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The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events., Competing Interests: Conflicts of interest The author(s) declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Since some speciation mechanisms are more likely to generate morphological disparity than others, the general failure of vascular plant taxonomists to recognize cryptic diversity may bias perceptions about speciation process in plants. While the exceptional floristic richness of the South African Cape has largely been attributed to adaptive divergence ('ecological' speciation), a combination of climatic dynamism and complex topography has likely provided ample opportunities for 'non-ecological' vicariant speciation, a mechanism which is perhaps more likely to produce cryptic species. We explore the role of topography as a driver of 'non-ecological' speciation in the high-elevation sedge Tetraria triangularis. Within this species, molecular and morphological data reveal five cryptic or semi-cryptic lineages of Miocene-Pliocene age which qualify as evolutionary species. At least three of these maintain their distinctness in sites of sympatry, identifying them as biological species. Negligible range overlap, and the identification of topography as a significant predictor of range turnover, identifies speciation as allopatric and a result of impeded gene flow across low-elevation topographic features. Weak morphological and ecological divergence implies a limited role for adaptive divergence in powering speciation, with character displacement in sympatry possibly arising as a consequence of interspecific competition. Although we cannot exclude a role for disruptive selection in species differentiation, we identify isolation of populations on topographically separated mountains as the principal motor of speciation. We suggest that the importance of topography in the genesis of Cape floristic diversity has been inadequately acknowledged., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Nuclear DNA is widely used to estimate phylogenetic and phylogeographic relationships. Nuclear gene variants may be present in an individual's genome, and these result in Intra-Individual Site Polymorphisms (2ISP; pronounced "twisp") in direct-PCR or individual-consensus sequences based on a sample of clones or fragment sequences from next generation sequencing (NGS). 2ISPs can occur fairly often, especially within, but not restricted to, high-copy-number regions such as the widely used internal transcribed spacers of the nuclear ribosomal cistron. Dealing with 2ISPs has been problematic as phylogeny reconstruction optimality criteria generally do not take account of this variation. Here we test whether an approach that treats 2ISPs as additional (termed "informative"), rather than ambiguous, characters offers improved support in three common criteria used for phylogenetic inference: Minimum Evolution (via Neighbour Joining), Maximum Parsimony, and Maximum Likelihood. We demonstrate significant improvements using the 2ISP-informative treatment with simulated, real-world, and case-study data sets. We envisage that this 2ISP-informative approach will greatly aid phylogenetic inference using any nuclear DNA regions that contain polymorphisms within individuals (including consensus sequences generated from NGS), especially at the intrageneric or intraspecific level.

One of the biggest challenges for conservation biology is to provide conservation planners with ways to prioritize effort. Much attention has been focused on biodiversity hotspots. However, the conservation of evolutionary process is now also acknowledged as a priority in the face of global change. Phylogenetic diversity (PD) is a biodiversity index that measures the length of evolutionary pathways that connect a given set of taxa. PD therefore identifies sets of taxa that maximize the accumulation of 'feature diversity'. Recent studies, however, concluded that taxon richness is a good surrogate for PD. Here we show taxon richness to be decoupled from PD, using a biome-wide phylogenetic analysis of the flora of an undisputed biodiversity hotspot--the Cape of South Africa. We demonstrate that this decoupling has real-world importance for conservation planning. Finally, using a database of medicinal and economic plant use, we demonstrate that PD protection is the best strategy for preserving feature diversity in the Cape. We should be able to use PD to identify those key regions that maximize future options, both for the continuing evolution of life on Earth and for the benefit of society.

Phylogenetic analyses of Polytrichales were conducted using morphology and sequence data from the chloroplast genes rbcL and rps4 plus the trnL-F gene region, part of the mitochondrial nad5 and the nuclear-encoded 18S rDNA. Our analyses included 46 species representing all genera of Polytrichales. Phylogenetic trees were constructed with simultaneous parsimony analyses of all sequences plus morphology and separate combinations of sequence data only. Results lend support for recognition of Polytrichales as a monophyletic entity. Oedipodium griffithianum appears as a sister taxon to Polytrichales or as a sister taxon of all mosses excluding Sphagnales and Andreaeles. Within Polytrichales, Alophosia and Atrichopsis, species without the adaxial lamellae (in Atrichopsis present but poorly developed on male gametophyte) otherwise typical of the group are sister to the remaining species followed by a clade including Bartramiopsis and Lyellia, species with adaxial lamellae covering only the central portion of the leaves. Six taxa with an exclusively Southern Hemisphere distribution form a grade between the basal lineages and a clade including genera that are mostly confined to the Northern Hemisphere.

Phylogenetic relationships among the rattan palm genera Calamus, Daemonorops, Ceratolobus, Calospatha, Pogonotium, and Retispatha were investigated using DNA sequences from the nontranscribed spacer of 5S nrDNA. Moderate levels of intragenome polymorphism were identified, indicating that concerted evolution is not completely homogenizing the multiple copies of the 5S nrDNA repeat present in the nuclear genome. The existence of intragenome polymorphism did not excessively interfere with phylogeny reconstruction because, in the majority of cases, multiple clones obtained from individual species were resolved as monophyletic groups. The highly speciose genus Calamus was found to be nonmonophyletic with all five remaining genera being embedded within it. A number of major lineages within Calamus were resolved, one of which included the monotypic genus Calospatha, another included the monotypic genus Retispatha, and a third included a monophyletic group comprising Daemonorops, Ceratolobus, and Pogonotium. While the findings indicate that generic circumscriptions require revision, a nomenclatural solution was not sought at this stage because inadequate sampling and lack of support at basal nodes suggested that the topologies obtained might not be entirely reliable. Under these circumstances, name changes to such an important group would be both unhelpful and irresponsible., (Copyright 2000 Academic Press.)

Phylogenetic relationships among the 22 genera of the palm subfamily Calamoideae were investigated using DNA sequence data from the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast rps16 intron. The rps16 intron displayed low levels of variation, corroborating previous reports that the chloroplast genome of palms is highly conserved. High levels of within-individual polymorphism were identified in the ITS region, indicating that concerted evolution is not effectively homogenizing the ITS repeats. In the majority of cases, multiple clones from individuals resolved as monophyletic. However, the high levels of homoplasy in the ITS dataset, along with generally poor jackknife support for many clades, led to concerns that topologies obtained from these data might be unreliable. Nevertheless, congruence between trees based on ITS data alone and those based on rps16 intron data was high. Simultaneous analyses of both datasets yielded well-resolved topologies with high levels of jackknife support. A number of exciting groups emerged from the analyses: the African rattan clade comprising the endemic African rattan genera Laccosperma, Eremospatha, and Oncocalamus; the Lepidocaryeae-Raphia clade comprising the fan-leaved New World tribe Lepidocaryeae and the African genus Raphia; and the Asian clade comprising all Asian genera except Eugeissona. The position of Eugeissona was variable, although it did not resolve inside any of the three major clades mentioned above., (Copyright 2000 Academic Press.)