Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach

Chromalveolates are a large, diverse supergroup of unicellulareukaryotes that includes Apicomplexa, dinoflagellates, ciliates(three lineages that form the alveolate branch), heterokonts,haptophytes, and cryptomonads (three lineages comprising thechromist branch). All sequenced genomes of chromalveolates haverelatively low intron density in protein-coding genes, and fewintron positions are shared between chromalveolate lineages.In contrast, genes of different chromalveolates share many intronpositions with orthologous genes from other eukaryotic supergroups,in particular, the intron-rich orthologs from animals and plants.Reconstruction of the history of intron gain and loss duringthe evolution of chromalveolates using a general and flexiblemaximum-likelihood approach indicates that genes of the ancestorsof chromalveolates and, particularly, alveolates had unexpectedlyhigh intron densities. It is estimated that the chromalveolateancestor had, approximately, two-third of the human intron density,whereas the intron density in the genes of the alveolate ancestoris estimated to be slightly greater than the human intron density.Accordingly, it is inferred that the evolution of chromalveolateswas dominated by intron loss. The conclusion that ancestralchromalveolate forms had high intron densities is unexpectedbecause all extant unicellular eukaryotes have relatively fewintrons and are thought to be unable to maintain numerous intronsdue to intense purifying selection in their, typically, largepopulations. It is suggested that, at early stages of evolution,chromalveolates went through major population bottlenecks thatwere accompanied by intron invasion.     

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

1. Download high-res image (392KB)
2. Download full-size image

     

Species concepts and the recognition of ancestors

Whether or not ancestral species can be recognised depends on the species concept adopted. A “metaspecies”; is a species that completely lacks autapomorphies, and which might (or might not) be ancestral to other species. Such taxa have been identified among both living and fossil organisms. Under the most commonly‐used species concepts (biological, evolutionary, phenetic, phylogenetic, ecological, recognition and cohesion), “metaspecies”; can be assumed to be ancestral. Even if the known members of a metaspecies are not ancestral to anything, parsimony dictates that the (as yet unknown) ancestral lineage is identical to the metaspecies and, under these species concepts, assignable to the same species. Only the cladistic and monophyletic species concepts would deny “metaspecies”; ancestral status, but these species concepts are problematical and have never been used by practising systematists.     

Putative genome donors ofArachis hypogaea (Fabaceae), evidence from crosses with synthetic amphidiploids

Chromosome pairing, pollen and pod fertility in hybrids between cultivated tetraploidArachis hypogaea and 15 synthetic amphidiploids from 8 diploid species (7 of the A genome and 1 of the B genome) of sect.Arachis have been utilized for the identification of putative genome donors in the evolution of cultivatedA. hypogaea. These results, in conjunction with evidence from morphological similarities, phytogeographical distribution and some phytochemical features, confirm the segmental amphidiploid origin ofA. hypogaea. A. batizocoi andA. duranensis are suggested as the donors of the B genome and the A genome respectively.     

Geographic views of human development

Human development can be divided into three stages: human ancestors (Lower Palaeolithic), early human races (Middle Palaeolithic) and modern humans (Upper Palaeolithic). Regional differentiation has been detected in the Lower Palaeolithic and is strongly developed in the Middle Palaeolithic but continues into the Upper Palaeolithic less marked. Clearly mixture at all levels accounts for this. Early humans absorbed the pre-existing regionalizations even as they further differentiated. Modern humans resulted from Upper Palaeolithic people spreading across the world and again absorbing the previous differentiations.