Reconstruct evolutionary history

Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes and their time of occurrence can shed light on the biology of each species, clade and their evolutionary history.

16p vigalileogalilei 27-02-2022 17 1   Download

Deciphering the history of life on Earth has long been regarded as one of the most central tasks in biology. In past years, widespread discordance between the evolutionary histories of different groups of orthologous genes of prokaryotes have been revealed, primarily due to horizontal gene transfers (HGTs). Nonetheless, evidence that support a strong tree-like signal of evolution have been uncovered, despite the presence of HGT events. Therefore, a challenging task is to distill this tree-like signal from the noise induced by all sources of non-tree-like events.

11p vitzuyu2711 29-09-2021 8 1   Download

Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains.

10p vijeeni2711 30-06-2021 8 1   Download

Orang-utans comprise three critically endangered species endemic to the islands of Borneo and Sumatra. Though whole-genome sequencing has recently accelerated our understanding of their evolutionary history, the costs of implementing routine genome screening and diagnostics remain prohibitive.

9p vilichoo2711 25-06-2021 12 1   Download

Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computational efficiency has been a constraint on the applicability of distance methods on very large problem instances.

9p viwyoming2711 16-12-2020 14 1   Download

Cancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some peculiar aspects that depend on the technology used to obtain the data to analyze: Single Cell DNA Sequencing data have great specificity, but are affected by moderate false negative and missing value rates.

16p viwyoming2711 16-12-2020 14 0   Download

High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history and population frequency of the subclonal lineages of tumor cells present in the sample can be reconstructed from these SNV frequency measurements.

16p vikentucky2711 26-11-2020 7 0   Download

Maximum compatibility is a method of phylogenetic reconstruction that is seldom applied to molecular sequences. It may be ideal for certain applications, such as reconstructing phylogenies of closely-related bacteria on the basis of whole-genome sequencing.

12p vioklahoma2711 19-11-2020 10 1   Download

Maximum parsimony phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of hosts and parasites, genes and species, and other interdependent pairs.

9p vioklahoma2711 19-11-2020 13 1   Download

Phylogeny estimation for bacteria is likely to reflect their true evolutionary histories only if they are highly clonal. However, recombination events could occur during evolution for some species. The reconstruction of phylogenetic trees from an alignment without considering recombination could be misleading, since the relationships among strains in some parts of the genome might be different than in others.

15p vicoachella2711 27-10-2020 7 0   Download

Comparative genomics studies are growing in number partly because of their unique ability to provide insight into shared and divergent biology between species. Of particular interest is the use of phylogenetic methods to infer the evolutionary history of cis-regulatory sequence features, which contribute strongly to phenotypic divergence and are frequently gained and lost in eutherian genomes.

9p vicolorado2711 22-10-2020 16 0   Download

Facilitated by the rapid progress of sequencing technology, comparative genomic studies in plants have unveiled recurrent whole genome duplication (i.e. polyploidization) events throughout plant evolution.

19p vishikamaru2711 29-04-2020 12 1   Download

This paper was originally presented as the first in the Sol Plaatjie Lecture Series on Africa, jointly hosted by the Ministry of Education and the African Human Genome Initiative in November 2002. The author Himla Soodyall addresses the contribution towards the generation of knowledge concerning the evolutionary history of mankind made by genetic approaches to anthropological questions. She examines the use and relevance of genetic data as another ’tool’ in the reconstruction of our history. About the Author/sProfessor Himla Soodyall obtained a B.Sc (Hons) degree at the University...

28p quatet 10-01-2013 66 3   Download

Life on Earth originated and then evolved from a universal common ancestor approximately 3.7 billion years ago. Repeated speciation and the divergence of life can be inferred from shared sets of biochemical and morphological traits, or by shared DNA sequences. These homologous traits and sequences are more similar among species that share a more recent common ancestor, and can be used to reconstruct evolutionary histories, using both existing species and the fossil record. Existing patterns of biodiversity have been shaped both by speciation and by extinction....

56p kennybibo 10-07-2012 95 25   Download