The performance of protected-area expansions in representing tropical Andean species: past trends and climate change prospects.

Protected area (PA) extent has increased significantly over the last 150 years globally, but it is yet unclear whether progress in expanding coverage has been accompanied by improved performance in ecological representation. Here, we explore temporal trends in the performance of PA networks in representing > 16,000 vertebrate and plant species in tropical Andean countries based on species bioclimatic niche modelling. We use a randomization analysis to assess whether representation gains over time (1937-2015) are the expected consequence of increasing the overall area of the network or the result of better designed networks. We also explore the impact of climate change on protected-area representation based on projected species distributions in 2070. We found that PAs added in the last three to four decades were better at representing species diversity than random additions overall. Threatened species, amphibians and reptiles are the exception. Species representation is projected to decrease across PAs under climate change, although PA expansions over the last decade (2006-2015) better represented species' future bioclimatic niches than did sites selected at random for most evaluated groups. These findings indicate an unbalanced representation across taxa, and raises concern over under-represented groups, including threatened species, and species' representation under climate change scenarios. However, they also suggest that decisions related to locating protected areas have become more strategic in recent decades and illustrate that indicators tracking representativeness of networks are crucial in PA monitoring frameworks.

Ciclos anuales de colibríes (Aves: Trochilidae) en un bosque nublado, Parque Nacional Henri Pittier, Venezuela

El Paso de Portachuelo es un abra utilizado por una gran diversidad de especies de aves, bien sea como residentes o para movimientos estacionales o migratorios, en el cual se han reportado 32 especies de colibríes en la familia Trochilidae. Debido a esto nos planteamos como objetivo evaluar la dinámica del ensamble de colibríes que usa dicho Paso. Se realizaron salidas de campo mensuales desde abril 1990 hasta noviembre 1994, y desde junio 2010 hasta noviembre 2013. Se capturaron 14 685 individuos, pertenecientes a 38 especies. Las especies con poblaciones que presentaron mayores abundancias fueron: Heliodoxa leadbeateri y Sternoclyta cyanopectus. Con base en los resultados obtenidos, la comunidad de colibríes del área de Portachuelo se puede dividir en: seis especies altamente abundantes y que se observan durante todo o la mayor parte del año, siete especies que utilizan el paso durante la mayor parte del año pero con densidades bajas, cuatro especies que utilizan la zona de manera estacional y siete especies raras en las capturas debido al tipo de muestreo, o a que no presentan movimientos de desplazamiento y prefieren otros hábitats.

Portachuelo Pass is an open area used by a great diversity of bird species, either as residents or for seasonal or migratory movements, reporting 32 species of hummingbirds in the Trochilidae family. Due to this, our goal was evaluating the hummingbird assemblage dynamics in Portachuelo Pass, analyzing the abundance of the captures over four years of sampling and comparing these data with samples taken between 1990 and 2013. Monthly field trips were made from April 1990 to November 1994, and from June 2010 to November 2013, between 5 and 8 mist-nets were used to catch the birds. 14 685 individuals were captured, belonging to 25 species. The relative abundance per species was estimated in each of the sampling months, separating the community into four groups: A) Hummingbirds with high abundances, B) Hummingbirds with low abundances, C) Hummingbirds rare and D) Phaethornithinae. The species with the highest abundance populations were: Heliodoxa leadbeateri and Sternoclyta cyanopectus, followed by Aglaiocercus kingi, Chalybura buffoni, Chrysuronia oenone and Coeligena coeligena. For the rest of the species the densities in the mist-net captures were from low to medium. Based on the results obtained, the community of hummingbirds in the area of Portachuelo can be divided into: six highly abundant species that are observed throughout all or most of the year, seven species that use the passage during most of the year but with low densities, four species that use the area in a seasonal manner and seven rare species in the catches due to the type of sampling, or that do not present displacement movements and prefer other habitats. Statistically significant differences were found between the abundance of hummingbirds of sampling years, being the year with the highest abundance 1991, followed by 2013.

Comparison of gizzard and intestinal microbiota of wild neotropical birds.

Gut bacterial communities have been shown to be influenced by diet, host phylogeny and anatomy, but most of these studies have been done in captive animals. Here we compare the bacterial communities in the digestive tract of wild birds. We characterized the gizzard and intestinal microbiota among 8 wild Neotropical bird species, granivorous or frugivorous species of the orders Columbiformes and Passeriformes. We sequenced the V4 region of the 16S rRNA gene in 94 collected samples from 32 wild birds from 5 localities, and compared bacterial communities by foraging guild, organ, locality and bird taxonomy. 16S rRNA gene-based sequencing data were examined using QIIME with linear discriminant analysis effect size (LEfSe) and metabolic pathways were predicted using PICRUSt algorism. We identified 8 bacterial phyla, dominated by Firmicutes, Actinobacteria and Proteobacteria. Beta diversity analyses indicated significant separation of gut communities by bird orders (Columbiformes vs. Passerifomes) and between bird species (p<0.01). In lower intestine, PICRUSt shows a predominance of carbohydrate metabolism in granivorous birds and xenobiotics biodegradation pathways in frugivorous birds. Gizzard microbiota was significantly richer in granivorous, in relation to frugivorous birds (Chao 1; non-parametric t-test, p<0.05), suggesting a microbial gizzard function, beyond grinding food. The results suggest that the most important factor separating the bacterial community structure was bird taxonomy, followed by foraging guild. However, variation between localities is also likely to be important, but this could not been assessed with our study design.

Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites.

Haemosporidians are a diverse group of vector-borne parasitic protozoa that includes the agents of human malaria; however, most of the described species are found in birds and reptiles. Although our understanding of these parasites' diversity has expanded by analyses of their mitochondrial genes, there is limited information on these genes' evolutionary rates. Here, 114 mitochondrial genomes (mtDNA) were studied from species belonging to four genera: Leucocytozoon, Haemoproteus, Hepatocystis, and Plasmodium. Contrary to previous assertions, the mtDNA is phylogenetically informative. The inferred phylogeny showed that, like the genus Plasmodium, the Leucocytozoon and Haemoproteus genera are not monophyletic groups. Although sensitive to the assumptions of the molecular dating method used, the estimated times indicate that the diversification of the avian haemosporidian subgenera/genera took place after the Cretaceous-Paleogene boundary following the radiation of modern birds. Furthermore, parasite clade differences in mtDNA substitution rates and strength of negative selection were detected. These differences may affect the biological interpretation of mtDNA gene lineages used as a proxy to species in ecological and parasitological investigations. Given that the mitochondria are critically important in the parasite life cycle stages that take place in the vector and that the transmission of parasites belonging to particular clades has been linked to specific insect families/subfamilies, this study suggests that differences in vectors have affected the mode of evolution of haemosporidian mtDNA genes. The observed patterns also suggest that the radiation of haemosporidian parasites may be the result of community-level evolutionary processes between their vertebrate and invertebrate hosts.

Geographic variation and phylogenetic relationships of Myiopagis olallai (Aves: Passeriformes; Tyrannidae), with the description of two new taxa from the Northern Andes.

Geographic variation in vocalizations, morphology and plumage patterns in New World flycatchers is little understood, particularly in rare species with disjunct distributions. We discovered a distinct new flycatcher of the genus Myiopagis from cloud forests of the northern Central Andes in Antioquia, Colombia. Comparisons of vocalizations and external morphology, and molecular phylogenetic analyses, demonstrate that the "Antioquia Myiopagis" is a unique lineage of the M. caniceps-olallai group. We show that three specimens collected in 1940-1951 from cloud forests of Serranía de Perijá in Venezuela, and traditionally assigned to M. caniceps, represent another distinct taxon that is closer to the "Antioquia Myiopagis" and M. olallai. Both new taxa, from Antioquia and Perijá, are described as subspecies of M. olallai. We present a phylogenetic hypothesis for the M. caniceps-olallai group, in which M. olallai and the "Antioquia Myiopagis" are phylogenetically nested within the polytypic M. caniceps, which consists of at least four distinct lineages, indicating that species diversity in this group could be underestimated. 

Low occurrence of Helicobacter DNA in tropical wild birds, Venezuela.

Enteric Helicobacter species (Helicobacter pullorum, Helicobacter pametensis, Helicobacter canadensis, Helicobacter anseris, and Helicobacter brantae) have been found in birds from temperate latitudes. We evaluated the occurrence of Helicobacter spp. in terrestrial wild birds from Venezuela. A fragment of 16S rRNA gene was amplified by PCR with Helicobacter genus-specific primers. Helicobacter spp. were detected in four of 80 fecal and in three of 42 intestinal tissue samples. Analyses of 16S and 23S rRNA gene sequences confirm for the first time the presence of Helicobacter in tropical terrestrial wild birds. However, the occurrence of Helicobacter was low, suggesting these bacteria may be uncommon in the populations we studied.

Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders.

Mitochondrial (mt) genes and genomes are among the major sources of data for evolutionary studies in birds. This places mitogenomic studies in birds at the core of intense debates in avian evolutionary biology. Indeed, complete mt genomes are actively been used to unveil the phylogenetic relationships among major orders, whereas single genes (e.g., cytochrome c oxidase I [COX1]) are considered standard for species identification and defining species boundaries (DNA barcoding). In this investigation, we study the time of origin and evolutionary relationships among Neoaves orders using complete mt genomes. First, we were able to solve polytomies previously observed at the deep nodes of the Neoaves phylogeny by analyzing 80 mt genomes, including 17 new sequences reported in this investigation. As an example, we found evidence indicating that columbiforms and charadriforms are sister groups. Overall, our analyses indicate that by improving the taxonomic sampling, complete mt genomes can solve the evolutionary relationships among major bird groups. Second, we used our phylogenetic hypotheses to estimate the time of origin of major avian orders as a way to test if their diversification took place prior to the Cretaceous/Tertiary (K/T) boundary. Such timetrees were estimated using several molecular dating approaches and conservative calibration points. Whereas we found time estimates slightly younger than those reported by others, most of the major orders originated prior to the K/T boundary. Finally, we used our timetrees to estimate the rate of evolution of each mt gene. We found great variation on the mutation rates among mt genes and within different bird groups. COX1 was the gene with less variation among Neoaves orders and the one with the least amount of rate heterogeneity across lineages. Such findings support the choice of COX 1 among mt genes as target for developing DNA barcoding approaches in birds.