Delimiting species without monophyletic gene trees.

By L. Lacey Knowles, Bryan C. Carstens, John Weins. Systematic Biology, 2007

729 citations recorded by the source corpus.

Subfields: Ecological Modeling, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/72ec6323e497bfcd25b52d82f5c04733dbc9d202

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Citations in the corpus

Inferring Phylogenies from RAD Sequence Data (2012, methodology): “Perhaps the greatest advantage of using RAD sequences for phylogeny reconstruction, as opposed to the traditional approach of using one to several genes, is that the RAD method samples data from many loci across the entire genome. This suggests that RAD sequence alignments could be profitably applie”
Phylogeography's past, present, and future: 10 years after Avise, 2000. (2010, methodology): “…delimitation and/or DNA-barcoding methods will be most effective when incorporating coalescent stochasticity (Hickerson et al., 2006b; Hudson and Coyne, 2002; Knowles and Carstens, 2007; Pons et al., 2006; Rosenberg, 2003, 2007) or using robust non-coalescent models (Meyer and Paulay, 2005).”
Deciphering the products of evolution at the species level: the need for an integrative taxonomy (2009, background): “The monophyly analyses are based on the assumption that coalescent patterns in gene genealogies are related to historical processes that originate separate lineages (Avise & Deette 1999; Avise 2000; Templeton 2001; Hewitt 2004; Knowles & Carstens 2007).”
The integrative future of taxonomy (2010, methodology): “Most promising are treebased methods that rely on coalescent theory [54, 74 ], because they can identify signals of species divergence even under complex circumstances of gene tree incongruence and non-monophyly [e.g.”
Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics (2021, background): “…criterion for species delimitation is intuitively appealing, metapopulation lineages may not be recovered as monophyletic of a number of reasons (Knowles and Carstens 2007), including incomplete lineage sorting in recently diverged species, introgression and hybridization (see below), porous or…”
Integrative taxonomy, or iterative taxonomy? (2011, background): “…and concatenation would be expected to perform poorly in these situations (Carstens & Knowles, 2007; Edwards et al., 2007; © 2010 CSIRO Systematic Entomology © 2010 The Royal Entomological Society, Systematic Entomology, 36, 209–217 Kubatko & Degnan, 2007; reviewed in Degnan & Rosenberg, 2009).”
Unveiling cryptic species of the bumblebee subgenus Bombus s. str. worldwide with COI barcodes (Hymenoptera: Apidae) (2012, background): “Reciprocal monophyly is rejected by some as a necessary condition of species (Knowles & Carstens, 2007), whereas pursuit of monophyletic taxa defines ‘best practice’ in systematics for others (Ebach & Carvalho, 2010).”
Accelerated species inventory on Madagascar using coalescent-based models of species delineation. (2009, methodology): “Taken together, 1 approach is to treat single locus data as a hypothesis to be tested with other data, such as additional genetic loci, geographical distribution, or morphological characters (e.g., DeSalle et al. 2005; Knowles and Carstens 2007; Shaffer and Thompson 2007).”
Molecules, ecology, morphology, and songs in concert: how many species is Arremon torquatus (Aves: Emberizidae)? (2009, neutral): “assimilis Krabbe et al. (2001) CD 4, #5 N.”
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 of Arctic Ocean holozooplankton for species identification and recognition (2010, background): “Neighbor-Joining is a useful indication of the reliability of the sequence for species identification, but is not the only approach to species identification using barcodes (e.g., Lef ebure et al., 2006; Kelly et al., 2007; Rach et al., 2008; Ross et al., 2008; Zhang et al., 2008), and monophyly may”
The art and science of species delimitation (2015, neutral): “Essentially all model-based species delimitation methods assume the existence of a species tree with gene trees determined by the MSC as described in the previous section.”
Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi (2011, methodology): “There may be problems with the molecular data themselves, particularly in recently diverged lineages (Knowles and Carstens 2007).”
Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets (2013, background): “…on the nature and origins of species use empirical tools to delimit evolutionarily example, reproductive isolation (Coyne and Orr 1998; yet by Knowles and Carstens 2007), ecological divergence (Fontaneto et al. 2007; Leaché et al. 2009), and other traits (Feulner et al. 2007), rather than…”