Biology subjects

Moore-Pollard, E. R.

Publications and source records attributed to Moore-Pollard, E. R..

5 recordsLinked to original sources

bioRxiv2025

Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae

The flowering plant order Asterales exhibits a striking disparity in species richness, with >30,000 species in Asteraceae compared to <50 in its sister family Calyceraceae. To investigate the genomic basis of this imbalance, we assembled three new chromosome-level genomes, including the first for Calyceraceae, and re-annotated five additional genomes. Comparative analyses revealed exceptionally high repeat content in both Asteraceae and Calyceraceae, pervasive chromosomal rearrangements, and evidence for shared and lineage-specific WGDs. In Asteraceae, tandem and dispersed duplications disproportionately drove expansions of gene families linked to secondary metabolism and stress response, while segmental duplicates bore signatures of adaptive selection for the regulation of biosynthetic and metabolic processes. Selective pressures on flowering time regulators suggest an evolved balance between regulatory flexibility and developmental constraint in floral diversification. These patterns reveal that, beyond ancient polyploidy, small-scale duplications and selective fine-tuning of regulatory networks underpinned the ecological versatility in Asteraceae, fueling its extraordinary diversification.

genomics↗

bioRxiv2025

Phylogenomic challenges in polyploid-rich lineages: Insights from orthology inference and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae)

AO_SCPLOWBSTRACTC_SCPLOWPhylogenomic discordance is pervasive and cannot always be resolved by increasing the amount of sequencing data alone. Biological processes such as polyploidy, hybridization, and incomplete lineage sorting are major contributors to discordance and must be accounted for to avoid misleading evolutionary interpretations. To better understand how these processes influence phylogenetic reconstruction, we conducted a comprehensive phylogenomic study in the complex genus Packera. With over 90 species and varieties, 40% of which exhibit polyploidy, aneuploidy, or other cytological complexities, Packera presents significant challenges for phylogenetic reconstruction. Given these complexities, we assessed different published paralog processing methods on the resulting evolutionary relationships and phylogenetic support of this group. We then applied three of these methods to evaluate their impact on tree topology and our understanding of Packeras evolutionary history by constructing a time-calibrated phylogeny, reconstructing historical biogeography, and testing for ancient reticulation. Phylogenetic outcomes varied based on the paralog processing method used, with no method performing the best over others. Our findings highlight the large impact of orthology inference and paralog processing on phylogenomic analyses, particularly in polyploid-rich groups such as Packera, and we offer guidance on methodological impacts along with practical recommendations. We note that gaining a robust understanding of Packeras evolutionary history requires more than computational approaches alone. While technological advancements have greatly expanded our ability to analyze genomic data, effective phylogenomic research still relies on strong taxon sampling and detailed species knowledge. Without careful attention to the biological context, such as reproductive boundaries, cytological variation, ecological interactions, and historical biogeographic processes, phylogenomic studies risk misinterpreting evolutionary history and processes. By accounting for these factors, we can begin to improve the accuracy of evolutionary reconstructions and gain deeper insights into the complex history of plant diversification.

plant biology↗

bioRxiv2023

From paralogy to hybridization: Investigating causes of underlying phylogenomic discordance using the complex genus Packera (Senecioneae; Asteraceae)

Premise of the studyUnderlying discordance in phylogenomic studies is becoming more common, and the answer is not as simple as adding more data. Biological processes such as polyploidy, hybridization, and incomplete lineage sorting are main contributors to these issues and must be considered when generating phylogenies. Otherwise, interpretations of evolutionary relationships could be misleading. MethodsTo obtain a better understanding of potential gene flow and its effect on phylogenetic trees, we investigated the causes and consequences of nuclear discordance using the genus Packera to understand how they influence the phylogenetic patterns seen in this complex group. To do this, we compared the topology and support values of Packera phylogenies resulting from various paralog selection or pruning methods. We then investigated whether pruning the paralogs instead of performing a selection process affected the topology and support of our phylogeny. To investigate hybridization and its effect on species relationships in our tree, we used likelihood methods to infer phylogenetic networks to find any evidence of gene flow among species lineages in this complicated genus. Key resultsWe found that performing different paralog selection or pruning methods does impact our understanding of the evolutionary relationships within Packera, and that addressing these paralogs with more rigorous methods than the typical pipeline increases concordance within the resulting phylogenies. Additionally, investigating reticulation events within highly discordant clades showed that ancestral hybridization and reticulation events are common throughout Packera. ConclusionsInvestigating underlying biological processes by testing various methods can provide further insight into complex species relationships and levels of discordance within phylogenomic studies.

evolutionary biology↗

bioRxiv2023

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

PremiseThe sunflower family specific probe set, Compositae-1061, has enabled family-wide phylogenomic studies and investigations at lower-taxonomic levels by targeting 1,000+ genes. However, it generally lacks resolution at the genus to species level, especially in groups with complex evolutionary histories including polyploidy and hybridization. MethodsIn this study, we developed a new Hyb-Seq probe set, Compositae-ParaLoss-1272, designed to target orthologous loci in Asteraceae family members. We tested its efficiency across the family by simulating target-enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in genus Packera which has a complex evolutionary and taxonomic history. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 taxa which were previously studied using the Compositae-1061 probe set. Sequences from both probe sets were used to generate phylogenies, compare topologies, and assess node support. ResultsWe report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members. Additionally, Compositae-ParaLoss-1272 had less gene tree discordance, recovered considerably fewer paralogous sequences, and retained longer loci than Compositae-1061. DiscussionGiven the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate this new probe set will provide improved resolution and utility for studies at lower-taxonomic levels and complex groups in the sunflower family.

plant biology↗

bioRxiv2023

Resolving evolutionary relationships in the groundsels: phylogenomics, divergence time estimates, and biogeography of Packera (Asteraceae: Senecioneae)

The genus Packera belongs to the sunflower family and contains an estimated 64 species and varieties endemic to North America. Some Packera are known to hybridize or exhibit polyploidy, making it difficult to reconstruct evolutionary relationships within the group. Previous molecular phylogenetic studies of Packera employing ITS data recovered low resolution trees, providing little information on the evolutionary relationships within this complex genus. Therefore, we used next-generation sequencing data to infer nuclear and plastid phylogenies of Packera and related Senecioneae taxa. The nuclear phylogeny was calibrated to produce a timetree, then used to reconstruct the macroevolutionary history of Packera, including its historical biogeography. We then compared the reconstructed evolutionary history to previously published scenarios based on phylogenetic and geohistorical data. We found that the nuclear and plastid phylogenies were highly incongruent, with the nuclear tree presenting higher resolution than the plastid tree which had an apparent lack of plastid diversity. The nuclear tree indicated that geography may have played a major role in the evolution and taxonomic diversification of Packera. The estimated origin of Packera at approximately 19.2MY - 25.9MY (late Oligocene to early Miocene) is older than in most other studies. Nonetheless, it aligns well with previous geohistorical predictions, which suggest that speciation and diversification events in Packera were driven by changes in geography and climate in North America. Moreover, Packera likely originated in the western United States or Mexico, and subsequently diversified north and east into the rest of North America and Russia, in agreement with other studies.

plant biology↗