Biology subjects

Luqman, H.

Publications and source records attributed to Luqman, H..

7 recordsLinked to original sources

bioRxiv2026

Rapid convergence toward an agriculturalist regulatory landscape following lifestyle transition in Bornean hunter-gatherers

The transition from hunter-gatherer to agricultural lifestyles is one of the landmarks in the history of human societies, but its phenotypic and immediate molecular consequences remain poorly understood. The Punan of Borneo clarify this question: two closely related groups -- the Punan Batu, still practising mobile foraging, and the Punan Tubu, resettled and farming within the last three generations -- share deep common ancestry and no detectable post-split gene flow from agricultural neighbours, allowing the molecular consequences of lifestyle change to be separated from underlying genetic architecture. We applied a multi-omics approach across these two groups and a neighbouring agriculturalist community, the Lundayeh, profiling whole-genome sequences, blood transcriptomes, and DNA methylation arrays. Despite their shared ancestry, the resettled Punan exhibit transcriptomic and methylation profiles more similar to the agriculturalists than to their still-foraging Punan relatives, with 87% fewer differentially expressed genes and substantially fewer differentially methylated sites in the Punan Tubu versus Lundayeh comparison, and show a 77% shift towards an agricultural state. Genes associated with fat metabolism and immune function are the main components of this molecular convergence. These findings demonstrate that lifestyle transition can reshape the human transcriptome and DNA methylation on timescales far shorter than genomic evolution, with implications for understanding the biological consequences of rapid subsistence change in Indigenous communities worldwide.

evolutionary biology↗

bioRxiv2025

Soil heterogeneity and pleiotropy contribute to polygenic soil adaptation during postglacial range expansion in an alpine plant

1) Plants colonized new abiotic environments during postglacial range expansions. Little is known about whether populations adapt to different soil conditions during range expansion and, if so, which mechanisms underlie presumably polygenic adaptation. It remains unclear how pleiotropy and soil heterogeneity contribute to such adaptation. 2) We studied 43 populations of Dianthus sylvestris with characterized soil conditions along its postglacial range expansion in the Alps. We leveraged genome-wide data and variation in multiple soil variables to identify polygenic signatures of selection in soil-associated alleles using environmental association analysis, generalized dissimilarity models, and polygenic scores. 3) We found signatures of selection in 814 single nucleotide polymorphisms (SNPs) and the largest magnitude of allele frequency change in candidate SNPs associated with K, Mg, and Al. Candidate genes showed higher pleiotropy than randomly sampled genes. We found soil heterogeneity shaping the populations adaptive genetic variation in the landscape. 4) Our results suggest that populations of D. sylvestris adapted to contrasting soil chemical properties during postglacial range expansion through polygenic adaptation. Pleiotropy likely plays an important role in polygenic adaptation to novel selective pressures and soil heterogeneity is an important factor contributing to the maintenance of adaptive genetic variation.

evolutionary biology↗

bioRxiv2025

From sporulation to village differentiation: the shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia

Despite established roles in human health and profound global diversity, existing gut microbiome datasets are biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a novel gut microbiome dataset from 116 Indonesians representing a cline from transitional hunter-gatherers to rural agricultural to urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species (15%) and subspecies level (50%) novelty. Novel taxa are rare, often village-specific, and depleted for sporulation genes, revealing a direct link between bacterial physiology, transmission, prevalence and discovery. We identify a rural-to-urban cline across multiple levels of biological organisation, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, variation in diet is strongly predictive of microbiome composition, offering compelling evidence that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.

