28 Works

Data from: Cross-species hybridization and the origin of North African date palms

Jonathan M. Flowers, Khaled M. Hazzouri, Muriel Gros-Balthazard, Ziyi Mo, Konstantina Koutroumpa, Andreas Perrakis, Sylvie Ferrand, Hussam S. M. Khierallah, Dorian Q. Fuller, Frederique Aberlenc, Christini Fournaraki & Michael D. Purugganan
Date palm (Phoenix dactylifera L.) is a major fruit crop of arid regions that were domesticated 7,000 y ago in the Near or Middle East. This species is cultivated widely in the Middle East and North Africa, and previous population genetic studies have shown genetic differentiation between these regions. We investigated the evolutionary history of P. dactylifera and its wild relatives by resequencing the genomes of date palm varieties and five of its closest relatives....

Local ecological knowledge of fisheries charts decline of sharks in data-poor regions

Dareen Almojil
Scientific knowledge is lacking on marine species of economic and conservation importance, hindering their sustainable management. Local Ecological Knowledge (LEK) has the potential to provide valuable insights on large (spatial and temporal) scales, by drawing on the collective experiences of those who work closely with the taxa of interest. This study explored the status of shark population over time in four countries across eastern and southern Arabia (i.e. Kuwait, Bahrain, Oman and Yemen). Results indicate...

A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird

Guillermo Friis
The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior and evolutionary biology for over a century. It is composed by at least six distinct, geographically structured forms of recent evolutionary origin presenting remarkable variation in phenotypic traits, migratory behavior and habitat. Here we report a high-quality genome assembly and annotation of the dark-eyed junco generated using...

What Peer-review Experiences Can Offer To Early Career Scientists And To The Scientific Community

Gwenaëlle Gremion, Mathieu Casado, Kelsey Aho, Jilda Alicia Caccavo, Nicolas Champollion, Emily Choy, Sarah L. Connors, Rahul Dey, Alfonso Fernandez, Gerlis Fugmann, Juan Höfer, Shridhar Jawak, Martine Lizotte, Sarah Maes, Kyle Mayers, Katja Mintenbeck, Jhon Fredy Mojica Moncada, Prashant H. Pandit, Elvira Poloczanska, Paul Rosenbaum, Elisa Seyboth, Sarah Shakil & Maud van Soest

Data from: The genome and phenome of the green alga Chloroidium sp. UTEX 3007 reveal adaptive traits for desert acclimatization

David R. Nelson, Basel Khraiwesh, Weiqi Fu, Saleh Alseekh, Ashish Jaiswal, Amphun Chaiboonchoe, Khaled Hazzouri, Matthew J. O’Connor, Glenn L. Butterfoss, Nizar Drou, Jillian D. Rowe, Jamil Harb, Alisdair R. Fernie, Kristin C. Gunsalus & Kourosh Salehi-Ashtiani
To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sources, including several desiccation tolerance-promoting sugars and unusually large stores of palmitate. Growth assays revealed capacities to grow in salinities from zero...

Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

Jae Young Choi & Michael D. Purugganan
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between...

Supplementary datasets for: Large-scale genome sequencing reveals the driving forces of viruses in microalgal evolution

David Nelson
Microalgae are integral primary producers for global ecosystems whose genomes can be mined for ecological insights, but representative genome sequences are lacking for many phyla. We cultured and sequenced 107 microalgae species from 11 different phyla indigenous to varied geographies and climates. This genome collection was used to resolve genomic differences between saltwater and freshwater microalgae. Freshwater species showed domain-centric ontology enrichment for nuclear and nuclear membrane functions, while saltwater species were enriched in organellar...

Data from: Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

Annalise B. Paaby, Amelia G. White, David D. Riccardi, Kristin C. Gunsalus, Fabio Piano & Matthew V. Rockman
Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of C. elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants...

A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina

Guillermo Friis, Joel Vizueta, David R. Nelson, Basel Khraiwesh, Enas Qudeimat, Kourosh Salehi-Ashtiani, Alejandra Ortega, Alyssa Marshell, Carlos M. Duarte & Edward Smith
The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level...

Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

Yann Bourgeois, Robert Ruggiero, Imtiyaz Hariyani & Stephane Boissinot
The interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole ( Anolis carolinensis...

