Blanca E. Hernández-Baños

Bird faunas of the humid montane forests of Mesoamerica: biogeographic patterns and priorities for conservation

Summary The distribution of 335 species of birds in 33 islands of humid montane forest in Mesoamerica is summarized, and patterns of distribution, diversity and endemism are analysed. The montane forests of Costa Rica and western Panama far exceed other habitat islands considered for species-richness, richness of species endemic to Mesoamerica, and richness of species ecologically restricted to humid montane forests. Other regions, such as the Sierra Madre del Sur of Guerrero and Oaxaca, the Los Tuxtlas region of southern Veracruz and the mountains of Chiapas and Guatemala, also hold rich and endemic avifaunas. Based on patterns of similarity of avifaunas, the region can be divided into seven regions holding distinctive avifaunas (Costa Rica and western Panama; northern Central America and northern Chiapas; southern Chiapas; eastern Mexico north of the Isthmus of Tehuantepec; Sierra Madre del Sur; interior Oaxaca; and Transvolcanic Belt and Sierra Madre Occidental), which serve as useful guides for the setting of priorities for conservation action. Se resumen las distribuciones de 335 especies de aves en 33 islas de bosque humedo de montana en Mesoamerica, y se analizan patrones de distribution, diversidad y endemismo. Los bosques montanos de Costa Rica y del oeste de Panama tienen la mas alta riqueza de especies, riqueza de especies endemicas a Mesoamerica, y riqueza de especies ecologicamente restringidas a bosque humedo de montana. Otras regiones, tales como la Sierra Madre del Sur de Guerrero y Oaxaca, la region de Los Tuxtlas y las montanas de Chiapas y Guatemala, tambien tienen avifaunas ricas en especies y en endemicas. Basado en patrones de similitud de avifaunas, se puede dividir Mesoamerica en siete regiones que tienen avifaunas distintas (Costa Rica y el oeste de Panama; el norte de Centroamerica y el norte de Chiapas; el sur de Chiapas; el este de Mexico; la Sierra Madre del Sur; el interior de Oaxaca; y el Eje Neovolcanico y la Sierra Madre Occidental), las cuales pueden servir como guias en el establecimiento de prioridades para la conservation.

Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus

The temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood, and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing whether the use of different units of biodiversity (i.e. biological species and statistically inferred species) impacted diversification rates and inferences regarding important biogeographic breaks in the genus. We found that the best‐fit model of diversification for the biological species data set was a declining rate of diversification; whereas a model of constant diversification was the best‐fit model for statistically inferred species or subspecies. Moreover, the relative importance of different landscape features in delimiting genetic structure across the landscape varied across data sets with differing units of biodiversity. Patterns based on divergence times among biological species indicated old speciation events across major geographic and river barriers. In contrast, data sets more inclusive of the diversity in Forpus illustrate the role of both old divergence across major landscape features and more recent divergences that are possibly attributed to Pleistocene climatic changes. Overall, these results indicate that conflicting models on the temporal origins of Neotropical birds may be attributable to sampling biases.

Phylogeography and population genetics of the Amethyst-throated Hummingbird (Lampornis amethystinus)

We analyzed mitochondrial DNA sequence variation across 69 Amethyst-throated Hummingbirds (Lampornis amethystinus), comparing with samples of related taxa. Although this group shows discrete phenotypic variation in throat color among populations in Oaxaca and Guerrero (Mexico), the only phylogeographic structure observed was between phenotypically similar populations north and south of the Isthmus of Tehuantepec. As such, it appears that throat color variation is of recent origin and likely based only on minor genetic differences.

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

Speciation is a continuous and dynamic process, and studying organisms during the early stages of this process can aid in identifying speciation mechanisms. The mallard (Anas platyrhynchos) and Mexican duck (A. [p.] diazi) are two recently diverged taxa with a history of hybridization and controversial taxonomy. To understand their evolutionary history, we conducted genomic scans to characterize patterns of genetic diversity and divergence across the mitochondrial DNA (mtDNA) control region, 3523 autosomal loci and 172 Z‐linked sex chromosome loci. Between the two taxa, Z‐linked loci (ΦST = 0.088) were 5.2 times more differentiated than autosomal DNA (ΦST = 0.017) but comparable to mtDNA (ΦST = 0.092). This elevated Z differentiation deviated from neutral expectations inferred from simulated data that incorporated demographic history and differences in effective population sizes between marker types. Furthermore, 3% of Z‐linked loci, compared to <0.1% of autosomal loci, were detected as outlier loci under divergent selection with elevated relative (ΦST) and absolute (dXY) estimates of divergence. In contrast, the ratio of Z‐linked and autosomal differentiation among the seven Mexican duck sampling locations was close to 1:1 (ΦST = 0.018 for both markers). We conclude that between mallards and Mexican ducks, divergence at autosomal markers is largely neutral, whereas greater divergence on the Z chromosome (or some portions thereof) is likely the product of selection that has been important in speciation. Our results contribute to a growing body of literature indicating elevated divergence on the Z chromosome and its likely importance in avian speciation.

