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30 July 2020

Novel Molecular Resources to Facilitate Future Genetics Research on Freshwater Mussels (Bivalvia: Unionidae)

and
1
Wetland and Aquatic Research Center, U.S. Geological Survey, 7920 NW 71st Street, Gainesville, FL 32653, USA
2
Biology Department, Baylor University, Waco, TX 76798, USA
3
Department of Integrative Biology, University of Texas at Austin, 2415 Speedway, Austin, TX 78712, USA
*
Authors to whom correspondence should be addressed.
Data2020, 5(3), 65;https://doi.org/10.3390/data5030065
This article belongs to the Section Computational Biology, Bioinformatics, and Biomedical Data Science
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Abstract

Molecular data have been an integral tool in the resolution of the evolutionary relationships and systematics of freshwater mussels, despite the limited number of nuclear markers available for Sanger sequencing. To facilitate future studies, we evaluated the phylogenetic informativeness of loci from the recently published anchored hybrid enrichment (AHE) probe set Unioverse and developed novel Sanger primer sets to amplify two protein-coding nuclear loci with high net phylogenetic informativeness scores: fem-1 homolog C (FEM1) and UbiA prenyltransferase domain-containing protein 1 (UbiA). We report the methods used for marker development, along with the primer sequences and optimized PCR and thermal cycling conditions. To demonstrate the utility of these markers, we provide haplotype networks, DNA alignments, and summary statistics regarding the sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA). Additionally, we compare the DNA sequence variation of FEM1 and UbiA to three loci commonly used in freshwater mussel genetic studies: the mitochondrial genes cytochrome c oxidase subunit 1 (CO1) and NADH dehydrogenase subunit 1 (ND1), and the nuclear internal transcribed spacer 1 (ITS1). All five loci distinguish among the three focal species (Potamilus fragilis, Potamilus inflatus, and Potamilus purpuratus), and the sequence variation was highest for ND1, followed by CO1, ITS1, UbiA, and FEM1, respectively. The newly developed Sanger PCR primers and methodologies for extracting additional loci from AHE probe sets have great potential to facilitate molecular investigations targeting supraspecific relationships in freshwater mussels, but may be of limited utility at shallow taxonomic scales.
Dataset:https://doi.org/10.5066/P9Q3CFL5.
Dataset License: CC0. This work was authored as part of the Contributor’s official duties as an Employee of the United States Government and is therefore a work of the United States Government. In accordance with 17 U.S.C. 105, no copyright protection is available for such works under U.S. Law. This is an open access article that has been identified as being free of known restrictions under copyright law, including all related and neighboring rights (https://creativecommons.org/publicdomain/mark/1.0/). You can copy, modify, distribute, and perform the work, even for commercial purposes, all without asking permission.

