Joana I Meier

Verified

Joana verified their affiliation via an institutional email.

Learn more

Verified

Joana verified their affiliation via an institutional email.

Learn more

• PhD
• Group Leader at Wellcome Sanger Institute

Modes and mechanisms of speciation are best studied in young species pairs. In older taxa it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pu...

Understanding why some evolutionary lineages generate exceptionally high species diversity is an important goal in evolutionary biology. Haplochromine cichlid fishes of Africa’s Lake Victoria region encompass >700 diverse species that all evolved in the last 150,000 years. How this ‘Lake Victoria Region Superflock’ could evolve on such rapid timesc...

Speciation is often thought of as a slow process due to the waiting times for mutations that cause incompatibilities, and permit ecological differentiation or assortative mating. Cases of rapid speciation and particularly cases of rapid adaptive radiation into multiple sympatric species have remained somewhat mysterious. We review recent findings f...

Studies on polymorphisms have been foundational to our understanding of evolution. The presence of different phenotypic morphs is sometimes considered a precursor to speciation in which morphs evolve into different species. While speciation should initially reduce genetic variation in daughter versus parental species, a common pattern is the recurr...

Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequen...

We present a genome assembly from a female specimen of Podarcis filfolensis (Maltese wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,506.95 megabases and 1,404.02 megabases. Most of haplotype 1 (98.73%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z s...

We present a genome assembly from a female specimen of Podarcis erhardii (Erhard's wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,495.98 megabases and 1,477.75 megabases. Most of haplotype 1 (99.28%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex...

We present a genome assembly from a female specimen of Larus michahellis (Yellow-legged Gull; Chordata; Aves; Charadriiformes; Laridae). The genome sequence has a total length of 1,405.56 megabases. Most of the assembly (90.55%) is scaffolded into 35 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has al...

New species typically evolve over several million years. However, rates of speciation and ecological diversification vary by orders of magnitude across the tree of life, with the fastest shown by some adaptive radiations. Eight hundred endemic species of cichlid fishes emerged and formed entire food webs in Lake Victoria and nearby lakes in East Af...

Background The endosymbiotic relationship between Wolbachia bacteria and insects has been of interest for many years due to their diverse types of host reproductive phenotypic manipulation and potential role in the host’s evolutionary history and population dynamics. Even though infection rates are high in Lepidoptera and specifically in butterflie...

Speciation is a complex process that can unfold in many different ways. Speciation researchers sometimes simplify core principles in their writing in a way that implies misconceptions about the speciation process. While we think that these misconceptions are usually inadvertently implied (and not actively believed) by the researchers, they nonethel...

Niche partitioning within variable habitats can expose species to distinct sensory information. Vision is the primary sensory modality used by many animals to interact with their habitat. However, within diurnal terrestrial ecosystems, little is known if, and how, variation in light environments impact species assemblages and visual system evolutio...

Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery...

A major question in evolutionary biology is what drives the diversification of lineages. Rapid, recent radiations are ideal systems for addressing how new species arise because they still show key morphological and ecological adaptations associated with speciation. While most studied recent radiations have evolved in an insular environment, less re...

We present a genome assembly from an individual female Spicauda simplicius (the Plain Longtail butterfly; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 610.1 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also bee...

Hybridization, or interbreeding between different taxa, was traditionally considered to be rare and to have a largely detrimental impact on biodiversity, sometimes leading to the breakdown of reproductive isolation and even to the reversal of speciation. However, modern genomic and analytical methods have shown that hybridization is common in some...

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...

The black soldier fly (Hermetia illucens) is the prime species in the developing global industry of insects as food and feed, but the genetic basis of its domestication has not been studied. We obtained whole genome sequences for 54 individuals from both wild and captive populations. We identified two genetic lineages at least 3 million years diver...

