Sample collection and lake profiling
Tissue samples (~1cm3) were collected
from 168 individuals of Suberites diversicolor (Fig 1, Table 1).
One lagoon was sampled in Darwin, Australia (DAR), one lagoon and three
marine lakes were sampled in Berau (Bay, B.1, B.2 and B.3), and six
marine lakes were sampled in Raja Ampat (P.27, P.30, P.32, P.1, P.4 and
P.5). Of these locations, nine overlap with the sponge phylogeography
study of Becking et al. (2013) and five with the microbial community
analysis of Ferreira et al. (2020) (Supplemental Table 1 for
corresponding lake codes between the three studies). Samples were
collected between 1-5m depth while snorkeling. Some lakes had very low
densities of S. diversicolor , therefore sample sizes were lower
(see Becking et al., 2013 Table 2 for densities). In the field,
tissue samples were immediately preserved in 99% ethanol or RNAlater
after excision at 0-4°C (4-8 weeks), and upon returning to the
laboratory stored in a -20°C freezer until further use.
Lake characterization was performed concordant with a protocol published
in Maas et al. (2018). In brief, lake area (m2) was
approximated using Google Earth Pro (v. 7.3.2), maximum depth was
measured using a handheld sonar system (Hawkeye), and water parameters
(temperature (°C) and salinity (ppt) were measured with an YSI
Professional Plus multimeter at 10 locations per lake at 1m intervals
from the surface to 5m depth. To define connection to the surrounding
sea we measured maximum tidal amplitude simultaneously in the lake and
the sea using Hobo water-level loggers. The ratio of maximum tidal
amplitude in meters of the lake compared to the sea was used as a proxy
to determine as the degree of physical connection between the lake and
sea (conform to calculations in Maas et al., 2018).