Research
Supergenes in seaweed flies
Gene flow and recombination directly oppose adaptation and speciation because they homogenize critical allele combinations. Supergenes are tightly linked sets of loci that control complex phenotypes and which maintain these favorable trait combinations in the face of gene flow or gene flux. Recent advances have shown that the genomic architecture of supergenes usually includes a structural variant (e.g., inversion, fusion, etc.) but we still understand little about how supergenes evolve and persist in nature. The structural variants that underlie supergenes are themselves under selection but also alter the efficacy of selection within the mutated region by modifying recombination rate and Ne, shifting the evolutionary trajectory of the population. My research incorporates theoretical and empirical techniques to push forward our current knowledge on the evolution of supergenes and structural variants in natural populations, and their role in adaptation and genome evolution.
I use both theoretical and empirical tools to determine how supergenes evolve in natural populations and their role in adaptation and speciation. As a real world example I use the seaweed fly, Coelopa frigida, which is adapted to live in piles of rotting seaweed on the beach and has a very large supergene on chromosome 1. Recent work has concentrated on elucidating the various selective forces on the inversion as well looking at genomic and transcriptomic patterns across populations (Berdan et al. 2018; Mérot et al. 2021; Berdan et al. 2021). This allows me to determine the forces acting on the inversion and to make specific predictions of future patterns of variation.
My theoretical work has revealed that a Muller's ratchet-like process occurs in polymorphic inversions leading to the accumulation of deleterious recessive alleles (Berdan et al. 2021). I am currently expanding this work to generate predictions that may be tested with sequence data from C. frigida.
Ecological genomics of the wrackbed environment
Unlike most other ecosystems, beaches have little to no primary productivity. Instead, deposited organic matter, such as algae and carrion, forms the basis of the sandy beach ecosystem. The processing of this material, primarily by bacteria, drives the wrackbed ecosystem. The degradation of the algae supports a diverse invertebrate community and allows nutrients to be leached back into the sea (reviewed in Hyndes, Berdan, et al., in review). My research focuses on two keystones of the wrackbed ecosystem: the microbial community and Coelopa frigida. Coelopa frigida larvae feed primarily on the microbiome of the wrackbed as well as promoting bacterial growth and algae degradation by aerating the wrackbed. In addition, C. frigida are adapted to their wrackbed composition (i.e. the species of algae present; Berdan, et al. 2018). I am collaborating with ecologists to determine how nutrients leach from wrackbeds to the ocean during algae degradation and what role C. frigida plays in this process (Long et al., in prep). I have also conducted a preliminary amplicon sequencing study to determine how the bacterial community varies along a salinity gradient and how the larval microbiome compares to it (Berdan et al., in review). The data show strong shifts in the microbial community likely driven by differences in polysaccharide content of the algae. I plan to follow up on this work with both metagenomic studies as well as controlled laboratory experiments to quantify differences between C. frigida adapted to different wrackbed conditions and with different supergene genotypes.
Speciation in crickets and grasshoppers
Many species differ primarily by signals they use to attract mates and the preferences for these signals. This leads to behavioral isolation, one of the most common forms of reproductive isolation. While a member of the GENART project at the Museum für Naturkunde in Berlin I used a two systems (sister species of crickets, and three species of grasshoppers) to explore the evolution of behavioral isolation and the mark it leaves on the genome. Additionally, I generated many different genomic resources for these n0n-model organisms (Berdan et al. 2016, Berdan et al. 2017). Our work revealed that behavioral isolation is strong in both systems and often multi-modal (Finck et al. 2016). Despite this, genomic data revealed that neutral processes and natural selection have left stronger marks on the genome than the sexual selection driving this behavioral divergence (Berdan et al. 2015, Blankers et al. 2018).
Speciation in fish
During my PhD, I concentrated on discerning the association between behavioral isolation and ecological divergence in a pair of fish species that experience gene flow, Lucania goodei and L. parva. These two species have diverged in salinity tolerance: L. parva tolerates a wide range of salinities while L. goodei can only tolerate freshwater. I tested for sensory drive and found strong behavioural isolation regardless of salinity and both males and female preferred conspecific mates (Berdan and Fuller 2012). Based on the results from this study, I considered the contribution of non-ecological selection to behavioural isolation by determining if reinforcement played a role. I group found reinforcement of male preferences in the Lucania system as well as cascade reinforcement occurring in females (Gregorio et. al 2012; Kozak et. al. 2015). The final part of my thesis focused on the role of a chromosomal rearrangement (and the potential reduced recombination it provides) in speciation. Lucania parva and L. goodei have undergone a chromosomal rearrangement that differs between the two species. I performed a QTL analysis using a SNP linkage map I developed along with colleagues (Berdan, Kozak et al. 2014). I found QTL for salinity tolerance scattered along the genome and sometimes co-localizing with loci underlying reproductive isolation, but not present on the fused chromosome (Berdan, Fuller, et. al., 2020).
