Genomic analyses lead to a list of candidate genes, including one with a major effect.
The Ground Tit (Pseudopodoces humilis) is a peculiar species. Based on its morphology – specifically its long, curved beak – ornithologists thought this small songbird belonged to the family Corvidae (crows, ravens, jays and their relatives). Hence, they referred to it as Hume’s Ground Jay or Tibetan Ground jay. Molecular analyses, however, showed that the Ground Tit is the largest member of a completely different bird family: the Paridae (tits, chickadees, and titmice). A good reminder that morphology is not always a reliable guide in taxonomy. Correctly classifying this species raised an intriguing question: Where did this long, curved beak come from? The shape of the beak seems to be an adaptation to foraging on the open grasslands of the Qinghai-Tibet Plateau. As its name suggests, the Ground Tit collects its food on the ground, eating a wide range of arthropods. Although it also searches rock crevices and holes for a tasty grub. A recent study in the journal Molecular Biology and Evolution tried to unravel the genetic underpinnings of this long beak.
In a previous blog post and a YouTube-video, I discussed the genetic basis of beak morphology. Analyses of 72 bird genomes indicated that coding and non-coding regions work together to create the spectacular diversity of avian beaks. And although there are some common underlying developmental pathways (such as Wnt signalling pathway and the ESC pluripotency pathways), it seems that different protein-coding genes are under selection in different species. For example, in Darwin’s Finches several genes are associated with beak morphology (e.g., BMP4, CALM1, ALX1 and HGMA), while a different gene (COL4A5) determines the beak morphology of Great Tits (Parus major). So, what about its relative, the Ground Tit?
To answer this question, Yalin Cheng and his colleagues compared the genome of the Ground Tit with 13 short-beaked parid species. The researchers applied two methods to identify genomic regions that differed between these species. First, they calculated Z-transformed FST-values for different genomic regions. FST is a measure for genetic differentiation and can be standardized with a Z-transformation, which allows for easier comparison between species. Next, they compared genetic outliers with beak lengths using a partial Mantel test. These analyses resulted in 25 genomic regions, containing 23 candidate genes.
Among these 23 candidate genes were two genes (FZD3 and ROR1) involved in the Wnt signalling pathway, highlighting the importance of common developmental pathways in the evolution of beak morphology. To narrow down the list of candidates, the researchers performed several tests to detect signatures of selection (such as Tajiima’s D and Fu & Li’s D). These tests showed the strongest positive selection in the gene COL27A1. Interestingly, this gene is homologous to COL4A5, which is associated with the elongated beak of Great Tits as a response to supplementary feeding at bird feeders. A closer look at the genetic code of COL27A1 indicated several mutations under positive selection, including two in a particular domain of the protein that probably changed its biological function. This finding suggests that COL27A1 has a major effect on the extreme beak evolution in the Ground Tit.
Cheng, Y., Miller, M. J., Zhang, D., Song, G., Jia, C., Qu, Y., & Lei, F. (2020). Comparative genomics reveals evolution of a beak morphology locus in a high-altitude songbird. Molecular biology and evolution, 37(10), 2983-2988.
Featured image: Ground Tit (Pseudopodoces humilis) © Dibyendu Ash | Wikimedia Commons