Genomic study looks for signatures of population expansion or contraction.
For many bird species, their evolutionary history is a series of population expansions and contractions. This is especially apparent during the Pleistocene (between 2.5 million and 11,000 years ago) when the climate fluctuated between cold and warm periods. As the climate warmed, certain vegetation types expanded, followed by the bird species that reside within them. These expansion and contraction dynamics leave traces in the genetic make-up of the bird populations. Several population genetic statistics have been developed to detect the signatures of these processes.
In 1989, for example, the Japanese researcher Fumio Tajima introduced a statistic to discriminate between population expansion and contraction: Tajima’s D. I will not go into the mathematical details (you can check out the excellent video by Mohamed Noor below), but in general you can interpret this statistic as follows: a negative Tajima’s D points to population expansion, while a positive Tajima’s D suggests population contraction. However, similar patterns can also arise due to different selection events (e.g., balancing selection or selective sweeps). That is why it is important to calculate other population genetic statistics to tease these processes apart. Or you could take a modelling approach where you compare different demographic models and see which one explains the data best. And that is exactly what researchers in a recent study in the journal BMC Evolutionary Biology did.
Kritika Garg and her colleagues focused on three scrubwren species on Mt. Wilhelm, the highest mountain of Papua New Guinea. These small passerines occur at different altitudes along this mountain. The buff-faced scrubwren (Aethomys perspicillatus) is restricted to lower montane forest at 1500–2450 meters, while the Papuan scrubwren (A. papuensis) can be observed in the upper montane habitat above 2000 meters. The third species – the large scrubwren (Sericornis nouhuysi) – can be found across the widest range, from 1500 to over 2000 meters. The researchers sequenced the DNA of 74 individuals and applied Approximate Bayesian Computation (ABC) analyses to the data. This computational method allows you to estimate the likelihood of several parameters under particular demographic models. In this case, we are interested in the population sizes over time.
The demographic analyses revealed that all three species experienced a population expansion between 27,000 and 29,000 years ago. This timeframe coincides with the Ålesund Interstadial that occurred about 30,000 years ago when a drop in global temperatures impacted the distribution of vegetation on Mt. Wilhelm.
The strong cooling would have shifted elevational belts down the slope, expanding the area of habitat available to montane forest birds such as the three scrubwrens, and sometimes even connecting populations that would have previously been stranded on separate mountain ranges.
The genetic consequences of these population expansions are also reflected in the lack of population genetic structure in the three species. As individuals expanded their range and potentially interbred with other populations, any differences between subpopulations would be erased. The researchers also calculated Tajima’s D for the three scrubwren species and unsurprisingly it was negative in all species. Hence, all the evidence clearly points to population expansions.
Garg, K. M., Chattopadhyay, B., Koane, B., Sam, K., & Rheindt, F. E. (2020). Last Glacial Maximum led to community-wide population expansion in a montane songbird radiation in highland Papua New Guinea. BMC evolutionary biology, 20(1), 1-10.
Featured image: Large Scrubwren (Sericornis nouhuysi) © Katerina Tvardikova