Supplemental Table Captions
Supplemental Table 1. GT-seq primers, probes, and variants for the 325
single nucleotide polymorphism loci from white sturgeon.
References Cited
Anders, P. J., Drauch-Schreier, A., Rodzen, J., Powell, M. S., Narum,
S., & Crossman, J. A. (2011). A review of genetic evaluation tools for
conservation and management of North American sturgeons: Roles,
benefits, and limitations. Journal of Applied Ichthyology . doi:
10.1111/j.1439-0426.2011.01830.x
Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery
rate: a practical and powerful approach to multiple testing.Journal of the Royal Statistical Society, Series B , 57 (1),
289–300.
Beyea, M. M., Benfey, T. J., & Kieffer, J. D. (2005). Hematology and
stress physiology of juvenile diploid and triploid shortnose sturgeon
(Acipenser brevirostrum). Fish Physiology and Biochemistry ,31 , 303–313. doi: 10.1007/s10695-005-1552-y
Blankenship, S. M., Schumer, G., Van Eenennaam, J. P., & Jackson, Z. J.
(2017). Estimating number of spawning white sturgeon adults from embryo
relatedness. Fisheries Management and Ecology . doi:
10.1111/fme.12217
Blischak, P. D., Kubatko, L. S., & Wolfe, A. D. (2018). SNP genotyping
and parameter estimation in polyploids using low-coverage sequencing
data. Bioinformatics . doi: 10.1093/bioinformatics/btx587
Campbell, N. R., Harmon, S. A., & Narum, S. R. (2015).
Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP
genotyping method based on custom amplicon sequencing. Molecular
Ecology Resources , 15 (4), 855–867. doi: 10.1111/1755-0998.12357
Catchen, J. M., Amores, A., Hohenlohe, P. A., Cresko, W. A., &
Postlethwait, J. H. (2011). Stacks: Building and Genotyping Loci De Novo
From Short-Read Sequences. G3: Genes, Genomes, Genetics‘ ,1 , 3171–3182.
Clark, L. V., & Schreier, A. D. (2017). Resolving microsatellite
genotype ambiguity in populations of allopolyploid and diploidized
autopolyploid organisms using negative correlations between allelic
variables. Molecular Ecology Resources . doi:
10.1111/1755-0998.12639
Comai, L. (2005). The advantages and disadvantages of being polyploid.Nature Reviews Genetics . doi: 10.1038/nrg1711
Crow, K. D., Stadler, P. F., Lynch, V. J., Amemiya, C., & Wagner, G. P.
(2006). The “fish-specific” Hox cluster duplication is coincident with
the origin of teleosts. Molecular Biology and Evolution . doi:
10.1093/molbev/msj020
Dehal, P., & Boore, J. L. (2005). Two rounds of whole genome
duplication in the ancestral vertebrate. PLoS Biology . doi:
10.1371/journal.pbio.0030314
Drauch Schreier, A., Gille, D., Mahardja, B., & May, B. (2011). Neutral
markers confirm the octoploid origin and reveal spontaneous
autopolyploidy in white sturgeon, Acipenser transmontanus. Journal
of Applied Ichthyology . doi: 10.1111/j.1439-0426.2011.01873.x
Du, K., Stöck, M., Kneitz, S., Klopp, C., Woltering, J. M., Adolfi, M.
C., … Schartl, M. (2020). The sterlet sturgeon genome sequence
and the mechanisms of segmental rediploidization. Nature Ecology
and Evolution . doi: 10.1038/s41559-020-1166-x
Dufresne, F., Stift, M., Vergilino, R., & Mable, B. K. (2014). Recent
progress and challenges in population genetics of polyploid organisms:
An overview of current state-of-the-art molecular and statistical tools.Molecular Ecology . doi: 10.1111/mec.12581
Fiske, J. A., Van Eenennaam, J. P., Todgham, A. E., Young, S. P.,
Holem-Bell, C. E., Goodbla, A. M., & Schreier, A. D. (2019). A
comparison of methods for determining ploidy in white sturgeon
(Acipenser transmontanus). Aquaculture . doi:
10.1016/j.aquaculture.2019.03.009
Gille, D. A., Famula, T. R., May, B. P., & Schreier, A. D. (2015).
