Yurco and Keeney BMC Res Notes (2018) 11:204 https://doi.org/10.1186/s13104-018-3301-1 BMC Research Notes

RESEARCH NOTE Open Access Characterization of tri and tetra‑nucleotide microsatellite loci for the freshwater snails Promenetus exacuous (Planorbidae) and tricarinata () and their utility in population genetic studies Patrick Yurco and Devon B. Keeney*

Abstract Objective: Promenetus exacuous and Valvata tricarinata are with widespread distributions throughout North America. Information regarding their genetic diversity and population connectivity are currently lacking. We utilized next generation sequencing to develop the frst microsatellites for each species to investigate genetic diversity within and diferentiation among populations. Results: Sixteen and seventeen microsatellite loci were developed for P. exacuous and V. tricarinata, respectively, and tested in a total of 43 P. exacuous and 48 V. tricarinata from two lakes approximately 183 km apart in New York State, USA. Fifteen P. exacuous loci were polymorphic in at least one lake and possessed 1–23 alleles and observed heterozygosities of 0.00–0.96 within individual lakes. Seventeen polymorphic V. tricarinata loci possessed 2–19 alleles and observed heterozygosities of 0.04–0.96 within lakes. Bayesian clustering using 12 loci for each species identifed two distinct genetic populations, refecting the two lakes. High assignment scores for individual snails to the lakes they were collected from supported strong population structure with minimal admixture at the scale of this study. These loci will be useful for investigating the genetic diversity and population structure of these species and indicate genetic diferentiation may be common among their populations. Keywords: Microsatellite loci, Promenetus exacuous, Valvata tricarinata, Population genetics, Gastropod genetic diversity

Introduction gastropods, Promenetus exacuous (Say, 1821) and Val- Despite their diversity, importance to ecosystems, and vata tricarinata (Say, 1817). Microsatellites were devel- conservation concerns, basic taxonomic and biological oped for these particular species for future studies information is lacking for many freshwater gastropods comparing their genetic connectivity throughout New throughout North America [1, 2]. We report here the York State based on the species’ disjunct and often sym- development of independent sets of 16 and 17 micros- patric populations throughout the region, their phyloge- atellite loci for two understudied species of freshwater netic divergence and difering biological characteristics ofering comparative insights into gastropod population connectivity throughout New York, and their current *Correspondence: [email protected] Department of Biological and Environmental Sciences, Le Moyne College, lack of genetic data and available microsatellite loci [3]. 1419 Salt Springs Road, Syracuse, NY 13214‑1301, USA In addition, both species have widespread distributions

© The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Yurco and Keeney BMC Res Notes (2018) 11:204 Page 2 of 6

