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1. On the potential of Angiosperms353 for population genomic studies

   https://doi.org/10.1002/aps3.11419  

   Slimp, Madeline; Williams, Lindsay D.; Hale, Haley; Johnson, Matthew G. (June 2021, Applications in Plant Sciences)

   null (Ed.)

   PREMISE The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate the need for specific marker development, while retaining the benefits of full-gene sequences in population-level analyses. However, whether the Angiosperms353 markers provide sufficient variation within species to calculate demographic parameters is untested. METHODS Using herbarium specimens from a 50-year-old floristic survey in Texas, we sequenced 95 samples from 24 species using the Angiosperms353 probe set. Our data workflow calls variants within species and prepares data for population genetic analysis using standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations and displayed limited phylogenetic bias. RESULTS We identified over 1000 segregating variants with zero missing data for 92% of species and demonstrate that Angiosperms353 markers contain sufficient variation to estimate pairwise nucleotide diversity (π)—typically between 0.002 and 0.010, with most variation found in flanking non-coding regions. In a subset of variants that were filtered to reduce linkage, we uncovered high heterozygosity in many species, suggesting that denser sampling within species should permit estimation of gene flow and population dynamics. DISCUSSION Angiosperms353 should benefit conservation genetic studies by providing universal repeatable markers, low missing data, and haplotype information, while permitting inclusion of decades-old herbarium specimens. 

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2. Resolving taxonomic uncertainty and exploring evolutionary relationships in the Cymopterus terebinthinus (Apiaceae) species complex

   https://doi.org/10.1002/tax.13344  

   Taylor, Annie; Mansfield, Don; Buerki, Sven; Feist, Mary Ann; Darrach, Mark; Smith, James F (May 2025, TAXON)

   Abstract Speciation processes in plants can be difficult to evaluate, but are essential to understanding evolutionary processes that lead to diversification. Determining the juncture at which a genetically and/or morphologically divergent population can be reliably considered a separate species is often challenging. This is particularly so with respect to recent divergences amongst closely related taxa wherein factors such as incomplete lineage sorting may yield confounding results. Taxa in theCymopterus terebinthinus(Apiaceae) species complex have long puzzled botanists. Named entities in this group display similar, yet apparently distinct morphologies that have been classified as varieties under various generic names highlighting long‐standing nomenclatural instability. Previous phylogenetic studies have challenged the monophyly of this complex. This study aims to clarify taxonomic boundaries and infer evolutionary relationships among the fourC. terebinthinusvarieties andC. petraeusby applying phylogenetic inference and incorporating ecological, morphological, and geographical evidence. We sampled from populations of all varieties ofC. terebinthinusandC. petraeusfor target capture with the Angiosperms353 bait kit. We performed phylogenetic analyses with maximum likelihood (RAxML and IQ‐TREE) and coalescent‐based phylogenetic analysis (ASTRAL). We also conducted principal component analysis of soil samples and climatic variables. We find thatC. terebinthinusand its varietal infrataxa comprise a monophyletic clade that includesC. petraeus. Clade groupings correspond to previous taxonomic assignments and morphology. Clades are often closely associated with geographical variables and at times correlated with ecological variables. Exceptions to this are here attributed to various evolutionary factors that often confound other phylogenetic analyses such as incomplete lineage sorting, introgression, and paralogous loci. Our findings suggests that geographical factors might play a major role in genetic and morphological differentiation in this complex. Despite finding well‐supported clades that correspond to defined morphological characters; further sampling amongC. petraeuspopulations is required to make taxonomic decisions. 

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3. Research in Boraginaceae: A new variety of Cryptantha maritima, Cryptantha pondii resurrected, and Johnstonella echinosepala transferred back to Cryptantha

   https://doi.org/10.11646/phytotaxa.509.2.3  

   SIMPSON, MICHAEL G.; REBMAN, JON P. (June 2021, Phytotaxa)

   A review of the species Cryptantha maritima (Boraginaceae) supports the continued recognition of the three varieties, these differing in corolla size, ovule and nutlet number, and calyx vestiture. Mapping of these taxa from verified specimens demonstrates some geographic trends, but also some overlap in ranges. In the process of our study, we discovered a new taxonomic entity. Cryptantha maritima var. vizcainensis is described as new. This variety is restricted to the Vizcaíno Desert of Baja California Sur, Mexico and should be considered rare, as it is known to date from only eleven collections. It differs from the other three varieties of the species in having a canescent, appressed-strigose stem vestiture lacking spreading trichomes, in having a relatively large corolla, and in having a fruit derived from two 1-ovuled ovary lobes, developing into two heteromorphic nutlets. We also discovered that the species Cryptantha pondii, previously treated as a synonym of C. patula, should be resurrected as a distinct taxon. Cryptantha pondii is restricted to the western Vizcaíno Desert and to Natividad Island of Baja California Sur. It is morphologically distinctive in having bracteate flowers, relatively large corollas, and four smooth nutlets heteromorphic by size. It is to date known from only three collections and should be considered extremely rare. We also reviewed the morphological and phylogenetic status of Johnstonella echinosepala. This taxon shows similarities to Cryptantha maritima and also exhibits some morphological discontinuity between Pacific and Gulf populations in Baja California Sur. Evidence from both morphological and phylogenetic studies supports the transfer of this species from the genus Johnstonella back to the genus Cryptantha. Finally, we propose that both C. pondii and C. echinosepala are likely close relatives of C. maritima, all of the “Maritimae clade,” a group distantly related to the main core of the genus Cryptantha. This study confirms the great importance of studying herbarium specimens in taxonomic research. 

