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

Borja Milá,M Alex Smith,Jordan Karubian,Allan J Baker,Alberto Muñoz Saldaña,Erika S Tavares,Thomas B Smith

doi:10.1371/journal.pone.0040541

Abstract

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.

Highlights

Species richness in highly diverse and relatively understudied tropical regions is severely underestimated
Three additional species with more restricted ranges were included in the analysis for comparative purposes: two sister species within the flycatcher genus Mionectes (M. oleagineus and M. macconnelli, the former widely distributed in Amazonia and the latter restricted to the Guianan Shield), and Thalurania fannyi, a hummingbird species restricted to the Chocobut closely related to T. furcata, one of the species used in the trans-Amazonian comparison
The magnitude of the divergence was highly variable in different species, yet over 50% of them showed intraspecific lineage distances above 3%, much larger than the 0.23% mean intraspecific divergence found within species in North America and temperate regions of South America (0.24%) (Figs. 2, 3)

Summary

Introduction

Species richness in highly diverse and relatively understudied tropical regions is severely underestimated. A more accurate estimate of tropical diversity requires establishing species limits in numerous taxa for which little information on geographic variation is often available. Robust taxonomic assessment of taxa for establishing species limits requires extensive field sampling across often large geographic ranges and labor-intensive analysis of both molecular and phenotypic datasets. In Amazonian birds, the challenge is daunting, as evidenced by the fact that adequate phylogeographic studies documenting patterns of intraspecific genetic structure are available for about 1% of the more than 1000 species in the region. The use of mitochondrial DNA markers to describe patterns of intraspecific genetic structure and reveal divergent lineages provides a relatively efficient approach to detecting potential new species [2,5,6]. Molecular data are not in themselves sufficient for species designation [7], they provide valuable information on patterns of lineage divergence and gene flow among populations that, when combined with data on phenotypic traits (e.g., plumage coloration, song and behavior) can be instrumental in designating species-level taxa [8,9]

Methods

Results

Conclusion