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.
Citation: Milá B, Tavares ES, Muñoz Saldaña A, Karubian J, Smith TB, Baker AJ (2012) A Trans-Amazonian Screening of mtDNA Reveals Deep Intraspecific Divergence in Forest Birds and Suggests a Vast Underestimation of Species Diversity. PLoS ONE 7(7): e40541. https://doi.org/10.1371/journal.pone.0040541
Editor: M. Alex Smith, University of Guelph, Canada
Received: November 18, 2011; Accepted: June 11, 2012; Published: July 17, 2012
Copyright: © 2012 Milá et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Field work was funded through grants from the Centre National de la Recherche Scientifique (France) to BM, and grants from NSF (National Science Foundation) (IRCEB9977072) and NASA (National Aeronautics and Space Administration) (IDS/03-0169-0347) to TBS. Laboratory work was supported by funding through the Canadian Barcode of Life Network from Genome Canada through the Ontario Genomics Institute, Natural Sciences and Engineering Research Council of Canada (NSERC), and other sponsors (listed on http://www.barcodinglife.org ), and the ROM Governors’ Fund. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Species richness in highly diverse and relatively understudied tropical regions is severely underestimated. Recent molecular systematic studies on tropical taxa have revealed that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent true biological species upon close taxonomic scrutiny –. A more accurate estimate of tropical diversity requires establishing species limits in numerous taxa for which little information on geographic variation is often available. In birds, 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 particularly 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.
Given the magnitude of the task at hand, time- and cost-effective techniques are needed to identify potential taxa and lineages of interest, which can then be subjected to in-depth taxonomic study. 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 , , . Although molecular data are not in themselves sufficient for species designation , 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 , .
Variation in mtDNA coding genes such as cytochrome c oxidase I (COI), has shown reasonably good congruence with species boundaries in birds of North America , , the Palearctic , Argentina , , South America  and the Korean Peninsula , revealing small intraspecific differences (<1% divergence) relative to differences among species. An emerging pattern in these regional assessments of COI variation is one of higher intraspecific divergence and more marked phylogeographic structure in the tropics than in temperate areas, with a number of genetically isolated populations suggesting the existence of species not recognized by current taxonomy . As one of the most diverse areas within the Neotropical region, the Amazon basin has received relatively little attention, although phylogeographic studies conducted to date in a limited number of Amazonian species – indicate that (1) intraspecific genetic distances are often larger than in the temperate zone, (2) lineage phylogeny often does not match current subspecific taxonomy, and (3) some intraspecific lineages are likely to represent new species given congruent levels of genetic and phenotypic divergence. This emerging pattern suggests a potentially serious underestimation of Amazonian avian richness , , and warrants increased research emphasis on intraspecific phylogeography across multiple taxa.
Here we screen patterns of variation in the cytochrome c oxidase I (COI) gene across 42 species of Amazonian forest birds by comparing sequences from individuals within and between two trans-Amazonian areas: the lowlands of eastern Ecuador in western Amazonia, and French Guiana in eastern Amazonia (Fig. 1). For some of the taxa, we also include sequences from the Chocó region of western Ecuador, which is separated from the Amazon basin by the Andes cordillera, to assess the relative contribution of trans-Andean differentiation to intraspecific variation in those species. These three sampling areas correspond to three of the eight main regions of avian endemism in tropical South America , and the large geographic distances involved relative to the species ranges ensure that observed patterns of divergence are likely to be relevant in the context of overall intraspecific variation. The 43 species included in the analysis belong to 6 orders and 17 families, 13 of them within the order Passeriformes (Table 1), and correspond mainly to terra firme lowland tropical forest specialists.
Detailed locality data are provided in Table S1.
Our specific objectives are to (1) describe patterns of trans-Amazonian intraspecific genetic distances for a subset of forest bird species, for most of which no molecular data were previously available; (2) to compare patterns of intraspecific mtDNA divergence with those found in better-studied temperate zone species; (3) to assess whether patterns of intraspecific genetic divergence are generally associated with patterns of plumage color divergence; (4) to identify potentially polyphyletic taxa and divergent intraspecific lineages that may represent potential new species and thus deserve future in-depth taxonomic scrutiny; and (5) to evaluate the prospect of mtDNA gene sequences as markers for avian species discovery in the Neotropics.
Materials and Methods
Birds were captured in the field using mist-nets at various localities in Ecuador (between 1999 and 2004) and French Guiana (between 2007 and 2008) (Fig. 1, Table S1). Each individual captured was identified, photographed, and a blood sample was collected by venipuncture for genetic analysis. Species selected for the study were those whose Amazonian distribution included both Ecuador and French Guiana, and we included trans-Andean samples from western Ecuador when available. Forty species were sampled in both east Ecuador and French Guiana, and twelve of them were also sampled in the west-Ecuadorian Chocó. 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 Chocó but closely related to T. furcata, one of the species used in the trans-Amazonian comparison. In total we obtained sequences from 758 individuals (Table 1, Table S1). We follow Restall et al.  for species taxonomy and nomenclature.
DNA was extracted from blood by membrane purification with 96-well glass fiber filtration plates (Acroprep 96 Filter Plate, 1.0 µm Glass, PALL Corp.) . Cycle conditions were based on previous analyses . A stable segment of ∼910 bp of the cytochrome oxidase I gene was amplified with primers LTyr (TGTAAAAAGGWCTACAGCCTAACGC, Oliver Haddrath, pers. com.), and COI907aH2 (GTRGCNGAYGTRAARTATGCTCG, ). Amplified products were purified by excising bands from the agarose gel and filtering each through a filter tip , then sequenced in both directions using an automated sequencer ABI 3730 (Applied Biosystems), according to the manufacturer’s suggested protocols. The primers used in the sequencing reaction were Ltyr and COI748Ht (TGGGARATAATTCCRAAGCCTGG, ), except for Platyrinchus coronatus, for which COI907aH2 was used as the reverse primer instead.
We aligned sequences using Sequencher 4.1.4 (Gene Codes) and Geneious 5.3.6 (Biomatters), and polymorphisms were checked visually for accuracy. Sequences have been deposited in GenBank, and original trace files are available in the BOLD project “Neotropical Birds” (www.barcodinglife.org). We calculated sequence divergence using a Kimura-two-parameter (K2P) model of sequence evolution and corrected distances across the Amazon (trans-Amazonian) and across the Andes (trans-Andean) for intra-population polymorphism using Arlequin 3.1 . All samples within each of the three main regions (French Guiana, East Ecuador and West Ecuador) were grouped together to estimate intra-population polymorphism. To examine phylogenetic relationships among haplotypes we constructed haplotype networks for each species using the median-joining algorithm in the program Network 4.6.0 (Fluxus Technologies Inc.). Statistical significance of network branches was estimated by 1000 bootstrap replicates on neighbor-joining trees generated for each species in MEGA 5.0 .
We calculated genetic diversity indices and demographic history parameters for Amazonian species with sufficient sample sizes (n ≥6 in both Ecuador and French Guiana). We calculated haplotype and nucleotide diversity indices in DnaSP  and tested for rapid changes in population size indicating past population expansions using Fu’s test of neutrality  and calculated values of Fs in Arlequin 3.1 .
We estimated phenotypic differences among intraspecific lineages by scoring the degree of plumage color divergence in at least one of the sexes, using a four-code key and the following arbitrary criteria: (1) no apparent differences in plumage and no subspecific designations in current taxonomy; (2) slight but diagnosable differences in color shade, intensity or extension, but no difference in the color itself or in color patterning; (3) marked differences in color shade, intensity or extension, but no differences in the color itself or in color patterning; (4) marked divergence in color or patterning. To standardize scoring as much as possible, we restricted the sources of subspecific phenotypic information to the color plates and verbal descriptions in Restall et al.  and our own photographic vouchers. Summary descriptions of phenotypic differences on which scores were based are provided in Table S2 in the Supplementary Materials. To test for an association between genetic distances and phenotypic scores we used a model II simple linear regression with a major axis (MA) regression method as implemented in the lmodel2 package in R 2.10.1 (R Development Core Team).
