Network of 25 haplotypes.

<p>Branch lengths are relative to their differences in eleven loci (shortest branches are equivalent to a single mutation). Pie chart shading colors represent the frequency of nuclear DNA identity. Dark: ITS-A in haplogroup D (<i>Ruppia maritima</i>), haplogroup E (Ancient hybrids in <i>Ruppia cirrhosa</i> complex) and some within haplotype B1 or C1 (recent hybrids); white: ITS-B in haplogroup B and C (<i>Ruppia cirrhosa</i>); and shaded: ITS-C in haplogroup A (<i>Ruppia drepanensis</i>). Note the large number of differences between haplogroup D and E, but sharing ITS-A.</p

Maximum Likelihood Tree of 25 haplotypes.

<p>Two haplogroup complexes of <i>Ruppia cirrhosa</i> and of <i>Ruppia maritima</i> are fully supported. Within haplogroups, only support (>70) was given to haplotypes D and E. The basal lineages of each haplogroup contain populations of Africa. The <i>Ruppia cirrhosa</i> complex with haplogroups B and C represent tetraploid populations (ITS-B) from the most marine-lagoonal habitats whereas others haplogroups (A, D) contained diploid populations (ITS-A and ITS-C) mostly from brackish water and inland saline wetlands, including ephemeral habitats.</p

Analysis of Molecular Variance.

<p>AMOVA) of <i>Ruppia cirrhosa</i> cpDNA haplotypes from 106 sites divided over two continental parts and over twelve seas or regions (d.f. = degree of freedom).</p

Data collection and haplotype diversity.

<p>Collection details and diversity in 12 European and Mediterranean regions of 2221 <i>Ruppia cirrhosa</i> individuals from 106 coastal lagoons and inland saline waterbodies. Additional locality details, haplotypes, ITS identity and ploidy levels of 2843 individuals of both <i>Ruppia cirrhosa</i> and <i>Ruppia maritima</i> complex are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104264#pone.0104264.s005" target="_blank">Table S1</a>.</p

Haplotype frequency distribution.

<p>Populations of the <i>Ruppia cirrhosa</i> complex (including <i>Ruppia drepanensis</i> haplogroup A and hybrid lineages of haplogroup E) are pooled in 12 coastal zones or regions as given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104264#pone-0104264-t001" target="_blank">Table 1</a> (Northern Baltic, Ostsee/Southern Baltic, North Sea, Atlantic, Inland Spain, Alboran/Algerian, Balearic, Tyrrhenic, Adriatic, Ionian, Northern Aegean, Levantine/Nile/Middle East). The size of pie charts is relative to their haplotype diversity. A detailed overview with pie charts relative to sample sizes at population level is provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104264#pone.0104264.s001" target="_blank">Figures S1</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104264#pone.0104264.s002" target="_blank">S2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104264#pone.0104264.s003" target="_blank">S3</a>.</p

Within population diversity along latitudinal gradient.

<p>Haplotype diversity in 72 populations (30 m transects) plotted against latitudes (°N) with indication of threshold values obtained from a Classification and Regression Tree analysis. Highest within population diversity resides in regions <40°N. Note the large number of monomorph sites across all latitudes.</p

Table_2_Inferring Connectivity Range in Submerged Aquatic Populations (Ruppia L.) Along European Coastal Lagoons From Genetic Imprint and Simulated Dispersal Trajectories.DOCX