1. Summary

Recent studies utilizing molecular tools have been integral in resolving the evolutionary history of freshwater mussels (Bivalvia: Unionida), despite a heavy reliance on the Sanger sequencing of mitochondrial DNA (mtDNA). Nearly all phylogenetic studies on freshwater mussels have largely relied on the commonly used marker internal transcribed spacer 1 (ITS1) to incorporate inference from the nuclear genome [,,,,,], which was first used in freshwater mussels nearly 20 years ago []. Even though researchers continue to utilize this locus, the number of studies reporting issues related to excessive heterozygosity, primarily due to length polymorphisms, continues to increase [,,,,,,,,,]. Other nuclear loci, such as histone H3 and 28S, have been utilized in freshwater mussel phylogenetic studies; however, these markers are well known to show limited diversity at shallow taxonomic scales and have primarily been used to resolve deep level phylogeny [,,,,,].
In recent years, the decreasing costs of next-generation sequencing platforms have significantly increased the ability to generate molecular supermatrices in non-model taxa [,], including freshwater mussels [,]. In particular, the recently developed anchored hybrid enrichment (AHE) probe set Unioverse [] has drastically improved the ability to resolve phylogeny in freshwater mussels. The Unioverse probe set consists of 811 protein-coding loci derived from genomic and transcriptomic resources across Bivalvia that can be captured across all freshwater mussels to resolve phylogenetic relationships. Despite the decreasing costs of next-generation sequencing, the utilization of AHE probe sets can be cost-prohibitive for small-scale projects or molecular investigations that incorporate hundreds of individuals to investigate intra- or interspecific relationships. However, AHE probe sets offer opportunities for the development of primers for the amplification and Sanger sequencing of select protein-coding loci that can be used for small-scale projects.
Here, we evaluated the phylogenetic informativeness of loci in the Universe probe set and report the development of novel primer pairs for the amplification of two protein-coding nuclear genes fem-1 homolog C (FEM1) and UbiA prenyltransferase domain-containing protein 1 (UbiA). To demonstrate the utility of these markers and facilitate their use in future studies, we provide the PCR primer sequences, optimized PCR conditions and thermal cycling parameters, haplotype networks, DNA alignments, and summary statistics regarding sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA) and three loci that are commonly used in studies in freshwater mussels: the mitochondrial genes cytochrome c oxidase subunit 1 (CO1) and NADH dehydrogenase subunit 1 (ND1), and the nuclear ITS1 locus. All five loci distinguish among the three focal species (Potamilus fragilis, Potamilus inflatus, and Potamilus purpuratus) and should be amplifiable across the subfamily Ambleminae. The observed sequence variation was highest for ND1, followed by CO1, ITS1, UbiA, and FEM1, respectively (Figure 1). We also provide the detailed methodology used in the marker selection to expedite the identification of additional candidate loci and primer development from available AHE data. The newly developed Sanger PCR primers and methodologies for extracting additional loci have great potential to facilitate molecular investigations targeting supraspecific relationships in freshwater mussels, but may be of limited utility at shallow taxonomic scales.
Figure 1. TCS haplotype networks for (A) cytochrome c oxidase subunit 1 (CO1), (B) fem-1 homolog C (FEM1), (C) internal transcribed spacer 1 (ITS1), (D) NADH dehydrogenase subunit 1 (ND1), and (E) UbiA prenyltransferase domain-containing protein 1 (UbiA). Each colored circle represents a unique haplotype, the colors correspond to individual species, the black circles represent unsampled haplotypes, and the hash marks indicate nucleotide differences between haplotypes.

2. Data Description

2.1. Specimen Details

All the metadata related to the specimens used in this study, including the collection location, GPS coordinates, and museum catalog numbers, are provided (https://doi.org/10.5066/P9Q3CFL5) [].

2.2. Molecular Data

We present the DNA sequence data from five markers: the mitochondrial genes CO1 and ND1, the nuclear non-coding marker ITS1, and the protein-coding nuclear genes FEM1 and UbiA. Our five-locus DNA alignment consisted of 3368 bp of mitochondrial and nuclear sequence data (CO1 = 657 bp; ND1 = 900 bp; FEM1 = 501 bp; UBiA = 765 bp; ITS1 = 545 bp). The number of loci sequenced for each individual varies from two to five loci, with all loci available for 28 individuals (Table 1). The specific sample sizes for each locus are as follows: CO1 (n = 102); ND1 (n = 103); FEM1 (n = 29); UBiA (n = 29); and ITS1 (n = 31). A subset of individuals was chosen for the additional nDNA loci due to the high prevalence of multiple copies at ITS1 and low genetic diversity at FEM1 and UbiA. All the DNA alignment files are available in Phylip format (.phy), with the first line indicating the number of taxa and number of nucleotides and subsequent lines containing a taxon identifier, catalog number, and GenBank Accession number in the first column (each separated by underscore), and the DNA sequence in the second column. The file names are as follows: CO1.phy; ND1.phy; FEM1.phy; UbiA.phy; ITS1.phy; and 5_locus.phy (https://doi.org/10.5066/P9Q3CFL5) [].
Table 1. Collection information and GenBank or SRA accession numbers for all the specimens and loci analyzed in this study. Museum abbreviations are as follows: UA—Alabama Museum of Natural History; UF—Florida Museum.