The plumage divergence scores used here represent a very coarse estimate of differentiation, and were produced with two main objectives in mind: (1) showing overall patterns of genetic-phenotypic association (or lack thereof), and (2) identifying potential candidate lineages for new species designation, with the understanding that detailed phenotypic (including plumage, song, and behavioral data) and molecular analyses will be necessary before final taxonomic decisions are made. We realize that for taxonomic purposes, proper analysis of variation in plumage color should be based on more quantitative measures of color (such as those provided by spectrophotometry) taken on study skins rather than qualitative assessments extracted from color plates, verbal descriptions and subspecific designations in Restall et al. , although the latter are of course the result of extensive examination of study skins. We are also aware of the fact that human perception likely underestimates color differences perceived by the avian eye , , yet because most avian alpha taxonomy has been based on qualitative, subjective assessments of differences in plumage color as perceived by human taxonomists, we feel the method is justified within the confines of the stated objectives.
Patterns of Intraspecific Genetic Divergence
The majority of species used in the trans-Amazonian intraspecific comparisons in our sample (33 of 40, excluding Thalurania fannyi and the interspecific comparison in Mionectes), showed a consistent and clear separation between Ecuadorian and French Guianan haplogroups (Table 1, Fig. 2). Mean divergence in intraspecific COI lineages was 3.45% across the Amazon basin and 3.85% across the Andes, for a total mean value of intraspecific lineage divergence for our sample of 3.56%. 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). Mean intraspecific divergence, which takes into account overall divergence among all sequences and not just the distance among divergent intraspecific lineages, was 2.13%, an order of magnitude larger than that found in temperate regions (Fig. 3). In temperate areas, mean intraspecific divergence below 1% was found in about 94% of species in North America and Argentina , , compared to only 25% of species in our Neotropical sample (Fig. 3). This percentage is also lower than that reported in a study on species from throughout South America (78%, ), although the study included many species from temperate areas and more limited intraspecific sampling.
Blue histograms correspond to total mean distances, calculated as percent K2P divergence corrected for intrapopulation polymorphism (see Table 2). Orange histograms represent values for phenotypic differentiation (plumage color divergence scored between 1 and 4, see Table S2). The red hatched line represents the average percent value for intraspecific lineage divergence for species in this study, and the black hatched line represents intraspecific divergence in temperate species from North America  and temperate and subtropical areas of Argentina .
Green bars: percent mean intraspecific divergence in North American bird species examined by Kerr et al. (2007) ; Blue bars: percent mean intraspecific divergence found in South American species examined by Tavares et al. (2011) ; Red bars: percent mean distance among intraspecific lineages in 40 Neotropical species included in this study; Orange bars: percent mean intraspecific divergence in 40 Neotropical species included in this study. Mean intraspecific divergence is the average K2P distance among all sequences within a species, whereas mean distance among intraspecific lineages is the mean distance among divergent haplogroups across the Amazon and across the Andes (see Table 1). Thalurania fannyi, Mionectes oleagineus and M. macconnelli not included.
Within the main group of 33 species showing clear divergence across Amazonia, some also showed complex patterns of lineage divergence (Fig. 4). Indeed, some lineages were almost as divergent within eastern Ecuador and French Guiana as between the two areas across Amazonia (Thalurania furcata, Glyphorynchus spirurus, Hypocnemis cantator, Dixiphia pipra, Schiffornis turdina, and Lanio fulvus). In contrast, 5 species (Geotrygon montana, Chloroceryle aenea, Myrmotherula axillaris, Hylophylax naevius and Cyanocompsa cyanoides) showed limited divergence among haplotypes within both regions (<1%). Only 3 species (Pithys albifrons, Pipra erythrocephala and Turdus albicollis) showed no divergence across Amazonia and shared at least one haplotype among localities, although one of them (Pithys albifrons) showed marked differences in haplotype frequencies (Fig. 4).
Circles represent individual COI haplotypes, their size is proportional to their frequency in the sample, and colors correspond to those used in Fig. 1. Branches among haplotypes correspond to one nucleotide change and hatch marks represent additional changes. Figures next to black squares along branches indicate the number of nucleotide changes when greater than 3. Asterisks indicate node support from a bootstrap analysis (1000 replicates) on a neighbor-joining tree (*: 90–96%, **: 97–100%). Species appear in phylogenetic order (see Fig. 2).
The 12 species for which we had west-Ecuadorian Chocó samples in addition to Amazonian samples allowed us to obtain a better measure of intraspecific divergence and compare the relative magnitude of intraspecific distances across the Andes and across Amazonia. Five of the 12 species showed greater divergence across the Andes than across the Amazon (Trogon rufus, Sclerurus mexicanus, Platyrinchus coronatus, Pipra erythrocephala and Cyanocompsa cyanoides), 3 showed greater divergence across the Amazon than across the Andes (Automolus ochrolaemus, Dendrocincla fuliginosa, and Schiffornis turdina), and 4 of them showed approximately equal distance between the three haplogroups (Geotrygon montana, Glyphorynchus spirurus, Myrmotherula axillaris, and Xenops minutus) (Table 1, Fig. 4). In the hummingbird genus Thalurania, the distance between the trans-Andean species Thalurania fannyi and the east-Ecuadorian haplogroup of T. furcata was actually smaller than the distance between trans-Amazonian populations of T. furcata, making the latter paraphyletic.
Genetic Diversity and Demographic History
For a subset of species with sufficient sample sizes (n ≥6 in both Amazonian regions), we calculated indices of genetic diversity and values of Fs to test for past events of rapid population growth. As with intraspecific genetic distances, patterns of genetic diversity and demographic change revealed high heterogeneity across species (Table 2), suggesting diverse demographic and evolutionary histories. Nucleotide diversity ranged from 0 in Platyrinchus coronatus to 0.266 in Dixiphia pipra, with higher values reflecting the presence of divergent intraspecific lineages within a population, and inter-population comparisons reaching differences above an order of magnitude in three species (Pithys albifrons, Dixiphia pipra and Platyrinchus coronatus). Haplotypic diversity was generally similar in trans-Amazonian comparisons, with marked differences detected only in Pithys albifrons and Platyrinchus coronatus. Fs values revealed marked differences in demographic history between trans-Amazonian populations of several species, with some showing evidence of past expansions only in western Amazonia (Thalurania, Myrmotherula axillaris, Hyllophylax poecilinotus and H. naevius) and some only in eastern Amazonia (Glyphorynchus, Thamnomanes, Pithys, Dixiphia, Mionectes macconnelli and Turdus). When both populations were combined, Turdus albicollis showed a significant signature of population growth (Fs = −5.350, P = 0.003), suggesting a recent Amazon-wide population expansion.
Congruence between Genetic and Plumage Divergence
A cursory analysis of differentiation across Amazonia in overall plumage coloration revealed a wide range of patterns, with 6 species showing no apparent differences (value of 1), 11 species showing slight differences in shade or intensity (value of 2), 8 species showing marked differences in shade or intensity (value of 3), and 16 species showing marked differences in color and patterning (value of 4) (Table S2). The relationship between overall plumage divergence and genetic distance among trans-Amazonian haplogroups did not reveal a consistent pattern (Fig. 2) and the correlation between the two variables was not significant (r2 = 0.0083, n = 39, P = 0.290). Moreover, species with a phenotypic divergence value of 1 included both highly genetically divergent and closely related haplogroups (Myiobius barbatus and Geotrygon montana, respectively). The same was true for species with a plumage divergence value of 4, with species like Hylophilus ochraceiceps or Cyphorhinus arada showing high genetic divergence, yet some like Pithys albifrons showing very low divergence (Fig. 2).
