Mycobacterial Mutagenesis and Drug Resistance Are Controlled by Phosphorylation- and Cardiolipin-Mediated Inhibition of the RecA Coprotease.

Infection with Mycobacterium tuberculosis continues to cause substantial human mortality, in part because of the emergence of antimicrobial resistance. Antimicrobial resistance in tuberculosis is solely the result of chromosomal mutations that modify drug activators or targets, yet the mechanisms controlling the mycobacterial DNA-damage response (DDR) remain incompletely defined. Here, we identify RecA serine 207 as a multifunctional signaling hub that controls the DDR in mycobacteria. RecA S207 is phosphorylated after DNA damage, which suppresses the emergence of antibiotic resistance by selectively inhibiting the LexA coprotease function of RecA without affecting its ATPase or strand exchange functions. Additionally, RecA associates with the cytoplasmic membrane during the mycobacterial DDR, where cardiolipin can specifically inhibit the LexA coprotease function of unmodified, but not S207 phosphorylated, RecA. These findings reveal that RecA S207 controls mutagenesis and antibiotic resistance in mycobacteria through phosphorylation and cardiolipin-mediated inhibition of RecA coprotease function.

Seladelpar treatment reduces IL-31 and pruritus in patients with primary biliary cholangitis.

BACKGROUND AND AIMS: Pruritus is a debilitating symptom for many people living with primary biliary cholangitis (PBC). In studies with seladelpar, a selective peroxisome proliferator-activated receptor-delta agonist, patients with PBC experienced significant improvement in pruritus and reduction of serum bile acids. Interleukin-31 (IL-31) is a cytokine known to mediate pruritus, and blocking IL-31 signaling provides relief in pruritic skin diseases. This study examined the connection between seladelpar's antipruritic effects and IL-31 and bile acid levels in patients with PBC. APPROACH AND RESULTS: IL-31 levels were quantified in serum samples from the ENHANCE study of patients with PBC receiving daily oral doses of placebo (n = 55), seladelpar 5 mg (n = 53) or 10 mg (n = 53) for 3 months, and for healthy volunteers (n = 55). IL-31 levels were compared with pruritus using a numerical rating scale (NRS, 0-10) and with bile acid levels. Baseline IL-31 levels closely correlated with pruritus NRS ( r = 0.54, p < 0.0001), and total ( r = 0.54, p < 0.0001) and conjugated bile acids (up to 0.64, p < 0.0001). Decreases in IL-31 were observed with seladelpar 5 mg (-30%, p = 0.0003) and 10 mg (-52%, p < 0.0001) versus placebo (+31%). Patients with clinically meaningful improvement in pruritus (NRS ≥ 2 decrease) demonstrated greater dose-dependent reductions in IL-31 compared to those without pruritus improvement (NRS < 2 decrease). Strong correlations were observed for the changes between levels of IL-31 and total bile acids ( r = 0.63, p < 0.0001) in the seladelpar 10 mg group. CONCLUSIONS: Seladelpar decreased serum IL-31 and bile acids in patients with PBC. The reductions of IL-31 and bile acids correlated closely with each other and pruritus improvement, suggesting a mechanism to explain seladelpar's antipruritic effects.

Seladelpar combined with complementary therapies improves fibrosis, inflammation, and liver injury in a mouse model of nonalcoholic steatohepatitis.

