Abstract
Birds are one of the most recognizable and diverse groups of organisms on earth. This group has played an important role in many fields, including the development of methods in behavioral ecology and evolutionary theory. The use of population genomics took off following the advent of high-throughput sequencing in various taxa. Several features of avian genomes make them particularly amenable for work in this field, including their nucleated red blood cells permitting easy DNA extraction and small, compact genomes. We review the latest findings in the population genomics of birds here, emphasizing questions related to behavior, ecology, evolution, and conservation. Additionally, we include insights in trait mapping and the ability to obtain accurate estimates of important summary statistics for conservation (e.g., genetic diversity and inbreeding). We highlight roadblocks that will need to be overcome in order to advance work on the population genomics of birds and prospects for future work. Roadblocks include the assembly of more contiguous reference genomes using long-reads and optical mapping. Prospects include the integration of population genomics with additional fields (e.g., landscape genetics, phylogeography, and genomic mapping) along with studies beyond genetic variants (e.g., epigenetics).
Highlights
Birds have played a central role in our understanding of many research fields
We follow this division in this chapter, introducing some of the latest findings from birds, highlighting the benefits of applying population genomics tools to these questions, and finishing by outlining future prospects along this trajectory
Information on these dynamics is essential for understanding the evolution of species, populations and traits and important for setting baselines beyond which evolutionary processes can be examined. This is especially true in the current literature, where genome scans are being used to identify loci associated with phenotypic traits and/or involved in adaptation and speciation
Summary
Birds have played a central role in our understanding of many research fields. Notable examples include (1) the development of methods essential for behavior and ecology by Margaret Nice [1] using populations of song sparrows (Melospiza melodia), and (2) the definition of species as groups of populations reproductively isolated from one another by Ernst Mayr [2], inspired by the geographic distribution of birds and galvanizing the field of evolution. The last 10 years has seen a change in both the scale and depth of genetic analyses, with the transition from the use of one or a few genetic markers to tens of thousands of markers genome-wide marking the development of population genomics This transition was stimulated by de novo assembly of reference genomes along with the advent of high-throughput sequencing (HTS). Work at the genome level informs our understanding of population processes (e.g., demography and population structure), while work at the locus level helps identify genomic regions affected by mutation, drift, selection and/or gene flow [3] We follow this division in this chapter, introducing some of the latest findings from birds, highlighting the benefits of applying population genomics tools to these questions (vs traditional population genetic techniques with fewer markers), and finishing by outlining future prospects along this trajectory
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