Intraspecific Divergence in Amazonian Birds
Our study reveals consistently large values of intraspecific divergence across the northern Amazon in 40 species of forest understory birds. The presence of clear genetic separation between trans-Amazonian samples in 33 out of 40 species studied suggests that this pattern might be widespread among Amazonian forest understory birds. The mean value of trans-Amazonian intraspecific lineage divergence in the COI gene was 3.45%, and including trans-Andean comparisons the total mean value of intraspecific lineage divergence for our sample was 3.56%. These values are about 15 times higher than those found for temperate areas of the world such as North America (0.23%)  and Korea (0.26%) , as well as temperate and sub-tropical areas of South America like Argentina (0.24%) , . Our mean values of intraspecific lineage divergence are also higher than those found in a study of 561 species across South America , where over 75% of species had values of intraspecific divergence below 1%, although both temperate and tropical species were included in that study. Our results are instead consistent with the relatively few thorough species-specific phylogeographic studies conducted to date in Amazonian species, including Pyrrhura picta-leucotis (cyt b: 1.1–5.6%, 1.1–2.2% within picta group , Glyphorynchus spirurus (cyt b + ND2&3: 1.3–7.5%, ), Xiphorhynchus elegans (cyt b:1.6–1.9% , Dendrocincla fuliginosa-merula (cyt b: 0.5–6.8%, ND2: 0.11–9.0%, COI: 0.17–6.5% ), Lepidothrix coronata (cyt b + ND2&3: 1.5–4.3%, ), Schiffornis turdina (cyt b + COI + ND2: 0.8–9.6%, ), or Phaeotlypis fulvicauda-rivularis (cyt b + COI&II + ND2+ ATPase 6&8: 4.6–6.1%, ). Our results suggest that tropical intraspecific distances are larger than those found in other latitudes. Although previous surveys of COI variation in temperate areas included limited within-species sampling and thus might have underestimated intraspecific divergence, most thorough phylogeographic studies of temperate species are consistent with low levels of genetic structure and divergence –.
A critical question with important implications for taxonomy, evolutionary biology, and conservation, is whether intraspecific genetic distances in the Neotropics are indeed larger than in the temperate zone, or whether this pattern is instead an artifact of incorrect species limits that underestimate species richness. Recent studies suggest that rates of phenotypic evolution of plumage coloration and song characteristics, both typically involved in avian reproductive isolation, are slower in tropical areas than in the temperate zone , , which is consistent with studies suggesting that speciation rates are faster in the latter than in the former , . Thus slower rates of reproductive isolation towards the equator would predict the existence of relatively divergent lineages that have not necessarily speciated. However, it is widely accepted that a high proportion of tropical bird species remains undescribed relative to the temperate zone, and this taxonomic bias is likely to have a strong influence on our understanding of the processes underlying the latitudinal gradient in species richness, so the issue remains a matter of debate –.
As phylogeographic and alpha taxonomic research progresses, it will become apparent whether patterns of both intra and inter-specific genetic distances are similar across temperate and tropical latitudes. Despite our limited sampling, mean divergence among taxonomic families in this study was 13%, very similar to the 12% found in a North American birds  and the 13% found for a worldwide sample . Whether this apparent uniformity at the family level also applies to the species level will require further research. Those cases in which molecular and phenotypic data have been used to revise species limits in previously polytypic tropical species, intraspecific distances have dropped to temperate zone values. For example, when Schistocichla (Percnostola) leucostigma was divided into S. leucostigma and S. saturata, intraspecific distance was reduced from 9% to less than 1% (ATPase 6+ND2+ND3, Braun et al. ), and the taxonomic split of Capito niger into four species reduced mean intraspecific divergence from 6% to again less than 1% (cyt b+ COI, Armenta et al. ).
The consistent pattern of trans-Amazonian divergence in most species we examined suggests both a pattern of long-term co-distribution and a shared response to past environmental events, both central dictums of comparative phylogeography . Identifying the factors driving trans-Amazonian divergence will require additional sampling across the region to determine the degree to which the geographic distribution of haplogroups shows discrete discontinuities at contact zones associated with known geographic barriers (such as prominent tributaries of the Amazon river, like the Negro or Branco rivers), or whether divergence is the product of clinal variation across geographic distance . Investigating these patterns through range-wide phylogeographic studies, preferably involving the collection of voucher specimens, will be essential to shed light on both evolutionary process and the resulting patterns of species richness.
Divergent Lineages and Species Discovery
Our screening of mtDNA variation revealed the presence of divergent lineages both across and sometimes within trans-Amazonian sampling areas. Marked patterns of both genetic and phenotypic intraspecific divergence in some taxa suggest that subspecific lineages are likely to represent new species not recognized by current taxonomic treatments. This is well illustrated by taxa like Cyphorhinus arada, Microcerculus bambla, and Hylophilus ochraceiceps, all showing congruent divergence in mtDNA and phenotype (Fig. 2 and 1). In taxa with continuous distributions across the region, establishing species limits that are consistent with this variation will require thorough geographic sampling to determine patterns of gene flow and introgression at contact zones among forms (e.g., Cyphorhinus and Hylophilus). In contrast, species delimitation should be easier in cases like Microcerculus bambla, where the geographic range of the differentiated lineages is markedly allopatric .
Limitations and Caveats of Our mtDNA Screening Approach
Our screening of intraspecific divergence is based largely on two main localities, which is unlikely to be representative of true intraspecific variation in many of the species targeted. As shown by the subset of species with trans-Andean samples, which considerably increased mean values of intraspecific divergence, our assessment is likely conservative. Previous studies have shown that other major geographic barriers in the region such as the Amazon river and many of its tributaries, or the Cerrado biome separating the coastal Atlantic forest of Brazil from the main Amazonian forest mass, can also account for marked genetic divergence within species of understory birds , .
Sampling for this study was carried out using mist nets located on the floor of terra firme rainforest, and the sampling is thus biased towards understory specialists. Speciose groups such as canopy specialists and species restricted to seasonally flooded habitats with potentially higher dispersal capacity have shown different biogeographic patterns and lower intraspecific divergence than understory species , . For example, genetic studies conducted on species associated with rivers and seasonally flooded forests such as Xiphorhynchus kienerii and X. obsoletus  and Chrysomus icterocephalus  have revealed very low levels of sequence divergence and widespread haplotype sharing, likely due to higher rates of gene flow along waterways.
Because of their overwhelming predominance in the rainforest understory, our sample is also biased towards passerines, and our conclusions may not apply to other avian orders. However, our data suggest that most of the variance in genetic divergence and diversity is observed within species and between closely related species rather than between higher taxonomic levels (genera, families or orders). In fact, variation in intraspecific divergence can be high even among closely related congeners, as demonstrated by the three species of Myrmotherula antwrens included in the study. Divergence within M. axillaris was minimal both across the Amazon (0.43% between east Ecuador and French Guiana) and across the Andes (0.53% between east and west Ecuador), in sharp contrast to a 5% trans-Amazonian divergence in M. longipennis and an intermediate 1.5% in M. menetriesii. This range of intra-genus divergence values has also been shown within non-passerine genera , .
