References
Andrews, K., Good, J., Miller, M., Gordon L., Hohenlohe P.A. (2016)
Harnessing the power of RADseq for ecological and evolutionary
genomics. Nat Rev Genet 17, 81–92.
https://doi.org/10.1038/nrg.2015.28
Avise JC, Arnold J, Ball RM et al. (1987) Intraspecific
Phylogeography: The Mitochondrial DNA Bridge Between Population Genetics
and Systematics. Annual Review of Ecology and Systematics ,18 , 489–522.
Björk CR (2010). Distribution patterns of disjunct and endemic vascular
plants in the interior wetbelt of northwest North
America. Botany . 88 (4):
409-428. https://doi.org/10.1139/B10-030
Brent RP (1974) Algorithms for Minimization Without Derivatives.IEEE Transactions on Automatic Control , 19 , 632–633.
Breiman, L. (2001). Random forests. Mach. Learn. 45, 5-32
Brunsfeld SJ, Sullivan J, Soltis DE, Soltis PS (2001) Comparative
phylogeography of north- western North America : a synthesis. In:Integrating ecological and evolutionary processes in a spatial
context , pp. 319–339.
Brunsfeld SJ, Miller TA, Carstens BC (2007) Insights into the
Biogeography of the Pacific Northwest of North America: Evidence from
the Phylogeography of Salix melanopsis. Systematic Biology ,32 , 129–139.
Burbrink FT, Chan YL, Myers EA, Ruane S, Smith BT, Hickerson MJ. (2016)
Asynchronous demographic responses to Pleistocene climate change in
eastern Nearctic vertebrates. Ecol Lett. 19:1457–67.
Carstens BC, Stevenson AL, Degenhardt JD, Sullivan J (2004) Testing
nested phylogenetic and phylogeographic hypotheses in the Plethodon
vandykei species group. Systematic biology , 53 ,
781–792.
Cartens, B.C., Brunsfeld, S.J., Demboski, J.R., Good, J.M. and Sullivan,
J. (2005), INVESTIGATING THE EVOLUTIONARY HISTORY OF THE PACIFIC
NORTHWEST MESIC FOREST ECOSYSTEM: HYPOTHESIS TESTING WITHIN A
COMPARATIVE PHYLOGEOGRAPHIC FRAMEWORK. Evolution, 59: 1639-1652.
doi:10.1111/j.0014-3820.2005.tb01815.x
Carstens BC, Brennan RS, Chua V et al. (2013) Model selection as
a tool for phylogeographic inference: An example from the willow Salix
melanopsis. Molecular Ecology .
Chan YL, Schanzenbach D, Hickerson MJ. (2014) Detecting concerted
demographic response across community assemblages using hierarchical
approximate Bayesian computation. Mol Biol Evol. 31:2501–15.
Chase, M., C. Bleskie, I. R. Walker, D. G. Gavin, and F. S. Hu. 2008.
Midge-inferred Holocene summer temperatures in Southeastern British
Columbia, Canada. Palaeogeography Palaeoclimatology Palaeoecology
257:244-259.
Clements, F.E. (1916) Plant succession: an analysis of the development
of vegetation. Carnegie institution of Washington, Washington, USA.
Davis M.B. (1981) Quaternary History and the Stability of Forest
Communities. In: West D.C., Shugart H.H., Botkin D.B. (eds) Forest
Succession. Springer Advanced Texts in Life Sciences. Springer, New
York, NY
De La Torre, A. R., Li, Z., Van de Peer, Y., & Ingvarsson, P. K.
(2017). Contrasting Rates of Molecular Evolution and Patterns of
Selection among Gymnosperms and Flowering Plants. Molecular
biology and evolution , 34 (6), 1363–1377.
https://doi.org/10.1093/molbev/msx069
Dettman JR, Taylor, JW. 2004. Mutation and evolution of microsatellite
loci in Neurospora. Genetics, 168:1231-1248.
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small
quantities of fresh leaf tissue. Phytochemical Bulletin , 19,
11–15.
Earl, DA. and vonHoldt, B M. (2012) STRUCTURE HARVESTER: a
website and program for visualizing STRUCTURE output and implementing
the Evanno method. Conservation Genetics Resources vol. 4 (2) pp.
359-361 doi: 10.1007/s12686-011-9548-7
Eaton DAR (2014) PyRAD: Assembly of de novo RADseq loci for phylogenetic
analyses. Bioinformatics , 30, 1844–1849.
