Local adaptation in an alpine finch, GWAS and FST output files

Understanding patterns and mechanisms underlying local adaptation is becoming increasingly important for species conservation amid anthropogenically driven environmental change. Alpine systems are experiencing particularly intense pressure from environmental change resulting from increased rates of warming and corresponding loss of snow and ice. We integrate morphological and genetic analyses to identify traits important for local adaptation in one of the highest elevation breeding birds in North America, the Sierra Nevada Gray-crowned Rosy Finch. We performed an in-depth analysis of how traits with known links to thermoregulation in birds, such as wing length, bill size, and feather microstructure, vary between two populations at sites with contrasting climate and environmental conditions. We identified loci underlying these traits using a genome-wide association study and further examined regions of the genome related to altitude adaptation and cold tolerance using FST outlier tests. ...,
Sample Collection
A total of 171 Gray-crowned Rosy Finches were collected using potter traps in the White Mountains (n=98) and Piute Pass (n=73) in June and July, the peak of the species’ breeding season (MacDougall-Shackleton et al., 2000). Birds showing signs of stress were released, resulting in slight variation in the types of data collected for each individual. Blood samples were collected from 150 of the captured birds using the brachial wing vein and stored in Queen’s lysis buffer at room temperature (Owen, 2011; Seutin et al., 1991). At the same time, morphological measurements - tarsus length, wing chord, beak width, beak length, beak depth, and nare length - were also collected from 154 of the birds using an electronic caliper, and 5-10 body feathers were collected from the breast of all individuals. Birds were banded to allow for identification of the individuals and to avoid recapture, then released. All handling and banding of birds was done following the guidelines and pr..., # Local adaptation in an alpine finch, GWAS and FST output files

Dataset DOI: [10.5061/dryad.kwh70rzhs](https://doi.org/10.5061/dryad.kwh70rzhs)

## Description of the data and file structure

#### Overview

This repository contains data and analysis outputs associated with the study:

**The Genetic and Morphological Basis of Local Adaptation to Elevational Extremes in an Alpine Finch**

The dataset stored here includes:

* Genome-wide association study (GWAS) outputs
* FST outlier analyses
* Gene annotation and candidate gene identification outputs

These data were used to investigate patterns of local adaptation in the **Gray-crowned Rosy Finch (*Leucosticte tephrocotis dawsonii*)** through the integration of genomic and phenotypic variation.

#### Study Design Summary

Samples were collected from alpine populations and included:

* Morphological measurements (e.g., beak traits, wing chord, body size metrics)
* Feather microstructure measurements (e.g., barbule density, node density)..., ,