DOI: 10.5061/dryad.76hdr7t4p
title: Archaeogenomic analysis of Chesapeake Atlantic sturgeon illustrates shaping of its populations in recovery from severe overexploitation

description: Atlantic sturgeon (Acipenser oxyrinchus ssp. oxyrinchus) has been a food
 resource in North America for millennia. However, industrial-scale fishing
 activities following the establishment of European colonies led to
 multiple collapses of sturgeon stocks, driving populations such as those
 in the Chesapeake area close to extinction. While recent conservation
 efforts have been successful in restoring census numbers, little is known
 regarding genomic consequences of the population bottleneck. Here, we
 characterise its effect on present-day population structuring and genomic
 diversity in James River populations. To establish a pre-collapse
 baseline, we collected genomic data from archaeological remains from
 Middle Woodland Maycock’s Point (c. 200-900 CE), as well as Jamestown and
 Williamsburg colonial sites. Demographic analysis of recovered mitogenomes
 reveals a historical collapse in effective population size, also reflected
 in diminished present-day mitogenomic diversity and structure. We infer
 that James River fall and spring spawning populations likely took shape in
 recent years of population recovery, where genetic drift enhanced the
 degree of population structure. The mismatch of mitogenomic lineages to
 geographical-seasonal groupings implies that despite their homing instinct
 and differential adaptation to season-specific behaviour, colonisation of
 new rivers has been a key ecological strategy for Atlantic sturgeon over
 evolutionary timescales.
description: This dataset comprises the intermediary files obained from
 bioinformatic processing of raw DNA sequnces obtained through high
 throughput sequencing of Atlantic sturgeon (AS). Sources of modern AS
 data: fin clips from James River (Chesapeake DPS) fall and spring
 populations; Great PeeDee River (South Carolina DPS) fall and spring
 populations. Sources of archaeological AS data: remains in the form of
 bones and scutes from Jamestown Colony, Williamsburg Colony and
 Maycock's point (Middle Woodland site).
 Specifically, the datasets produced are based on variants called
 from target captured exonic DNA and mitogenomes sequenced with the aid of
 target capture. The population genomic and phylogenomic analytical steps
 conducted in the publication are outlined here.
description: # Archaeogenomic analysis of Chesapeake Atlantic sturgeon illustrates
 shaping of its populations in recovery from severe overexploitation
 [https://doi.org/10.5061/dryad.76hdr7t4p](https://doi.org/10.5061/dryad.76hdr7t4p) This dataset contains files and associated scripts, arranged into 7 sections, corresponding to different analytical processes conducted for the manuscript.  See file `0. READ ME Chesapeake Atlantic Sturgeon workflow` within the zip folder for more details. ## Description of the data and file structure 1\. Alignment files (nuclear and mitochondrial) 2\. Files for ADMIXTURE analysis 3\. PCA and Procrustes PCA - fitting of poorly genotyped ancient samples to population structure analysis 4\. James River fall/spring population assignment tests - testing affinity of ancient samples 5\. Nucleotide diversity estimations for modern samples 6\. Alignments used in phylogenetic and Bayesian Skyline analyses 7\. (Supplementary) files used for currentNe ## Sharing/Access information Links to other publicly accessible locations of the data: NCBI (to be linked here in due course) TreeBase (to be linked here in due course) ## Code/Software See `0. READ ME Chesapeake Atlantic Sturgeon workflow`