1. Evolutionary Biology
  2. Genetics and Genomics

Seasonally migratory songbirds have different historic population size characteristics than resident relatives

  1. Kevin Winker  Is a corresponding author
  2. Kira Delmore
  1. University of Alaska Museum and Department of Biology and Wildlife, United States
  2. Department of Biology, Texas A&M University, United States
  3. Ecology, Evolution, and Environmental Biology, Columbia University, United States
https://doi.org/10.7554/eLife.90848.3
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  1. Kevin Winker
  2. Kira Delmore
(2025)
Seasonally migratory songbirds have different historic population size characteristics than resident relatives
eLife 12:RP90848.
https://doi.org/10.7554/eLife.90848.3
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6 figures, 3 tables and 2 additional files

Figures

Figure 1
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The phylogenetic tree of the songbird lineages in this study, from the genera Catharus and Hylocichla.

Neotropical residents are shaded in gray.

Figure 2
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Distribution maps of the thrush taxa in this study.

Among seasonal migrants, green indicates breeding range and yellow is wintering range. Among sedentary lineages (those shaded in gray), purple indicates year-round range. Data are from Bird Life International and the Handbook of the Birds of the World, 2021. Available at http://datazone.birdlife.org/species/requestdis.

Figure 3
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Partial historic effective population size curves from all lineages in this study, based on pairwise sequentially Markovian coalescent (PSMC) analyses.

Each peak of initial growth is set to zero years to set a common framework in which to visualize the periods and magnitudes of initial growth among migrant (red) and resident (blue) lineages. See specific lineages with their bootstrapped results in Figure 5.

Figure 4
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Historic effective population size curves from all lineages, based on pairwise sequentially Markovian coalescent (PSMC) analyses.

Migrant lineages are in red and resident lineages in blue. See specific lineages with their bootstrapped results in Figure 5.

Figure 5
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Montage of the historic effective population size curves of all lineages analyzed in this study, with each lineage in a separate panel (based on pairwise sequentially Markovian coalescent [PSMC] analyses).

Sedentary lineages are highlighted in gray. Note that scales on both axes vary among panels, and that the X axis is on a log scale. Bold red lines are the main curves from the original data, and pink lines reflect 100 replicates from bootstrapped sequences. Bold red curves are all overlaid on common axes in the single panel of Figure 4.

Figure 6
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Graphic presentation of the C. minimus pairwise sequentially Markovian coalescent (PSMC) dataset, showing effective population size (Ne×104) from 50 Kyr back in time to the lineages’ origins as estimated from genomic data.

The variables in our analyses are the mean and SD of the effective population size (Ne) values, deltaT of initial growth (timetrough – timepeak), the degree of that growth (1 – [Ntrough/Npeak]), and the rate of that growth (degree/deltaT).

Tables

Table 1
Data from pairwise sequentially Markovian coalescent (PSMC) analyses reflecting effective population sizes (Ne×104) through history at depths > 50 Kyr and the five variables derived and analyzed from that output.

Taxa shaded in gray are Neotropical residents.

TaxonMean Ne (±SD)SD/meanDegree of early growth 1 - (Ntrough/Npeak)Rate of early growth degree/deltaTdeltaT
H. mustelina35.63 (±20.11)0.560.862.92E-072,946,862
Catharus fuscescens95.59 (±50.99)0.530.831.93E-074,284,020
Catharus guttatus E75.34 (±65.69)0.870.904.48E-072,021,768
Catharus guttatus W39.72 (±24.20)0.610.813.28E-072,477,684
Catharus minimus63.71 (±28.83)0.450.782.17E-073,594,914
Catharus ustulatus swainsonii76.61 (±66.61)0.870.792.12E-073,740,764
Catharus ustulatus ustulatus39.56 (±12.15)0.310.632.14E-072,943,763
Catharus bicknelli46.90 (±24.12)0.510.782.79E-072,781,554
Catharus aurantiirostris12.38 (±2.83)0.23–0.75–1.00E-06747,451
Catharus fuscater11.38 (±1.66)0.150.396.18E-07627,449
Catharus frantzii24.71 (±8.41)0.340.172.20E-07774,024
Catharus gracilirostris29.98 (±9.28)0.310.583.52E-071,637,663
Catharus mexicanus37.10 (±16.18)0.440.753.34E-072,250,295
Catharus occidentalis76.40 (±53.14)0.700.912.11E-074,292,405
Means (±SD)
Migrants59.34 (±35.70)*0.57 (±0.20)*0.798 (±0.08)*2.73E-7 (±0.85E-7)3,098,906 (±732,563)*
Residents31.99 (±15.25)0.36 (±0.19)0.341 (±0.59)1.23E-7 (±5.69E-7)1,721,547 (+1,409,939)
  1. *

    p<0.05.

