The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data.

The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological and biogeographic transitions within the clade. We used target capture sequencing with the Angiosperms353 probes, taxon-sampling encompassing nearly all genera of the family, tree-based sequence curation, and multiple phylogenetic approaches to investigate the major clades of Primulaceae and their relationship to other Ericales. We generated dated phylogenetic trees and conducted broad-scale biogeographic analyses as well as stochastic character mapping of growth habit. We show that Ardisia, a pantropical genus and the largest in the family, is not monophyletic, with at least 19 smaller genera nested within it. Neotropical members of Ardisia and several smaller genera form a clade, an ancestor of which arrived in the Neotropics and began diversifying about 20 Ma. This Neotropical clade is most closely related to Elingamita and Tapeinosperma, which are most diverse on islands of the Pacific. Both Androsace and Primula are non-monophyletic by the inclusion of smaller genera. Ancestral state reconstructions revealed that there have either been parallel transitions to an herbaceous habit in Primuloideae, Samolus, and at least three lineages of Myrsinoideae, or a common ancestor of nearly all Primulaceae was herbaceous. Our results provide a robust estimate of phylogenetic relationships across Primulaceae and show that a revised classification of Myrsinoideae and several other clades within the family is necessary to render all genera monophyletic.

Divergent Specialization of Simple Venom Gene Profiles among Rear-Fanged Snake Genera (Helicops and Leptodeira, Dipsadinae, Colubridae).

Many venomous animals express toxins that show extraordinary levels of variation both within and among species. In snakes, most studies of venom variation focus on front-fanged species in the families Viperidae and Elapidae, even though rear-fanged snakes in other families vary along the same ecological axes important to venom evolution. Here we characterized venom gland transcriptomes from 19 snakes across two dipsadine rear-fanged genera (Leptodeira and Helicops, Colubridae) and two front-fanged genera (Bothrops, Viperidae; Micrurus, Elapidae). We compared patterns of composition, variation, and diversity in venom transcripts within and among all four genera. Venom gland transcriptomes of rear-fanged Helicops and Leptodeira and front-fanged Micrurus are each dominated by expression of single toxin families (C-type lectins, snake venom metalloproteinase, and phospholipase A2, respectively), unlike highly diverse front-fanged Bothrops venoms. In addition, expression patterns of congeners are much more similar to each other than they are to species from other genera. These results illustrate the repeatability of simple venom profiles in rear-fanged snakes and the potential for relatively constrained venom composition within genera.

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set.

PREMISE: To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS: We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS: Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS: High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

Under the rug: Abandoning persistent misconceptions that obfuscate organelle evolution.

The advent and advance of next generation sequencing over the past two decades made it possible to accumulate large quantities of sequence reads that could be used to assemble complete or nearly complete organelle genomes (plastome or mitogenome). The result has been an explosive increase in the availability of organelle genome sequences with over 4000 different species of green plants currently available on GenBank. During the same time period, plant molecular biologists greatly enhanced the understanding of the structure, repair, replication, recombination, transcription and translation, and inheritance of organelle DNA. Unfortunately many plant evolutionary biologists are unaware of or have overlooked this knowledge, resulting in misrepresentation of several phenomena that are critical for phylogenetic and evolutionary studies using organelle genomes. We believe that confronting these misconceptions about organelle genome organization, composition, and inheritance will improve our understanding of the evolutionary processes that underly organelle evolution. Here we discuss four misconceptions that can limit evolutionary biology studies and lead to inaccurate phylogenies and incorrect structure of the organellar DNA used to infer organelle evolution.

Historical biogeography of Vochysiaceae reveals an unexpected perspective of plant evolution in the Neotropics.

PREMISE: Despite the fast pace of exploration of the patterns and processes influencing Neotropical plant hyperdiversity, the taxa explored are mostly from large groups that are widely distributed, morphologically diverse, or economically important. Vochysiaceae is an example of an undersampled taxon, providing an excellent system for investigating Neotropical biogeography. We present a phylogenomics-based hypothesis of species relationships in Vochysiaceae to investigate its evolutionary history through space and time. METHODS: We inferred a phylogeny for 122 species from Vochysiaceae and seven other families of Myrtales. Fossils from four myrtalean families were used to estimate the divergence times within Vochysiaceae. Historical biogeography was estimated using ancestral range probabilities and stochastic mapping. RESULTS: Monophyly of all genera was supported except for Qualea, which was split by Ruizterania into two clades. Vochysiaceae originated ~100 mya, splitting into an Afrotropical and a Neotropical lineage ~50 mya, and its ancestral range is in the area currently occupied by the Cerrado. CONCLUSIONS: The most recent common ancestor of Vochysiaceae + Myrtaceae had a West Gondwanan distribution, supporting a South American + African ancestral range of Vochysiaceae. On a global scale, geographic range reduction was the principal biogeographic event. At a finer scale, initial range reduction was also important and the Cerrado region was the most ancestral area with multiple colonization events to the Amazon, Central America, and the Atlantic Forest. Colonization events occurred from open areas to forest vegetation, an unusual finding regarding the evolution of plants in the Neotropics.

Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes.

The current classification of angiosperms is based primarily on concatenated plastid markers and maximum likelihood (ML) inference. This approach has been justified by the assumption that plastid DNA (ptDNA) is inherited as a single locus and that its individual genes produce congruent trees. However, structural and functional characteristics of ptDNA suggest that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces. To examine this idea, we produced new complete plastid genome (plastome) sequences of 27 species and combined these data with publicly available sequences to produce a final dataset that includes 78 plastid genes for 89 species of rosids and five outgroups. We used four data matrices (i.e., gene, exon, codon-aligned, and amino acid) to infer species and gene trees using ML and multispecies coalescent (MSC) methods. Rosids include about one third of all angiosperms and their two major clades, fabids and malvids, were recovered in almost all analyses. However, we detected incongruence between species trees inferred with different matrices and methods and previously published plastid and nuclear phylogenies. We visualized and tested the significance of incongruence between gene trees and species trees. We then measured the distribution of phylogenetic signal across sites and genes supporting alternative placements of five controversial nodes at different taxonomic levels. Gene trees inferred with plastid data often disagree with species trees inferred using both ML (with unpartitioned or partitioned data) and MSC. Species trees inferred with both methods produced alternative topologies for a few taxa. Our results show that, in a phylogenetic context, plastid protein-coding genes may not be fully linked and behaving as a single locus. Furthermore, concatenated matrices may produce highly supported phylogenies that are discordant with individual gene trees. We also show that phylogenies inferred with MSC are accurate. We therefore emphasize the importance of considering variation in phylogenetic signal across plastid genes and the exploration of plastome data to increase accuracy of estimating relationships. We also support the use of MSC with plastome matrices in future phylogenomic investigations.