3. Methods

3.1. Taxon Sampling and DNA Extraction

We present molecular data on 103 specimens representing Potamilus fragilis (n = 22), Potamilus inflatus (n = 14), and Potamilus purpuratus (n = 67) used in Smith and Johnson [] (Table 1). All specimens were collected from four Gulf of Mexico river drainages in the southeastern United States: Mobile, Pascagoula, Pearl, and Pontchartrain. Genomic DNA was extracted from mantle tissue clips from vouchered individuals using the Qiagen PureGene DNA extraction kit with the standard extraction protocol (Qiagen, Hilden, Germany).

3.2. Novel Primer Design and Gene Annotation

We compiled data from a recent study [] utilizing the AHE probe set Unioverse to develop novel primer sets for amplifying protein-coding nuclear loci for use in the freshwater mussel genus Potamilus. To screen for loci in the dataset that were informative at shallow phylogenetic scales, we measured the net phylogenetic informativeness (PI) using an arbitrary time scale []. This methodology has been used in previous studies to calculate the power of individual loci in AHE datasets [,]. First, we reconstructed a phylogeny from a concatenated alignment of probe loci using IQ-TREE v 1.6.11 [,], and the consensus tree was arbitrarily dated with a molecular clock (i.e., tips = time 0, root = time 1) using the program PATHd8 []. A concatenated alignment partitioned by the probe and the ultrametric tree from PATHd8 were uploaded into the web application PhyDesign [] (http://phydesign.townsend.yale.edu/) to estimate the PI using the HyPhy substitution rates algorithm with the GTR model of nucleotide evolution and empirical base frequencies []. We used the R script PhyDesign.r [] to identify specific nucleotide positions in the alignment with unusually high substitution rates that could be contributing phylogenetic noise. Nucleotide positions with rate values higher than five were removed from the alignment manually and the filtered matrices were re-uploaded to PhyDesign as above for a final analysis.
Three nucleotides were removed from the dataset due to unusually high substitution rates (rate value > 5 = “phantom spikes”). In the filtered dataset, the probe regions with a 100% capture efficiency across Ambleminae had an average net PI of 4.62 and ranged from 0.32 to 23.09 (Table 2). Using the results from PhyDesign, we selected two candidate loci for primer development and PCR validation: locus 156 and locus 412. Locus 156 and locus 412 exhibited a 100% capture efficiency in our dataset, had suitable candidate primers that could be cross amplified across Potamilus, displayed high levels of average PI (9.22 and 11.61, respectively), and were able to discriminate our focal species. We were unable to develop compatible primers for the other candidate loci with high net PI scores (e.g., locus 70 and locus 413).
Table 2. Average, minimum, and maximum net phylogenetic informativeness (PI), and the time at maximum PI for the 55 loci with a 100% capture efficiency across Ambleminae. Time at max PI represents an arbitrary time scale, with values closer to zero providing the maximum phylogenetic signal at shallower taxonomic scales. Loci are ordered from the highest to lowest average net PI.
We used BLASTX [] to annotate the gene and protein names for our candidate loci []. Briefly, the probe region sequences of both loci for P. inflatus were searched against the non-redundant protein database using BLASTX, which returned 172 and 118 BLAST hits for locus 156 and locus 412, respectively. Locus 156 was identified as UbiA prenyltransferase domain-containing protein 1, and the highest homology was to genes in the marine bivalves Crassostrea virginica (74.62%) and C. gigas (72.31%). Locus 412 was identified as a fem-1 homolog, and the highest homology was to genes in the unionid bivalves Hyriopsis schlegelii (99.44%) and H. cumingii (98.89%), and the marine bivalves Mizuhopecten yessoensis (87.22%), Pecten maximus (87.22%), C. virginica (86.11%), and C. gigas (86.11%). There were inconsistencies regarding whether the region was a fem-1 homolog A or fem-1 homolog C. All the blast hits except for H. cumingii and H. schlegelii indicated the sequence was representative of fem-1 homolog C; therefore, we annotated the locus as fem-1 homolog C.

