Hannes Becher

Biological invasions and range expansions act as natural experiments for understanding evolutionary processes at and beyond a species’ range margin. However, unlike manipulative experiments, invasions and range expansions are less genetically tractable and often involve genotypes of uncertain origin that are subject to complex evolutionary pressures. Here, we replay the earliest stages of the colonization of the widespread North American plant species Mimulus guttatus (synonym Erythranthe guttata) in the United Kingdom. We established a common garden in the invaded range using northern and southern native genotypes, allowed plants to freely mate and recruit, and quantified the genomic contribution made after five growing seasons using whole genome pooled sequencing (Pool-Seq). Despite having lower genome-wide variation, northern genotypes contributed disproportionately to the experimental population, which showed a two-fold excess of northern relative to southern ancestry, with 63%–70% northern contribution across chromosomes. The experimental population also showed extensive individual admixture, which we detected using diagnostic short sequences (k-mers) in the Pool-Seq data. Our results indicate that preadaptation of northern genotypes, despite reduced genome-wide variation, may have facilitated the successful range expansion of M. guttatus into the UK. This work also demonstrates how “invade and resequence” experiments can be used to dissect the genomic processes underlying expansion beyond a species’ native range.

Stem cell-based models resembling murine blastocysts represent a useful system to investigate subsequent developmental processes. While existing cell lines derived from epiblast and trophectoderm can be aggregated to form ‘blastoids’, some previously tested in vitro cultured extraembryonic endoderm cells tended to progress to later stages of development, so integrated inefficiently into blastoids. We attempted to capture the precursor population for extraembryonic endoderm in vitro by reproducing the mechanical environment of the in vivo peri-implantation embryo as closely as possible. We investigated expression of candidate cell adhesion receptor integrins in the blastocyst inner cell mass, and from this information we assembled an extracellular matrix intended to support primitive endoderm growth by promoting signalling pathways responsible for specification of this lineage. In addition, inner cell mass cells from blastocysts were plated on soft or stiff substrates to investigate whether an appropriate mechano-environment could enhance their self-renewal as primitive endoderm in culture. We could expand nascent primitive endoderm cell lines over several passages, which provided a reproducible, albeit short-term, system sufficient to identify some essential requirements for early primitive endoderm expansion and function.

Summary: Inherited aneuploidy is one of the most common causes of human genetic disease affecting approximately 20% of all human embryos and is the major cause of non-conception in older women. Inherited aneuploidies typically arise from meiotic chromosome segregation errors and are strongly affected by maternal age. Cohesin, a protein complex that mediates cohesion between sister chromatids, becomes depleted from oocyte chromosomes with age in mice, potentially contributing to the high rate of aneuploidy in older mouse oocytes. However, it remains unclear at which stage of oogenesis ageing affects chromatid cohesion in mice and whether ageing similarly affects cohesin in human oocytes. Here we use fluorescence in situ hybridisation to assess at which stages of oogenesis ageing alters chromatid separation in mice and in humans. We show that chromatid separation increases with age while oocytes remain dormant in primordial follicles in both mice and humans and that this effect of age on chromatid separation is detectable in fertile women of child-bearing age. Furthermore, we show that this age-dependent increase in chromatid separation is accompanied by age-dependent depletion of the acetylated SMC3-marked cohesive subpopulation of cohesin from oocytes at the dormant primordial follicle stage in both mice and humans. These data suggest that ageing impacts on oocyte chromosomes while they remain dormant in primordial follicles, and that this aspect of oocyte chromosome ageing is shared in both mice and humans. Improving our understanding of these pathways may allow strategies to slow or prevent this aspect of oocyte ageing to be developed.

Mammalian enhancers can regulate genes over large genomic distances, often skipping over other genes. Despite this, precise developmental regulation suggests that mechanisms exist to ensure enhancers only activate their correct targets. Sculpting of three-dimensional chromosome organization through cohesin-dependent loop extrusion is thought to be important for facilitating and constraining enhancer action. The boundaries of topologically associating domains (TADs) are thought to prevent enhancers acting on genes in adjacent TADs. However, there are examples where enhancers appear to act across TAD boundaries, but it has remained unclear whether a single enhancer can simultaneously activate genes in different TADs. Here we show that some Shh enhancers can activate transcription concurrently not only at Shh but also at Mnx1 located in an adjacent TAD. This occurs in the context of a chromatin conformation maintaining genes and enhancers in close proximity and is influenced by cohesin. To our knowledge, this is the first report of two endogenous mammalian genes transcribed concurrently under the control of the same enhancer and across a TAD boundary. These findings have implications for understanding the design rules of gene regulatory landscapes and are consistent with a transcription cluster model of enhancer–promoter communication.

Africa has a uniquely rich cattle diversity of ∼150 breeds comprising the Bos taurus indicus sub-species, Bos taurus taurus , and their crosses. These represent ∼23% of the global cattle population. However, high quality, representative assemblies are limited for African cattle and especially for indicine breeds. Here we built high quality de novo assemblies for five important African indigenous cattle breeds using PacBio HiFi sequencing: Lagune ( Bos taurus taurus) , Gudali, Iringa Red and Singida White ( Bos taurus indicus ), and Mpwapwa ( Bos taurus taurus x Bos taurus indicus ). These new assemblies are the most contiguous and complete African cattle assemblies produced so far, with genome sizes of 3.25 - 3.36Gb, contiguity N50s ranging from 83.59Mb to 97.87Mb and scaffold N50s from 100.30Mb to 113.37Mb. BUSCO genome completeness scores were also higher than 99.68%, indicative of highly contiguous assemblies. These improved and highly contiguous genome assemblies are consequently a valuable resource for future African and global livestock genomic studies.

