Biology subjects

Baird, S. J. E.

Publications and source records attributed to Baird, S. J. E..

10 recordsLinked to original sources

bioRxiv2026

diempy: fast and reference-free genome polarisation

Most ancestry-assignment methods rely on putatively pure reference panels, which are often unrealistic and bias inference. The genome polarisation algorithm diem, introduced previously, avoids reference panels by jointly inferring the polarity of common allelic states and quantifying variant diagnosticity via an expectation-maximisation procedure. Here we present diempy, an efficient python implementation of diem coupled with tools that turn polarised calls into analysis-ready outputs. diempy offers lossless VCF-to-diem BED conversion; ploidy-aware handling of individuals and chromosomes; flexible masking of sites, regions and individuals; and interactive visualisation of polarised genomes, hybrid indices, clines and ternary plots. Post-processing functions include DI thresholding, kernel smoothing, and automatic detection and run-length encoding of contiguous ancestry tracts. BED-based I/O facilitates integration with population-genomic workflows (e.g. filtering by annotation or ploidy). These features make reference-free genome polarisation with diempy practical and reproducible for studies of population structure, admixture and species barriers.

evolutionary biology↗

bioRxiv2025

Eroding species barriers: hybridising canids remain distinct around centromeres

Species barriers are shaped by variation in recombination coupled with natural selection [1-3]. Canids lost the Prdm9 gene 40-60 million years ago [4-6], stabilising low recombination at the centromeric ends [7] of acrocentric autosomes despite overall high recombination rates [6]. We predict canid recombination architecture will tend to maintain barriers to gene flow at one end of autosomes while eroding them at the other. Polarization [8] of 31 million single nucleotide variants (SNVs) across 980 canid genomes reveals elevated barriers to gene flow at pericentromeric regions between grey wolves, coyotes and golden jackals. Highly diagnostic SNVs are six-fold enriched in pericentromeric regions. The exception is the barrier to gene flow between dogs and wolves, which accumulated divergence differently from other comparisons: genomes of domesticated dogs preserve ancient genetic diversity lost in contemporary grey wolf populations, positioning them as reservoirs of ancestral alleles. Our results show that genome architecture modulates permeability of barriers to gene flow, pointing to pericentromeric regions as targets for reinforcement selection that may maintain canid taxa.

zoology↗

bioRxiv2024

Genomic regions of current low hybridisation mark long-term barriers to gene flow in scarce swallowtail butterflies

Many closely related species continue to hybridise after millions of generations of divergence. However, the extent to which current patterning in hybrid zones connects back to the speciation process remains unclear: does evidence for current multilocus barriers support the hypothesis of speciation due to multilocus divergence? We analyse whole-genome sequencing data to investigate the speciation history of the scarce swallowtails Iphiclides podalirius and I. feisthamelii, which abut at a narrow ([~]25 km) contact zone north of the Pyrenees. We first quantify the heterogeneity of effective migration rate under a model of isolation with migration, using genomes sampled across the range to identify long-term barriers to gene flow. Secondly, we investigate the recent ancestry of individuals from the hybrid zone using genome polarisation and estimate the coupling coefficient under a model of a multilocus barrier. We infer a low rate of long-term gene flow from I. feisthamelii into I. podalirius the direction of which matches the admixture across the hybrid zone and complete reproductive isolation across{approx} 33% of the genome. Our contrast of recent and long-term gene flow shows that regions of low recent hybridisation are indeed enriched for long-term barriers which maintain divergence between these hybridising sister species. This paves the way for future analysis of the evolution of reproductive isolation along the speciation continuum. Author summaryEfforts to understand how new species evolve typically approach the problem through either: 1) investigating patterns of genetic exchange across hybrid zones -- where closely related species interbreed -- or 2) modelling the demographic history of closely related species. Both approaches are capable of quantifying variation in genetic exchange, or gene flow, along the genome to identify regions of reproductive isolation; yet they leverage genetic signatures across vastly different timescales. The former exploits very recent signatures, while the latter averages long-term signatures over the history of divergence. Hence, we can contrast the genomic distribution of barriers acting on these very different timescales to test how patterns of gene flow change across the speciation continuum. Here we use this strategy to capture the speciation dynamics of a pair of hybridising papilionid butterflies. Our results show that not only are these species continuing to produce hybrids after more than a million years since the onset of divergence, but there is a significant degree of concordance between patterns of gene flow observed along the genome across time scales.

