Decoupling of genetic and phenotypic evolution in the Tawny-Crowned Greenlet

Study finds deep genomic divergence despite little morphological changes.

South America houses high levels of cryptic bird diversity. Although some populations look morphologically similar, they often exhibit drastic genetic differences. Because the taxonomy of Neotropical birds is largely based on the study of museum specimens, we are probably missing a lot of species.

A notable example concerns the Tawny-Crowned Greenlet (Tunchiornis ochraceiceps). This small songbird can be found from the lowlands of Central America to the Amazon region. Based on subtle differences in plumage and morphometrics, ornithologists have recognized 10 subspecies. Genetic data, however, paint a drastically different picture. Analyses of mitochondrial DNA showed that some of these subspecies diverged ca. 10 million years ago. That would be a distinct species in anyone’s book.

A recent study in the journal Molecular Phylogenetics and Evolution undertook a more detailed analysis of the Tawny-Crowned Greenlet, combining plumage coloration, morphometrics, vocalizations and genomic data. How many cryptic species are hiding in the tropical rainforests?

Six Lineages

Let’s start with the genomic patterns. Based on more than 2000 ultraconserved elements (UCEs), the researchers could delineate six separate lineages (of which two showed signs of substructure). The main split in the phylogenetic tree – dated to about 9 million years ago – differentiates between the western and the eastern lineages. The western group falls apart into populations on both sides of the Andes, whereas the eastern group is subdivided by different Amazonian rivers. The figure below provides a nice overview of the complex geographical distribution of these genetic lineages.

Genomic analyses suggested six distinct lineages across Central and South America. From: Buainain et al. (2021).

Phenotypic Boundaries

But can we also discriminate between these lineages with phenotypic data or vocalizations? When it comes to morphometrics and song, the answer is no. The authors indicate that “no clear spatial separation between samples belonging to the two [genetic] clusters can be seen in the [morphological] classification graph” and “the quantitative analysis shows no diagnostic vocal characters for any of the populations of T. ochraceiceps.”

In terms of plumage coloration, the situation is slightly better. One plumage character – the coloration of the forehead and crown – can be used to distinguish between three groups, namely populations in the west, northeast of the Amazon and southeast of the Amazon. Other plumage traits were not diagnostic for different populations, but did show variation across the distribution of the Tawny-Crowned Greenlet. In most cases, the geographic extremes were clearly different with a large area of intermediate phenotypes in between. Drawing clear phenotypic boundaries between populations is difficult, at best.

Some examples of plumage traits that distinguished some populations of the Tawny-Crowned Greenlet. In general, however, it was difficult to determine clear phenotypic boundaries. From: Buainain et al. (2021).

A Conservative Species

These analyses reveal an interesting evolutionary pattern: the decoupling of genetic and phenotypic evolution. Although the Tawny-Crowned Greenlet is composed of genetically distinct populations, this differentiation is not reflected in the phenotypic variation. Why is the phenotype of this (group of) species so conserved? The researchers offer several explanations that require further investigation:

  • Stabilizing selection: there is no selective pressure – social or ecological – to develop morphological or vocal differences.
  • Habitat specialist: the Tawny-Crowned Greenlet follows a specific habitat type which does not require it to adapt morphologically.

Finally, the authors propose a taxonomic arrangement for the six genetic lineages. They divide them into four distinct species, of which two species are further separated into two subspecies: T. o. ochraceiceps, T. o. bulunensis, T. ferrugineifrons, T. luteifrons, T. r. rubrifrons and T. r. lutescens. This classification might change in the future. Stay tuned.

Geographical distribution of the six taxa (species and subspecies) in the Tawny-Crowned Greenlet. From: Buainain et al. (2021).


Buainain, N., Maximiano, M. F., Ferreira, M., Aleixo, A., Faircloth, B. C., Brumfield, R. T., … & Ribas, C. C. (2021). Multiple species and deep genomic divergences despite little phenotypic differentiation in an ancient Neotropical songbird, Tunchiornis ochraceiceps (Sclater, 1860)(Aves: Vireonidae). Molecular Phylogenetics and Evolution162, 107206.

Milá, B., Tavares, E. S., Munoz Saldana, A., Karubian, J., Smith, T. B., & Baker, A. J. (2012). A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity. PLoS One7(7), e40541.

Featured image: Tawny-Crowned Greenlet (Tunchiornis ochraceiceps) © Dominic Sherony | Wikimedia Commons

The Warbling Vireo comprises of two cryptic species

Genetic analyses confirm behavioral differences between two main groups.

There is more to avian diversity than meets the eye. Some species might look very similar although they are genetically and behaviorally distinct. An example that most European birders will be familiar with concerns the Chiffchaff (Phylloscopus collybita) and the Willow Warbler (Phylloscopus trochilus). Morphologically, these passerines are difficult to tell apart. But when they start singing, it is easy to discriminate between the two-syllable song of the Chiffchaff and the string of notes produced by the Willow Warbler. Recently, a study in the journal Ornithology (previously The Auk) described a similar case in North America where the Warbling Vireo (Vireo gilvus) might actually comprise two cryptic species.

Genetic Markers

Currently, the Warbling Vireo is classified into four subspecies that can be assigned to two main groups. The gilvus group houses only one subspecies (gilvus) and can be observed in deciduous forests across eastern North America. The swainsoni group holds three subspecies (swainsoni, victoriae, and leucopolius) that occur in the deciduous and mixed forests of western North America. Both groups meet along a contact zone in central Alberta (Canada). Some ornithologists suggested that these two groups might represent distinct species, but the evidence supporting this taxonomic arrangement is limited. Hence, Scott Lovell and his colleagues decided to unravel the genetics of this species complex by sequencing some mitochondrial and nuclear DNA.

The mitochondrial gene cytochrome b (cytb) supported the two groups described above, separated by 35 mutations. The genetic divergence between these mitochondrial clades amounted to 4% which translates into a divergence time between 1.9 and 2.5 million years ago (depending on the chosen mutation rate). The nuclear markers corroborated this pattern, clearly dividing most individuals into the gilvus and swainsoni groups. I write “most individuals”, because the genetic analyses uncovered some hybrids. Nine out of 145 individuals showed signs of mixed ancestry. These hybrids were detected within and near the contact zone, suggesting limited introgression outside of this area.

The mitochondrial DNA clearly separates the two groups. From: Lovell et al. (2021) The Auk.

Migratory Divide

Genetic data is just one line of evidence to support a taxonomic split. The two groups do show some minor differences in morphology and song, but the main difference probably relates to their migratory behavior. Individuals from the gilvus and swainsoni groups follow distinct migration routes: gilvus individuals fly through the mid-western and eastern USA whereas swainsoni individuals follow a route across the western USA and Mexico. Moreover, the two taxa arrive on the breeding grounds at different times: swainsoni individuals settle about two weeks earlier. This mismatch in timing reduces the possibility of mixed couples, allowing these taxa to diverge genetically. Hence, the authors argue to recognize these two groups as distinct species. In addition, they write that “future work may determine that additional cryptic species occur within the swainsoni group.” Who know what taxonomic discoveries lie ahead?

Analyses of the nuclear DNA discriminated between the two groups, but also uncovered some hybrids (green squares). Yellow triangles represent individuals with mismatches between nuclear and mitochondrial assignment. From: Lovell et al. (2021) The Auk.


Lovell, S. F., Lein, M. R., & Rogers, S. M. (2021). Cryptic speciation in the Warbling Vireo (Vireo gilvus). The Auk138(1), ukaa071.

Featured image: Warbling Vireo (Vireo gilvus) © Francesco Veronesi | Wikimedia Commons