17. Extinctions, Genetics and Future Possibilities

Avian Genetics:  We are living in a Genetic Revolution.

Cody Limber, 

Yale University, New Haven, CT

cody.limber@yale.edu

This presentation begins at 5 hours 18 minutes on the video recording of this conference:  COA's Birds and the Environment Science Conference - Online - YouTube

We are in the midst of a genetic revolution. Over the past 20 years, the cost of sequencing a genome has come down from over a billion dollars to ~1,000 dollars as of 2020. This means that we are now able to sequence more genomes from different species across the tree of life. In part due to efforts like the 10k avian genomes project, we have full genomes from over 500 species representing 92% of avian families. 

What do we do with all these data? We can use genetic data to build trees. Not trees in the forest, but trees of life representing the evolutionary history of bird evolution and showing who is related to whom. Traditionally, this was done with morphological characters, but genetic data allows for increased resolution and accuracy. Genetics also allows us to describe new species. By comparing gene sequences from similar species, we are able to look for differences or similarities that enable us to make informed decisions about what to call a species. We can also analyze birds of unknown parentage genetically to reveal their family histories. 

Functional genetics is a new and expanding field asking questions about what these different genes in different species do and how they contribute to their unique morphologies. By comparing birds with different beak shapes, we are able to look for genes that may be involved in shaping these bills, something Darwin never even dreamed of doing. 

Genetics is also important in conservation especially in the face of the current biodiversity crisis. One area of concern looks at genetic diversity in species with small population sizes. Genetic diversity is extremely important in maintaining the health of a population and efforts to increase genetic diversity have had mixed success. There are also efforts to bring species that are extinct back to life. Although we are able to sequence genomes from extinct species, we currently lack the knowledge and technology required to bring back these extinct species. Conservation money is better spent on preserving what we still have instead of bringing back the species we have lost. 

If you have questions, you can explore the references below, or contact me by email:  cody.limber@yale.edu

References:

(Bravo et al., 2021; Burga et al., 2017; Feng et al., 2020; Lamichhaney et al., 2015; Lane et al., 2021; Mussmann et al., 2017; Prum et al., 2015; Rosenberg et al., 2019; Toews et al., 2018)

Bravo, G.A., Schmitt, C.J., and Edwards, S.V. (2021). What Have We Learned from the First 500 Avian Genomes? Annual Review of Ecology, Evolution, and Systematics 52. 

Burga, A., Wang, W., Ben-David, E., Wolf, P.C., Ramey, A.M., Verdugo, C., Lyons, K., Parker, P.G., and Kruglyak, L. (2017). A genetic signature of the evolution of loss of flight in the Galapagos cormorant. Science 356. 

Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, A.H., Xie, D., Chen, G., Guo, C., and Faircloth, B.C. (2020). Dense sampling of bird diversity increases power of comparative genomics. Nature 587, 252-257. 

Lamichhaney, S., Berglund, J., Almén, M.S., Maqbool, K., Grabherr, M., Martinez-Barrio, A., Promerová, M., Rubin, C.-J., Wang, C., and Zamani, N. (2015). Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature 518, 371-375. 

Lane, D.F., Aponte Justiniano, M.A., Terrill, R.S., Rheindt, F.E., Klicka, L.B., Rosenberg, G.H., Schmitt, C.J., and Burns, K.J. (2021). A new genus and species of tanager (Passeriformes, Thraupidae) from the lower Yungas of western Bolivia and southern Peru. Ornithology. 

Mussmann, S., Douglas, M., Anthonysamy, W., Davis, M.A., Simpson, S., Louis, W., and Douglas, M. (2017). Genetic rescue, the greater prairie chicken and the problem of conservation reliance in the Anthropocene. Royal Society open science 4, 160736. 

Prum, R.O., Berv, J.S., Dornburg, A., Field, D.J., Townsend, J.P., Lemmon, E.M., and Lemmon, A.R. (2015). A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, 569. 

Rosenberg, K.V., Dokter, A.M., Blancher, P.J., Sauer, J.R., Smith, A.C., Smith, P.A., Stanton, J.C., Panjabi, A., Helft, L., and Parr, M. (2019). Decline of the North American avifauna. Science 366, 120-124. 

Toews, D.P., Streby, H.M., Burket, L., and Taylor, S.A. (2018). A wood-warbler produced through both interspecific and intergeneric hybridization. Biology letters 14, 20180557.