evolutionary biology↗

bioRxiv2022

diemr: Genome polarisation for detecting barriers to geneflow in R

O_LISemi-permeable barriers to geneflow in principle allow distantly related organisms to capture and exchange pre-adapted genes potentially speeding adaptation. However, describing barriers to geneflow on a genomic scale is non-trivial. C_LIO_LIWe extend classic diagnostic allele counting measures of geneflow across a barrier to the case of genome-scale data. Diagnostic index expectation maximisation (diem) polarises the labelling of bistate markers with respect to the sides of a barrier. An initial state of ignorance is enforced by starting with randomly generated marker polarisations. This means there is no prior on population or taxon membership of the genomes concerned. Using a deterministic data labelling, small numbers of classic diagnostic markers can be replaced by large numbers of markers, each with a diagnostic index. Individuals hybrid indices (genome admixture proportions) are then calculated genome wide conditioned on marker diagnosticity; within diploid, haplodiploid and/or haploid genome compartments; or indeed over any subset of markers, allowing classical cline width/barrier strength comparisons along genomes. Along-genome barrier strength hetero-geneity allows for barrier regions to be identified. Further, blocks of genetic material that have introgressed across a barrier are easily identified with high power. C_LIO_LIdiem indicates panmixis among Myotis myotis bat genomes, with a barrier separating low data quality outliers. In a Mus musculus domesticus/Mus spretus system, diem adds multiple introgressions of olfactory (and vomeronasal) gene clusters in one direction to previous demon-strations of a pesticide resistance gene introgressing in the opposite direction across a strong species barrier. C_LIO_LIdiem is a genomes analysis solution which scales over reduced representation genomics of thousands of markers to treatment of all variant sites in large genomes. While the method lends itself to visualisation, its output of markers with barrier-informative annotation will fuel research in population genetics, phylogenetics and association studies. diem can equip such downstream applications with millions of informative markers. C_LI

bioinformatics↗

bioRxiv2021

Copy number variation of the putative speciation genes in the European house mouse hybrid zone

AO_SCPLOWBSTRACTC_SCPLOWHybrid zones have long been described as "windows on the evolutionary process", and studying them has become even more important since the advance in the genome analysis tools. The hybrid zone between two subspecies of the house mouse (Mus musculus musculus and Mus m. domesticus) is a unique model speciation system to study fine scale interactions of recently diverged genomes. Here, we explore the role of gene Copy Number Variation in shaping the barrier to introgression in the hybrid zone within a previously established transect in Central Europe. The CNV of seven pre-selected candidate genes was determined via droplet-digital PCR and analyzed in the context of ~500k SNPs, with the ancestral population (i.e. musculus or domesticus) of every SNP allele previously inferred in the admixed individuals (Baird et al., in prep.). The copy numbers of five genes were clearly associated with the prevalence of either musculus or domesticus genomes across the hybrid zone. In three cases, the highest and/or outlying levels of association were observed at or very close to the annotated positions of the respective gene amplicons, demonstrating the power of our approach in confirming the reference locations of copy number variants. Notably, several other reference locations were recognized as positive outliers in the association with particular CNV genes, possibly representing the extra gene copies and/or their epistatic interaction sites.

evolutionary biology↗

bioRxiv2021

Genomic evidence of paternal genome elimination in globular springtails

AO_SCPLOWBSTRACTC_SCPLOWPaternal genome elimination (PGE) - a type of reproduction in which males inherit but fail to pass on their fathers genome - evolved independently in six to eight arthropod clades. Thousands of species, including several important for agriculture, reproduce via this mode of reproduction. While PGE is well established in some of the clades, the evidence in globular springtails (Symphypleona) remains elusive, even though they represent the oldest and most species rich clade putatively reproducing via PGE. We sequenced genomic DNA from whole bodies of Allacma fusca males with high fractions (>27.5%) of sperm to conclusively confirm that all the sperm carry one parental haplotype only. Although it is suggestive that the single haplotype present in sperm is maternally inherited, definitive genetic proof of the parent of origin is still needed. The genomic approach we developed allows for detection of genotypic differences between germline and soma in all species with sufficiently high fraction of germline in their bodies. This opens new opportunities for scans of reproductive modes in small organisms.

genomics↗

bioRxiv2020

A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridising fire-bellied toads (Bombina bombina and B. variegata)