Eaton DAR, Overcast I ( 2020) ipyrad: Interactive assembly and analysis
of RADseq datasets, Bioinformatics, https://doi.org/10.1093/bioinformatics/btz966
Edgar RC (2010) Search and clustering orders of magnitude faster than
BLAST. Bioinformatics , 26 (19):
2460-2461. doi:10.1093/bioinformatics/btq461
Espíndola A, Ruffley M, Smith ML et al. (2016) Identifying
cryptic diversity with predictive phylogeography. Proceedings of
the Royal Society B: Biological Sciences , 283 , 20161529.
Evanno, G., Regnaut, S. and Goudet, J. (2005), Detecting the number of
clusters of individuals using the software structure: a
simulation study. Molecular Ecology, 14: 2611-2620.
doi:10.1111/j.1365-294X.2005.02553.x
Excoffier L, Foll M (2011) fastsimcoal: A continuous-time coalescent
simulator of genomic diversity under arbitrarily complex evolutionary
scenarios. Bioinformatics , 27 , 1332–1334.
Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M (2013)
Robust Demographic Inference from Genomic and SNP Data. PLoS
Genetics , 9 .
Faegri, K., and J. Iversen. 1992. Textbook of Pollen Analysis. Hafner,
New York.
Falush D, Stephens M, Pritchard JK (2003) Inference of population
structure using multilocus genotype data: Linked loci and correlated
allele frequencies. Genetics , 164 , 1567–1587.
Fernandez, MC, Hu, FS, Gavin, DG, et al. (2021) A tale of two conifers:
Migration across a dispersal barrier outpaced regional expansion from
refugia. Journal of
Biogeography , 00 , 1– 11. https://doi.org/10.1111/jbi.14209
Fick, S.E. and Hijmans, R.J. (2017), WorldClim 2: new 1‐km spatial
resolution climate surfaces for global land areas. Int. J. Climatol, 37:
4302-4315. doi:10.1002/joc.5086
Flessa, K. W., S. T. Jackson, J. D. Aber, M. A. Arthur, P. R. Crane, D.
H. Erwin, R. W. Graham, J. B. C. Jackson, S. M. Kidwell, C. G. Maples,
C. H. Peterson, and O. J. Reichman. 2005. The Geological Record of
Ecological Dynamics: Understanding the Biotic effects of Future
Environmental Change. National Academies Press, Washington, D.C.
Garrick, R. C., Bonatelli, I. A. S., Hyseni, C. Morales, A., Pelletier,
T. A., Perez, M. F., Carstens, B. C. (2015). The evolution of
phylogeographic datasets. Molecular
Ecology , 24 , 1164–1171.
Gavin, D. G., L. B. Brubaker, J. S. McLachlan, and W. W. Oswald. 2005.
Correspondence of pollen assemblages with forest zones across steep
environmental gradients, Olympic Peninsula, Washington, USA. Holocene
15:648-662.
Gavin, D. G., and F. S. Hu. 2006. Spatial variation of climatic and
non-climatic controls on species distribution: the range limit of Tsuga
heterophylla. Journal of Biogeography 33:1384-1396.
Gavin DG, Hu FS, Walker IR, Westover K (2009) The Northern Inland
Temperate Rainforest of British Columbia: Old Forests with a Young
History? Northwest Science , 83 , 70–78.
Gehara, M, Garda, AA, Werneck, FP, et al. (2017) Estimating synchronous
demographic changes across populations using hABC and its application
for a herpetological community from northeastern Brazil. Mol
Ecol . 26: 4756– 4771. https://doi.org/10.1111/mec.14239
Gleason, H. A. (1926). The Individualistic Concept of the Plant
Association. Bulletin of the Torrey Botanical Club , 53 (1),
7–26. doi: 10.2307/2479933
Gottesfeld AS, Swanson FJ, Gottesfeld LMJ. (1981) A Pleistocene
low-elevation subalpine forest in the wester cascades, Oregon. Northwest
Sci. 55: 157-167
Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009)
Inferring the joint demographic history of multiple populations from
multidimensional SNP frequency data. PLoS Genetics , 5 .
Habeck, J. R. (1987). Present-Day Vegetation in the Northern Rocky
Mountains. Annals of the Missouri Botanical Garden , 74 (4),
804–840. doi: 10.2307/2399451
Hebda RJ, Mathewes RW. (1984) Holocene history of cedar and native
indian cultures of the North American Pacific Coast. Science 225:
711-713.