Although some lineages of animals and plants have made impressive adaptive radiations when provided with ecological opportunity, the propensities to radiate vary profoundly among lineages for unknown reasons. In Africa’s Lake Victoria region, one cichlid lineage radiated in every lake, with the largest radiation taking place in a lake less than 16,...

The repeated evolution of phenotypes provides clear evidence for the role of natural selection in driving evolutionary change. However, the evolutionary origin of repeated phenotypes can be difficult to disentangle as it can arise from a combination of factors such as gene flow, shared ancestral polymorphisms or mutation. Here, we investigate the p...

Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery...

A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive...

The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Müllerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Recent studies on the ecology and genetics of speciation in Ithomiini have suggested that sexual p...

The repeated evolution of phenotypes is ubiquitous in nature and offers some of the clearest evidence of the role of natural selection in evolution. The genomic basis of repeated phenotypic evolution is often complex and can arise from a combination of gene flow, shared ancestral polymorphism and de novo mutation. Here, we investigate the genomic b...

Repeated evolution can provide insight into the mechanisms that facilitate adaptation to novel or changing environments. Here we study adaptation to altitude in two tropical butterflies, Heliconius erato and H. melpomene , which have repeatedly and independently adapted to montane habitats on either side of the Andes. We sequenced 518 whole genomes...

The ithomiine butterflies (Nymphalidae: Danainae) represent the largest known radiation of Mullerian mimetic butterflies. They dominate by number the mimetic butterfly communities, which include species such as the iconic neotropical Heliconius genus. Despite recent studies carried out on ithomiine ecology and genetic structure, no reference genome...

Intraspecific colour polymorphisms (CPs) present unique opportunities to study fundamental evolutionary questions, such as the link between ecology and phenotype, mechanisms maintaining genetic diversity and their putative role in speciation. Wrasses are highly diverse in ecology and morphology and harbour a variety of colour-polymorphic species. I...

Repeated evolution can provide insight into the mechanisms that facilitate adaptation to novel or changing environments. Here we study adaptation to high altitude in two divergent tropical butterflies, H. erato and H. melpomene, which have repeatedly and independently adapted to high elevations on either side of the Andean mountains. We sequenced 5...

Understanding how organisms adapt to their local environment is central to evolution. With new whole‐genome sequencing technologies and the explosion of data, deciphering the genomic basis of complex traits that are ecologically relevant is becoming increasingly feasible. Here we study the genomic basis of wing shape in two Neotropical butterflies...

Significance A defining goal in genetics is linking variation in DNA sequence to trait evolution between populations and, ultimately, species. Genome sequencing efficiently captures such variation but typically in millions of tiny fragments that omit haplotype or linkage information. We present “haplotagging,” a simple, rapid linked-read sequencing...

If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic c...

Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid f...

Understanding how organisms adapt to their local environment is central to evolution. With new whole-genome sequencing technologies and the explosion of data, deciphering the genomic basis of complex traits that are ecologically relevant is becoming increasingly feasible. Here we study the genomic basis of wing shape in two Neotropical butterflies...

Speciation rates vary considerably among lineages, and our understanding of what drives the rapid succession of speciation events within young adaptive radiations remains incomplete1–11. The cichlid fish family provides a notable example of such variation, with many slowly speciating lineages as well as several exceptionally large and rapid radiati...

African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral sh...

Background Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before as...

The East African cichlid radiations are characterized by repeated and rapid diversification into many distinct species with different ecological specializations and by a history of hybridization events between nonsister species. Such hybridization might provide important fuel for adaptive radiation. Interspecific hybrids can have extreme trait valu...

Hybridization between invasive and native species has raised global concern, given the dramatic increase in species range shifts and pest outbreaks due to anthropogenic dispersal. Nevertheless, secondary contact between sister lineages of local and invasive species provides a natural laboratory to understand the factors that determine introgression...

