Biology subjects

Streisfeld, M. A.

Publications and source records attributed to Streisfeld, M. A..

7 recordsLinked to original sources

bioRxiv2024

The genomic outcomes of hybridization vary over time within a monkeyflower radiation

The accumulation of genetic differences through time can lead to reproductive isolation between populations and the origin of new species. However, hybridization between emerging species can occur at any point before isolation is complete. The evolutionary consequences of this hybridization may vary depending on when it occurred. If hybridization occurred later during the process, when ecological and genetic differences have accumulated between diverging lineages, low hybrid fitness can result in selection against gene flow. If hybridization occurred earlier, when barriers present were too weak to limit introgression, then hybridization can lead to genetic swamping. Alternatively, adaptive introgression can occur at any point during speciation. Thus, by understanding the history and genomic consequences of hybridization at different points along the speciation continuum, we can begin to understand how variation present within populations translates to divergence between species. Here, we identified the genomic signals of introgressive hybridization at different points during the divergence of two monkeyflower taxa endemic to the Channel Islands of California. We found that both ancient and recent introgression have shaped their genomes, but the impacts of selection on this foreign material varied. There was no signal of selection against ancient introgression, but we did find strong evidence for selection against recent introgression, potentially because there are more reproductive barriers in place now, reducing fitness in recent hybrids. Thus, this study reveals that hybridization can occur at multiple points throughout the divergence history of a radiation, but the processes shaping genome wide levels of introgression can change over time.

evolutionary biology↗

bioRxiv2024

Inheritance of somatic mutations can affect fitness in monkeyflowers

Plants possess the unique ability to transmit mutations to progeny that arise both through meiotic and mitotic (somatic) cell divisions. This is because the same meristem cells responsible for vegetative growth also generate gametes for sexual reproduction. Despite the potential for somatic mutations to be an additional source of genetic variation for adaptation, their role in plant evolution remains largely unexplored. We performed multiple experiments in the bush monkeyflower (Mimulus aurantiacus) to determine the fitness effects of somatic mutations inherited across generations. We tracked somatic mutations transmitted to progeny by generating self-pollinations within a flower (autogamy) or between stems of the same plant (geitonogamy). Autogamy and geitonogamy lead to different segregation patterns of somatic mutations among stems, making it possible to compare average fitness due to somatic variants. We found increased fecundity following autogamy, as well as significant impacts on drought tolerance, survival, and biomass. The variance in fitness was also greater following autogamy, consistent with the effects of somatic mutations impacting fitness. Effect sizes were small, but predictable, given that M. aurantiacus is a long-lived, drought-adapted shrub. These results reveal the importance of inherited somatic mutations as a source of genetic variation that can be relevant for plant adaptation.

evolutionary biology↗

bioRxiv2024

The genome of Lolium multiflorum reveals the genetic architecture of paraquat resistance

- Herbicide resistance in agricultural weeds has become one of the greatest challenges for sustainable crop production. The repeated evolution of herbicide resistance provides an excellent opportunity to study the genetic and physiological basis of the resistance phenotype and the evolutionary responses to human-mediated selection pressures. Lolium multiflorum is a ubiquitous weed that has evolved herbicide resistance repeatedly around the world in various cropping systems. - We assembled and annotated a chromosome-scale genome for L. multiflorum and elucidated the genetic architecture of paraquat resistance by performing quantitative trait loci analysis, genome-wide association studies, genetic divergence analysis, and transcriptome analyses from paraquat-resistant and -susceptible L. multiflorum populations. - Results suggested that two regions of chromosome 5 were associated with paraquat resistance. The regions contain candidate genes that encode cellular transport functions, including a novel multidrug and toxin extrusion (MATE) protein, and a cation transporter previously shown to interact with polyamines. - Our results reveal the genetic architecture of paraquat resistance and identified promising candidate genes for future functional studies. Given that L. multiflorum is a weed and a cultivated crop species, the genomic resources generated will prove valuable to a wide spectrum of the plant science community.

