Population genomics with pedigrees: new approaches for studying contemporary evolution

PROJECT SUMMARY
There are now many beautiful examples of phenotypic evolution on ecological timescales. Nevertheless,
technological challenges and limited availability of temporal genomic data have left a large gap in knowledge of
short-term evolutionary dynamics at the genomic level. Indeed, measuring evolution of natural populations in
real-time remains challenging, and systems with sufficient data to study contemporary genetic evolution are
rare. The proposed work combines evolutionary genomics with long-term demographic and pedigree data to
investigate the evolution of natural populations on short timescales. Long-term, individual-based studies that
have accumulated extensive phenotypic, environmental, and fitness data for thousands of individuals on a
multigenerational pedigree provide a unique opportunity to study how short-term evolution occurs. In particular,
knowledge of the population pedigree, the relationships among all individuals in a population over time,
provides the ability to observe directly the actual processes underlying allele frequency change. The PI
developed the Florida Scrub-Jay (Aphelocoma coerulescens) as a model for evolutionary genomics by adding
substantial genomic data to a 50-year demographic study and formed collaborations with other groups with
similar long-term datasets. This study will track the inheritance of the entire genome down the pedigree, as it is
broken up by recombination over the generations, in two classic study systems: the Florida Scrub-Jay and the
Soay sheep. Elucidating how an individual's genome is distributed across its descendants from generation to
generation provides a powerful framework for determining how individual variation in lifetime reproductive
success predicts variation in individual genetic contributions to future generations and allele frequency change
and for identifying genomic regions associated with fitness. This project will also develop haplotype-dropping
methods that simulate Mendelian transmission of haplotypes down the pedigree to test for short-term selection
and improve selection component methods to test for selection at different life-history stages. Application of
these methods to the Florida Scrub-Jays will increase understanding of the role of fluctuating selection and life-
history trade-offs in maintaining adaptive genetic variation in natural populations. Furthermore, the proposed
work will quantify the long-term contributions of immigrants to population genetic diversity and fitness by
tracing the frequency and fitness impact of specific immigrant haplotypes across generations. Developing more
advanced methods that effectively use pedigree information unlocks unprecedented opportunities to directly
measure contemporary evolution and study many key questions in evolutionary biology. The proposed
framework outlines a powerful approach for future evolutionary and human genomics research. A better
understanding of evolution on ecological time scales offers valuable insights to studies of organismal response
to rapid environmental change, as well as the evolution of drug and pesticide resistance.

Grant Number: 5R35GM133412-05
NIH Institute/Center: NIH
Principal Investigator: Nancy Chen