Winter connectivity and leapfrog migration in a migratory passerine.

Technological advances in migratory tracking tools have revealed a remarkable diversity in migratory patterns. One such pattern is leapfrog migration, where individuals that breed further north migrate to locations further south. Here, we analyzed migration patterns in the Painted Bunting (Passerina ciris) using a genetic-based approach. We started by mapping patterns of genetic variation across geographic space (called a genoscape) using 386 individuals from 25 populations across the breeding range. We then genotyped an additional 230 samples from 31 migration stopover locations and 178 samples from 16 wintering locations to map patterns of migratory connectivity. Our analyses of genetic variation across the breeding range show the existence of four genetically distinct groups within the species: Eastern, Southwestern, Louisiana, and Central groups. Subsequent assignment of migrating and wintering birds to genetic groups illustrated that birds from the Central group migrated during the fall via western Mexico or southern Texas, spent the winter from northeastern Mexico to Panama, and migrated north via the Gulf Coast of Mexico. While Louisiana birds overlapped with Central birds on their spring migratory routes along the Gulf Coast, we found that Louisiana birds had a more restricted wintering distribution in the Yucatan Peninsula and Central America. Further estimation of the straight-line distance from the predicted breeding location to the wintering location revealed that individuals sampled at lower winter latitudes traveled to greater distances (i.e., the predicted breeding area was further north; p > .001), confirming that these species exhibit a leapfrog migration pattern. Overall, these results demonstrate the utility of a genoscape-based approach for identifying range-wide patterns of migratory connectivity such as leapfrog migration with a high degree of clarity.

High Prevalence of Avian Influenza Virus Among Wild Waterbirds and Land Birds of Mexico.

Aquatic wild birds, especially waterfowl, have been long considered the main reservoirs of the avian influenza A virus; however, recent surveys have found an important prevalence of these viruses among land birds as well. Migration has been suggested as an important factor in the avian influenza virus dissemination. We aimed to estimate the prevalence of influenza A viruses in wild birds (waterbirds and land birds; resident and migratory) in eastern Mexico, where the three main North American migration flyways converge and where there was no previous information on this subject. We detected influenza with reverse transcription coupled with a PCR approach. Of the 534 birds sampled between 2010 and 2012, we detected the influenza A virus in a high proportion of birds (39%). Prevalence was particularly high in land birds (49%) when compared to aquatic birds (26%); there was no difference in overall prevalence between resident (39%) and migratory birds (39%). The high prevalence of the avian influenza virus in land birds was noteworthy in the innermost sampling areas in northern Mexico (Coahuila [82%] and Nuevo Leon [43%]).

Alta prevalencia del virus de la influenza aviar entre aves acuáticas silvestres y aves terrestres de México. Las aves silvestres acuáticas, especialmente las aves anseriformes, han sido consideradas durante mucho tiempo los principales reservorios del virus de la influenza aviar A; sin embargo, muestreos recientes también han encontrado una importante prevalencia de estos virus entre las aves terrestres. Se ha sugerido que la migración es un factor importante en la diseminación del virus de la influenza aviar. El objetivo de este estudio fue estimar la prevalencia de los virus de la influenza A en aves silvestres (aves acuáticas y terrestres; residentes y migratorias) en el este de México, donde convergen las tres rutas migratorias principales de América del Norte y donde no había información previa sobre este tema. Se detectó al virus de influenza mediante transcripción reversa acoplada a PCR. De las 534 aves muestreadas entre los años 2010 y 2012, se detectó al virus de la influenza A en una alta proporción de aves (39%). La prevalencia fue particularmente alta en las aves terrestres (49%) en comparación con las aves acuáticas (26%); no se observó diferencia en la prevalencia general entre las aves residentes (39%) y las migratorias (39%). La alta prevalencia del virus de la influenza aviar en las aves terrestres fue notable en las áreas de muestreo hacia el interior del norte de México (Coahuila [82%] y Nuevo León [43%]).

