@phdthesis{18515,
  abstract     = {Understanding the role of evolutionary processes in shaping genetic variation has been a
primary goal in evolutionary genetics. In this regard, a key question is how genetically
distinct populations evolve in the face of gene flow, thereby generating genetic and
phenotypic divergence and reproductive isolation (RI). This requires quantifying the role
and relative contributions of prezygotic and postzygotic isolating mechanisms on the
reduction of gene exchange between populations, and identifying regions in the genome
that mediate RI, which is often polygenic. Further, this needs distinguishing neutral and
selected regions in the genome, and discerning how selection influences patterns of neutral
divergence.
Population structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is
structured in space and shapes the neutral null model. Availability of large scale spatial
genomic datasets now enables us to detect signatures of population structure in genetic
data and infer population genetic parameters. Such inferences are crucial and have wide
applications in biodiversity, conservation genetics, population management and medical
genetics. However, inferences are based on assumptions that do not always match the
complex reality, thus leading to erroneous conclusions. Moreover, the role and interaction
of heterogeneous population density and dispersal, which are ubiquitous in nature, has
been challenging to study owing to their mathematical complexity. In such scenarios,
feedback between theory, data and simulations can prove to be useful.
In this thesis, I examine the effect of population structure on neutral genetic variation
and barriers to gene exchange in hybridising populations, thereby bridging together the
fields of spatial population genetics and speciation.
Despite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative
definition and has been used and measured differently across different fields. Chapter 2
gives a quantitative definition of RI, in terms of the effect of genetic differences on gene
flow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.
In addition to this, we discuss current measures of RI and their limitations, and propose
the need for new measures that combine organismal and genetic perspectives of RI.
In chapter 3, I examine the combined effect of assortative mating, sexual selection
and viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a
mainland-island model. We obtain novel theoretical predictions for molecular divergence
in terms of effective migration rates, which bears a simple relationship to measurable
fitness components of migrants and various early generation hybrids. We explore the
conditions under which local adaptation can be maintained despite maladaptive gene flow
and quantify the relative contributions of viability and sexual selection to genome-wide
barriers to gene flow.
The next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that
consist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow
flowered A.m. striatum. Previous studies have suggested that flower colour is target of
pollinator mediated selection and is influenced only by few genes. While these regions
show high genetic differentiation between the subspecies, the rest of the genome is seen
to be well mixed. Chapter 4 examines the effects of heterogeneous population density
and leptokurtic dispersal on isolation by distance and the distribution of heterozygosity
by focusing on non-flower colour markers.
Chapter 5 analyses cline shapes and associations among 6 focal flower colour markers to
understand how selection and dispersal maintain this hybrid zone. We see sharp coincident
stepped clines at all loci and positive associations throughout the hybrid zone, contrary to
the expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal
combined with multilocus simulations, we show that stepped clines do not reflect genetic
barriers to gene flow, but are rather a result of long-distance migration. This framework
allows us to get realistic estimates gene flow and selection and shows how traditional cline
analysis may lead to inaccurate conclusions when assumptions of the theory are not met.
Overall, this thesis investigates how different features of population structure leave
detectable signatures in genetic variation, namely in patterns of isolation by distance,
linkage disequilibrium and genetic divergence. It also highlights how effective migration
rates provide useful way of analysing polygenic architectures and shed new light into
hybrid zones. In doing so, I identify scenarios when simple models become insufficient
and suggest possibe directions by combining genetic data with simulations.},
  author       = {Surendranadh, Parvathy},
  issn         = {2663-337X},
  pages        = {219},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Effect of population structure on neutral genetic variation and barriers to gene exchange}},
  doi          = {10.15479/at:ista:18515},
  year         = {2024},
}

@article{18908,
  abstract     = {Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for > 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.},
  author       = {Le Moan, Alan and Stankowski, Sean and Rafajlović, Marina and Ortega-Martinez, Olga and Faria, Rui and Butlin, Roger K and Johannesson, Kerstin},
  issn         = {2056-3744},
  journal      = {Evolution Letters},
  number       = {4},
  pages        = {575--586},
  publisher    = {Oxford University Press},
  title        = {{Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes}},
  doi          = {10.1093/evlett/qrae014},
  volume       = {8},
  year         = {2024},
}