microbiology↗

bioRxiv2024

Adaptation across a precipitation gradient from niche center to niche edge

Evaluating the potential for species to adapt to changing climate relies on an appreciation of current patterns of adaptive variation and selection, which might vary in intensity across a species niche, affecting our inference of where adaptation might be most important in the future. Here we investigate the genetic basis of adaptation in Lactuca serriola, the wild relative of the common lettuce, growing along a steep precipitation gradient in Israel approaching the species arid niche limit, and used candidate loci to inform predictions of its past and future adaptive evolution. Environmental association analyses combined with generalized dissimilarity models revealed 98 candidate genes showing non-linear shifts in allele frequencies across the gradient, with a large proportion under strong directional selection near the dry niche edge. Selection acts on genes with separate suites of biological functions, specifically related to osmotic stress and phenological adjustments at the dry edge, and related to biotic interactions at the niche center. The adaptive genetic composition of populations, as inferred through polygenic risk scores, indicates that intensified selection may be the key determinant of the dry niche edge. However, inference of past and future evolutionary change suggests larger adaptive shifts in the mesic part of the range, which is most affected by climate change. Our study highlights that non-linear spatial variation in selection has implications for predicting past and future responses to climate change.

genomics↗

bioRxiv2022

Climate-induced range shifts drive adaptive response via spatio-temporal sorting of alleles

Quaternary climate fluctuations drove many species to shift their geographic ranges, in turn shaping their genetic structures. Recently, it has been argued that adaptation may have accompanied species range shifts via the "sieving" of genotypes during colonisation and establishment. However, this has not been directly demonstrated, and knowledge remains limited on how different evolutionary forces, that are typically investigated separately, interacted to jointly mediate species responses to past climatic change. Here, through whole-genome resequencing of over 1200 individuals of the carnation Dianthus sylvestris coupled with integrated population genomic and gene-environment models, we reconstruct the past neutral and adaptive landscape of this species as it was shaped by the Quaternary glacial cycles. We show that adaptive responses emerged concomitantly with the post-glacial range shifts and expansions of this species in the last 20 thousand years. This was due to the spatial sorting of adaptive alleles through time, as populations expanded out of restrictive glacial refugia into the broader and more heterogeneous range of habitats available in the present-day inter-glacial. Our results reveal a tightly-linked interplay of migration and adaptation under past climate-induced range shifts that has acted to shape the spatial patterns of adaptive genetic variation we see in the species today.

evolutionary biology↗

bioRxiv2021

Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae)

Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution - the independent evolution of similar phenotypes in different populations - provides a powerful framework to investigate the evolutionary potential of populations, the constraints of evolution, its repeatability and therefore its predictability. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae), and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling support a previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying divergence within each replicate ecotype pair, with a strikingly low amount of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by significant expression divergence are largely consistent across ecotype pairs, in strong contrast to the non-shared genetic basis. The remarkable redundancy of differential gene expression indicates a polygenic architecture for the diverged adaptive traits. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.

evolutionary biology↗

bioRxiv2020

Identifying loci under selection via explicit demographic models

Adaptive genetic variation is a function of both selective and neutral forces. To accurately identify adaptive loci, it is thus critical to account for demographic history. Theory suggests that signatures of selection can be inferred using the coalescent, following the premise that genealogies of selected loci deviate from neutral expectations. Here, we build on this theory to develop an analytical framework to identify Loci under Selection via explicit Demographic models (LSD). Under this framework, signatures of selection are inferred through deviations in demographic parameters, rather than through summary statistics directly, and demographic history is accounted for explicitly. Leveraging on the property of demographic models to incorporate directionality, we show that LSD can provide information on the environment in which selection acts on a population. This can prove useful in elucidating the selective processes underlying local adaptation, by characterising genetic trade-offs and extending the concepts of antagonistic pleiotropy and conditional neutrality from ecological theory to practical application in genomic data. We implement LSD via Approximate Bayesian Computation and demonstrate, via simulations, that LSD has i) high power to identify selected loci across a large range of demographic-selection regimes, ii) outperforms commonly applied genome-scan methods under complex demographies, and iii) accurately infers the directionality of selection for identified candidates. Using the same simulations, we further characterise the behaviour of isolation-with-migration models conducive to the study of local adaptation under regimes of selection. Finally, we demonstrate an application of LSD by detecting loci and characterising genetic trade-offs underlying flower colour in Antirrhinum majus.

evolutionary biology↗