Finally, the use of a single mtDNA coding gene to detect divergent lineages has important limitations. Due to the relatively slow mutation rate of mtDNA coding regions, recently diverged species may show incomplete lineage sorting in mtDNA , , and cases of mtDNA introgression through past hybridization may conceal true levels of evolutionary divergence , . Mitochondrial markers will continue to be useful for recovering inter- and intraspecific phylogenies and detecting divergent lineages , yet more variable markers including biparentally inherited loci will often be necessary to fully reveal Neotropical genetic structure, and thus estimates from a single mtDNA coding gene likely constitute a conservative estimate.
Implications for DNA Barcoding in Neotropical Birds
The universality of COI as a barcode for bird identification, with its many practical applications , , remains promising even in tropical areas. The utility of this gene to identify a good proportion of tropical bird species has been previously demonstrated –, and today its universality seems to be mostly limited by incorrect species limits in many groups. The diversity and complexity of phylogeographic patterns found to date indicate that most currently recognized Amazonian species contain markedly divergent phylogroups that may represent new, separate species. As in-depth phylogeographic studies of Neotropical species contribute to the establishment of proper species limits and reveal general patterns of intraspecific divergence, we will be able to assess whether the high across-species variance in intraspecific distances is a true characteristic of Neotropical taxa, or instead is an artifact of uneven taxonomic coverage. Specifically, it will become apparent whether patterns of variation converge towards those found in temperate regions, or whether intraspecific lineages in the Neotropics are indeed older and therefore more structured. To the extent that COI variation reveals marked structure within current species, sequences from COI and other mtDNA genes will be useful in species identification (as DNA barcodes) even if current intraspecific clades are raised to the level of taxonomic species in the future.
The Need for a Phylogeographic Approach to Species Discovery
The use of mtDNA markers has already been instrumental in taxonomic revisions of several Neotropical avian groups , , –, and molecular work produced in just the last decade has had a major impact on taxonomy. However, most studies to date have focused on interspecific phylogenies based on incomplete or limited subspecific sampling that has often prevented definitive resolution of species limits. Phylogeographic studies that survey genetic variation across entire geographic ranges encompassing known patterns of phenotypic variation are still rare, yet are essential to properly describe species limits and richness.
Because plumage color is almost always under natural and/or sexual selection, numerous cases of rapid plumage divergence , , plumage convergence in divergent taxa , and cryptic speciation ,  have been reported that can lead to taxonomic classifications that do not reflect the evolutionary history of taxa . Therefore, combining data from neutrally evolving molecular markers with phenotypic traits is essential for establishing taxonomic species limits that are biologically meaningful ,  and truly contribute to taxonomic progress .
The establishment of proper species limits in many taxa will not only better reflect patterns of diversity in the Amazon relative to other tropical regions and the temperate zone, but should also significantly improve attempts at understanding patterns of endemism , the evolution of range size , diversification hypotheses –, speciation rates , , species distribution models  and conservation strategies –.
Specimens sampled per species and per locality. Species are listed in alphabetical order.
John McCormack, Jason Weir and anonymous reviewers provided useful comments on previous versions of the manuscript. Enrique Arbeláez-Cortés provided the map for Fig. 1. For help with field sampling in Ecuador we thank Gabriela Castañeda, Jaime Chaves, Juan Fernando Freile, Tatiana Santander, Brandt T. Ryder, Daniela Gross, Juan Diego Ortiz, Orfa Rodríguez, María Fernanda Salazar, Suzanne Tomassi, John McCormack, Brenda Larison, Luis Carrasco, and Marcelo Tobar. For field sampling in French Guiana we thank CNRS Guyane, Philippe Gaucher, Christophe Thébaud, Iván de la Hera, and Gonzalo Milá. We also thank Alberto Castillo Solís and Nicole Leung for help with sample processing in the laboratory.
Conceived and designed the experiments: BM. Performed the experiments: BM EST AMS. Analyzed the data: BM EST AMS. Contributed reagents/materials/analysis tools: BM JK TBS AJB. Wrote the paper: BM. Provided comments on the manuscript: all authors.
- 1. Vieites DR, Wollenberg KC, Andreone F, Köhler J, Glaw F, et al. (2009) Vast underestimation of Madagascar’s biodiversity evidenced by an integrative amphibian inventory. Proceedings of the National Academy of Sciences 106: 8267–8272.DR VieitesKC WollenbergF. AndreoneJ. KöhlerF. Glaw2009Vast underestimation of Madagascar’s biodiversity evidenced by an integrative amphibian inventory.Proceedings of the National Academy of Sciences10682678272
- 2. Bradley RD, Baker RJ (2001) A test of the genetic species concept: cytochrome-b sequences and mammals Journal of Mammalogy 82: 960–973.RD BradleyRJ Baker2001A test of the genetic species concept: cytochrome-b sequences and mammals Journal of Mammalogy82960973
- 3. Monaghan MT, Balke M, Gregory TR, Vogler AP (2005) DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1925–1933.MT MonaghanM. BalkeTR GregoryAP Vogler2005DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers.Philosophical Transactions of the Royal Society B: Biological Sciences36019251933
- 4. Isler ML, Isler PR, Whitney BM (2007) Species limits in antbirds (Thamnophilidae): the warbling antbird (Hypocnemis cantator) complex. Auk 124: 11–28.ML IslerPR IslerBM Whitney2007Species limits in antbirds (Thamnophilidae): the warbling antbird (Hypocnemis cantator) complex.Auk1241128
- 5. Dincă V, Zakharov EV, Hebert PDN, Vila R (2011) Complete DNA barcode reference library for a country’s butterfly fauna reveals high performance for temperate Europe. Proceedings of the Royal Society B: Biological Sciences 278: 347–355.V. DincăEV ZakharovPDN HebertR. Vila2011Complete DNA barcode reference library for a country’s butterfly fauna reveals high performance for temperate Europe.Proceedings of the Royal Society B: Biological Sciences278347355
- 6. Clare EL, Kim BK, Fenton MB, Hebert PDN (2011) Neotropical bats: estimating species diversity with DNA barcodes. PLOS One 6: e22648.EL ClareBK KimMB FentonPDN Hebert2011Neotropical bats: estimating species diversity with DNA barcodes.PLOS One6e22648
- 7. Moritz C, Cicero C (2004) DNA barcoding: promise and pitfalls. PLoS Biol 2: e354.C. MoritzC. Cicero2004DNA barcoding: promise and pitfalls.PLoS Biol2e354
- 8. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in Genetics 23: 167–172.M. HajibabaeiGAC SingerPDN HebertDA Hickey2007DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics.Trends in Genetics23167172
- 9. Janzen DH, Hajibabaei M, Burns JM, Hallwachs W, Remigio E, et al. (2005) Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1835–1845.DH JanzenM. HajibabaeiJM BurnsW. HallwachsE. Remigio2005Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding.Philosophical Transactions of the Royal Society B: Biological Sciences36018351845
