Joana F. Costa

Adaptive Traits Are Maintained on Steep Selective Gradients despite Gene Flow and Hybridization in the Intertidal Zone

Gene flow among hybridizing species with incomplete reproductive barriers blurs species boundaries, while selection under heterogeneous local ecological conditions or along strong gradients may counteract this tendency. Congeneric, externally-fertilizing fucoid brown algae occur as distinct morphotypes along intertidal exposure gradients despite gene flow. Combining analyses of genetic and phenotypic traits, we investigate the potential for physiological resilience to emersion stressors to act as an isolating mechanism in the face of gene flow. Along vertical exposure gradients in the intertidal zone of Northern Portugal and Northwest France, the mid-low shore species Fucus vesiculosus, the upper shore species Fucus spiralis, and an intermediate distinctive morphotype of F. spiralis var. platycarpus were morphologically characterized. Two diagnostic microsatellite loci recovered 3 genetic clusters consistent with prior morphological assignment. Phylogenetic analysis based on single nucleotide polymorphisms in 14 protein coding regions unambiguously resolved 3 clades; sympatric F. vesiculosus, F. spiralis, and the allopatric (in southern Iberia) population of F. spiralis var. platycarpus. In contrast, the sympatric F. spiralis var. platycarpus (from Northern Portugal) was distributed across the 3 clades, strongly suggesting hybridization/introgression with both other entities. Common garden experiments showed that physiological resilience following exposure to desiccation/heat stress differed significantly between the 3 sympatric genetic taxa; consistent with their respective vertical distribution on steep environmental clines in exposure time. Phylogenetic analyses indicate that F. spiralis var. platycarpus is a distinct entity in allopatry, but that extensive gene flow occurs with both higher and lower shore species in sympatry. Experimental results suggest that strong selection on physiological traits across steep intertidal exposure gradients acts to maintain the 3 distinct genetic and morphological taxa within their preferred vertical distribution ranges. On the strength of distributional, genetic, physiological and morphological differences, we propose elevation of F. spiralis var. platycarpus from variety to species level, as F. guiryi.

Wider sampling reveals a non-sister relationship for geographically contiguous lineages of a marine mussel

The accuracy of phylogenetic inference can be significantly improved by the addition of more taxa and by increasing the spatial coverage of sampling. In previous studies, the brown mussel Perna perna showed a sister–lineage relationship between eastern and western individuals contiguously distributed along the South African coastline. We used mitochondrial (COI) and nuclear (ITS) sequence data to further analyze phylogeographic patterns within P. perna. Significant expansion of the geographical coverage revealed an unexpected pattern. The western South African lineage shared the most recent common ancestor (MRCA) with specimens from Angola, Venezuela, and Namibia, whereas eastern South African specimens and Mozambique grouped together, indicating a non-sister relationship for the two South African lineages. Two plausible biogeographic scenarios to explain their origin were both supported by the hypotheses-testing analysis. One includes an Indo-Pacific origin for P. perna, dispersal into the Mediterranean and Atlantic through the Tethys seaway, followed by recent secondary contact after southward expansion of the western and eastern South African lineages. The other scenario (Out of South Africa) suggests an ancient vicariant divergence of the two lineages followed by their northward expansion. Nevertheless, the “Out of South Africa” hypothesis would require a more ancient divergence between the two lineages. Instead, our estimates indicated that they diverged very recently (310 kyr), providing a better support for an Indo-Pacific origin of the two South African lineages. The arrival of the MRCA of P. perna in Brazil was estimated at 10 [0–40] kyr. Thus, the hypothesis of a recent introduction in Brazil through hull fouling in wooden vessels involved in the transatlantic itineraries of the slave trade did not receive strong support, but given the range for this estimate, it could not be discarded. Wider geographic sampling of marine organisms shows that lineages with contiguous distributions need not share a common ancestry.

