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1. Evolution of conserved noncoding sequences in Arabidopsis thaliana

   https://doi.org/10.1093/molbev/msab042  

   Yocca, Alan E; Lu, Zefu; Schmitz, Robert J; Freeling, Michael; Edger, Patrick P (February 2021, Molecular Biology and Evolution)

   Wittkopp, Patricia (Ed.)

   Abstract Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only PAV and positional variation (PosV) but that diversity in CNS is non-random, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting roles for conserved and variable CNS in gene regulation. Additionally, our data suggests transposable elements contribute to CNS variation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype. 

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2. Asia Pacific Sporolithon (Corallinophycidae, Rhodophyta) species revised based on DNA sequencing of type specimens and including S. crypticum sp. nov., S. immotum sp. nov . and S. nodosum sp. nov.

   https://doi.org/10.1080/00318884.2023.2225309  

   Gabrielson, Paul W.; Hughey, Jeffery R.; Peña, Viviana; Richards, Joseph L.; Saunders, Gary W.; Twist, Brenton; Farr, Tracy; Nelson, Wendy A. (November 2023, Phycologia)

   To address the taxonomic uncertainty of Sporolithon species named in the early to mid-20th century, targeted PCR sequencing was performed on eight historical type specimens and on recently collected specimens. Six type specimens amplified for the rbcL gene and were Sanger sequenced yielding sequences ranging in length from 118 to 280 base pairs (bp). One, S. australasicum, failed to amplify and another, S. howei, was amplified for the psbA gene yielding a sequence 544 bp in length. The 118 bp long rbcL sequence of the lectotype of S. crassiramosum showed that it is a later, heterotypic synonym of S. molle. The rbcL sequences of type specimens of S. episoredion, S. schmidtii, S. sibogae and S. timorense ranged from 118 to 228 bp, and each is a distinct species. The 544 bp long psbA sequence of S. howei is also unique. The 280 bp long rbcL sequence of the lectotype of S. durum did not match any sequence with that name in any public repository, including the previously published complete plastome and mitogenome sequences. However, it was identical in sequence to a specimen in GenBank from the southern coast of Western Australia as well as several other sequences generated from field-collected specimens from the states of South Australia and Western Australia. The rhodolith specimens from New Zealand previously called S. durum are S. nodosum sp. nov. The species is endemic to New Zealand. The epilithic specimens from New Zealand previously called S. durum are S. immotum sp. nov., which is also found along the southeastern coast of Australia. Sporolithon crypticum sp. nov. is described from the southern coast of Western Australia. RAxML and Bayesian phylogenetic analyses of Sporolithon psbA and rbcL sequences are congruent between the two plastid encoded genes. DNA sequencing of type specimens of species of corallines is demonstrated to be the only reliable method to correctly apply names. 

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3. Target Enrichment and Extensive Population Sampling Help Untangle the Recent, Rapid Radiation of Oenothera Sect. Calylophus

   https://doi.org/10.1093/sysbio/syac032  

   Cooper, Benjamin J.; Moore, Michael J.; Douglas, Norman A.; Wagner, Warren L.; Johnson, Matthew G.; Overson, Rick P.; Kinosian, Sylvia P.; McDonnell, Angela J.; Levin, Rachel A.; Raguso, Robert A.; et al (May 2022, Systematic Biology)

   Abstract Oenothera sect. Calylophus is a North American group of 13 recognized taxa in the evening primrose family (Onagraceae) with an evolutionary history that may include independent origins of bee pollination, edaphic endemism, and permanent translocation heterozygosity. Like other groups that radiated relatively recently and rapidly, taxon boundaries within Oenothera sect. Calylophus have remained challenging to circumscribe. In this study, we used target enrichment, flanking noncoding regions, gene tree/species tree methods, tests for gene flow modified for target-enrichment data, and morphometric analysis to reconstruct phylogenetic hypotheses, evaluate current taxon circumscriptions, and examine character evolution in Oenothera sect. Calylophus. Because sect. Calylophus comprises a clade with a relatively restricted geographic range, we were able to extensively sample across the range of geographic, edaphic, and morphological diversity in the group. We found that the combination of exons and flanking noncoding regions led to improved support for species relationships. We reconstructed potential hybrid origins of some accessions and note that if processes such as hybridization are not taken into account, the number of inferred evolutionary transitions may be artificially inflated. We recovered strong evidence for multiple evolutionary origins of bee pollination from ancestral hawkmoth pollination, edaphic specialization on gypsum, and permanent translocation heterozygosity. This study applies newly emerging techniques alongside dense infraspecific sampling and morphological analyses to effectively reconstruct the recalcitrant history of a rapid radiation. [Gypsum endemism; Oenothera sect. Calylophus; Onagraceae; phylogenomics; pollinator shift; recent radiation; target enrichment.] 

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4. A New Pipeline for Removing Paralogs in Target Enrichment Data

   https://doi.org/10.1093/sysbio/syab044  

   Zhou, Wenbin; Soghigian, John; Xiang, Qiu-Yun (June 2021, Systematic Biology)

   null (Ed.)

   Abstract Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperm 353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of datasets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene datasets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperm 353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study. 

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5. Maximizing Molecular Data From Low-Quality Fluid-Preserved Specimens in Natural History Collections

   https://doi.org/10.3389/fevo.2022.893088  

   Bernstein, Justin M.; Ruane, Sara (June 2022, Frontiers in Ecology and Evolution)

   Over the past decade, museum genomics studies have focused on obtaining DNA of sufficient quality and quantity for sequencing from fluid-preserved natural history specimens, primarily to be used in systematic studies. While these studies have opened windows to evolutionary and biodiversity knowledge of many species worldwide, published works often focus on the success of these DNA sequencing efforts, which is undoubtedly less common than obtaining minimal or sometimes no DNA or unusable sequence data from specimens in natural history collections. Here, we attempt to obtain and sequence DNA extracts from 115 fresh and 41 degraded samples of homalopsid snakes, as well as from two degraded samples of a poorly known snake, Hydrablabes periops . Hydrablabes has been suggested to belong to at least two different families (Natricidae and Homalopsidae) and with no fresh tissues known to be available, intractable museum specimens currently provide the only opportunity to determine this snake’s taxonomic affinity. Although our aim was to generate a target-capture dataset for these samples, to be included in a broader phylogenetic study, results were less than ideal due to large amounts of missing data, especially using the same downstream methods as with standard, high-quality samples. However, rather than discount results entirely, we used mapping methods with references and pseudoreferences, along with phylogenetic analyses, to maximize any usable molecular data from our sequencing efforts, identify the taxonomic affinity of H. periops , and compare sequencing success between fresh and degraded tissue samples. This resulted in largely complete mitochondrial genomes for five specimens and hundreds to thousands of nuclear loci (ultra-conserved loci, anchored-hybrid enrichment loci, and a variety of loci frequently used in squamate phylogenetic studies) from fluid-preserved snakes, including a specimen of H. periops from the Field Museum of Natural History collection. We combined our H. periops data with previously published genomic and Sanger-sequenced datasets to confirm the familial designation of this taxon, reject previous taxonomic hypotheses, and make biogeographic inferences for Hydrablabes . A second H. periops specimen, despite being seemingly similar for initial raw sequencing results and after being put through the same protocols, resulted in little usable molecular data. We discuss the successes and failures of using different pipelines and methods to maximize the products from these data and provide expectations for others who are looking to use DNA sequencing efforts on specimens that likely have degraded DNA. Life Science Identifier ( Hydrablabes periops ) urn:lsid:zoobank.org :pub:F2AA44 E2-D2EF-4747-972A-652C34C2C09D. 

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