@article{18944,
  abstract     = {Understanding connectivity patterns exhibited by endangered species living in fragmented habitats is fundamental to improving management and conservation actions. Such improvements can be particularly pressing at the trailing edges of these habitats, where populations are facing the greatest challenges from climate change, and appear even more crucial if the species is commercially harvested. Seascape genetics have been increasingly used to meet these needs. In this study, we examined connectivity patterns among 32 populations of the oarweed kelp <jats:italic>Lam</jats:italic><jats:italic>inaria digitata</jats:italic> located at the species’ southern range limit. The distance (or sampling gap) between neighboring populations ranged from a few km to a few 100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses of population structure; (2) test whether on-shelf islands are genetically more differentiated than mainland populations; (3) evaluate the relative importance of various abiotic conditions in shaping the genetic structure; and (4) evaluate if the relative importance of each environmental factor varied according to sampling schemes. Our analyses revealed a positive relationship between connectivity links and genetic diversity: populations with high levels of connectivity were genetically enriched while isolated populations showed signs of genetic erosion. The genetically impoverished populations corresponded to the southernmost populations as well as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay) and the northernmost population in Pas-de-Calais. By performing distance-based redundancy analysis on various sampling schemes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor when analyzing at a final spatial resolution.},
  author       = {Fouqueau, Louise and Reynes, L and Tempera, F and Bajjouk, T and Blanfuné, A and Chevalier, C and Laurans, M and Mauger, S and Sourisseau, M and Assis, J and Lévêque, L and Valero, M},
  issn         = {1616-1599},
  journal      = {Marine Ecology Progress Series},
  pages        = {23--42},
  publisher    = {Inter-Research Science Center},
  title        = {{Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes}},
  doi          = {10.3354/meps14640},
  volume       = {740},
  year         = {2024},
}

@article{18949,
  abstract     = {Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research: (i) scientific integration, through the bringing together of ideas, data, and approaches; and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (i) the multidisciplinary nature of speciation research, (ii) the complex language of speciation; (iii) a bias toward certain study systems; (iv) the challenges of working across scales; and (v) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.},
  author       = {Stankowski, Sean and Cutter, Asher D and Satokangas, Ina and Lerch, Brian A and Rolland, Jonathan and Smadja, Carole M and Segami Marzal, J Carolina and Cooney, Christopher R and Feulner, Philine G D and Domingos, Fabricius Maia Chaves Bicalho and North, Henry L and Yamaguchi, Ryo and Butlin, Roger K and Wolf, Jochen B W and Coughlan, Jenn and Heidbreder, Patrick and Hernández-Gutiérrez, Rebeca and Barnard-Kubow, Karen B and Peede, David and Rancilhac, Loïs and Salvador, Rodrigo Brincalepe and Thompson, Ken A and Stacy, Elizabeth A and Moyle, Leonie C and Garlovsky, Martin D and Maulana, Arif and Kantelinen, Annina and Cacho, N Ivalú and Schneemann, Hilde and Domínguez, Marisol and Dopman, Erik B and Lohse, Konrad and Rometsch, Sina J and Comeault, Aaron A and Merrill, Richard M and Scordato, Elizabeth S C and Singhal, Sonal and Pärssinen, Varpu and Lackey, Alycia C R and Kumar, Sanghamitra and Meier, Joana I and Barton, Nicholas H and Fraisse, Christelle and Ravinet, Mark and Kulmuni, Jonna},
  issn         = {2752-938X},
  journal      = {Evolutionary Journal of the Linnean Society},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{Toward the integration of speciation research}},
  doi          = {10.1093/evolinnean/kzae001},
  volume       = {3},
  year         = {2024},
}

