Microsatellite genotypes of Gracilaria chilensis from New Zealand and Chile

This readme file describes the microsatellites genotypes for a red algae: Gracilaria chilensis. The file include data for 187 individuals collected from eight natural populations from New Zealand (including the Chatham Islands) and 410 individuals collected along the Chilean coast. G. chilensis is extensively cultivated in Chile for agar production, however, only natural populations (i.e. non cultivated ones) are reported in this data set. The five microsatellite loci are named according to Guillemin et al. (2005, Development of microsatellites DNA markers in the cultivated seaweed Gracilaria chilensis (Gracilariales Rhodophyta). Mol Ecol Notes 5, 155–157.). All individuals are diploids. “0” correspond to missing data. For any further queries please contact [email protected]

Genetic population structure of New Zealand and Chilean <i>Gracilaria</i> populations.

<p>(A) based on Bayesian analysis with STRUCTURE software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039-Pritchard1" target="_blank">[37]</a>, proportions of individual multilocus genotypes were assigned to each of the 5 virtual genetic clusters indicated by the different colours; (B) based on graph analysis with POPULATION GRAPH software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039-Dyer1" target="_blank">[40]</a>, differences in node size reflect differences in within population variability whereas edge lengths represent the genetic variation between pairs of samples, there were significantly more edges within New Zealand and Chilean groups than between the two groups (P&lt;0.0001). Node colour corresponds to the 5 clusters as determined by STRUCTURE. For both analyses: N = 7 New Zealand populations, 11 Chilean populations, 567 individuals, 5 codominant loci. Population codes are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039.s002" target="_blank">Table S1</a>.</p

Tests of demographic changes based on ITS2 sequences.

<p>Departure from neutrality tested using Fu’s Fs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039-Fu1" target="_blank">[42]</a> and Ramos-Onsins and Rozas’ R₂ statistic <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039-RamosOnsins1" target="_blank">[43]</a>. Significance determined using 10,000 simulated data sets implemented by DnaSP version 5.10.01 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039-Rozas1" target="_blank">[44]</a>. τ-values estimated from demographic expansion models using ARLEQUIN v 3.11 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039-Excoffier1" target="_blank">[33]</a>. Goodness of fit tests for a model of population expansion calculated from the sum of squared deviation (SSD) and the Harpending’s raggedness index (Rag). Significance assessed by bootstrapping (10,000 replicates; ARLEQUIN v 3.11) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039-Excoffier1" target="_blank">[33]</a>.</p>$<p>All East New Zealand populations excluding Chatham;</p>‡<p>P values of (Expected SSD &gt; Observed SSD) or P (Expected Rag &gt; Observed Rag) superior to 0.05 means the null hypothesis of spatial expansion can’t be rejected;</p>#<p>nc: τ-value not calculated when spatial expansion is rejected.</p><p>Tests of demographic changes based on ITS2 sequences.</p

Location of the sampling sites.

<p>ITS2 ribotype distribution and ITS2 network including 201 sequences of 481 nucleotides. Pie charts represent ribotype frequency in each population. Ribotype network was constructed using a median-joining algorithm with programme NETWORK <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039-Bandelt1" target="_blank">[36]</a>. Colours of the network correspond to those mapped with rare ribotypes in each “region” pooled under the same colour for clarity. Circle sizes are proportional to total ribotype frequency and connection lengths correspond to mutation steps (most of the ribotypes are separated by one mutational step but eight mutations separate r4 from r6).</p

Number of alleles observed in each of the 10 allele frequency classes defined in New Zealand and Chilean populations (pooled data from each side of the South Pacific coast).

<p>Reduced number of low frequency alleles is characteristic of a bottleneck <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114039#pone.0114039-Keller1" target="_blank">[47]</a>.</p

A) Electrophoresis pattern of sex marker products amplified in six diploid sporophytes of <i>L</i>. <i>digitata</i>. M: male marker (M_68_16_1); F: female marker (M_68_58_3). B) Electrophoresis pattern of sex marker products amplified in a diploid sporophyte and female partheno-sporophyte of <i>Undaria pinnatifida</i>. M: male marker (M_68_16_2), F: female marker (M_285_20_2), PAR gene (M_285_26_1); SP: sporophyte, pSP: partheno-sporophyte.

<p>A) Electrophoresis pattern of sex marker products amplified in six diploid sporophytes of <i>L</i>. <i>digitata</i>. M: male marker (M_68_16_1); F: female marker (M_68_58_3). B) Electrophoresis pattern of sex marker products amplified in a diploid sporophyte and female partheno-sporophyte of <i>Undaria pinnatifida</i>. M: male marker (M_68_16_2), F: female marker (M_285_20_2), PAR gene (M_285_26_1); SP: sporophyte, pSP: partheno-sporophyte.</p

Schematic representation of a kelp life cycle.

<p>The sexual cycle consists of an alternation between a macroscopic diploid sporophyte and microscopic, haploid, dioicous (male and female) gametophytes. The zoospores produced by the sporophyte are released and develop as male (carrying the V sex chromosome) or female (carrying the U sex chromosome) gametophytes. Egg and sperm produced by the gametophyte fuse to return to the diploid, asexual sporophyte generation, which carries both the U and the V sex chromosomes.</p

Origins of the kelp gametophyte clones used in this study.

<p>*Asexual sporophyte, carrying both male and female sex chromosomes</p><p>**Partheno-sporophyte derived from female gametophyte (through parthenogenetic development of unfertilized eggs)</p><p>Origins of the kelp gametophyte clones used in this study.</p

Primer information and PCR conditions for the sex-specific marker tests carried out on the three Laminariales species <i>L</i>. <i>digitata</i>, <i>M</i>. <i>pyrifera</i> and <i>U</i>. <i>pinnatifida</i>.

<p>*D–denaturation time, A–annealing time, E–elongation time, TA- annealing temperature.</p><p>**NA–no amplification</p><p>Primer information and PCR conditions for the sex-specific marker tests carried out on the three Laminariales species <i>L</i>. <i>digitata</i>, <i>M</i>. <i>pyrifera</i> and <i>U</i>. <i>pinnatifida</i>.</p

Mean population growth (± SE) for central and marginal populations from both species of <i>Lessonia nigrescens</i> under the five tested temperature treatments.

<p>Mean population growth (± SE) for central and marginal populations from both species of <i>Lessonia nigrescens</i> under the five tested temperature treatments.</p