Luis A. Sánchez-González

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.

CLIMATE-DRIVEN DIVERSIFICATION AND PLEISTOCENE REFUGIA IN PHILIPPINE BIRDS: EVIDENCE FROM PHYLOGEOGRAPHIC STRUCTURE AND PALEOENVIRONMENTAL NICHE MODELING

Avian diversification in oceanic archipelagos is largely attributed to isolation across marine barriers. During glacial maxima, lowered sea levels resulted in repeated land connections between islands joined by shallow seas. Consequently, such islands are not expected to show endemism. However, if climate fluctuations simultaneously caused shifts in suitable environmental conditions, limiting populations to refugia, then occurrence on and dispersal across periodic land bridges are not tenable. To assess the degree to which paleoclimate barriers, rather than marine barriers, drove avian diversification in the Philippine Archipelago, we produced ecological niche models for current‐day, glacial maxima, and interglacial climate scenarios to infer potential Pleistocene distributions and paleoclimate barriers. We then tested marine and paleoclimate barriers for correspondence to geographic patterns of population divergence, inferred from DNA sequences from eight codistributed bird species. In all species, deep‐water channels corresponded to zones of genetic differentiation, but six species exhibited deeper divergence associated with a periodic land bridge in the southern Philippines. Ecological niche models for these species identified a common paleoclimate barrier that coincided with deep genetic structure among populations. Although dry land connections joined southern Philippine islands during low sea level stands, unfavorable environmental conditions limited populations within landmasses, resulting in long‐term isolation and genetic differentiation. These results highlight the complex nature of diversification in archipelagos: marine barriers, changes in connectivity due to sea level change, and climate‐induced refugia acted in concert to produce great species diversity and endemism in the Philippines.

Molecular systematics and species limits in the Philippine fantails (Aves: Rhipidura).

Islands have long-attracted scientists because of their relatively simple biotas and stark geographic boundaries. However, for many islands and archipelagos, this simplicity may be overstated because of methodological and conceptual limitations when these biotas were described. One archipelago that has received relatively little recent attention is the Philippine islands. Although much of its biota was documented long ago, taxonomic revision and evolutionary study has been surprisingly scarce, and only a few molecular phylogenetic studies are beginning to appear. We present a molecular phylogeny and taxonomic revision for the Philippine fantails (Aves: Rhipidura) using nuclear and mitochondrial DNA sequences. Our results suggest that current taxonomy underestimates diversity in the group. Some morphologically distinct subspecies warrant species status, whereas one was indistinguishable genetically and morphologically and should not be retained. A few taxa require additional sampling for thorough taxonomic assessment. Patterns of diversity within Philippine Rhipidura mostly corroborate predictions of the Pleistocene aggregate island complex (PAIC) hypothesis, in which diversity is expected to be partitioned by deep water channels separating Pleistocene aggregate islands rather than by current islands. Substantial structure within PAIC clades indicates that additional drivers of diversification should be considered.

Phylogeography of the Robsonius Ground-Warblers (Passeriformes: Locustellidae) Reveals an Undescribed Species from Northeastern Luzon, Philippines

Abstract. The Robsonius ground-warblers are forest birds endemic to the Luzon Island complex in the Philippine archipelago. Their systematic relationships have long remained ambiguous; until recently they were included in the timaliid genus Napothera. Two Robsonius species are currently recognized on the basis of plumage differences: R. rabori from northern Luzon in the Cordillera Central and the northern Sierra Madre, and R. sorsogonensis from southern Luzon and Catanduanes Island. Recent specimen collections, including the first adult specimen from the Cordillera Central, establish plumage differences between populations of R. rabori in the Cordillera Central and Sierra Madre and reveal a third diagnosable population within Luzon. These differences have gone unnoticed because R. rabori (sensu stricto) had been known only from the juvenile holotype. Molecular phylogenetic data further support the hypothesis that three highly divergent taxa occur across the Luzon Island complex: Robsonius rabori is known only from the northern Cordillera Central in Ilocos Norte; an undescribed taxon (formerly included in R. rabori) occurs in the northern Sierra Madre in Cagayan, Isabela, Aurora, and Nueva Vizcaya provinces; and R. sorsogonensis occurs in southern Luzon (Bulacan and Laguna provinces), the Bicol Peninsula, and on Catanduanes Island. The existence of three putatively allopatric species within the Luzon island complex highlights the role of in situ diversification in island systems, and brings attention to the need for forest conservation to protect geographically restricted populations throughout the Luzon Island complex.

