Testing species delimitation in sympatric species complexes: The case of an African tropical tree, Carapa spp. (Meliaceae)

How to fail at species delimitation

“…However, it is a mistake to characterize the entire field as adopting the GLC or to assume that the GLC is a prerequisite for species delimitation (e.g. Rosell et al 2010;Barrett & Freudenstein 2011;Duminil et al 2012). However, it is good practice to define some species concept when reporting investigation that includes a substantial species delimitation component, if only because this articulation enforces the need for a clear argument regarding the criteria used to recognize species.…”

Population Genetics Methods Applied to a Species Delimitation Problem: Endemic Trumpet Daffodils (NarcissusSectionPseudonarcissi) from the Southern Iberian Peninsula

“…cause populations may have not been isolated long enough to accumulate differences, and both morphological and genetic markers would be likely to show low levels of differentiation (Whittall et al 2004;Shaffer and Thomson 2007;Schö nswetter et al 2009;Lega et al 2012;Slová k et al 2012). An alternative and powerful tool for delimiting the boundaries of closely related taxa in complex groups of plants are population genetics approaches that rely on large sets of informative and independent genetic markers (Drummond and Hamilton 2007;Joly and Bruneau 2007;Kučera et al 2008;Duminil and di Michele 2009;Duminil et al 2012). Because of their genomewide sampling, high reproducibility, and ability to resolve even extremely small genetic differences, amplified fragment length polymorphisms (AFLPs) are among the most efficient markers 502 INTERNATIONAL JOURNAL OF PLANT SCIENCES for discrimination between closely related species and for studies of species boundaries (Meudt and Clarke 2007;Mereďa et al 2008;Minder and Widmer 2008;Frey et al 2012;Garrido et al 2012).…”

“…One indirect way of incorporating the geographic context when assessing species boundaries is to analyze whether divergence among genetically isolated lineages occurs independently of their degree of geographic separation (Good and Wake 1992; Sites andMarshall 2003, 2004). Findings revealing that geographically distant populations of the same evolving lineage are genetically more closely related to each other than to geographically proximate populations of other lineages or that highly genetically divergent lineages are found in sympatry would be strong arguments for the recognition of truly distinct species (Minder and Widmer 2008;Koffi et al 2010;Duminil et al 2012).…”

Forest tree genomics: 10 achievements from the past 10 years and future prospects

“…This facilitates adaptation from standing genetic variation, which is particularly relevant during rapid range expansion (Keller et al 2010;Lascoux and Petit 2010). Bayesian clustering algorithms (reviewed in François and Durand 2010) have proved useful for tree species delimitation (Duminil et al 2012;Guichoux et al 2013). However, population sampling must account for the presence of gene flow by including evolutionarily important areas, such as secondary contact zones or hybrid zones (Eckert et al 2008;Scotti-Saintagne et al 2013a).…”