Herring EM, Gavin DG (2015) Climate and vegetation since the Last
Interglacial (MIS 5e) in a putative glacial refugium, northern Idaho,
USA. Quaternary Science Reviews . 117: 82-95.
https://doi.org/10.1016/j.quascirev.2015.03.028.
Hickerson MJ, Stahl EA, Lessios HA. (2006) Test for simultaneous
divergence using approximate Bayesian computation. Evolution.
60:2435–53.
Janes, JK, Miller, JM, Dupuis, JR, et al. (2017) The K = 2
conundrum. Mol Ecol . 26: 3594
– 3602. https://doi.org/10.1111/mec.14187
Kirkwood JE (1922). Forest distribution in the northern Rocky Mountains.
Univ. Montana Studies, Bull. 247: 1-180.
Kruschke, J. K. 2011. Doing Bayesian data analysis: a tutorial
with R and BUGS. Burlington, MA: Academic Press.
Liaw, A. & Wiener, M. (2002). Classification and Regression by
randomForest. R news ., 2/3, 18-22.
Meng X-L, Rubin DB (1993) Maximum Likelihood Estimation via the ECM
Algorithm: A General Framework. Biometrika , 80 ,
267–278.
Mehringer, P. J., Jr. (1996). Columbia River Basin Ecosystems: Late
Quaternary Environments. Contract Report. Interior Columbia Basin
Ecosystem Management Project.
Metzger G, Espindola A, Waits LP, Sullivan J (2015) Genetic structure
across broad spatial and temporal scales: Rocky mountain tailed frogs
(Ascaphus montanus; Anura: Ascaphidae) in the Inland Temperate
Rainforest. Journal of Heredity , 106 , 700–710.
Minore, Don. 1990. Thuja plicata Donn ex D. Don western redcedar.
In: Burns, Russell M.; Honkala, Barbara H., technical coordinators.
Silvics of North America. Volume 1. Conifers. Agric. Handb. 654.
Washington, DC: U.S. Department of Agriculture, Forest Service: 590-600.
[13419]
Nielson M, Lohman K, Sullivan J (2001) Phylogeography of the Tailed Frog
(Ascaphus truei ): Implications for the Biogeography of the
Pacific Northwest. Evolution , 55 , 147–160.
Newmaster, S. G., R. J. Belland, A. Arsenault, and D. H. Vitt. 2003.
Patterns of bryophyte diversity in humid coastal and inland
cedar-hemlock forests of British Columbia. Environmental Reviews
11:S159-S185.
Novembre, J. 2016. Pritchard, Stephens, and Donnelly on Population
Structure. Genetics 204, 391-393.
O’Connell, L.M., Ritland, K. & Thompson, S.L. (2008). Patterns of
post-glacial colonization by western redcedar (Thuja plicata ,
Cupressaceae) as revealed by microsatellite markers. Botany , 86,
194–203.
Owens, John N.; Molder, Marje. 1984. The reproductive cycles of western
and mountain hemlock. Victoria, BC: Ministry of Forests, Information
Services Branch. 32 p. [19144]
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double
digest RADseq: An inexpensive method for de novo SNP discovery and
genotyping in model and non-model species. PLoS ONE , 7.
Priest GR (1990) Volcanic and Tectonic Evolution of the Cascade Volcanic
Arc , Central Oregon. Journal of Geophysical Research ,95 , 19583–19599.
Pritchard, J.K., Stephens, M. & Donnelly, P. (2000). Inference of
population structure using multilocus genotype data. Genetics ,
155, 945–959.
Puechmaille, S. J. 2016. The program STRUCTURE does not reliably recover
the correct population structure when sampling is uneven: subsampling
and new estimators alleviate the problem. Molecular Ecology Resources
16, 608-627.
Pudlo P, et al. (2015) Reliable ABC model choice via random forests.
Bioinformatics 32(6):859–866.
Rankin AM, Wilke T, Lucid M, Leonard W, Espíndola AE, Smith ML, Carstens
BC, Sullivan J (2019) Complex interplay of ancient vicariance and recent
patterns of geographical speciation in north-western North American
temperate rainforests explains the phylogeny of jumping slugs
(Hemphillia spp. ), Biological Journal of the Linnean
Society , Volume 127, Issue 4, Pages
876–889, https://doi.org/10.1093/biolinnean/blz040
Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: a
versatile open source tool for metagenomics. PeerJ , 4, e2584.