Diversification in the Andes: the Atlapetes brush-finches

With nearly 30 species, the Atlapetes brush‐finches are one of the most species‐rich genera in the New World sparrows (Passerellidae). Atlapetes is mainly distributed in highland forests from Mexico to north‐western Argentina, with a few taxa in the foothills (<1000 m). Species diversity is highest in South America, because of high rates of local replacement but few cases of local co‐occurrence, creating a mosaic of forms with different plumage colours. With the purpose of understanding phylogenetic and environmental determinants of trait evolution, we reconstructed a molecular phylogeny based on full ND2 mtDNA sequences, with focus on the core group of Andean Atlapetes species and related outgroups. Phylogenetic relationships revealed that most Andean species are closely related to a geographical neighbour, although these neighbours may often be phenotypically quite different, with yellow‐plumaged species sister to grey‐plumaged taxa. Biogeographic analyses suggest Mesoamerica as the area of origin for Atlapetes, which dispersed through the Panama Isthmus to the eastern Andean slope, then the western Andes and finally the southern Andes. Diversification in the genus was apparently influenced by the glacial cycles that affected the distribution of montane forests in the Neotropics, particularly during the last million years. Phenotypic plumage changes may be associated with ecological conditions, with black dorsum in the wettest areas and a pale dorsum in a group of closely related species in dry environments on the Pacific slope. Local sympatry and ecological segregation presumably does not lead to increased divergence in plumage signals or song.

Avifaunal Surveys of the Upper Apurímac River Valley, Ayacucho and Cuzco Departments, Peru: New Distributional Records and Biogeographic, Taxonomic, and Conservation Implications

ABSTRACT The sliver of humid tropical and montane forest on the east slope of the Andes in Ayacucho Department ranks among the least surveyed sectors of the Peruvian Andes. This mountainous region, along with adjacent Apurímac Department and western Cuzco Department, comprise the Apurímac River Valley, a putative biogeographic barrier. Hence, understanding avian distributions in the vicinity of the Apurímac River Valley is fundamental to understanding faunal turnover across it. Here, we report results of recent avifaunal surveys (2008–2012) from five sites in the Apurímac Valley region. We report 35 bird species previously undocumented in Ayacucho, six of which represent range extensions, including records of the endemic Black-spectacled Brush-Finch (Atlapetes melanopsis), Marcapata Spinetail (Cranioleuca marcapatae), and Chestnut-breasted Mountain-Finch (Poospiza caesar); the remaining records filled perceived range gaps. Specimen evidence suggests little phenotypic introgression between differentiated forms across the region, except for apparent introgression zones in Superciliaried Hemispingus (Hemispingus superciliaris) and Mountain Cacique (Cacicus chrysonotus); these observations uphold the idea that the Apurímac River Valley functions to isolate bird populations. Specimens of two Grallaria sp. and one Scytalopus sp. may represent new taxa, two of which appear to be endemic to Ayacucho (the third extends into adjacent Junín Department). More generally, montane forest bird species richness and avian endemism in eastern Ayacucho are similar to those of Cuzco and Pasco departments; previous assessments that considered Ayacucho as an area of reduced diversity were misled by sparse sampling effort.

Genetic Differentiation in Insular Lowland Rainforests: Insights from Historical Demographic Patterns in Philippine Birds

Phylogeographic studies of Philippine birds support that deep genetic structure occurs across continuous lowland forests within islands, despite the lack of obvious contemporary isolation mechanisms. To examine the pattern and tempo of diversification within Philippine island forests, and test if common mechanisms are responsible for observed differentiation, we focused on three co-distributed lowland bird taxa endemic to Greater Luzon and Greater Negros-Panay: Blue-headed Fantail (Rhipidura cyaniceps), White-browed Shama (Copsychus luzoniensis), and Lemon-throated Leaf-Warbler (Phylloscopus cebuensis). Each species has two described subspecies within Greater Luzon, and a single described subspecies on Greater Negros/Panay. Each of the three focal species showed a common geographic pattern of two monophyletic groups in Greater Luzon sister to a third monophyletic group found in Greater Negros-Panay, suggesting that common or similar biogeographic processes may have produced similar distributions. However, studied species displayed variable levels of mitochondrial DNA differentiation between clades, and genetic differentiation within Luzon was not necessarily concordant with described subspecies boundaries. Population genetic parameters for the three species suggested both rapid population growth from small numbers and geographic expansion across Luzon Island. Estimates of the timing of population expansion further supported that these events occurred asynchronously throughout the Pleistocene in the focal species, demanding particular explanations for differentiation, and support that co-distribution may be secondarily congruent.

