Biology subjects

Suissa, J. S.

Publications and source records attributed to Suissa, J. S..

3 recordsLinked to original sources

bioRxiv2023

Comparative phylogenomic analyses of SNP versus full locus datasets: insights and recommendations for researchers

PremiseIn phylogenomic analyses, no consensus exists on whether using single nucleotide polymorphisms (SNPs) or including flanking regions (full locus) is best, nor how strictly missing data should be filtered. Moreover, empirical evidence on whether SNP-only trees are suitable for downstream phylogenetic comparative methods such as divergence time estimation and ancestral state reconstructions is lacking. MethodsUsing GBS data from 22 taxa of Glycine, we addressed the effects of SNP vs. locus usage and filtering stringency on phylogenomic inference and phylogenetic comparative methods. We compared branch length, node support, and divergence time estimation across eight datasets with varying amounts of missing data and total size. ResultsOur results reveal five aspects of phylogenomic data usage: 1. tree topology is largely congruent regardless of data type or filtering parameters; 2. filtering missing data too strictly reduces the confidence in some relationships; 3. absolute branch lengths vary by two orders of magnitude between datasets; 4. data type and branch length variation have little effect on divergence time estimation; 5. phylograms significantly alter the estimation of ancestral states. DiscussionWhen conducting phylogenomic analyses we recommend not to filter datasets too strictly to minimize the risk of misleading topologies, low support, and inaccurate divergence times.

evolutionary biology↗

bioRxiv2020

Revealing the evolutionary history of a reticulate polyploid complex in the genus Isoëtes

O_LIPolyploidy and hybridization are important processes in the evolution of spore-dispersed plants. Few studies, however, focus these dynamics in heterosporous lycophytes, such as Isoetes, where polyploid hybrids are common and thought to be important in the generation of their extant diversity. We investigate reticulate evolution in a complex of western North American quillworts (Isoetes) and provide insights into the evolutionary history of hybrids, and the role of polyploidy in maintaining novel diversity. C_LIO_LIWe utilize low copy nuclear markers, whole plastomes, restriction site-associated DNA sequencing, cytology, and reproductive status (fertile or sterile) to investigate the reticulate evolutionary history of western North American Isoetes. C_LIO_LIWe reconstruct the reticulate evolutionary history and directionality of hybridization events in this complex. The presence of high level polyploids, plus frequent homoploid and interploid hybridization suggests that there are low prezygotic reproductive barriers in this complex, hybridization is common and bidirectional between similar--but not divergent--cytotypes, and that allopolyploidization is important to restore fertility in some hybrid taxa. C_LIO_LIOur data provide five lines of evidence suggesting that hybridization and polyploidy can occur with frequency in the genus, and these evolutionary processes may be important in shaping extant Isoetes diversity. C_LI

evolutionary biology↗

bioRxiv2019

Low atmospheric CO2 induces nocturnal carbon accumulation in the lycophyte genus Isoetes

Background and AimsCrassulacean Acid Metabolism (CAM) is an adaptation to increase water use efficiency in dry environments. Oddly, similar biochemical patterns occur in the submerged aquatic lycophyte genus Isoetes. It has long been assumed that CAM-like nocturnal carbon accumulation in aquatic plants is an adaptation to low daytime carbon levels in aquatic ecosystems, but this has never been directly tested. MethodsTo test this hypothesis, populations of terrestrial Isoetes engelmannii and I. tuckermanii were grown in climate-controlled chambers and starved of atmospheric CO2 during the day while pH was measured for 24-hours. Key resultsWe demonstrate that terrestrial plants exposed to low atmospheric CO2 display diel acidity cycles similar to those in both xerophytic CAM plants and submerged Isoetes. ConclusionsCO2 starvation induces CAM-like nocturnal carbon accumulation in terrestrial Isoetes, substantiating the hypothesis that carbon starvation is a selective pressure for nocturnal carbon accumulation in Isoetes. Furthermore, while aquatic carbon levels undoubtedly promote nocturnal carbon accumulation in extant Isoetes, the induction of this behavior in terrestrial plants suggests a possible earlier terrestrial evolution of this metabolism in Isoetalean ancestors in response to low atmospheric CO2 levels. We both provide support for a long-standing assumption about nocturnal carbon accumulation Isoetes as well as suggest an earlier evolution of this behavior.

plant biology↗