Microclimatic variability in tropical forests plays a key role in shaping species distributions and their ability to cope with environmental change, especially for ectotherms. Nonetheless, currently available climatic datasets lack data from the forest interior and, furthermore, our knowledge of thermal tolerance among tropical ectotherms is limite...

Background Diploid genome assembly is typically impeded by heterozygosity, as it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution which exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assem...

African cichlid fishes are a prime model for studying the mechanisms of speciation. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for variation in cichlid phenotypes. Cichlids have some of the largest known shifts in vertebrate visual sensitivity. These...

Microclimatic variability in tropical forests plays a key role in shaping species distributions and their ability to cope with environmental change, especially for ectotherms. Yet, currently available climatic datasets lack data from the forest interior and our knowledge of thermal tolerance among tropical ectotherms is limited. To tackle this, we...

Hybridization between invasive and native species has raised global concern given the dramatic increase in species range shifts and pest outbreaks due to climate change, development of suitable agroecosystems, and anthropogenic dispersal. Nevertheless, secondary contact between sister lineages of local and invasive species provides a natural labora...

The process of adaptive radiation was classically hypothesized to require isolation of a lineage from its source (no gene flow) and from related species (no competition). Alternatively, hybridization between species may generate genetic variation that facilitates adaptive radiation. Here we study haplochromine cichlid assemblages in two African Gre...

Interspecific hybridization is the process where closely related species mate and produce offspring with admixed genomes. The genomic revolution has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive an...

Phenotypic divergence between closely related species has long interested biologists. Taxa that inhabit a range of environments and have diverse natural histories can help understand how selection drives phenotypic divergence. In butterflies, wing colour patterns have been extensively studied but diversity in wing shape and size is less well unders...

Phenotypic divergence between closely related species has long interested biologists. Taxa that inhabit a range of environments and have known and diverse, natural histories, can help understand how different selection pressures shape diverging traits. In butterflies, wing colour patterns have been extensively studied, whereas wing shape diversity...

Mating behavior between recently diverged species in secondary contact can impede or promote reproductive isolation. Traditionally, researchers focus on the importance of female mate choice and male‐male competition in maintaining or eroding species barriers. Although female‐female competition is widespread, little is known about its role in the sp...

While gene flow can reduce the potential for local adaptation, hybridization may conversely provide genetic variation that increases the potential for local adaptation. Hybridization may also affect adaptation through altering sexual dimorphism and sexual conflict, but this remains largely unstudied. Here, we discuss how hybridization may affect se...

Adaptive radiation research typically relies on the study of evolution in retrospective, leaving the predictive value of the concept hard to evaluate. Several radiations, including the cichlid fishes in the East African Great Lakes, have been studied extensively, yet no study has investigated the onset of the intraspecific processes of niche expans...

Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F...

While gene flow can reduce the potential for local adaptation, hybridization may conversely provide genetic variation that increases the potential for local adaptation. Hybridization may also affect adaptation through altering sexual dimorphism and sexual conflict, but this remains largely unstudied. Here, we discuss how hybridization may affect se...

The genetic basis of parallel evolution of similar species is of great interest in evolutionary biology. In the adaptive radiation of Lake Victoria cichlid fishes, sister species with either blue or red-back male nuptial coloration have evolved repeatedly, often associated with shallower and deeper water, respectively. One such case are blue and re...

Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F...

Supplementary Figures, Supplementary Tables, Supplementary Discussion, Supplementary Methods and Supplementary References

Groups, missing data proportions and number of polymorphic sites.

Ancestry informative SNPs at the LWS opsin gene.

Taxon sampling.

Ecological speciation is the evolution of reproductive isolation as a consequence of direct divergent natural selection or ecologically mediated divergent sexual selection. While the genomic signature of the former has been extensively studied in recent years, only few examples exist for genomic differentiation where environment-dependent sexual se...

Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection. Most genomic studies of ecological speciation have investigated allopatric populations, making it difficult to infer reproductive isolation. The few studies on sympatric ecotypes h...

Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the...