LAUSR

Understanding the factors that influence extinction and persistence of species is one of the key goals of genetical, evolutionary, and ecological aspects of conservation biology. Passenger pigeons (PP), perhaps the most abundant bird species ever with estimates of 3–5 billion birds, went extinct in 1914. This extinction was primarily the result of new and efficient hunting techniques introduced in the 19th century that included the new technology of the telegraph, which was used to inform hunters where the flocks were migrating and roosting, and the newly developed railroads, which provided transportation for the hunters and for shipping the killed birds to cities for food. Using current molecular analysis and in an effort to provide insight into this extinction, Murray et al. (2017) have now examined the impact of natural selection on the PP genome by comparing to its closest living relative, the band-tailed pigeon (BP). Overall, Murray et al. (2017) found that the average diversity in PP was twice as high as that in BP (average nucleotide diversities π of 0.08 in PP and 0.04 in BP). However, this difference was much less than that expected under a population genetics model if the population size of PP was several orders of magnitude larger than that of current BP population size estimates. Murray et al. (2017) concluded that this difference is the result of the “surprisingly pervasive influence of natural selection” and not past population instability as suggested by Hung et al. (2014). Their most striking finding was the pattern of genetic diversity over the PP genome with quite high variation of diversity in different chromosomal regions compared to the very uniform diversity over the genome in BP (see Figure 2B in Murray et al. 2017). In fact, PP had nucleotide diversity that varied around 10-fold between genomic regions with purported high recombination rates (the ends of the ten macrochromosomes and the microchromosomes) also having high nucleotide diversity around or approaching 0.02, while genomic regions with low purported recombination rates (centers of the ten macrochromosomes) had low nucleotide diversity of around 0.002. The correlation of nucleotide diversity with recombination could be the result of several factors. First, it could be the result of selective sweeps of adaptive variants. Although selective sweeps of adaptive variants reduce diversity at nearby sites, positive selection is thought to be more efficient and important in regions of higher recombination and diversity (Charlesworth and Campos 2014). In support of positive selection, Murray et al. (2017) identified 32 genes that showed the evidence of adaptive evolution in PP, some of which they suggested were adaptive to living in high density. They also provided some evidence that has been a faster rate of adaptive evolution in PP than in BP. Second, the positive association of diversity and recombination rates is also expected to occur when there is purifying selection against deleterious variants (Charlesworth and Campos 2014). Finally, Murray et al. (2017) also suggested that biased gene conversion rates are expected to be higher in regions with higher recombination. Murray et al. (2017) provided evidence that all three factors were significant but it would be important to know how much contribution each of these factors make to the extreme variation in nucleotide diversity over the PP genome. The most recognized genetic reason for extinction risk is inbreeding depression and there are many examples of high inbreeding depression in bird species, for example, in the great tit (Szulkin et al. 2007), collared flycatchers (Kruuk et al. 2002), and house sparrows (Jensen et al. 2007). The recent number of documented cases of large inbreeding depression appears partly due to the examination of additional fitness components besides viability, such as fecundity and mating success, and partly due to measuring inbreeding depression in more stressful natural environments. For example in red deer, which has large population numbers, given an inbreeding level equivalent to that in * PW Hedrick [email protected]