A new approach to modeling the effects of Hill-Robertson interference on levels of adaptation and patterns of variability in a nonrecombining genome or genomic region is described. The model assumes a set of L diallelic sites subject to reversible mutations between beneficial and deleterious alleles, with the same selection coefficient at each site. The assumption of reversibility allows the system to reach a stable statistical equilibrium with respect to the frequencies of deleterious mutations, in contrast to many previous models that assume irreversible mutations to deleterious alleles. The model is therefore appropriate for understanding the long-term properties of nonrecombining genomes such as Y chromosomes, and is applicable to haploid genomes or to diploid genomes when there is intermediate dominance with respect to the effects of mutations on fitness. Approximations are derived for the equilibrium frequencies of deleterious mutations, the effective population size that controls the fixation probabilities of mutations at sites under selection, the nucleotide site diversity at neutral sites located within the nonrecombining region, and the site frequency spectrum for segregating neutral variants. The approximations take into account the effects of linkage disequilibrium on the genetic variance at sites under selection. Comparisons with published and new computer simulation results show that the approximations are sufficiently accurate to be useful, and can provide insights into a wider range of parameter sets than is accessible by simulation. The relevance of the findings to data on nonrecombining genome regions is discussed.

Background: Pedigrees continue to be extremely important in agriculture and conservation genetics with the pedigrees of modern breeding programmes easily comprising millions of records. The structure of such pedigrees is challenging to visualise. Being directed acyclic graphs, pedigrees can be represented as matrices. Common choices are the numerator relationship matrix, A , and the adjacency matrix T . With these matrices, the structure of pedigrees can then, in principle, be visualised via principal component analysis (PCA). However, the naive PCA of matrices for large pedigrees is challenging due to computational and memory constraints. Results: We present the open-access R package randPedPCA for rapid pedigree PCA using sparse matrices and randomised linear algebra. Our rapid pedigree PCA builds on the fact that matrix-vector multiplications with the numerator relationship matrix can be carried out implicitly using the extremely sparse inverse Cholesky factor of the numerator relationship matrix. We demonstrate the utility of randPedPCA using several simulated datasets of pedigrees and SNPs. We then demonstrate the performance of randPedPCA by analysing the pedigree of the UK Labrador Retriever breeding population of almost 1.5 million individuals. Conclusions: The structure of pedigrees can be efficiently and rapidly visualised using scatter plots of principal component scores. For large pedigrees, this is considerably faster than rendering plots of a pedigree graph.

A new approach to modeling the effects of Hill-Robertson interference on levels of adaptation and patterns of variability in a non-recombining genome or genomic region is described. The model assumes a set of L diallelic sites subject to reversible mutations between beneficial and deleterious alleles, with the same selection coefficient at each site. The assumption of reversibility allows the system to reach a stable statistical equilibrium with respect to the frequencies of deleterious mutations, in contrast to many previous models that assume irreversible mutations to deleterious alleles. The model is therefore appropriate for understanding the long-term properties of non-recombining genomes such as Y chromosomes, and is applicable to haploid genomes or to diploid genomes when there is intermediate dominance with respect to the effects of mutations on fitness. Approximations are derived for the equilibrium frequencies of deleterious mutations, the effective population size that controls the fixation probabilities of mutations at sites under selection, the nucleotide site diversity at neutral sites located within the non-recombining region, and the site frequency spectrum for segregating neutral variants. The approximations take into account the effects of linkage disequilibrium on the genetic variance at sites under selection. Comparisons with published and new computer simulation results show that the approximations are sufficiently accurate to be useful, and can provide insights into a wider range of parameter sets than is accessible by simulation. The relevance of the findings to data on non-recombining genome regions is discussed.

Enhancers in the mammalian genome are able to control their target genes over very large genomic distances, often across intervening genes. Yet the spatial and temporal specificity of developmental gene regulation would seem to demand that enhancers are constrained so that they only activate the correct target gene. The sculpting of three-dimensional chromosome organization, especially that brought about through cohesin-dependent loop extrusion, is thought to be important for facilitating and constraining the action of enhancers. In particular, the boundaries of topologically associating domains (TADs) are thought to delimit regulatory landscapes and prevent enhancers acting on genes close in the linear genome, but located in adjacent TADs. However, there are some examples where enhancers appear to act across TAD boundaries. In these cases it was not determined whether an enhancer can simultaneously activate transcription at genes in its own TAD and in an adjacent TAD. Here, using a combination of mouse developmental genetics, and synthetic activators in stem cells, we show that some Shh enhancers can activate transcription simultaneously, not only of Shh but also at a gene Mnx1 located in an adjacent TAD. This occurs in the context of a chromatin configuration that maintains both genes and the enhancers close together and is influenced by cohesin. To the best of our knowledge this is the first report of two endogenous mammalian genes transcribed simultanously under the control of the same enhancer, and across a TAD boundary. Our data have implications for understanding the design rules of gene regulatory landscapes, and are most consistent with a transcription hub model of enhancer-promoter communication.