2006
DOI: 10.1111/j.1365-294x.2006.02961.x
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Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders

Abstract: Delimiting the boundaries of species involved in radiations is critical to understanding the tempo and mode of lineage formation. Single locus gene trees may or may not reflect the underlying pattern of population divergence and lineage formation, yet they constitute the vast majority of the empirical data in species radiations. In this study we make use of an expressed sequence tag (EST) database to perform nuclear (nDNA) and mitochondrial (mtDNA) genealogical tests of species boundaries in Ambystoma ordinari… Show more

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Cited by 71 publications
(77 citation statements)
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“…It is gener− ally evident that nuclear gene fragments have some highly divergent regions that can discriminate even very closely related species (Sonnenberg et al 2007), hence amplifying and sequencing the complete 18S rDNA fragment during the future continuation of this study can be expected to show higher divergences between and within species. It is indeed clear that the COI fragment is suitable across a broad taxonomic range to delimit species, but also the complementation by a nu− clear marker system proved to be of advantage (Weisrock et al 2006;Knowles and Carstens 2007;Boissin et al 2008;O'Meara 2010;Ross et al 2010). Sonnenberg et al (2007) showed that a mitochondrial transfer can be detected using nuclear fragments (D1 and D2 regions) since the nuclear sequence confirmed the taxo− nomic assignment, whereas the mitochondrial sequence led to the wrong identifi− cation.…”
Section: Discussionmentioning
confidence: 99%
“…It is gener− ally evident that nuclear gene fragments have some highly divergent regions that can discriminate even very closely related species (Sonnenberg et al 2007), hence amplifying and sequencing the complete 18S rDNA fragment during the future continuation of this study can be expected to show higher divergences between and within species. It is indeed clear that the COI fragment is suitable across a broad taxonomic range to delimit species, but also the complementation by a nu− clear marker system proved to be of advantage (Weisrock et al 2006;Knowles and Carstens 2007;Boissin et al 2008;O'Meara 2010;Ross et al 2010). Sonnenberg et al (2007) showed that a mitochondrial transfer can be detected using nuclear fragments (D1 and D2 regions) since the nuclear sequence confirmed the taxo− nomic assignment, whereas the mitochondrial sequence led to the wrong identifi− cation.…”
Section: Discussionmentioning
confidence: 99%
“…Given the very low levels of nuclear divergence among members of the tiger salamander complex, including some of our target taxa (Weisrock et al 2006), we focused exclusively on mitochondrial DNA in this study. We designed oligonucleotide primers for the mitochondrial control region (CR), and NADH dehydrogenase subunit 2 (ND2) using Primer3 (Rozen and Skaletsky 2000) and sequences downloaded from GenBank.…”
Section: Dna Extraction and Amplificationmentioning
confidence: 99%
“…EU057196-EU057514 and EU342218-EU342345. ] In recent years, the increasing amount of genomic sequence data available for major evolutionary lineages has been paralleled by an increase in the use of multilocus phylogenetic approaches to resolve difficult and previously intractable evolutionary relationships (Rokas et al 2003;Murphy et al 2004;James et al 2006;Weisrock et al 2006). Some of these studies have been based exclusively on publicly available databases, mining DNA sequence information to yield large data sets, a number of which contain hundreds of thousands of orthologous nucleotide positions (Bapteste et al 2002;Rokas et al 2003;Pollard et al 2006;Cannarozzi et al 2007;Nikolaev et al 2007).…”
mentioning
confidence: 99%