Title

Genetic variation at the species and population levels in the Rocky Mountain ridged mussel (Gonidea angulata) – Supplementary Material

Description

Freshwater mussels in western North America are threatened by water diversions, climate change, loss of required host fish, and other factors, and have experienced marked decline in the past several decades. All four of the primary lineages (potentially species) of freshwater mussels in the western U.S. and Canada are widespread and have somewhat generalist host fish requirements. Of these lineages, perhaps the most poorly understood and of greatest conservation concern is Gonidea angulata (Rocky Mountain ridged mussel). Gonidea is a monotypic genus occurring only in the western continental U.S. and southern Canada. Here we describe the patterns of genetic variation across the species range, including several populations in the Okanagan Valley at the northern edge of the range. We detected only ten mitochondrial cytochrome oxidase I haplotypes, three of which are commonly found across major hydrologic basins, and the remainder of which were basin-specific variants. Haplotypes differed by a maximum of 5 of 537 nucleotides. New microsatellite loci were developed for G. angulata as a part of this study. Data from these microsatellite loci indicated that the population in the Chehalis River, Washington, was distinct from other locations, and that the Okanagan lake population was somewhat diverged from the remaining populations in the Columbia River and Klamath Lake. Only low levels of inbreeding were detected, in contrast to previous findings in Margartifera falcata, suggesting that hermaphroditism is not common. The population with the least diversity, according to microsatellite data, was the northern-most known population in Okanagan Lake. We discuss the biogeographic and conservation implications of our findings and provide supplementary material of our research including sequencing data and narrative of microsatellite development.

Document Type

Dataset

DCMI Type

Dataset

File Format

.pdf, txt, sh, fasta, xlsx, fastq.gz

Viewing Instructions

Instructions to concatenate files for use included in the README.txt file

Publication Date

11-6-2020

Funder

British Columbia Ministry of Environment and Climate Change Strategy (Conservation Science Section)

Publisher

Utah State University

Methodology

Samples were collected from the Okanagan, Chehalis, Columbia, Klamath, and Sacramento River Basins using non-lethal collection techniques. Paired-end 'Shotgun' sequences were aligned, process, and optimized for multiplex conditions. Additional information can be found in the Microsatellite Development Narrative (Document S1)

Scientfic Names

Gonidea angulata

Language

eng

Code Lists

See Document_S1_Microsatellite_Development_Narrative.pdf for code list.

Comments

Description of files:

Document S1: Microsatellite Development Narrative

Documents S2-1 to S2-4: Raw sequence data divided into 4 parts. (See instructions for concatenation in the README.txt file)

Document S3: Screening Scripts

Document S4: Filtered Sequences

Document S5: Primer Design

Document S6: Microsatellite Genotype Data

Figure S1: Structure Harvester Results

Table S1: Sampling Locations (Generalized location data is provided. For more detailed location information contact the authors listed above.)

Table S2: Microsatellite Loci and Multiplexing

Table S3: COI Genbank Accessions

Disciplines

Natural Resources Management and Policy

Files

README.txt (6 kB)
MD5: 9f567b19fed2e202618867f9329f8634

Document_S1_Microsatellite_Development_Narrative.pdf (171 kB)
MD5: 7a8f83de2f2a6f97d2a02d14fd41c7e5

Document_S2-1_gonideaF_read1_aa_fastq.gz (2184713 kB)
MD5: 3c18b9c34ef8436fb00ff8c745cefb56

Document_S2-2_gonideaF_read1_ab_fastq.gz (2206431 kB)
MD5: 6201ad389065a7afd0912c918832981c

Document_S2-3_gonideaR_read2_aa_fastq.gz (2481653 kB)
MD5: c2466f752c89a8d7029e0c4eb106e54a

Document_S2-4_gonideaR_read2_ab_fastq.gz (2536552 kB)
MD5: 296ea4aa9745642b1b8b97201b529dd3

Document_S3_Screening_Scripts.sh (7 kB)
MD5: 7db46d685853a553dde7e770784a37b7

Document_S4_Filtered_Sequences.fasta (543 kB)
MD5: e04240322fa7c962c3df3697b8e1b13a

Document_S5_Primer_Design.xlsx (129 kB)
MD5: 605b58be37d55a590e9a18f59e4fa931

Document_S6_Microsatellite_Genotype_Data.xlsx (100 kB)
MD5: 7b79c68f0ecbb01a8f49ff7eb0c8aea6

Figure_S1_Structure_Harvester_Results.pdf (112 kB)
MD5: dab7d2944f8d21198d03b4aad368695c

Table_S1_Sampling_Locations.xlsx (12 kB)
MD5: b68690d134138e2d65226cab01ea8884

Table_S2_ Microsatellite_Loci_and_Multiplexing.pdf (143 kB)
MD5: 79d7b91d8f327eef60ff32bb5fd138f1

Table_S3_COI_GenBank_Accessions.pdf (131 kB)
MD5: 99b779862bb52b999b4c92bbf5648ddc

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