Molecular Phylogenetics and Evolution最新文献

Coccocarpia Pers. currently comprises 28 mostly broadly distributed tropical species of fungi associated with cyanobacteria. Three of these taxa, C. erythroxyli, C. palmicola, and C. pellita, are presumably pantropical to subcosmopolitan, with broad morphological variation across their range. This study provides the first global phylogeny of the genus, to test current species concepts and infer distribution patterns, based on samples from Colombia, Puerto Rico, Gabon, Kenya, Thailand, Fiji, and Hawaii. We also estimate divergence times within the clade and provide a first reconstruction of its biogeographic history. Based on phylogenetic reconstructions inferred from maximum likelihood and Bayesian approaches of four molecular markers (mtSSU, nuLSU, ITS, RPB2), Coccocarpia was recovered as monophyletic. However, the currently accepted taxa are largely polyphyletic entities and the underlying diversity in this genus is much higher than currently understood. Different methods for species delimitation boundaries came to agree on a scenario involving more than 150 species in the available, albeit still small, dataset. This suggests that with broader sampling, Coccocarpia may indeed represent a hyper-diverse genus, potentially containing over 200 species. The phylogeny is geographically structured: one clade is exclusive to the Paleotropics, one to the Neotropics, and one is pantropical. Coccocarpia likely emerged during the Late Cretaceous (90 ± 10 Mya) in the tropical regions of Australasia-Oceania, initially colonizing Oceania, and Asia and subsequently the Neotropics. The three main clades diverged between the Late Cretaceous and the Paleocene, with significant diversification in the Oligocene, during which the neotropical clade gave rise to morphological novelties, including the epiphylla and stellata clades.

Copepods are small crustaceans that are ubiquitous in aquatic environments. They are particularly abundant in marine and freshwater plankton, marine sediments, and as parasites or commensals of other aquatic organisms. Despite their abundance and importance, phylogenetic relationships among copepods are poorly resolved. The validity of higher-level taxa, including several orders, has continued to be controversial throughout the 21st century. This study has two main goals: first, to use phylogenomic data to assess relationships among the four major copepod orders: Calanoida, Cyclopoida, Harpacticoida, and Siphonostomatoida, which together include more than 98 % of copepod species diversity, and second, to test the validity of the recently proposed order Canuelloida. Towards these goals, we sampled 28 copepod transcriptomes and genomes spanning 20 families and 5 orders, including the first transcriptome of a representative of Canuelloida. We identified 2,527 single copy protein coding genes comprising 939,460 amino acid (aa) positions and 530,269 informative sites. All phylogenetic analyses support a monophyletic Podoplea (i.e., the superorder comprising all copepod orders except for Calanoida and Platycopioida) with Calanoida as its sister taxon. We find robust support across all methods for Canuelloida as a distinct order separate from the traditionally recognized Harpacticoida (Oligoarthra). Contrary to several recent studies of smaller sets of nuclear genes or mitochondrial genomes, we recover Cyclopoida and Harpacticoida as sister taxa and find that gene tree discordance analysis rejects the alternative topologies. Transcriptomic data are promising for resolving the backbone of the copepod phylogeny but collecting and sequencing the nearly 15,000 species of copepods, many of which are infrequently encountered and less than 1 mm in size, remains a major hurdle.