<p>Coastal salt- and brackish water lagoons are unique shallow habitats characterized by beds of submerged seagrasses and salt-tolerant Ruppia species. Established long-term and large-scale patterns of connectivity in lagoon systems can be strongly determined by patterns of nearshore and coastal currents next to local bird-mediated seed dispersal. Despite the importance of dispersal in landscape ecology, characterizing patterns of connectivity remains challenging in aquatic systems. Here, we aimed at inferring connectivity distances of Ruppia cirrhosa along European coastal lagoons using a population genetic imprint and modeled dispersal trajectories using an eddy-resolving numerical ocean model that includes tidal forcing. We investigated 1,303 individuals of 46 populations alongside subbasins of the Mediterranean (Balearic, Tyrrhenian, Ionian) and the Atlantic to Baltic Sea coastline over maximum distances of 563–2,684 km. Ten microsatellite loci under an autotetraploid condition revealed a mixed sexual and vegetative reproduction mode. A pairwise F_ST permutation test of populations revealed high levels of historical connectivity only for distance classes up to 104–280 km. Since full range analysis was not fully explanatory, we assessed connectivity in more detail at coastline and subbasin level using four approaches. Firstly, a regression over restricted geographical distances (300 km) was done though remained comparable to full range analysis. Secondly, piecewise linear regression analyses yielded much better explained variance but the obtained breakpoints were shifted toward greater geographical distances due to a flat slope of regression lines that most likely reflect genetic drift. Thirdly, classification and regression tree analyses revealed threshold values of 47–179 km. Finally, simulated ocean surface dispersal trajectories for propagules with floating periods of 1–4 weeks, were congruent with inferred distances, a spatial Bayesian admixed gene pool clustering and a barrier detection method. A kinship based spatial autocorrelation showed a contemporary within-lagoon connectivity up to 20 km. Our findings indicate that strong differentiation or admixtures shaped historical connectivity and that a pre- and post LGM genetic imprint of R. cirrhosa along the European coasts was maintained from their occurrence in primary habitats. Additionally, this study demonstrates the importance of unraveling thresholds of genetic breaks in combination with ocean dispersal modeling to infer patterns of connectivity.</p

Table_1_Inferring Connectivity Range in Submerged Aquatic Populations (Ruppia L.) Along European Coastal Lagoons From Genetic Imprint and Simulated Dispersal Trajectories.DOCX

<p>Coastal salt- and brackish water lagoons are unique shallow habitats characterized by beds of submerged seagrasses and salt-tolerant Ruppia species. Established long-term and large-scale patterns of connectivity in lagoon systems can be strongly determined by patterns of nearshore and coastal currents next to local bird-mediated seed dispersal. Despite the importance of dispersal in landscape ecology, characterizing patterns of connectivity remains challenging in aquatic systems. Here, we aimed at inferring connectivity distances of Ruppia cirrhosa along European coastal lagoons using a population genetic imprint and modeled dispersal trajectories using an eddy-resolving numerical ocean model that includes tidal forcing. We investigated 1,303 individuals of 46 populations alongside subbasins of the Mediterranean (Balearic, Tyrrhenian, Ionian) and the Atlantic to Baltic Sea coastline over maximum distances of 563–2,684 km. Ten microsatellite loci under an autotetraploid condition revealed a mixed sexual and vegetative reproduction mode. A pairwise F_ST permutation test of populations revealed high levels of historical connectivity only for distance classes up to 104–280 km. Since full range analysis was not fully explanatory, we assessed connectivity in more detail at coastline and subbasin level using four approaches. Firstly, a regression over restricted geographical distances (300 km) was done though remained comparable to full range analysis. Secondly, piecewise linear regression analyses yielded much better explained variance but the obtained breakpoints were shifted toward greater geographical distances due to a flat slope of regression lines that most likely reflect genetic drift. Thirdly, classification and regression tree analyses revealed threshold values of 47–179 km. Finally, simulated ocean surface dispersal trajectories for propagules with floating periods of 1–4 weeks, were congruent with inferred distances, a spatial Bayesian admixed gene pool clustering and a barrier detection method. A kinship based spatial autocorrelation showed a contemporary within-lagoon connectivity up to 20 km. Our findings indicate that strong differentiation or admixtures shaped historical connectivity and that a pre- and post LGM genetic imprint of R. cirrhosa along the European coasts was maintained from their occurrence in primary habitats. Additionally, this study demonstrates the importance of unraveling thresholds of genetic breaks in combination with ocean dispersal modeling to infer patterns of connectivity.</p

Genetic diversity measures and characteristics of twenty microsatellite loci from <i>C</i>. <i>papyrus</i> genets (Total N = 141, per population = 47) of three populations of Lake Tana (Ethiopia).

<p>Genetic diversity measures and characteristics of twenty microsatellite loci from <i>C</i>. <i>papyrus</i> genets (Total N = 141, per population = 47) of three populations of Lake Tana (Ethiopia).</p

Clonal diversity and structure measures of <i>C</i>. <i>papyrus</i> ramets sampled in three papyrus swamps in Lake Tana under two sedimentation regimes during 2014 and 2016.

<p>Clonal diversity and structure measures of <i>C</i>. <i>papyrus</i> ramets sampled in three papyrus swamps in Lake Tana under two sedimentation regimes during 2014 and 2016.</p