A method to estimate effective population size from linkage disequilibrium when generations overlap

Effective population size (Ne) is a key parameter in evolutionary and conservation studies. It characterises the number of unique or distinct individuals in a population, and can be used to establish management programmes. Several methods have been developed to estimate this parameter. Currently, for studies with one sample in time, the simplest methods are based on linkage disequilibrium. These methods rely on simple models, and biases have been shown when populations deviate from the assumptions made in those models. This occurs in particular when populations are age-structured or have overlapping generations. Recently, several methods have been developed to correct such biases. Here, we develop analytical equations to predict linkage disequilibrium within age groups, and use such results to infer cohort size from samples of newborn individuals. We can in turn use these equations to estimate Ne accurately for a variety of species. Furthermore, using publicly available data, we apply our method to the white-crowned sparrow (Zonotrichia leucophrys).

Long-term changes of plumage between urban and rural populations of white-crowned sparrows (Zonotrichia leucophrys)

Urbanization is one of the most extreme forms of land transformation and results in changes to ecosystems and species compositions. As a result, there are strong directional selection pressures compared to nearby rural areas. Despite a surge in research on the different selection pressures on acoustic communication in urban and rural areas, there has been comparatively little investigation into traits involved with visual communication. We measured the plumage of museum specimens of white-crowned sparrows (Zonotrichia leucophrys) from urban and adjacent rural habitats in San Francisco, CA, to assess the effects of divergent habitats on plumage. We found significant differences in dorsal plumage, but not crown plumage, between urban and rural populations that have been diverging over the past 100 years. Urban birds have increasingly darker and duller dorsal plumage, whereas rural birds in adjacent areas have plumage with richer hues and more color complexity. Our findings suggest a newly observed adaptation to urban environments by native species and suggest that many traits, in addition to acoustic signals, may be changing in response to urban selection pressures. Additional collections in urban areas are needed to explore likely divergences in plumage coloration between urban and rural environments.

Anthropogenic noise affects winter song structure of a long-distance migrant, Gambel’s white-crowned sparrow

Many animals learn to produce acoustic signals that are used to attract mates and defend territories. The structure of these signals can be influenced by external features of the environment, including the anthropogenic soundscape. In many sedentary species, habitat features and soundscape appears to influence the cultural evolution of songs, often with tradeoffs for better transmission over sexually selected song structure. However, none have investigated whether noise on the wintering grounds affects song structure, which for long-distance migrants may result in an acoustic ‘mismatch’ when returning to a breeding ground. This study investigates urban noise effects on song structure in a long-distance migrant, Zonotrichia leucophrys gambelii, on the wintering grounds in the Fresno Clovis Metropolitan Area and in outlying non-urban areas. Songs and background noise levels were recorded concurrently, and song measurements of frequency and duration were examined differences across noise levels and habitats . We found that the buzz and trill decrease in bandwidth in the presence of noise. The length of the whistle and buzz portion of the song also tends to decreases with noise in urban habitats. This trend toward short, pure tones in noisy areas may transmit better in noisy urban winter habitats, but may not be adaptive on quieter breeding grounds. We suggest that future studies should consider whether winter auditory feedback and song learning environments have consequences for song crystallization and breeding success for long-distance migrants.