DOI: 10.5061/dryad.vx0k6dk5m
title: Data from: Gene flow blurs species boundaries in the <em>Juncus ensifolius</em> – <em>saximontanus</em> (Poales: Juncaceae) species complex

description: We investigated species boundaries between Juncus ensifolius, J.
 saximontanus, and their putative closest relative [or sister taxon] J.
 macrandrus, three members of a group of seven species of Juncus that are
 native to North America and have iris-like leaves. Juncus ensifolius and
 J. saximontanus have overlapping ranges in the central portion of Western
 North America, but J. ensifolius has a more northerly distribution, while
 J. saximontanus has a more southerly distribution. The distinctions
 between the two species have long been unclear, primarily due to the
 presence of individuals with a variable number of stamens, which is the
 primary character used to differentiate them. J. macrandrus is
 distinguished from our focal species by the length of its anthers, and is
 found only in the California floristic province, where the ranges of J.
 ensifolius and J. saximontanus overlap. We generated genotyping by
 sequencing data for 95 individuals of our two focal species and one
 individual from J. macrandrus, our putative outgroup. We used phylogenetic
 inference, evolutionary clustering, principal components analyses of
 morphological measurements, and other methods to investigate species
 boundaries in this group. We found that introgression with closely related
 species in the group such as J. macrandrus, but not between J. ensifolius
 and J. saximontanus, is a primary driver of uncertainty about species
 distinctions. We also found evidence for an independently evolving lineage
 in J. saximontanus that may deserve recognition at the species level. We
 determined that J. saximontanus and J. ensifolius are distinct species and
 can be recognized based on stamen number as well as number of heads per
 inflorescence. We propose that individuals with intermediate characters
 are most likely the result of hybridization with J. macrandrus or another
 closely related species.
description: # Data from: Gene flow blurs species boundaries in the *Juncus ensifolius*
 – *saximontanus* (Poales: Juncaceae) species complex Dataset DOI:
 [10.5061/dryad.vx0k6dk5m](https://doi.org/10.5061/dryad.vx0k6dk5m) ##
 Description of the data and file structure These data were collected as
 part of a study to clarify the species delimitation of *Juncus
 saximontanus* and *Juncus ensifolius*.  ### Files and variables #### File:
 morpho_measurements.csv **Description:** Morphological trait data for
 individuals included in the study. NA values indicate measurements that
 were not possible on that specimen.  ##### Variables * Sci_name_hyp:
 Species hypothesis * Site: Collection site * sample: sample identifier  *
 num_stamen: number of stamens * num_flw_heads: number of flower heads *
 flw_per_head1: number of flowers per head one * flw_per_head2: number of
 flowers per head two * auricles: auricles present or absent?  *
 anther_length_mm: anther length in mm * fil_length_mm: filament length mm
 * style_length_mm: style length mm * seed_length: seed length mm *
 seed_app: seed appendages present or absent * tepal_color: tepal color *
 comments: comments (none = no comments) #### File:
 ref_based_alignment_trimmed.phy **Description:** Final multi-sequence
 alignment for the loci mapped to the *J. effusus* reference genome and
 including the reference genome as a homozygous individual.  #### File:
 denovo_alignement_trimmed.phy **Description:** Final multi-sequence
 alignment for the loci generated using denovo clustering in ipyrad.  ####
 File: vcf_plus_J_eff_filter.vcf **Description:** Final vcf file including
 the *J. effusus* reference as a homozygous individual  #### File:
 denovo_data.loci **Description:** Results from denovo clustering in .loci
 format #### File: denovo_data.phy **Description:** Results from denovo
 clustering in phylip format #### File: denovo_data.vcf
 **Description:** Results from denovo clustering in vcf format #### File:
 denovo_data.snps **Description:** Results from denovo clustering in .snps
 format ## Code/software Code to recreate analyses can be found
 at [https://github.com/reedjohnkenny/J_ens_sax_sp_delim](https://github.com/reedjohnkenny/J_ens_sax_sp_delim)