Evidence for a maternal origin of spontaneous autopolyploidy in cultured
white sturgeon (Acipenser transmontanus). Aquaculture . doi:
10.1016/j.aquaculture.2014.10.002
Havelka, M., Bytyutskyy, D., Symonová, R., Ráb, P., & Flajšhans, M.
(2016). The second highest chromosome count among vertebrates is
observed in cultured sturgeon and is associated with genome plasticity.Genetics Selection Evolution . doi: 10.1186/s12711-016-0194-0
Hildebrand, L. R., Drauch Schreier, A., Lepla, K., McAdam, S. O.,
McLellan, J., Parsley, M. J., … Young, S. P. (2016). Status of
White Sturgeon (Acipenser transmontanus Richardson, 1863) throughout the
species range, threats to survival, and prognosis for the future.Journal of Applied Ichthyology . doi: 10.1111/jai.13243
Holland, P. W. H., Garcia-Fernandez, J., Williams, N. A., & Sidow, A.
(1994). Gene duplications and the origins of vertebrate development.Development .
Huang, K., Guo, S. T., Shattuck, M. R., Chen, S. T., Qi, X. G., Zhang,
P., & Li, B. G. (2015). A maximum-likelihood estimation of pairwise
relatedness for autopolyploids. Heredity . doi:
10.1038/hdy.2014.88
Huang, Kang, Dunn, D. W., Ritland, K., & Li, B. (2020). polygene:
Population genetics analyses for autopolyploids based on allelic
phenotypes. Methods in Ecology and Evolution . doi:
10.1111/2041-210X.13338
Ilut, D. C., Nydam, M. L., & Hare, M. P. (2014). Defining loci in
restriction-based reduced representation genomic data from nonmodel
species: Sources of bias and diagnostics for optimal clustering.BioMed Research International . doi: 10.1155/2014/675158
Jager, H. I. (2005). Genetic and demographic implications of aquaculture
in white sturgeon (Acipenser transmontanus) conservation. Canadian
Journal of Fisheries and Aquatic Sciences . doi: 10.1139/f05-106
Jay, K., Crossman, J. A., & Scribner, K. T. (2014). Estimates of
Effective Number of Breeding Adults and Reproductive Success for White
Sturgeon. Transactions of the American Fisheries Society . doi:
10.1080/00028487.2014.931301
Jombart, T. (2008). Adegenet: A R package for the multivariate analysis
of genetic markers. Bioinformatics . doi:
10.1093/bioinformatics/btn129
Jones, O. R., & Wang, J. (2010). COLONY: A program for parentage and
sibship inference from multilocus genotype data. Molecular Ecology
Resources . doi: 10.1111/j.1755-0998.2009.02787.x
Leal, M. J., Clark, B. E., Van Eenennaam, J. P., Schreier, A. D., &
Todgham, A. E. (2018). The effects of warm temperature acclimation on
constitutive stress, immunity, and metabolism in white sturgeon
(Acipenser transmontanus) of different ploidies. Comparative
Biochemistry and Physiology -Part A : Molecular and Integrative
Physiology . doi: 10.1016/j.cbpa.2018.05.021
Leal, M. J., Van Eenennaam, J. P., Schreier, A. D., & Todgham, A. E.
(2020). Diploid and triploid white sturgeon (Acipenser transmontanus)
differ in magnitude but not kinetics of physiological responses to
exhaustive exercise at ambient and elevated temperatures. Canadian
Journal of Fisheries and Aquatic Sciences . doi: 10.1139/cjfas-2019-0289
Ludwig, A., Belfiore, N. M., Pitra, C., Svirsky, V., & Jenneckens, I.