3.3. PCR and Sequencing

PCRs were conducted using a 25 µL mixture of the following: molecular grade water (9.5 µL), MyTaqTM Red Mix (12.5 µL; Bioline, London, UK), primers (1.0 µL each), and DNA template (100 ng). The primers for all loci and thermal cycling conditions for CO1, ND1, and ITS1 are reported in Table 3. The thermal cycling conditions for FEM1 and UbiA were as follows: an initial denaturation at 95 °C for 3 min, followed by 35 cycles of 95 °C for 30 s, 51/60 °C (FEM1/UbiA) for 30 s, and 72 °C for 90 s. The products were sent to Molecular Cloning Laboratories (McLAB, South San Francisco, CA, USA) for bi-directional sequencing on an ABI 3730. Geneious v 10.2.3 [] was used to assemble the contigs and edit chromatograms, and the sequences were aligned in Mesquite v 3.61 [] using MAFFT v 7.311 []. The loci were aligned independently using the L-INS-i method in MAFFT and translated into amino acids to ensure the absence of stop codons and gaps.
Table 3. PCR primer sequences and cycling conditions used in this study.

3.4. Sequence Variation and Haplotype Analysis

We created haplotype networks (Figure 1) and calculated the nucleotide diversity, number of haplotypes, number of segregating sites, and number of parsimony-informative sites (Table 4) to compare the amounts of sequence variation across all five loci used in this study. The TCS haplotype networks and sequence variation statistics were calculated using PopART 1.7 []. All five loci distinguish among the three focal species (Figure 1). The sequence variation was highest for ND1, followed by CO1, ITS1, UbiA, and FEM1, respectively (Table 4). Despite selecting loci from the AHE probe set with a high net PI, the level of sequence variation remains low when compared to mtDNA and ITS1, suggesting the limited utility of the probes at intraspecific levels.
Table 4. Summary of diversity indices based on all five loci utilized in this study. Abbreviations and symbols are as follows: cytochrome c oxidase subunit 1 (CO1); fem-1 homolog C (FEM1); internal transcribed spacer 1 (ITS1); NADH dehydrogenase subunit 1 (ND1); UbiA prenyltransferase domain-containing protein 1 (UbiA); sample size (n); nucleotide diversity (π); number of haplotypes (nh); number of segregating sites (S); and number of parsimony-informative sites (P).

4. User Notes

All the data and metadata described in this study are at https://doi.org/10.5066/P9Q3CFL5 [], and all the novel GenBank accessions for this study were as follows: CO1: MT662002–MT662099; FEM1: MT669773–MT669799; ITS1: MT661766–MT661792; ND1: MT669647–MT669745; and UbiA: MT669746–MT669772 (Table 1).

Author Contributions

Conceptualization, N.A.J. and C.H.S.; methodology, N.A.J. and C.H.S.; validation, N.A.J. and C.H.S.; formal analysis, N.A.J. and C.H.S.; investigation, N.A.J. and C.H.S.; resources, N.A.J. and C.H.S.; data curation, N.A.J. and C.H.S.; writing—original draft preparation, N.A.J.; writing—review and editing, C.H.S.; visualization, N.A.J.; supervision, N.A.J.; project administration, N.A.J.; funding acquisition, N.A.J. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the U.S. Fish and Wildlife Service and U.S. Geological Survey.