- 10. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biology 2: 1657–1663.PDN HebertMY StoeckleTS ZemlakCM Francis2004Identification of birds through DNA barcodes.PLoS Biology216571663
- 11. Kerr KCR, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, et al. (2007) Comprehensive DNA barcode coverage of North American birds. Molecular Ecology Notes 7: 535–543.KCR KerrMY StoeckleCJ DoveLA WeigtCM Francis2007Comprehensive DNA barcode coverage of North American birds.Molecular Ecology Notes7535543
- 12. Kerr K, Birks S, Kalyakin M, Red’kin Y, Koblik E, et al. (2009) Filling the gap - COI barcode resolution in eastern Palearctic birds. Frontiers in Zoology 6: 29.K. KerrS. BirksM. KalyakinY. Red’kinE. Koblik2009Filling the gap - COI barcode resolution in eastern Palearctic birds.Frontiers in Zoology629
- 13. Lijtmaer DA, Kerr KCR, Barreira AS, Hebert PDN, Tubaro PL (2011) DNA barcode libraries provide insight into continental patterns of avian diversification. PLoS One 6: e20744.DA LijtmaerKCR KerrAS BarreiraPDN HebertPL Tubaro2011DNA barcode libraries provide insight into continental patterns of avian diversification.PLoS One6e20744
- 14. Kerr KCR, Lijtmaer DA, Barreira AS, Hebert PDN, Tubaro PL (2009) Probing evolutionary patterns in Neotropical birds through DNA barcodes. PLoS One 4: e4379.KCR KerrDA LijtmaerAS BarreiraPDN HebertPL Tubaro2009Probing evolutionary patterns in Neotropical birds through DNA barcodes.PLoS One4e4379
- 15. Tavares ES, Gonçalves P, Miyaki CY, Baker AJ (2011) DNA barcode detects high genetic structure within Neotropical bird species. PLoS One 6: e28543.ES TavaresP. GonçalvesCY MiyakiAJ Baker2011DNA barcode detects high genetic structure within Neotropical bird species.PLoS One6e28543
- 16. Yoo HS, Eah J-Y, Kim JS, Kim Y-J, Min M-S, et al. (2006) DNA barcoding Korean birds. Molecules and Cells 22: 323–327.HS YooJ-Y EahJS KimY-J KimM-S Min2006DNA barcoding Korean birds.Molecules and Cells22323327
- 17. Aleixo A (2004) Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification. Evolution 58: 1303–1317.A. Aleixo2004Historical diversification of a terra-firme forest bird superspecies: a phylogeographic perspective on the role of different hypotheses of Amazonian diversification.Evolution5813031317
- 18. Cheviron ZA, Hackett SJ, Capparella AP (2005) Complex evolutionary history of a Neotropical lowland forest bird (Lepidothrix coronata) and its implications for historical hypotheses of the origin of Neotropical avian diversity. Molecular Phylogenetics and Evolution 36: 338–357.ZA ChevironSJ HackettAP Capparella2005Complex evolutionary history of a Neotropical lowland forest bird (Lepidothrix coronata) and its implications for historical hypotheses of the origin of Neotropical avian diversity.Molecular Phylogenetics and Evolution36338357
- 19. Marks BD, Hackett SJ, Capparella AP (2002) Historical relationships among Neotropical lowland forest areas of endemism as determined by mitochondrial DNA sequence variation within the Wedge-billed Woodcreeper (Aves: Dendrocolaptidae: Glyphorynchus spirurus). Molecular Phylogenetics and Evolution 24: 153–167.BD MarksSJ HackettAP Capparella2002Historical relationships among Neotropical lowland forest areas of endemism as determined by mitochondrial DNA sequence variation within the Wedge-billed Woodcreeper (Aves: Dendrocolaptidae: Glyphorynchus spirurus).Molecular Phylogenetics and Evolution24153167
- 20. Nyári AS (2007) Phylogeographic patterns, molecular and vocal differentiation, and species limits in Schiffornis turdina (Aves). Molecular Phylogenetics and Evolution 44: 154–164.AS Nyári2007Phylogeographic patterns, molecular and vocal differentiation, and species limits in Schiffornis turdina (Aves).Molecular Phylogenetics and Evolution44154164
- 21. Ribas CC, Joseph L, Miyaki CY, Johnson KP (2006) Molecular systematics and patterns of diversification in Pyrrhura (Psittacidae), with special reference to the picta-leucotis complex. The Auk 123: 660–680.CC RibasL. JosephCY MiyakiKP Johnson2006Molecular systematics and patterns of diversification in Pyrrhura (Psittacidae), with special reference to the picta-leucotis complex.The Auk123660680
- 22. Miller MJ, Bermingham E, Klicka J, Escalante P, Raposo do Amaral FS, et al. (2008) Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher. Proceedings of the Royal Society B: Biological Sciences 275: 1133–1142.MJ MillerE. BerminghamJ. KlickaP. EscalanteFS Raposo do Amaral2008Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher.Proceedings of the Royal Society B: Biological Sciences27511331142
- 23. Weir JT, Price M (2011) Andean uplift promotes lowland speciation through vicariance and dispersal in Dendrocincla woodcreepers. Molecular Ecology 20: 4550–4563.JT WeirM. Price2011Andean uplift promotes lowland speciation through vicariance and dispersal in Dendrocincla woodcreepers.Molecular Ecology2045504563
- 24. Bates JM, Hackett SJ, Goerck JM (1999) High levels of mitochondrial DNA differentiation in two lineages of antbirds (Drymophila and Hypocnemis). Auk 116: 1093–1106.JM BatesSJ HackettJM Goerck1999High levels of mitochondrial DNA differentiation in two lineages of antbirds (Drymophila and Hypocnemis).Auk11610931106
- 25. Navarro-Sigüenza A, Peterson AT (2004) An alternative species taxonomy of the birds of Mexico. Biota Neotropica 4: 1–32.A. Navarro-SigüenzaAT Peterson2004An alternative species taxonomy of the birds of Mexico.Biota Neotropica4132
- 26. Cracraft J (1985) Historical biogeography and patterns of differentiation within the South American areas of endemism. Ornithological Monographs 36: 49–84.J. Cracraft1985Historical biogeography and patterns of differentiation within the South American areas of endemism.Ornithological Monographs364984
- 27. Restall R, Rodner C, Lentino M (2006) Birds of Northern South America: An Identification Guide. New Haven: Yale University Press. R. RestallC. RodnerM. Lentino2006Birds of Northern South America: An Identification Guide.New Haven: Yale University Press
- 28. Ivanova NV, DeWaard JR, Hebert PDN (2006) An inexpensive, automation friendly protocol for recovering high quality DNA. Molecular Ecology Notes 6: 998–1002.NV IvanovaJR DeWaardPDN Hebert2006An inexpensive, automation friendly protocol for recovering high quality DNA.Molecular Ecology Notes69981002
- 29. Tavares ES, Baker AJ (2008) Single mitochondrial gene barcodes reliably indentify sister-species in diverse clades of birds. BMC Evolutionary Biology 8: 81.ES TavaresAJ Baker2008Single mitochondrial gene barcodes reliably indentify sister-species in diverse clades of birds.BMC Evolutionary Biology881
- 30. Dean AD, Greenwald JE (1995) Use of filtered pipet tips to elute DNA from agarose gels. Biotechniques 18: 980.AD DeanJE Greenwald1995Use of filtered pipet tips to elute DNA from agarose gels.Biotechniques18980
- 31. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47–50.L. ExcoffierG. LavalS. Schneider2005Arlequin ver. 3.0: An integrated software package for population genetics data analysis.Evolutionary Bioinformatics Online14750
- 32. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731–2739.K. TamuraD. PetersonN. PetersonG. StecherM. Nei2011MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.Molecular Biology and Evolution2827312739
- 33. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496–2497.J. RozasJC Sanchez-DelBarrioX. MesseguerR. Rozas2003DnaSP, DNA polymorphism analyses by the coalescent and other methods.Bioinformatics1924962497