Seladelpar, a selective peroxisome proliferator-activated receptor δ (PPARδ) agonist, improves markers of hepatic injury in human liver diseases, but histological improvement of nonalcoholic steatohepatitis (NASH) and liver fibrosis has been challenging with any single agent. To discover how complementary agents could work with seladelpar to achieve optimal outcomes, this study evaluated a variety of therapeutics (alone and in combination) in a mouse model of NASH. Mice on a high-fat amylin liver NASH (AMLN) diet were treated for 12 wk with seladelpar, GLP-1-R (glucagon-like peptide-1 receptor) agonist liraglutide, apoptosis signal-regulating kinase 1 (ASK1) inhibitor selonsertib, farnesoid X receptor (FXR) agonist obeticholic acid, and with seladelpar in combination with liraglutide or selonsertib. Seladelpar treatment markedly improved plasma markers of liver function. Seladelpar alone or in combination resulted in stark reductions in liver fibrosis (hydroxyproline, new collagen synthesis rate, mRNA indices of fibrosis, and fibrosis staining) compared with vehicle and the other single agents. Robust reductions in liver steatosis were also observed. Seladelpar produced a reorganization of metabolic gene expression, particularly for those genes promoting peroxisomal and mitochondrial lipid oxidation. In summary, substantial improvements in NASH and NASH-induced fibrosis were observed with seladelpar alone and in combination with liraglutide in this model. Broad gene expression analysis suggests seladelpar should be effective in concert with diverse mechanisms of action.NEW & NOTEWORTHY NASH is a chronic, progressive, and increasingly problematic liver disease that has been resistant to treatment with individual therapeutics. In this study using a diet-induced mouse model of NASH, we found that the PPARδ agonist seladelpar reduced fibrosis and NASH pathology alone and in combinations with a GLP-1-R agonist (liraglutide) or an ASK1 inhibitor (selonsertib). Liver transcriptome analysis comparing each agent and coadministration suggests seladelpar should be effective in combination with a variety of therapeutics.

Phylogenomics of the extinct Heath Hen provides support for sex-biased introgression among extant prairie grouse.

Rapid divergence and subsequent reoccurring patterns of gene flow can complicate our ability to discern phylogenetic relationships among closely related species. To what degree such patterns may differ across the genome can provide an opportunity to extrapolate better how life history constraints may influence species boundaries. By exploring differences between autosomal and Z (or X) chromosomal-derived phylogenetic patterns, we can better identify factors that may limit introgression despite patterns of incomplete lineage sorting among closely related taxa. Here, using a whole-genome resequencing approach coupled with an exhaustive sampling of subspecies within the recently divergent prairie grouse complex (genus: Tympanuchus), including the extinct Heath Hen (T. cupido cupido), we show that their phylogenomic history differs depending on autosomal or Z-chromosome partitioned SNPs. Because the Heath Hen was allopatric relative to the other prairie grouse taxa, its phylogenetic signature should not be influenced by gene flow. In contrast, all the other extant prairie grouse taxa, except Attwater's Prairie-chicken (T. c. attwateri), possess overlapping contemporary geographic distributions and have been known to hybridize. After excluding samples that were likely translocated prairie grouse from the Midwest to the eastern coastal states or their resulting hybrids with mainland Heath Hens, species tree analyses based on autosomal SNPs consistently identified a paraphyletic relationship with regard to the Heath Hen with Lesser Prairie-chicken (T. pallidicinctus) sister to Greater Prairie-chicken (T. c. pinnatus) regardless of genic or intergenic partitions. In contrast, species trees based on the Z-chromosome were consistent with Heath Hen sister to a clade that included its conspecifics, Greater and Attwater's Prairie-chickens (T. c. attwateri). These results were further explained by historic gene flow, as shown with an excess of autosomal SNPs shared between Lesser and Greater Prairie-chickens but not with the Z-chromosome. Phylogenetic placement of Sharp-tailed Grouse (T. phasianellus), however, did not differ among analyses and was sister to a clade that included all other prairie grouse despite low levels of autosomal gene flow with Greater Prairie-chicken. These results, along with strong sexual selection (i.e., male hybrid behavioral isolation) and a lek breeding system (i.e., high variance in male mating success), are consistent with a pattern of female-biased introgression between prairie grouse taxa with overlapping geographic distributions. Additional study is warranted to explore how genomic components associated with the Z-chromosome influence the phenotype and thereby impact species limits among prairie grouse taxa despite ongoing contemporary gene flow.

