Phylogenetic relationships and systematics of a subclade of Mesoamerican emerald hummingbirds (Aves: Trochilidae: Trochilini).

Phylogenetic relationships among major hummingbird clades are relatively well resolved, yet due to the lack of morphological synapomorphies and relative phenotypic homogeneity, the systematics of several hummingbird groups remain unresolved. Here, we present the results of a multilocus study of a clade of emerald hummingbirds composed of Cynanthus, Chlorostilbon, Riccordia and Phaeoptila (sensu Stiles et al. 2017). We include taxa not analyzed in previous studies (C. lawrencei, C. auriceps and C. forficatus, from Tres Marías Islands, Western Mexico, and Cozumel Island, respectively), and this allows us to develop a new hypothesis for the phylogenetic relationships within this group. We found that this clade originated in Mesoamerica about 12 million years ago, and comprises four geographically congruent clades: (a) the most basal clade, Phaeoptila sordida, of the Balsas River basin, Mexico; (b) Riccordia bicolor, R. maugaeus, R. ricordii and R. swainsonii of the West Indies; (c) Chlorostilbon assimilis, C. aureoventris, C. melanorhynchus, C. mellisugus, C. poortmani and C. pucherani, all of South America, except C. assimilis of Central America; and (d) a Mesoamerican clade with two Cynanthus subclades: a widespread Mexican clade that includes species formerly belonging to the genus Chlorostilbon: Cynanthus auriceps, C. canivetii, C. doubledayi and C. forficatus; and a clade restricted to the west coast of Mexico and the Tres Marías Islands and composed of C. latirostris and C. lawrencei. Our results help clarify the systematics of this group of emeralds, reconstruct its true evolutionary history, and advance understanding of phenotypic evolution in hummingbirds.

A Novel and Divergent Gyrovirus with Unusual Genomic Features Detected in Wild Passerine Birds from a Remote Rainforest in French Guiana.

Sequence-independent amplification techniques have become important tools for virus discovery, metagenomics, and exploration of viral diversity at the global scale, especially in remote areas. Here, we describe the detection and genetic characterization of a novel gyrovirus, named GyV11, present in cloacal, oral, and blood samples from neotropical wild birds in French Guiana. The molecular epidemiology revealed the presence of GyV11 only in passerine birds from three different species at a low prevalence (0.73%). This is the first characterization and prevalence study of a gyrovirus carried out in resident wild bird populations in a remote region, and provides evidence of the fecal-oral route transmission and local circulation of the virus. The molecular phylogeny of gyroviruses reveals the existence of two distinct gyrovirus lineages in which GyV11 is phylogenetically distinct from previously reported gyroviruses. Furthermore, GyV11 is placed basal in the gyrovirus phylogeny, likely owing to its ancestral origin and marked divergence. This study also provides important insights into the ecology, epidemiology, and genomic features of gyroviruses in a remote neotropical rainforest. The pathogenesis of this virus in avian species or whether GyV11 can infect humans and/or chickens needs to be further investigated.

Systematics of the Dendropsophus leucophyllatus species complex (Anura: Hylidae): Cryptic diversity and the description of two new species.

Genetic data in studies of systematics of Amazonian amphibians frequently reveal that purportedly widespread single species in reality comprise species complexes. This means that real species richness may be significantly higher than current estimates. Here we combine genetic, morphological, and bioacoustic data to assess the phylogenetic relationships and species boundaries of two Amazonian species of the Dendropsophus leucophyllatus species group: D. leucophyllatus and D. triangulum. Our results uncovered the existence of five confirmed and four unconfirmed candidate species. Among the confirmed candidate species, three have available names: Dendropsophus leucophyllatus, Dendropsophus triangulum, and Dendropsophus reticulatus, this last being removed from the synonymy of D. triangulum. A neotype of D. leucophyllatus is designated. We describe the remaining two confirmed candidate species, one from Bolivia and another from Peru. All confirmed candidate species are morphologically distinct and have much smaller geographic ranges than those previously reported for D. leucophyllatus and D. triangulum sensu lato. Dendropsophus leucophyllatus sensu stricto occurs in the Guianan region. Dendropsophus reticulatus comb. nov. corresponds to populations in the Amazon basin of Brazil, Ecuador, and Peru previously referred to as D. triangulum. Dendropsophus triangulum sensu stricto is the most widely distributed species; it occurs in Amazonian Ecuador, Peru and Brazil, reaching the state of Pará. We provide accounts for all described species including an assessment of their conservation status.

