Darwin the Scientist

Browne, Janet

doi:10.1101/sqb.2009.74.047

Cited by 10 publications

(8 citation statements)

References 8 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Restricted recombination within the LR-PC region is expected to impact upon its gene evolution (see Introduction), leading to increased non-synonymous substitution (π a ), relative to the synonymous rate (π s ) (Charlesworth et al ., 2009). To test this prediction, gene-based π a , π s and π a /π s values were explored in wild barley ( H. spontaneum ).…”

Section: Resultsmentioning

confidence: 99%

“…Lack of recombination in the PC regions renders the genes within it relatively inaccessible to breeders, who need to re-assort alleles to achieve crop improvement. Restricted recombination also has potential impact upon gene evolution (Begun and Aquadro, 1992; Hudson, 1994; Nordborg et al ., 2005; Wright et al ., 2006; Charlesworth et al ., 2009). Multi-gene haplotypes in low-recombining (LR) regions are expected to evolve as concerted units with low diversity, which should be further reduced by the preferred selfing habit of most cereal crop species, including barley.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

The low‐recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

et al. 2014

View full text Add to dashboard Cite

The low-recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low-recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole-genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The low‐recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

et al. 2014

View full text Add to dashboard Cite

show abstract

“…Moreover, the models might contradict each other as in the case of the conflict between the ecotype model [75] and the biological species concept for Bacteria [76]. For this reason, it has been called into question whether a robust species concept can be obtained using theory-based algorithms [78]. In contrast, clustering optimization only aims at maximizing conservatism (in the sense of minimal changes of the previous classification) and consistency (in the sense of minimal deviations in character divergence between the resulting clusters) [54].…”

Section: Resultsmentioning

confidence: 99%

“…This flexibility also allows its use in optimizing distance functions for molecular taxonomy [59]. Whether species are ‘real’ or not is not of interest for clustering optimization, much like in [78], but we maintain that biologists can hardly do without the species category in practice because of its importance as a means for managing the deposition of and the access to biological material [79]. It is likely that such a pragmatic view on the species category will remain dominant in the future; for instance, current Prokaryote taxonomy appears to be largely unaffected by the proposed ‘paradigm shift’ [75] in species delineation.…”

Section: Resultsmentioning

confidence: 99%

Species Delimitation in Taxonomically Difficult Fungi: The Case of Hymenogaster

et al. 2011

View full text Add to dashboard Cite

BackgroundFalse truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions.MethodologyIn this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software.ConclusionsAmong distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season). In particular, taxa described in the 19th century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-)automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general.

show abstract

“…Microbes have rapid generations and large populations, and new technologies allow discovery of mutations throughout their genomes 16–19 . Samples can be frozen and revived, allowing phylogenies and mutational histories to be constructed and analyzed 18,19 .…”

mentioning

confidence: 99%

Genomic analysis of a key innovation in an experimental Escherichia coli population

Blount

Barrick

Davidson

et al. 2012

Nature

559

636

View full text Add to dashboard Cite

Evolutionary novelties have been important in the history of life, but their origins are usually difficult to examine in detail. We previously described the evolution of a novel trait, aerobic citrate utilization (Cit+), in an experimental population of Escherichia coli. Here we analyze genome sequences to investigate the history and genetic basis of this trait. At least three distinct clades coexisted for more than 10,000 generations prior to its emergence. The Cit+ trait originated in one clade by a tandem duplication that captured an aerobically-expressed promoter for the expression of a previously silent citrate transporter. The clades varied in their propensity to evolve this novel trait, although genotypes able to do so existed in all three clades, implying that multiple potentiating mutations arose during the population’s history. Our findings illustrate the importance of promoter capture and altered gene regulation in mediating the exaptation events that often underlie evolutionary innovations.

show abstract

Darwin the Scientist

Cited by 10 publications

References 8 publications

The low‐recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

The low‐recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

Species Delimitation in Taxonomically Difficult Fungi: The Case of Hymenogaster

Genomic analysis of a key innovation in an experimental Escherichia coli population

Contact Info

Product

Resources

About