Conserving the evolutionary history of birds.

In the midst of the sixth mass extinction, limited resources are forcing conservationists to prioritize which species and places will receive conservation action. Evolutionary distinctiveness measures the isolation of a species on its phylogenetic tree. Combining a species' evolutionary distinctiveness with its globally endangered status creates an EDGE score. We use EDGE scores to prioritize the places and species that should be managed to conserve bird evolutionary history. We analyzed all birds in all countries and important bird areas. We examined parrots, raptors, and seabirds in depth because these groups are especially threatened and relatively speciose. The three focal groups had greater median threatened evolutionary history than other taxa, making them important for conserving bird evolutionary history. Australia, Brazil, Indonesia, Madagascar, New Zealand, and the Philippines were especially critical countries for bird conservation because they had the most threatened evolutionary history for endemic birds and are important for parrots, raptors, and seabirds. Increased enforcement of international agreements for the conservation of parrots, raptors, and seabirds is needed because these agreements protect hundreds of millions of years of threatened bird evolutionary history. Decisive action is required to conserve the evolutionary history of birds into the Anthropocene.

En medio de la sexta extinción masiva, los recursos limitados están obligando a los conservacionistas a priorizar cuáles especies y lugares recibirán acciones de conservación. La peculiaridad evolutiva mide el aislamiento de una especie con respecto a su árbol filogenético. La combinación entre la peculiaridad evolutiva de una especie y su estado de conservación mundial genera un puntaje EDGE. Usamos estos puntajes para priorizar los lugares y especies que se deben gestionar para conservar la historia evolutiva ornitológica. Analizamos todas las especies de aves en todos los países y áreas de importancia ornitológica. Estudiamos a profundidad a los psitácidos, rapaces, y aves marinas por el nivel de amenaza que enfrentan estos grupos y porque cuentan con muchas especies. Estos tres grupos tuvieron una mayor mediana de historia evolutiva amenazada que los demás taxones, por lo que son de suma importancia para la conservación de la historia evolutiva ornitológica. Australia, Brasil, Indonesia, Madagascar, Nueva Zelanda y las Filipinas fueron países particularmente críticos para la conservación de las aves pues cuentan con la mayor historia evolutiva amenazada de aves endémicas y son localidades importantes para nuestros tres grupos focales. Se requiere de un incremento en la aplicación de los acuerdos internaciones para la conservación de los psitácidos, rapaces y aves marinas ya que estos acuerdos protegen cientos de millones de años de historia evolutiva ornitológica. Se necesitan acciones decisivas para conservar la historia evolutiva de las aves en el Antropoceno.

Host Mesothelin Expression Increases Ovarian Cancer Metastasis in the Peritoneal Microenvironment.

Mesothelin (MSLN), a glycoprotein normally expressed by mesothelial cells, is overexpressed in ovarian cancer (OvCa) suggesting a role in tumor progression, although the biological function is not fully understood. OvCa has a high mortality rate due to diagnosis at advanced stage disease with intraperitoneal metastasis. Tumor cells detach from the primary tumor as single cells or multicellular aggregates (MCAs) and attach to the mesothelium of organs within the peritoneal cavity producing widely disseminated secondary lesions. To investigate the role of host MSLN in the peritoneal cavity we used a mouse model with a null mutation in the MSLN gene (MSLNKO). The deletion of host MSLN expression modified the peritoneal ultrastructure resulting in abnormal mesothelial cell surface architecture and altered omental collagen fibril organization. Co-culture of murine OvCa cells with primary mesothelial cells regardless of MSLN expression formed compact MCAs. However, co-culture with MSLNKO mesothelial cells resulted in smaller MCAs. An allograft tumor study, using wild-type mice (MSLNWT) or MSLNKO mice injected intraperitoneally with murine OvCa cells demonstrated a significant decrease in peritoneal metastatic tumor burden in MSLNKO mice compared to MSLNWT mice. Together, these data support a role for host MSLN in the progression of OvCa metastasis.