Multilocus analysis of intraspecific differentiation in three endemic bird species from the northern Neotropical dry forest.

Among-species phylogeographic concordance provides insight into the common processes driving lineage divergence in a particular region. However, identifying the processes that caused phylogeographic breaks is not always straight forward, and inferring past environmental conditions in combination with documented geologic events is sometimes necessary to explain current patterns. We searched for concordant phylogeographic patterns and investigated their causes in three bird species (Momotus mexicanus, Melanerpes chrysogenys, and Passerina leclancherii) that belong to three different avian orders and are endemic to the northernmost range of the Neotropical dry forest. We obtained mitochondrial DNA (ND2 and COI or cyt b) and nuclear DNA (20454, GAPDH, MUSK, and TGFB) sequences for at least one locus from 162 individuals across all species and defined climatically stable areas using environmental niche model projections for the last 130,000 years to have a paleoenvironmental framework for the phylogeographic results. All three species showed marked phylogeographic structure, with breaks found in roughly similar areas, such as the border between the Mexican states of Guerrero and Oaxaca, and between southern Jalisco and Michoacán. Both of these regions are known biogeographic breaks among other taxa. Patterns of genetic diversity and differentiation were partially compatible with climatically stable areas. Coalescent analyses revealed recent population growth and estimated the deeper haplogroup divergence of all three taxa to have occurred within the last 600,000 years. The phylogeographic patterns found are noteworthy because they are maintained in a relatively small area for bird species with continuous ranges, and highlight a unique situation when compared to phylogeographic patterns found in other studies of Neotropical birds that have stressed the role of geographic barriers to explain intraspecific differentiation. Our results point to a scenario of population isolation resulting in the present phylogeographic structure, likely a result of historical climate fluctuations that have fragmented and reconnected the Neotropical dry forest. This study contributes to a growing body of evidence indicating active diversification of endemic lineages in the northern Neotropical dry forest region.

Speciation on oceanic islands: rapid adaptive divergence vs. cryptic speciation in a Guadalupe Island songbird (Aves: Junco).

The evolutionary divergence of island populations, and in particular the tempo and relative importance of neutral and selective factors, is of central interest to the study of speciation. The rate of phenotypic evolution upon island colonization can vary greatly among taxa, and cases of convergent evolution can further confound the inference of correct evolutionary histories. Given the potential lability of phenotypic characters, molecular dating of insular lineages analyzed in a phylogenetic framework provides a critical tool to test hypotheses of phenotypic divergence since colonization. The Guadalupe junco is the only insular form of the polymorphic dark-eyed junco (Junco hyemalis), and shares eye and plumage color with continental morphs, yet presents an enlarged bill and reduced body size. Here we use variation in mtDNA sequence, morphological traits and song variables to test whether the Guadalupe junco evolved rapidly following a recent colonization by a mainland form of the dark-eyed junco, or instead represents a well-differentiated "cryptic" lineage adapted to the insular environment through long-term isolation, with plumage coloration a result of evolutionary convergence. We found high mtDNA divergence of the island lineage with respect to both continental J. hyemalis and J. phaeonotus, representing a history of isolation of about 600,000 years. The island lineage was also significantly differentiated in morphological and male song variables. Moreover, and contrary to predictions regarding diversity loss on small oceanic islands, we document relatively high levels of both haplotypic and song-unit diversity on Guadalupe Island despite long-term isolation in a very small geographic area. In contrast to prevailing taxonomy, the Guadalupe junco is an old, well-differentiated evolutionary lineage, whose similarity to mainland juncos in plumage and eye color is due to evolutionary convergence. Our findings confirm the role of remote islands in driving divergence and speciation, but also their potential role as repositories of ancestral diversity.

