Biology subjects

Rahnamae, N.

Publications and source records attributed to Rahnamae, N..

6 recordsLinked to original sources

bioRxiv2026

A reusable neural approach to recombination mapping for model and non-model species

Pedigree and crossing experiments can measure crossovers directly and provide the gold standard for recombination mapping, but their cost restricts fine-scale recombination mapping to only a few species. Patterns of linkage disequilibrium (LD) provide an alternative statistical approach for inferring variation in recombination along the genome. LD, however, is confounded by many evolutionary factors, such as demographic changes, life-history traits, and genomic structural variation. We present fastrho, a state-space neural-network estimator trained across a range of simulation-based priors. In simulated bottleneck and expansion scenarios, the fixed checkpoint recovered local map shape without target-specific retraining; comparisons with pyrho used lookup tables constructed under the simulation-generating history. We further evaluated generalizability across multiple species and, to account for additional confounders not represented in the initial training data, designed specialized models for inference in selfing plants, structured Arabis populations, and large- malaria-vector populations. A major biological application of the mosquito model was the construction of a five-arm recombination atlas spanning 13 Ag3 populations, providing a detailed view of recombination-rate variation across the dataset. Recombination maps inferred from Ag3 pedigrees provided independent, coarse-scale support for this atlas. Finally, analyses of resistance loci and redpoll bird supergenes demonstrate how selection and structural variation influence LD. Throughout our study, we use experimental maps for independent validation. Together, our results establish fastrho as a flexible framework for robust recombination mapping across diverse biological systems.

evolutionary biology↗

bioRxiv2026

Species-specific drivers of genetic diversity are decoupled from plant community diversity

Understanding how habitat connectivity shapes biodiversity remains a major ecological challenge. In particular, the roles of connectivity and ecological heterogeneity on co-variation in plant species diversity and intraspecific genetic diversity is not understood. We combined species distribution modelling, resistance-to-movement mapping, landscape connectivity analysis and population genomics to investigate diversity patterns in three wet meadow herbs, Scorzonera humilis, Oenanthe peucedanifolia and Lychnis flos-cuculi, and their surrounding plant communities. Genetic diversity patterns differed strongly among co-occurring species. Connectivity metrics explained genetic diversity only in O. peucedanifolia, and environmental drivers of genetic diversity were highly species specific. Importantly, genetic diversity changed with the presence of some species in the community, but it was consistently unrelated to indicators of local plant community diversity. Overall, the processes shaping within-species biodiversity may differ fundamentally from those structuring habitat connectivity and plant species communities, with important implications for conservation.

ecology↗

bioRxiv2026

Evolutionary transitions to self-fertilization influence the inference of introgression history

The availability of polymorphism data and statistical inference methods allows documenting the widespread occurrence of introgression and hybridization across the tree of life. However, these methods are primarily optimized for outcrossing species without generation overlap or seed banking, thereby ignoring the consequences of life-history traits (and their evolution) on genome-wide polymorphism patterns. We investigate how a transition from outcrossing to selfing, a common feature of plant species, may affect the inference of introgression history. We simulate six demographic models with different histories of gene flow under two mating-system scenarios: a constant high selfing rate and a transition-to-selfing scenario. Using an Approximate Bayesian Computation framework with random forests, we compare model choice based on genotypic summary statistics alone and in combination with coalescent statistics derived from coalescent tree sequences. Including coalescent information substantially improves model classification, especially for distinguishing secondary contact and continuous gene flow. Cross-classification of pseudo-observed datasets shows that ignoring a transition to selfing can lead to false demographic inferences, with transition-to-selfing data often misclassified as ancient gene flow or secondary contact when analyzed under a constant selfing model. We then apply this inference framework to genomic data from Arabis nemorensis and Arabis sagittata, two predominantly selfing species with evidence for post-split hybridization. Our analyses reveal a likely transition to selfing roughly 470,000-890,000 years ago, and a likely continuous level of gene flow after the species split. The latter results lead us to revisit our previous scenario of gene flow due to secondary contact between species inferred under constant selfing. Changes in mating systems and, by extension, life-history traits can therefore bias inference about introgression if they are not explicitly modeled. Tree-sequence-based coalescent statistics provide useful information for inferring complex demographic histories that involve both gene flow and transitions to selfing.

evolutionary biology↗

bioRxiv2025

The complex molecular basis of enhanced stress resilience in extreme drought-tolerant Arabis grassland species