@unpublished{19520,
  abstract     = {Vertebrates exhibit a wide range of motor behaviors, ranging from swimming to complex limb-based movements. Here we take advantage of frog metamorphosis, which captures a swim-to-limb-based movement transformation during the development of a single organism, to explore changes in the underlying spinal circuits. We find that the tadpole spinal cord contains small and largely homogeneous populations of motor neurons (MNs) and V1 interneurons (V1s) at early escape swimming stages. These neuronal populations only modestly increase in number and subtype heterogeneity with the emergence of free swimming. In contrast, during frog metamorphosis and the emergence of limb movement, there is a dramatic expansion of MN and V1 interneuron number and transcriptional heterogeneity, culminating in cohorts of neurons that exhibit striking molecular similarity to mammalian motor circuits. CRISPR/Cas9-mediated gene disruption of the limb MN and V1 determinants FoxP1 and Engrailed-1, respectively, results in severe but selective deficits in tail and limb function. Our work thus demonstrates that neural diversity scales exponentially with increasing behavioral complexity and illustrates striking evolutionary conservation in the molecular organization and function of motor circuits across species.},
  author       = {Vijatovic, David and Toma, Florina Alexandra  and Harrington, Zoe P and Sommer, Christoph M and Hauschild, Robert and Trevisan, Alexandra J. and Chapman, Phillip and Julseth, Mara and Brenner-Morton, Susan and Gabitto, Mariano I. and Dasen, Jeremy S. and Bikoff, Jay B. and Sweeney, Lora Beatrice Jaeger},
  booktitle    = {bioRxiv},
  title        = {{Spinal neuron diversity scales exponentially with swim-to-limb transformation during frog metamorphosis}},
  doi          = {10.1101/2024.09.20.614050},
  year         = {2024},
}

@article{17207,
  author       = {Fouqueau, Louise and Polechova, Jitka},
  issn         = {1420-9101},
  journal      = {Journal of evolutionary biology},
  number       = {6},
  pages        = {579--587},
  publisher    = {Oxford University Press},
  title        = {{Eco-evolutionary dynamics in changing environments: Integrating theory with data}},
  doi          = {10.1093/jeb/voae067},
  volume       = {37},
  year         = {2024},
}

@article{17237,
  abstract     = {The impact of climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of 4 populations of the cold-water kelp Laminaria digitata by analyzing their spatial and temporal genomic variations using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at 2 time points, spanning at least 2 generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species’ demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change.},
  author       = {Reynes, Lauric and Fouqueau, Louise and Aurelle, Didier and Mauger, Stephane and Destombe, Christophe and Valero, Myriam},
  issn         = {1420-9101},
  journal      = {Journal of Evolutionary Biology},
  number       = {6},
  pages        = {677--692},
  publisher    = {Oxford University Press},
  title        = {{Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations}},
  doi          = {10.1093/jeb/voae048},
  volume       = {37},
  year         = {2024},
}

@article{17238,
  abstract     = {We know that heritable variation is abundant, and that selection causes all but the smallest populations to rapidly shift beyond their original trait distribution. So then, what limits the range of a species? There are physical constraints and also population genetic limits to the effectiveness of selection, ultimately set by population size. Global adaptation, where the same genotype is favoured over the whole range, is most efficient when based on a multitude of weakly selected alleles and is effective even when local demes are small, provided that there is some gene flow. In contrast, local adaptation is sensitive to gene flow and may require alleles with substantial effect. How can populations combine the advantages of large effective size with the ability to specialise into local niches? To what extent does reproductive isolation help resolve this tension? I address these questions using eco-evolutionary models of polygenic adaptation, contrasting discrete demes with continuousspace.},
  author       = {Barton, Nicholas H},
  issn         = {1420-9101},
  journal      = {Journal of Evolutionary Biology},
  number       = {6},
  pages        = {605--615},
  publisher    = {Oxford University Press},
  title        = {{Limits to species' range: The tension between local and global adaptation}},
  doi          = {10.1093/jeb/voae052},
  volume       = {37},
  year         = {2024},
}

@misc{17344,
  abstract     = {This file contains the Mathematica notebook associated with the paper Effect of assortative mating and sexual selection on polygenic barriers to gene flow. It contains the numerical approximations, analyses, and simulations used in the study. },
  author       = {Surendranadh, Parvathy and Sachdeva, Himani},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Mathematica notebook for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'}},
  doi          = {10.15479/AT:ISTA:17344},
  year         = {2024},
}

