Biology subjects

Sinn, B. T.

Publications and source records attributed to Sinn, B. T..

7 recordsLinked to original sources

bioRxiv2026

Unexpected excess heterozygosity in a threatened, mycoheterotrophic, self-pollinating orchid

Self-fertilization results in reduction of heterozygosity over time, accelerated by small population sizes, restricted ranges, and fragmented habitats. Yet some species maintain heterozygosity despite these factors. One is Corallorhiza bentleyi, a threatened, mycoheterotrophic, self-pollinating orchid restricted to Virginia and West Virginia, USA. Reduced representation sequencing was employed across five of the ~12 known localities of C. bentleyi, including representatives of sister species C. involuta from Mexico, to quantify patterns of population structure and genomic diversity. Surveys of C. bentleyi revealed a predominance of the cleistogamous (closed-flowered) growth form. Differentiation was observed between the two species but with weak population structure in C. bentleyi. Surprisingly, excess heterozygosity and negative inbreeding were recovered in both species, counter to expectations. Analyses provided evidence against bioinformatic artifacts (collapsed paralogs), small-sample bias (Robertson effect), and accumulation of mutations along chromosomes due to low recombination associated with selfing (Meselson effect) as explanations for excess heterozygosity. Demographic analyses favored a model of post-glacial divergence among C. bentleyi and C. involuta lacking bottlenecks. Finally, simulations under alternative selection scenarios favored models of overdominance vs. those of negative frequency dependent selection. It was concluded that overdominance, namely selection against selfed homozygotes, is the most likely explanation for elevated heterozygosity in C. bentleyi. Conservation concerns are discussed in light of these findings and the threats of extinction for one of the most vulnerable orchid species in North America.

evolutionary biology↗

bioRxiv2025

Organellar data sets confirm overall angiosperm relationships if problematic RNA-edit sites are accounted for in mitochondrial genomes

PremisePlastid-based data sets continue to play a major role in our understanding of early flowering-plant relationships, although organellar genomes of major lineages outside the monocots and eudicots remain under-sampled. A tendency of mitochondrial RNA-edit sites to mislead phylogenetic analysis in mixed transcriptomic/genomic data sets needs attention in angiosperm-wide studies, which only rarely consider mitochondrial genomes. MethodsWe compared mitochondrial- vs. plastid-based phylogenomic inferences, examined the effect of removing putative RNA-edit sites from mitochondrial data, and performed combined organellar analysis (plastid plus filtered mitochondrial genomes). We expanded taxon sampling for multiple angiosperm lineages for phylogenomic analysis using both organellar genomes, representing several poorly sampled lineages (in particular Degeneriaceae, Trimeniaceae) with smaller (few-gene) data sets. ResultsPlastid-based inferences recover well-supported relationships that align with and build upon previous studies, and recover well-supported internal relationships for two ANA-grade families (Hydatellaceae, Trimeniaceae) sampled for nearly all species. By contrast, unfiltered mitochondrial inferences of angiosperm phylogeny are generally poorly supported, and recover anomalous relationships compared to plastid-based inferences. However, removing putative mitochondrial RNA-edit sites dramatically reduces inter-organellar conflict and improves overall branch support. ConclusionsWe accounted for phylogenomic discordance between the two organellar genomes regarding overall angiosperm-wide relationships and filled in taxonomic gaps (poorly sampled lineages). Removing RNA edit sites substantially improves congruence in interorganellar inferences by effectively correcting a systematic bias in mitochondrial data. Uncertain relationships persist among five major mesangiosperm lineages in plastid-based inferences, but a clade comprising Chloranthales, Ceratophyllales and eudicots is well supported by filtered mitochondrial data.

plant biology↗

bioRxiv2023

A case study of Whirly1 (WHY1) evolution in the angiosperms: altered sequence, splicing, and expression in a clade of early-transitional mycoheterotrophic orchids