Appendix 1—table 1
Specimen data and NCBI-SRA numbers (PRJNA1112856).

Vouchered specimens are housed in the following institutions: UAM (University of Alaska Museum), MSB (Museum of Southwestern Biology, University of New Mexico), LSUMNS (Louisiana State University Museum of Natural Science), and FMNH (Field Museum of Natural History).

InstitutionCatalog #SpeciesYearField no.LocalityNCBI-SRA
UAM28620H. mustelina2010KSW5403Belize: Toledo District; Big FallsSRR29089747
UAM27774C. fuscescens2007KSW5151Belize: Toledo District; Big FallsSRR29089742
UAM15202C. guttatus E1992KSW4013USA: Vermont; BrandonSRR29089748
UAM26337C. guttatus W2008UAMX5095USA: Alaska; KodiakSRR29089739
UAM22642C. minimus2003KSW5000USA: Alaska; FairbanksSRR29089741
n.a. (blood)KF15K01C. ustulatus swainsonii2011KF15K01Canada: British Columbia, KamloopsPending
n.a. (blood)KF01K01C. u. ustulatus2011KF01K01Canada: British Columbia, KamloopsSRS18060177
UAM19996C. bicknelli2000KSW3633USA: Vermont; Mt MansfieldSRR29089740
UAM25341C. aurantiirostris2004MJM1154Panama: Chiriqui; El SaltoSRR29089749
MSB31939C. fuscater2008MSB31939Peru: Amazonas; 4.5 km N TullanyaSRR29089746
UAM25098C. frantzii2004KSW4485Panama: Chiriqui; Volcan BaruSRR29089744
LSUMNS138784C. gracilirostris1990JMB1065; B-16270Costa Rica: San Jose; Cerro de la MuerteSRR29089750
UAM10352C. mexicanus1994PEP2489Mexico: Veracruz; Volcan San MartinSRR29089743
FMNH343305C. occidentalis1989MEX408Mexico: Oaxaca; TotontepecSRR29089745
Appendix 1—table 2
Data from pairwise sequentially Markovian coalescent (PSMC) analyses reflecting effective population sizes (Ne) (×104) through history at depths >50 Kyr (using variable generation times) and the five variables derived and analyzed from that output.

Taxa shaded in gray are Neotropical residents.

TaxonMean Ne (+SD)SD/meanDegree of early growth 1 - (Ntrough/Npeak)Rate of early growth degree/deltaTdeltaT
H. mustelina35.63 (+20.11)0.560.863.03E-072,834,197
C. fuscescens95.77 (+56.07)0.580.831.79E-074,627,125
C. guttatus E78.69 (+76.09)0.970.904.89E-071,850,522
C. guttatus W40.15 (+24.11)0.600.813.59E-072,266,059
C. minimus63.71 (+28.83)0.450.782.35E-073,323,013
C. ustulatus swainsonii76.61 (+66.61)0.870.792.12E-073,740,764
C. ustulatus ustulatus39.56 (+12.15)0.310.632.16E-072,909,628
C. bicknelli46.90 (+24.12)0.510.783.01E-072,580,641
C. aurantiirostris12.39 (+2.78)0.22–0.75–7.93E-07942,318
C. fuscater11.33 (+1.66)0.150.395.57E-07713,817
C. frantzii24.97 (+8.61)0.340.171.93E-07886,294
C. gracilirostris30.80 (+11.08)0.360.583.25E-071,775,757
C. mexicanus37.10 (+16.18)0.440.752.92E-072,575,082
C. occidentalis76.39 (+53.14)0.700.911.97E-074,595,855
Means (+SD)
Migrants59.63 (+38.48)†0.61 (+0.21)*0.798 (+0.08)*2.87E-7 (+1.01E-7)3,016,494 (+875,860)*
Residents32.16 (+15.58)0.36 (+0.19)0.342 (+0.59)1.284E-7 (+4.71E-7)1,914,854 (+1,489,246)
  1. *

    *p<0.05.

  2. †

    p<0.01.

Additional files

MDAR checklist
https://cdn.elifesciences.org/articles/90848/elife-90848-mdarchecklist1-v1.docx
Supplementary file 1

Specimen data, NCBI-SRA numbers, and alternative generation time PSMC results.

https://cdn.elifesciences.org/articles/90848/elife-90848-supp1-v1.docx

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  1. Kevin Winker
  2. Kira Delmore
(2025)
Seasonally migratory songbirds have different historic population size characteristics than resident relatives
eLife 12:RP90848.
https://doi.org/10.7554/eLife.90848.3