Biology subjects

Grimm, G. W.

Publications and source records attributed to Grimm, G. W..

5 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

Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

BackgroundDrosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum together with the highly succulent and species-rich tribe Ruschieae constitute the core ruschioids in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.\n\nMethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species represented by multiple accessions of Drosanthemum. A well-curated, geo-referenced occurrence data set comprising the phylogenetically studied and 867 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.\n\nResultsPhylogenetic inference supports nine clades within Drosanthemum, seven of them group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region revealed phylogenetic affinities not obvious in the phylogenetic tree. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are molecular and morphologically diverse. In contrast, less species-rich, molecularly less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest initial rapid radiation generating the main lineages, with some clades showing subsequent diversification.

evolutionary biology↗

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↗

bioRxiv2017

An updated infrageneric classification of the oaks: review of previous taxonomic schemes and synthesis of evolutionary patterns

In this paper, we review major classification schemes proposed for oaks by John Claudius Loudon, Anders Sandoe Orsted, William Trelease, Otto Karl Anton Schwarz, Aimee Antoinette Camus, Yuri Leonardovich Menitsky, and Kevin C. Nixon. Classifications of oaks (Fig. 1) have thus far been based entirely on morphological characters. They differed profoundly from each other because each taxonomist gave a different weight to distinguishing characters; often characters that are homoplastic in oaks. With the advent of molecular phylogenetics our view has considerably changed. One of the most profound changes has been the realisation that the traditional split between the East Asian subtropical to tropical subgenus Cyclobalanopsis and the subgenus Quercus that includes all other oaks is artificial. The traditional concept has been replaced by that of two major clades, each comprising three infrageneric groups: a Palearctic-Indomalayan clade including Group Ilex (Ilex oaks), Group Cerris (Cerris oaks) and Group Cyclobalanopsis (cycle-cup oaks), and a predominantly Nearctic clade including Group Protobalanus (intermediate or golden cup oaks), Group Lobatae (red oaks) and Group Quercus (white oaks, with most species in America and some 30 species in Eurasia). The main morphological feature characterising these phylogenetic lineages is pollen morphology, a character overlooked in traditional classifications. This realisation, along with the now available (molecular-)phylogenetic framework, opens new avenues for biogeographic, ecological and evolutionary studies and a re-appraisal of the fossil record. We provide an overview about recent advances in these fields and outline how the results of these studies contribute to the establishment of a unifying systematic scheme of oaks. Ultimately, we propose an updated classification of Quercus recognising two subgenera with eight sections. This classification considers morphological traits, molecular-phylogenetic relationships, and the evolutionary history of one of the most important temperate woody plant genera.\n\nO_FIG O_LINKSMALLFIG WIDTH=156 HEIGHT=200 SRC=\"FIGDIR/small/168146_fig1.gif\" ALT=\"Figure 1\">\nView larger version (49K):\norg.highwire.dtl.DTLVardef@d5a05org.highwire.dtl.DTLVardef@91295forg.highwire.dtl.DTLVardef@3338fcorg.highwire.dtl.DTLVardef@e24a58_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Classification schemes for Quercus from Loudon to Nixon (see Appendix). Colour coding denotes the actual systematic affiliation of species included in each taxon: of the Old World or mid-latitude clade section Cyclobalanopsis (cycle-cup oaks, yellow), section Cerris (Cerris oaks; orange), and section Ilex (Ilex oaks; green); and of the New World or high-latitude clade section Quercus (white oaks s.str.; blue), sections Virentes (cyan) and Ponticae (dark blue), section Protobalanus (intermediate oaks; purple), and section Lobatae (red oaks; red). Colour gradients are proportional, i.e. reflect the proportion of species with different systematic affiliation included in each taxon. Note: Menitsky (1984) and Trelease (1924) only treated the Eurasian and American oaks, respectively, and provided classifications in (nearly) full agreement with current phylogenies.\n\nC_FIG

plant biology↗