Biology subjects

Simeone, M. C.

Publications and source records attributed to Simeone, M. C..

4 recordsLinked to original sources

bioRxiv2025

Whole chloroplast genomes reveal a complex genetic legacy of lost lineages, past radiations and secondary contacts in the dominant temperate deciduous tree genus Fagus

Background--Major northern temperate tree genera emerged in the Eocene and now have vast ranges across the Northern Hemisphere. Here we undertake a multi-discipline study to provide novel insights into the formation and biogeographic history of a dominant, yet understudied temperate tree genus, Fagus L. Data and methodology--A whole chloroplast genome phylogeny (eighty-two chloroplast genomes) with multi-accessions of most species was determined and contrasted with the timing of lineage diversification inferred from three different nuclear and chloroplast gene time-calibrated phylogenies using 101 fossils as age priors. Main results--Five deeply diverged chloroplast lineages were revealed that, with the exception of a Eurasian lineage, underwent divergence decoupled from speciation predating modern species lineages by up to 28 million years (Ma). The geographic distribution of chloroplast lineages reflects a complex history of genetic admixture during past contact between extinct and modern species including between different subgenera in East Asia and long-term persistence particularly in Japan which is the hotspot of plastome diversity. Conclusion--Modern Fagus forests are the consequence of 62 million years of evolution, migration, genetic exchange and species extinction with most modern species harbouring a mosaic of genetic material, a legacy of multiple admixture events in deep time.

evolutionary biology↗

bioRxiv2021

High-Throughput Sequencing of 5S-IGS rDNA in Fagus L. (Fagaceae) reveals complex evolutionary patterns and hybrid origin of modern species

Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata - F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4,963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years. Significance statementThe evolution of extra-tropical wind-pollinated tree genera involves dynamic speciation processes. High-throughput sequencing of the multi-copy, potentially multi-locus 5S rDNA reveals a complex history of hybrid origins, lineage sorting and mixing, and intra-genomic competition between paralogous-homeologous loci in the core group of Eurasian beech trees (genus Fagus) and their distant relative, F. japonica. The modern species are genetic mosaics and represent a striking case of at least 55 million years of ongoing reticulate evolution.

evolutionary biology↗

bioRxiv2019

Genetic diversity and taxonomic issues in Gastridium P.Beauv (Poaceae) inferred from plastid and nuclear DNA sequence analysis

Incomplete taxonomic knowledge may seriously hamper biodiversity conservation efforts that are crucial in a context of global change. Gastridium P.Beauv. is a Mediterranean-Paleotropical member of the Poaceae family, inhabiting ephemeral grass habitats, whose species number and diversity are still imperfectly known. In order to progress towards a comprehensive taxonomic treatment of this genus, we examined patterns of DNA diversity in the four taxa (Gastridium lainzii, G. phleoides, G. scabrum, and G. ventricosum) that have been recently advanced by different authors, based on new morpho-ecological descriptors. We explored nucleotide sequence variation at two plastid (trnH-psbA, trnL-F) and one nuclear (ITS) DNA markers in 44 total individuals. Diversity data were treated with multiple statistical and phylogenetic tools, and integrated with available GenBank sequences of Gastridium and other closely related genera. Despite the limited variability detected, evidence of within-taxon genetic cohesion and estimates of molecular divergence comparable with those of species in the same subtribal lineage (Agrostidinae) were recovered. The identified plastid genealogies appeared congruent with a subdivision of the genus into (at least) three distinct entities, and coherent with collected morphological descriptors. Phylogenetic reconstructions with ITS were less corresponding to taxa identities, likely due to reticulation and polyploidization. Once placed in a broader taxonomic context, the investigated dataset produced plastid and nuclear tree topologies consistent with previous assessments, highlighting the overall little resolution of species and genera within Agrostidinae. In the plastid tree, a sister relationship between Gastridium and Triplachne was weakly supported. In the ITS tree, relationships among these genera were unresolved. The hypothesis of closely related but separately evolving lineages within Gastridium is discussed, suggesting a re-evaluation of its current assessment in taxonomic authorities to enhance our knowledge of the grass family, and assist future biodiversity surveys of key Mediterranean grassland ecosystems.

genetics↗

bioRxiv2019

Genomic landscape of the global oak phylogeny

O_LIThe tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity.\nC_LIO_LIWe utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the worlds oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.\nC_LIO_LIOak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity.\nC_LIO_LIThe support we find for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.\nC_LI

evolutionary biology↗