Molecular data of cryptic species in the Sphagnum magellanicum complex (Bryophyta) in North America
Data files
Jun 10, 2024 version files 119.64 GB
-
bcdp-80p-633_samples.phy
9.12 MB
-
demultiplexed_sample_data-insilico.tar.gz
313.52 MB
-
demultiplexed_sample_data-radseq1.tar.gz
17.21 GB
-
demultiplexed_sample_data-radseq2.tar.gz
17.75 GB
-
demultiplexed_sample_data-radseq3.tar.gz
24.65 GB
-
demultiplexed_sample_data-radseq4.tar.gz
25.71 GB
-
demultiplexed_sample_data-radseq5.tar.gz
22.03 GB
-
demultiplexed_sample_data-radseq6.tar.gz
11.97 GB
-
md5sum.txt
585 B
-
README.md
3.47 KB
Abstract
Sphagnum magellanicum (Sphagnaceae, Bryophyta) has been considered to be a single semi-cosmopolitan species, but recent molecular analyses have shown that it comprises a complex of at least seven reciprocally monophyletic groups, that are, however, difficult or impossible to distinguish morphologically. Newly developed barcode markers and RADseq analyses were used to identify species among 808 samples from 119 sites. Molecular approaches are used here to assess the geographic ranges of four North American species, the frequency at which they occur sympatrically, and ecological differentiation among them. Microhabitats were classified with regard to hydrology and shade. Hierarchical Modelling of Species Communities was used to assess climate variation among the species. Climate niches were projected back to 22,000 years bp to assess the likelihood that the North American species had sympatric ranges during the late Pleistocene. The species exhibit parallel morphological variation, making it extremely difficult to distinguish phenotypically. Two to three species frequently co-occur within peatlands. They have broadly overlapping micro-habitat and climate niches. Barcode- versus RADseq-based identifications were in conflict for 6% of the samples, and always involved S. diabolicum vs. S. magniae. These species co-occur within peatlands at scales that could permit interbreeding, yet they remain largely distinct genetically and phylogenetically. The four cryptic species exhibit individualistic geographic and ecological patterns. Conflicting identifications from barcode vs. RADseq analyses for S. diabolicum versus S. magniae could reflect incomplete speciation or hybridization. They comprise a valuable study system for additional work on climate adaptation.
https://doi.org/10.5061/dryad.37pvmcvtk
Principal Investigator/Corresponding author: Marta Nieto-Lugilde, Duke University, marta.nietolugilde@duke.edu
Data prepared by: Marta Nieto-Lugilde, Duke University, marta.nietolugilde@duke.edu
Co-investigators:
Diego Nieto-Lugilde, Universidad de Cordoba
Bryan Piatkowski, Oak Ridge National Laboratory
Aaron M. Duffy, Duke University
Sean C. Robinson, SUNY Oneonta
Blanka Aguero, Duke University
Scott Schuette, Pennsylvania Natural Heritage Program
Richard Wilkens, Salisbury University
Joseph Yavitt, Cornell University
A. Jonathan Shaw, Duke University
Date collected:
2019-2024
These datasets DNA sequences for Sphagnum magellanicum group plants collected from the following countries:
Canada (Alberta, British Columbia, Labrador, New Brunswick, Newfoundland, Nova Scotia, Quebec), USA (Alabama, Alaska, Arkansas, Connecticut, Delaware, Florida, Georgia, Kentucky, Maine, Maryland, Michigan, Minnesota, Mississippi, New Hampshire, New Jersey, New York, North Carolina, Pennsylvania, South Carolina, Tennessee, Vermont, Virginia, Washington, West Virginia, Wisconsin). Collection locations for specific samples included in this dataset can be found in Table S1 of the associated manuscript.
Data and file overview:
bcdp-80p-633_samples.phy: Phylip format alignment of 2140 RADseq loci generated by ipyrad for Sphagnum samples.
demultiplexed_sample_data-insilico.tar.gz: Zipped folder of zipped fastq format “RADseq-like” reads from 66 in silico digested genome resequencing samples. 10 copies of each read (enough to pass downstream depth filters) with quality values all set to “E” (high enough to pass downstream quality filters). File names match the sample name. 2024-06-03
demultiplexed_sample_data-radseq1.tar.gz: Zipped folder of demultiplexed zipped fastq format Illumina reads from 100 Sphagnum RADseq samples. File names match the sample name. 2024-06-03
demultiplexed_sample_data-radseq2.tar.gz: Zipped folder of demultiplexed zipped fastq format Illumina reads from 100 Sphagnum RADseq samples. File names match the sample name. 2024-06-03
demultiplexed_sample_data-radseq3.tar.gz: Zipped folder of demultiplexed zipped fastq format Illumina reads from 100 Sphagnum RADseq samples. File names match the sample name. 2024-06-03
demultiplexed_sample_data-radseq4.tar.gz: Zipped folder of demultiplexed zipped fastq format Illumina reads from 100 Sphagnum RADseq samples. File names match the sample name. 2024-06-03
demultiplexed_sample_data-radseq5.tar.gz: Zipped folder of demultiplexed zipped fastq format Illumina reads from 100 Sphagnum RADseq samples. File names match the sample name. 2024-06-03
demultiplexed_sample_data-radseq6.tar.gz: Zipped folder of demultiplexed zipped fastq format Illumina reads from 67 Sphagnum RADseq samples. File names match the sample name. 2024-06-03
md5sum.txt: A text file containing md5 checksum values for each of the data files. 2024-06-03
Additional information on specific samples included in this dataset can be found in Table S1 of the associated manuscript.
Sharing and access information:
This work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license.