Schematic of the major flight feathers of black-throated blue warbler.

<p>Primaries (P1-P9) and secondaries (S1-S6) are numbered from the center of the wing. Rectrices (R1-R6) are numbered from the center of the tail outward. Illustration modified from an original drawing by Jacqueline Mask.</p

Variation of <i>δ</i>²H_<i>F</i> in plumage of black-throated blue warblers in the Big Santeetlah Creek watershed.

<p>Box plots depict minimum values, first quartile, median, third quartile, and maximum values observed among population samples for primaries (P1-P9), secondaries (S1-S6), rectrices (R1-R6), and ventral contour feathers (V1-V3). Data are presented by year (2013 and 2014).</p

Primers used in the ancient DNA analysis (5′-3′ direction).

<p>Primers used in the ancient DNA analysis (5′-3′ direction).</p

Ancient samples: sampling locations, units and dates in calendar years based on direct radiocarbon dating of bones (samples in italics) or of associated shell middens.

<p>45CA24B70  =  Ozette site; 45CA400  =  Shell midden deposit; 45CA23  =  Shell midden on Quilleute Indian reservation.</p

Phylogenetic network and tree constructed from modern and ancient gray whale haplotypes.

<p>(<b>a</b>) Haplogroup network for ancient eastern Pacific and modern eastern and western Pacific samples (constructed in TCS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035039#pone.0035039-Clement1" target="_blank">[52]</a>). Haplogroups were defined by grouping together sequences with one or zero differences. (<b>b</b>) Neighbor-joining (midpoint-rooted) tree using ancient and modern haplotypes from PAUP* <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035039#pone.0035039-Swofford1" target="_blank">[53]</a>. The HKY85 model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035039#pone.0035039-Hasegawa1" target="_blank">[75]</a> was used to correct genetic distances. Ancient samples have the prefix BAL and are denoted with an arrow. Each haplotype is represented only once in the tree.</p

Bayesian skyline plots using empirical ancient and eastern Pacific modern datasets.

<p>(black solid line = median; black dashed lines = 95% highest posterior density intervals (HPDIs)), and for a simulated dataset in which bottleneck from 96,000 to 22,000 individuals occurred 1200 ybp (gray solid line = median; gray dashed lines = 95% HPDIs). BSP results were averaged across five replicate runs. NB: The BSP analysis used here assumes a single panmictic population.</p

Posterior density distributions for Approximate Bayesian Computation results.

<p>Based on ancient eastern Pacific and modern eastern samples (shaded area) and prior uniform sampling distributions based on one million iterations for (a) time of bottleneck in generations (t_bot); (b) minimum female effective population size at bottleneck (N_ef(bot)); and (c) pre-bottleneck female effective population size (N_ef(prebot)).</p

Appendix A. A table comparing the gut contents of California sheephead in 1980–1982 and 2007.

A table comparing the gut contents of California sheephead in 1980–1982 and 2007

Mean stable isotope values for modern (USNM), modern corrected (USNM (maximum Suess)) and ancient (Ozette) samples; error bars represent standard errors.

<p>No significant overall difference between ancient and modern samples is observed once modern samples are corrected for the Suess effect. The Suess effect results in an average shift in δ¹³C of 0.3%.</p

Simulated demographic scenario.

<p>The size of the ancient population is assumed to range from 20,000–116,000 (census size). The modern population is assumed to have a census size of 22,000. The size and timing of the bottleneck (pictured here at 10,000 individuals and 10 generations ago) were varied between 100–10,000 (census size) and 1–100 generations ago.</p