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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. [ABSTRACT FROM AUTHOR]

The passerine superfamily Certhioidea lacks a complete phylogeny despite decades of recognition as a clade and extensive systematic work within all its constituent families. Here, we inferred a near-complete species-level phylogeny of Certhioidea from a molecular supermatrix, including the first comprehensive sampling of the wrens (Troglodytidae), and used this phylogeny to infer its biogeographic and diversification histories. We also inferred an expanded phylogeny including nearly 100 putative phylospecies previously documented in the literature, and we found that including this diversity had notable impacts on the inferred evolutionary history of Certhioidea. This phylospecies-level tree documented a few instances of species paraphyly, some previously described in the literature and some novel. We found that Certhioidea originated largely in Eurasia and dispersed into North America five times in the last 20 million years, including at the origin of the "New World certhioids," wrens and gnatcatchers, a clade herein named Orthourae. After this initial dispersal event, both wrens and gnatcatchers diversified extensively across the hemisphere, with both lineages repeatedly crossing between continents. However, we detected no notable impact of the formation of the Isthmus of Panama on the frequency of dispersal events between North and South America. The inclusion of phylospecies altered this biogeographic inference in some portions of the tree but overall was largely consistent. With species-level sampling, we found that diversification rates within Certhioidea were largely constant through time with a detectable deceleration toward the present. By contrast, phylospecies-level sampling recovered a different diversification history with a significant rate increase at the crown node of Orthourae after dispersing into the Americas and increased speciation rates particularly within the genera Polioptila and Henicorhina. This largely resolved phylogeny for Certhioidea has yielded important insights into the evolutionary history of this group and provides a framework for future comparative work on this fascinating clade. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We evaluated geographic variation and subspecific taxonomy in the Le Conte's thrasher Toxostoma lecontei by analyzing DNA sequences from 16 nuclear loci, one mitochondrial DNA locus, and four study skin characters, and compared these data sets with previously published data on plumage coloration and different mtDNA genes. Morphological support for the southernmost taxon, T. l. arenicola, is relatively weak: multivariate analyses of morphometrics or back coloration do not provide diagnostic support, although one color character differs statistically. However, combined DNA analyses indicate that T. l. arenicola is diagnosable and reciprocally monophyletic, diverging from T. l. lecontei at least 140 000 yr ago. Little to no past introgression across a very short geographic distance despite the long period of isolation is strong evidence of independently evolving taxa. We suggest that the lack of morphological divergence in traits related to niche use has prevented the two taxa from invading each other's range. Despite relatively weak morphological differences we suggest that these two deeply divergent lineages merit species status, and we suggest Vizcaíno thrasher for the common name corresponding to T. l. arenicola. The population size of T. l. arenicola is small and the taxon is in need of preservation attention. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

[Display omitted] • The plants and animals of the Baja Peninsula include diverse geographic patterns of evolutionary divergence. • The patterns likely stemmed from common events in earth history, such as a mid-peninsular seaway. • We compared phylogenetic analyses of multilocus sequence data to previous studies of mitochondrial and nuclear DNA. • All data sets agree that three species are concordantly differentiated at the Vizcaino Desert, and one species, the California gnatcatcher, shows no geographic differentiation. • The phylogenetic patterns of genetic divergence aid conservation by suggesting areas for reserves, and showing that some subspecies are distinct evolutionary or taxonomic units. 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. [ABSTRACT FROM AUTHOR]

The article explores the phylogeography of the Rufous-naped Wren or Campylorhynchus rufinucha in the dry forests of Mesoamerica based on the study conducted by the authors. About 35 unique haplotypes were discovered in 128 Rufous-naped Wrens. The highest haplotype diversity was found in Guatemala. Genetic differentiation was 67% among populations within forms, including intermixed populations from Guatemala and Laguna La Joya.

[Display omitted] • Multilocus nuclear data significantly improve phylogeny estimates for Campylorhynchus wrens. • Most intercontinental dispersal in the genus occurred after closure of the Isthmus of Panama. • Sex linkage appears to improve phylogeny estimation on a per node but not per locus basis. • We argue denser sampling of the avian Z chromosome by target enrichment arrays is warranted. 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. [ABSTRACT FROM AUTHOR]

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. © The Willi Hennig Society 2007. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

