Showing papers by "Daniel Ortiz-Barrientos published in 2022"
TL;DR: In this article , the authors explore patterns of replicated evolution across the plant kingdom and discuss the processes responsible for such patterns, and highlight where future efforts can help us bridge the understanding of replicating evolution across different levels of biological organization.
Abstract: Similar traits and functions commonly evolve in nature. Here, we explore patterns of replicated evolution across the plant kingdom and discuss the processes responsible for such patterns. We begin this review by defining replicated evolution and the theoretical, genetic, and ecological concepts that help explain it. We then focus our attention on empirical cases of replicated evolution at the phenotypic and genotypic levels. We find that replication at the ecotype level is common, but evidence for repeated ecological speciation is surprisingly sparse. On the other hand, the replicated evolution of ecological strategies and physiological mechanisms across similar biomes appears to be pervasive. We conclude by highlighting where future efforts can help us bridge the understanding of replicated evolution across different levels of biological organization. Earth's landscape is diverse but also repeats itself. Organisms seem to have followed suit. Expected final online publication date for the Annual Review of Plant Biology, Volume 74 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
3 citations
TL;DR: In this paper , the authors propose to represent individual genes with hyperedges, and simultaneously test each gene against many features/vertices, and further explore gene/hyperedge interactions using the line graph representations, which also reduces the complexity of dense hypergraphs.
Abstract: Multidisciplinary approaches can significantly advance our understanding of complex systems. For instance, gene co-expression networks align prior knowledge of biological systems with studies in graph theory, emphasising pairwise gene to gene interactions. In this paper, we extend these ideas, promoting hypergraphs as an investigative tool for studying multi-way interactions in gene expression data. Additional freedoms are achieved by representing individual genes with hyperedges, and simultaneous testing each gene against many features/vertices. Further gene/hyperedge interactions can be captured and explored using the line graph representations, a techniques that also reduces the complexity of dense hypergraphs. Such an approach provides access to graph centrality measures, which in turn identify salient features within a data set, for instance dominant or hub-like hyperedges leading to key knowledge on gene expression. The validity of this approach is established through the study of gene expression data for the plant species Senecio lautus and results will be interpreted within this biological setting.
TL;DR: In this article , the authors investigated the genetic basis of anthropophily in a non-model mosquito species group, the Anopheles farauti complex from the southwest Pacific, by performing tests of selection and assessing evolutionary patterns for >200 olfactory genes from nine genomes.
TL;DR: In this paper , the authors employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity.
Abstract: Abstract Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity. Multiple population genetic analyses indicate the presence of four genetic clusters and show that the most genetically differentiated cluster contains accessions imported from Southeast Asia (mainly those from Thailand). We find that genetic structure was strongly associated with three traits: trunk circumference, fruit blush colour and intensity in M. indica . This suggests that the history of these accessions could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype can improve the accuracy of genomic selection, which can assist the future development of new cultivars.
10 Jun 2022
TL;DR: In this article , a case of speciation by reinforcement in Drosophila was examined, and it was shown that reinforced mating discrimination is inherited as a dominant trait, exhibits variability within species, and may be influenced by a known set of candidate genes involved in olfaction.
Abstract: Reinforcement occurs when natural selection strengthens behavioral discrimination to prevent costly interpopulation matings, such as when matings produce sterile hybrids. This evolutionary process can complete speciation, thereby providing a direct link between Darwin’s theory of natural selection and the origin of new species. My dissertation presents the first study on the genetics of reinforcement. This study is framed in a conceptual body that explains how genomic architecture, selection and recombination, interact to facilitate divergence in the presence of gene flow. In addition, in my dissertation I produced a dense recombination map for D. pseudoobscura, which together with the genome sequence opens many possibilities for classic population genetic and genomic analyses in this system. I examine a case of speciation by reinforcement in Drosophila. I present the first high-resolution genetic study of variation within species for female mating discrimination that is enhanced by natural selection. I show that reinforced mating discrimination is inherited as a dominant trait, exhibits variability within species, and may be influenced by a known set of candidate genes involved in olfaction. My results show that the genetics of reinforced mating discrimination is different from the genetics of mating discrimination between species, suggesting that overall mating discrimination might be a composite phenomenon, which in Drosophila could involve both auditory and olfactory cues. Examining the genetics of reinforcement provides a unique opportunity for both understanding the origin of new species in the face of gene flow and identifying the genetic basis of adaptive female species preferences, two major gaps in our understanding of speciation.