Alexandra Anh-Thu Weber

Alexandra Anh-Thu Weber
Eawag: Das Wasserforschungs-Institut des ETH-Bereichs | Eawag · Department of Aquatic Ecology

PhD
Adaptation & Conservation Genomics

About

46
Publications
13,653
Reads
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874
Citations
Introduction
I am an evolutionary biologist interested in deciphering the genomic mechanisms leading to adaptation and speciation. I also use genomic resources to implement conservation strategies for freshwater bivalves.
Additional affiliations
February 2022 - present
Eawag: Das Wasserforschungs-Institut des ETH-Bereichs
Position
  • Group Leader
January 2021 - January 2022
Institut Français de Recherche pour l'Exploitation de la Mer
Position
  • Marie Sklodowska-Curie Global Fellow
October 2018 - January 2021
Museum Victoria
Position
  • Marie Sklodowska-Curie Global Fellow
Education
October 2011 - January 2015
IMBE, Aix-Marseille Université
Field of study
  • Marine biology - population genetics - evolution - comparative transcriptomics
September 2009 - June 2011
Aix-Marseille Université
Field of study
  • Oceanography - Marine biology and ecology
September 2006 - June 2009
University of Lausanne
Field of study
  • Biology

Publications

Publications (46)
Article
Full-text available
Genetic diversity is the amount of variation observed between DNA sequences from distinct individuals of a given species. This pivotal concept of population genetics has implications for species health, domestication, management and conservation. Levels of genetic diversity seem to vary greatly in natural populations and species, but the determinan...
Article
Closely related species are key models to investigate mechanisms leading to reproductive isolation and early stages of diversification, also at the genomic level. The brittle star cryptic species complex Ophioderma longicauda encompasses the sympatric broadcast spawning species C3 and the internal brooding species C5. Here we used de novo transcrip...
Article
Full-text available
The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations, however their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated...
Preprint
Full-text available
Understanding the drivers and dynamics of diversification is a central topic in evolutionary biology. Here, we investigated the dynamics of diversification in the cichlid fish Astatotilapia burtoni that diverged along a lake-stream environmental gradient. Whole-genome and morphometric analyses revealed that divergent selection was essential at the...
Article
Full-text available
Hybrid conferences are in-person events that have an online component. This type of meeting format was rare before the COVID-19 pandemic, but started to become more common recently given the asynchronous global progression of the pandemic, the uneven access to vaccines and different travel regulations among countries that led to a large proportion...
Preprint
Full-text available
Hybrid conferences are in-person events that are also accessible online. This type of meeting format was rare pre-COVID-19 but started to become more common recently given the asynchronous global progression of the pandemic and the uneven access and distribution of vaccines that led to a large proportion of participants being unable to attend inter...
Article
Full-text available
Reticulated evolution -i.e. secondary introgression / admixture between sister taxa-is increasingly recognized as playing a key role in structuring infra-specific genetic variation and revealing cryptic genetic connectivity patterns. When admixture zones coincide with ecological transitions, the connectivity patterns often follow environmental vari...
Article
Full-text available
Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream populatio...
Preprint
Full-text available
The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations, however their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated...
Article
Full-text available
The conspicuous Mediterranean brittle star Ophioderma longicauda (Bruzelius, 1805) has been discovered to represent a cryptic species complex, consisting of six nuclear clusters with contrasting reproductive modes (broadcast spawners and brooders). Here, O. longicauda is re-described. It is distinguished by a dark reddish-brown colouration both dor...
Article
Accurate species delimitation is essential to properly assess biodiversity, but also for management and conservation purposes. Yet, it is not always trivial to accurately define species boundaries in closely related species due to incomplete lineage sorting. Additional difficulties may be caused by hybridization, now evidenced as a frequent phenome...
Article
Full-text available
Why sex chromosomes turn over and remain undifferentiated in some taxa, whereas they degenerate in others, is still an area of ongoing research. The recurrent occurrence of homologous and homomorphic sex chromosomes in distantly related taxa suggests their independent evolution or continued recombination since their first emergence. Fishes display...
Article
Full-text available
Xenophyophores are important megafaunal organisms in the abyssal Clarion-Clipperton Zone (CCZ; equatorial Pacific), a region hosting commercially significant deposits of polymetallic nodules. Previous studies assigned those with attached, fan-like tests to Psammina limbata, a species described from the central CCZ based on morphology. Here, we rede...
Article
Understanding how reproductive barriers evolve and which barriers contribute to speciation requires the examination of organismal lineages that are still in the process of diversification and the study of the full range of reproductive barriers acting at different life stages. Lake and river ecotypes of the East African cichlid fish Astatotilapia b...
Article
Based on a combination of morphological and molecular data, we describe five new species and two new genera of xenophyophores from the Clarion-Clipperton Zone (abyssal eastern Pacific), an area with commercially valuable seafloor deposits of polymetallic nodules. Bizarria bryiformis gen. et sp. nov. displays unusual features, notably an organic-wal...
Article
Full-text available
Adaptive phenotypic plasticity and fixed genotypic differences have long been considered opposing strategies in adaptation. More recently, these mechanisms have been proposed to act complementarily and under certain conditions jointly facilitate evolution, speciation, and even adaptive radiations. Here, we investigate the relative contributions of...
