A primary challenge for modern phylogeography is understanding how ecology and geography, both contemporary and historical, shape the spatial distribution and evolutionary histories of species. Phylogeographic patterns are the result of many factors, including geology, climate, habitat, colonization history, and lineage-specific constraints. Assessing the relative influences of these factors is difficult because few species, regions, and environments are sampled in enough detail to compare competing hypotheses rigorously and because a particular phylogeographic pattern can potentially result from different evolutionary scenarios. The silky anoles (Anolis sericeus complex) of Central America and Mexico are abundant and found in all types of lowland terrestrial habitat, offering an excellent opportunity to test the relative influences of the factors affecting diversification. Here, we performed a range-wide statistical phylogeographic analysis on restriction-site associated DNA (RAD) markers from silky anoles and compared the phylogeographic patterns we recovered to historical and contemporary environmental and topographic data. We constructed niche models to compare niche overlap between sister lineages and conducted coalescent simulations to characterize how the major lineages of silky anoles have diverged. Our results revealed that the mode of divergence for major lineage diversification events was geographic isolation, resulting in ecological divergence between lineages, followed by secondary contact. Moreover, comparisons of parapatric sister lineages suggest that ecological niche divergence contributed to isolation by environment in this system, reflecting the natural history differences among populations in divergent environments.
ANSE_caribtehuan
Caribbean silky anole localities used for Tehuantepec-only ENMs
ANSE_pactehuan
Pacific silky anole localities used for Tehuantepec-only ENMs
ANSE_RAxML_infile
Infile for RAxML analyses for 75 silky anoles + 1 outgroup (Anolis laeviventris)
ANSE_RAxML_result
Output for RAxML analysis of 75 silky anoles + 1 outgroup (Anolis laeviventris)
infile_ANSE_mrbayes
Infile for MrBayes analyses for 75 silky anoles + 1 outgroup (Anolis laeviventris), including partitions
ANSE_consensus_mrbayes
MrBayes consensus results for analysis of 75 silky anoles + 1 outgroup (Anolis laeviventris)
ANSE_samplingforDryad
File with coordinates and field/museum numbers for localities used in phylogeographic analyses and generating ecological niche models.
DHL412_R1.fq
Raw Illumina reads for DHL412
DHL413_R1.fq
Raw Illumina reads for DHL413
FRMP94_R1.fq
Raw Illumina reads for FRMP94
JAC24546_R1.fq
Raw Illumina reads for JAC24546
AMH432_R1.fq
Raw Illumina reads for AMH432
RVG265_R1.fq
Raw Illumina reads for RVG265
RVG275_R1.fq
Raw Illumina reads for RVG275
LNG0029_R1.fq
Raw Illumina reads for LNG0029
POE4321_R1.fq
Raw Illumina reads for POE4321
POE4349_R1.fq
Raw Illumina reads for POE4349
POE4092_R1.fq
Raw Illumina reads for POE4092
LNG0172_R1.fq
Raw Illumina reads for LNG0172
LNG0173_R1.fq
Raw Illumina reads for LNG0173
LNG0170_R1.fq
Raw Illumina reads for LNG0170
LNG0179_R1.fq
Raw Illumina reads for LNG0179
LNG0177_R1.fq
Raw Illumina reads for LNG0177
LNG0174_R1.fq
Raw Illumina reads for LNG0174
LNG0186_R1.fq
Raw Illumina reads for LNG0186
LNG0171_R1.fq
Raw Illumina reads for LNG0171
LNG0169_R1.fq
Raw Illumina reads for LNG0169
LNG0168_R1.fq
Raw Illumina reads for LNG0168
POE4359_R1.fq
Raw Illumina reads for POE4359
POE4070_R1.fq
Raw Illumina reads for POE4070
POE4090_R1.fq
Raw Illumina reads for POE4090
ANMO1852_R1.fq
Raw Illumina reads for ANMO1852
POE4058_R1.fq
Raw Illumina reads for POE4058
POE4053_R1.fq
Raw Illumina reads for POE4053
POE4078_R1.fq
Raw Illumina reads for POE4078
LNG0068_R1.fq
Raw Illumina reads for LNG0068
LNG0106_R1.fq
Raw Illumina reads for LNG0106
LNG0105_R1.fq
Raw Illumina reads for LNG0105
LNG0104_R1.fq
Raw Illumina reads for LNG0104
LNG0066_R1.fq
Raw Illumina reads for LNG0066
LNG0103_R1.fq
Raw Illumina reads for LNG0103
LNG0092_R1.fq
Raw Illumina reads for LNG0092
LNG0095_R1.fq
Raw Illumina reads for LNG0095
LNG0102_R1.fq
Raw Illumina reads for LNG0102
LNG0100_R1.fq
Raw Illumina reads for LNG0100
POE4081_R1.fq
Raw Illumina reads for POE4081
POE3966_R1.fq
Raw Illumina reads for POE3966
LNG0062_R1.fq
Raw Illumina reads for LNG0062
LNG0067_R1.fq
Raw Illumina reads for LNG0067
LNG0122_R1.fq
Raw Illumina reads for LNG0122
LNG0113_R1.fq
Raw Illumina reads for LNG0113
LNG0123_R1.fq
Raw Illumina reads for LNG0123
LNG0055_R1.fq
Raw Illumina reads for LNG0055
LNG0071_R1.fq
Raw Illumina reads for LNG0071
LNG0094_R1.fq
Raw Illumina reads for LNG0094
LNG0112_R1.fq
Raw Illumina reads for LNG0112
LNG0076_R1.fq
Raw Illumina reads for LNG0076
LNG0130_R1.fq
Raw Illumina reads for LNG0130
LNG0074_R1.fq
Raw Illumina reads for LNG0074
LNG0056_R1.fq
Raw Illumina reads for LNG0056
LNG0143_R1.fq
Raw Illumina reads for LNG0143
LNG0142_R1.fq
Raw Illumina reads for LNG0142
LNG0144_R1.fq
Raw Illumina reads for LNG0144
LNG0145_R1.fq
Raw Illumina reads for LNG0145
LNG0147_R1.fq
Raw Illumina reads for LNG0147
LNG0146_R1.fq
Raw Illumina reads for LNG0146
POE4143_R1.fq
Raw Illumina reads for POE4143
POE4306_R1.fq
Raw Illumina reads for POE4306
POE4172_R1.fq
Raw Illumina reads for POE4172
POE4332_R1.fq
Raw Illumina reads for POE4332
LNG0082_R1.fq
Raw Illumina reads for LNG0082
LNG0081_R1.fq
Raw Illumina reads for LNG0081
POE3481_R1.fq
Raw Illumina reads for POE3481
POE3503_R1.fq
Raw Illumina reads for POE3503
POE3519_R1.fq
Raw Illumina reads for POE3519
POE3404_R1.fq
Raw Illumina reads for POE3404
POE4260_R1.fq
Raw Illumina reads for POE4260
POE3403_R1.fq
Raw Illumina reads for POE3403
POE3604_R1.fq
Raw Illumina reads for POE3604
POE3603_R1.fq
Raw Illumina reads for POE3603
POE3616_R1.fq
Raw Illumina reads for POE3616
JS818_R1.fq
Raw Illumina reads for JS818