DOI: 10.5061/dryad.70h1h
title: Data from: From the mountains to the coast and back again: ancient biogeography in a radiation of short-range endemic harvestmen from California

description: The harvestmen genus Calicina is represented by 25 short-range endemic
 species occurring in the western Sierra Nevada, Transverse and Coast
 Ranges of California. Our principal aim was to reconstruct the temporal
 and spatial biogeographic history of this arachnid lineage. We inferred a
 time-calibrated species tree for 21 of 25 described Calicina species using
 multiple genes and multilocus coalescent-based methods. This species tree
 was used as a framework for algorithmic biogeographic and divergence time
 analyses, and a phylogenetic canonical correlation analysis (CCA) was used
 to examine the relationship between morphological evolution and
 environmental variables. Species tree and biogeographic analyses indicate
 that high-elevation Sierran taxa are early-diverging in Calicina, with
 subsequent biogeographic “criss-crossing” of lineages from the Sierra
 Nevada to the Coast Ranges, back to the Sierra Nevada, then back to Coast
 Ranges. In both the Sierra Nevada and Coast Ranges, distantly-related
 parapatric lineages essentially never occur in sympatry. CCA reveals that
 in both the Coast Ranges and the Sierra Nevada, distant phylogenetic
 relatives evolve convergent morphologies. Our evidence shows that Calicina
 is clearly dispersal-limited, with an ancient biogeographic history that
 provides unique insight into the complex geologic evolution of California
 since the mid-Paleogene.
description: Calicina Raw
 Morphological Data MatrixCombined morphological
 data matrix used for comparative analyses showing unique specimen ID
 (KEM#), species idenfitication, text locality information, and sex for
 each specimen measured. Raw measurements of Scute Length (measured
 dorsally at the midline in mm) and Leg II Length (combined length of
 individual segments starting with the trochanter in mm) were treated as
 continuous characters in comparative analyses. Eye development was treated
 as a binary character (present vs. absent).CalicinaMorphDryad.xlsxPhased RNA Polymerase II Transcription Factor AlignmentPhased RNA Polymerase II Transcription Factor alignment used in the final *BEAST species tree inference. Heterozygous haplotypes were reconstructed using the program PHASE v2.1 (Stephens et al., 2001).This gene region is orthologous to Ixodes protein ISCW004924.B9_B10AlignPhasedF_19April2015.fastaPhased Uroporphyrinogen Decarboxylase AlignmentPhased Uroporphyrinogen Decarboxylase alignment used in the final *BEAST species tree inference. Heterozygous haplotypes were reconstructed using the program PHASE v2.1 (Stephens et al., 2001).This gene region is orthologous to Ixodes protein ISCW020804.D7_D8AlignPhasedF_19April2015.fastaPhased Ski-Interacting Protein AlignmentPhased Ski-Interacting Protein alignment used in the final *BEAST species tree inference. Heterozygous haplotypes were reconstructed using the program PHASE v2.1 (Stephens et al., 2001).This gene region is orthologous to Ixodes protein ISCW021146.E1_E2AlignPhasedF_19April2015.fastaRaw Climatic DataRaw climatic data for all known published (Ubick and Briggs, 1989) and SDSU Museum of Biodiversity collection localities for Calicina specimens from Bioclimatic layers 1-19 of the WORLDCLIM dataset v.1.4 Data were extracted at 30 arc-second (1 km) resolution (Hijmans et al., 2005) using the program DIVA-GIS (Hijmans et al., 2004).CalicinaClimData.csv