Integrative taxonomy of the Lesser Short-toed Lark and Sand Lark species complex

The combination of genetic and non-genetic data points to four distinct species.

The advent of genetic – and later genomic – data turned out to be a double-edged sword for taxonomists. On the one hand, DNA sequences allow researchers to discriminate between morphologically similar species. On the other hand, the ability to detect ever more fine-scaled genetic differentiation between populations complicates the drawing of species boundaries. Several species delimitation programs using molecular data have been developed, but it remains a daunting task to translate the output of these programs into clear taxonomic arrangements. Jeet Sukumaran and Lacey Knowles nicely described this issue in a PNAS paper: “Until new methods are developed that can discriminate between structure due to population-level processes and that due to species boundaries, genomic-based results should only be considered a hypothesis that requires validation of delimited species with multiple data types, such as phenotypic and ecological information.” In other words, genetic patterns will need to be corroborated by non-genetic data.

Five Lark Lineages

Several months ago, I covered a molecular study on the Lesser Short-toed Lark (Alaudala rufescens) and Sand Lark (A. raytal) species complex (see this blog post). The genetic analyses pointed to five genetic lineages that could be classified into four distinct species. Indeed, the researchers wrote that “our results call for a taxonomic revision, and we tentatively suggest that at least four species should be recognized, although we stress the need for an approach integrating molecular, morphological and other data that are not yet available.” A follow-up study in the journal Molecular Phylogenetics and Evolution provides these missing data, using plumage patterns, biometrics, songs, geographical distributions and bioclimatic factors to evaluate the genetic patterns.

A slightly more elaborate genetic analysis uncovered the same five lineages as the previous study. In addition, the species delimitation program STACEY suggested that four lineages were sufficiently divergent to warrant a species status, namely the heinei clade, the raytal clade, the rufescens clade and the cheleensis + leucophaea clade (see figure below). But what about the non-genetic data? The researchers performed several detailed analyses and an exhaustive overview of the results is not feasible within the scope of a short blog post. So, I will try to summarize the main findings below:

  • The five lineages could not be separated by plumage. This is probably a consequence of the convergent evolution due to adaptation to a similar habitats.
  • Classification analyses based on the wing, tail and bill lengths discriminated between all clades, except for the cheleensis and leucophaea clades. Several individuals from these groups were misclassified.
  • Song characteristics were significantly different between the five clades, although the songs of cheleensis and leucophaea seemed to show a clinal pattern.
  • All five lineages occur in open habitats with scant vegetation, but there appear to be some differences in habitat preferences.
  • Bioclimatic parameters, such as rainfall and temperature, could discriminate between the different lineages.
Genetic analyses indicated five distinct clades. Do they all represent different species? From: Alström et al. (2021) Molecular Phylogenetics and Evolution.

Integrative Taxonomy

Based on these patterns, the researchers concluded that “the rufescens, heinei and raytal clades were unanimously supported as independent lineages by mtDNA, morphology and bioacoustics as well as by the STACEY multilocus analysis. The raytal clade was also supported by its unique habitat. The combined cheleensis and leucophaea clade was also supported by the same datasets.” The latter two clades could not be confidently separated, because they showed clinal variation in several traits. The proposed taxonomy thus includes four species:

  • Lesser Short-toed Lark (A. rufescens)
  • Heine’s Short-toed Lark (A. heinei)
  • Asian Short-toed Lark (A. cheleensis)
  • Sand Lark (A. raytal)

This study nicely illustrates the use of multiple data sources to inform taxonomic decisions (an approach known as integrative taxonomy). It is interesting to see how the genomic revolution has drawn attention to the taxonomic importance of non-genetic data, such as morphology, behavior and bioacoustics. Several authors have highlighted this perspective. I recently argued that genomics provides another line of evidence in the pluralistic approach to species classification (see this book chapter). Similarly, Carlos Daniel Cadena and Felipe Zapata called for the integration of genomic and phenotypic data in avian taxonomy (see this paper). The development of new genetic techniques is bringing us back to the basics.


Alström, P., van Linschooten, J., Donald, P. F., Sundev, G., Mohammadi, Z., Ghorbani, F., Shafaeipour, A., van den Berg, A., Robb, M., Aliabadian, M., Wei, C., Lei, F., Oxelman, B. & Olsson, U. (2021). Multiple species delimitation approaches applied to the avian lark genus AlaudalaMolecular Phylogenetics and Evolution154, 106994.

Featured image: Lesser Short-toed Lark (A. rufescens) © Juan Emilio | Wikimedia Commons

Uncovering cryptic diversity in the lesser short-toed lark species complex

Genetic analyses reveal several distinct lineages within this morphologically uniform bird group.

“Few groups of birds show the same level of disagreement between taxonomy based on morphology and phylogenetic relationships as inferred from DNA sequences.” This statement refers to the bird family Alaudidae: the larks. These brownish birds mostly reside in open habitat where strong selection for camouflage resulted in little morphological differences. Such bird groups can be a taxonomists’ nightmare, especially if the researcher solely focuses on morphological characteristics to pigeon-hole the specimens. Luckily, molecular data can provide some clarity. A recent study in the journal Zoologica Scripta investigated one species complex within the lark family. Does molecular data work where morphology fails?

The short-toed lark, nicely camouflaged in its natural habitat. © Juan Emilio | Wikimedia Commons


No Consensus

An international team of researchers took a closer look at the lesser short-toed lark (Alaudala rufescens) species complex. Due to the morphological similarities, the taxonomy of these birds has been heavily debated and up to 16 different taxa have been recognized. Some authors treated all taxa as a single species, while others split it into two species: the lesser short-toed lark and the Asian short-toed lark (A. cheleensis). Because morphological analyses did not lead a consensus, the researchers turned to molecular data. They sequenced one mitochondrial and eleven nuclear genes.

The genetic analyses revealed four distinct lineages within the species complex that separated between 1.6 and 3.2 million years ago. The authors indicate that the complex could be separated into at least four species, namely the heinei clade, the raytal clade, the rufescens clade and the cheleensis + leucophaea clade. The latter two subspecies are grouped together because they could not be confidently separated by the nuclear genes. This cryptic diversity has been masked by the slight plumage differentiation within complex.

Genetic analyses revealed five separate groups that probably represent four distinct species. From: Ghorbani et al. (2020) Zoological Scripta


Evolutionary Questions

This study highlights the power of molecular data to uncover cryptic diversity and inform taxonomic decisions. Although it is important to create a solid taxonomic framework, the debates about which taxa should be classified as species or subspecies are secondary to more interesting evolutionary questions. As I have argued before, instead of focusing on minor morphological differences to draw arbitrary lines between “species”, we should try to understand how this diversity originated. In case of these larks, we can unravel the genetic basis of their impressive camouflage. Do the same genes underlie this diversity or are different genes under selection in different taxa. Such questions are more exciting than deciding to call something a species or not. The birds themselves couldn’t care less…



Ghorbani, F., Aliabadian, M., Zhang, R., Irestedt, M., Hao, Y., Sundev, G., Lei, F., Ma, M., Olsson, U. & Alström, P. (2020). Densely sampled phylogenetic analyses of the Lesser Short‐toed Lark (Alaudala rufescens) – Sand Lark (A. raytal) species complex (Aves, Passeriformes) reveal cryptic diversity. Zoologica Scripta.