@article{20325,
abstract = {Inferring genealogical relationships of wild populations is useful because it gives direct estimates of mating patterns and variance in reproductive success. Inference can be improved by including information about parentage shared between siblings, or by modelling phenotypes or population data related to mating. However, we currently lack a framework to infer parent–offspring relationships, sibships and population parameters in a single analysis. To address this, we here extend a previous method, Fractional Analysis of Paternity and Sibships, to include population data for the case where one parent is known. We illustrate this with the example of pollen dispersal in a natural hybrid zone population of the snapdragon Antirrhinum majus. Pollen dispersal is leptokurtic, with half of mating events occurring within 30 m, but with a long tail of mating events up to 859 m. Using simulations, we find that both sibship and population information substantially improve pedigree reconstruction, and that we can expect to resolve median dispersal distances with high accuracy.},
author = {Ellis, Thomas and Field, David and Barton, Nicholas H},
issn = {1365-294X},
journal = {Molecular Ecology},
number = {15},
publisher = {Wiley},
title = {{Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone}},
doi = {10.1111/mec.70051},
volume = {34},
year = {2025},
}
@article{20330,
abstract = {The evolution of sexual dimorphism (the difference in average trait values between females and males, SD), is often thought to be constrained by shared genetic architecture between the sexes. Indeed, it is commonly expected that SD should negatively correlate with the intersex correlation (the genetic correlation between effects of segregating variants in females and males, r fm), either because (1) traits with ancestrally low r fm are less constrained in their ability to respond to sex-specific selection and thus evolve to be more dimorphic, or because (2) sex-specific selection, driving sexual dimorphism evolution, also acts to reduce r fm. Despite the intuitive appeal and prominence of these ideas, their generality and the conditions in which they hold remain unclear. Here, we develop models incorporating sex-specific stabilizing selection, mutation and genetic drift to examine the relationship between r fm and SD. We show that the two commonly-discussed mechanisms with the potential to generate a negative correlation between SD and r fm could just as easily generate a positive association, since the standard line of reasoning hinges on a hidden assumption that sex-specific adaptation more frequently favors increased dimorphism than reduced dimorphism. Our results provide, to our knowledge, the first mechanistic framework for understanding the conditions under which a correlation between r fm and SD may arise and offer a compelling explanation for inconsistent empirical evidence. We also make the intriguing observation that—even when selection between the two sexes is identical—drift generates nonzero SD. We quantify this effect and discuss its significance.},
author = {Puixeu Sala, Gemma and Hayward, Laura},
issn = {1943-2631},
journal = {Genetics},
number = {3},
publisher = {Oxford University Press},
title = {{The relationship between sexual dimorphism and intersex correlation: Do models support intuition?}},
doi = {10.1093/genetics/iyaf175},
volume = {231},
year = {2025},
}
@article{20429,
abstract = {Plant–plant interactions are key to understanding ecosystem services and shaping restoration strategies, as they can produce either negative or positive effects, determining species establishment and growth. Recognizing these interactions during early-life stages provides valuable insights for restoration in human-disturbed areas. One promising approach is nucleation planting, which establishes small clusters of native species in strategically selected sites, being particularly useful in sites with large herbivores. In southern Patagonia, livestock production has historically been the main economic activity, severely impacting extensive areas of Nothofagus antarctica forest through grazing and intentional burning to increase forage. In this context, nucleation planting with Berberis microphylla, a non-palatable shrub, could foster forest recovery in degraded sites. To evaluate this, we conducted an experiment testing the response of trees to varying shrub number, while also assessing intraspecific effects in both species. We measured survival, biomass, and functional traits. Results showed that the combination of four shrubs surrounding a single tree maintained tree survival at levels comparable to trees growing alone, while seedlings exhibited conspecific negative plant number dependence. Additionally, B. microphylla increased its below- to above-ground biomass ratio under higher plant number, indicating resource reallocation and niche differentiation through spatial separation of root systems.},
