Using the Multiple Analysis Approach to Reconstruct Phylogenetic Relationships among Planktonic Foraminifera from Highly Divergent and Length-polymorphic SSU rDNA Sequences

Abstract

The high sequence divergence within the small subunit ribosomal RNA gene (SSU rDNA) of foraminifera makes it difficult to establish the homology of individual nucleotides across taxa. Alignment-based approaches so far relied on time-consuming manual alignments and discarded up to 50% of the sequenced nucleotides prior to phylogenetic inference. Here, we investigate the potential of the multiple analysis approach to infer a molecular phylogeny of all modern planktonic foraminiferal taxa by using a matrix of 146 new and 153 previously published SSU rDNA sequences. Our multiple analysis approach is based on eleven different automated alignments, analysed separately under the maximum likelihood criterion. The high degree of congruence between the phylogenies derived from our novel approach, traditional manually homologized culled alignments and the fossil record indicates that poorly resolved nucleotide homology does not represent the most significant obstacle when exploring the phylogenetic structure of the SSU rDNA in planktonic foraminifera. We show that approaches designed to extract phylogenetically valuable signals from complete sequences show more promise to resolve the backbone of the planktonic foraminifer tree than attempts to establish strictly homologous base calls in a manual alignment.

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

“…3), but only 0 to 30 % of the morphological assemblages (Kucera et al, 2005). The microperforate clade appears to have significantly lower rDNA substitution rates (Aurahs et al, 2009) and here we observe no mismatch between the primer and the reference sequences within this clade.…”

“…This observation is consistent with preferential PCR amplification. The rDNA of planktonic foraminifera is characterized by high and variable substitution rates (de Vargas et al, 1997), and two of the four above species exhibit some of the highest mutation rates (Aurahs et al, 2009). The manual inspection of a multiple sequence alignment containing the reference database sequences revealed the presence of up to five mismatches between these species sequences and the primer sequences used to generate the dataset.…”

Assessing the role of cladogenesis in macroevolution by integrating fossil and molecular evidence

“…One noted exception to monophyly among extant morphospecies is Globigerinoides ruber, which is now recognized as comprising two distinct clades on the basis of molecular evidence (35). Inconsistencies between molecular and fossil data are largely confined to the placement of higher-order clades, where SSU rDNA divergences are high and relationships are difficult to resolve (36).…”

Methodology for Single-Cell Genetic Analysis of Planktonic Foraminifera for Studies of Protist Diversity and Evolution

“…This can be attributed to highly variable expansion segments integrated as loops in the helices of the SSU rDNA. The foraminifera SSU rDNA contains three unique variable regions (37/f, 41/f, and 47/f; Pawlowski and Lecroq, 2010) that differ widely between the different groups, complicating automated sequence alignments (de Vargas et al, 1997;Aurahs et al, 2009b). Furthermore, rates of SSU rDNA evolution in planktonic foraminifera vary significantly between the different species and are one of the highest known (de Vargas et al, 1997).…”

“…Planktonic foraminifera are thus a prime example of a group with fully resolved morphological taxonomy that could be tested by genetic information (Aurahs et al, 2009b) and where the extent of hidden genetic diversity could be established in great detail (Darling and Wade, 2008). Since the development of DNA extraction methods which leave the calcite shell intact, the DNA sequences can be directly associated with the morphology of the same individual, establishing a definitive link between genetic diversity and subtle morphological variability (e.g., Morard et al, 2009Morard et al, , 2011Quillévéré et al, 2013).…”