- NSF-PAR ID:
- 10233346
- Date Published:
- Journal Name:
- Applications in Plant Sciences
- ISSN:
- 2168-0450
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract— The genus Solidago represents a taxonomically challenging group due to its sheer number of species, putative hybridization, polyploidy, and shallow genetic divergence among species. Here we use a dataset obtained exclusively from herbarium specimens to evaluate the status of Solidago ulmifolia var. palmeri , a morphologically subtle taxon potentially confined to Alabama, Arkansas, Mississippi, and Missouri. A multivariate analysis of both discrete and continuous morphological data revealed no clear distinction between S. ulmifolia var. palmeri and Solidago ulmifolia var. ulmifolia . Solidago ulmifolia var. palmeri ’s status was also assessed with a phylogenomic and SNP clustering analysis of data generated with the “Angiosperms353” probe kit. Neither analysis supported Solidago ulmifolia var. palmeri as a distinct taxon, and we suggest that this name should be discarded. The status of Solidago delicatula (formerly known as Solidago ulmifolia var. microphylla ) was also assessed. Both morphological and phylogenetic analyses supported the species status of S. delicatula and we suggest maintaining this species at its current rank. These results highlight the utility of the Angiosperms353 probe kit, both with herbarium tissue and at lower taxonomic levels. Indeed, this is the first study to utilize this kit to identify genetic groups within a species.more » « less
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Premise Divergence depends on the strength of selection and frequency of gene flow between taxa, while reproductive isolation relies on mating barriers and geographic distance. Less is known about how these processes interact at early stages of speciation. Here, we compared population‐level differentiation in floral phenotype and genetic sequence variation among recently diverged
Castilleja to explore patterns of diversification under different scenarios of reproductive isolation.Methods Using target enrichment enabled by the Angiosperms353 probe set, we assessed genetic distance among 50 populations of four
Castilleja species. We investigated whether patterns of genetic divergence are explained by floral trait variation or geographic distance in two focal groups: the widespreadC. sessiliflora and the more restrictedC. purpurea species complex.Results We document that
C. sessiliflora and theC. purpurea complex are characterized by high diversity in floral color across varying geographic scales. Despite phenotypic divergence, groups were not well supported in phylogenetic analyses, and little genetic differentiation was found across targeted Angiosperms353 loci. Nonetheless, a principal coordinate analysis of single nucleotide polymorphisms revealed differentiation withinC. sessiliflora across floral morphs and geography and less differentiation among species of theC. purpurea complex.Conclusions Patterns of genetic distance in
C. sessiliflora suggest species cohesion maintained over long distances despite variation in floral traits. In theC. purpurea complex, divergence in floral color across narrow geographic clines may be driven by recent selection on floral color. These contrasting patterns of floral and genetic differentiation reveal that divergence can arise via multiple eco‐evolutionary paths. -
Background Vestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM) seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed for
Escarpia spp. could be amplified in the GoM seep tubeworm,Seepiophila jonesi . Additionally, we determine if cross-amplified loci can reliably uncover the same signatures of high gene flow seen in a previous investigation ofS. jonesi .Methods Seventy-seven
S. jonesi individuals were collected from eight seep sites across the upper Louisiana slope (<1,000 m) in the GoM. Forty-eight microsatellite loci that were originally developed forEscarpia laminata (18 loci) andEscarpia southwardae (30 loci) were tested to determine if they were homologous and polymorphic inS. jonesi . Loci found to be both polymorphic and of high quality were used to test for significant population structuring inS. jonesi. Results Microsatellite pre-screening identified 13 (27%) of the
Escarpia loci were homologous and polymorphic inS. jonesi , revealing that microsatellites can be amplified within the escarpiid clade of vestimentiferans. Our findings uncovered low levels of heterozygosity and a lack of genetic differentiation amongstS. jonesi from various sites and regions, in line with previous investigations that employed species-specific polymorphic loci onS. jonesi individuals retrieved from both the same and different seep sites. The lack of genetic structure identified from these populations supports the presence of significant gene flow via larval dispersal in mixed oceanic currents. Discussion The ability to develop “universal” microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show that
S. jonesi collected from various localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen inEscarpia spp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species. -
Premise Phylogenetic studies in the Compositae are challenging due to the sheer size of the family and the challenges they pose for molecular tools, ranging from the genomic impact of polyploid events to their very conserved plastid genomes. The search for better molecular tools for phylogenetic studies led to the development of the family‐specific Compositae1061 probe set, as well as the universal Angiosperms353 probe set designed for all flowering plants. In this study, we evaluate the extent to which data generated using the family‐specific kit and those obtained with the universal kit can be merged for downstream analyses.
Methods We used comparative methods to verify the presence of shared loci between probe sets. Using two sets of eight samples sequenced with Compositae1061 and Angiosperms353, we ran phylogenetic analyses with and without loci flagged as paralogs, a gene tree discordance analysis, and a complementary phylogenetic analysis mixing samples from both sample sets.
Results Our results show that the Compositae1061 kit provides an average of 721 loci, with 9–46% of them presenting paralogs, while the Angiosperms353 set yields an average of 287 loci, which are less affected by paralogy. Analyses mixing samples from both sets showed that the presence of 30 shared loci in the probe sets allows the combination of data generated in different ways.
Discussion Combining data generated using different probe sets opens up the possibility of collaborative efforts and shared data within the synantherological community.
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Charleston, Michael (Ed.)Abstract We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. Although codon partitioning did not result in any substantial topological differences, the inclusion of flanking noncoding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of data sets increased convergence between analysis methods but did not reduce gene-tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. Although the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of data sets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution. [Artocarpus; Moraceae; noncoding sequences; phylogenomics; target enrichment.]more » « less