- 34. Fu YX (1997) Statistical neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915–925.YX Fu1997Statistical neutrality of mutations against population growth, hitchhiking and background selection.Genetics147915925
- 35. Bleiweiss R (2004) Ultraviolet plumage reflectance distinguishes sibling bird species. Proceedings of the National Academy of Sciences 101: 16561–16564.R. Bleiweiss2004Ultraviolet plumage reflectance distinguishes sibling bird species.Proceedings of the National Academy of Sciences1011656116564
- 36. Eaton MD (2005) Human vision fails to distinguish widespread sexual dichromatism among sexually “monochromatic” birds. Proceedings of the National Academy of Sciences 102: 10942–10946.MD Eaton2005Human vision fails to distinguish widespread sexual dichromatism among sexually “monochromatic” birds.Proceedings of the National Academy of Sciences1021094210946
- 37. Lovette IJ (2004) Molecular phylogeny and plumage signal evolution in a trans Andean and circum Amazonian avian species complex. Molecular Phylogenetics and Evolution 32: 512–523.IJ Lovette2004Molecular phylogeny and plumage signal evolution in a trans Andean and circum Amazonian avian species complex.Molecular Phylogenetics and Evolution32512523
- 38. Merilä J, Bjorklund M, Baker A (1997) Historical demography and present day population structure of the greenfinch, Carduelis chloris - an analysis of mtDNA control-region sequences. Evolution 51: 946–956.J. MeriläM. BjorklundA. Baker1997Historical demography and present day population structure of the greenfinch, Carduelis chloris - an analysis of mtDNA control-region sequences.Evolution51946956
- 39. Milá B, McCormack JE, Castañeda G, Wayne RK, Smith TB (2007) Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco. Proceedings of the Royal Society B 274: 2653–2660.B. MiláJE McCormackG. CastañedaRK WayneTB Smith2007Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco.Proceedings of the Royal Society B27426532660
- 40. Pérez-Tris J, Bensch S, Carbonell R, Helbig AJ, Tellería JL (2004) Historical diversification of migration patterns in a passerine bird. Evolution 58: 1819–1832.J. Pérez-TrisS. BenschR. CarbonellAJ HelbigJL Tellería2004Historical diversification of migration patterns in a passerine bird.Evolution5818191832
- 41. Seutin G, Ratcliffe LM, Boag PT (1995) Mitochondrial DNA homogeneity in the phenotypically diverse redpoll finch complex (Aves: Carduelinae: Carduelis flammea-hornemanni). Evolution 49: 962–973.G. SeutinLM RatcliffePT Boag1995Mitochondrial DNA homogeneity in the phenotypically diverse redpoll finch complex (Aves: Carduelinae: Carduelis flammea-hornemanni).Evolution49962973
- 42. Zink RM (1997) Phylogeographic studies of North American birds. Avian Molecular Evolution and Systematics: Academic Press. pp. 301–324.RM Zink1997Phylogeographic studies of North American birds.Avian Molecular Evolution and Systematics: Academic Press301324
- 43. Zink RM, Dittman DL (1993) Gene flow, refugia, and evolution of geographic variation in the song sparrow (Melospiza melodia). Evolution 47: 717–729.RM ZinkDL Dittman1993Gene flow, refugia, and evolution of geographic variation in the song sparrow (Melospiza melodia).Evolution47717729
- 44. Pavlova A, Zink RM, Drovetski SV, Red’kin Y, Rohwer S (2003) Phylogeographic patterns in Motacilla flava and Motacilla citreola: species limits and population history. Auk 123: 744–758.A. PavlovaRM ZinkSV DrovetskiY. Red’kinS. Rohwer2003Phylogeographic patterns in Motacilla flava and Motacilla citreola: species limits and population history.Auk123744758
- 45. Buerkle CA (1999) The historical pattern of gene flow among migratory and nonmigratory populations of prairie warblers (Aves: Parulinae). Evolution 53: 1915–1924.CA Buerkle1999The historical pattern of gene flow among migratory and nonmigratory populations of prairie warblers (Aves: Parulinae).Evolution5319151924
- 46. Kimura M, Clegg SM, Lovette IJ, R HK, Girman DJ, et al. (2002) Phylogeographical approaches to assessing demographic connectivity between breeding and overwintering regions in a Nearctic-Neotropical warbler (Wilsonia pusilla). Molecular Ecology 11: 1605–1616.M. KimuraSM CleggIJ LovetteHK RDJ Girman2002Phylogeographical approaches to assessing demographic connectivity between breeding and overwintering regions in a Nearctic-Neotropical warbler (Wilsonia pusilla).Molecular Ecology1116051616
- 47. Milá B, Girman DJ, Kimura M, Smith TB (2000) Genetic evidence for the effect of a postglacial population expansion on the phylogeography of a North American songbird. Proceedings of the Royal Society Biological Sciences Series B 267: 1033–1040.B. MiláDJ GirmanM. KimuraTB Smith2000Genetic evidence for the effect of a postglacial population expansion on the phylogeography of a North American songbird.Proceedings of the Royal Society Biological Sciences Series B26710331040
- 48. Milá B, Smith TB, Wayne RK (2006) Postglacial population expansion drives the evolution of long-distance migration in a songbird. Evolution 60: 2403–2409.B. MiláTB SmithRK Wayne2006Postglacial population expansion drives the evolution of long-distance migration in a songbird.Evolution6024032409
- 49. Martin PR, Montgomerie R, Loughheed SC (2009) Rapid sympatry explains greater color pattern divergence in high latitude birds. Evolution 64: 336–347.PR MartinR. MontgomerieSC Loughheed2009Rapid sympatry explains greater color pattern divergence in high latitude birds.Evolution64336347
- 50. Weir JT, Wheatcroft D (2011) A latitudinal gradient in rates of evolution of avian syllable diversity and song length. Proceedings of the Royal Society B 278: 1713–1720.JT WeirD. Wheatcroft2011A latitudinal gradient in rates of evolution of avian syllable diversity and song length.Proceedings of the Royal Society B27817131720
- 51. Weir JT, Price T (2011) Limits to speciation inferred from times to secondary sympatry and ages of hybridizing species along a latitudinal gradient. American Naturalist 177: 462–469.JT WeirT. Price2011Limits to speciation inferred from times to secondary sympatry and ages of hybridizing species along a latitudinal gradient.American Naturalist177462469
- 52. Weir JT, Schluter D (2007) The latitudinal gradient in recent speciation and extinction rates of birds and mammals. Science 315: 1574–1576.JT WeirD. Schluter2007The latitudinal gradient in recent speciation and extinction rates of birds and mammals.Science31515741576
- 53. Tobias JA, Bates JM, Hackett SJ, Seddon N (2008) Comment on “The latitudinal gradient in recent speciation and extinction rates of birds and mammals” Science 319: 901c.JA TobiasJM BatesSJ HackettN. Seddon2008Comment on “The latitudinal gradient in recent speciation and extinction rates of birds and mammals”Science319901c
- 54. Cardillo M, Orme CD, Owens IPF (2005) Testing for latitudinal bias in diversification rates: an example using New World birds. Ecology 86: 2278–2287.M. CardilloCD OrmeIPF Owens2005Testing for latitudinal bias in diversification rates: an example using New World birds.Ecology8622782287
- 55. Ricklefs RE (2006) Global variation in the diversification rate of passerine birds. Ecology 87: 2468–2478.RE Ricklefs2006Global variation in the diversification rate of passerine birds.Ecology8724682478
- 56. Johns GC, Avise JC (1998) A comparative summary of genetic distances in the vertebrates from the Mitochondrial cytochrome b gene. Mol Biol Evol 15: 1481–1490.GC JohnsJC Avise1998A comparative summary of genetic distances in the vertebrates from the Mitochondrial cytochrome b gene.Mol Biol Evol1514811490