The evolution of a female genital trait widely distributed in the Lepidoptera: comparative evidence for an effect of sexual coevolution.

Background Sexual coevolution is considered responsible for the evolution of many male genital traits, but its effect on female genital morphology is poorly understood. In many lepidopterans, females become temporarily unreceptive after mating and the length of this refractory period is inversely related to the amount of spermatophore remaining in their genital tracts. Sperm competition can select for males that delay female remating by transferring spermatophores with thick spermatophore envelopes that take more time to be broken. These envelopes could select for signa, sclerotized sharp structures located within the female genital tract, that are used for breaking spermatophores. Thus, this hypothesis predicts that thick spermatophore envelopes and signa evolve in polyandrous species, and that these adaptations are lost when monandry evolves subsequently. Here we test the expected associations between female mating pattern and presence/absence of signa, and review the scant information available on the thickness of spermatophore envelopes. Methodology/Principal Findings We made a literature review and found information on female mating pattern (monandry/polyandry), presence/absence of signa and phylogenetic position for 37 taxa. We built a phylogenetic supertree for these taxa, mapped both traits on it, and tested for the predicted association by using Pagels test for correlated evolution. We found that, as predicted by our hypothesis, monandry evolved eight times and in five of them signa were lost; preliminary evidence suggests that at least in two of the three exceptions males imposed monandry on females by means of specially thick spermatophore envelopes. Previously published data on six genera of Papilionidae is in agreement with the predicted associations between mating pattern and the characteristics of spermatophore envelopes and signa. Conclusions/Significance Our results support the hypothesis that signa are a product of sexually antagonistic coevolution with spermatophore envelopes.

The Chimalapas Region, Oaxaca, Mexico: a high-priority region for bird conservation in Mesoamerica

The Chimalapas region, in eastern Oaxaca, Mexico, holds lowland rainforests, tropical dry forests, and cloud forests typical of the Neotropics, as well as montane pine and pine-oak forests more typical of the Nearctic. Totaling more than 600,000 ha, much of the region is forested, and in a good state of preservation. The Chimalapas avifauna is by far the most diverse for any region of comparable size in the country, totalling at least 464 species in the region as a whole (with more than 300 species in the lowland rainforest) representing 44% of the bird species known from Mexico. Within the region, the humid Atlantic lowlands hold 317 species, the montane regions 113 species, and the southern dry forested lowlands 216 species. Important species present in the region include Harpy Eagle Harpia harpyja and several other large eagles, Black Penelopina nigra and probably Horned Oreophasis derbianus Guans, Scarlet Macaw Ara macao , Cinnamon-tailed Sparrow Aimophila sumichrasti , Rose-bellied Bunting Passerina rositae , and Resplendent Quetzal Pharomachrus mocinno . The area holds immense lowland rainforests and cloud forests that rank among the largest and best preserved in all of Mesoamerica, including a complete lowland-to-highland continuum, with entire watersheds preserved more or less intact.

Coalescent analyses show isolation without migration in two closely related tropical orioles: the case of Icterus graduacauda and Icterus chrysater.

The Isthmus of Tehuantepec has played an important role in shaping the avian diversity of Mexico, as well as the rest of the Western Hemisphere. It has been both a barrier and a land connector between North and South America for many groups of birds. Furthermore, climatic change over the Pleistocene has resulted in ecological fluctuations that led to periods of connection and isolation of the highlands in this area. Here we studied the divergence of two species of orioles whose distribution in the highlands is separated by the lowlands of the Isthmus of Tehuantepec: Icterus graduacauda (west of the Isthmus) and Icterus chrysater (east of the Isthmus). We sequenced multiple loci (one mitochondrial gene and six nuclear introns) and performed coalescent analyses (Isolation with Migration) to test whether their divergence resulted from prior occupancy of the ancestral area followed by a vicariant event or recent dispersal from one side or the other of this Isthmus. Results strongly indicate a vicariant event roughly 300,000 years ago in the Pleistocene followed by little or no gene flow. Both mitochondrial and nuclear genes show that the Isthmus of Tehuantepec is a strong barrier to gene flow. Thus, these two species appear to not exchange genes despite their recent divergence and the close geographic proximity of their ranges.