Adaptive genetic diversity and evidence of population genetic structure in the endangered Sierra Madre Sparrow (Xenospiza baileyi).

The magnitude and distribution of genetic diversity through space and time can provide useful information relating to evolutionary potential and conservation status in threatened species. In assessing genetic diversity in species that are of conservation concern, several studies have focused on the use of Toll-like receptors (TLRs). TLRs are innate immune genes related to pathogen resistance, and polymorphisms may reflect not only levels of functional diversity, but may also be used to assess genetic diversity within and among populations. Here, we combined four potentially adaptive markers (TLRs) with one mitochondrial (COI) marker to evaluate genetic variation in the endangered Sierra Madre Sparrow (Xenospiza baileyi). This species offers an ideal model to investigate population and evolutionary genetic processes that may be occurring in a habitat restricted endangered species with disjunct populations (Mexico City and Durango), the census sizes of which differ by an order of magnitude. TLRs diversity in the Sierra Madre Sparrow was relatively high, which was not expected given its two small, geographically isolated populations. Genetic diversity was different (but not significantly so) between the two populations, with less diversity seen in the smaller Durango population. Population genetic structure between populations was due to isolation and different selective forces acting on different TLRs; population structure was also evident in COI. Reduction of genetic diversity in COI was observed over 20 years in the Durango population, a result likely caused by habitat loss, a factor which may be the main cause of diversity decline generally. Our results provide information related to the ways in which adaptive variation can be altered by demographic changes due to human-mediated habitat alterations. Furthermore, our findings may help to guide conservation schemes for both populations and their restricted habitat.

Dense Geographic and Genomic Sampling Reveals Paraphyly and a Cryptic Lineage in a Classic Sibling Species Complex.

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis/Empidonax occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the US Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this article, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E. occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

A new species of Trachymyrmex (Hymenoptera, Formicidae) fungus-growing ant from the Sierra Madre Oriental of northeastern Mexico.

Here we describe a new species of Trachymyrmex, T. pakawasp. n., from the Gran Sierra Plegada range of the Sierra Madre Oriental, in the states of Coahuila and Nuevo Leon, northeastern Mexico. Trachymyrmex pakawa is a large-sized species compared to other North American Trachymyrmex. Its geographic distribution includes the piedmont of the Gran Sierra Plegada at La Estanzuela, Monterrey, as well as peripheral mountains segregated from the Sierra Madre Oriental (Cerro de las Mitras, Sierra de Zapalinamé, Cañon de San Lorenzo, Cerro de las Letras). The preferred habitats of T. pakawa include oak-pine forest at La Estanzuela, xeric oak forest at Zapalinamé and mesic Chihuahuan desert scrub with sotol (Dasylirion) at other sites. All localities are on slopes, on very rocky, shallow lithosols overlaying large boulders. This species nests under and between large boulders and rocks. It has not been observed on alluvial or better developed, deeper soils, and it is absent from sites with human activity (urban, disturbed, and landscaped areas). It is closely related to and morphologically similar to Trachymyrmex smithi. The known distribution ranges of T. pakawa and T. smithi almost overlap in Saltillo, Coahuila state. The main character that distinguishes the new species from T. smithi is longer antennal scapes in T. pakawa; also, different nesting habits (rocky slopes vs. alluvial sites or deep sand in T. smithi), and geographic distribution. Phylogenetic analysis of DNA sequences from the mitochondrial marker cytochrome c oxidase subunit I (COI) and the first intron of the F1 copy of the nuclear protein-coding gene Elongation Factor 1- α (EF1-α-F1) confirm a sister-species relationship between T. pakawa and T. smithi. Bayesian coalescent analyses indicate a divergence time of about 8.00 million years before present (95% confidence interval: 4.8-11.5 mya) between T. pakawa and T. smithi. The divergence of the lineages of T. pakawa and T. smithi could have been driven by the Pliocene-Holocene desertification of southwestern North America. This process resulted in isolated mesic refugia and forests in the Madrean ranges and piedmonts of northeastern Mexico (the current habitat of T. pakawa) while T. smithi adapted to the deeper, often sandy soils on the drier desert plains of Coahuila and Chihuahua states in Mexico, and New Mexico and Texas in the USA. Within the Nearctic species of the Trachymyrmex septentrionalis species group, T. pakawa is the species that is closest (by geographical distribution) to Neotropical species of Trachymyrmex like T. saussurei.