throughout North America and secure global conserva- 72 °C for 30 s. Te 30 cycles were followed by a fnal tion status with localized areas of concern, potentially extension of 30 min at 60 °C. An initial round of PCRs increasing the interest of these microsatellites to other was performed with a gradient of annealing tempera- researchers [4–6]. tures ranging from 50 to 70 °C to determine optimal annealing temperatures. All optimized loci utilized an Main text annealing temperature of 60 °C, except Pex1877 and Materials and methods Pex2263 (56 °C), and Pex 216 (53 °C). Genotypes were Valvata tricarinata and P. exacuous were collected from determined on an ABI 3730 × 1 96-capillary Genetic Round Lake (43° 02′ 55.6″N, 75° 58′ 24.1″W) and Lake Analyzer at the DNA Analysis Facility at Yale Univer- Saratoga (43° 03′ 12.6″N, 73° 43′ 11.8″W) using dip nets. sity. PCR products from up to four loci utilizing difer- Both lakes are in New York State and are approximately ent fuorescent dyes were combined in each well prior 183 km apart. To develop microsatellite loci, genomic to submission. Alleles were scored using Geneious ver. DNA for next generation sequencing was extracted from 8.1 [7]. the foot of a single V. tricarinata from Round Lake and MICRO-CHECKER ver. 2.2 [12] was used to iden- a single P. exacuous from Lake Saratoga using a Qiagen tify potential scoring errors from stuttering, large allele ® ­Dneasy Tissue kit. DNA was eluted with 75 µl ­H2O and dropout, and/or the presence of null alleles. Alleles quantifed using a NanoDrop 2000 (Termo Scientifc). were analyzed for deviations from Hardy–Weinberg Approximately 3 µg of RNA-free genomic DNA from expectations within sites and overall linkage disequilib- each species was sent to the University of Wisconsin- rium using Genepop on the Web [13, 14]. Signifcance Madison Biotechnology Center for DNA fragmentation tests with multiple comparisons used an adjusted criti- and sequencing. Next generation sequencing was per- cal value based on the B-Y False Discovery Rate (FDR) formed using an ION Torrent PGM system with each [15]. STRUCTURE ver. 2.4.3 [16] was used to deter- species allocated approximately 25% of a 318 chip. Raw mine if loci could infer population diferentiation by genomic data were converted to FASTA format using using genotypes to assign individuals to genetic clus- Geneious ver. 8.1 [7]. Microsatellite motifs were identi- ters and estimate the actual number of genetic popula- fed using msatcommander 1.0.8 [8]. Parameters were set tions using a Bayesian approach. A highly conservative to search for perfect tri- and tetranucleotide repeats with subset of twelve loci for each species that did not dis- a minimum length of eight repeat units to decrease the play deviations from Hardy–Weinberg expectations in potential for genotyping errors due to stuttering common either site, did not include loci displaying linkage with with dinucleotide repeats, and increase the likelihood of each other, and that failed to amplify in no more than polymorphism [9, 10]. Primer %GC was set to 35–65%, two snails in either population (P. exacuous: Pex577, optimal annealing temperature was 60 °C, and one Pex757, Pex1009, Pex1877, Pex2091, Pex2181, Pex2263, primer from each pair was designed to have a 5′ CAG tag Pex2471, Pex2889, Pex2908, Pex2958, and Pex2972; (CAGTCGGGCGTCATCA) (Table 1). Default settings V. tricarinata: Vtr99, Vtr565, Vtr828, Vtr835, Vtr980, were used for the remaining parameters. Vtr1099, Vtr1279, Vtr2328, Vtr2388, Vtr2492, Vtr4154, DNA was extracted from 24 V. tricarinata