Skip to main content

Phylogenetics Could Provide Early Warning for Endangered Bird Species

NEW YORK (GenomeWeb News) – British bird species that share genes may also share some population perils, new research suggests.
Imperial College London population biologist Gavin Thomas created an evolutionary tree showing the phylogenetic relationships between nearly 250 different British bird species. The research, appearing today in Proceedings of the Royal Society B, suggests that birds that flock together phylogenetically also share comparable risks of population declines — information that could help conservation biologists decide which species they should keep an eye on.
“The data clearly shows a link between closely related birds and chances of population decline, which could be useful for conservationists,” Thomas said in a statement. Still, he added, “[conservationists] will need to take other factors, such as range contraction, into account.”
When forecasting future extinction risks, biologists often rely on measures of birds’ life history and ecological data. They also take into account factors such as population trends, abundance, and range size, Thomas noted. Although these and many other factors need to be considered, he added, phylogeny holds the potential to enlighten discussions about bird species conservation.
Until now, though, British bird classification has been largely based on features such as conservation concern as opposed to molecular phylogeny. Using the bioinformatics software Geneious, Thomas searched GenBank for sequence data related to 12 mitochondrial protein-encoding genes and one published sequence for cytochrome b.
From these, he used a relaxed clock Bayesian inference method to construct a phylogenetic tree that included some 93 percent of the bird species that breed or winter in Britain. When he overlaid this tree with data on species with decreasing population numbers and looked for phylogenetic clustering, Thomas found an interesting trend: birds exhibiting population declines tended to group together phylogenetically as did those with highly concentrated populations.
Based on this type of reasoning, Thomas noted in a statement, birds such as greenfinch and ptarmigan — among others — may see population declines in the future. That’s because the greenfinch is a close relative of at least two bird species in decline: the linnet and the bullfinch. Similarly, the ptarmigan is related to the black grouse and the grey partridge, both of which are experiencing population decreases. And they’re not alone.
“Numbers of the common blackbird are currently not perceived as threatened at all,” Thomas said. “[H]owever, it has close relatives, including the song thrush, that are experiencing severe levels of population decline. This could mean that populations of blackbirds in the UK are at risk of declining in the future.”
But there were limits to the predictive power of phylogeny, he noted. While phylogenetic relationships between different bird species can be used to glean information about population declines, they’re not necessarily accurate predictors of bird species that may become endangered due to factors such as range contraction. Sequence data was also patchy for the 248 birds tested, he said, making it difficult to draw firm conclusions.
“[W]hile phylogeny has the potential to provide an insight into the types of species that are likely to be susceptible to extinction risk or decline in some cases, a degree of caution is required where different, and potentially conflicting, conservation metrics are lumped into single indices,” Thomas wrote, noting that, “In contrast to the list of species that have suffered population declines, range-contracting species appear idiosyncratic with respect to their biological characteristics.”

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.