(2001). Genome duplication events and functional reduction of ploidy
levels in sturgeon (Acipenser, Huso and Scaphirhynchus).Genetics .
Lynch, M., & Conery, J. S. (2000). The evolutionary fate and
consequences of duplicate genes. Science . doi:
10.1126/science.290.5494.1151
Meirmans, P. G., Liu, S., & Van Tienderen, P. H. (2018). The Analysis
of Polyploid Genetic Data. Journal of Heredity . doi:
10.1093/jhered/esy006
Meirmans, P. G., & Van Tienderen, P. H. (2013). The effects of
inheritance in tetraploids on genetic diversity and population
divergence. Heredity . doi: 10.1038/hdy.2012.80
Meyer, A., & Van De Peer, Y. (2005). From 2R to 3R: Evidence for a
fish-specific genome duplication (FSGD). BioEssays . doi:
10.1002/bies.20293
Miller, M. R., Dunham, J. P., Amores, A., Cresko, W. A., & Johnson, E.
A. (2007). Rapid and cost-effective polymorphism identification and
genotyping using restriction site associated DNA (RAD) markers.Genome Research . doi: 10.1101/gr.5681207
Nei, M. (1973). Analysis of gene diversity in subdivided populations.Proceedings of the National Academy of Sciences of the United
States of America . doi: 10.1073/pnas.70.12.3321
O’Leary, S. J., Puritz, J. B., Willis, S. C., Hollenbeck, C. M., &
Portnoy, D. S. (2018). These aren’t the loci you’re looking for:
Principles of effective SNP filtering for molecular ecologists.Molecular Ecology , 0 (ja). doi: 10.1111/mec.14792
Ogden, R., Gharbi, K., Mugue, N., Martinsohn, J., Senn, H., Davey, J.
W., … Congiu, L. (2013). Sturgeon conservation genomics: SNP
discovery and validation using RAD sequencing. Molecular Ecology .
doi: 10.1111/mec.12234
Ohno, S. (1971). Evolution by Gene Duplication. Population (French
Edition) . doi: 10.2307/1530208
Puritz, J. B., Matz, M. V, Toonen, R. J., Weber, J. N., Bolnick, D. I.,
& Bird, C. E. (2014). Demystifying the RAD fad. Molecular
Ecology , 23 (24), 5937–5942.
Rajkov, J., Shao, Z., & Berrebi, P. (2014). Evolution of polyploidy and
functional diploidization in sturgeons: Microsatellite analysis in 10
sturgeon species. Journal of Heredity . doi: 10.1093/jhered/esu027
Raymond, M., & Rousset, F. (1995). An exact test for population
differentiation. Evolution , 49 , 1280–1283. doi:
10.1111/j.1558-5646.1995.tb04456.x
Rodzen, J. A., Famula, T. R., & May, B. (2004). Estimation of parentage
and relatedness in the polyploid white sturgeon (Acipenser
transmontanus) using a dominant marker approach for duplicated
microsatellite loci. Aquaculture . doi:
10.1016/S0044-8486(03)00450-2
Ronfort, J., Jenczewski, E., Bataillon, T., & Rousset, F. (1998).
Analysis of population structure in autotetraploid species.Genetics .
Roques, S., Chancerel, E., Boury, C., Pierre, M., & Acolas, M. L.