snails and Vtr4287) were used for STRUCTURE analyses. from each lake and 24 and 19 P. exacuous from Round STRUCTURE runs used an admixture model with fve Lake and Lake Saratoga, respectively. For each DNA iterations, a burnin length of 100,000 and 100,000 steps extraction, the foot was removed and transferred to in the Monte Carlo Markov Chain (MCMC). Separate 400 µl of 5% Chelex containing 0.1 mg/ml protein- runs for each species utilized LnPD as the selection cri- ase K. Te solution was incubated for approximately terion and the number of genetic populations (K) was 8 h at 60 °C followed by eight minutes at 95 °C. DNA allowed to range from 1 to 6. was utilized directly from these extractions. Micros- atellite loci were amplifed using three primer poly- Results and discussion merase chain reactions (PCRs) [11] on individual loci Fifteen polymorphic P. exacuous loci possessed 1–23 with the Qiagen Type-it Microsatellite Kit. Each 10 µl alleles and observed heterozygosities ranged from reaction included 1X Type-it Multiplex PCR (Qiagen) 0.00 to 0.96 within individual lakes (Table 1). One reaction mix, 0.2 µM standard locus primer, 0.02 µM locus deviated from Hardy–Weinberg expectations locus primer with CAG tag sequence, and 0.2 µM fu- in Round Lake (Pex2117), potentially from null alleles orescent-labeled CAG tag (PET, NED, 6-FAM, or VIC). and/or stuttering issues. Null alleles may also be pre- Te parameters of the PCRs were 5 min heat activa- sent in Pex216 and Pex2117 in Lake Saratoga, with low tion at 95 °C followed by 30 cycles of denaturation at amplifcation success likely prohibiting statistical sig- 95 °C for 30 s, annealing for 90 s, and an extension at nifcance. An additional sixteenth locus (Pex2416) was Yurco and Keeney BMC Res Notes (2018) 11:204 Page 3 of 6 E /H O H 0.89/0.89 0.76/0.85 0.33/0.70 0.84/0.86 0.95/0.90 0.57/0.79 0.41/0.47 0.32/0.33 0.61/0.50 0.89/0.84 0.56/0.68 0.50/0.51 0.00/0.00 0.84/0.89 0.94/0.94 0.94/0.97 3 6 4 5 2 9 5 4 1 A 11 11 11 12 10 15 23 6 Lake Saratoga Lake n 19 18 14 17 19 18 19 18 18 18 19 19 19 18 18 E /H O H 0.83/0.82 0.79/0.80 0.50/0.53 0.00/0.00 0.46/0.51 0.00/0.00 0.79/0.82 0.36*/0.63 0.17/0.22 0.00/0.00 0.00/0.00 0.96/0.79 0.00/0.00 0.75/0.86 0.88/0.91 0.95/0.91 8 5 4 1 3 1 8 3 2 1 1 7 1 A 10 15 13 n Round lake 24 24 24 23 24 24 23 24 24 24 22 24 22 24 24 24 165–261 272–368 158–226 248–384 166–226 239–278 243–276 169–197 305–326 244–284 192–208 86–162 146–170 250–262 128–184 314 Allele range (bp) range Allele 6 - FAM 6 - FAM PET PET PET VIC 6 - FAM 6 - FAM VIC NED VIC VIC PET PET NED NED Label GTCAGCTACGTGATCTTGGC GTAGTCTAGGCCTTCGGTCC CTGTCAGAAATACGCGGCTC GAGTGTTTCGGTGCCACAG GCATCCATATTTCAAAGCTGGG CTGCTATGGACGTGAGGGAG GTCATCTACGCATGGGAAGC TTAACGGTTCTGGCTTCCAC TGGTACTGGGACTTCATGGC TGTCATAAATCCGGCACTGC TAGGGAGGCATACAAACGGAG AACTTGGAATTGGCTGCCTC F: CAGTCGGGCGTCATC F: CAGTCGGGCGTCATCA GCTGTCTTTCATGGTTCCGG F: AAATGTGTCTGCAGGCGTAC R: CAGTCGGGCGTCATC TGAGAGCCCTTAAGTCGTGG F: R: CAGTCGGGCGTCATCA TTATTGCCACTCACGTACGC F: R: CAGTCGGGCGTCATCA AGCTTTGGAGTATGCTTGCC F: CAGTCGGGCGTCATC F: CAGTCGGGCGTCATCA AACCTGCAAGAAAGACCTGC F: CAGTCGGGCGTCATC AATGTAAGTGCGTGTGTAGCC F: CAGTCGGGCGTCATC F: CAGTCGGGCGTCATCA F: CAGTCGGGCGTCATCA AGGCAAACAGATGAGCTATGTC F: R: CAGTCGGGCGTCATCA TACTGACTTGACGCCAATGC F: R: CAGTCGGGCGTCATCA ACCTGCATGCCTAGCTACTG F: R: CAGTCGGGCGTCATCA F: CAGTCGGGCGTCATCA F: CAGTCGGGCGTCATCA Primer sequence (5 ′ –3 ) sequence Primer R: ACTGAAGTCCCTGAAGTGGC R: GGCTTAAACTGGGACGATGC R: CCTTTCCACCACATCACAGG R: CTAAGATTGGGAAGCCGCTG R: GCAAAGGCCGGATATTTCGATC R: ACTTCGCGTTTGTAGGTAGG R: TTCGCTCAATACCCAGTGATC R: GGCGCGAAATGGACTAACTG R: AAATAGTGCCGAATGTGCCG R: TATTGATGGGCGGACGGATG 15 8 18 10 9 12 11 17 16 15 11 11 12 9 8 10 (AAC) Repeat motif Repeat (AAC) (ACCT) (AACT) (AAAG) (AGAT ) (ACTC) (ACT) (ACCT) (AGAT ) (AACT) (AAAG) (ACC) (AAT ) (AACT) (AACT) Valvata tricarinata Valvata and (b) (a) Promenetus exacuous for loci developed Microsatellite Pex216 Pex1009 Pex2908 Pex1877 Pex2889 Pex2958 Pex757 Pex2416 Pex2181 Pex2091 Pex516 Pex2263 Pex2471 Pex577 Pex2117 Pex2972 Promenetus exacuous (a) Promenetus 1 Table Locus Yurco and Keeney BMC Res Notes (2018) 11:204 Page 4 of 6 E /H O H 0.63/0.56 0.75/0.75 0.92/0.90 0.96/0.95 0.75/0.81 0.71/0.76 0.42/0.59 0.67/0.76 0.38/0.40 0.46/0.52 0.45/0.59 0.67/0.87 0.23*/0.79 0.20/0.39 0.67/0.71 0.67/0.84 0.58*/0.76 4 5 6 5 7 6 5 3 8 6 2 9 A 14 19 13 11 10 Lake Saratoga Lake n 24 24 24 24 23 24 24 24 24 24 22 24 13 20 24 24 24 E /H O H 0.04/0.04 0.71/0.75 0.33/0.34 0.58/0.73 0.65/0.85 0.08/0.08 0.67/0.61 0.63/0.75 0.58/0.55 0.67/0.76 0.29/0.25 0.75/0.80 0.29/0.27 0.50/0.42 0.79/0.81 0.83/0.77 0.83/0.92 2 8 6 8 7 2 7 8 3 8 2 9 4 2 A 10 10 14 n Round lake 24 24 24 24 23 24 24 24 24 24 24 24 24 24 24 24 24 209–221 126–162 266–318 127–163 186–270 203–224 127–169 248–296 258–279 141–348 103–118 190–235 221–263 182–236 324–354 227–314 117–132 Allele range (bp) range Allele PET NED 6 - FAM NED 6 - FAM PET NED VIC VIC 6 - FAM NED PET VIC VIC VIC NED PET Label CCTTCATTCCACCTCAGCAG GAGTACCATCAAAGACGGCG GTAACCCAGTCCGTGCTCG CCTACAGATCAGAGACGTACAC CCTTCATTCACCTCAGCAGC TAGAGTCCAAGTGTGAGGCG TAGAGTCCAAGTGTGAGGCG TCTAGGGAAAGCGTGAGTGG TTGCTCCTTGGATTGGGATC TGGGCACTGAAATCTCGTATG TCTCTGCCAGCTTACCACTG TGTAGTGCCCATAGTCATGTAC CAACAACCTAGTGTGCCCTTC ACAGAGGTTCAAATCCCGGC F: CAGTCGGGCGTCATC CTTTGCCTCTTCCGGACATGF: R: CAGTCGGGCGTCATCA ACGGACTACAGGTGAATACAAC F: AGAAGTTCAATTTCGGCATGAG R: CAGTCGGGCGTCATC F: CAGTCGGGCGTCATCA TGTCAGATCACTCTTGGGCG F: R: CAGTCGGGCGTCAT F: CTCGTTTCCTGGCTGTTGTC R: CAGTCGGGCGTCATCA ACGCTAAGCTTTGTACAGTGC F: R: CAGTCGGGCGTCATCA ATTCAGTGCAGACATTCGGG F: CAGTCGGGCGTCATC AGCGAAGACAGAAATCCTCC F: CAGTCGGGCGTCATC F: CAGTCGGGCGTCATCA CCACAGGGCCAATAAATAACTG F: R: CAGTCGGGCGTCATCA F: CAGTCGGGCGTCATCA CAGGCCAAGATTCACACTGAC F: R: CAGTCGGGCGTCATCA F: CAGTCGGGCGTCATCA F: CAGTCGGGCGTCATCA F: CAGTCGGGCGTCATCA F: CAGTCGGGCGTCATCA Primer sequence (5 ′ –3 ) sequence Primer R: TTGCAGATCAAGGTTGTCGC R: CTTTGCCTCTTCCGGACATG R: AGTTGATCATCCCGCCGTAG R: ACAAATATATTTCGGTGCGCG R: CTGCAGCCTCGTGAATTGAC R: CTTACGCCACTGCCACTAAC R: ACGCGTTCTCTTTAATACCTGC R: GCCCACTACAACAAGCGAAG R: GGACGTTGTGCTTCTATTCTCC R: CAGCCCATTTCATCCTTGCC 14 12 8 8 14 12 19 10 11 10 25 10 25 20 9 9 10 (AATC) Repeat motif Repeat (AAT ) (ATC) (AAT ) (AAG) (AAAC) (AAC) (AAG) (AGC) (AGC) (AAG) (AAT ) (AAT ) (AAT ) (ACT) (AAT ) (AAG) Indicates statistically signifcant deviation from expected heterozygosity. GenBank expected heterozygosity. from deviation signifcant * Indicates statistically 5 ′ primer of the primer tag is underlined sequence. The based on the 5 ′ beginning and varied ) heterozygosities. E ­ (H continued )/expected O Vtr99 Vtr565 Vtr1099 Vtr2492 Vtr980 Vtr2349 Vtr828 Vtr972 Vtr4287 Vtr115 Vtr1730 Vtr1279 Vtr2388 Vtr4154 Vtr835 Vtr2508 Vtr2328 Valvata tricarinata (b) Valvata 1 Table and site-specifc and observed of alleles, range number of amplifed individuals ( n ), alleles (A), size total label, dye fuorescent primer sequences, allele, motif of sequenced repeat by name is followed Locus ­ (H Locus MH000435–MH000451 tricarinata MH000452–MH000467, V. exacuous Numbers: P. Accession Yurco and Keeney BMC Res Notes (2018) 11:204 Page 5 of 6