Bird feathers are potential biomonitors for airborne elemental carbon.

Birds can serve as effective biomonitors of air pollution, yet few studies have quantified external particulate matter accumulation on bird feathers. Biomonitoring of airborne elemental carbon (EC) is of critical significance because EC is a component of particulate matter with adverse effects on air quality and human health. To assess their effectiveness for use in EC monitoring, we compared EC accumulation on bird feathers at two sites that differed in vehicular traffic volume in an urban environment within the Dallas-Fort Worth Metropolitan Area, USA. Moulted flight feathers from domestic chickens were experimentally exposed to ambient EC pollution for 5 days in two urban microenvironments 1.5 km distant from each other that differed in traffic volume--adjacent to an interstate highway and a university campus bus stop. Feathers near the highway accumulated approximately eight times more EC (307 ± 34 µg m-2 day-1), on average, than feathers near the bus stop (40 ± 9 µg m-2 day-1). These findings indicate that EC accumulation on feathers varies over short distances within urban areas and that bird feathers potentially can be used for biomonitoring airborne EC.

Towards reconciliation of the four world bird lists: hotspots of disagreement in taxonomy of raptors.

There are currently four world bird lists referenced by different stakeholders including governments, academic journals, museums and citizen scientists. Consolidation of these lists is a conservation and research priority. In reconciling lists, care must be taken to ensure agreement in taxonomic concepts-the actual groups of individual organisms circumscribed by a given scientific epithet. Here, we compare species-level taxonomic concepts for raptors across the four lists, highlighting areas of disagreement. Of the 665 species-level raptor taxa observed at least once among the four lists, only 453 (68%) were consistent across all four lists. The Howard and Moore Checklist of the Birds of the World contains the fewest raptor species (528), whereas the International Ornithological Community World Bird List contains the most (580) and these two lists are in the most disagreement. Of the disagreements, 67% involved owls, and Indonesia was the country containing the most disagreed upon species (169). Finally, we calculated the amount of species-level agreement across lists for each avian order and found raptor orders spread throughout the rankings of agreement. Our results emphasize the need to reconcile the four world bird lists for all avian orders, highlight broad disagreements across lists and identify hotspots of disagreement for raptors, in particular.

Extensive shared polymorphism at non-MHC immune genes in recently diverged North American prairie grouse.

Gene polymorphisms shared between recently diverged species are thought to be widespread and most commonly reflect introgression from hybridization or retention of ancestral polymorphism through incomplete lineage sorting. Shared genetic diversity resulting from incomplete lineage sorting is usually maintained for a relatively short period of time, but under strong balancing selection it may persist for millions of years beyond species divergence (balanced trans-species polymorphism), as in the case of the major histocompatibility complex (MHC) genes. However, balancing selection is much less likely to act on non-MHC immune genes. The aim of this study was to investigate the patterns of shared polymorphism and selection at non-MHC immune genes in five grouse species from Centrocercus and Tympanuchus genera. For this purpose, we genotyped five non-MHC immune genes that do not interact directly with pathogens, but are involved in signaling and regulate immune cell growth. In contrast to previous studies with MHC, we found no evidence for balancing selection or balanced trans-species polymorphism among the non-MHC immune genes. No haplotypes were shared between genera and in most cases more similar allelic variants sorted by genus. Between species within genera, however, we found extensive shared polymorphism, which was most likely attributable to introgression or incomplete lineage sorting following recent divergence and large ancestral effective population size (i.e., weak genetic drift). Our study suggests that North American prairie grouse may have attained relatively low degree of reciprocal monophyly at nuclear loci and reinforces the rarity of balancing selection in non-MHC immune genes.

Major histocompatibility complex variation and blood parasites in resident and migratory populations of the common yellowthroat.