The plastid-targeted transcription factor Whirly1 (WHY1) has been implicated in chloroplast biogenesis, plastid genome stability, and fungal defense response, which together represent characteristics of interest for the study of autotrophic losses across the angiosperms. While gene loss in the plastid and nuclear genomes has been well studied in mycoheterotrophic plants, the evolution of the molecular mechanisms impacting genome stability are completely unknown. Here we characterize the evolution of WHY1 in four early-transitional mycoheterotrophic orchid species in the genus Corallorhiza by synthesizing the results of phylogenetic, transcriptomic, and comparative genomic analyses with WHY1 genomic sequences sampled from 21 orders of angiosperms. We found an increased number of non-canonical WHY1 isoforms assembled from all but the greenest Corallorhiza species, including intron retention in some isoforms. Within Corallorhiza, phylotranscriptomic analyses revealed the presence of tissue-specific differential expression of WHY1 in only the most photosynthetically capable species and a coincident increase in the number of non-canonical WHY1 isoforms assembled from fully mycoheterotrophic species. Gene- and codon-level tests of WHY1 selective regimes did not infer significant signal of either relaxed selection or episodic diversifying selection in Corallorhiza, but did so for relaxed selection in the late-stage full mycoheterotrophic orchids Epipogium aphyllum and Gastrodia elata. Taken together, this study provides the most comprehensive view of WHY1 evolution in angiosperms to date. Our analyses reveal that splicing alteration and decreased expression of WHY1 are coincident with deceased plastome stability in a group of early-transitional mycoheterotrophic orchids and that these changes may precede the selective shifts observed in late-stage mycoheterotrophic species.

evolutionary biology↗

bioRxiv2020

ISSRseq: an extensible, low-cost, and efficient method for reduced representation sequencing

O_LIThe capability to generate densely sampled single nucleotide polymorphism (SNP) data is essential in diverse subdisciplines of biology, including crop breeding, pathology, forensics, forestry, ecology, evolution, and conservation. However, the wet-lab expertise and bioinformatics training required to conduct genome-scale variant discovery remain limiting factors for investigators with limited resources. C_LIO_LIHere we present ISSRseq, a PCR-based method for reduced representation of genomic variation using simple sequence repeats as priming sites to sequence inter simple sequence repeat (ISSR) regions. Briefly, ISSR regions are amplified with single primers, pooled, used to construct sequencing libraries with a commercially-available kit, and sequenced on the Illumina platform. We also present a flexible bioinformatic pipeline that assembles ISSR loci, calls and hard filters variants, outputs data matrices in common formats, and conducts population analyses using R. C_LIO_LIUsing three angiosperm species as case studies, we demonstrate that ISSRseq is highly repeatable, necessitates only simple wet-lab skills and commonplace instrumentation, is flexible in terms of the number of single primers used, and can generate genomic-scale variant discovery on par with existing RRS methods which require more complex wet lab procedures. C_LIO_LIISSRseq represents a straightforward approach to SNP genotyping in any organism, and we predict that this method will be particularly useful for those studying population genomics and phylogeography of non-model organisms. Furthermore, the ease of ISSRseq relative to other RRS methods should prove useful to those lacking advanced expertise in wet lab methods or bioinformatics. C_LI

genomics↗

bioRxiv2020

Integrating genetics, morphology, and fungal host specificity in conservation studies of a vulnerable, selfing, mycoheterotrophic orchid

