Mining the EST Databases to Determine Evolutionary Events in the Legumes and Grasses

Schlueter, Jessica A.; Dixon, P. M.; Granger, Cheryl L.; Shoemaker, Randy C.

doi:10.1007/0-387-24187-6_12

Cited by 7 publications

(6 citation statements)

References 62 publications

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“…Duplications and losses of genes –‘birth and death’– are common features of eukaryotic genomes (Lynch & Conery, 2000), and not all involve polyploidy. The divergence date estimated for the two paralogues of ncpGS is around 4.5 mya (Doyle et al ., 2003), which is only about a third of the estimate based on synonymous substitution distances calculated from over 250 pairs of duplicated genes (Schlueter et al ., 2003). This does not necessarily rule out polyploidy as the cause for the ncpGS duplication, however.…”

Section: Introductionmentioning

confidence: 91%

Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (GlycinesubgenusGlycine)

et al. 2003

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SummaryThe perennial soybeans ( Glycine subgenus Glycine ), are the sister group of the annual cultivated soybean ( G. max ). Among the approximately 20 species are diploids and polyploids, the former confined to Australia and neighboring islands and the latter more widespread. Although most subgenus Glycine species reproduce predominantly by selfing in cleistogamous flowers, phylogenetic evidence exists for reticulate evolution throughout the history of the subgenus. The entire genus is a paleopolyploid, and could possibly be allopolyploid, though there is as yet no evidence for a hybrid origin. Incongruence among the major nuclear genome groups in nuclear and chloroplast gene trees can be explained by several ancient introgressions. Within the B-genome group there is substantial incongruence between chloroplast and nuclear single copy gene trees that is explained better by introgressive hybridization than by stochastic sorting of ancestral lineages. Several allopolyploids originated by hybridization among a subset of genome groups to form a single large interconnected polyploid complex. A number of allopolyploid combinations have arisen recurrently, some bidirectionally. Some recurrent polyploids show evidence of lineage recombination, indicating that their populations comprise a single biological species. Neopolyploidy has involved hybridization among a subset of subgenus Glycine genome groups, and appears to have occurred recently, whereas hybridization at the diploid level has occurred throughout the history of the group.

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Section: Introductionmentioning

confidence: 91%

Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (GlycinesubgenusGlycine)

et al. 2003

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“…The common bean and soybean diverged nearly 20 million years ago, around the time of the major duplication event in soybean (Lavin et al 2005;Schlueter et al 2004). Synteny analysis indicates that most segments of any single common bean linkage group are highly similar to two soybean chromosomes (Galeano et al 2009).…”

Section: Genomic Tools and Germplasm Collectionsmentioning

confidence: 97%

Genomics of Origin, Domestication and Evolution of Phaseolus vulgaris

Bellucci

Bitocchi

Rau

et al. 2013

Genomics of Plant Genetic Resources

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“…Another potential solution is the application of genomics data to dating specific events. In Schlueter & al. (2004), EST assemblies from legumes Glycine and Medicago (Fabaceae) coupled with BLAST searches (Altschul & al., 1990) were used to group putative gene sequences into best matching paralogous pairs.…”

Section: Discussionmentioning

confidence: 99%

“…(2004), EST assemblies from legumes Glycine and Medicago (Fabaceae) coupled with BLAST searches (Altschul & al., 1990) were used to group putative gene sequences into best matching paralogous pairs. The analysis of synonymous distance among these hundreds of pairs by Schlueter & al. (2004) produced a distribution that was best explained by the presence of two polyploid events in last 60 million years or so in the lineage leading to Glycine (consistent with expectations), with at least one in the Medicago lineage in this time (see also Blanc & Wolfe, 2004).…”

Section: Discussionmentioning

confidence: 99%

The effect of incongruence on molecular dates

Pfeil

2009

TAXON

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Despite what is known about processes that can cause topological incongruence among datasets, combined analysis of concatenated datasets (simultaneous analysis) without examination of congruence is still advocated and practiced. Although the danger in such cases of inferring the incorrect topology is known (and sometimes ignored), here I examine an under‐appreciated effect of the combined analysis of incongruent datasets on molecular date inferences. Using simulated character matrices, a bias towards either increased or decreased dates is demonstrated that increases in its effect with greater proportion of incongruent characters. A general prediction is made regarding the behaviour of molecular date estimates based on the phylogenetic position of taxa that are incongruent. This prediction is borne out in a case study using real data from incongruent nuclear genes in Medicago (Fabaceae).

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Mining the EST Databases to Determine Evolutionary Events in the Legumes and Grasses

Cited by 7 publications

References 62 publications

Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (GlycinesubgenusGlycine)

Diploid and polyploid reticulate evolution throughout the history of the perennial soybeans (GlycinesubgenusGlycine)

Genomics of Origin, Domestication and Evolution of Phaseolus vulgaris

The effect of incongruence on molecular dates

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