Genes of the major histocompatibility complex (MHC) are a critical part of the adaptive immune response, and the most polymorphic genes in the vertebrate genome, especially in passerine birds. This diversity is thought to be influenced by exposure to pathogens which can vary in relation to numerous factors. Migratory behaviour may be a particularly important trait to consider because migratory birds are exposed to a greater number of different pathogens and parasites at both breeding (i.e. temperate) and overwintering (i.e. tropical and subtropical) areas, as well as at stopover sites during migration. Thus, migrants are predicted to have greater MHC diversity than residents. We compared MHC variation, at both class I and II, and levels of haemosporidian infection between one resident and two migratory populations of the common yellowthroat (Geothlypis trichas). We found that residents were less likely to be infected with haemosporidian parasites and had lower MHC diversity at class I; however, variation at MHC class II was greater in residents than migrants, contrary to our prediction. These patterns were not likely to be caused by differences in population demography as genomewide heterozygosity (based on 9225 single nucleotide polymorphisms) was high in all three populations and not correlated with MHC variation. Our different results for MHC class I and II suggest that studies of immune gene variation in relation to life history need to consider that there could be different selection pressures arising from intracellular (class I) and extracellular (class II) pathogens in different populations.

Protease-activated Receptor-2 (PAR-2)-mediated Nf-κB Activation Suppresses Inflammation-associated Tumor Suppressor MicroRNAs in Oral Squamous Cell Carcinoma.

Oral cancer is the sixth most common cause of death from cancer with an estimated 400,000 deaths worldwide and a low (50%) 5-year survival rate. The most common form of oral cancer is oral squamous cell carcinoma (OSCC). OSCC is highly inflammatory and invasive, and the degree of inflammation correlates with tumor aggressiveness. The G protein-coupled receptor protease-activated receptor-2 (PAR-2) plays a key role in inflammation. PAR-2 is activated via proteolytic cleavage by trypsin-like serine proteases, including kallikrein-5 (KLK5), or by treatment with activating peptides. PAR-2 activation induces G protein-α-mediated signaling, mobilizing intracellular calcium and Nf-κB signaling, leading to the increased expression of pro-inflammatory mRNAs. Little is known, however, about PAR-2 regulation of inflammation-related microRNAs. Here, we assess PAR-2 expression and function in OSCC cell lines and tissues. Stimulation of PAR-2 activates Nf-κB signaling, resulting in RelA nuclear translocation and enhanced expression of pro-inflammatory mRNAs. Concomitantly, suppression of the anti-inflammatory tumor suppressor microRNAs let-7d, miR-23b, and miR-200c was observed following PAR-2 stimulation. Analysis of orthotopic oral tumors generated by cells with reduced KLK5 expression showed smaller, less aggressive lesions with reduced inflammatory infiltrate relative to tumors generated by KLK5-expressing control cells. Together, these data support a model wherein KLK5-mediated PAR-2 activation regulates the expression of inflammation-associated mRNAs and microRNAs, thereby modulating progression of oral tumors.

Spatial Microbial Composition Along the Gastrointestinal Tract of Captive Attwater's Prairie Chicken.

Gastrointestinal microbiota is increasingly recognized as an important component of individual health, and therefore, our ability to quantify its diversity accurately is central for exploring different ways to improve health. Non-invasive sampling methods, such as cloaca swabs, are often used to measure gastrointestinal microbiota diversity within an individual. However, few studies have addressed to what degree differences exist in microbial community composition along the gastrointestinal tract, and measures obtained from the cloaca may not actually represent the diversity present elsewhere in the gastrointestinal tract. In this study, we systematically characterized the gastrointestinal microbial community of the critically endangered Attwater's Prairie chicken (Tympanuchus cupido attwateri) by opportunistically sampling four different locations (ileum, cecum, large intestine, and cloaca) along the gastrointestinal tract of eight individuals. Spatial variation of microbial community was observed at different sampling locations within the gastrointestinal tract. The cecum harbored the most diverse and significantly different microbiota from the other locations, while the microbial α- and ß-diversities were similar in the ileum, large intestine, and cloaca. The results of this study provide evidence that microbiota diversity can differ depending on sampling location and metric used to quantify diversity. As shown here, non-invasive cloacal sampling strategies may reflect microbiota diversity elsewhere in the gastrointestinal tract, yet caution is warranted when making generalizations in terms of the microbiota diversity correlations when samples are obtained from a single location within the gastrointestinal tract.