Mycoheterotrophic plants derive most or all carbon and nutrients from fungal partners and represent poorly understood components of forest biodiversity. Many are rare or endangered yet can be ecological indicators of forest ecosystem function due to their often highly specific fungal host requirements. One such species is the IUCN red-listed ( vulnerable), fully mycoheterotrophic orchid, Corallorhiza bentleyi. This recently described species is among the rarest plants in Appalachia, known from five counties in Virginia and West Virginia, USA. The species has a restricted range, small population size, and is self-pollinating. Here we take an integrative approach to conservation genetic assessment in C. bentleyi using floral morphometrics, simple-sequence repeats, and fungal host DNA to characterize variation within and among sampling localities. Morphology reveals some differentiation among individuals from six sampling localities. Surprisingly, most genetic variation is found within localities, contra to the expectation for a selfing species. Fungal host DNA reveals extreme specificity upon a few genotypes of a single ectomycorrhizal host species, Tomentella fuscocinerea, across all localities. We discuss the conservation implications of morphological, genetic, and symbiotic diversity in this vulnerable species, and recommend additional assessment of conservation status based on: an obligate reproductive mode of selfing, preventing benefits of outcrossing among genetically non-identical individuals; extreme host specificity, severely restricting niche space; and highly fragmented habitat under threat from anthropogenic disturbance. This study underscores the importance of integrative conservation assessment, analyzing multiple data sources, and reveals patterns not readily apparent from census-based assessments alone.

evolutionary biology↗

bioRxiv2020

Genetic, morphological, and niche variation in the widely hybridizing Rhus integrifolia-Rhus ovata species complex.

Hybridization and introgression are common processes among numerous plant species that present both challenges and opportunities for studies of species delimitation, phylogenetics, taxonomy, and adaptation. Rhus integrifolia and R. ovata are two ecologically important shrubs native to the southwestern USA and Mexico, and are known to hybridize frequently, but the morphological, genetic, and ecological implications of hybridization in these species are poorly studied on a broad geographic scale. Analyses were conducted using leaf morphology, genetic variation of plastid and nuclear loci, and species distribution models for both species and their putative hybrid introgressants across 19 localities in California and Arizona, USA. These analyses revealed evidence for morphological and genetic distinction among localities comprising putative parental species, but a high degree of morpho-genetic intermediacy among localities with putative hybrids. Comparison of morphological and genetic population structure among localities revealed evidence for putative local adaptation or widespread phenotypic plasticity. Multiple regression models identified a weak but statistically significant negative association between leaf area and precipitation. Finally, species distribution modeling inferred northward range shifts over time, with both species predicted to occupy more coastal regions in the future, possibly increasing the frequency of hybridization among them. These findings underscore the importance of integrative assessment of multiple data sources in the study of hybridizing species and highlight the Rhus integrifolia-ovata complex as a powerful model for investigating the adaptive implications of hybridization.

evolutionary biology↗

bioRxiv2019

Degradation of key photosynthetic genes in the critically endangered semi-aquatic flowering plant Saniculiphyllum guangxiense (Saxifragaceae)

BackgroundPlastid gene loss and pseudogenization has been widely documented in parasitic and mycoheterotrophic plants, which have relaxed selective constraints on photosynthetic function. More enigmatic are sporadic reports of degradation and loss of important photosynthesis genes in lineages thought to be fully photosynthetic. Here we report the complete plastid genome of Saniculiphyllum guangxiense, a critically endangered and phylogenetically isolated plant lineage, along with genomic evidence of reduced chloroplast function. We also report 22 additional plastid genomes representing the diversity of its containing clade Saxifragales, characterizing gene content and placing variation in a broader phylogenetic context. ResultsWe find that the plastid genome of Saniculiphyllum has experienced pseudogenization of five genes of the NDH complex (ndhA, ndhB, ndhD, ndhF, and ndhK), previously reported in flowering plants with an aquatic habit, as well as the more surprising pseudogenization of two genes more central to photosynthesis (ccsA and cemA), contrasting with strong phylogenetic conservatism of plastid gene content in all other sampled Saxifragales. These genes participate in photooxidative protection, cytochrome synthesis, and carbon uptake. Nuclear paralogs exist for all seven plastid pseudogenes, yet these are also unlikely to be functional. ConclusionsSaniculiphyllum appears to represent the greatest degree of plastid gene loss observed to date in any fully photosynthetic lineage, yet plastid genome length, structure, and substitution rate are within the variation previously reported for photosynthetic plants. These results highlight the increasingly appreciated dynamism of plastid genomes, otherwise highly conserved across a billion years of green plant evolution, in plants with highly specialized life history traits.

evolutionary biology↗