author = {Bustamante, Gimena Noemí and Arena, Miriam Elisabet and Selzer, Luciano and Ruggirello, Matthew and Rodríguez, Paula and Pedrazzani, Samuele and Navarro-Cano, Jose Antonio and Soler Schaller, Rosina Matilde},
issn = {1573-5052},
journal = {Plant Ecology},
pages = {1301--1313},
publisher = {Springer Nature},
title = {{Biotic interactions between trees and colonizing shrubs: Implications for active restoration in southern Patagonian forests}},
doi = {10.1007/s11258-025-01568-0},
volume = {226},
year = {2025},
}
@article{20531,
abstract = {Genetic drift is potentially an important component of selection for sex, as it is a source of statistical associations between alleles at selected loci. By increasing local drift, population structure may thus amplify the evolutionary advantage of sex. However, most previous models have focused either on haploid populations or on diploid populations without spatial structure. In this article, we use two- and three-locus analytical models and multilocus simulations to explore selection for sex in a diploid population structured according to the island model, in the presence of recurrent deleterious mutations. Our results show that selection generally favors an intermediate rate of sex that decreases as the direct cost of sex increases and increases moderately as the degree of population structure increases. Selection for sex is generated by multiple effects involving genetic associations within and between loci. When selection occurs at many loci, it is generally dominated by interference effects involving deleterious alleles at different loci, captured by our three-locus model. In our multilocus simulations, we observed an irreversible spread of asexual mutants under strong costs of sex, and when deleterious mutations are partially recessive. However, population structure may prevent this spread of asexual mutants when dispersal rates are sufficiently small.},
author = {Fouqueau, Louise and Roze, Denis},
issn = {1558-5646},
journal = {Evolution},
number = {10},
pages = {2167--2180},
publisher = {Oxford University Press},
title = {{Deleterious mutations and selection for sex in spatially structured, diploid populations}},
doi = {10.1093/evolut/qpaf143},
volume = {79},
year = {2025},
}
@phdthesis{20694,
abstract = {Understanding the mechanisms underlying speciation is a central aim of evolutionary biology.
A persistent challenge in the field is to identify loci that contribute to reproductive isolation,
while disentangling signals of selection from demography, linkage and intrinsic genomic
features. Traditional population genomic approaches that rely on site-based statistics in
arbitrary fixed windows face inherent limitations, as they conflate historical and
contemporary processes of divergence and overlook haplotype structure. Recent advances in
whole-genome sequencing and methods to infer ancestral recombination graphs (ARGs) now
offer the opportunity to study genealogical relationships explicitly, revealing how lineages
coalesce and recombine through time. By directly analysing haplotype clustering by species
or phenotype and their patterns of coalescence, ARG-based methods show promise for
diagnosing sweeps, identifying barrier loci maintained under divergent selection amid gene
flow, and tracing their evolutionary history.
In this thesis, I explore the utility of genealogical approaches for studying species
divergence. In chapter 2, I propose a conceptual framework for defining haplotype blocks
through the structure of the ARG, using simulations and empirical data to highlight how
genealogical processes generate rich and often overlooked haplotypic patterns.
In chapter 3, I examine the genomic basis of a key evolutionary innovation in marine
snails Littorina. These snails offer a unique opportunity to study an innovation because they
include a very recent transition from egg-laying to live bearing, yet snails with the different
reproductive modes are not reciprocally monophyletic. I exploited this by using topology
clustering in ARG-derived local genealogical trees to pinpoint narrow genomic regions or
haplotype blocks that carry swept alleles, thus revealing that the transition from egg-laying
to live-bearing involves multiple, live-bearer-specific sweeps.
Chapter 4 establishes a population-scale, phased genomic resource for Antirrhinum
majus, using cost-effective haplotagging, then optimizes imputation from low-coverage data
against high-accuracy KASP sequencing to maximize sequence completeness with modest
accuracy trade-offs against a traditional short-read sequence pipeline. A hybrid phasing
strategy combines molecular phasing with statistical phasing to generate phased whole
genome sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing
costs.