High diversity and suggested endemicity of culturable Actinobacteria in an extremely oligotrophic desert oasis.

The phylum Actinobacteria constitutes one of the largest and anciently divergent phyla within the Bacteria domain. Actinobacterial diversity has been thoroughly researched in various environments due to its unique biotechnological potential. Such studies have focused mostly on soil communities, but more recently marine and extreme environments have also been explored, finding rare taxa and demonstrating dispersal limitation and biogeographic patterns for Streptomyces. To test the distribution of Actinobacteria populations on a small scale, we chose the extremely oligotrophic and biodiverse Cuatro Cienegas Basin (CCB), an endangered oasis in the Chihuahuan desert to assess the diversity and uniqueness of Actinobacteria in the Churince System with a culture-dependent approach over a period of three years, using nine selective media. The 16S rDNA of putative Actinobacteria were sequenced using both bacteria universal and phylum-specific primer pairs. Phylogenetic reconstructions were performed to analyze OTUs clustering and taxonomic identification of the isolates in an evolutionary context, using validated type species of Streptomyces from previously phylogenies as a reference. Rarefaction analysis for total Actinobacteria and for Streptomyces isolates were performed to estimate species' richness in the intermediate lagoon (IL) in the oligotrophic Churince system. A total of 350 morphologically and nutritionally diverse isolates were successfully cultured and characterized as members of the Phylum Actinobacteria. A total of 105 from the total isolates were successfully subcultured, processed for DNA extraction and 16S-rDNA sequenced. All strains belong to the order Actinomycetales, encompassing 11 genera of Actinobacteria; the genus Streptomyces was found to be the most abundant taxa in all the media tested throughout the 3-year sampling period. Phylogenetic analysis of our isolates and another 667 reference strains of the family Streptomycetaceae shows that our isolation effort produced 38 unique OTUs in six new monophyletic clades. This high biodiversity and uniqueness of Actinobacteria in an extreme oligotrophic environment, which has previously been reported for its diversity and endemicity, is a suggestive sign of microbial biogeography of Actinobacteria and it also represents an invaluable source of biological material for future ecological and bioprospecting studies.

Molecular evolution and expression profile of the chemerine encoding gene RARRES2 in baboon and chimpanzee.

BACKGROUND: Chemerin, encoded by the retinoic acid receptor responder 2 (RARRES2) gene is an adipocytesecreted protein with autocrine/paracrine functions in adipose tissue, metabolism and inflammation with a recently described function in vascular tone regulation, liver, steatosis, etc. This molecule is believed to represent a critical endocrine signal linking obesity to diabetes. There are no data available regarding evolution of RARRES2 in non-human primates and great apes. Expression profile and orthology in RARRES2 genes are unknown aspects in the biology of this multigene family in primates. Thus; we attempt to describe expression profile and phylogenetic relationship as complementary knowledge in the function of this gene in primates. To do that, we performed A RT-PCR from different tissues obtained during necropsies. Also we tested the hypotheses of positive evolution, purifying selection, and neutrality. And finally a phylogenetic analysis was made between primates RARRES2 protein. RESULTS: RARRES2 transcripts were present in liver, lung, adipose tissue, ovary, pancreas, heart, hypothalamus and pituitary tissues. Expression in kidney and leukocytes were not detectable in either species. It was determined that the studied genes are orthologous. CONCLUSIONS: RARRES2 evolution fits the hypothesis of purifying selection. Expression profiles of the RARRES2 gene are similar in baboons and chimpanzees and are also phylogenetically related.