Preprint
Full-text available
Accurate species delimitation is essential to properly assess biodiversity, but also for management and conservation purposes. Yet, it is not always trivial to accurately define species boundaries in closely related species due to incomplete lineage sorting. Additional difficulties may be caused by hybridization, now evidenced as a frequent phenome...
Preprint
Full-text available
Reticulated evolution-i.e. secondary introgression/admixture between sister taxa-is increasingly recognized as a key evolutionary process that may play a role in promoting adaptation. Mytilus spp. is an ideal system to assess its importance, because these marine mussels form semi-isolated species that remain reproductively compatible over large tim...
Article
Full-text available
Based on a combination of morphological and molecular data, we describe five new species and two new genera of xenophyophores from the Clarion-Clipperton Zone (abyssal eastern Pacific), an area with commercially valuable seafloor deposits of polymetallic nodules. Bizarria bryiformis gen. et sp. nov. displays unusual features, notably an organic-wal...
Article
Genetic diversity is crucial for species’ maintenance and persistence, yet is often overlooked in conservation studies. Species diversity is more often reported due to practical constraints, but it is unknown if these measures of diversity are correlated. In marine invertebrates, adults are often sessile or sedentary and populations exchange genes...
Article
Full-text available
We describe Aschemonella monile Gooday and Holzmann sp. nov. from the Clarion-Clipperton Zone (CCZ, abys-sal eastern equatorial Pacific), a region characterized by commercially significant concentrations of polymetallic nod-ules. The new species is the most abundant xenophyophore (giant agglutinated foraminifera) in our main sampling area (12-14°N;...
Presentation
Full-text available
Unnoticed by the public, initiatives for oil exploration are advanced in Africa’s largest freshwater reservoirs, including Lakes Tanganyika, Malawi and lately Albert, threatening their ecosystems and biota. It is imperative that environmental impact assessments are conducted by independent organizations to ensure that decisions on this matter are b...
Article
Full-text available
Xenophyophores, giant, fragile, agglutinated foraminifera (protists), are major constituents of the abyssal megafauna in the equatorial Pacific Clarion-Clipperton Zone (CCZ), a region where seabed mining of polymetallic nodules may occur in the future. As part of a baseline study of benthic communities we made extensive collections of xenophyophore...
Article
Full-text available
Xenophyophores, giant, fragile, agglutinated foraminifera (protists), are major constituents of the abyssal megafauna in the equatorial Pacific Clarion-Clipperton Zone (CCZ), a region where seabed mining of polymetallic nodules may occur in the future. As part of a baseline study of benthic communities we made extensive collections of xenophyophore...
Article
Full-text available
As the world’s demands for hydrocarbons increase, remote areas previously made inaccessible by technological limitations are now being prospected for oil and gas deposits. Virtually unnoticed by the public, such activities are ongoing in the East African Great Lakes region, threatening these ecosystems famed for their hyper-diverse biota, includin...
Poster
Full-text available
With about 2,000 species, cichlid fishes from the East African Great Lakes are textbook examples of adaptive radiations. An example of ongoing adaptive divergence has recently been identified in the habitat generalist Astatotilapia burtoni, which occurs in Lake Tanganyika and inflowing rivers. Several lake-stream populations have been characterized...
Article
Full-text available
Closely related species with divergent life-history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatr...
Article
Full-text available
Cryptic species are numerous in the marine environment. The brittle star Ophioderma longicauda is composed of six mitochondrial lineages, encompassing brooders, which form a monophyletic group, and broadcasters, from which the brooders are derived. To clarify the species limits within O. longicauda, we compared the reproductive status of the sympat...
Poster
Full-text available
Here we compared the connectivity and genetic diversity between the broadcasting and the brooding species of the Ophioderma longicauda species complex
Article
Full-text available
Protists are key players in microbial communities, yet our understanding of their role in ecosystem functioning is seriously impeded by difficulties in identification of protistan species and their quantification. Current microscopy-based methods used for determining the abundance of protists are tedious and often show a low taxonomic resolution. R...
Data
Restriction fragments generated after digestion of PCR products of Allogromia , Rosalina and Bolivina by Dra I and Cfo I restriction enzymes. (DOC)
Data
Number of cells of each species used for the experimental mixes. (DOC)
Data
SSU rDNA copy number estimation for Allogromia , Rosalina and Bolivina inferred from qPCR data and corresponding copy number factors relatively to Bolivina results, used for normalization of the sequence data. (DOC)
Data
Number of rDNA sequences of Allogromia , Rosalina , Bolivina found after cloning and sequencing of five PCR products of the mixes of species (Replicate 1), RFLP analysis of five PCR products of the mixes of species (Replicates 2 and 3). (DOC)
Data
Number of cDNA sequences of Allogromia , Rosalina , Bolivina found after cloning and sequencing of PCR products of the five mixes of species and RFLP analysis. (DOC)
Data
PCR primers used for this study. (DOC)
Data
SSU rRNA expression level for Allogromia , Rosalina and Bolivina inferred from qPCR data and corresponding Expression Level Factors (ELF) relatively to Bolivina results, used for normalization of the sequence data. (DOC)
Article
Full-text available
Global warming is expected to change marine species distributions; it is thus critical to understand species current thermotolerance. The brittle star species complex Ophioderma longicauda comprises a broadcast spawning lineage L1 and a brooding lineage L3. We collected L1 specimens from Marseilles and Crete, and L3 specimens from Crete. We monitor...