Acknowledgments

The authors thank John Pfeiffer for providing preliminary data and advice during the marker development stage of this project and Matt Cannister for assistance with preparing the metadata file for sharing on ScienceBase. Special thanks to Jeff Powell for help obtaining funding, which was provided by the U.S. Fish and Wildlife Service and U.S. Geological Survey. The specimens utilized in this study were either from museum collections or collected under the U.S. Fish and Wildlife Service permit TE 697819-4. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Smith, C.H.; Johnson, N.A.; Pfeiffer, J.M.; Gangloff, M.M. Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus). Mol. Phylogenet. Evol. 2018, 119, 50–62. [Google Scholar] [CrossRef] [PubMed]
  2. Johnson, N.A.; Smith, C.H.; Pfeiffer, J.M.; Randklev, C.R.; Williams, J.D.; Austin, J.D. Integrative taxonomy resolves taxonomic uncertainty for freshwater mussels being considered for protection under the U.S. Endangered Species Act. Sci. Rep. 2018, 8, 1–16. [Google Scholar] [CrossRef] [PubMed]
  3. Keogh, S.M.; Simons, A.M. Molecules and morphology reveal ‘new’ widespread North American freshwater mussel species (Bivalvia: Unionidae). Mol. Phylogenet. Evol. 2019, 138, 182–192. [Google Scholar] [CrossRef]
  4. Inoue, K.; McQueen, A.L.; Harris, J.L.; Berg, D.J. Molecular phylogenetics and morphological variation reveal recent speciation in freshwater mussels of the genera Arcidens and Arkansia (Bivalvia: Unionidae). Biol. J. Linn. Soc. 2014, 112, 535–545. [Google Scholar] [CrossRef]
  5. Inoue, K.; Hayes, D.M.; Harris, J.L.; Christian, A.D. Phylogenetic and morphometric analyses reveal ecophenotypic plasticity in freshwater mussels Obovaria jacksoniana and Villosa arkansasensis (Bivalvia: Unionidae). Ecol. Evol. 2013, 3, 2670–2683. [Google Scholar] [CrossRef] [PubMed]
  6. Campbell, D.C.; Lydeard, C. The genera of Pleurobemini (Bivalvia: Unionidae: Ambleminae). Am. Malacol. Bull. 2012, 30, 19–38. [Google Scholar] [CrossRef]
  7. King, T.L.; Eackles, M.S.; Gjetvaj, B.; Hoeh, W.R. Intraspecific phylogeography of Lasmigona subviridis (Bivalvia: Unionidae): Conservation implications of range discontinuity. Mol. Ecol. 1999, 8, S65–S78. [Google Scholar] [CrossRef]
  8. Jones, J.W.; Neves, R.J.; Ahlstedt, S.A.; Hallerman, E.M. A holistic approach to taxonomic evaluation of two closely related endangered freshwater mussel species, the oyster mussel Epioblasma capsaeformis and tan riffleshell Epioblasma florentina walkeri (Bivalvia: Unionidae). J. Molluscan Stud. 2006, 72, 267–283. [Google Scholar] [CrossRef]
  9. Campbell, D.C.; Johnson, P.D.; Williams, J.D.; Rindsberg, A.K.; Serb, J.M.; Small, K.K.; Lydeard, C. Identification of ‘extinct’ freshwater mussel species using DNA barcoding. Mol. Ecol. Resour. 2008, 8, 711–724. [Google Scholar] [CrossRef]
  10. Pfeiffer, J.M.; Johnson, N.A.; Randklev, C.R.; Howells, R.G.; Williams, J.D. Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896). Conserv. Genet. 2016, 17, 279–292. [Google Scholar] [CrossRef]
  11. Smith, C.H.; Johnson, N.A.; Pfeiffer, J.M.; Gangloff, M.M. Molecular and morphological data to facilitate future research on freshwater mussels (Bivalvia: Unionidae: Anodontinae). Data Brief. 2018, 17, 95–104. [Google Scholar] [CrossRef] [PubMed]
  12. Smith, C.H.; Johnson, N.A.; Havlik, K.; Doyle, R.D.; Randklev, C.R. Resolving species boundaries in the critically imperiled freshwater mussel species, Fusconaia mitchelli (Bivalvia: Unionidae). J. Zool. Syst. Evol. Res. 2020, in press. [Google Scholar] [CrossRef]