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4. Molecular phylogenetic analyses support the validity of Ceratiomyxa porioides (Amoebozoa, Eumycetozoa) at species level

   https://doi.org/10.1016/j.ejop.2024.126083  

   Fry, Nicholas W.; Jones, Robert E.; Blandenier, Quentin; Tice, Alexander K.; Porfirio-Sousa, Alfredo L.; Kleitz-Singleton, Felicity; Henderson, Tristan C.; Brown, Matthew W. (June 2024, European Journal of Protistology)

   The frequently encountered macroscopic slime molds of the genus Ceratiomyxa have long been recognized by mycologists and protistologists for hundreds of years. These organisms are amoebozoan amoebae that live and grow inside and on the surface of decaying wood. When conditions are favorable, they form subaerial sporulating structures called fruiting bodies which take on a variety of forms. These forms are typically some arrangement of column and/or branches, but one is uniquely poroid, forming folds instead. Originally, this poroid morphology was designated as its own species. However, it was not always clear what significance fruiting body morphology held in determining species. Currently, Ceratiomyxa fruticulosa var. porioides, the poroid form, is considered a taxonomic variety of Ceratiomyxa fruticulosa based on morphological designation alone. Despite its long history of observation and study, the genus Ceratiomyxa has been paid little molecular attention to alleviate these morphological issues. We have obtained the first transcriptomes of the taxon C. fruticulosa var. porioides and found single gene phylogenetic and multigene phylogenomic support to separate it from C. fruticulosa. This provides molecular evidence that fruiting body morphology does correspond to species level diversity. Therefore, we formally restore Ceratiomyxa porioides stat. nov. to its original status. 

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5. Detecting and Removing Sample Contamination in Phylogenomic Data: An Example and its Implications for Cicadidae Phylogeny (Insecta: Hemiptera)

   https://doi.org/10.1093/sysbio/syac043  

   Owen, Christopher L; Marshall, David C; Wade, Elizabeth J; Meister, Russ; Goemans, Geert; Kunte, Krushnamegh; Moulds, Max; Hill, Kathy; Villet, M; Pham, Thai-Hong; et al (June 2022, Systematic Biology)

   Esselstyn, Jacob (Ed.)

   Abstract Contamination of a genetic sample with DNA from one or more nontarget species is a continuing concern of molecular phylogenetic studies, both Sanger sequencing studies and next-generation sequencing studies. We developed an automated pipeline for identifying and excluding likely cross-contaminated loci based on the detection of bimodal distributions of patristic distances across gene trees. When contamination occurs between samples within a data set, a comparison between a contaminated sample and its contaminant taxon will yield bimodal distributions with one peak close to zero patristic distance. This new method does not rely on a priori knowledge of taxon relatedness nor does it determine the causes(s) of the contamination. Exclusion of putatively contaminated loci from a data set generated for the insect family Cicadidae showed that these sequences were affecting some topological patterns and branch supports, although the effects were sometimes subtle, with some contamination-influenced relationships exhibiting strong bootstrap support. Long tip branches and outlier values for one anchored phylogenomic pipeline statistic (AvgNHomologs) were correlated with the presence of contamination. While the anchored hybrid enrichment markers used here, which target hemipteroid taxa, proved effective in resolving deep and shallow level Cicadidae relationships in aggregate, individual markers contained inadequate phylogenetic signal, in part probably due to short length. The cleaned data set, consisting of 429 loci, from 90 genera representing 44 of 56 current Cicadidae tribes, supported three of the four sampled Cicadidae subfamilies in concatenated-matrix maximum likelihood (ML) and multispecies coalescent-based species tree analyses, with the fourth subfamily weakly supported in the ML trees. No well-supported patterns from previous family-level Sanger sequencing studies of Cicadidae phylogeny were contradicted. One taxon (Aragualna plenalinea) did not fall with its current subfamily in the genetic tree, and this genus and its tribe Aragualnini is reclassified to Tibicininae following morphological re-examination. Only subtle differences were observed in trees after the removal of loci for which divergent base frequencies were detected. Greater success may be achieved by increased taxon sampling and developing a probe set targeting a more recent common ancestor and longer loci. Searches for contamination are an essential step in phylogenomic analyses of all kinds and our pipeline is an effective solution. [Auchenorrhyncha; base-composition bias; Cicadidae; Cicadoidea; Hemiptera; phylogenetic conflict.] 

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