Chloroplast genomes as a tool to resolve red algal phylogenies: a case study in the Nemaliales

Obtaining strongly supported phylogenies that permit confident taxonomic and evolutionary interpretations has been a challenge in algal biology. High-throughput sequencing has improved the capacity to generate data and yields more informative datasets. We sequenced and analysed the chloroplast genomes of 22 species of the order Nemaliales as a case study in the use of phylogenomics as an approach to achieve well-supported phylogenies of red algae.Australian Research Council/[FT110100585]/ARC/AustraliaAustralian Biological Resources Study/[RFL213-08]/ABRS/AustraliaMillennium Scientific Initiative/[NC120030]/MSI/Nueva JerseyUniversity of Melbourne///AustraliaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Ciencias del Mar y Limnología (CIMAR

Comparative analyses of chloroplast genome data representing nine green algae in Sphaeropleales (Chlorophyceae, Chlorophyta)

The chloroplast genomes of green algae are highly variable in their architecture. In this article we summarize gene content across newly obtained and published chloroplast genomes in Chlorophyceae, including new data from nine of species in Sphaeropleales (Chlorophyceae, Chlorophyta). We present genome architecture information, including genome synteny analysis across two groups of species. Also, we provide a phylogenetic tree obtained from analysis of gene order data for species in Chlorophyceae with fully sequenced chloroplast genomes. Further analyses and interpretation of the data can be found in “Chloroplast phylogenomic data from the green algal order Sphaeropleales (Chlorophyceae, Chlorophyta) reveal complex patterns of sequence evolution” (Fučíková et al., In review) [1]

Data from: Population of origin and environment interact to determine oomycete infections in spotted salamander populations

Spatial variation in disease risk in wild populations can depend both on environmental and genetic factors. Understanding the various contributions of each factor requires experimental manipulation of both the environment and genetic composition of populations under natural field conditions. We first examined natural patterns of oomycete composition and infection in the eggs of 13 populations of the spotted salamander Ambystoma maculatum. We then performed a fully factorial field transplant of the eggs of six populations to separate the contributions from population of origin and the environment on oomycete resistance in spotted salamanders. Among wild ponds, we found strong variation in oomycete infections in spotted salamander populations and differences in the composition of oomycete communities. In transplant experiments, salamander populations differed in their resistance to oomycete infections via a significant interaction between population of origin and environment. However, not all populations were locally adapted to local conditions. One population was significantly adapted to its home environment, and another one was significantly maladapted. These population effects could originate from differential adaptation of salamander populations to local oomycete communities or environmental conditions that mediate resistance, local adaptation and maladaptation of oomycetes to hosts, or from maternal transmission. Accounting for both environment and population of origin will often be necessary to understand disease dynamics in wild populations

Data from: Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal Tree of Life.

Premise of the study: Phylogenomic analyses across the green algae are resolving relationships at the class, order and family levels, and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. Methods: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using Next-Generation sequencing methods. Plastomes were characterized and gene order and content were compared with plastomes spanning the Sphaeropleales. Single-gene and concatenated-gene phylogenetic analyses of plastid and mitochondrial genes were performed. Key results: The Hydrodictyaceae contain the largest sphaeroplealean plastomes thus far fully sequenced. Conservation of plastome gene order within Hydrodictyaceae is striking compared with more dynamic patterns revealed across Sphaeropleales. Phylogenetic analyses resolve Hydrodictyon sister to a monophyletic Pediastrum, though the morphologically distinct P. angulosum and P. duplex continue to be polyphyletic. Analyses of plastid data supported the neochloridacean genus Chlorotetraëdron as sister to Hydrodictyaceae, while conflicting signal was found in the mitochondrial data. Conclusions: A phylogenomic approach resolved within-family relationships not obtainable with previous phylogenetic analyses. Denser taxon sampling across Sphaeropleales is necessary to capture patterns in plastome evolution, and further taxa and studies are needed to fully resolve sister lineage to Hydrodictyaceae and polyphyly of Pediastrum angulosum and P. duplex