Hybrid zones that result from secondary contact between diverged populations offer unparalleled insight into the genetic architecture of emerging reproductive barriers and so shed light on the process of speciation. Natural selection and recombination jointly determine their dynamics, leading to a range of outcomes from finely fragmented mixtures of the parental genomes that facilitate introgression to a situation where strong selection against recombinants retains large unrecombined genomic blocks that act as strong barriers to gene flow. In the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae), two anciently diverged and ecologically distinct taxa meet and produce abundant, fertile hybrids. The dense linkage map presented here enables genomic analysis of the selection-recombination balance that keeps the two gene pools from merging into one. We mapped 4,775 newly developed marker loci from bait-enriched genomic libraries in F2 crosses. The enrichment targets were selected from a draft assembly of the B. variegata genome, after filtering highly repetitive sequences. We developed a novel approach to infer the most likely diplotype per sample and locus from the raw read mapping data, which is robust to over-merging and obviates arbitrary filtering thresholds. Large-scale synteny between Bombina and Xenopus tropicalis supports the resulting linkage map. By assessing the sex of late-stage F2 tadpoles from histological sections, we also identified the sex-determining region in the Bombina genome to 7 cM on LG5, which is homologous to X. tropicalis chromosome 5, and inferred male heterogamety, suggestive of an XY sex determination mechanism. Interestingly, chromosome 5 has been repeatedly recruited as a sex chromosome in anurans with XY sex determination.

evolutionary biology↗

bioRxiv2019

Widespread introgression of the Mus musculus musculus Y chromosome in Central Europe

According to Haldanes rule, sex chromosomes should harbour more incompatibilities than autosomes. As a consequence, transmission of sex-linked genes across a genetic barrier is expected to be hampered. A remarkable example of a contradiction of this assumption was reported from the hybrid zone between two house mouse subspecies in western Czechia and south-eastern Germany where unidirectional east[->]west Y chromosome introgression was observed. Since the phenomenon was coupled with differences in sex ratio, this was hypothesised to be caused by a genetic conflict between sex-specific genes on sex chromosomes or elsewhere in the genome. Here we capitalise on a large material consisting of almost 7500 mice collected across a vast area from the Baltic Sea to the Alps embracing a ~900 km long portion of the zone with the aim to (i) detect its exact course and (ii) reveal the extent and pattern of the Y chromosome introgression in Central Europe. We show that the path of the zone is quite tortuous even at the global scale and the introgression is rather a rule than an exception. We also show that although sex ratio perturbations described in our previous study appear also in other introgression areas, they may not be ubiquitous. Finally, we reveal that although not all Y chromosome types are associated with the introgression, it is not restricted to a single winning haplotype.

evolutionary biology↗

bioRxiv2019

Intensity of infection with intracellular Eimeria spp. and pinworms is reduced in hybrid mice compared to parental subspecies

The longstanding impression that hybrid mice are more highly parasitized and therefore less fit than parentals persists despite the findings of recent studies. Working across a novel transect of the European House Mouse hybrid zone we assessed intracellular infections by Eimeria, a parasite of high pathogenicity, and infections by pinworms, assumed to be less pathogenic. For Eimeria we found lower intensities in hybrid hosts than in parental mice but no evidence of lowered probability of infection in the centre of the hybrid zone. This means ecological and epidemiological factors are very unlikely to be responsible for the reduced load of infected hybrids. Focussing on parasite intensity (load in infected hosts) we also corroborated reduced pinworm loads reported for hybrid mice in previous studies. In addition we questioned whether differences in body condition during infection would indicate different impacts on hybrid vs. parental hosts health. We couldnt show such an effect. We conclude that intensity of diverse parasites, including the previously unstudied Eimeria, is reduced in hybrid mice compared to parental subspecies. We suggest caution in extrapolating this to differences in hybrid host fitness in the absence of, for example, evidence for a link between parasitemia and health.

evolutionary biology↗

bioRxiv2019

Sperm quality parameters are increased and asymmetric in house mouse hybrids

Spermatogenesis is a tuned cascade of processes producing sperm; impairment of any phase of this process can affect fitness of males. The level of impairment can be pronounced in hybrids between genetically divergent populations. To explore the effect of hybridization on sperm quality we produced F1 hybrids from 29 wild derived strains of two house mouse subspecies, M. m. musculus and M. m. domesticus, which diverged 0.5 MY ago. The measured sperm quality traits did not significantly differ between intrasubspecific crosses. Effects of intersubspecific hybridization were dependent on sperm trait and cross direction. The proportion of sperm head abnormalities was increased in F1 intersubspecific hybrids. The frequency of dissociated sperm heads was increased in the M. m. musculus x M. m. domesticus ([female]x[male]) F1 but decreased in M. m. domesticus x M. m. musculus ([female]x[male]) F1 hybrids, with the difference in medians being more than 180%. We deduce that the dissociated sperm heads trait is associated with the X chromosome and modulated by interaction with the Y chromosome; nevertheless, the high proportion of unexplained variance (55.46 %) suggests the presence of polymorphic autosomal interactions. The reported differences in sperm quality between cross types may be highly relevant to male fitness in zones of secondary contact between the two subspecies. The cross direction asymmetry in frequency of dissociated sperm heads should favour the M. m. musculus Y chromosome. This is consistent with the spread of the M. m. musculus Y chromosome in nature across the hybrid zone between these two subspecies.

evolutionary biology↗