Identification of a human papillomavirus-associated oncogenic miRNA panel in human oropharyngeal squamous cell carcinoma validated by bioinformatics analysis of the Cancer Genome Atlas.

High-risk human papillomavirus (HPV) is a causative agent for an increasing subset of oropharyngeal squamous cell carcinomas (OPSCCs), and current evidence supports these tumors as having identifiable risk factors and improved response to therapy. However, the biochemical and molecular alterations underlying the pathobiology of HPV-associated OPSCC (designated HPV(+) OPSCC) remain unclear. Herein, we profile miRNA expression patterns in HPV(+) OPSCC to provide a more detailed understanding of pathologic molecular events and to identify biomarkers that may have applicability for early diagnosis, improved staging, and prognostic stratification. Differentially expressed miRNAs were identified in RNA isolated from an initial clinical cohort of HPV(+/-) OPSCC tumors by quantitative PCR-based miRNA profiling. This oncogenic miRNA panel was validated using miRNA sequencing and clinical data from The Cancer Genome Atlas and miRNA in situ hybridization. The HPV-associated oncogenic miRNA panel has potential utility in diagnosis and disease stratification and in mechanistic elucidation of molecular factors that contribute to OPSCC development, progression, and differential response to therapy.

Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater's prairie-chicken.

The negative effects of inbreeding on fitness are serious concerns for populations of endangered species. Reduced fitness has been associated with lower genome-wide heterozygosity and immune gene diversity in the wild; however, it is rare that both types of genetic measures are included in the same study. Thus, it is often unclear whether the variation in fitness is due to the general effects of inbreeding, immunity-related genes or both. Here, we tested whether genome-wide heterozygosity (20 990 SNPs) and diversity at nine immune genes were better predictors of two measures of fitness (immune response and survival) in the endangered Attwater's prairie-chicken (Tympanuchus cupido attwateri). We found that postrelease survival of captive-bred birds was related to alleles of the innate (Toll-like receptors, TLRs) and adaptive (major histocompatibility complex, MHC) immune systems, but not to genome-wide heterozygosity. Likewise, we found that the immune response at the time of release was related to TLR and MHC alleles, and not to genome-wide heterozygosity. Overall, this study demonstrates that immune genes may serve as important genetic markers when monitoring fitness in inbred populations and that in some populations specific functional genes may be better predictors of fitness than genome-wide heterozygosity.

Multi-locus phylogenetic inference among New World Vultures (Aves: Cathartidae).

New World Vultures are large-bodied carrion feeding birds in the family Cathartidae, currently consisting of seven species from five genera with geographic distributions in North and South America. No study to date has included all cathartid species in a single phylogenetic analysis. In this study, we investigated the phylogenetic relationships among all cathartid species using five nuclear (nuc; 4060bp) and two mitochondrial (mt; 2165bp) DNA loci with fossil calibrated gene tree (27 outgroup taxa) and coalescent-based species tree (2 outgroup taxa) analyses. We also included an additional four nuclear loci (2578bp) for the species tree analysis to explore changes in nodal support values. Although the stem lineage is inferred to have originated ∼69 million years ago (Ma; 74.5-64.9 credible interval), a more recent basal split within Cathartidae was recovered at ∼14Ma (17.1-11.1 credible interval). Two primary clades were identified: (1) Black Vulture (Coragyps atratus) together with the three Cathartes species (Lesser C. burrovianus and Greater C. melambrotus Yellow-headed Vultures, and Turkey Vulture C. aura), and (2) King Vulture (Sarcoramphus papa), California (Gymnogyps californianus) and Andean (Vultur gryphus) Condors. Support for taxon relationships within the two basal clades were inconsistent between analyses with the exception of Black Vulture sister to a monophyletic Cathartes clade. Increased support for a yellow-headed vulture clade was recovered in the species tree analysis using the four additional nuclear loci. Overall, these results are in agreement with cathartid life history (e.g. olfaction ability and behavior) and contrasting habitat affinities among sister taxa with overlapping geographic distributions. More research is needed using additional molecular loci to further resolve the phylogenetic relationships within the two basal cathartid clades, as speciation appeared to have occurred in a relatively short period of time.