Intraspecific morphological and genetic variation of common species predicts ranges of threatened ones.

Predicting where threatened species occur is useful for making informed conservation decisions. However, because they are usually rare, surveying threatened species is often expensive and time intensive. Here, we show how regions where common species exhibit high genetic and morphological divergence among populations can be used to predict the occurrence of species of conservation concern. Intraspecific variation of common species of birds, bats and frogs from Ecuador were found to be a significantly better predictor for the occurrence of threatened species than suites of environmental variables or the occurrence of amphibians and birds. Fully 93 per cent of the threatened species analysed had their range adequately represented by the geographical distribution of the morphological and genetic variation found in seven common species. Both higher numbers of threatened species and greater genetic and morphological variation of common species occurred along elevation gradients. Higher levels of intraspecific divergence may be the result of disruptive selection and/or introgression along gradients. We suggest that collecting data on genetic and morphological variation in common species can be a cost effective tool for conservation planning, and that future biodiversity inventories include surveying genetic and morphological data of common species whenever feasible.

A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys are urgently needed to avoid underestimating tropical diversity, and the use of mtDNA markers can be instrumental in identifying and prioritizing taxa for species discovery.

Speciation in an avian complex endemic to the mountains of Middle America (Ergaticus, Aves: Parulidae).

The implementation of the phylogeographic approach for the study of biodiversity is critical in poorly sampled regions like the montane systems of Middle America, as complex evolutionary histories often result in the presence of independent lineages not properly considered by traditional taxonomy. Herein we sequenced 2370 bp of mtDNA (ND2, cyt b and ATPase) from 81 individuals of Ergaticus, a complex of birds endemic to the montane forests of Middle America. Although current taxonomy recognizes two species, the results reveal considerable genetic structure with the presence of four mtDNA lineages. Two of these lineages within Ergaticus ruber evidence the need of a revaluation of the species limits for this taxon. The general phylogeographic pattern can be explained as a consequence of relative isolation of the populations in different mountain ranges separated by low elevation barriers. Most population groups did not show signals of demographic expansion with the exception of the one corresponding to clade 1. The divergence time estimates point to the Pleistocene as an important time period for the diversification of this complex.

Stable isotopes as indicators of altitudinal distributions and movements in an Ecuadorean hummingbird community.

Altitudinal migration and dispersal is an important component of the life history of several temperate and tropical birds but remains poorly understood due to the limited success of mark and recapture techniques. Stable isotopes of hydrogen (deltaD) in rainfall, and to a lesser extent, carbon (delta13C) in plants are known to change with altitude and hence may provide the basis of a technique for tracking the altitudinal movements in birds and other wildlife. We investigated the potential for this technique by measuring delta13C, deltaD, and delta15N values in tail feathers of eight species of hummingbirds ( Phaethornis malaris, P. syrmatophorus, P. guy, Adelomyia melanogenys, Coeligena torquata, C. lutetiae, Metallura baroni, M. williami) along an altitudinal gradient (300-3,290 m asl) in the Andes Mountains of Ecuador. Feather delta13C and deltaD values were correlated and each changed significantly with elevation above 400 m. In general, we found good agreement between feather deltaD values and those predicted from a generalized relationship of precipitation and surface water deltaD with altitude. Similarly, feather delta13C values showed an enrichment of approximately 1.5 per thousand per 1,000 m over the linear portion of the elevational response. Stable-nitrogen isotope values were variable, and so did not provide useful information on elevation in birds, apart from trophic effects. Overall there appears to be good potential for using the (deltaD, delta13C) stable isotope approach to track altitudinal movements and to elucidate previously unrecognized patterns of life history variation in both temperate and tropical species that migrate across elevational isotopic gradients.