  13. Smith, C.H.; Johnson, N.A.; Inoue, K.; Doyle, R.D.; Randklev, C.R. Integrative taxonomy reveals a new species of freshwater mussel, Potamilus streckersoni sp. nov. (Bivalvia: Unionidae): Implications for conservation and management. Syst. Biodivers. 2019, 17, 331–348. [Google Scholar] [CrossRef]
  14. Grobler, P.J.; Jones, J.W.; Johnson, N.A.; Beaty, B.; Struthers, J.; Neves, R.J.; Hallerman, E.M. Patterns of genetic differentiation and conservation of the Slabside Pearlymussel, Lexingtonia dolabelloides (Lea, 1840) in the Tennessee River drainage. J. Molluscan Stud. 2006, 72, 65–75. [Google Scholar] [CrossRef]
  15. Lopes-Lima, M.; Froufe, E.; Do, V.T.; Ghamizi, M.; Mock, K.E.; Kebapçı, Ü.; Klishko, O.; Kovitvadhi, S.; Kovitvadhi, U.; Paulo, O.S.; et al. Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes. Mol. Phylogenet. Evol. 2017, 106, 174–191. [Google Scholar] [CrossRef]
  16. Pfeiffer, J.M.; Sharpe, A.E.; Johnson, N.A.; Emery, K.F.; Page, L.M. Molecular phylogeny of the Nearctic and Mesoamerican freshwater mussel genus Megalonaias. Hydrobiologia 2018, 811, 139–151. [Google Scholar] [CrossRef]
  17. Jeratthitikul, E.; Phuangphong, S.; Sutcharit, C.; Prasankok, P.; Kongim, B.; Panha, S. Integrative taxonomy reveals phenotypic plasticity in the freshwater mussel Contradens contradens (Bivalvia: Unionidae) in Thailand, with a description of a new species. Syst. Biodivers. 2019, 1–14. [Google Scholar] [CrossRef]
  18. Whelan, N.V.; Geneva, A.J.; Graf, D.L. Molecular phylogenetic analysis of tropical freshwater mussels (Mollusca: Bivalvia: Unionoida) resolves the position of Coelatura and supports a monophyletic Unionidae. Mol. Phylogenet. Evol. 2011, 61, 504–514. [Google Scholar] [CrossRef]
  19. Huang, X.-C.; Su, J.-H.; Ouyang, J.-X.; Ouyang, S.; Zhou, C.-H.; Wu, X.-P. Towards a global phylogeny of freshwater mussels (Bivalvia: Unionida): Species delimitation of Chinese taxa, mitochondrial phylogenomics, and diversification patterns. Mol. Phylogenet. Evol. 2019, 130, 45–59. [Google Scholar] [CrossRef]
  20. Huff, S.W.; Campbell, D.; Gustafson, D.L.; Lydeard, C.; Altaba, C.R.; Giribet, G. Investigations into the phylogenetic relationships of freshwater pearl mussels (Bivalvia: Margaritiferidae) based on molecular data: Implications for their taxonomy and biogeography. J. Molluscan Stud. 2004, 70, 379–388. [Google Scholar] [CrossRef]
  21. Ekblom, R.; Galindo, J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity 2011, 107, 1–15. [Google Scholar] [CrossRef] [PubMed]
  22. Ellegren, H. Genome sequencing and population genomics in non-model organisms. Trends Ecol. Evol. 2014, 29, 51–63. [Google Scholar] [CrossRef] [PubMed]
  23. Pfeiffer, J.M.; Breinholt, J.W.; Page, L.M. Unioverse: Phylogenomic resources for reconstructing the evolution of freshwater mussels (Unionoida). Mol. Phylogenet. Evol. 2019, 137, 114–126. [Google Scholar] [CrossRef]
  24. Smith, C.H.; Pfeiffer, J.M.; Johnson, N.A. Comparative phylogenomics reveal complex evolution of life history strategies in a clade of bivalves with parasitic larvae (Bivalvia: Unionoida: Ambleminae). Cladistics 2020. [Google Scholar] [CrossRef]
  25. Johnson, N.A.; Smith, C.H. Novel genetic resources to facilitate future molecular studies in freshwater mussels (Bivalvia: Unionidae). U.S. Geological Survey Data Release 2020. Available online: https://doi.org/10.5066/P9Q3CFL5 (accessed on 29 July 2020).