The plastid genome of the red alga Laurencia

We present the 174,935 nt long plastid genome of the red alga Laurencia sp. JFC0032. It is the third plastid genome characterized for the largest order of red algae (Ceramiales). The circular‐mapping plastid genome is small compared to most florideophyte red algae, and our comparisons show a trend toward smaller plastid genome sizes in the family Rhodomelaceae, independent from a similar trend in Cyanidiophyceae. The Laurencia genome is densely packed with 200 annotated protein‐coding genes (188 widely conserved, 3 open reading frames shared with other red algae and 9 hypothetical coding regions). It has 29 tRNAs, a single‐copy ribosomal RNA cistron, a tmRNA, and the RNase P RNA.

Intraspecific genetic lineages of a marine mussel show behavioural divergence and spatial segregation over a tropical/subtropical biogeographic transition

BackgroundIntraspecific variability is seen as a central component of biodiversity. We investigated genetic differentiation, contemporary patterns of demographic connectivity and intraspecific variation of adaptive behavioural traits in two lineages of an intertidal mussel (Perna perna) across a tropical/subtropical biogeographic transition.ResultsMicrosatellite analyses revealed clear genetic differentiation between western (temperate) and eastern (subtropical/tropical) populations, confirming divergence previously detected with mitochondrial (COI) and nuclear (ITS) markers.Gene flow between regions was predominantly east-to-west and was only moderate, with higher heterozygote deficiency where the two lineages co-occur. This can be explained by differential selection and/or oceanographic dynamics acting as a barrier to larval dispersal.Common garden experiments showed that gaping (periodic closure and opening of the shell) and attachment to the substratum differed significantly between the two lineages. Western individuals gaped more and attached less strongly to the substratum than eastern ones.ConclusionsThese behavioural differences are consistent with the geographic and intertidal distributions of each lineage along sharp environmental clines, indicating their strong adaptive significance. We highlight the functional role of diversity below the species level in evolutionary trends and the need to understand this when predicting biodiversity responses to environmental change.

Molecular Survey of Codium Species Diversity in Southern Madagascar

Abstract We present a molecular survey of the species in the green algal genus Codium that were collected as part of the Atimo Vatae expedition to southern Madagascar. Based on clustering analysis of partial tufA and rbcL sequences, we recognize 11–12 species-level clusters in this area. Through a combination of morphological identifications and DNA comparisons, these clusters are identified as C. mozambiquense, C. spongiosum, C. lucasii subsp. capense, C. duthieae, C. decorticatum, C. prostratum, C. dwarkense, C. taylorii, C. arenicola and C. cf. cicatrix, and a new ball-shaped species. We present a phylogenetic tree inferred from a concatenated alignment with tufA, rbcL and rps3-rpl16 to show the placement of these species in the broader context of the genus and to analyse the biogeographic affinities of the southern Madagascan Codium flora. We conclude that the Madagascan flora shares elements with temperate South Africa and contains tropical Indo-Pacific elements. It also has endemic elements, some clearly at the species level, some possibly representing isolated populations of more widely-ranging species.

DNA barcodes and morphometric data indicate that Codium fragile (Bryopsidales, Chlorophyta) may consist of two species

Abstract: The siphonous green alga Codium fragile currently has 10 accepted subspecies, among which is the problematic invasive subsp. fragile. The subspecies are defined on the basis of five polymorphic nucleotides in the plastid rps3–rpl16 spacer region, and this subdivision into subspecies has not been investigated in detail with other DNA markers. Here, we compiled a data set of the green algal DNA barcoding marker tufA that includes 110 C. fragile specimens and an additional 80 specimens of eight related Codium species. Our tufA haplotype tree showed two distinct clades within C. fragile, and the three algorithmic species delimitation methods that were applied agreed that these are likely to represent separate species. The first clade consisted of the invasive subspecies fragile, whereas the second contained the remaining subspecies present among our sequences. Using a newly developed morphometric method to capture fine details of utricle morphology, we show that the two molecular clades also have subtle morphological differences. Despite all this new evidence in favour of two species being present in C. fragile, we refrain from making formal taxonomic changes, chiefly because our tufA data do not agree with previous rps3–rpl16 results. We propose four complementary approaches to resolve these conflicts.

