Background The southern hemisphere kelps in the genus Lessonia play an important role in coastal ecosystems along the shores of South America, New Zealand & Tasmania. In Chile, the harvest of Lessonia algae has great economic importance. In the past they have been many mis- and reclassifications of Lessonia species, specifically in the Magellanic region. Molecular research has revealed cryptic diversity in the Chilean and Australasian Lessonia lineages. The species of the Magellanic region, however, have not been subjected to comprehensive phylogenetic analyses.
Objectives The main objective of the study is a phylogenetic reconstruction for the genus Lessonia, comprising its entire geographic range. Secondly, I aim to clarify persisting taxonomic uncertainty in the Magellanic Lessonia lineages. Further, I aim to investigate the divergence times of the Lessonia lineages and derive an evolutionary hypothesis for the genus Lessonia with particular focus on the Magellanic Lessonia lineages.
Methods This investigation is based on a de novo transcriptome assembly of paired-end RNA sequences (RnaSpades). In silico transcriptome curation was done with Transrate & FragGeneScan. For biological filtering Diamond Blast, the NCBI stamenopile database and BUSCO were used. RSEM with bowtie 2 was used to map the RNA fragments onto the transcriptome. Finally, after allele phasing and locus selection (samtools), multiple sequence alignments and loci selection were performed using translator X, MUSCLE, and Gblocks using a custom python script (locus_pipe.py). The working dataset for phylogenomic analysis comprised paired-end sequences for 58 single copy loci of 24 Lessonia and two outgroup samples, Laminaria digitata and L. ochroleuca. Maximum likelihood and Bayesian phylogenetic analyses were performed using MrBayes, IQ-TREE2 and BEAST2 software. For more detailed results polymorphism aware and concordance factor analysis were performed (IQ-TREE 2) as well as species delimitation analysis using SODA.
Results Maximum likelihood and Bayesian trees had coherent topologies and branch lengths for all major branches as well as high boot strap support/ posterior probabilities (>90/ 0.9). Gene concordance was low whilst concordance among sites was high. Three main clusters could be distinguished, separating the Chilean, Magellanic and Australasian species. Among these, the Chilean cluster was the oldest and most divergent from all remaining lineages. A total of 14 species were distinguished in the SODA analysis, of which four were cryptic lineages in the Lessonia variegata species complex and one was a potentially new sister lineage to Lessonia searlesiana. Diversification of the genus Lessonia occurred within the past 2 M years. The split between L. searlesiana and L. flavicans happened before the geographic divergence between Falkland and Patagonian lineages. These latter geographic divergences occurred in two separate parallel events, between 300 and 150 Kya.
Conclusions The present study is one of the most comprehensive ones on the kelp genus Lessonia and the first detailed genealogical analysis of the diversity within the Magellanic Lessonia species. Formerly described cryptic species were confirmed in this study and a new evolutionary hypothesis is presented. A potentially new cryptic species is reported from the Magellanic region. These results may have important implications for the sustainable management and conservation of Lessonia in the light of global change.
Background The southern hemisphere kelps in the genus Lessonia play an important role in coastal ecosystems along the shores of South America, New Zealand & Tasmania. In Chile, the harvest of Lessonia algae has great economic importance. In the past they have been many mis- and reclassifications of Lessonia species, specifically in the Magellanic region. Molecular research has revealed cryptic diversity in the Chilean and Australasian Lessonia lineages. The species of the Magellanic region, however, have not been subjected to comprehensive phylogenetic analyses.
Objectives The main objective of the study is a phylogenetic reconstruction for the genus Lessonia, comprising its entire geographic range. Secondly, I aim to clarify persisting taxonomic uncertainty in the Magellanic Lessonia lineages. Further, I aim to investigate the divergence times of the Lessonia lineages and derive an evolutionary hypothesis for the genus Lessonia with particular focus on the Magellanic Lessonia lineages.
Methods This investigation is based on a de novo transcriptome assembly of paired-end RNA sequences (RnaSpades). In silico transcriptome curation was done with Transrate & FragGeneScan. For biological filtering Diamond Blast, the NCBI stamenopile database and BUSCO were used. RSEM with bowtie 2 was used to map the RNA fragments onto the transcriptome. Finally, after allele phasing and locus selection (samtools), multiple sequence alignments and loci selection were performed using translator X, MUSCLE, and Gblocks using a custom python script (locus_pipe.py). The working dataset for phylogenomic analysis comprised paired-end sequences for 58 single copy loci of 24 Lessonia and two outgroup samples, Laminaria digitata and L. ochroleuca. Maximum likelihood and Bayesian phylogenetic analyses were performed using MrBayes, IQ-TREE2 and BEAST2 software. For more detailed results polymorphism aware and concordance factor analysis were performed (IQ-TREE 2) as well as species delimitation analysis using SODA.
Results Maximum likelihood and Bayesian trees had coherent topologies and branch lengths for all major branches as well as high boot strap support/ posterior probabilities (>90/ 0.9). Gene concordance was low whilst concordance among sites was high. Three main clusters could be distinguished, separating the Chilean, Magellanic and Australasian species. Among these, the Chilean cluster was the oldest and most divergent from all remaining lineages. A total of 14 species were distinguished in the SODA analysis, of which four were cryptic lineages in the Lessonia variegata species complex and one was a potentially new sister lineage to Lessonia searlesiana. Diversification of the genus Lessonia occurred within the past 2 M years. The split between L. searlesiana and L. flavicans happened before the geographic divergence between Falkland and Patagonian lineages. These latter geographic divergences occurred in two separate parallel events, between 300 and 150 Kya.
Conclusions The present study is one of the most comprehensive ones on the kelp genus Lessonia and the first detailed genealogical analysis of the diversity within the Magellanic Lessonia species. Formerly described cryptic species were confirmed in this study and a new evolutionary hypothesis is presented. A potentially new cryptic species is reported from the Magellanic region. These results may have important implications for the sustainable management and conservation of Lessonia in the light of global change.