Patterns of volatile diversity yield insights into the genetics and biochemistry of the date palm fruit volatilome

Jonathan Flowers, Khaled Hazzouri, Alain Lemansour, Tiago Capote, Muriel Gros-Balthazard, Sylvie Ferrand, Marc Lebrun, Khaled Amiri & Michael Purugganan
Volatile organic compounds are key components of the fruit metabolome that contribute to traits such as aroma and taste. Here we report on the diversity of 90 flavor-related fruit traits in date palms (Phoenix dactylifera L.) including 80 volatile organic compounds, which collectively represent the fruit volatilome, as well as 6 organic acids, and 4 sugars in tree-ripened fruits. We characterize these traits in 148 date palms representing 135 varieties using headspace solid-phase microextraction gas...

Rapid evolutionary divergence of a songbird population following recent colonization of an urban area

Guillermo Friis, Jonathan Atwell, Adam Fudickar, Timothy Greives, Pamela Yeh, Trevor Price, Ellen Ketterson & Borja Milá
Colonization of a novel environment by a small group of individuals can lead to rapid evolutionary change, yet evidence of the relative contributions of neutral and selective factors in promoting divergence during the early stages of colonization remain scarce. Here, we use genome-wide SNP data to test the role of neutral and selective forces in driving the divergence of a unique urban population of the Oregon junco (Junco hyemalis oreganus), which became established on the...

Data from: Synopsis and taxonomic revision of three genera in the snake tribe Sonorini

Christian L. Cox, Alison R. Davis Rabosky, Iris A. Holmes, Jacobo Reyes-Velasco, Corey E. Roelke, Eric N. Smith, Oscar Flores-Villel, Jimmy A. McGuire & Jonathan A. Campbell
Delimiting species is a crucial goal of integrative biology, and yet can be misled by homoplasy and high levels of morphological variation. The snake tribe Sonorini contains three genera that have long confounded taxonomists: Chilomeniscus, Chionactis and Sonora. Dynamic colour evolution in this group, including rampant geographic variation in colour and colour polymorphism, has led to a chaotic taxonomy. We used mitochondrial and high-throughput nuclear data (ddRADseq) and complete taxonomic sampling of each genus to...

Data from: Adaptive changes in sexual signaling in response to urbanization

Wouter Halfwerk, Michiel Blaas, Lars Kramer, Nadia Hijner, Paula A. Trillo, Ximena E. Bernal, Rachel A. Page, Sandra Goutte, Michael J. Ryan & Jacintha Ellers
Urbanization can cause species to adjust their sexual displays, as the effectiveness of mating signals is impacted by environmental conditions. Despite many examples showing that mating signals in urban conditions differ from those in rural conditions, we do not know whether these differences provide a combined reproductive and survival benefit to the urban phenotype. Here we show that male túngara frogs have increased the conspicuousness of their calls, which is under strong sexual and natural...

Data from: Whole genome resequencing reveals extensive natural variation in the model green alga Chlamydomonas reinhardtii

Jonathan M. Flowers, Khaled M. Hazzouri, Gina M. Pham, Ulises Rosas, Tayebeh Bahmani, Basel Khraiwesh, David R. Nelson, Kenan Jijakli, Rasha Abdrabu, Elizabeth H. Harris, Paul A. Lefebvre, Erik F. Y. Hom, Kourosh Salehi-Ashtiani & Michael D. Purugganan
We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. Nucleotide diversity is ∼3% and is geographically structured in North America with some evidence of admixture among sampling locales. Examination of predicted loss-of-function mutations in field isolates indicates...

Data from: The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ

Remi N. Ketchum, Melissa B. DeBiasse, Joseph F. Ryan, John A. Burt & Adam M. Reitzel
The complete mitogenome of Echinometra sp. EZ has been described and fully annotated in this study. Cytochrome subunit one phylogenetic analysis of six Echinometra species confirms that our sample is E. sp. EZ. The mitogenome is 15,698 bp in length and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a non-coding region with an identical organization to other Echinoidea. The E. sp. EZ mitogenome shared ~99.1% identity to the published Echinometra mathaei mitogenome, differing...

Data from: Differential effect of selection against LINE retrotransposons among vertebrates inferred from whole-genome data and demographic modeling

Alexander T Xue, Robert P. Ruggiero, Michael J. Hickerson & Stéphane Boissinot
Variation in LINE composition is one of the major determinants for the substantial size and structural differences among vertebrate genomes. In particular, the larger genomes of mammals are characterized by hundreds of thousands of copies from a single LINE clade, L1, whereas nonmammalian vertebrates possess a much greater diversity of LINEs, yet with orders of magnitude less in copy number. It has been proposed that such variation in copy number among vertebrates is due to...

