Additional file 1: of Complex signatures of genomic variation of two non-model marine species in a homogeneous environment

Tables S1 – S5 and Figure S1 – S4 as referred to in the text. (DOCX 1086 kb

Additional file 7: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Histograms showing the distribution of selected nodes from BEAST analyses 1 and 2. (PNG 327 kb

Additional file 6: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

BEAST analysis 2 output log file. (LOG 106 kb

Additional file 8: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Mitochondrial genome structure with genome size, gene annotations, GC-content in blue and AT-content in green. (PNG 327 kb

Additional file 1: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Species list and ezRAD library information. (XLSX 52 kb

Additional file 3: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

XML BEAST file including data matrix and parameter setup as described in Materials and Methods. (XML 291 kb

Additional file 9: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Time calibrated phylogeny of BEAST analysis 1 plotted on stratigraphic chart. New sequenced species are in dark green and bold. Taxonomic clades of interest are shaded in light gray. Error bars on node ages are in dark turquoise. Nodes of interest are marked with a capital letters A-F on the nodes and correspond to node ages listed in Table 1. The capital letter R specifies the root age of the dated phylogeny. (PNG 913 kb

Additional file 5: of Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

Tracer statistics of turnover, diversification and sampling proportion of the two runs and the prior from BEAST analysis 2. (PNG 138 kb

Annual nutrient concentrations and flux of the groundwater background and land cover/use zones.

<p>Annual nutrient concentrations and flux of the groundwater background and land cover/use zones.</p

Linked land-sea modeling framework.

<p>Based on (A) climate, groundwater recharge, and recharge nutrient concentration data, (B) groundwater flow (m³.yr^-1) and nutrients concentrations (mg.L^-1) were modeled using MODFLOW and MT3D-MS. (C) Nutrient flux (kg.yr^-1) from anthropogenic drivers were added to the background nutrient flux. (D) A land-sea link was created using MODPATH. (E) The coastal discharge models used the groundwater flow (m³.yr^-1) and nutrients flux (kg.yr^-1) and GIS distance-based models to generate the terrestrial driver grid data. (F) The SWAN wave model and bathymetry data were coupled with (G) GIS-based models to generate the marine driver grid data. (H) The coral reef predictive models were calibrated on coral reef survey data. (I) Outputs were: (1) response curves, (2) maps of benthic (% cover) and fish (g.m^-2) indicators, and (3) a linked land-sea decision-support tool. (The wave model image in panel G is reprinted from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193230#pone.0193230.ref066" target="_blank">66</a>] under a CC BY license, with permission from Charles Fletcher, original copyright 2009. Refer to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193230#pone.0193230.s001" target="_blank">S1 File</a>).</p