Towards a species-level phylogeny for Neotropical Myrtaceae: Notes on topology and resources for future studies.

PREMISE: Increasingly complete phylogenies underpin studies in systematics, ecology, and evolution. Myrteae (Myrtaceae), with ~2700 species, is a key component of the exceptionally diverse Neotropical flora, but given its complicated taxonomy, automated assembling of molecular supermatrices from public databases often lead to unreliable topologies due to poor species identification. METHODS: Here, we build a taxonomically verified molecular supermatrix of Neotropical Myrteae by assembling 3909 published and 1004 unpublished sequences from two nuclear and seven plastid molecular markers. We infer a time-calibrated phylogenetic tree that covers 712 species of Myrteae (~28% of the total diversity in the clade) and evaluate geographic and taxonomic gaps in sampling. RESULTS: The tree inferred from the fully concatenated matrix mostly reflects the topology of the plastid data set and there is a moderate to strong incongruence between trees inferred from nuclear and plastid partitions. Large, species-rich genera are still the poorest sampled within the group. Eastern South America is the best-represented area in proportion to its species diversity, while Western Amazon, Mesoamerica, and the Caribbean are the least represented. CONCLUSIONS: We provide a time-calibrated tree that can be more reliably used to address finer-scale eco-evolutionary questions that involve this group in the Neotropics. Gaps to be filled by future studies include improving representation of taxa and areas that remain poorly sampled, investigating causes of conflict between nuclear and plastid partitions, and the role of hybridization and incomplete lineage sorting in relationships that are poorly supported.

Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification.

PREMISE: To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target-enriched nuclear data to improve our understanding of phylogenetic relationships in the family. METHODS: We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in Brunellia, and several outgroup taxa. We removed loci that indicated biased inference of relationships and applied concatenated and coalescent methods to infer Brunellia phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage sorting events and assessed their impact on phylogenetic inference. Finally, we performed ancestral-state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in Brunellia. RESULTS: Brunellia comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses. CONCLUSIONS: Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene-tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character-state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in Brunellia, the relationships among subclades remain incompletely understood.

-Complete plastid genome sequences of two species of the Neotropical genus Brunellia (Brunelliaceae).

Here we present the first two complete plastid genomes for Brunelliaceae, a Neotropical family with a single genus, Brunellia. We surveyed the entire plastid genome in order to find variable cpDNA regions for further phylogenetic analyses across the family. We sampled morphologically different species, B. antioquensis and B. trianae, and found that the plastid genomes are 157,685 and 157,775 bp in length and display the typical quadripartite structure found in angiosperms. Despite the clear morphological distinction between both species, the molecular data show a very low level of divergence. The amount of nucleotide substitutions per site is one of the lowest reported to date among published congeneric studies (π = 0.00025). The plastid genomes have gene order and content coincident with other COM (Celastrales, Oxalidales, Malpighiales) relatives. Phylogenetic analyses of selected superrosid representatives show high bootstrap support for the ((C,M)O) topology. The N-fixing clade appears as the sister group of the COM clade and Zygophyllales as the sister to the rest of the fabids group.

Historical biogeographical patterns in continental Australia: congruence among areas of endemism of two major clades of eucalypts.

Published phylogenies of two eucalypt clades, red bloodwoods Corymbia subgenus Corymbia and eudesmids Eucalyptus subgenus Eudesmia (Myrtaceae), were combined for an analysis of historical biogeographical area relationships within continental Australia. The method of paralogy-free subtree analysis was used to eliminate geographical paralogy; the paralogy-free subtrees were coded as characters for parsimony analysis to find the minimal and area cladogram, which proved to be informative of a continent-wide pattern. The eucalypt fossil record and molecular dating studies allow an interpretation of the biogeographical history in terms of major vicariance events that date from the early Paleogene. The summary area cladogram shows the wet jarrah forest region of South-West Western Australia, a region of high endemism, as the earliest to differentiate from all other areas, isolated by marine inundation across southern Australia and climatic cooling in the Late Eocene-Early Oligocene. From about this time, regionalization continued, with warmer conditions and monsoonal climate developing in central and northern Australia, and cooling in the south-east. Northern and eastern humid and semi-humid areas were related as a track, but with increased aridity in the interior of the continent, the monsoonal climate contracted northwards. The Australian Monsoon Tropics (AMT: Kimberley, Top End, Arnhem, Cape York and inland north-east Queensland) differentiated from eastern areas (Queensland wet tropics to McPherson-Macleay). Our results also show all arid and semi-arid regions as related, suggestive of a historically cohesive interior biota rather than repeated colonizations of the interior from the periphery of the continent. Climate largely differentiates hot arid areas in the north (Pilbara, Northern and Central deserts) from arid areas in the south (south-west interzone, Wheatbelt, Goldfields and Great Victoria Desert). © The Willi Hennig Society 2010.