Contrasting patterns of selection and drift between two categories of immune genes in prairie-chickens.

Immune-receptor genes of the adaptive immune system, such as the major histocompatibility complex (MHC), are involved in recognizing specific pathogens and are known to have high rates of adaptive evolution, presumably as a consequence of rapid co-evolution between hosts and pathogens. In contrast, many 'mediating' genes of the immune system do not interact directly with specific pathogens and are involved in signalling (e.g. cytokines) or controlling immune cell growth. As a consequence, we might expect stronger selection at immune-receptor than mediating genes, but these two types of genes have not been compared directly in wild populations. Here, we tested the hypothesis that selection differs between MHC (class I and II) and mediating genes by comparing levels of population differentiation across the range of greater prairie-chickens (Tympanuchus cupido). As predicted, there was stronger population differentiation and isolation by distance at immune receptor (MHC) than at either mediating genes or neutral microsatellites, suggesting a stronger role of local adaptation at the MHC. In contrast, mediating genes displayed weaker differentiation between populations than neutral microsatellites, consistent with selection favouring similar alleles across populations for mediating genes. In addition to selection, drift also had a stronger effect on immune receptor (MHC) than mediating genes as indicated by the stronger decline of MHC variation in relation to population size. This is the first study in the wild to show that the effects of selection and drift on immune genes vary across populations depending on their functional role.

Differential introgression and effective size of marker type influence phylogenetic inference of a recently divergent avian group (Phasianidae: Tympanuchus).

Life history strategies can influence the effective population size (Ne) of loci differently based on their mode of inheritance. Recognizing how this may affect the rate of lineage sorting among marker types is important for studies focused on resolving phylogenetic relationships among recently divergent taxa. In this study, we use gene tree, coalescent-based species tree, and isolation-with-migration analyses to explore the differences between marker types (autosomal, Z-linked, and mitochondrial) in resolving phylogenetic relationships among North American prairie grouse (Tympanuchus). We found that Z-linked loci were more likely to identify monophyletic relationships among prairie grouse species compared to autosomal and mtDNA loci in both species and gene tree analyses, with species tree analyses outperforming gene trees. These results were further supported with isolation-with-migration analyses, where Z-linked loci largely followed a strict isolation model while autosomal loci were more likely to fit a model with gene flow between species following population divergence. While accounting for differences in inheritance pattern (or Ne) for marker type, results suggest that additional factors, such as strong sexual selection and sex-biased introgression (i.e., male-biased postzygotic hybrid behavioral isolation or "unsexy son"), may further explain the decreased diversity levels and increased rate of lineage sorting observed with the Z-linked loci relative to autosomal and mtDNA loci. In fact, to our knowledge no hybrid male prairie grouse have been observed breeding in the wild, yet hybrid females along with backcross females are known to produce viable offspring. Overall, this study highlights that more work is needed to determine how complex models of gene flow (i.e., sex biased introgression) and differences in the effective size among marker types based on differing life history strategies influence divergence date estimation and species delimitation.

Rapid diversification of falcons (Aves: Falconidae) due to expansion of open habitats in the Late Miocene.