In chapter 5, I analyse hybridising populations from two replicate hybrid zones to find
a parallel genetic basis of flower colour, amidst the noise in genomic differentiation landscape
driven by variation in demographic history. While outlier genome scans of FST failed to dissect
the causes of differentiation, ARG-based topology clustering revealed a reuse of colour
associated haplotypes across hybrid zones. In addition to the biological insight, this chapter
also presents a comparison of the latest ARG inference tools, showing that signals of
Abstract
viii
topological clustering qualitatively agree between methods, despite differences in the tree
sequences.
Next, in chapter 6, by leveraging ~1000 individuals in one of the hybrid zones, I
integrated genome-wide association studies of floral pigmentation with genealogical
inference, to test for additional colour loci, and confirm the effect of previously described loci.
This work demonstrates that flower colour variation is driven by a small number of large effect
loci, while also hinting at the presence of a new candidate regulatory factor.
Finally in chapter 7, in a preliminary analysis, I begin to dissect the genomic island of
speciation around Rosea/Eluta to understand its evolutionary origins. My results show that it
consists of 5 highly divergent loci, each of which is associated with flower colour. Using
patterns of coalescence in genealogical trees, I find evidence of staggered selective sweeps
and a persistent localized barrier to gene flow within an otherwise permeable genome.
Together, these chapters add to the increasing pool of studies using genealogical
approaches to complement and extend site-based statistics to use haplotype structures in
speciation research. By tracking haplotypes directly and connecting genealogical clustering to
population processes, ARG-based inference promises to provide new insights into how local
selective pressures, demographic history, and long-term barriers interact to shape the
genomic architecture of divergence. By underscoring the value of ARGs in revealing the finescale origins and maintenance of biodiversity, this thesis presents cautious optimism about
the benefits of using genealogical inference to learn more than what site-based statistics
could tell us.},
author = {Pal, Arka},
issn = {2663-337X},
pages = {268},
publisher = {Institute of Science and Technology Austria},
title = {{Using genealogies to study the genomic basis of species divergence}},
doi = {10.15479/AT-ISTA-20694},
year = {2025},
}
@article{20190,
abstract = {A major goal of speciation research is identifying loci that underpin barriers to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome for molecular signatures of processes that drive or maintain divergence. However, interpreting the ‘genomic landscape’ of speciation is complicated, because genome scans conflate multiple processes, most of which are not informative about gene flow. However, studying replicated population contrasts, including multiple incidences of secondary contact, can strengthen inferences. In this paper, we use linked-read sequencing (haplotagging), FST scans and genealogical methods to characterise the genomic landscape associated with replicate hybrid zone formation. We studied two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies majus, that form secondary hybrid zones in multiple independent valleys in the Pyrenees. Consistent with past work, we found very low differentiation at one well-studied zone (Planoles). However, at a second zone (Avellanet), we found stronger differentiation and greater heterogeneity, which we argue is due to differences in the amount of introgression following secondary contact. Topology weighting of genealogical trees identified loci where haplotype diversity was associated with the two snapdragon varieties. Two of the strongest associations were at previously identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta, two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence times provides additional evidence for selective sweeps at these loci and barriers to gene flow. Our study highlights the impact of demographic history on the differentiation landscape, emphasising the need to distinguish between historical divergence and recent introgression.},
author = {Pal, Arka and Shipilina, Daria and Le Moan, Alan and Mcnairn, Adrian J. and Grenier, Jennifer K. and Kucka, Marek and Coop, Graham and Chan, Yingguang Frank and Barton, Nicholas H and Field, David and Stankowski, Sean},
issn = {1365-294X},
journal = {Molecular Ecology},
number = {22},
publisher = {Wiley},
title = {{Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum}},
doi = {10.1111/mec.70067},
volume = {34},
year = {2025},
}
@unpublished{21967,
abstract = {Selection against deleterious mutations, called purifying selection, plays a central role in evolution and acts in all populations. It is known that the genetic patterns observed in genomic regions undergoing purifying selection differ from those resulting from neutral evolution. However, a comprehensive understanding of the underlying mechanisms shaping those patterns is still lacking.
