to obtain a deeper understanding of historical population trends than that typically available from microsatellites or mtDNA. We compared our estimated population history, a long-term history of the fire regime and ecological niche models representing the mid-Holocene, last glacial maximum, and last interglacial. Our Bayesian skyline plots showed a pattern of historical population fluctuation that was consistent with changing fire regimes. Genetic data suggest that the species is genetically unstructured, and that the current population should be orders of magnitude larger than it is at present. We suggest that fire suppression and habitat loss are primary factors contributing to the recent decline of the BCVI, although the role of climate change since the last glacial maximum is unclear at present.

Biogeographical patterns of the avifaunas of the Caribbean Basin Islands: a parsimony perspective.

We analyzed the avifaunas of the Caribbean islands and nearby continental areas and their relationships using Parsimony Analysis of Endemicity (PAE), in order to assess biogeographical patterns and their concordance with geological and phylogenetic evidence. Using distributional information of birds obtained from published literature, a presence/absence matrix for 695 genera and 2026 species of land and freshwater birds was constructed and analyzed. Three different analyses were performed: for species, for genera, and for species and genera combined. In the combined analysis, the Lesser Antilles appear paraphyletic at the base of the cladogram. Then, two major clades are identified: South America (Andes, Venezuelan lowlands, Dutch West Indies and Trinidad and Tobago) and North America, including the Greater Antilles in a clade that is the sister area to Yucatan and the Central American countries nested from north to south. PAE results support Caribbean vicariant models and cladistic biogeographical hypotheses on area relationships, and show relative congruence with available phylogenetic data. Bird biogeography on the Caribbean islands appears to have been caused by both vicariance and dispersal processes.