A population genetics toolbox for the threatened canopy-forming brown seaweeds Cystoseira tamariscifolia and C. amentacea (Fucales, Sargassaceae)

The brown macroalga Cystoseira tamariscifolia is a foundation species along the northeastern Atlantic and western Mediterranean Sea. It occurs from lower intertidal rock pools to the shallow subtidal. Anthropogenic pollution and rising seawater temperatures can threaten its local distributions. In order to address impacts of historical and current environmental changes, to quantify effective dispersal and population connectivity, and to provide genetic tools for restoration and coastal management strategies, we have developed ten microsatellite markers, validated on 48 individuals from a single population. With 2–11 alleles per locus, the observed heterozygosity varied between 0.244 and 0.875. All of the developed microsatellites cross-amplified also on Cystoseira amentacea. The ten microsatellite loci developed here show high genetic diversity, making them useful for connectivity and population genetic studies aimed at small to large spatial scales, and provide essential insight for the development of conservation strategies for this important but threatened foundation species.

Evolutionary dynamics of algal traits and diversity

Algae have a particularly rich evolutionary history that has not yet been comprehensively explored. We review statistical techniques to infer patterns of trait evolution and species diversification from phylogenies. We illustrate these methods using the evolution of algal thermal niches and its interaction with species diversification as a case study. We offer some perspectives for the application of these methods in other fields of phycology and the integration of microand macroevolutionary approaches.

Organization of plastid genomes in the freshwater red algal order Batrachospermales (Rhodophyta)

Little is known about genome organization in members of the order Batrachospermales, and the infra‐ordinal relationship remains unresolved. Plastid (cp) genomes of seven members of the freshwater red algal order Batrachospermales were sequenced, with the following aims: (i) to describe the characteristics of cp genomes and compare these with other red algal groups; (ii) to infer the phylogenetic relationships among these members to better understand the infra‐ordinal classification. Cp genomes of Batrachospermales are large, with several cases of gene loss, they are gene‐dense (high gene content for the genome size and short intergenic regions) and have highly conserved gene order. Phylogenetic analyses based on concatenated nucleotide genome data roughly supports the current taxonomic system for the order. Comparative analyses confirm data for members of the class Florideophyceae that cp genomes in Batrachospermales is highly conserved, with little variation in gene composition. However, relevant new features were revealed in our study: genome sizes in members of Batrachospermales are close to the lowest values reported for Florideophyceae; differences in cp genome size within the order are large in comparison with other orders (Ceramiales, Gelidiales, Gracilariales, Hildenbrandiales, and Nemaliales); and members of Batrachospermales have the lowest number of protein‐coding genes among the Florideophyceae. In terms of gene loss, apcF, which encodes the allophycocyanin beta subunit, is absent in all sequenced taxa of Batrachospermales. We reinforce that the interordinal relationships between the freshwater orders Batrachospermales and Thoreales within the Nemaliophycidae is not well resolved due to limited taxon sampling.

High-throughput sequencing for algal systematics

ABSTRACT In recent years, the use of molecular data in algal systematics has increased as high-throughput sequencing (HTS) has become more accessible, generating very large datasets at a reasonable cost. In this perspectives paper, our goal is to describe how HTS technologies can advance algal systematics. Following an introduction to some common HTS technologies, we discuss how metabarcoding can accelerate algal species discovery. We show how various HTS methods can be applied to generate datasets for accurate species delimitation, and how HTS can be applied to historical type specimens to assist the nomenclature process. Finally, we discuss how HTS data such as organellar genomes and transcriptomes can be used to construct well-resolved phylogenies, leading to a stable and natural classification of algal groups. We include examples of bioinformatic workflows that may be applied to process data for each purpose, along with common programs used to achieve each step. We also discuss possible strategies and the new skill set that will be required to fully embrace HTS as a part of algal systematics, along with considerations of cost and experimental design. HTS technology has revolutionized many fields in biology, and will certainly do the same in algal systematics.