Aissi A, Beghami Y, Heuertz M (2019) Le chêne faginé (Quercus faginea, Fagaceae) en Algérie: potentiel germinatif et variabilité morphologique des glands et des semis. Plant Ecol Evol 152:437–449
Google Scholar
Aissi A, Beghami Y, Lepais O, Véla E (2021) Morphological and taxonomic analysis of Quercus faginea (Fagaceae) complex in Algeria. Botany 99:99–113
Google Scholar
Alberto F, Niort J, Derory J, Lepais O, Vitalis R, Galop D et al. (2010) Population differentiation of sessile oak at the altitudinal front of migration in the French Pyrenees. Mol Ecol 19:2626–2639
Google Scholar
Allendorf FW, Luikart G (2007) Conservation and the genetics of populations. Blackwell Pub
De Barba M, Miquel C, Lobréaux S, Quenette PY, Swenson JE, Taberlet P (2016) High-throughput microsatellite genotyping in ecology: Improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA. Mol Ecol Resour 17:492–507
Google Scholar
Barthe S, Gugerli F, Barkley NA, Maggia L, Cardi C, Scotti I (2012) Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences. PLoS One 7:e40699
Google Scholar
Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian computation in population genetics. Genetics 162:2025–35
Google Scholar
Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier (France)
Bradbury IR, Wringe BF, Watson B, Paterson I, Horne J, Beiko R et al. (2018) Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery. Evol Appl 11:918–930
Google Scholar
Buschbom J, Yanbaev Y, Degen B (2011) Efficient long-distance gene flow into an isolated relict oak stand. J Hered 102:464–472
Google Scholar
Chapuis M, Raynal L, Plantamp C, Meynard CN, Blondin L, Marin J et al. (2020) A young age of subspecific divergence in the desert locust inferred by ABC Random Forest. Mol Ecol 29:4542–4558
Google Scholar
Cornuet J-M, Ravigné V, Estoup A (2010) Inference on population history and model checking using DNA sequence and microsatellite data with the software DIYABC (v1.0). BMC Bioinforma 11:401
Google Scholar
Crow JF, Aoki K (1984) Group selection for a polygenic behavioral trait: Estimating the degree of population subdivision. Proc Natl Acad Sci USA 81:6073–6077
Google Scholar
Curto M, Winter S, Seiter A, Schmid L, Scheicher K, Barthel LMF et al. (2019) Application of a SSR-GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics. Ecol Evol 9:2814–2832
Google Scholar
Darby BJ, Erickson SF, Hervey SD, Ellis-Felege SN (2016) Digital fragment analysis of short tandem repeats by high-throughput amplicon sequencing. Ecol Evol 6:4502–4512
Google Scholar
Dickey AM, Hall PM, Shatters RG, Mckenzie CL (2013) Evolution and homoplasy at the Bem6 microsatellite locus in three sweetpotato whitefly (Bemisia tabaci) cryptic species. BMC Res Notes 6:249
Google Scholar
Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR (2013) NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol Ecol Resour 14:209–214
Google Scholar
Durand J, Bodenes C, Chancerel E, Frigerio JM, Vendramin G, Sebastiani F et al. (2010) A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study. BMC Genomics 11:570
Google Scholar
Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361
Google Scholar
Estoup A, Jarne P, Cornuet J-M (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol Ecol 11:1591–1604
Google Scholar
Estoup A, Raynal L, Verdu P, Marin J-M (2018) Model choice using Approximate Bayesian Computation and Random Forests: analyses based on model grouping to make inferences about the genetic history of Pygmy human populations. J la Société Fr Stat 159:167–190
Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M (2013) Robust demographic inference from genomic and SNP data. PLoS Genet 9:e1003905
Google Scholar
Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567
Google Scholar
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–87
Google Scholar
Feliner GN (2014) Patterns and processes in plant phylogeography in the Mediterranean Basin. A review. Perspect Plant Ecol, Evol Syst 16:265–278
Google Scholar
Flagel L, Brandvain Y, Schrider DR (2019) The unreasonable effectiveness of convolutional neural networks in population genetic inference. Mol Biol Evol 36:220–238
Google Scholar
Foll M, Gaggiotti O (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: A Bayesian perspective. Genetics 180:977–993
Google Scholar
Gaggiotti OE, Chao A, Peres-Neto P, Chiu CH, Edwards C, Fortin MJ et al. (2018) Diversity from genes to ecosystems: A unifying framework to study variation across biological metrics and scales. Evol Appl 11:1176–1193
Google Scholar
García Murillo P., Harvey-Brown Y (2017) Quercus canariensis. In: The IUCN Red List of Threatened Species,, p e.T78809256A80570536
GBIF Secratariat (2021a) Quercus faginea Lam. In: GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omeiaccessed via GBIF.org on 2022-05-10
GBIF Secratariat (2021b). Quercus canariensis Willd. In: GBIF Backbone Taxonomy. Checklist dataset https://doi.org/10.15468/39omeiaccessed via GBIF.org on 2022-05-10
Gómez A, Lunt DH (2007) Refugia within refugia: Patterns of phylogeographic concordance in the Iberian peninsula. In: Weiss S, Ferrand N (eds) Phylogeography of Southern European Refugia. Springer Netherlands, Dordrecht, p 155–188
Google Scholar
Gorener V, Harvey-Brown Y, Barstow M (2017) Quercus canariensis. IUCN red List Threat species e.T7880925
Goudet J (1995) FSTAT (Version 1.2): A computer program to calculate F-statistics. J Hered 86:485–486
Google Scholar
Hampe A, Petit RJ (2005) Conserving biodiversity under climate change: the rear edge matters. Ecol Lett 8:461–7
Google Scholar
Hardy OJ, Charbonnel N, Fréville H, Heuertz M (2003) Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation. Genetics 163:1467–82
Google Scholar
Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620
Google Scholar
Harvey-Brown Y, García Murillo PG, Buira A (2017) Quercus faginea. IUCN Red List Threat Species: e.T78916251A80570540.