Molecular evolution and expression profile of the chemerine encoding gene RARRES2 in baboon and chimpanzee

BACKGROUND: Chemerin, encoded by the retinoic acid receptor responder 2 (RARRES2) gene is an adipocytesecreted protein with autocrine/paracrine functions in adipose tissue, metabolism and inflammation with a recently described function in vascular tone regulation, liver, steatosis, etc. This molecule is believed to represent a critical endocrine signal linking obesity to diabetes. There are no data available regarding evolution of RARRES2 in non-human primates and great apes. Expression profile and orthology in RARRES2 genes are unknown aspects in the biology of this multigene family in primates. Thus; we attempt to describe expression profile and phylogenetic relationship as complementary knowledge in the function of this gene in primates. To do that, we performed A RT-PCR from different tissues obtained during necropsies. Also we tested the hypotheses of positive evolution, purifying selection, and neutrality. And finally a phylogenetic analysis was made between primates RARRES2 protein. RESULTS: RARRES2 transcripts were present in liver, lung, adipose tissue, ovary, pancreas, heart, hypothalamus and pituitary tissues. Expression in kidney and leukocytes were not detectable in either species. It was determined that the studied genes are orthologous. CONCLUSIONS: RARRES2 evolution fits the hypothesis of purifying selection. Expression profiles of the RARRES2 gene are similar in baboons and chimpanzees and are also phylogenetically related.

Functional synthetic Antennapedia genes and the dual roles of YPWM motif and linker size in transcriptional activation and repression.

Segmental identity along the anteroposterior axis of bilateral animals is specified by Hox genes. These genes encode transcription factors, harboring the conserved homeodomain and, generally, a YPWM motif, which binds Hox cofactors and increases Hox transcriptional specificity in vivo. Here we derive synthetic Drosophila Antennapedia genes, consisting only of the YPWM motif and homeodomain, and investigate their functional role throughout development. Synthetic peptides and full-length Antennapedia proteins cause head-to-thorax transformations in the embryo, as well as antenna-to-tarsus and eye-to-wing transformations in the adult, thus converting the entire head to a mesothorax. This conversion is achieved by repression of genes required for head and antennal development and ectopic activation of genes promoting thoracic and tarsal fates, respectively. Synthetic Antennapedia peptides bind DNA specifically and interact with Extradenticle and Bric-à-brac interacting protein 2 cofactors in vitro and ex vivo. Substitution of the YPWM motif by alanines abolishes Antennapedia homeotic function, whereas substitution of YPWM by the WRPW repressor motif, which binds the transcriptional corepressor Groucho, allows all proteins to act as repressors only. Finally, naturally occurring variations in the size of the linker between the homeodomain and YPWM motif enhance Antennapedia repressive or activating efficiency, emphasizing the importance of linker size, rather than sequence, for specificity. Our results clearly show that synthetic Antennapedia genes are functional in vivo and therefore provide powerful tools for synthetic biology. Moreover, the YPWM motif is necessary--whereas the entire N terminus of the protein is dispensable--for Antennapedia homeotic function, indicating its dual role in transcriptional activation and repression by recruiting either coactivators or corepressors.

Molecular phylogenetic analysis of an endangered Mexican sparrow: Spizella wortheni.

The Worthen's Sparrow (Spizella wortheni) is an endemic bird species of the Mexican Plateau that is protected by Mexican law. Considering its limited range (25 km(2)), small population size (100-120 individuals), and declining population, it is one of the most endangered avian species in North America. Although it has been assumed to be the sister taxon of the Field Sparrow (Spizella pusilla), the systematic and evolutionary relationships of Worthen's Sparrow have never been tested using modern molecular phylogenetic methods. We addressed the molecular phylogeny of S. wortheni analyzing six mitochondrial genes (3571 bp) from all of the natural members of the genus Spizella. Our maximum likelihood and Bayeasian analysis indicate that despite the superficial similarity, S. wortheni is not the sister taxon of S. pusilla, but is instead most closely related to the Brewer's Sparrow (Spizella breweri). Also new insights about the phylogenetics relationships of the Spizella genera are presented.