Additional file 1 of Ecological and biogeographic features shaped the complex evolutionary history of an iconic apex predator (Galeocerdo cuvier)
Creators: name: Lesturgie, Pierre
name: Lainé, Hugo
name: Suwalski, Arnaud
name: Chifflet-Belle, Pascaline
name: Maisano Delser, Pierpaolo
name: Clua, Eric
name: Jaquemet, Sébastien
name: Magalon, Hélène
name: Mona, Stefano
Publisher: name: figshare
Year: 2024
Subjects: subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: Additional file 1: Figure S1. Isolation by distance (IBD) plot within the Indo-Pacific. Pairwise genetic distances (FST/(1-FST)) are plotted against geographic distances between Indo-Pacific sampling sites. Figure S2. Principal Component Analysis (PCA) computed with: (A) all individuals (n = 50) and (B) Indo-Pacific individuals only (n = 43). The axes represented in both panels are the first and the third component. Figure S3. Ancestry proportions retrieved using the nmf algorithm with K = 2 ancestral populations for Indo-Pacific samples performed with PCAngsd. Figure S4. Evolutionary scenarios used to investigate the population structure of the Atlantic Ocean based on data from Brazil population through an Approximate Bayesian Computation (ABC) framework. NS (No Structure) is an unstructured model where the modern effective size ( $${\mathrm{N}}_{\mathrm{mod}}$$ N mod ) instantaneously changes to $${\mathrm{N}}_{\mathrm{anc}}$$ N anc , at time shift $${\mathrm{T}}_{\mathrm{s}}$$ T s generations. FIM (Finite Island Meta-population) represents a finite island meta-population model with 100 demes that have been instantaneously colonised $${\mathrm{T}}_{\mathrm{col}}$$ T col generations ago, from an ancestral population of size $${\mathrm{N}}_{\mathrm{anc}}$$ N anc . Demes are allowed to exchange migrants with any other. SS (Stepping-Stone) is similar to FIM but the migrants are only exchanged between the four nearest neighbours in a two-dimensional grid. Figure S5. Akaike Information Criterion (AIC) values for the five isolation/migration models and the associated ranking on the x-axis. Boxplots represent the likelihood distribution of the data evaluated under the best parameter estimates for each of the five models (presented in Fig. 2) after 100 replicates. The models are presented from the richest in parameters (IM-full, 13 parameters) to the poorest (IM-div, 8 parameters). Figure S6. Maximum likelihood for the parameter estimated by fastsimcoal under model IM-bsc, representing two populations from each ocean basin with an effective size that changed $${\mathrm{T}}_{{\mathrm{s}}_{\mathrm{IP}}}$$ T s IP and $${\mathrm{T}}_{{\mathrm{s}}_{\mathrm{AO}}}$$ T s AO years ago from a modern effective size ( $${\mathrm{N}}_{{\mathrm{mod}}_{\mathrm{IP}}}$$ N mod IP and $${\mathrm{N}}_{{\mathrm{mod}}_{\mathrm{AO}}}$$ N mod AO ) to an ancestral effective size ( $${\mathrm{N}}_{{\mathrm{anc}}_{\mathrm{IP}}}$$ N anc IP and $${\mathrm{N}}_{{\mathrm{anc}}_{\mathrm{AO}}}$$ N anc AO ). The two populations are connected by an asymmetrical number of migrants constant from 0 to $${\mathrm{T}}_{\mathrm{div}}$$ T div ( $${\mathrm{Nm}}_{\mathrm{IP}\to \mathrm{AO}}$$ Nm IP → AO and $${\mathrm{Nm}}_{\mathrm{AO}\to \mathrm{IP}}$$ Nm AO → IP ) and diverged $${\mathrm{T}}_{\mathrm{div}}$$ T div years ago from an ancestral population of size $${\mathrm{N}}_{\mathrm{anc}}$$ N anc .