Data from: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach

Edward G. Smith, Remi N. Ketchum & John A. Burt
Analysis of the widely used ITS region is confounded by the presence of intragenomic variants (IGVs). In Symbiodinium, the algal symbionts of reef building corals, deep-sequencing analyses are used to characterise communities within corals, yet these analyses largely overlook IGVs. Here we consider that distinct ITS2 sequences could represent IGVs rather than distinct symbiont types and argue that symbionts can be distinguished by their proportional composition of IGVs, described as their ITS2 metahaplotype. Using our...

Allometric escape from acoustic constraints in frog calls is rare

Joao Filipe Tonini, Diogo Provete, Natan Maciel, Alessandro Morais, Sandra Goutte, Felipe Toledo & R. Alexander Pyron
Allometric constraint is a product of natural selection, particularly with respect to body size and traits constrained by physical properties thereof, such as metabolism, longevity, and vocal frequency. Parameters describing allometric relationships are conserved across most lineages, indicating that physical constraints dictate scaling patterns in deep time, despite substantial genetic and ecological divergence among organisms. Acoustic allometry (sound frequency ~ body size) is conserved across frogs, in defiance of massive variation in both body size...

Perl scripts from: The genomes of ancient date palms germinated from 2,000-year-old seeds

Muriel Gros-Balthazard & Jonathan Flowers
Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated from the fourth century BCE to the second century CE, were recovered from archaeological sites in the Southern Levant and germinated to yield viable plants. We conducted whole-genome sequencing of these germinated ancient samples and used single-nucleotide polymorphism data to examine the genetics of these previously extinct Judean date palms. We find that the oldest seeds from the fourth to first century BCE are related to...

Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients

Remi Ketchum, Edward Smith, Grace Vaughan, Dain McParland, Noura Al-Mansoori, John Burt & Adam Reitzel
Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species’ range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20℃ - 37℃) and is connected to the Gulf of Oman which experiences more...

Data from: Diversification in wild populations of the model organism Anolis carolinensis: a genome-wide phylogeographic investigation

Joseph D. Manthey, Marc Tollis, Alan R. Lemmon, Emily Moriarty Lemmon & Stephane Boissinot
The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among...

Data from: Genetic structure of coral-Symbiodinium symbioses on the world’s warmest reefs

Edward G. Smith, Benjamin C. C. Hume, Patrice Delaney, Jörg Wiedenmann & John A. Burt
Corals in the Arabian/Persian Gulf (PAG) survive extreme sea temperatures (summer mean: >34°C), and it is unclear whether these corals have genetically adapted or physiologically acclimated to these conditions. In order to elucidate the processes involved in the thermal tolerance of PAG corals, it is essential to understand the connectivity between reefs within and outside of the PAG. To this end, this study set out to investigate the genetic structure of the coral, Platygyra daedalea,...

Data from: GPCR genes as activators of surface colonization pathways in a model marine diatom

Ashish Kumar Jaiswal, Weiqi Fu, Amphun Chaiboonchoe, Bushra Dohai, Mehar Sultana, Kristos Baffour, Amnah Alzahmi, James Weston, Dina Al-Khairy, Sarah Daakour, Ashish Jaiswal, David Nelson, Alexandra Mystikou, Sigurdur Brynjolfsson & Kourosh Salehi-Ashtiani
Surface colonization allows diatoms, a dominant group of phytoplankton in oceans, to adapt to harsh marine environments while mediating biofoulings to human-made underwater facilities. The regulatory pathways underlying diatom surface colonization, which involves morphotype switching in some species, remain mostly unknown. Here, we describe the identifications of 61 signaling genes, including G-protein-coupled receptors (GPCRs) and protein kinases, that are differentially regulated during surface colonization in the model diatom species, Phaeodactylum tricornutum. We show that the...

Environmental and morphological constraints interact to drive the evolution of communication signals in frogs

Matías Muñoz, Sandra Goutte, Jacintha Ellers & Wouter Halfwerk
Animals show a rich diversity of signals and displays. Among the many selective forces driving the evolution of communication between individuals, one widely recognized factor is the structure of the environment in which signals are produced, transmitted and received. In particular, animals communicating by sounds often emit acoustic signals from specific locations, such as high up in the air, from the ground or in the water. The properties of these different display sites will impose...

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