Sean Stankowski

University of Sussex · Department of Ecology and Evolution

Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic “landscape” of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use...

A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that sur...

Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even...

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 repr...

Short-read whole-genome sequencing helps us to understand the genetic mechanisms underpinning evolution. To go from raw reads to variants requires a bioinformatic pipeline. Processing sequence data in bioinformatic pipelines is intricate, with several intermediate steps that have a plethora of parameters and options. A default variant-discovery pip...

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 experim...

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 effec...

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 b...

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 t...

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 experim...

Chromosomal rearrangements lead to the coupling of reproductive barriers, but whether and how they contribute to completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between taxa segregating for inversion arrangements, providing opportunities to study this question. Here, we analysed two adjace...

Understanding the origin of species is no easy task. Academic studies of speciation usually take place over a few years, while the process itself usually occurs over evolutionary timescales. How, then, can we possibly hope to understand speciation from start to finish? The idea of a “speciation continuum” has been presented as something of a soluti...

Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used w...

Abstract: Key innovations are fundamental to biological diversification, but their genetic architecture is poorly understood. A recent transition from egg-laying to live-bearing in Littorina snails provides the opportunity to study the architecture of a young innovation. Samples do not cluster by reproductive mode in a genome-wide phylogeny, but lo...

Understanding the phenotypic and genetic architecture of reproductive isolation is a longstanding goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine ‘top‐down’ and...

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 de...

The term “haplotype block” is commonly used in the developing field of haplotype‐based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relation b...

Hybrid speciation—the origin of new species resulting from the hybridization of genetically divergent lineages—was once considered rare, but genomic data suggest that it may occur more often than once thought. In this study, Noguerales and Ortego (2022) find genomic evidence supporting the hybrid origin of a grasshopper that is able to exploit a br...

Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing th...

Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex‐determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex‐determining region. Chromosomal inversions may contribute to recom...

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 dispers...

The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relation b...

The term "haplotype block" is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relation b...

Understanding the phenotypic and genetic architecture of reproductive isolation is a longstanding goal of speciation research. In many systems, candidate barrier traits and loci have been identified, but causal connections between them are rarely made. In this study, we combine ‘top-down’ and ‘bottom-up’ approaches with demographic modeling toward...

Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species,...

This document gives basic instructions for how to install and use an interactive dashboard to explore and analyze the results of an online survey of speciation researchers. The purpose of the survey was to gauge thoughts about concepts and ideas that are central to speciation research along with respondent information about their research interests...

Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wid...

Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics i...

The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism ge...

The Oxford English Dictionary defines a concept as, "an idea of a class of objects, a general notion". It follows from this definition that a concept cannot be rejected in the way that an hypothesis might be rejected if its predictions are inconsistent with observations. Instead, a concept must be judged by its heuristic value: does it help in maki...

Hybrid zones, where distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Studying clines in genetic loci and adaptive traits across hybrid zones is a powerful method for understanding how selection drives differentiation within a single species, but can also be used to com...

Hybrid zones, where phenotypically distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Divergence in quantitative traits, controlled by multiple loci, may require stronger barriers to gene flow than traits controlled by few, major effect loci. The butterflies Heliconius e...

Hybrid zones, where phenotypically distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Divergence in quantitative traits, controlled by multiple loci, may require stronger barriers to gene flow than traits controlled by few, major effect loci. The butterflies Heliconius e...

Many forms of reproductive isolation contribute to speciation, and early acting barriers may be especially important, because they have the first opportunity to limit gene flow. Ecogeographic isolation occurs when intrinsic traits of taxa contribute to disjunct geographic distributions, reducing the frequency of inter‐taxon mating. Characterizing t...

Understanding the drivers and dynamics of speciation within oceanic islands is fundamental to achieve a process-based understanding of the assembly and structure of island communities. While there has been much interest in the non-neutral drivers of divergent evolution within islands, such as natural selection, there has been less focus on neutral...

In the Dampier Archipelago, Western Australia, land snails of the genus Rhagada are exceptional in two respects: (1) they show greater morphological diversity over distances of less than 70 km than does the rest of the genus over distances of up to 2,000 km; (2) the island morphospecies have complex, interspersed distributions , contrasting with th...

Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic ‘landscape’ of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use...

Premise of the study: Evolutionary radiations provide excellent opportunities to study the origins of biodiversity, but rapid divergence and ongoing gene flow make inferring evolutionary relationships among taxa difficult. Consequently, combining morphological and genomic analyses will be necessary to clarify the evolutionary history of radiations...

Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and...

Phylogenetic diversity of Rhagada land snails is high on the Burrup Peninsula, Western Australia, with four distinct clades, representing three of the four major clades of the Pilbara region. Detailed sampling indicated little geographic overlap of the four clades, conforming to the general rarity of congeneric sympatry in Australian camaenids. The...

Phylogenetic diversity of Rhagada land snails is high on the Burrup Peninsula, Western Australia, with four distinct clades, representing three of the four major clades of the Pilbara region. Detailed sampling indicated little geographic overlap of the four clades, conforming to the general rarity of congeneric sympatry in Australian camaenids. The...

A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic, or environmental data that might enhanc...

A major goal of speciation research is to reveal the genomic signatures that accompany the speciation process. Genome scans are routinely used to explore genome-wide variation and identify highly differentiated loci that may contribute to ecological divergence, but they do not incorporate spatial, phenotypic, or environmental data that might enhanc...

Ecological adaptation is the driving force during divergence-with-gene-flow and generates reproductive isolation early in speciation. Although gene flow opposes divergence, local adaptation can be facilitated by factors that prevent the breakup of favorable allelic combinations. We investigated how selection, genetic architecture, and geography hav...

A primary goal in evolutionary biology is to identify the historical events that have facilitated the origin and spread of adaptations. When these adaptations also lead to reproductive isolation, we can learn about the evolutionary mechanisms contributing to speciation. We reveal the complex history of the gene MaMyb2 in shaping flower colour diver...

The Western Australian camaenid genera Plectorhagada and Strepsitaurus have morphological similarities and mutually exclusive ranges near Cape Range. Sequences of ctyochrome c oxidase subunit I (COI) and 16S mitochondrial DNA (mtDNA) genes confirmed that the two genera are genetically close sister clades. Targeted sampling showed that Strepsitaurus...

The predictability of evolution depends on the roles that selection and historical contingency play in determining its outcomes, but the relative importance of these evolutionary mechanisms has attracted considerable debate. One view is that historical events have such a profound impact on the genetic structure of populations that patterns of pheno...

Camaenid land snails are often the focus of targeted biodiversity surveys in Australia, but can be difficult to locate because they hibernate for most of the year. Searches would be more effective if the density of live snails could be predicted from features of the habitat, or from the abundance of empty shells from long dead individuals. In 53 po...

In island archipelagos, where islands have experienced repeated periods of fragmentation and connection through cyclic changes in sea level, complex among-island distributions might reflect historical distributional changes or local evolution. We test the relative importance of these mechanisms in an endemic radiation of Rhagada land snails in the...

Fragmentation is generally considered to have negative impacts on widespread outbreeders but impacts on gene flow and diversity in patchy, naturally rare, self-compatible plant species remain unclear. We investigated diversity, gene flow and contemporary pollen-mediated gene immigration in the rare, narrowly distributed endemic shrub Calothamnus qu...

Speciation is the process by which reproductive isolation evolves between populations. Two general models of speciation have been proposed: ecological speciation, where reproductive barriers evolve due to ecologically based divergent selection, and mutation-order speciation, where populations fix different mutations as they adapt to similar selecti...

Three species of camaenid land snails occur on Barrow Island: Quistrachia barrowensis and two previously unassigned species of Rhagada. Based on morphological re-evaluation and analysis of sequences of the mitochondrial gene COI, we have revised the taxonomy of these species, providing a clearer understanding of their geographic distributions and o...

On Rosemary Island, a small continental island (11 km2) in the Dampier Archipelago, Western Australia, snails of the genus Rhagada have extremely diverse morphologies. Their shells vary remarkably in size and shape, with the latter ranging from globose to keeled‐flat, spanning the range of variation in the entire genus. Based primarily on variation...

Atriplex nummularia is a polyploid Australian saltbush which has been identified as a suitable species for use in the rehabilitation of agricultural land affected by salinity. We isolated 12 polymorphic loci for a preliminary assessment of genetic variability and structure within the species as a basis for a breeding programme. Preliminary screenin...

In recent years there has been a marked increase in the number of Australian universities offering courses or units in conservation biology. Consequently, there has been an increased demand for a student text which relates the intricacies of the discipline to the unique circumstances associated with the Australian continent. In response, Lindenmaye...