- 57. Braun MJ, Isler ML, Isler PR, Bates JM, Robbins MB (2005) Avian speciation in the Pantepui: the case of the Roraiman antbird (Percnostola [Schistocichla] “leucostigma” saturata). Condor 107: 327–341.MJ BraunML IslerPR IslerJM BatesMB Robbins2005Avian speciation in the Pantepui: the case of the Roraiman antbird (Percnostola [Schistocichla] “leucostigma” saturata).Condor107327341
- 58. Armenta JK, Weckstein JD, Lane DF (2005) Geographic variation in mitochondrial DNA sequences of an Amazonian nonpasserine: the black-spotted barbet complex. Condor 107: 527–536.JK ArmentaJD WecksteinDF Lane2005Geographic variation in mitochondrial DNA sequences of an Amazonian nonpasserine: the black-spotted barbet complex.Condor107527536
- 59. Zink RM (1996) Comparative phylogeography in North American birds. Evolution 50: 308–317.RM Zink1996Comparative phylogeography in North American birds.Evolution50308317
- 60. Brumfield RT (2005) Mitochondrial variation in Bolivian populations of the Variable Antshrike (Thamnophilus caerulescens). Auk 122: 414–432.RT Brumfield2005Mitochondrial variation in Bolivian populations of the Variable Antshrike (Thamnophilus caerulescens).Auk122414432
- 61. Cabanne GS, D’Horta FM, Meyer D, SIlva JMC, Miyaki CY (2011) Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic forest. Biological Journal of the Linnean Society 103: 801–820.GS CabanneFM D’HortaD. MeyerJMC SIlvaCY Miyaki2011Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic forest.Biological Journal of the Linnean Society103801820
- 62. Cracraft J, Prum RO (1988) Patterns and processes of diversification: speciation and historical congruence in some neotropical birds. Evolution 42: 603–620.J. CracraftRO Prum1988Patterns and processes of diversification: speciation and historical congruence in some neotropical birds.Evolution42603620
- 63. Burney CW, Brumfield RT (2009) Ecology predicts levels of genetic differentiation in Neotropical birds. American Naturalist 174: 358–368.CW BurneyRT Brumfield2009Ecology predicts levels of genetic differentiation in Neotropical birds.American Naturalist174358368
- 64. Aleixo A (2006) Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves:Dendrocolaptidae). Biological Journal of the Linnean Society 89: 383–395.A. Aleixo2006Historical diversification of floodplain forest specialist species in the Amazon: a case study with two species of the avian genus Xiphorhynchus (Aves:Dendrocolaptidae).Biological Journal of the Linnean Society89383395
- 65. Cadena CD, Gutiérrez-Pinto N, Dávila N, Terry Chesser R (2011) No population genetic structure in a widespread aquatic songbird from the Neotropics. Molecular Phylogenetics and Evolution 58: 540–545.CD CadenaN. Gutiérrez-PintoN. DávilaR. Terry Chesser2011No population genetic structure in a widespread aquatic songbird from the Neotropics.Molecular Phylogenetics and Evolution58540545
- 66. Puebla-Olivares F, Bonaccorso E, Espinosa de los Monteros A, Omland KE, Llorente-Bousquets JE, et al. (2008) Speciation in the Emerald Toucanet (Aulachorhynchus prasinus) complex. Auk 125: 39–50.F. Puebla-OlivaresE. BonaccorsoA. Espinosa de los MonterosKE OmlandJE Llorente-Bousquets2008Speciation in the Emerald Toucanet (Aulachorhynchus prasinus) complex.Auk1253950
- 67. Milá B, Toews DPL, Smith TB, Wayne RK (2011) A cryptic contact zone between divergent mitochondrial DNA lineages in southwestern North America supports past introgressive hybridization in the yellow-rumped warbler complex (Aves: Dendroica coronata). Biol J Linn Soc 103: 696–706.B. MiláDPL ToewsTB SmithRK Wayne2011A cryptic contact zone between divergent mitochondrial DNA lineages in southwestern North America supports past introgressive hybridization in the yellow-rumped warbler complex (Aves: Dendroica coronata).Biol J Linn Soc103696706
- 68. Irwin DE, Rubstov AS, Panov EN (2009) Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes). Biological Journal of the Linnean Society 98: 422–438.DE IrwinAS RubstovEN Panov2009Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes).Biological Journal of the Linnean Society98422438
- 69. Zink RM, Barrowclough GF (2008) Mitochondrial DNA under siege in avian phylogeography. Molecular Ecology 17: 2107–2121.RM ZinkGF Barrowclough2008Mitochondrial DNA under siege in avian phylogeography.Molecular Ecology1721072121
- 70. Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Systematic Biology 54: 852–859.PDN HebertTR Gregory2005The promise of DNA barcoding for taxonomy.Systematic Biology54852859
- 71. Burns KJ, Naoki K (2004) Molecular phylogenetics and biogeography of Neotropical tanagers in the genus Tangara. Molecular Phylogenetics and Evolution 32: 838–854.KJ BurnsK. Naoki2004Molecular phylogenetics and biogeography of Neotropical tanagers in the genus Tangara.Molecular Phylogenetics and Evolution32838854
- 72. Cadena CD, Klicka J, Ricklefs RE (2007) Evolutionary differentiation in the Neotropical montane region: molecular phylogenetics and phylogeography of Buarremon brush-finches (Aves, Emberizidae). Molecular Phylogenetics and Evolution 44: 993–1016.CD CadenaJ. KlickaRE Ricklefs2007Evolutionary differentiation in the Neotropical montane region: molecular phylogenetics and phylogeography of Buarremon brush-finches (Aves, Emberizidae).Molecular Phylogenetics and Evolution449931016
- 73. Hackett SJ, Rosenberg KV (1990) Comparison of phenotypic and genetic differentiation in South American antwtrens (Formicaridae). Auk 107: 473–489.SJ HackettKV Rosenberg1990Comparison of phenotypic and genetic differentiation in South American antwtrens (Formicaridae).Auk107473489
- 74. Lovette IJ, Pérez-Emán JL, Sullivan JP, Banks RC, Fiorentino I, et al. (2010) A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves). Molecular Phylogenetics and Evolution 57: 753–770.IJ LovetteJL Pérez-EmánJP SullivanRC BanksI. Fiorentino2010A comprehensive multilocus phylogeny for the wood-warblers and a revised classification of the Parulidae (Aves).Molecular Phylogenetics and Evolution57753770
- 75. McGuire JA, Witt CC, Altshuler DL, Remsen JVJ (2007) Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy. Systematic Biology 56: 837–856.JA McGuireCC WittDL AltshulerJVJ Remsen2007Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy.Systematic Biology56837856
- 76. Voelker G, Rohwer S, Bowie RCK, Outlaw DC (2007) Molecular systematics of a speciose, cosmopolitan songbird genus: defining the limits of, and relationships among, the Turdus thrushes. Molecular Phylogenetics and Evolution 42: 422–434.G. VoelkerS. RohwerRCK BowieDC Outlaw2007Molecular systematics of a speciose, cosmopolitan songbird genus: defining the limits of, and relationships among, the Turdus thrushes.Molecular Phylogenetics and Evolution42422434
- 77. Hackett SJ (1996) Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Molecular Phylogenetics and Evolution 5: 368–382.SJ Hackett1996Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves).Molecular Phylogenetics and Evolution5368382
- 78. Eberhard JR, Bermingham E (2004) Phylogeny and biogeography of the Amazona ochrocephala (Aves; Psittacidae) complex. Auk 121: 318–332.JR EberhardE. Bermingham2004Phylogeny and biogeography of the Amazona ochrocephala (Aves; Psittacidae) complex.Auk121318332
