Genetic load: genomic estimates and applications in non-model animals

Nature Reviews Genetics, Journal Year: 2022, Volume and Issue: 23(8), P. 492 - 503

Published: Feb. 8, 2022

Language: Английский

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Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(12), P. 5782 - 5805

Published: Sept. 1, 2021

Abstract Drosophila melanogaster is a leading model in population genetics and genomics, growing number of whole-genome data sets from natural populations this species have been published over the last years. A major challenge integration disparate sets, often generated using different sequencing technologies bioinformatic pipelines, which hampers our ability to address questions about evolution species. Here we these issues by developing bioinformatics pipeline that maps pooled (Pool-Seq) reads D. hologenome consisting fly symbiont genomes estimates allele frequencies either heuristic (PoolSNP) or probabilistic variant caller (SNAPE-pooled). We use generate largest repository genomic available for date, encompassing 271 previously unpublished samples 100 locations >20 countries on four continents. Several sampled at seasons across multiple This set, call Evolution Space Time (DEST), coupled with sampling environmental metadata. web-based genome browser web portal provide easy access SNP set. further guidelines how Pool-Seq model-based demographic inference. Our aim scalable platform as community resource can be easily extended via future efforts an even more extensive cosmopolitan will enable geneticists analyze spatiotemporal genetic patterns evolutionary dynamics unprecedented detail.

Language: Английский

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Meta‐analysis suggests negative, but p CO ₂ ‐specific, effects of ocean acidification on the structural and functional properties of crustacean biomaterials

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(6)

Published: June 1, 2022

Crustaceans comprise an ecologically and morphologically diverse taxonomic group. They are typically considered resilient to many environmental perturbations found in marine coastal environments, due effective physiological regulation of ions hemolymph pH, a robust exoskeleton. Ocean acidification can affect the ability calcifying organisms build maintain mineralized tissue poses threat for all taxa. Currently, there is no consensus on how ocean will alter relevant exoskeletal properties crustaceans. Here, we present systematic review meta-analysis effects crustacean exoskeleton, assessing both ion content (calcium magnesium) functional (biomechanical resistance cuticle thickness). Our results suggest that effect varies based upon seawater

Language: Английский

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From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles

Molecular Ecology, Journal Year: 2021, Volume and Issue: 30(23), P. 6417 - 6433

Published: May 8, 2021

The northern acorn barnacle (Semibalanus balanoides) is a robust system to study the genetic basis of adaptations highly heterogeneous environments. Adult barnacles may be exposed dissimilar levels thermal stress depending on where they settle in intertidal (i.e., closer upper or lower tidal boundary). For instance, near limit experience episodic summer temperatures above recorded heat coma levels. This differential at microhabitat level also dependent aspect sun exposure. In present study, we used pool-seq approaches conduct genome wide screen for loci responding zonation across North Atlantic basin (Maine, Rhode Island, and Norway). Our analysis discovered 382 genomic regions containing SNPs which are consistently zonated whose frequencies vary their position rocky intertidal) all surveyed habitats. Notably, most young private Atlantic. These show high differentiation ecologically extreme microhabitats concomitant with elevated variation Tajima's D, suggesting action non-neutral processes. Overall, these findings support hypothesis that spatially selection general repeatable feature this species, natural can maintain functional

Language: Английский

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Trans‐Specific Polymorphisms Between Cryptic Daphnia Species Affect Fitness and Behavior

Molecular Ecology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 24, 2024

Shared polymorphisms, loci with identical alleles across species, are of unique interest in evolutionary biology as they may represent cases selection maintaining ancient genetic variation post-speciation, or contemporary promoting convergent evolution. In this study, we investigate the abundance shared polymorphism between two members Daphnia pulex species complex. We test whether presence mutations is consistent action balancing alternative hypotheses such hybridization, incomplete lineage sorting analyzed over 2,000 genomes from six taxa D. group and examined prevalence distribution focal pair, North American European pulex. show that diverged 10 million years ago, yet retained tens thousands polymorphisms. suggest number polymorphisms cannot be fully explained by hybridization alone. most could product evolution, a limited appear to old trans-specific affecting alike. Finally, provide evidence blue wavelength opsin gene has functional effects on behavior fitness wild.

Language: Английский

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Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions

Marine Biotechnology, Journal Year: 2021, Volume and Issue: 23(3), P. 402 - 416

Published: May 1, 2021

Barnacles are key marine crustaceans in several habitats, and they constitute a common practical problem by causing biofouling on man-made constructions ships. Despite considerable ecological economic impacts, there is surprising void of basic genomic knowledge, barnacle reference genome lacking. We here set out to characterize the bay Balanus improvisus (= Amphibalanus improvisus) based short-read whole-genome sequencing experimental size estimation. show both experimentally (DNA staining flow cytometry) computationally (k-mer analysis) that B. has haploid ~ 740 Mbp. A pilot assembly rendered total 600 Mbp was highly fragmented with an N50 only 2.2 kbp. Further assembly-based assembly-free analyses revealed very limited contiguity due having extremely high nucleotide diversity (π) coding regions (average π ≈ 5% average fourfold degenerate sites 20%), overall repeat content (at least 40%). also report variation α-octopamine receptor OctA = 3.6%), which might increase risk populations evolve resistance toward antifouling agents. The features described can help planning for future high-quality genome, urgently needed properly explore understand proteins interest biology biotechnology developing better strategies.