@article{17888,
  abstract     = {Context: Biotic resource exploitation is a critical determinant of species’ distributions. However, quantifying resource exploitation patterns through space and time can be difficult, complicating their incorporation in spatial ecology studies. Therefore, understanding the local drivers of spatial patterns of resource exploitation may contribute to better large-scale species distribution models.
Objectives: We investigated (1) how the resource exploitation patterns of two trophic interactions (plant–insect) are explained by insect behaviour, resource aggregation, and potential insect-insect interactions. We also analyzed how (2) resource patch size and (3) resource accessibility in a heterogeneous landscape affected host exploitation patterns.
Methods: We quantified nectar robbing by insects in the genus Bombus (bumblebees) and seed predation by Brachypterolus vestitus larvae (Antirrhinum beetle) on Antirrhinum majus L. (wild snapdragons) in the Pyrenees Mountains, Catalonia, Spain. We tested hypotheses about resource exploitation by integrating spatial analyses at multiple scales.
Results: Both trophic interactions were aggregated, explained by the aggregation of their resource. At some scales, nectar robbing is more aggregated than the resource. Trophic interaction abundance is proportional to resource patch size, following the ideal free distribution model. Landscape features do not explain the locations exploited. Nectar robbing and seed predation occur together more often than expected.
Conclusions: Our findings suggest that multiple biotic and ecological spatial factors may simultaneously affect resource exploitation at a local scale. These findings should be considered when developing agricultural projects, management plans and conservation policies.},
  author       = {Pocull Belles, Guillem and Baskett, Carina and Barton, Nicholas H},
  issn         = {1572-9761},
  journal      = {Landscape Ecology},
  number       = {9},
  publisher    = {Springer Nature},
  title        = {{Multiscale spatial analysis of two plant–insect interactions: Effects of landscape, resource distribution, and other insects}},
  doi          = {10.1007/s10980-024-01899-9},
  volume       = {39},
  year         = {2024},
}

@article{18525,
  abstract     = {As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance in cis- and in trans-, break the latter down by effect propagation order, assess the trans- variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of nontranscriptional (including environmental) effects.},
  author       = {Ruzickova, Natalia and Hledik, Michal and Tkačik, Gašper},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {44},
  publisher    = {National Academy of Sciences},
  title        = {{Quantitative omnigenic model discovers interpretable genome-wide associations}},
  doi          = {10.1073/pnas.2402340121},
  volume       = {121},
  year         = {2024},
}

@article{14796,
  abstract     = {Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.},
  author       = {Stankowski, Sean and Zagrodzka, Zuzanna B. and Garlovsky, Martin D. and Pal, Arka and Shipilina, Daria and Garcia Castillo, Diego Fernando and Lifchitz, Hila and Le Moan, Alan and Leder, Erica and Reeve, James and Johannesson, Kerstin and Westram, Anja M and Butlin, Roger K.},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6678},
  pages        = {114--119},
  publisher    = {American Association for the Advancement of Science},
  title        = {{The genetic basis of a recent transition to live-bearing in marine snails}},
  doi          = {10.1126/science.adi2982},
  volume       = {383},
  year         = {2024},
}

@article{11479,
  abstract     = {Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results.},
  author       = {De Jode, Aurélien and Le Moan, Alan and Johannesson, Kerstin and Faria, Rui and Stankowski, Sean and Westram, Anja M and Butlin, Roger K. and Rafajlović, Marina and Fraisse, Christelle},
  issn         = {1752-4571},
  journal      = {Evolutionary Applications},
  number       = {2},
  pages        = {542--559},
  publisher    = {Wiley},
  title        = {{Ten years of demographic modelling of divergence and speciation in the sea}},
  doi          = {10.1111/eva.13428},
  volume       = {16},
  year         = {2023},
}

@article{12166,
  abstract     = {Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings.},
  author       = {Westram, Anja M and Butlin, Roger},
  issn         = {1365-294X},
  journal      = {Molecular Ecology},
  keywords     = {Genetics, Ecology, Evolution, Behavior and Systematics},
  number       = {1},
  pages        = {26--29},
  publisher    = {Wiley},
  title        = {{Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize}},
  doi          = {10.1111/mec.16779},
  volume       = {32},
  year         = {2023},
}

