Biology subjects

Bobo, D.

Publications and source records attributed to Bobo, D..

5 recordsLinked to original sources

bioRxiv2025

First Genomic Insights into an Aeshnidae Dragonfly: Unveiling the Genome of a Holarctic Species, Aeshna juncea

Temperature oscillations in the Arctic may present a unique opportunity to study how insect species respond to such changes. Aeshna juncea, a Holarctic species of the family Aeshnidae thrives in this environment; molecular adaptations that allow it to survive in the Arctic have yet to be evaluated. Here, we present the first assembled and annotated draft genome assembly and annotation of A. juncea. The assembly is both highly contiguous and complete. This resource is presented and used here to provide further evidence that transposons and unclassified repetitive elements are a major driver behind genome size variation in Odonata and show that the effective population size of A. juncea populations from Alaska went through bottlenecks during the most recent ice age. We believe this genome will be an important resource in understanding how species like Aeshna juncea survive in Arctic habitats.

evolutionary biology↗

bioRxiv2025

The information content of species: formal definitions of pangenome complexity track with bacterial lifestyle

Genes and other genomic elements have variable presence absence patterns across most bacterial species. Pangenome fluidity is often invoked to measure this genome flux. Fluid pangenomes contain genes found only in subsets of species strains. Tighter pangenomes contain more genes that define a shared core. Species definitions are often tied to this pangenome diversity. In any global comparative framework, pangenomes must be calculated across all known species. But defining pangenomes is fraught with computational and biological challenges, requiring assembly, annotation, alignment, and phylogenetics of millions of orthologs. We offer an alternate view that de-centers the gene and emphasizes the raw information content of sequences. Information is data that reduces uncertainty. Tight pangenomes, with elements repeated across every strain in a species ensemble, contain more complete information. In contrast, fluid pangenomes have more uncertainty, higher complexity, and higher information diversity. Bacterial lifestyle has been shown to drive this information diversity. For example, challenging environments often increase information diversity by encouraging the accrual of auxiliary genes. Here, we employ agile complexity metrics to quantify this increase. Ensembles of free-living, motile, and non-pathogenic species have high genomic complexity. Ensemble complexity decreases in species bound to specific hosts. Because we eliminate annotation and alignment, our method is fast enough to evaluate species across all known bacterial genomes. The approach democratizes classification and our results highlight how broad the term "species" has become.

genomics↗

bioRxiv2019

Exome Sequencing Reveals a High Prevalence of BRCA1 and BRCA2 Founder Variants in a Diverse Population-Based Biobank

Pathogenic variants in BRCA1 and BRCA2 (BRCA1/2) lead to increased risk of breast, ovarian, and other cancers, but most variant positive individuals in the general population are unaware of their risk, and little is known about the prevalence of pathogenic BRCA1/2 variants in non-European populations. We investigated BRCA1/2 prevalence and impact using exome sequencing and electronic health record (EHR) data from 30,223 adult participants of the BioMe Biobank in New York City. There were 218 (0.7%) individuals harboring expected pathogenic variants, resulting in an overall prevalence of 1 in 139. In sub-populations defined by genetic ancestry, the highest prevalence was in individuals of Ashkenazi Jewish (AJ; 1 in 49), Filipino and Southeast Asian (1 in 81), and Non-AJ European (1 in 103) descent. Among 218 variant positive individuals, 112 (51.4%) harbored known founder variants: 80 had AJ founder variants (BRCA1 c.5266dupC and c.68_69delAG, and BRCA2 c.5946delT), 7 had a Puerto Rican founder variant (BRCA2 c.3922G>T), and 25 had one of 19 other founder variants. Non-European populations were more likely to harbor BRCA1/2 variants that were not classified in ClinVar, or that had uncertain or conflicting evidence for pathogenicity. Within mixed ancestry populations, such as Hispanic/Latinos with genetic ancestry from Africa, Europe, and the Americas, there was a strong correlation between the proportion African genetic ancestry and the likelihood of harboring a BRCA1/2 variant with uncertain or conflicting evidence for pathogenicity. Based on EHR and participant questionnaire data, [~]28% of variant positive individuals had a personal history, and [~]45% a personal or family history of BRCA1/2-associated cancers. Approximately 27% of variant positive individuals had evidence of prior clinical genetic testing for BRCA1/2. However, individuals with AJ founder variants were twice as likely to have had a clinical test (38%) than those with other pathogenic variants (19%). These findings deepen our knowledge about BRCA1/2 variants and associated cancer risk in diverse populations, indicate a gap in knowledge about potential cancer-related variants in non-European populations, and suggest that genomic screening in diverse patient populations may be an effective tool to identify at-risk individuals.

genomics↗

bioRxiv2018

Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics

ABSTARCTDespite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early Medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data was consistent with the proposed long-distance migration from Pannonia to Northern Italy.

genetics↗

bioRxiv2017

Fine-scale human population structure in southern Africa reflects ecogeographic boundaries

Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until about 2,000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for more than one hundred South Africans from the =Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking =Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu-speakers, approximately 14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.\n\nData depositionData files are freely available on the Henn Lab website: http://ecoevo.stonybrook.edu/hennlab/data-software/\n\nSummaryDistinct, spatially organized ancestries demonstrate fine-scale population structure in southern Africa, implying a more complex history of the KhoeSan than previously thought. Southern KhoeSan ancestry in the Nama and =Khomani is shared in a rim around the Kalahari Desert. We hypothesize that there was recent migration of pastoralists from East Africa into southern Africa, independent of the Bantu-expansion, but the spread of pastoralism within southern Africa occurred largely by cultural diffusion.

genetics↗