DOI: 10.5061/dryad.p2ngf1vxb
title: Supplementary material for: Intermittent migration can induce pulses of speciation in a two-island system

description: Geographic barriers can come and go depending on natural conditions. These
 fluctuations cause population cycles of expansion and contraction,
 introducing intermittent migrations that may not hinder speciation but
 rather promote diversification. Here, we study a neutral two-island
 speciation model with intermittent migration driven by sea-level
 fluctuations. Seabed depth modulates isolation and connection periods
 between the islands, with migration occurring during connection periods
 with a certain probability. Mating is restricted to genetically compatible
 individuals on the same island, and offspring inherit genomes from both
 parents through recombination. We observe speciation pulses that would not
 occur under strict isolation or continuous migration, with infrequent,
 temporary increases in species richness happening at different times
 depending on the combination of geographic settings and migration
 probability. The resulting dynamic patterns of richness exhibit
 contrasting behavior between connected and isolated scenarios, often
 including species that do not persist.  Prolonged isolation can
 reduce richness to one species per island, resembling patterns commonly
 associated with archipelagos under sea-level fluctuations. Together with
 other studies, our results in out-of-equilibrium populations support the
 relevance of investigating the impact of variable migration on
 diversification, particularly in regions of high diversity.
description: # Supplementary Material for "Intermittent migration can induce
 pulses of speciation in a two-island system" **supplementary.pdf**
 contains the Supplementary Information to the manuscript. We provide one
 code, written in FORTRAN: **"Program\_intermittent.f90"** This
 program has one input file, **"input\_sea.txt"**, and one
 output, **"Temporal.txt"**: ``` a) The input\_sea.txt provides
 in the first line five parameters (the values in the parentheses refer to
 the values in the file): a.1) Number of iterations (2000) a.2) Initial
 migration probability (0.4) a.3) Number of repetitions for the set of
 parameters (1) a.4) Mutation rate (0.001) a.5) Time interval that species
 identification is made (10 iterations) The remaining lines provide the
 step iteration and the value of migration. The migration variation period
 (written over the subsequent lines) is based on the sea level data
 assuming a seabed of h=-50m. ``` Other parameters, such as minimal genetic
 similarity, genome size, and population size, can be adjusted in the main
 program. ``` b) The output "Temporal.txt" has 7 columns labeled
 as: b.1) pop - the number of total individuals inhabiting the islands
 (parameter) b.2) rep - the number of the simulation repetition (parameter)
 b.3) mig - the migration rate (parameter) b.4) tem - the time iteration;
 saved as multiple of (a.5) b.5) esp - the ID of the species (initially,
 all individuals are conal, and their species ID is 1) b.6) abund1 -
 abundance of esp on island 1 at time iteration tem b.7) abund2 - abundance
 of esp on island 2 at time iteration tem ```