Biology subjects

Fama, N. M.

Publications and source records attributed to Fama, N. M..

3 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↗

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↗