An important step in conservation is to identify whether threatened populations are evolutionarily discrete and significant to the species. A prior mitochondrial DNA (mtDNA) phylogeographic study of the California Gnatcatcher (Polioptila californica) revealed no geographic structure and, thus, did not support the subspecies validity of the threatened coastal California Gnatcatcher (P. c. californica). The U.S. Fish and Wildlife Service concluded that mtDNA data alone were insufficient to test subspecies taxonomy. We sequenced eight nuclear loci to search for historically discrete groupings that might have been missed by the mtDNA study (which we confirmed with new ND2 sequences). Phylogenetic analyses of the nuclear loci revealed no historically significant groupings and a low level of divergence (GST = 0.013). Sequence data suggested an older population increase in southern populations, consistent with niche modeling that suggested a northward range expansion following the Last Glacial Maximum (LGM). The signal of population increase was most evident in the mtDNA data, revealing the importance of including loci with short coalescence times. The threatened subspecies inhabits the distinctive Coastal Sage Scrub ecosystem, which might indicate ecological differentiation, but a test of niche divergence was insignificant. The best available genetic, morphological, and ecological data indicate a southward population displacement during the LGM followed by northward range expansion, without the occurrence of significant isolating barriers having led to the existence of evolutionarily discrete subspecies or distinct population segments that would qualify as listable units under the Endangered Species Act. [ABSTRACT FROM AUTHOR]

This paper presents a high-performance torque and flux control strategy for high-power induction motor drives. The control method uses the torque error to control the load angle, obtaining the appropriate flux vector trajectory from which the voltage vector is directly derived based on direct torque control principles. The voltage vector is then generated by an asymmetric cascaded multilevel inverter without need of modulation and filter. Due to the high output quality of the inverter, the torque response presents nearly no ripple. In addition, switching losses are greatly reduced since 80% of the power is delivered by the high-power cell of the asymmetric inverter, which commutates at fundamental frequency. Simulation and experimental results for 81-level inverter are presented. [ABSTRACT FROM AUTHOR]

Objective. To determine the epidemiological and clinic characteristics of gastroenteritis caused by Vibrio parahaemolyticus strains of the pandemic group in Peru. Material and methods. Clinical and laboratory records were searched in 100 cases of gastroenteritis caused by V parahaemolyticus, either of the pandemic or non pandemic group. Clinical and epidemiological data were collected and statistical analysis was done to evaluate if the severity of illness was associated with the pandemic group. Results. Epidemiological data were collected in 85% of cases, and clinical data were only available in 37% of cases, mainly on those hospitalized. Cases associated with the pandemic strains had a higher probability of liquid stools (96.3% vs. 62.5%, p<0.05), moderate or severe dehydration (100% vs. 60%, p<0.05), and hospital care (98% vs. 42.9%, p<0.0001). Cases aged thirty or older were associated with the pandemic strains (63% vs. 39.5%, p<0.05). Conclusions. Vibrio parahaemolyticus of the pandemic group causes more severe gastrointestinal disease than none pandemic strains, with higher probability of requiring hospital care. Based on this report, it is advisable to include the identification of V. parahaemolyticus in the etiological diagnosis of agents causing severe gastroenteritis in the Peruvian health system. [ABSTRACT FROM AUTHOR]

Grinding mill drives play an important role in the mining industry. Almost 60% of the electrical energy consumed by modem concentrator plants goes to grinding mill drives. Different technologies are used in grinding systems presenting special characteristics from the electrical and process points of view. This paper presents a technical evaluation and practical experience of two different technologies used in high-power grinding mill drives. The analysis is focused on the static power converter and associated control scheme required to drive the motor. Cycloconverters and load-commutated inverters are analyzed in terms of power grid interaction, motor interaction, and the required control scheme. The evaluation is supported with practical results obtained in different concentrator plant facilities. [ABSTRACT FROM AUTHOR]

High-power pulsewidth-modulated inverters for medium-voltage applications operate at switching frequencies below 1 kHz to keep the dynamic losses of the power devices at a permitted level. Also, the sampling rate of the digital signal processing system is then low, which introduces considerable signal delays. These have adverse effects on the dynamics of the current control system and introduce undesired cross coupling between the current components id and iq. To overcome this problem, complex state variables are used to derive more accurate models of the machine and the inverter. From these, a novel current controller structure employing single-complex zeros is synthesized. Experimental results demonstrate that high dynamic performance and zero cross coupling is achieved even at very low switching frequency. [ABSTRACT FROM AUTHOR]

Electric Wining haul trucks are one of the most challenging applications of power electronics in automotive systems. This paper presents some advances in very-high-power trucks used in copper mines. The special operational and environmental requirement for this application are highlighted It is established that the use of inverter-fed three-phase induction motors with vector control is the preferred Solution to reach the required high starting torque and good dynamic performance required by these vehicles. Packaging is a key issue and special attention is dedicated to the forced-air cooling system, because the air has a high dust level including conductive and corrosive materials. The truck's high-performance electric retarding system is described along with a novel use of trolley lines in a diesel boost mode as a way to increase the power and speed of the truck and reduce fuel consumption. Advanced features like remote monitoring, the use of global Positioning systems and Internet diagnostic and troubleshooting are also discussed. The paper clearly shows that modem electric haul trucks are highly sophisticated systems that make full use of advances in modem technologies to increase safety and Productivity levels. [ABSTRACT FROM AUTHOR]