The aims of this study for the WAMSI Dredging Science Program were:
1. To establish fundamental knowledge on the genetic diversity of seagrass meadows; and if this varies among sites and with
different environmental conditions, particularly clear and turbid water;
2. To understand the gene flow among populations; and
3. To inform the design of mesocosm and laboratory experiments on seagrass resilience.
This study was the first of its kind to examine the patterns of genetic diversity in seagrasses in the Pilbara region of
WA. Three species were assessed: Halophila ovalis (6 populations), Halodule uninervis (8 populations) and Thalassia hemprichii
(3 populations) at a range of spatial scales, within a meadow (centimetres−metres), among meadows at a local scale (2−60
km) and among meadows at a regional scale (up to 500 km). Due to the varied distribution of species we could not sample
all species across the same spatial scale and range of environments, so we designed a nested approach, with sites replicated
at a distance of 2−5 km, and then different species at varied larger spatial scales.
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Microsatellite markers and single nucleotide polymorphism markers
Three species of seagrass, H. ovalis, H. uninervis and Thalassia hemprichii (Ehrenberg) Ascherson (year) were assessed across
a range of spatial scales to determine:
- the variation in genetic diversity within and among sites;
- the patterns in connectivity among sites; and
- the relationship between genetic diversity and relevant environmental conditions.
Four spatial scales were assessed: fine scale (metres); small scale (10-100s km); regional spatial scale (100-500 km); and
large scale (>500 km), from Indonesia to the Pilbara.
A site was defined as a circular area of 50 m diameter. At each site, 50 samples were randomly collected based on randomly
generated bearings and distances along the bearing which were located using compasses and transect tapes to identify positions
along. Each sample was separated by a minimum of 2 m and if no seagrass was present at the randomly allocated position,
it was collected from the next closest patch of seagrass, and the position recorded. Each sample consisted of a seagrass ramet
with 1−3 connected shoots. Samples were stored in seawater at ambient temperature until processing. For H. ovalis apical
meristems and young leaves were extracted from each sample, and for H. uninervis and T. hemprichii the young part of the
leaves without epiphytes were extracted. All extracted samples were cleaned and stored in silica gel to preserve the DNA
within 8 hours of collection. A herbarium voucher specimen of each species from each site was also created.
For the ‘fine’ scale, all seagrass was harvested from 3 replicate 50 cm diameter cores. Up to 12 independent ramets were
identified, and preserved for DNA extraction as described below. Only H. ovalis was analysed at this scale.
DNA was extracted from 2−3 leaf pairs, growing tips and/or shoots of silica-dried plant material. All extractions were performed
using AGRF extraction service (www.agrf.org.au).
Further information on genotyping and genetic analysis is available from final report