Nests, Nest Placement, and Eggs of Three Philippine Endemic Birds

Abstract We describe the nest and eggs of two Philippine endemic passerines, the Rusty-faced Babbler (Robsonius rabori) and the Blue-breasted Blue Flycatcher (Cyornis herioti). We also describe a novel type of nest and nest placement for the Short-crested Monarch (Hypothymis helenae), and provide the first description of the eggs of this species. We discuss similarities among eggs and nests of these species with their relatives, and the need for more information regarding natural history and breeding habits for the Philippine avifauna.

Concerted Pleistocene dispersal and genetic differentiation in passerine birds from the Tres Marías Archipelago, Mexico

ABSTRACT Studies in evolutionary biology have commonly been focused on insular systems because of their natural geographic isolation and relatively simpler biotas. Using mitochondrial DNA sequences of 4 passerine bird species distributed in the Tres Marías Archipelago (TMA) and the nearby mainland of western Mexico—Cardinalis cardinalis, Turdus rufopalliatus, Vireo hypochryseus, and Icterus pustulatus—we determined interspecific and intraspecific phylogenetic relationships between insular and mainland populations, conducted insular age-based time calibration for the estimation of divergence times, and used Bayesian analyses to examine the colonization history of islands. Specifically, we tested whether the study species from the TMA share the same colonization history since the emergence of the islands ∼120 kya, taking advantage of the reduced isolation due to sea-level fluctuations during the Pleistocene, or whether there were independent colonization events. We also looked for evidence in the genetic structure of the island populations that would support the idea of colonization by a small number of individuals. Phylogenetic relationships consistently recovered lineage divergence between the TMA and mainland populations, with strong support in 3 of the 4 species. Our estimates for the sea level and coastline of the west coast of Mexico during the Pleistocene showed that the distance between the TMA and the mainland was ∼25 km. We tested several island colonization scenarios according to the phylogenetic relationships, haplotype networks, divergence time estimates, historical demography, and different glaciation dates. The most supported scenario of colonization of the TMA suggests that a single event occurred ∼120 kya when the islands emerged, which is highly concordant with geological evidence, and simultaneously affected the 4 species.

An integrative species delimitation approach reveals fine-scale endemism and substantial unrecognized avian diversity in the Philippine Archipelago

The Philippine archipelago is recognized as a biodiversity hotspot because of its high levels of endemism and numerous threatened species. Avian lineages in the Philippines feature morphologically distinct allopatric taxa, which have been variably treated either as species or subspecies depending on species concepts and recognition criteria. To understand how alternative species limits would alter diversity metrics and patterns of endemism in the Philippines, we selected 19 focal lineages of birds, each containing multiple described taxa within the Mindanao Island Group. We delimited species in an integrative, lineage-based framework using three operational criteria: species must (1) form well-supported, geographically circumscribed clades, (2) be monophyletic with significant genetic differentiation identified by a coalescent model, and (3) feature fixed differences in phenotypic characters. Our criteria identified 40 species from the original 19 focal lineages, a 50–74% increase over recent comprehensive taxonomic treatments. Genetic criteria in isolation identified an additional 10 populations that could be cryptic species in need of further study. We identified fine-scale endemism within the Mindanao Island Group, with multiple unrecognized avian endemics restricted to Samar/Leyte, Bohol Island, and the Zamboanga Peninsula. Genetic and phenotypic information support the hypothesis that polytypic bird species in the Philippines tend to be composed of evolutionarily distinct, range-restricted, allopatric replacements rather than widespread and variable “superspecies”. We conclude that lack of species recognition has resulted in underestimates of species diversity and overlooked fine-scale endemism in the Philippines. Recognizing this diversity would alter conservation priorities, shifting efforts to protect microendemics on smaller islands and finer scale endemic areas within larger islands.