A Trans-Amazonian Screening of mtDNA Reveals Deep Intraspecific Divergence in Forest Birds and Suggests a Vast Underestimation of Species Diversity

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.

The multiple applications of DNA barcodes in avian evolutionary studies

“…There are many different areas of occurrence of these splits and varying levels of intraspecific genetic divergence and geographic patterns among species occupying similar distributional ranges (Kerr et al 2009a;Tavares et al 2011;Milá et al 2012). Many of the highly divergent species are polytypic, with several taxonomically recognized subspecies, but the number and geographic distribution of the genetic lineages discovered in COI are not always congruent with those of the subspecies, suggesting that observable phenotypic differentiation and genetic divergence in neutral markers might occur at different rates.…”

“…This is particularly true for the Neotropics, where these splits occur more often and with more complex geographic patterns compared to the Nearctic and Palearctic (Lijtmaer et al 2011;Tavares et al 2011;Milá et al 2012). The results obtained in those cases that have been analyzed in depth indicate that it is very likely that COI divergence is accompanied by differentiation in other genetic loci and in behavioural and phenotypic traits, making these species a promising research subject for ornithology and evolutionary biology.…”

“…In contrast, continental species are more likely to show similar patterns in their genetic structure, reflecting a common geological history (Newton 2003). Many studies focused on continental species of different realms to study general biogeographic patterns of COI variation as a means to determine the diversifying factors that affected them (Johnsen et al 2010;Lijtmaer et al 2011;Tavares et al 2011;Milá et al 2012;Chaves et al 2015). We review these studies in the next paragraphs.…”

“…In addition, Neotropical species show complex biogeographic patterns with a large range of intraspecific genetic distances in species of the same areas, which could reflect the occurrence of multiple diversifying events at different geological times in this region, multiple dispersal events after a large isolation process, or considerable variation in the rate of evolution among species (Tavares et al 2011). In the lower latitudes of the Neotropics, Milá et al (2012) have studied genetic diversification between eastern and western Amazonian populations of tropical for-est species and also compared these with trans-Andean populations. They found large levels of intraspecific divergence among these geographic areas in most cases.…”

“…In turn, some cases of deep genetic divergence in DNA barcodes within species were further investigated with other molecular and phenotypic markers and were found to be cases of evolutionarily isolated lineages, some of which even deserved species status (Sanin et al 2009;Efe et al 2009;Kerr and Dove 2013;Lavinia et al 2015a;García et al 2016). Moreover, the large geographic coverage of bird DNA barcoding projects allowed researchers to compare the patterns of genetic divergence across different biogeographic regions to study the diversifying factors acting in each of them (Lohman et al 2010;Lijtmaer et al 2011;Tavares et al 2011;Milá et al 2012;Campagna et al 2012b;Nishiumi and Kim 2015). DNA barcodes were also employed to study mechanisms and patterns of mitochondrial gene evolution (Kerr 2010(Kerr , 2011Stoeckle and Kerr 2012;Stoeckle and Thaler 2014;Lavinia et al 2016), among many other applications.…”