Emma L. Berdan

Bio: Emma L. Berdan is an academic researcher from University of Gothenburg. The author has contributed to research in topics: Coelopa frigida & Population. The author has an hindex of 11, co-authored 41 publications receiving 442 citations. Previous affiliations of Emma L. Berdan include Instituto Gulbenkian de Ciência & Museum für Naturkunde.

Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification

Abstract: Although single-nucleotide polymorphism (SNPs) were initially thought to make-up the majority of selectable variation (Morin et al. 2004; Sachidanandam et al. 2001), it is becoming increasingly recognized that structural variation represents a significant, yet often poorly understood, source of genetic variation. It is only within the past 10 years, aided by the development of genomic technologies such as high-throughput and later 3rd generation sequencing, that the extent of intra-and interspecific structural variation has been investigated in a number of non-model species (Chain & Feulner 2014; Fan & Meyer 2014). This article is protected by copyright. All rights reserved.

Functional and population genomic divergence within and between two species of killifish adapted to different osmotic niches.

Abstract: Adaptation to salinity affects species distributions, promotes speciation, and guides many evolutionary patterns in fishes. To uncover the basis of a complex trait like osmoregulation, genome-level analyses are sensible. We combine population genomic scans with genome expression profiling to discover candidate genes and pathways associated with divergence between osmotic environments. We compared transcriptome sequence divergence between multiple freshwater and saltwater populations of the rainwater killifish, Lucania parva. We also compared sequence divergence between L. parva and its sister species, Lucania goodei, a freshwater specialist. We found highly differentiated single nucleotide polymorphisms (SNPs) between freshwater and saltwater L. parva populations in cell junction and ion transport genes, including V-type H + ATPase. Between species, we found divergence in reproduction and osmotic stress genes. Genes that were differentially expressed between species during osmotic acclimation included genes involved in ion transport and cell volume regulation. Gene sets that were divergent in coding sequence and divergent in expression did not overlap, although they did converge in function. Like many studies using genomic scans, our approach may miss some loci that contribute to adaptation but have complicated patterns of allelic variation. Our study suggests that gene expression and coding sequence may evolve independently as populations adapt to a complex physiological challenge.

The Genomic Architecture and Evolutionary Fates of Supergenes.

Abstract: Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic architecture as well as the mode of origin of supergenes across diverse organismal systems. Although the role of genomic architecture for the origin of supergenes has been much discussed, differences in the genomic architecture also subsequently affect the evolutionary trajectory of supergenes and the rate of degeneration of supergene haplotypes. In this review, we synthesize recent genomic work and historical models of supergene evolution, highlighting how the genomic architecture of supergenes affects their evolutionary fate. We discuss how recent findings on classic supergenes involved in governing ant colony social form, mimicry in butterflies, and heterostyly in flowering plants relate to theoretical expectations. Furthermore, we use forward simulations to demonstrate that differences in genomic architecture affect the degeneration of supergenes. Finally, we discuss implications of the evolution of supergene haplotypes for the long-term fate of balanced polymorphisms governed by supergenes.

Deleterious mutation accumulation and the long-term fate of chromosomal inversions.

Abstract: Chromosomal inversions contribute widely to adaptation and speciation, yet they present a unique evolutionary puzzle as both their allelic content and frequency evolve in a feedback loop. In this simulation study, we quantified the role of the allelic content in determining the long-term fate of the inversion. Recessive deleterious mutations accumulated on both arrangements with most of them being private to a given arrangement. This led to increasing overdominance, allowing for the maintenance of the inversion polymorphism and generating strong non-adaptive divergence between arrangements. The accumulation of mutations was mitigated by gene conversion but nevertheless led to the fitness decline of at least one homokaryotype under all considered conditions. Surprisingly, this fitness degradation could be permanently halted by the branching of an arrangement into multiple highly divergent haplotypes. Our results highlight the dynamic features of inversions by showing how the non-adaptive evolution of allelic content can play a major role in the fate of the inversion.

Behavioral Isolation due to Cascade Reinforcement in Lucania Killifish.

Abstract: Reinforcement occurs when behavioral isolation is strengthened between species due to selection against hybridization in sympatry. Mate preferences and their target traits may change in sympatry as a consequence of reinforcement. This can potentially generate further behavioral isolation within species if sympatric populations evolve extreme preferences or traits that cause them to reject individuals from foreign populations as mates or be rejected as mates. This process is known as cascade reinforcement. We measured behavioral isolation between sympatric and allopatric populations of Lucania killifish to determine whether isolation evolves due to reinforcement between species and whether reinforcement affects preferences within species, consistent with the cascade reinforcement hypothesis. We measured mate preferences in both sexes between species (Lucania parva vs. Lucania goodei) and within species (among populations of L. parva). Between species, both male and female preferences for conspecifi...

Human biochemical genetics

Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

Abstract: The analysis of polymorphism data is becoming increasingly important as a complementary tool to classical genetic analyses. Nevertheless, despite plunging sequencing costs, genomic sequencing of individuals at the population scale is still restricted to a few model species. Whole-genome sequencing of pools of individuals (Pool-seq) provides a cost-effective alternative to sequencing individuals separately. With the availability of custom-tailored software tools, Pool-seq is being increasingly used for population genomic research on both model and non-model organisms. In this Review, we not only demonstrate the breadth of questions that are being addressed by Pool-seq but also discuss its limitations and provide guidelines for users.

Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions.

Abstract: Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species’ demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, ...