Rohland N, Reich D (2012) Cost-effective, high-throughput DNA sequencing
libraries for multiplexed target capture. Genome Research , 22,
939–946.
Rosenberg, S.M. Walker, I.R. & Mathewes, RW (2003). Postglacial spread
of hemlock (Tsuga) and vegetation history in Mount Revelstoke National
Park, British Columbia, Canada. Canadian Journal of Botany. 81.
Ruffley M, Smith ML, Espındola A, Carstens BC, Sullivan J, Tank DC.
(2018) Combining allele frequency and tree-based approaches improves
phylogeographic inference from natural history collections. Mol Ecol.
2018;27:1012–1024. https://doi.org/10.1111/mec.14491
[dataset] Ruffley M, Smith ML, Turck D. 2021. Thuja plicata and
Tsuga heterophylla ddRADseq raw data. Pending DOI.
Smith ML, Ruffley M, Espındola A, Tank DC, Sullivan J, Carstens BC.
(2017) Demographic model selection using random forests and the site
frequency spectrum. Mol Ecol. 2017;26:4562–4573. https://doi.org/
10.1111/mec.14223
Smith ML, Ruffley M, Rankin AM, Espındola A, Tank DC, Sullivan J,
Carstens BC. (2018) Testing for the presence of cryptic diversity in
tail-dropper slugs (Prophysaon ) using molecular
data, Biological Journal of the Linnean Society , Volume 124,
Issue 3, July 2018, Pages
518–532, https://doi.org/10.1093/biolinnean/bly067
Smith, M.L. and Carstens, B.C. (2020), Process‐based species
delimitation leads to identification of more biologically relevant
species*. Evolution, 74: 216-229.
doi:10.1111/evo.13878
Soltis DE, Gitzendanner M a., Strenge DD, Soltis PS (1997) Chloroplast
DNA intraspecific phylogeography of plants from the Pacific Northwest of
North America. Plant Systematics and Evolution , 206 ,
353–373.
Sullivan J, Arellano E, Rogers DS (2000) Comparative Phylogeography of
Mesoamerican Highland Rodents: Concerted versus Independent Response to
Past Climatic Fluctuations. The American Naturalist ,155 , 755–768.
Sullivan, J, Smith, ML, Espíndola, A, Ruffley M, Rankin A, Tank DC,
Carstens BC. (2019) Integrating life history traits into predictive
phylogeography. Mol Ecol .
2019; 28: 2062– 2073. https://doi.org/10.1111/mec.15029
Steele CA, Carstens BC, Storfer A, Sullivan J (2005) Testing hypotheses
of speciation timing in Dicamptodon copei and Dicamptodon aterrimus
(Caudata: Dicamptodontidae). Molecular Phylogenetics and
Evolution , 36 , 90–100.
Tesky, Julie L. 1992. Tsuga heterophylla. In: Fire Effects Information
System, [Online]. U.S. Department of Agriculture, Forest Service,
Rocky Mountain Research Station, Fire Sciences Laboratory (Producer).
Available:
https://www.fs.fed.us/database/feis/plants/tree/tsuhet/all.html [2020,
April 14].
Turner, David P. 1985. Successional relationships and a comparison of
biological characteristics among six northwestern conifers. Bulletin of
the Torrey Botanical Club. 112(4): 421-428. [16784]
Waitt, R. B., and R. M. Thorson. 1983. The Cordilleran ice sheet in
Washington, Idaho, and Montana. Pp. 53-70 in S. C. Porter, ed.
Late-Quaternary environments of the United States. Minneapolis:
University of Minnesota Press.
Waring RH, Franklin JF (1979) Evergreen coniferous forests of the
pacific northwest. Science (New York, N.Y.) , 204 ,
1380–1386.
Whitlock, C. 1992. Vegetational and climatic history of the Pacific
Northwest during the last 20,000 years: implications for understanding
present day biodiversity. Northwest Environmental Journal 8:5-28.
Wilke, T & Duncan, N. (2004). Phylogeographical patterns in the
American Pacific Northwest: Lessons from the arionid slug Prophysaon
coeruleum. Molecular ecology. 13. 2303-15.
10.1111/j.1365-294X.2004.02234.x.
Xue AT, Hickerson MJ. (2015) The aggregate site frequency spectrum for
comparative population genomic inference. Mol Ecol. 24:6223–40.