- 79. Eberhard JR, Bermingham E (2005) Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans. Molecular Phylogenetics and Evolution 36: 288–304.JR EberhardE. Bermingham2005Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans.Molecular Phylogenetics and Evolution36288304
- 80. Russello MA, Amato G (2004) A molecular phylogeny of Amazona: implications for Neotropical parrot biogeography, taxonomy, and conservation. Molecular Phylogenetics and Evolution 30: 421–437.MA RusselloG. Amato2004A molecular phylogeny of Amazona: implications for Neotropical parrot biogeography, taxonomy, and conservation.Molecular Phylogenetics and Evolution30421437
- 81. Campagna L, Geale K, Handford P, Lijtmaer DA, Tubaro PL, et al. (2011) A molecular phylogeny of the Sierra-Finches (Phrygilus, Passeriformes): Extreme polyphyly in a group of Andean specialists. Molecular Phylogenetics and Evolution 61: 521–533.L. CampagnaK. GealeP. HandfordDA LijtmaerPL Tubaro2011A molecular phylogeny of the Sierra-Finches (Phrygilus, Passeriformes): Extreme polyphyly in a group of Andean specialists.Molecular Phylogenetics and Evolution61521533
- 82. McCormack JE, Peterson AT, Bonaccorso E, Smith TB (2008) Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina). Molecular Ecology 17: 2505–2521.JE McCormackAT PetersonE. BonaccorsoTB Smith2008Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina).Molecular Ecology1725052521
- 83. Aleixo A (2002) Molecular systematics and the role of the “varzea”-“terra firme” ecotone in the diversification of Xiphorhynchus woodcreepers (Aves: Dendrocolaptidae). Auk 119: 621–640.A. Aleixo2002Molecular systematics and the role of the “varzea”-“terra firme” ecotone in the diversification of Xiphorhynchus woodcreepers (Aves: Dendrocolaptidae).Auk119621640
- 84. Ribas CC, Gaban-Lima R, Miyaki CY, Cracraft J (2005) Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae). Journal of Biogeography 32: 1409–1427.CC RibasR. Gaban-LimaCY MiyakiJ. Cracraft2005Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae).Journal of Biogeography3214091427
- 85. Omland KE, Lanyon SM (2000) Reconstructing plumage evolution in orioles (Icterus): repeated convergence and reversal in patterns. Evolution 54: 2119–2133.KE OmlandSM Lanyon2000Reconstructing plumage evolution in orioles (Icterus): repeated convergence and reversal in patterns.Evolution5421192133
- 86. Moore WS, Weibel AC, Agius A (2006) Mitochondrial DNA phylogeny of the woodpecker genus Veniliornis (Picidae, Picinae) and related genera implies convergent evolution of plumage patterns. Biological Journal of the Linnean Society 87: 611–624.WS MooreAC WeibelA. Agius2006Mitochondrial DNA phylogeny of the woodpecker genus Veniliornis (Picidae, Picinae) and related genera implies convergent evolution of plumage patterns.Biological Journal of the Linnean Society87611624
- 87. Beheregaray LB, Caccone A (2007) Cryptic biodiversity in a changing world. Journal of Biology 6: 9.LB BeheregarayA. Caccone2007Cryptic biodiversity in a changing world.Journal of Biology69
- 88. Toews DPL, Irwin DE (2008) Cryptic speciation in a Holarctic passerine revealed by genetic and bioacoustic analyses. Molecular Ecology 17: 2691–2705.DPL ToewsDE Irwin2008Cryptic speciation in a Holarctic passerine revealed by genetic and bioacoustic analyses.Molecular Ecology1726912705
- 89. Dacosta JM, Klicka J (2008) The Great American Interchange in birds: a phylogenetic perspective with the genus Trogon. Molecular Ecology 17: 1328–1343.JM DacostaJ. Klicka2008The Great American Interchange in birds: a phylogenetic perspective with the genus Trogon.Molecular Ecology1713281343
- 90. Padial JM, De la Riva I (2010) A response to recent proposals for integrative taxonomy. Biological Journal of the Linnean Society 101: 747–756.JM PadialI. De la Riva2010A response to recent proposals for integrative taxonomy.Biological Journal of the Linnean Society101747756
- 91. Sites JWJ, Marshall JC (2004) Operational criteria for delimiting species. Annu Rev Ecol Evol Syst 35: 199–227.JWJ SitesJC Marshall2004Operational criteria for delimiting species.Annu Rev Ecol Evol Syst35199227
- 92. Sangster G (2009) Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation. Proceedings of the Royal Society B 276: 3185–3191.G. Sangster2009Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation.Proceedings of the Royal Society B27631853191
- 93. Blackburn TM, Gaston KJ (1996) Spatial patterns in the geographic range sizes of bird species in the New World. Phil Trans R Soc Lond B 351: 897–912.TM BlackburnKJ Gaston1996Spatial patterns in the geographic range sizes of bird species in the New World.Phil Trans R Soc Lond B351897912
- 94. Brumfield RT, Capparella AP (1996) Historical diversification of birds in northwestern south America: A molecular perspective on the role of vicariant events. Evolution 50: 1607–1624.RT BrumfieldAP Capparella1996Historical diversification of birds in northwestern south America: A molecular perspective on the role of vicariant events.Evolution5016071624
- 95. Brumfield RT, Edwards SV (2007) Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes. Evolution. pp. 346–367.RT BrumfieldSV Edwards2007Evolution into and out of the Andes: a Bayesian analysis of historical diversification in Thamnophilus antshrikes.Evolution346367
- 96. Beven S, Connor EF, Beven K (1984) Avian biogeography in the Amazon basin and the biological model of diversification. Journal of Biogeography 11: 383–399.S. BevenEF ConnorK. Beven1984Avian biogeography in the Amazon basin and the biological model of diversification.Journal of Biogeography11383399
- 97. Moritz C, Patton JL, Schneider CJ, Smith TB (2000) Diversification of rainforest faunas: an integrated molecular approach. Annual Review of Ecology and Systematics 31: 533–563.C. MoritzJL PattonCJ SchneiderTB Smith2000Diversification of rainforest faunas: an integrated molecular approach.Annual Review of Ecology and Systematics31533563
- 98. Avise JC, Walker D, Johns GC (1998) Speciation durations and Pleistocene effects on vertebrate phylogeography. Proc R Soc Lond B 265: 1707–1712.JC AviseD. WalkerGC Johns1998Speciation durations and Pleistocene effects on vertebrate phylogeography.Proc R Soc Lond B26517071712
- 99. Buermann W, Saatchi S, Smith TB, Zutta BR, Chaves JA, et al. (2008) Predicting species distrubutions across the Amazonian and Andean regions using remote sensing data. Journal of Biogeography 35: 1160–1176.W. BuermannS. SaatchiTB SmithBR ZuttaJA Chaves2008Predicting species distrubutions across the Amazonian and Andean regions using remote sensing data.Journal of Biogeography3511601176
- 100. Faith D (1994) Genetic diversity and taxonomic priorities for conservation. Biological Conservation 68: 69–74.D. Faith1994Genetic diversity and taxonomic priorities for conservation.Biological Conservation686974
- 101. Faith DP, Reid CAM, Hunter J (2004) Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment. Conservation Biology 18: 255–261.DP FaithCAM ReidJ. Hunter2004Integrating phylogenetic diversity, complementarity, and endemism for conservation assessment.Conservation Biology18255261
- 102. Thomassen HA, Buermann W, Milá B, Graham CH, Cameron SE, et al. (2009) Modeling environmentally associated morphological and genetic variation in a rainforest bird, and its application to conservation prioritization. Evolutionary Applications 3: 1–16.HA ThomassenW. BuermannB. MiláCH GrahamSE Cameron2009Modeling environmentally associated morphological and genetic variation in a rainforest bird, and its application to conservation prioritization.Evolutionary Applications3116