@article{12514,
  abstract     = {The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model.},
  author       = {Bolnick, Daniel I. and Hund, Amanda K. and Nosil, Patrik and Peng, Foen and Ravinet, Mark and Stankowski, Sean and Subramanian, Swapna and Wolf, Jochen B.W. and Yukilevich, Roman},
  issn         = {1558-5646},
  journal      = {Evolution: International journal of organic evolution},
  number       = {1},
  pages        = {318--328},
  publisher    = {Oxford University Press},
  title        = {{A multivariate view of the speciation continuum}},
  doi          = {10.1093/evolut/qpac004},
  volume       = {77},
  year         = {2023},
}

@misc{12933,
  abstract     = {Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster".},
  author       = {Puixeu Sala, Gemma},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster}},
  doi          = {10.15479/AT:ISTA:12933},
  year         = {2023},
}

@misc{12949,
  abstract     = {The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in  the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each  of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.},
  author       = {Barton, Nicholas H},
  keywords     = {Quantitative genetics, infinitesimal model},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The infinitesimal model with dominance}},
  doi          = {10.15479/AT:ISTA:12949},
  year         = {2023},
}

@phdthesis{14058,
  abstract     = {Females and males across species are subject to divergent selective pressures arising
from di↵erent reproductive interests and ecological niches. This often translates into a
intricate array of sex-specific natural and sexual selection on traits that have a shared
genetic basis between both sexes, causing a genetic sexual conflict. The resolution of
this conflict mostly relies on the evolution of sex-specific expression of the shared genes,
leading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought
to evolve via modifications of the genetic networks ultimately linked to sex-determining
transcription factors. Although much empirical and theoretical evidence supports this
standard picture of the molecular basis of sexual conflict resolution, there still are a
few open questions regarding the complex array of selective forces driving phenotypic
di↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.
First, how do patterns of phenotypic sexual dimorphism vary within populations,
as a response to the temporal and spatial changes in sex-specific selective forces? To
tackle this question, I analyze the patterns of sex-specific phenotypic variation along
three life stages and across populations spanning the whole geographical range of Rumex
hastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.
Second, how do gene expression patterns lead to phenotypic dimorphism, and what
are the molecular mechanisms underlying the observed transcriptomic variation? I
address this question by examining the sex- and tissue-specific expression variation in
newly-generated datasets of sex-specific expression in heads and gonads of Drosophila
melanogaster. I additionally used two complementary approaches for the study of the
genetic basis of sex di↵erences in gene expression in the second and third Chapters of
the thesis.
Third, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual
dimorphism? I develop models of sex-specific stabilizing selection, mutation and drift
to formalize common intuition regarding the patterns of covariation between intersex
correlation and sexual dimorphism in the fourth Chapter of the thesis.
Alltogether, the work described in this PhD thesis provides useful insights into the
links between genetic, transcriptomic and phenotypic layers of sex-specific variation,
and contributes to our general understanding of the dynamics of sexual dimorphism
evolution.},
  author       = {Puixeu Sala, Gemma},
  isbn         = {978-3-99078-035-0},
  issn         = {2663-337X},
  pages        = {230},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation}},
  doi          = {10.15479/at:ista:14058},
  year         = {2023},
}

@article{14077,
  abstract     = {The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed
so far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues
and biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila
melanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate
crosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,
testes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that
have been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation
of genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression
and can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis
variation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary
expression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance
as well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled
experimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.},
  author       = {Puixeu Sala, Gemma and Macon, Ariana and Vicoso, Beatriz},
  issn         = {2160-1836},
  journal      = {G3: Genes, Genomes, Genetics},
  keywords     = {Genetics (clinical), Genetics, Molecular Biology},
  number       = {8},
  publisher    = {Oxford University Press},
  title        = {{Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster}},
  doi          = {10.1093/g3journal/jkad121},
  volume       = {13},
  year         = {2023},
}

@article{14452,
  abstract     = {The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√⁠. We illustrate our results with some numerical examples.},
  author       = {Barton, Nicholas H and Etheridge, Alison M. and Véber, Amandine},
  issn         = {1943-2631},
  journal      = {Genetics},
  number       = {2},
  publisher    = {Oxford University Press},
  title        = {{The infinitesimal model with dominance}},
  doi          = {10.1093/genetics/iyad133},
  volume       = {225},
  year         = {2023},
}