Background and AimsPlant species in competitive meadows must tolerate extreme stress, yet the mechanisms underlying resilience remain poorly understood. Arabis nemorensis, an endangered selfing species of Euro- pean floodplain grasslands, experiences both flooding and drought and hybridizes with its close relative, A. sagittata. We investigated how these species differ in drought survival and the molec- ular basis of their responses. MethodsSympatric lineages of A. nemorensis and A. sagittata were compared in a controlled dry-down experiment, complemented by transcriptome and small RNA profiling, and machine-learning anal- ysis of cis-regulatory motifs. Key ResultsBoth species wilted at 5% soil moisture, but A. sagittata recovered more effectively (90% vs. 50%). This difference was not explained by a major QTL, suggesting a polygenic basis. Transcrip- tome profiling revealed stronger induction in A. sagittata (6,359 vs. 5,571 differentially expressed genes). Small RNA analysis identified species-specific regulation of miR408, a conserved drought regulator. Machine-learning identified 307 sequence motifs predictive of stress-responsive expres- sion, with motif distributions indicating distinct regulatory networks. ConclusionsThis study reveals the polygenic and regulatory complexity underlying divergent drought resili- ence strategies in the closely related species thriving in grassland environments. Arabis nemorensis and its close relative A. sagittata co-occur in a floodplain meadow exposed to flooding and drought. In dry-down experiments, A. sagittata recovered more effectively than A. nemorensis. Transcriptome and small RNA analyses revealed stronger stress responses in A. sagittata, including regulation of miR408. These differences result from different regulatory networks and have a polygenic basis.

plant biology↗

bioRxiv2025

Contemporary hybridization among Arabis floodplain species creates opportunities for adaptation

Hybridization between closely related species is increasingly recognized as a major source of biodiversity. Yet, whether it can create advantageous trait combinations while purging harmful alleles remains unknown. We studied Arabis nemorensis and A. sagittata, two endangered species that currently hybridize in a single hotspot. We measured 22 phenotypic traits and mapped their genetic basis in an F2 population, after generating high quality genome assemblies for both species. In total, 58 QTLs were identified for 20 traits, with additive and dominance effects best fitting Gaussian and logistic distributions, respectively. Six large-effect QTLs were linked to significant hybrid fitness loss. Two genomic regions showed strong transmission bias favoring A. sagittata alleles, potentially accelerating their introgression. However, 48% of QTLs were unlinked to reduced fitness or segregation distortion and may generate genotypes exceeding parental performance. Notably, a major QTL affecting flowering time explained 23% of phenotypic variation and implicated TFL1 as a candidate gene for life history adaptation. While most QTLs lacked overlap with past selective sweeps, indicating limited recent positive selection, 5 of 7 QTLs for rosette size overlapped with sweep signatures in the parental lineages. Overall, our findings offer unique insights into incipient stages of hybridization.

evolutionary biology↗

bioRxiv2024

Barcoding-inferred biodiversity of shallow-water Indo-Pacific demosponges

AimThe Indo-Pacific is the worlds largest marine biogeographic region. It is characterised by different degrees of connectivity among its subregions, and harbours the majority of demosponge species currently known to science. Comparisons between several regional sponge faunas have been undertaken in the past, mostly based on identifying the sponge species morphologically. The Sponge Barcoding Project, in tandem with other regional DNA taxonomy campaigns, provides one of the largest DNA-based taxonomic data collections from sponges of the Indo-Pacific. Here, we utilise the sponge barcoding data in the largest molecular biodiversity study of sponges to date, which reveals patterns of shallow-water demosponge faunal connectivity, endemism, and distribution in the Indo-Pacific with a level of resolution unavailable in prior morphology-based studies. LocationDemosponge specimens in this study cover 13 marine provinces of the Indo-Pacific, from the Red Sea to South East Polynesia. MethodsWe classified demosponge barcodes using the ribosomal subunit (28S rDNA) of 1,910 sponge samples into molecular operational taxonomic units (MOTUs). MOTU composition of the 13 marine provinces was compared based on Jaccard and Sorenson dissimilarities, and other biodiversity indices. ResultsOur data corroborated high levels of endemism among demosponges. Faunal overlaps were revealed between the Red Sea and the Gulf, which displayed relatively small connectivity with other marine provinces of the Western Indian Ocean. In the Western Indian Ocean, we observed a strong faunistic boundary to the Central Indo-Pacific. The Polynesian sponge faunas were comparatively isolated marine provinces of the Central Indo-Pacific. Main conclusionsOur data corroborate case studies on sponges that generally reject the presence of cosmopolitan or otherwise widespread sponge species, instead revealing high levels of regional endemism. This is consistent with similar observations and hypotheses in other marine invertebrates. Connectivity among Indo-Pacific marine provinces differs for demosponges in many aspects from that of other marine taxa, such as corals and fishes, probably due to their shorter pelagic larval phase.

zoology↗