DOI: 10.5061/dryad.pzgmsbcj3
title: Data from: Distribution and biogeography of Sanguina snow algae: fine-scale sequence analyses reveal previously unknown population structure

description: It has been previously suggested that snow algal species within the genus
 Sanguina (S. nivaloides and S. aurantia) show no population structure
 despite being found globally (S. nivaloides) or throughout the Northern
 Hemisphere (S. aurantia). However, systematic biogeographic research into
 global distributions is lacking due to few genetic and no genomic
 resources for these snow algae. Here, using all publicly available and
 previously unpublished Sanguina sequences of the Internal Transcribed
 Spacer 2 region, we investigate if this purported lack of population
 structure within Sanguina species is supported by additional evidence.
 Using a minimum entropy decomposition (MED) approach to examine fine-scale
 genetic population structure, we find that these snow algae populations
 are largely distinct regionally and have some interesting biogeographic
 structuring. This is in opposition to the currently accepted idea that
 Sanguina species lack any observable population structure across their
 vast ranges and highlights the utility of fine-scale (sub-OTU) analytical
 tools to delineate geographic and genetic population structure. This work
 extends the known range of S. aurantia and emphasizes the need for
 development of genetic and genomic tools for additional studies on snow
 algae biogeography.
description: We analyzed all available and verified ITS2 sequences at the time
 of analysis from <i>Sanguina </i>species<i>
 </i>from GenBank, SRA, and supplemental information from associated
 publications. We chose to analyze the ITS2 region as opposed to 18S or
 other gene targets because ITS2 has the most available data and ITS
 regions have great potential for species level population analysis for
 algae (An et al. 1999). We gathered the following
 Sanger sequences: 56 sequences from Segawa et al. (2018) collected from
 Alaska (USA), Svalbard (Norway), and Antarctica; 48 sequences from
 Procházková et al. (2019) from Austria, Italy, Slovakia, Switzerland,
 Norway, Colorado (USA), Argentina, and Antarctica; 29 sequences (Brown,
 unpublished using the primers ITS1-ITS4) from Lyman Basin, Washington
 (USA; 48º10’21” N, 120º53’50” W, 1880 m asl) and Niwot Ridge, Colorado
 (USA; 40º02’56” N, 105º34’51” W, 3514 m asl). Further, we gathered
 locus-targeted Illumina MiSeq sequence data: 1,600 sequences (Brown et al.
 2016) from Washington (USA) and Colorado (USA); 44,666 sequences (Brown
 and Jumpponen 2019) from Finland, Sweden, Norway, and Colorado (USA); and
 59,130 sequences (Tucker & Brown, unpublished<i>;</i>
 using fITS7-ITS4 primers) from Lyman Basin, Washington (USA; 48º10’27” N,
 120º53’26” W; 1818 m asl), Mt. Democrat, Colorado (USA; 39º20’38” N,
 106º07’45” W, 3950 m asl) and Medicine Bow Peak, Wyoming (USA, 41º20’45”
 N, 106º019’50” W; 3549 m asl). In all, we gathered 105,529 ITS2
 sequences. All sequences used were to the best of our
 knowledge from snows, generally perennial snowfields. To confirm that
 these sequences were from <i>Sanguina </i>snow algae, we
 extracted the ITS2 region (remove flanking 5.8S and LSU regions) from all
 sequences using the program ITSx (Bengtsson‐Palme et al. 2013), and MAFFT
 aligned (Katoh and Standley 2013) them to create a multiple sequence
 alignment (MSA). To initially confirm <i>Sanguina </i>origin
 of sequences, all sequences were initially clustered into OTUs using
 VSEARCH at 3% dissimilarity (Rognes et al. 2016) and representative
 sequences for these OTUs (see Appendix A1) were queried against GenBank
 (BLASTn nr/nt) and type sequences for both <i>Sanguina
 </i>species<i> </i>to confirm <i>Sanguina
 </i>identities. This resulted in two retained
 OTUs – the dominant OTU1 (best match to <i>Sanguina
 aurantia</i>, 96.63% match to accession MK728633.1 – 38,012 total
 sequences; 95.65% match to <i>S. aurantia </i>type specimen
 MK728634.1) and OTU2 (best match to <i>Sanguina nivaloides,
 </i>99.59% match to accession GU117577.1 – 22,065 total sequences,
 99.01% match to <i>S. nivaloides</i> type specimen
 MK728599.1), remaining sequences were determined to not belong to
 <i>Sanguina</i> and were discarded. Discarded sequences were
 mainly assigned to the Trebouxiophyceae, other non-<i>Sanguina
 </i>Chlorophyceae, or were poorly matched to any reference taxa. It
 may be that a few errant sequences not belonging to either target
 <i>Sanguina </i>species may have been included as part of the
 OTU clustering, but we have no evidence that casts doubt on the veracity
 of these sequences. These retained OTUs will hereafter be referred to as
 <i>S. aurantia</i> or <i>S. nivaloides</i>. All
 associated retained sequences were collected (Table 1, Appendix A1) and
 coded by location for <i>Sanguina </i>species specific MED
 analyses (<i>S. nivaloides</i> and <i>S.
 aurantia</i> were analyzed separately).