Language: Английский

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Chaotic Genetic Patchiness in the Highly Valued Atlantic Stalked Barnacle Pollicipes pollicipes From the Iberian Peninsula: Implications for Fisheries Management

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: March 15, 2022

The stalked barnacle Pollicipes pollicipes inhabits rocky shores from the Atlantic coasts of Brittany (France) to Senegal. Because culinary traditions southern Europe, barnacles represent an important target species for local fisheries on Iberian Peninsula. To manage this fishery sustainably, it is therefore assess dynamics populations over coast, and how they are interconnected at a wider scale using finely tuned genetic markers. In work, new enriched library GT microsatellites P. was prepared sequenced Ion Torrent™ Next Gen-Sequencing Technology. 1,423 adults juveniles were sampled in 15 localities three geographic regions: Portugal, Galicia Asturias (both northern Spain). Twenty polymorphic loci arranged five multiplex PCRs then tested validated as molecular tools address spatial temporal patterns . Our results revealed high diversity among adults. However, genetically more structured than their adult counterparts, which alternatively displayed much connectivity studied regions. lack heterogeneity may be due overlapping several generations settlers coming different origins, mainly depends orientation residual currents along coast during reproduction. differentiation indeed congruent with Peninsula hydrodynamics, can produce chaotic patchiness (CGP) small scales sweepstake reproductive success, collective dispersal and/or self-recruitment. Remarkably, most found work located Galicia, could admixture between distinct metapopulations or old refuge populations. conclude, variation lead false impression population panmixia by masking restricted current-driven larval exchanges This possibility should taken into consideration further specific management conservation plans

Language: Английский

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Genomic Adaptations to an Endoparasitic Lifestyle in the Morphologically Atypical CrustaceanSacculina carcini(Cirripedia: Rhizocephala)

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(10)

Published: Oct. 1, 2022

Abstract The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of refined developmental program, we produced draft genome sequence for comparison with genomes nonparasitic barnacles and characterized transcriptomes internal external tissues. clusters orthologous genes revealed depletion multiple gene families but also several unanticipated expansions compared to non-parasitic crustaceans. Transcriptomic analyses comparing interna externa tissues an unexpected variation expression between rootlets sampled around host midgut thoracic ganglia. Genes associated lipid uptake were strongly expressed by We identified candidate probably involved in manipulation (suppression ecdysis gonad development) including those encoding neurohormones juvenile hormone binding protein. evolution Rhizocephala therefore appears have rapid turnover (losses expansions) as well fine tuning expression.

Language: Английский

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Characterizing the cirri and gut microbiomes of the intertidal barnacle Semibalanus balanoides

Animal Microbiome, Journal Year: 2020, Volume and Issue: 2(1)

Published: Nov. 13, 2020

Abstract Background Natural populations inhabiting the rocky intertidal experience multiple ecological stressors and provide an opportunity to investigate how environmental differences influence microbiomes over small geographical scales. However, very few microbiome studies focus on animals that inhabit intertidal. In this study, we of barnacle Semibalanus balanoides . We first describe two body tissues: feeding appendages, or cirri, gut. Next, examine whether there are between each tissue barnacles collected from thermally extreme microhabitats shores’ upper lower tidal zones. Results Overall, S. consisted 18 phyla 408 genera. Our results showed although cirri gut shared a portion their amplicon sequence variants (ASVs), was distinct. Over 80% ASVs found in were also gut, 44% cirri. Notably, not subset microbiome. Additionally, identified responsive microhabitat differences. Conclusion study indicate maintains distinct its tissues, is more stable than extremes

Language: Английский

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A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Feb. 10, 2022

ABSTRACT Understanding the patterns of selection during plant evolution and recent crop improvement processes is central topic in breeding genetics. As an essential macronutrient for growth development, nitrogen (N) a key factor affecting adaptation improvement. The widespread adoption less expensive industrial N fixation has dramatically reshaped morphology by favoring compact maize plants to tolerant crowding stress. associated genetic changes, however, have not been systematically studied. Here, we investigated inbred lines developed before after 1960s — time point when inorganic fertilizer started be widely used production. We identified strong selective sweep exhibiting pronounced genomic differentiation between Old-Era (pre-1960s) New-Era (post-1960s) lines. Further study revealed population genetics statistics exhibited consistent with historical balancing selection. This balanced interval number morphological, physiological, metabolite traits related vegetative responses. A cluster three glutamate receptor-like (GLR) genes located within region targeted Functional characterizations suggested differences transcriptional activity GLR haplotypes carried likely play role mediating distinct identification both targets changes regulation responsive different eras sheds light on sensing pathways paves way developing resilient crops.

Language: Английский

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