In the present work, we use simulations combined with a genealogical approach to identify the effect of purifying selection on the ancestry and thus on the genetic diversity. Our analysis relies on the postulate that the genealogy belongs to the universality class of Beta-coalescents. Under this assumption, we derive statistics measuring the distortion of the genealogy. This approach allows us to consider a wide range of regimes (i.e. arbitrary selection and mutation strengths) and uncover a rich phase diagram. We find that, for strong selection, the limiting genealogy is given by Kingman’s coalescent on a polynomial timescale. As selection gets weaker, Muller’s ratchet starts operating, setting off the emergence of multiple mergers in the genealogical structures. Our results show that while multiple-merger coalescents are often interpreted as the signature of selective sweeps in rapidly adapting populations, these structures can also appear in the context of Muller’s ratchet.},
author = {Khudiakova, Kseniia and Boenkost, Florin and Tourniaire, Julie N},
booktitle = {bioRxiv},
title = {{Genealogies under purifying selection}},
doi = {10.1101/2024.10.15.618444},
year = {2024},
}
@article{14463,
abstract = {Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.},
author = {Reeve, James and Butlin, Roger K. and Koch, Eva L. and Stankowski, Sean and Faria, Rui},
issn = {1365-294X},
journal = {Molecular Ecology},
number = {24},
publisher = {Wiley},
title = {{Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)}},
doi = {10.1111/mec.17160},
volume = {33},
year = {2024},
}
@phdthesis{14711,
abstract = {In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.
For species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges
as well as in highly fragmented populations.
In this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.
Chapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.
In chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.
The focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.
Chapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.
Overall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management.},
author = {Olusanya, Oluwafunmilola O},
issn = {2663-337X},
pages = {183},
publisher = {Institute of Science and Technology Austria},
title = {{Local adaptation, genetic load and extinction in metapopulations}},
doi = {10.15479/at:ista:14711},
year = {2024},
}
@article{14850,
abstract = {Elaborate sexual signals are thought to have evolved and be maintained to serve as honest indicators of signaller quality. One measure of quality is health, which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal gecko that is often infested with ectoparasites in the wild, and males of this species express visual (coloured gular patches) and chemical (femoral gland secretions) traits that receivers could assess during social interactions. In this paper, we tested whether ectoparasites affect individual health, and whether signal quality is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite level was negatively correlated with body condition in both sexes. Moreover, some characteristics of both visual and chemical traits in males were strongly associated with ectoparasite levels. Specifically, males with higher ectoparasite levels had yellow gular patches with lower brightness and chroma, and chemical secretions with a lower proportion of aromatic compounds. We then determined whether ectoparasite levels in males influence female behaviour. Using sequential choice trials, wherein females were provided with either the visual or the chemical signals of wild-caught males that varied in ectoparasite level, we found that only chemical secretions evoked an elevated female response towards less parasitised males. Simultaneous choice trials in which females were exposed to the chemical secretions from males that varied in parasite level further confirmed a preference for males with lower parasites loads. Overall, we find that although health (body condition) or ectoparasite load can be honestly advertised through multiple modalities, the parasite-mediated female response is exclusively driven by chemical signals.},
author = {Pal, Arka and Joshi, Mihir and Thaker, Maria},
issn = {0022-0949},
journal = {Journal of Experimental Biology},
keywords = {Insect Science, Molecular Biology, Animal Science and Zoology, Aquatic Science, Physiology, Ecology, Evolution, Behavior and Systematics},
number = {1},
publisher = {The Company of Biologists},
title = {{Too much information? Males convey parasite levels using more signal modalities than females utilise}},
doi = {10.1242/jeb.246217},
volume = {227},
year = {2024},
}
@phdthesis{15020,
abstract = {This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.
Chapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?
Chapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.
Chapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.
Chapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.},
author = {Hledik, Michal},
issn = {2663-337X},
keywords = {Theoretical biology, Optimality, Evolution, Information},
pages = {158},
publisher = {Institute of Science and Technology Austria},
title = {{Genetic information and biological optimization}},
doi = {10.15479/at:ista:15020},
year = {2024},
}
@article{15099,
abstract = {Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.},
author = {Johannesson, Kerstin and Faria, Rui and Le Moan, Alan and Rafajlović, Marina and Westram, Anja M and Butlin, Roger K. and Stankowski, Sean},
issn = {1362-4555},
journal = {Trends in Genetics},
number = {4},
pages = {337--351},
publisher = {Elsevier},
title = {{Diverse pathways to speciation revealed by marine snails}},
doi = {10.1016/j.tig.2024.01.002},
volume = {40},
year = {2024},
}
@article{15358,
abstract = {We consider how a population of N haploid individuals responds to directional selection on standing variation, with no new variation from recombination or mutation. Individuals have trait values z1,…,zN, which are drawn from a distribution ψ; the fitness of individual i is proportional to [Formula: see text] . For illustration, we consider the Laplace and Gaussian distributions, which are parametrised only by the variance V0, and show that for large N, there is a scaling limit which depends on a single parameter NV0. When selection is weak relative to drift (NV0≪1), the variance decreases exponentially at rate 1/N, and the expected ultimate gain in log fitness (scaled by V0), is just NV0, which is the same as Robertson's (1960) prediction for a sexual population. In contrast, when selection is strong relative to drift (NV0≫1), the ultimate gain can be found by approximating the establishment of alleles by a branching process in which each allele competes independently with the population mean and the fittest allele to establish is certain to fix. Then, if the probability of survival to time t∼1/V0 of an allele with value z is P(z), with mean P¯, the winning allele is the fittest of NP¯ survivors drawn from a distribution ψP/P¯. The expected ultimate change is ∼2log(1.15NV0) for a Gaussian distribution, and ∼-12log0.36NV0-log-log0.36NV0 for a Laplace distribution. This approach also predicts the variability of the process, and its dynamics; we show that in the strong selection regime, the expected genetic variance decreases as ∼t-3 at large times. We discuss how these results may be related to selection on standing variation that is spread along a linear chromosome.},
author = {Barton, Nicholas H and Sachdeva, Himani},
issn = {1096-0325},
journal = {Theoretical Population Biology},
pages = {129--137},
publisher = {Elsevier},
title = {{Limits to selection on standing variation in an asexual population}},
doi = {10.1016/j.tpb.2024.04.001},
volume = {157},
year = {2024},
}
@article{18491,
abstract = {Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the intertidal snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. On the basis of spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions and transformation was both dramatic and rapid. Hence, adaptation can be predicted from knowledge of the phenotypic and genetic variation among populations.},
author = {Garcia Castillo, Diego Fernando and Barton, Nicholas H and Faria, Rui and Larsson, Jenny and Stankowski, Sean and Butlin, Roger and Johannesson, Kerstin and Westram, Anja M},
issn = {2375-2548},
journal = {Science Advances},
number = {41},
publisher = {AAAS},
title = {{Predicting rapid adaptation in time from adaptation in space: A 30-year field experiment in marine snails}},
doi = {10.1126/sciadv.adp2102},
volume = {10},
year = {2024},
}
@misc{18498,
abstract = {Scripts and data used in the research study Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails. https://doi.org/10.1101/2023.09.27.559715},
author = {Garcia Castillo, Diego Fernando and Barton, Nicholas H and Faria, Rui and Larsson, Jenny and Stankowski, Sean and Butlin, Roger and Johannesson, Kerstin and Westram, Anja M},
publisher = {Zenodo},
title = {{Data and code for: Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails}},
doi = {10.5281/ZENODO.12159343},
year = {2024},
}
@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 Laminaria digitata 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},
}