Understanding how and why lineages diversify is central to understanding the origins of biological diversity. The avian family Falconidae (caracaras, forest-falcons, falcons) has an uneven distribution of species among multiple well-supported clades, and provides a useful system for testing hypotheses about diversification rate and correlation with environmental changes. We analyzed eight independent loci for 1-7 individuals from each of the 64 currently recognized Falconidae species, together with two fossil falconid temporal calibrations, to assess phylogeny, absolute divergence times and potential shifts in diversification rate. Our analyses supported similar diversification ages in the Early to Middle Miocene for the three traditional subfamilies, Herpetotherinae, Polyborinae and Falconinae. We estimated that divergences within the subfamily Falconinae began about 16mya and divergences within the most species-rich genus, Falco, including about 60% of all Falconidae species, began about 7.5mya. We found evidence for a significant increase in diversification rate at the basal phylogenetic node for the genus Falco, and the timing for this rate shift correlates generally with expansion of C4 grasslands beginning around the Miocene/Pliocene transition. Concomitantly, Falco lineages that are distributed primarily in grassland or savannah habitats, as opposed to woodlands, and exhibit migratory, as opposed to sedentary, behavior experienced a higher diversification rate.

Mercury Concentrations in Birds from Two Atmospherically Contaminated Sites in North Texas, USA.

Mercury (Hg) is a ubiquitous and highly toxic contaminant that can have negative effects on wildlife. Only a few studies have measured Hg concentrations in birds from the south central United States, and the potential threat of Hg contamination to birds in this region is largely unknown. In the present study, we assess Hg concentrations in blood and feathers from five bird species [eastern bluebird (Sialis sialis), Carolina wren (Thryothorus ludovicianus), wood duck (Aix sponsa), great egret (Ardea alba), and great blue heron (Ardea herodias)] that occupy different trophic levels at Caddo Lake and Lewisville Lake, located in northeast and north central Texas, respectively. Both sites are contaminated with Hg from the atmosphere. Adult passerines had higher Hg concentrations in their blood than conspecific nestlings. Mercury concentrations in feathers differed between species by more than an order of magnitude with large piscivorous species having higher concentrations than smaller insectivorous species. Mercury concentrations in eastern bluebirds were higher at Caddo Lake than Lewisville Lake. The present study represents one of the first studies of Hg concentrations in multiple bird species in north Texas and suggests that Hg concentrations in birds from atmospherically polluted sites in this region may be high enough to compromise fitness in those species.

Conditionally induced RAGE expression by proximal airway epithelial cells in transgenic mice causes lung inflammation.

BACKGROUND: Receptors for advanced glycation end-products (RAGE) are multiligand cell-surface receptors expressed abundantly by distal pulmonary epithelium. Our lab has discovered RAGE-mediated effects in the orchestration of lung inflammation induced by tobacco smoke and environmental pollutants; however, the specific contribution of RAGE to the progression of proximal airway inflammation is still inadequately characterized. METHODS AND RESULTS: We generated a Tet-inducible transgenic mouse that conditionally overexpressed RAGE using the club cell (Clara) secretory protein (CCSP) promoter expressed by club (Clara) cells localized to the proximal airway. RAGE was induced for 40 days from weaning (20 days of age) until sacrifice date at 60 days. Immunohistochemistry, immunoblotting, and qPCR revealed significant RAGE up-regulation when compared to non-transgenic controls; however, H&E staining revealed no detectible morphological abnormalities and apoptosis was not enhanced during the 40 days of augmentation. Freshly procured bronchoalveolar lavage fluid (BALF) from CCSP-RAGE TG mice had significantly more total leukocytes and PMNs compared to age-matched control littermates. Furthermore, CCSP-RAGE TG mice expressed significantly more tumor necrosis factor alpha (TNF-α), interleukin 7 (IL-7), and interleukin 14 (IL-14) in whole lung homogenates compared to controls. CONCLUSIONS: These data support the concept that RAGE up-regulation specifically in lung airways may function in the progression of proximal airway inflammation.