Phylogeography of the red alga Gracilariopsis tenuifrons (Gracilariales) along the Brazilian coast.

Changes in the sea level during the Holocene are regarded as one of the most prevalent drivers of the diversity and distribution of macroalgae in Brazil, influenced by the emergence of the Vitória-Trindade seamount chain (VTC). Gracilariopsis tenuifrons has a wide geographic distribution along the Brazilian coast, from Maranhão state (2°48'64.3" S) to Santa Catarina state (27.5°73'83" S). The knowledge of historical processes affecting diversity may allow the development of conservation strategies in environments against anthropogenic influence. Therefore, knowledge about phylogeography and populational genetic diversity in G. tenuifrons is necessary. Six populations were sampled along the northeastern tropical (Maranhão-MA, Rio Grande do Norte-RN, Alagoas-AL, and Bahia-BA States) and southeastern subtropical (São Paulo "Ubatuba"-SP1 and São Paulo "Itanhaém"-SP2 States) regions along the Brazilian coast. The genetic diversity and structure of G. tenuifrons were inferred using mitochondrial (COI-5P and cox2-3 concatenated) DNA markers. Gracilariopsis tenuifrons populations showed an evident separation between the northeast (from 2°48'64.3" S to 14°18'23" S; 17 haplotypes) and the southeast (from 23°50'14.9" S to 24°20'04.7" S; 10 haplotypes) regions by two mutational steps between them. The main biogeographical barrier to gene flow is located nearby the VTC. The southeast region (São Paulo State) is separated by two subphylogroups (SP1, three haplotypes and SP2, six haplotypes), and Santos Bay (estuary) has been considered a biogeographical barrier between them. The presence of genetic structure and putative barriers to gene flow are in concordance with previous studies reporting biogeographic breaks in the southwest Atlantic Ocean, including the genetic isolation between northeast and southeast regions for red and brown algae in the vicinity of the VTC.

The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species.

Macroalgal (seaweed) genomic resources are generally lacking as compared with other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole-genome assemblies for two species (Gracilaria chilensis and Gracilaria gracilis), a draft genome assembly of Gracilaria caudata, and genome annotation of the previously published Gracilaria vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.

Dual influence of terrestrial and marine historical processes on the phylogeography of the Brazilian intertidal red alga Gracilaria caudata.

In this study, we explored how past terrestrial and marine climate changes have interacted to shape the phylogeographic patterns of the intertidal red seaweed Gracilaria caudata, an economically important species exploited for agar production in the Brazilian north-east. Seven sites were sampled along the north-east tropical and south-east sub-tropical Brazilian coast. The genetic diversity and structure of G. caudata was inferred using a combination of mitochondrial (COI and cox2-3), chloroplast (rbcL) and 15 nuclear microsatellite markers. A remarkable congruence between nuclear, mitochondrial and chloroplast data revealed clear separation between the north-east (from 03° S to 08° S) and the south-east (from 20° S to 23° S) coast of Brazil. These two clades differ in their demographic histories, with signatures of recent demographic expansions in the north-east and divergent populations in the south-east, suggesting the maintenance of several refugia during the last glacial maximum due to sea-level rise and fall. The Bahia region (around 12° S) occupies an intermediate position between both clades. Microsatellites and mtDNA markers showed additional levels of genetic structure within each sampled site located south of Bahia. The separation between the two main groups in G. caudata is likely recent, probably occurring during the Quaternary glacial cycles. The genetic breaks are concordant with (i) those separating terrestrial refugia, (ii) major river outflows and (iii) frontiers between tropical and subtropical regions. Taken together with previously published eco-physiological studies that showed differences in the physiological performance of the strains from distinct locations, these results suggest that the divergent clades in G. caudata correspond to distinct ecotypes in the process of incipient speciation and thus should be considered for the management policy of this commercially important species.

Phylogeography of the Hypnea musciformis species complex (Gigartinales, Rhodophyta) with the recognition of cryptic species in the western Atlantic Ocean.

Populations of the marine benthic red macroalgae Hypnea musciformis and Hypnea pseudomusciformis along the Atlantic and Pacific Oceans were tested for phylogeographic structure using the DNA barcode COI-5P combined with rbcL for the construction of the phylogenetic tree. Strong patterns of genetic structure were detected across 210 COI-5P DNA sequences, and 37 COI-5P haplotypes were found, using multiple statistical approaches. Hypnea musciformis was found in the Northeast and Northwest Atlantic, the Mediterrean Sea, Namibia, and along the Pacific coast of Mexico. Two new putative species were detected, Hypnea sp. 1 in the Caribbean Sea and Hypnea sp. 2 in the Dominican Republic. Three distinct marine phylogeographic provinces were recognized in the Southern Hemisphere for H. pseudomusciformis: Uruguay, South-Southeast Brazil, and Northeast Brazil. The degree of genetic isolation and distinctness among these provinces varied considerably. The Uruguay province was the most genetically distinct, as characterized by four unique haplotypes not shared with any of the Brazilian populations. Statistically significant results support both, isolation by distance and isolation by environment hypotheses, explaining the formation and mantainance of phylogeographic structuring along the Uruguay-Brazil coast. Geographic, taxonomic and molecular marker concordances were found between our H. pseudomusciformis results and published studies. Furthermore, our data indicate that the Hawaiian introduced populations of H. musciformis contain Hypnea sp. 1 haplotypes, the current known distribution of which is restricted to the Caribbean.