Henriques R, von der Heyden S, Matthee CA (2016) When homoplasy mimics hybridization: a case study of Cape hakes (Merluccius capensis and M. paradoxus). PeerJ 4:e1827
Google Scholar
Hewitt GM (1999) Post-glacial re-colonization of European biota. Biol J Linn Soc 68:87–112
Google Scholar
Hey J, Won YJ, Sivasundar A, Nielsen R, Markert JA (2004) Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species. Mol Ecol 13:909–919
Google Scholar
Hoban S, Bruford M, D’Urban Jackson J, Lopes-Fernandes M, Heuertz M, Hohenlohe PA et al. (2020) Genetic diversity targets and indicators in the CBD post-2020 Global Biodiversity Framework must be improved. Biol Conserv 248:108654
Google Scholar
Hoogenboom J, de Knijff P, Laros JFJ, de Leeuw RH, van der Gaag KJ, Sijen T (2016) FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise. Forensic Sci Int Genet 27:27–40
Google Scholar
Hothorn T, Hornik K, van de Wiel MA, Zeileis A (2008) Implementing a class of permutation tests: the coin package. J Stat Softw 28:1–23
Google Scholar
Jamieson IG, Allendorf FW (2012) How does the 50/500 rule apply to MVPs? Trends Ecol Evol 27:578–584
Google Scholar
Jerome D, Vasquez F (2018) Quercus faginea. IUCN Red List Threat Species e.T7891625
Kalinowski ST (2005) HP-RARE 1.0: A computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189
Google Scholar
Kampfer S, Lexer C, Glössl J, Steinkellner H (1998) Characterization of (GA)n microsatellite loci from Quercus robur. Hereditas 129:183–186
Google Scholar
Kivelä M, Arnaud-Haond S, Saramäki J (2015) EDENetworks: A user-friendly software to build and analyse networks in biogeography, ecology and population genetics. Mol Ecol Resour 15:117–122
Google Scholar
Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I (2015) Clumpak: A program for identifying clustering modes and packaging population structure inferences across K. Mol Ecol Resour 15:1179–1191
Google Scholar
Layton KKS, Dempson B, Snelgrove PVR, Duffy SJ, Messmer AM, Paterson IG et al. (2020) Resolving fine‐scale population structure and fishery exploitation using sequenced microsatellites in a northern fish. Evol Appl: eva.12922.
Lepais O, Chancerel E, Boury C, Salin F, Manicki A, Taillebois L et al. (2020) Fast sequence-based microsatellite genotyping development workflow. PeerJ 8:e9085
Google Scholar
Lepais O, Leger V, Gerber S (2006) Short note: high throughput microsatellite genotyping in oak species. Silvae Genet 55:238
Google Scholar
Lepais O, Muller SD, Ben Saad-Limam S, Benslama M, Rhazi L, Belouahem-Abed D et al. (2013) High genetic diversity and distinctiveness of rear-edge climate relicts maintained by ancient tetraploidisation for Alnus glutinosa. PLoS One 8:e75029
Google Scholar
Leroy T, Roux C, Villate L, Bodénès C, Romiguier J, Paiva JAP et al. (2017) Extensive recent secondary contacts between four European white oak species. N. Phytol 214:865–878
Google Scholar
Lye GC, Lepais O, Goulson D (2011) Reconstructing demographic events from population genetic data: the introduction of bumblebees to New Zealand. Mol Ecol 20:2888–900
Google Scholar
Magri D, Fineschi S, Bellarosa R, Buonamici A, Sebastiani F, Schirone B et al. (2007) The distribution of Quercus suber chloroplast haplotypes matches the palaeogeographical history of the western Mediterranean. Mol Ecol 16:5259–66
Google Scholar
Marin J, Pudlo P, Estoup A, Robert C (2018) Likelihood-free model choice. In: Sisson S A, Fan Y, Beaumont M (eds) Handbook of Approximate Bayesian Computation, CRC Press, pp. 153.
