Biology subjects

Alam, M. N. U.

Publications and source records attributed to Alam, M. N. U..

3 recordsLinked to original sources

bioRxiv2025

Mapping Animal Cultures: The Animal Culture Database (ACDB)

Socially transmitted behaviors are widespread across the animal kingdom, yet there is a lack of comprehensive datasets documenting their distribution and ecological significance. Knowledge of animal behavioral traditions could be essential for understanding many species responses to anthropogenic disturbances and further enhancing conservation efforts. Here, we introduce the first open-access database that synthesizes data on animal cultural behaviors and traditions. The Animal Culture Database (ACDB) contains descriptions of 128 behaviors including forms of vocal communication, migration, predator defense, foraging practices, habitat alteration, play, mating displays, and other social behaviors for a sample of 61 species. In addition to offering an open-access resource for researchers, educators, and conservationists, the ACDB represents a step toward recognizing the role of social learning in animal populations.

animal behavior and cognition↗

bioRxiv2025

Universal orthologs infer deep phylogenies and improve genome quality assessments

Universal single-copy orthologs are the most conserved components of genomes. Although they are routinely used for studying evolutionary histories and assessing new assemblies, current methods do not incorporate information from available genomic data. Here, we first determine the influence of evolutionary history on universal gene content in plants, fungi and animals. We find that across 11,098 genomes comprising 2,606 taxonomic groups, 215 groups significantly vary from their respective lineages in terms of their BUSCO (Benchmarking Universal Single Copy Orthologs) completeness. Additionally, 169 groups display an elevated complement of duplicated orthologs, likely as an artifact of whole genome duplication events. Secondly, we investigate the extent of taxonomic congruence in BUSCO-derived whole-genome phylogenies. For 275 suitable families out of 543 tested, sites evolving at higher rates produce at most 23.84% more taxonomically concordant, and at least 46.15% less terminally variable phylogenies compared to lower-rate sites. We find topological differences between BUSCO concatenated and coalescent trees to be marginal and conclude that higher rate sites from concatenated alignments produce the most congruent and least variable phylogenies. Finally, we show that BUSCO misannotations can lead to misrepresentations of assembly quality. To overcome this issue, we filter a Curated set of BUSCOs (CUSCOs) that provide up to 6.99% fewer false positives compared to the standard BUSCO search and introduce novel methods for comparing assemblies using BUSCO synteny. Overall, we highlight the importance of considering evolutionary histories during assembly evaluations and release the phyca software toolkit that reconstructs consistent phylogenies and reports phylogenetically informed assembly assessments.

genomics↗

bioRxiv2020

Comprehensive analysis and genome-wide association studies of biomass, chlorophyll, seed and salinity tolerance related traits in rice highlight genetic hotspots for crop improvement

Farmland is on the decline and worldwide food security is at risk. Rice is the staple of choice for over half the Earths people. To sustain current demands and ascertain a food secure future, substandard farmland affected by abiotic stresses must be utilized. For rapid crop improvement, a broader understanding of polygenic traits like stress tolerance and crop yield is indispensable. To this end, the hidden diversity of resilient and neglected wild varieties must be traced back to their genetic roots. In this study, we separately assayed 15 phenotypes in a panel of 176 diverse accessions predominantly comprised of local landraces from Bangladesh. We compiled high resolution sequence data for these accessions. We collectively studied the ties between the observed phenotypic differences and the examined additive genetic effects underlying these variations. We applied a sophisticated fixed effect model to associate phenotypes with genotypes on a genomic scale. Discovered QTLs were mapped to known genes. Candidate genes were sorted by tissue specific gene expression profiles and protein level consequence of existing polymorphisms. Our explorations yielded 17 QTLs related to various traits in multiple trait classes. 12 identified QTLs were equivalent to findings from previous studies. Integrative analysis assumes novel functionality for 21 candidate genes on multiple evidence levels. These findings will usher novel avenues for the bioengineering of high yielding crops of the future fortified with genetic defenses against abiotic stressors.

plant biology↗