Biology subjects

Magbanua, Z. V.

Publications and source records attributed to Magbanua, Z. V..

5 recordsLinked to original sources

bioRxiv2025

Population Genomics Informs Conservation Strategies for Critically Endangered Kokia Species in Hawaii

Island endemic species are particularly vulnerable to extinction due to their limited geographic ranges and small population sizes. Kokia is a genus found exclusively in the Hawaiian Islands, whose species were once major components of local forests but have experienced significant population reductions due to habitat destruction and the consequences of invasive species. Although conservation of Kokia species has been an ongoing topic for over a century, records regarding historical efforts are sparse. Recently generated genomes for each of the three extant species provide the foundation for understanding genetic diversity and population structure for future conservation work. Whole genome resequencing of K. cookei (n = 23 samples), K. drynarioides (n = 92), and K. kauaiensis (n = 45) suggests that K. drynarioides has the lowest overall diversity, reflecting propagation from a limited part of the remaining gene pool, whereas K. kauaiensis exhibits the most diversity. Diversity in the primarily graft-propagated K. cookei is higher than expected, and slightly higher than in the free-living K. drynarioides. Notably, our analyses identified a source of novel variation in K. cookei in a cultivated plant historically labeled K. drynarioides. Population structure analyses reveal a single population for K. cookei, but three groups for each of the other two species. Importantly, our analyses identify clusters of related individuals, reflected in genetic distance and clustering metrics, which provide valuable information for increasing diversity in managed populations and in ex situ conservation collections. These results provide a genomic framework for ongoing efforts in restoring and maintaining diversity in these critically endangered Hawaiian species.

genomics↗

bioRxiv2025

Comparative population genomics of relictual Caribbean island Gossypium hirsutum

Gossypium hirsutum is the worlds most important source of cotton fiber, yet the diversity and population structure of its wild forms remain largely unexplored. The complex domestication history of G. hirsutum combined with reciprocal introgression with a second domesticated species, G. barbadense, has generated a wealth of morphological forms and feral derivatives of both species and their interspecies recombinants, which collectively are scattered across a large geographic range in arid regions of the Caribbean basin. Here we assessed genetic diversity within and among populations from two Caribbean islands, Puerto Rico (n = 43, five sites) and Guadeloupe (n = 25, one site), which contain putative wild and/or introgressed forms. Using whole-genome resequencing data and a phylogenomic framework derived from a broader genomic survey, we parsed individuals into feral derivatives and truly wild forms. Feral cottons display uneven levels of genetic and morphological resemblance to domesticated cottons, with diverse patterns of genetic variation and heterozygosity. These patterns are inferred to reflect a complex history of interspecific and intraspecific gene flow that is spatially highly variable in its effects. Wild cottons in both Caribbean islands appear to be relatively inbred, especially the Guadeloupe samples. Our results highlight the dynamics of population demographics in relictual wild cottons that experienced profound genetic bottlenecks associated with repeated habitat destruction superimposed on a natural ecogeographical distribution comprising widely scattered populations. These results have implications for conservation and utilization of wild diversity in G. hirsutum.

evolutionary biology↗

bioRxiv2024

Assessment of the Genetic Diversity of Atlantic Bottlenose Dolphin (Tursiops truncatus) Strandings in the Mississippi Sound (USA)

The common bottlenose dolphin (Tursiops truncatus) is a key marine mammal species in the northern Gulf of Mexico, playing an essential role as a top predator. This study focuses on the genetic diversity and population structure of bottlenose dolphins stranded in the Mississippi Sound from 2010 to 2021. A total of 511 tissue samples (muscle, liver, lung, kidney, and brain) were collected from stranded dolphins, and mitochondrial DNA (mtDNA) was extracted for analysis. Using high-throughput sequencing methods, 417 samples were successfully amplified and sequenced, producing 386 complete mitogenomes. Genetic diversity metrics, such as nucleotide and haplotype diversity, were calculated, and population structure was inferred for both mitochondrial control region (mtCR) and whole mitogenome sequences. Using the whole mitogenome, the study identified four genetically distinct populations within the Mississippi Sound, demonstrating regional variation in dolphin populations. Notably, some individuals likely originated from populations outside the sampled area. The use of whole mitogenomes allowed for improved resolution of genetic diversity and population differentiation compared to previous studies using partial mtDNA sequences. These findings provide critical insights into the genetic structure of bottlenose dolphins in the region and highlight the value of using stranded animals for population genetic studies.

genomics↗

bioRxiv2022

A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination

Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechanism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.

genomics↗

bioRxiv2022

Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification

We present an improved ddRAD-Seq protocol for identifying single nucleotide polymorphisms (SNPs). It utilizes optimally sized restriction enzyme digestion fragments, quick acting ligases that are neutral with the restriction enzyme buffer eliminating buffer exchange steps, and adapters designed to be compatible with Illumina index primers. Library amplification and barcoding are completed in one PCR step, and magnetic beads are used to purify the genomic fragments from the ligation and library generation steps. Our protocol increases the efficiency and decreases the time to complete a ddRAD-Seq experiment. To demonstrate its utility, we compared SNPs from our protocol with those from whole genome resequencing data from Gossypium herbaceum and Gossypium arboreum. Principal component analysis demonstrated that the variability of the combined data was explained by the genotype (PC1) and methodology applied (PC2). Phylogenetic analysis showed that the SNPs from our method clustered with SNPs from the resequencing data of the corresponding genotype. Sequence alignments illustrated that for homozygous loci, more than 90% of the SNPs from the resequencing data were discovered by our method. Our analyses suggest that our ddRAD-Seq method is reliable in identifying SNPs suitable for phylogenetic and association genetic studies while reducing cost and time over known methods.

genomics↗