Comparison of maximum parsimony bootstrap support (in %) for clades of species of the <i>Racomitrium canescens</i> complex.

<p>The bootstrap analyses were performed using parts of the analyzed DNA regions <i>rps4-trnT-trnL</i> and nrITS, which can be amplified separately with established primers for species identification purposes (DNA barcoding). Two specimens with missing sequences were excluded from the analysis of <i>trnT-trnL</i>. Values before and after the dash are from analyses without and with indels included by simple indel coding (SIC), respectively; values >70% are in bold. Dashes denote clades that were not resolved in the respective phylogenetic reconstructions.</p

Sequence divergence percentages between species pairs in the <i>Racomitrium canescens</i> complex.

<p>Comparison of maximum intraspecific versus minimum interspecific divergence percentages for species pairs of five species (<i>R. canescens</i>, <i>R. elongatum</i>, <i>R. ericoides</i>, <i>R. japonicum</i>, <i>R. muticum</i>) with more than one specimen sequenced for the plastid <i>rps4-trnT-trnL</i> region (A) and its partitions <i>rps4-trnT</i> (B) and <i>trnT-trnL</i> (C) as well as the nrITS region (D) and its partitions ITS1 (E) and ITS2 (F).</p

Calculations of pairwise Fst estimates and p-values for five species of the <i>Racomitrium canescens</i> complex.

<p>Group comparisons based on the ITS sequence and indel data are indicated above the diagonal, whereas group comparisons based on the plastid sequence and indel data are shown below the diagonal. Significant p-values (significance level 0.05) are indicated by an asterisk.</p

Contrasting spatial, temporal and environmental patterns in observation and specimen based species occurrence data

<div><p>Species occurrence data records the location and time of an encounter with a species, and is valuable for many aspects of ecological and evolutionary analyses. A key distinction within species occurrence data is between (1) collected and preserved specimens that can be taxonomically validated (i.e., natural history collections), and (2) observations, which are more error prone but richer in terms of number and spread of observations. In this study we analyse the distribution in temporal, spatial, taxonomic and environmental coverage of specimen- and observation based species occurrence data for land plants in Norway, a region with strong climatic and human population density gradients. Of 4.8 million species occurrence records, the majority (78%) were observations. However, there was a greater species richness in the specimen record (N = 4691) than in the observation record (N = 3193) and most species were recorded more as specimens than observations. Specimen data was on average older, and collected later during the year. Both record types were highly influenced by a small number of prolific contributors. The species most highly represented in the observation data set were widespread or invasive, while in the specimen records, taxonomically challenging species were overrepresented. Species occurrence records were unevenly spatially distributed. Both specimen and observation records were concentrated in regions of Norway with high human population density and with high temperatures and precipitation, but in different regions within Norway. Observation and specimen records thus differ in taxonomic, temporal, spatial and environmental coverage for a well-sampled group and study region, potentially influencing the ecological inferences made from studies utilizing species occurrence data. The distribution of observation data dominates the dataset, so inferences of species diversity and distributions do not correspond to the evolutionary or physiological knowledge of species, which is based on specimen data. We make recommendations for users of biodiversity data, and collectors to better exploit the complementary strengths of these distinct biodiversity data types.</p></div

Contrasting spatial, temporal and environmental patterns in observation and specimen based species occurrence data - Fig 2

<p>(a) Number of human observation and preserved specimen records of each species. Species are plotted with symbols denoting their taxonomic class (Bryophyta and Marchantiophyta grouped as bryophytes). (b) The ratio of number of observations to number of specimen records for each species grouped by taxonomic class. Boxes represent interquartile ranges, with whiskers 1.5 times this range, and points showing species outside the range. The median is shown by a black line. Values above one show species with more observation records than specimen records. Vertical lines divide classes within the three phyla. (c) Species rank-abundance plot for each record type in the Norwegian Embryophyta dataset, showing the number of records (note log₁₀ y-axis) for each species plotted against the species’ rank when ordered from most to least abundant within each record type. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0196417#pone.0196417.t002" target="_blank">Table 2</a> gives the identity of the 10 most abundant species per record basis. (d) Recorder rank-abundance plot for each record type showing the log number of records made by each recorder, plotted against the recorders’ rank when ordered from the most to least abundant within each record type. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0196417#pone.0196417.s001" target="_blank">S1 Table</a> gives the identity of the 10 most abundant recorders per record basis.</p

Intra- versus interspecific pairwise distances of <i>rps4-trnT-trnL</i> and ITS sequences in the <i>Racomitrium canescens</i> complex.

<p>Kimura 2-parameter (K2P) distances are shown for the combined molecular markers and different partitions thereof. The upper two rows indicate the ranges of intraspecific and interspecific distances for all eight species of the <i>R. canescens</i> complex plus <i>R. varium</i>. The last row indicates the overlap between the maximum intraspecific and minimum interspecific distances.</p

Revised species identifications in the <i>Racomitrium canescens</i> species complex based on molecular data.

<p>Changes in species identification of 14 specimens analyzed in the present study are indicated by arrows. Arrow thickness is equivalent to the number of specimens transferred from one species to another (one, two, or four specimens, respectively). Grey or black arrows indicate changes within or between subsections <i>Canescens</i> and <i>Ericoides </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053134#pone.0053134-Larran1" target="_blank">[15]</a>, respectively.</p

Geographical distribution of genetic groups inferred by the software Structure for all samples of haploid <i>Sphagnum magellanicum</i> (below, colours as in Fig 1) and all samples of diploid <i>S</i>. <i>magellanicum</i> and <i>S</i>. <i>alaskense</i> (above).

<p>Genetic groups in the haploid plants differ in their total geographical distributions, but no spatial structure was found for diploid plants.</p

The number of species occurrence records of each record type plotted against the geographic range, here estimated as the number of 10x10 km grid cells within which that species had been recorded (as any record type).

<p>Outlying species are plotted as square points and labelled.</p

Principal coordinate analysis based on microsatellite loci of six groups of haploid <i>Sphagnum magellanicum</i> divided in geographical regions.

<p>Coloured symbols in the upper left corner show geographical origin of the samples and the coloured lines correspond to different genetic groups inferred by Structure (same colours as used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148447#pone.0148447.g002" target="_blank">Fig 2</a> lower map). The dots that are not enclosed are admixed between different genetic groups.</p