(2019). From microsatellites to single nucleotide polymorphisms for the
genetic monitoring of a critically endangered sturgeon. Ecology
and Evolution . doi: 10.1002/ece3.5268
Schreier, A. D., May, B., & Gille, D. A. (2013). Incidence of
spontaneous autopolyploidy in cultured populations of white sturgeon,
Acipenser transmontanus. Aquaculture . doi:
10.1016/j.aquaculture.2013.09.012
Schreier, A. Drauch, Mahardja, B., & May, B. (2013). Patterns of
population structure vary across the range of the white sturgeon.Transactions of the American Fisheries Society . doi:
10.1080/00028487.2013.788554
Schreier, A. Drauch, Rodzen, J., Ireland, S., & May, B. (2012). Genetic
techniques inform conservation aquaculture of the endangered Kootenai
river white sturgeon Acipenser transmontanus. Endangered Species
Research . doi: 10.3354/esr00387
Schreier, A., Stephenson, S., Rust, P., & Young, S. (2015). The case of
the endangered Kootenai River white sturgeon (Acipenser transmontanus)
highlights the importance of post-release genetic monitoring in captive
and supportive breeding programs. Biological Conservation . doi:
10.1016/j.biocon.2015.09.011
Schreier, Andrea Drauch, Mahardja, B., & May, B. (2012). Hierarchical
patterns of population structure in the endangered fraser river white
sturgeon (acipenser transmontanus) and implications for conservation.Canadian Journal of Fisheries and Aquatic Sciences , 69 ,
1968–1980. doi: 10.1139/f2012-120
Scott, W., & Crossman, E. (1973). Freshwater fishes of Canada,
Bulletin 184 . Fisheries Research Board of Canada, Ottawa.
Soltis, D. E., Visger, C. J., Blaine Marchant, D., & Soltis, P. S.
(2016). Polyploidy: Pitfalls and paths to a paradigm. American
Journal of Botany . doi: 10.3732/ajb.1500501
Spoelhof, J. P., Soltis, P. S., & Soltis, D. E. (2017). Pure
polyploidy: Closing the gaps in autopolyploid research. Journal of
Systematics and Evolution . doi: 10.1111/jse.12253
Thorstensen, M., Bates, P., Lepla, K., & Schreier, A. (2019). To breed
or not to breed? Maintaining genetic diversity in white sturgeon
supplementation programs. Conservation Genetics . doi:
10.1007/s10592-019-01190-4
Van Eenennaam, A. L., Murray, J. D., & Medrano, J. F. (1998).
Synaptonemal complex analysis in spermatocytes of white sturgeon,
Acipenser transmontanus richardson (pisces, acipenseridae), a fish with
a very high chromosome number. Genome , 41 , 51–61. doi:
10.1139/g97-101
Van Eenennaam, J. P., Fiske, A. J., Leal, M. J., Cooley-Rieders, C.,
Todgham, A. E., Conte, F. S., & Schreier, A. D. (2019). Mechanical
shock during egg de-adhesion and post-ovulatory ageing contribute to
spontaneous autopolyploidy in white sturgeon culture (Acipenser
transmontanus). Aquaculture . doi:
10.1016/j.aquaculture.2019.734530
Wang, J. (2018). Effects of sampling close relatives on some elementary
population genetics analyses. Molecular Ecology Resources . doi:
10.1111/1755-0998.12708
Wang, J., & Scribner, K. T. (2014). Parentage and sibship inference
from markers in polyploids. Molecular Ecology Resources . doi:
10.1111/1755-0998.12210
Waples, R. S., & Anderson, E. C. (2017). Purging putative siblings from
population genetic data sets: A cautionary view. Molecular
Ecology . doi: 10.1111/mec.14022
Weir, B. S. (1997). Genetic Data Analysis II. Biometrics . doi:
10.2307/2533134
Wendel, J. F. (2000). Genome evolution in polyploids. Plant
Molecular Biology . doi: 10.1023/A:1006392424384
Willis, S. C., Hollenbeck, C. M., Puritz, J. B., Gold, J. R., &
Portnoy, D. S. (2017). Haplotyping RAD loci: an efficient method to
filter paralogs and account for physical linkage. Molecular
Ecology Resources , 17 (5), 955–965. doi: 10.1111/1755-0998.12647
Wolfe, K. H. (2001). Yesterday’s polyploids and the mystery of
diploidization. Nature Reviews Genetics . doi: 10.1038/35072009