Page 55 - Dedola2011

Tang 2007). This method uses a stochastic optimization algorithm approach to retrieve
the posterior mode of the number of genetically diverged groups (i.e. K is estimated as a
random variable). The clustering was performed using the module for linked molecular
data and applying the codon linkage model which
is the appropriate choice for sequence data. Each analysis was performed ten times with
a vector ofvalues (1-22) for K each with six replicates.

Haplotypes were grouped into haplogroups that reflected clustering results; for
each sampling location we computed the proportion of a given haplogroup in order to
build interpolation maps ofthe haplogroup frequency in the Mediterranean. We used the
inversed weighted distance (IDW) method implemented in gstat (Pebesma 2004) and
interpolated the estimated values Raster (Hijmans and Van Etten 2011). These
computations were made with R 2.13.0 ofwhich these libraries are part (R development
core team 201l).The Analysis of Molecular Variance (AMOVA) was performed by
using the software package Arlequin 3.5.1.2 (Excoffier and Lischer 2010). Individuals
were grouped according to their geographical provenience. Furthermore pairwise <DsT
values based on Tamura and Nei (1993) genetic distances were calculated using the
gamma value (y) obtained in jModelTest. The significance of variance components and
F-statistics was tested by a permutation test with l ,000 replicates.

The fit of the data to ademographic expansion model was assessed by computing
the mismatch distribution (distribution of the pairwise differences). Additionally,
Tajima's D (Tajima, 1989; Nei and Kumar, 2000) and Fu's (1997), Fs neutrality tests
implemented in Arlequin were used to assess departures from mutation drif-equilibrium
model. Significant negative values for both tests are expected under recent population
expansion, selective sweeps, or purifying selection.

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Gìan Luca Dedola: ANALISI DELLA VARIABILITÀ GENETICA DI PATELLA FéRRUGINEA, PATEL-LA UL l'SSIPONENSIS (MOLLUSCA: GASTROPODA) E PINNA
NOBILIS (MOLLUSCA: BIVALVIA): lLCONTRJBUTO DEl DATI MOLECOLARI ALLA CONSERVAZIONE DI SPECIE MINACCIATE - Tesi di douorato in Scienze
della natura e delle sue risorse • indiri7.zo BK>logi.a Ambientale, Università degli Studi di Sassarl