  26. Smith, C.H.; Johnson, N.A. A comparative phylogeographic approach to facilitate recovery of an imperiled freshwater mussel (Bivalvia: Unionida: Potamilus inflatus). Diversity 2020, 12, 281. [Google Scholar] [CrossRef]
  27. Townsend, J.P. Profiling phylogenetic informativeness. Syst. Biol. 2007, 56, 222–231. [Google Scholar] [CrossRef]
  28. Bogarín, D.; Pérez-Escobar, O.A.; Groenenberg, D.; Holland, S.D.; Karremans, A.P.; Lemmon, E.M.; Lemmon, A.R.; Pupulin, F.; Smets, E.; Gravendeel, B. Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex. Mol. Phylogenet. Evol. 2018, 129, 27–47. [Google Scholar] [CrossRef]
  29. Fragoso-Martínez, I.; Salazar, G.A.; Martínez-Gordillo, M.; Magallón, S.; Sánchez-Reyes, L.; Moriarty Lemmon, E.; Lemmon, A.R.; Sazatornil, F.; Granados Mendoza, C. A pilot study applying the plant anchored hybrid enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae). Mol. Phylogenet. Evol. 2017, 117, 124–134. [Google Scholar] [CrossRef]
  30. Nguyen, L.-T.; Schmidt, H.A.; von Haeseler, A.; Minh, B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 2015, 32, 268–274. [Google Scholar] [CrossRef]
  31. Chernomor, O.; von Haeseler, A.; Minh, B.Q. Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol. 2016, 65, 997–1008. [Google Scholar] [CrossRef]
  32. Britton, T.; Anderson, C.L.; Jacquet, D.; Lundqvist, S.; Bremer, K. Estimating divergence times in large phylogenetic trees. Syst. Biol. 2007, 56, 741–752. [Google Scholar] [CrossRef] [PubMed]
  33. López-Giráldez, F.; Townsend, J.P. PhyDesign: An online application for profiling phylogenetic informativeness. BMC Evol. Biol. 2011, 11, 1–4. [Google Scholar] [CrossRef] [PubMed]
  34. Pond, S.L.K.; Frost, S.D.W.; Muse, S.V. HyPhy: Hypothesis testing using phylogenies. Bioinformatics 2005, 21, 676–679. [Google Scholar] [CrossRef] [PubMed]
  35. States, D.J.; Gish, W. Combined use of sequence similarity and codon bias for coding region identification. J. Comput. Biol. 1994, 1, 39–50. [Google Scholar] [CrossRef] [PubMed]
  36. Krauthammer, M.; Rzhetsky, A.; Morozov, P.; Friedman, C. Using BLAST for identifying gene and protein names in journal articles. Gene 2000, 259, 245–252. [Google Scholar] [CrossRef]
  37. Kearse, M.; Moir, R.; Wilson, A.; Stones-Havas, S.; Cheung, M.; Sturrock, S.; Buxton, S.; Cooper, A.; Markowitz, S.; Duran, C.; et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012, 28, 1647–1649. [Google Scholar] [CrossRef]
  38. Maddison, W.P.; Maddison, D.R. Mesquite: A modular system for evolutionary analysis. Version 3.61. 2019. Available online: https://www.mesquiteproject.org/ (accessed on 29 July 2020).
  39. Katoh, K.; Standley, D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013, 30, 772–780. [Google Scholar] [CrossRef]
  40. Campbell, D.C.; Serb, J.M.; Buhay, J.E.; Roe, K.J.; Minton, R.L.; Lydeard, C. Phylogeny of North American amblemines (Bivalvia, Unionoida): Prodigious polyphyly proves pervasive across genera. Invertebr. Biol. 2005, 124, 131–164. [Google Scholar] [CrossRef]
  41. Serb, J.M.; Buhay, J.E.; Lydeard, C. Molecular systesmatics of the North American freshwater bivalve genus Quadrula (Unionidae: Ambleminae) based on mitochondrial ND1 sequences. Mol. Phylogenet. Evol. 2003, 28, 1–11. [Google Scholar] [CrossRef]
  42. Leigh, J.W.; Bryant, D. popart: Full-Feature software for haplotype network construction. Methods Ecol. Evol. 2015, 6, 1110–1116. [Google Scholar] [CrossRef]

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