Médail F, Diadema K (2009) Glacial refugia influence plant diversity patterns in the Mediterranean Basin. J Biogeogr 36:1333–1345
Google Scholar
Moracho E, Moreno G, Jordano P, Hampe A (2016) Unusually limited pollen dispersal and connectivity of Pedunculate oak (Quercus robur) refugial populations at the species’ southern range margin. Mol Ecol 25:3319–3331
Google Scholar
Mountain JL, Knight A, Jobin M, Gignoux C, Miller A, Lin AA et al. (2002) SNPSTRs: Empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Res 12:1766–1772
Google Scholar
Muir G, Lowe AJ, Fleming CC, Vogl C (2004) High nuclear genetic diversity, high levels of outcrossing and low differentiation among remnant populations of Quercus petraea at the margin of its range in Ireland. Ann Bot 93:691–697
Google Scholar
Neophytou C, Gärtner SM, Vargas-Gaete R, Michiels H-G (2015) Genetic variation of Central European oaks: shaped by evolutionary factors and human intervention? Tree Genet Genomes 11:1–15
Google Scholar
Payseur BA, Cutter AD (2006) Integrating patterns of polymorphism at SNPs and STRs. Trends Genet 22:424–429
Google Scholar
Petit RJ, Brewer S, Bordács S, Burg K, Cheddadi R, Coart E et al. (2002) Identification of refugia and post-glacial colonisation routes of European white oaks based on chloroplast DNA and fossil pollen evidence. Ecol Manag 156:49–74
Google Scholar
Petit RJ, Hampe A, Cheddadi R (2005) Climate changes and tree phylogeography in the Mediterranean. Taxon 54:877–885
Google Scholar
Press MO, Hall AN, Morton EA, Queitsch C (2019) Substitutions are boring: Some arguments about parallel mutations and high mutation rates. Trends Genet 35:253–264
Google Scholar
Press MO, Mccoy RC, Hall AN, Akey JM, Queitsch C (2018) Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana. Genome Res 28:1169–1178
Google Scholar
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–59
Google Scholar
Pudlo P, Marin J-M, Estoup A, Cornuet J-M, Gautier M, Robert CP (2016) Reliable ABC model choice via random forests. Bioinformatics 32:859–866
Google Scholar
Ramakrishnan U, Mountain JL (2004) Precision and accuracy of divergence time estimates from STR and SNPSTR variation. Mol Biol Evol 21:1960–1971
Google Scholar
Raynal L, Marin J-M, Pudlo P, Ribatet M, Robert CP, Estoup A (2019) ABC random forests for Bayesian parameter inference. Bioinformatics 35:1720–1728
Google Scholar
Rodríguez-Sánchez F, Hampe A, Jordano P, Arroyo J (2010) Past tree range dynamics in the Iberian Peninsula inferred through phylogeography and palaeodistribution modelling: A review. Rev Palaeobot Palynol 162:507–521
Google Scholar
Šarhanová P, Pfanzelt S, Brandt R, Himmelbach A, Blattner FR (2018) SSR-seq: Genotyping of microsatellites using next-generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring. Ecol Evol 8:10817–10833
Google Scholar
Scotti-Saintagne C, Mariette S, Porth I, Goicoechea PG, Barreneche T, Bodénès C et al. (2004) Genome scanning for interspecific differentiation between two closely related oak species [Quercus robur L. and Q. petraea (Matt.) Liebl.]. Genetics 168:1615–26
Google Scholar
Vartia S, Villanueva-Cañas JL, Finarelli J, Farrell ED, Collins PC, Hughes GM et al. (2016) A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding. R Soc Open Sci 3:150565
Google Scholar
Viruel J, Haguenauer A, Juin M, Mirleau F, Bouteiller D, Boudagher-Kharrat M et al. (2018) Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae). Appl Plant Sci 6:e01201
Google Scholar
Wang J (2016) Individual identification from genetic marker data: developments and accuracy comparisons of methods. Mol Ecol Resour 16:163–175
Google Scholar
Waples RS, Do C (2010) Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: A largely untapped resource for applied conservation and evolution. Evol Appl 3:244–262
Google Scholar
Xie KT, Wang G, Thompson AC, Wucherpfennig JI, Reimchen TE, MacColl ADC et al. (2019) DNA fragility in the parallel evolution of pelvic reduction in stickleback fish. Science (80-) 363:81–84
Google Scholar
Source: Ecology - nature.com
