Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA

By Daniel J. Funk, K. Omland. 2003

2,237 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics

View Paper: https://www.semanticscholar.org/paper/754a3b88d07f988a941606a920362d65b94a8650

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Citations in the corpus

Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well (2008, background): “Indeed, paraphyly, broadly construed, is thought to be a widespread phenomenon in plants [25], [26].”
Revealing secret liaisons: DNA barcoding changes our understanding of food webs (2010, background): “Since clades in a mitochondrial gene tree may not always represent independently evolving species (Funk & Omland, 2003; Hurst & Jiggins, 2005; Knowles & Carstens, 2007; Lohse, 2009), we confirmed any patterns emerging from the COI material by sequencing a subset of members of all mitochondrial…”
DNA barcoding as a tool for coral reef conservation (2007, background): “The finding that the apparent incidence of paraphyly (which can be due to errors in identification or taxonomy) is lower in better-studied groups suggests this bias is significant (Funk and Omland 2003).”
Identifying Canadian Freshwater Fishes through DNA Barcodes (2008, background): “Several processes such as pseudogenes ontogenesis, introgressive hybridisation, and retention of ancestral polymorphism pose potential difficulties in capturing species boundaries using mtDNA sequences [29,30,31,32].”
SYSTEMATIC STUDIES ON SAWFLIES OF THE GENERA DOLERUS, EMPRIA, AND CALIROA (HYMENOPTERA: TENTHREDINIDAE) (2004, background): “Systematists generally agree that multiple specimens should be included at the level below the taxonomic rank of interest, and this should also apply to the species level (Funk & Omland, 2003).”
Phylogeography of the pool frog Rana (Pelophylax) lessonae in the Italian peninsula and Sicily: multiple refugia, glacial expansions and nuclear–mitochondrial discordance (2008, background): “…unparsimonious on the basis that it would imply that the independent signals at seven unlinked nuclear loci are less representative of the population history than is that of the single mtDNA genome (Funk & Omland, 2003; Avise, 2004; Ballard & Whitlock, 2004; but cf. Garcı́a-Parı́s et al., 2003).”
Ecological explanations for (incomplete) speciation. (2009, background): “For example, the degree of phenotypic divergence can vary quantitatively [3,7,10], as can the completeness of reproductive isolation [2,4–6,9,10,13–16], the degree of genotypic clustering [18,19], the sharpness of geographic clines in gene frequencies [21] and the extent of lineage sorting [22, 23 ]”
Integrative taxonomy, or iterative taxonomy? (2011, background): “Current surveys suggest that this will be the case most of the time, for mtDNA at least (Funk & Omland, 2003; Joseph & Omland, 2009).”
Identification of Birds through DNA Barcodes (2004, background): “The importance of sampling multiple individuals within each species is highlighted by a recent review which found evidence of species-level paraphyly or polyphyly in 23% of 2,319 animal species, including 16.7% of 331 bird species (Funk and Omland 2003).”
Sequence-based species delimitation for the DNA taxonomy of undescribed insects. (2006, background): “This raises the possibility of incongruent gene and species histories, in particular in the light of reported high propensity for gene flow of mtDNA between otherwise separated groups (Funk and Omland, 2003; Hudson and Coyne, 2002; Seberg et al., 2003; Will and Rubinoff, 2004).”
Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics (2021, background): “Therefore, emerging lineages nested within a paraphyletic residual have been accepted as recently evolving species under certain circumstances (Wheeler and Nixon 1990; Crisp and Chandler 1996; Wheeler and Platnik 2000; Funk and Omland 2003; Freudenstein et al.”
DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. (2006, background): “…literature that questions the theoretical justification for this requirement (Wheeler and Meier, 2000), but also the substantial empirical evidence indicating that a large proportion of currently recognized species are "paraphyletic" on gene trees (Crisp and Chandler, 1996; Funk and Omland, 2003).”
Comparative phylogeography and species boundaries in Echinolittorina snails in the central Indo‐West Pacific (2006, background): “As in another recent study (Lourie et al., 2005), we emphasize the value of comparisons among species within a genus, the ‘congeneric phylogeography’ approach (Funk & Omland, 2003).”
Species Delimitation: A Decade After the Renaissance (2013, positive): “However, the mitochondrial locus does not always meet assumptions of neutrality [100], and it frequently introgresses across species boundaries [101], so in our view it should be used to identify “candidate species” [102], which can then be verified with independent lines of evidence [103].”