Gene flow and recombination directly oppose adaptation and speciation because they homogenize critical allele combinations. Supergenes are tightly linked sets of loci that control complex phenotypes and which maintain these favorable trait combinations in the face of gene flow or gene flux. Recent advances have shown that the genomic architecture of supergenes usually includes a structural variant (e.g., inversion, fusion, etc.) but we still understand little about how supergenes evolve and persist in nature. The structural variants that underlie supergenes are themselves under selection but also alter the efficacy of selection within the mutated region by modifying recombination rate and Ne, shifting the evolutionary trajectory of the population. My research incorporates theoretical and empirical techniques to push forward our current knowledge on the evolution of supergenes and structural variants in natural populations, and their role in adaptation and genome evolution.
I use both theoretical and empirical tools to determine how supergenes evolve in natural populations and their role in adaptation and speciation. As a real world example I use the seaweed fly, Coelopa frigida, which is adapted to live in piles of rotting seaweed on the beach and has a very large supergene on chromosome 1. Recent work has concentrated on elucidating the various selective forces on the inversion as well looking at genomic and transcriptomic patterns across populations (Berdan et al. 2018; Mérot et al. 2021; Berdan et al. 2021). This allows me to determine the forces acting on the inversion and to make specific predictions of future patterns of variation.
My theoretical work has revealed that a Muller's ratchet-like process occurs in polymorphic inversions leading to the accumulation of deleterious recessive alleles (Berdan et al. 2021). I am currently expanding this work to generate predictions that may be tested with sequence data from C. frigida.
Ecological genomics of the wrackbed environment
Unlike most other ecosystems, beaches have little to no primary productivity. Instead, deposited organic matter, such as algae and carrion, forms the basis of the sandy beach ecosystem. The processing of this material, primarily by bacteria, drives the wrackbed ecosystem. The degradation of the algae supports a diverse invertebrate community and allows nutrients to be leached back into the sea (reviewed in Hyndes, Berdan, et al., in review). My research focuses on two keystones of the wrackbed ecosystem: the microbial community and Coelopa frigida. Coelopa frigida larvae feed primarily on the microbiome of the wrackbed as well as promoting bacterial growth and algae degradation by aerating the wrackbed. In addition, C. frigida are adapted to their wrackbed composition (i.e. the species of algae present; Berdan, et al. 2018). I am collaborating with ecologists to determine how nutrients leach from wrackbeds to the ocean during algae degradation and what role C. frigida plays in this process (Long et al., in prep). I have also conducted a preliminary amplicon sequencing study to determine how the bacterial community varies along a salinity gradient and how the larval microbiome compares to it (Berdan et al., in review). The data show strong shifts in the microbial community likely driven by differences in polysaccharide content of the algae. I plan to follow up on this work with both metagenomic studies as well as controlled laboratory experiments to quantify differences between C. frigida adapted to different wrackbed conditions and with different supergene genotypes.
Speciation in crickets and grasshoppers
Many species differ primarily by signals they use to attract mates and the preferences for these signals. This leads to behavioral isolation, one of the most common forms of reproductive isolation. While a member of the GENART project at the Museum für Naturkunde in Berlin I used a two systems (sister species of crickets, and three species of grasshoppers) to explore the evolution of behavioral isolation and the mark it leaves on the genome. Additionally, I generated many different genomic resources for these n0n-model organisms (Berdan et al. 2016, Berdan et al. 2017). Our work revealed that behavioral isolation is strong in both systems and often multi-modal (Finck et al. 2016). Despite this, genomic data revealed that neutral processes and natural selection have left stronger marks on the genome than the sexual selection driving this behavioral divergence (Berdan et al. 2015, Blankers et al. 2018).
Speciation in fish
During my PhD, I concentrated on discerning the association between behavioral isolation and ecological divergence in a pair of fish species that experience gene flow, Lucania goodei and L. parva. These two species have diverged in salinity tolerance: L. parva tolerates a wide range of salinities while L. goodei can only tolerate freshwater. I tested for sensory drive and found strong behavioural isolation regardless of salinity and both males and female preferred conspecific mates (Berdan and Fuller 2012). Based on the results from this study, I considered the contribution of non-ecological selection to behavioural isolation by determining if reinforcement played a role. I group found reinforcement of male preferences in the Lucania system as well as cascade reinforcement occurring in females (Gregorio et. al 2012; Kozak et. al. 2015). The final part of my thesis focused on the role of a chromosomal rearrangement (and the potential reduced recombination it provides) in speciation. Lucania parva and L. goodei have undergone a chromosomal rearrangement that differs between the two species. I performed a QTL analysis using a SNP linkage map I developed along with colleagues (Berdan, Kozak et al. 2014). I found QTL for salinity tolerance scattered along the genome and sometimes co-localizing with loci underlying reproductive isolation, but not present on the fused chromosome (Berdan, Fuller, et. al., 2020).