Geographic Variation and Genetic Structure in the Streak-Backed Oriole: Low Mitochondrial DNA Differentiation Reveals Recent Divergence

Abstract Many avian species from the temperate zone show low levels of genetic diversity when compared with species from the tropics, although there are some interesting exceptions, and species whose ranges occur across the temperate–tropical boundary could have characteristics of either or both zones. The distribution of the Streak-backed Oriole (Icterus pustulatus) extends from northwestern Sonora in Mexico south along the Pacific coast to Costa Rica. In addition, there is a population on the Tres Marías Islands. Northern populations are migratory and dichromatic (sexes different), whereas southern populations are nonmigratory and monochromatic (sexes alike). We sequenced mtDNA (control region domain I) from 102 individuals across the range of this species. Maximum parsimony and maximum likelihood analyses did not support the existence of multiple species within Icterus pustulatus based on mtDNA. However, populations from the Tres Marías Islands seem to have been isolated long enough to have fixed differences from populations on the mainland. The species complex shows an uncommon phylogeographic pattern, with shallow haplotype trees and weak geographic structure, suggesting that it has undergone recent population expansion. We recommend that the insular populations be considered a separate species, Icterus graysonii, given the fixed differences from mainland birds in multiple characteristics, including mtDNA and plumage patterns.

A multilocus analysis provides evidence for more than one species within Eugenes fulgens (Aves: Trochilidae).

The status of subspecies in systematic zoology is the focus of controversy. Recent studies use DNA sequences to evaluate the status of subspecies within species complexes and to recognize and delimit species. Here, we assessed the phylogenetic relationships, the taxonomic status of the proposed subspecies, and the species limits of the monotypic hummingbird genus Eugenes (E. fulgens with traditionally recognized subspecies E. f. fulgens, E. f. viridiceps, and E. f. spectabilis), using nuclear (Beta Fibrinogen BFib, Ornithine Decarboxylase ODC, and Muscle Skeletal Receptor Tyrosine Kinase MUSK) and mitochondrial (NADH dehydrogenase subunit 2 ND2, NADH dehydrogenase subunit 4 ND4, and Control Region CR) markers. We performed Bayesian and Bayesian Phylogenetics and Phylogeography analyses and found genetic differences between the three groups, suggesting the existence of two cryptic species (E. fulgens and E. viridiceps) and one phenotypically differentiated species (E. spectabilis). Our analyses show that the E. viridiceps and E. fulgens groups are more closely related with one another than with E. spectabilis.

Rapid radiation and hybridization contribute to weak differentiation and hinder phylogenetic inferences in the New World Mallard complex (Anas spp.)

ABSTRACT Of the 13 taxa composing the Mallard complex, 4 occur in North America: the sexually monochromatic American Black Duck (A. rubripes), Mexican Duck (A. [platyrhynchos] diazi), and Mottled Duck (A. fulvigula), and the dichromatic Mallard (Anas platyrhynchos). Although morphologically distinct, inferring the evolutionary relationships of this group is confounded by extensive genic sharing due to incomplete lineage sorting and ongoing hybridization. The objective of this study was to examine the underlying cause (i.e. incomplete lineage sorting vs. contemporary gene flow) of phylogenetic uncertainty. Whereas most taxa were fairly structured at mitochondrial DNA, a “starburst” pattern of divergence consistent with a rapid radiation was recovered with 17 nuclear introns. Furthermore, nuclear-based divergence estimates and tests of population structure recovered Florida and West Gulf Coast Mottled Ducks as well-differentiated and genetically diagnosable from each other and the remaining taxa, whereas Mallards, American Black Ducks, and Mexican Ducks were indistinguishable. In general, neither population structure analyses nor coalescent-based gene flow estimates conclusively identified the presence of hybrids or significant gene flow, suggesting that genetic similarity within the group is largely influenced by incomplete lineage sorting. However, we also cannot reject potentially high levels of gene flow. Moreover, inconsistent relationships among species trees indicated that phylogenetic results were sensitive to which individuals were included. Taxa within the New World group are phenotypically distinguishable, yet genetically similar and seemingly lack the apparent reproductive isolation that is consistent with early stages of (incomplete) speciation. Future work should focus on genomic regions under selection to better understand the stage of speciation among the various incipient forms.