Projects

Projects (3)
Project
The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations, however their molecular mechanisms remain understudied. Brittle stars, a very diverse group of marine invertebrates abundant in the deep-sea, colonized this environment several times independently, highlighting their strong adaptive abilities. In this project, we are investigating the molecular mechanisms underlying deep-sea adaptation in brittle stars using genomic methods (e.g. de novo genome assembly & annotation, whole-genome resequencing, exon-capture). By investigating different bathymetric transitions and spanning a wide phylogenetic range (from the within-species to the between-family resolution), we intend to obtain a comprehensive overview of the different adaptation mechanisms involved.
Project
In this project, we study adaptive divergence in East African cichlids, making use of replicate lake-stream population pairs in four cichlid species in the area of Lake Tanganyika, with a particular focus on Astatotilapia burtoni. Using population genomics, transplant experiments and mate-choice assays, our aim is to bring novel insights into cichlid speciation and to further advance the understanding of how selection acts on natural populations.
Project
In this project, we study the brittle star cryptic species complex Ophioderma longicauda, which encompasses six divergent mitochondrial lineages and two different reproductive strategies. Some mitochondrial lineages are broadcast spawners, whereas other are internal brooders. the aims of this project are: - to define species boundaries within this complex and inferring the most likely demographic scenario of divergence using multilocus data - to estimate the selective pressures arising from a change in reproductive mode - to compare connectivity between species displaying contrasting dispersal potentials - to infer if the thermotolerances of the brooding and the broadcasting species are different