plant biology↗

bioRxiv2023

Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation

The re-use of old genetic variation can promote rapid diversification in evolutionary radiations, but in most cases, the historical events underlying this divergence are not known. For example, ancient hybridization can generate new combinations of alleles that sort into descendant lineages, potentially providing the raw material to initiate divergence. In the Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members of this radiation. In addition, allelic variation in the MaMyb2 gene is responsible for differences in flower color between the closely related ecotypes of subspecies puniceus, contributing to reproductive isolation by pollinators. Previous work suggested that MaMyb2 was introgressed into the red-flowered ecotype of puniceus. However, additional taxa within the radiation have independently evolved red flowers from their yellow-flowered ancestors, raising the possibility that this introgression had a more ancient origin. In this study, we used repeated tests of admixture from whole-genome sequence data across this diverse radiation to demonstrate that there has been both ancient and recurrent hybridization in this group. However, most of the signal of this ancient introgression has been removed due to selection, suggesting that widespread barriers to gene flow are in place between taxa. Yet, a roughly 30 kb region that contains the MaMyb2 gene is currently shared among the red-flowered taxa. Patterns of admixture, sequence divergence, and extended haplotype homozygosity across this region confirm a history of ancient hybridization, where functional variants have been preserved due to positive selection in red-flowered taxa but lost in their yellow-flowered counterparts. The results of this study reveal that selection against gene flow can reduce genomic signatures of ancient hybridization, but that historical introgression can provide essential genetic variation that facilitates the repeated origins of phenotypic traits between lineages.

evolutionary biology↗

bioRxiv2022

Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone

Understanding the phenotypic and genetic architecture of reproductive isolation is a longstanding goal of speciation research. In many systems, candidate barrier traits and loci have been identified, but causal connections between them are rarely made. In this study, we combine top-down and bottom-up approaches with demographic modeling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work in this system suggests that pollinator-mediated reproductive isolation is a primary barrier to gene flow between two divergent red- and yellow-flowered ecotypes of Mimulus aurantiacus. Several candidate floral traits contributing to pollinator isolation have been identified, including a difference in flower color, which is caused primarily by a single large-effect locus (MaMyb2). Other anonymous SNP loci, potentially contributing to pollinator isolation, also have been identified, but their causal relationships remain untested. Here, we performed demographic analyses, which indicate that this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted in a large fraction of the genome by barrier loci. Using a cline-based genome scan (our bottom-up approach), we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few islands of speciation. A QTL analysis (our top-down approach) revealed most floral traits are highly polygenic, with little evidence that QTL co-localize, indicating that most traits are largely genetically independent. Finally, we find little convincing evidence for the overlap of QTL and candidate barrier loci, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow aside from pollinator isolation may play an important role in this system.

genetics↗

bioRxiv2020

Population genomic and historical analysis reveals a global invasion by bridgehead processes in Mimulus guttatus

Humans are transforming species ranges worldwide. While artificial translocations trigger biological invasions with negative effects on biodiversity, invasions provide exceptional opportunities to generate ecological and evolutionary hypotheses. Unfortunately, imperfect historical records and exceedingly complex demographic histories present challenges for the reconstruction of invasion histories. Here we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of yellow monkeyflowers (Mimulus guttatus) from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive North American M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by rapid admixture from multiple parts of the native range. Populations in the British Isles then appear to have served as a bridgehead for vanguard invasions worldwide into the rest of Europe, New Zealand and eastern North America. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments.

evolutionary biology↗

bioRxiv2018

The tempo of linked selection: emergence of a heterogeneous genomic landscape during a recent radiation of monkeyflowers

Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic landscape of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a recent radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine taxa in this radiation, we show that highly similar diversity ({pi}) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Thus, combined with existing evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the genomic basis of adaptation and speciation in this system.\n\nAuthor summaryWhat can patterns of genome-wide variation tell us about the speciation process? The answer to this question depends upon our ability to infer the evolutionary processes underlying these patterns. This, however, is difficult, because many processes can leave similar footprints, but some have nothing to do with speciation per se. For example, many studies have found highly heterogeneous levels of genetic differentiation when comparing the genomes of emerging species. These patterns are often referred to as differentiation landscapes because they appear as a rugged topography of peaks and valleys as one scans across the genome. It has often been argued that selection against deleterious mutations, a process referred to as background selection, is primarily responsible for shaping differentiation landscapes early in speciation. If this hypothesis is correct, then it is unlikely that patterns of differentiation will reveal much about the genomic basis of speciation. However, using genome sequences from nine emerging species of monkeyflower coupled with simulations of genomic divergence, we show that it is unlikely that background selection is the primary architect of these landscapes. Rather, differentiation landscapes have probably been shaped by adaptation and gene flow, which are processes that are central to our understanding of speciation. Therefore, our work has important implications for our understanding of what patterns of differentiation can tell us about the genetic basis of adaptation and speciation.

evolutionary biology↗