monomorphic in both populations, but is reported loci will be suitable for identifying gene fow patterns here as it may be polymorphic in other populations as among populations experiencing varying levels of observed between populations with several similar loci admixture. Multiple genetic groups were not detected in the present study. Linkage disequilibrium was not within sites. detected between any pair of P. exacuous loci. Te development of microsatellites in these two Seventeen polymorphic V. tricarinata loci possessed understudied, distantly related species will enable 2–19 alleles and observed heterozygosities of 0.04–0.96 researchers to examine the factors impacting the within lakes (Table 1). Two loci deviated from Hardy– genetic diversity within and population structure Weinberg expectations in Lake Saratoga (Vtr1730 and among their populations, and gain additional insights Vtr2349), potentially due to null alleles. Null alleles into the biology, evolution, and conservation of fresh- may also be present in Vtr2508 in Lake Saratoga. Link- water gastropods. While our interests are primarily the age disequilibrium was detected among Vtr115, Vtr972, dispersal and connectivity of these species throughout and Vtr4287. New York State and surrounding areas, these micros- STRUCTURE results for both species supported two atellites may be used by other labs to address diverse genetic populations (K = 2), refecting the two sam- questions in other regions. For example, although ple locations (Fig. 1). All snails were assigned to the both species are globally secure, there are conserva- population they were sampled from with a high prob- tion concerns for specifc populations throughout their ability (97–100% for all snails except a single V. tricari- range [4–6], and these markers may aid in conservation nata from Lake Saratoga with 92%), revealing minimal eforts. In addition, direct comparison of gastropods admixture between these populations for both species from diferent families over large geographic areas may (Fig. 1). Te high assignment values reveal that these reveal broad evolutionary dispersal patterns.

Fig. 1 Results of STRUCTURE cluster membership analyses for a Promenetus exacuous and b Valvata tricarinata for K 2. Vertical bars represent = proportion of membership of individual snails for two genetic clusters (gray Round Lake, black Lake Saratoga). Labels below graphs indicate = = original sample sites Yurco and Keeney BMC Res Notes (2018) 11:204 Page 6 of 6

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Received: 8 February 2018 Accepted: 20 March 2018

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