746 results match your criteria inferred shifts


Symbiont switching and trophic mode shifts in Orchidaceae.

New Phytol 2021 May 1. Epub 2021 May 1.

Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands.

• Mycorrhizal fungi are central to the biology of land plants. However, to what extent mycorrhizal shifts - broad evolutionary transitions in root-associated fungal symbionts - are related to changes in plant trophic modes remains poorly understood. • We built a comprehensive DNA dataset of Orchidaceae fungal symbionts and a dated plant molecular phylogeny to test the hypothesis that shifts in orchid trophic modes follow a stepwise pattern, from autotrophy over partial mycoheterotrophy (mixotrophy) to full mycoheterotrophy, and that these shifts are accompanied by switches in fungal symbionts. Read More

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Sediment archives reveal irreversible shifts in plankton communities after World War II and agricultural pollution.

Curr Biol 2021 Apr 17. Epub 2021 Apr 17.

CNRS, UMR 6538 Laboratoire Géosciences Océan (LGO), Université de Brest (UBO), 29280 Plouzané, France.

To evaluate the stability and resilience of coastal ecosystem communities to perturbations that occurred during the Anthropocene, pre-industrial biodiversity baselines inferred from paleoarchives are needed. The study of ancient DNA (aDNA) from sediments (sedaDNA) has provided valuable information about past dynamics of microbial species and communities in relation to ecosystem variations. Shifts in planktonic protist communities might significantly affect marine ecosystems through cascading effects, and therefore the analysis of this compartment is essential for the assessment of ecosystem variations. Read More

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Hydrologic and nutrient-driven regime shifts of cyanobacterial and eukaryotic algal communities in a large shallow lake: Evidence from empirical state indicator and ecological network analyses.

Sci Total Environ 2021 Apr 12;783:147059. Epub 2021 Apr 12.

State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.

The detection and prediction of lake ecosystem responses to environmental changes are pressing scientific challenge of major global relevance. Specifically, an understanding of lake ecosystem stability over long-term scales is urgently needed to identify impending ecosystem regime shifts induced by human activities and improve lake ecosystem protection. This study investigated regime shifts in cyanobacterial and eukaryotic algal communities in a large shallow lake over a century in response to nutrient enrichment and hydrologic regulation using evidence from empirical state indicators and ecological network analyses of sedimentary-inferred communities. Read More

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Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries.

Nat Commun 2021 04 13;12(1):2213. Epub 2021 Apr 13.

Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada.

Global oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. Read More

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Tomato agamous-like6 parthenocarpy is facilitated by ovule integument reprogramming involving the growth regulator KLUH.

Plant Physiol 2021 Apr;185(3):969-984

ARO, Volcani Center, Institute of Plant Sciences, HaMaccabbim Road 68, Rishon LeZion 7505101, Israel.

Fruit set is established during and soon after fertilization of the ovules inside the quiescent ovary, but the signaling pathways involved remain obscure. The tomato (Solanum lycopersicum) CRISPR loss-of-function mutant of the transcription factor gene AGAMOUS-like6 (SlAGL6; slagl6CR-sg1) is capable of fertilization-independent setting of normal, yet seedless (parthenocarpic), fruit. To gain insight into the mechanism of fleshy fruit set, in this study, we investigated how slagl6CR-sg1 uncouples fruit set from fertilization. Read More

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Absence of reliable physiological signature of illusory body ownership revealed by fine-grained autonomic measurement during the rubber hand illusion.

PLoS One 2021 1;16(4):e0237282. Epub 2021 Apr 1.

School of Psychology, University of Sussex, Brighton, United Kingdom.

The neural representation of a 'biological self' is linked theoretically to the control of bodily physiology. In an influential model, selfhood relates to internal agency and higher-order interoceptive representation, inferred from the predicted impact of efferent autonomic nervous activity on afferent viscerosensory feedback. Here we tested if an altered representation of physical self (illusory embodiment of an artificial hand) is accompanied by sustained shifts in autonomic activity. Read More

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Dietary ecology of Alaskan polar bears (Ursus maritimus) through time and in response to Arctic climate change.

Glob Chang Biol 2021 Apr 1. Epub 2021 Apr 1.

Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.

Arctic climate change poses serious threats to polar bears (Ursus maritimus) as reduced sea ice makes seal prey inaccessible and marine ecosystems undergo bottom-up reorganization. Polar bears' elongated skulls and reduced molar dentition, as compared to their sister species the grizzly bear (Ursus arctos), are adaptations associated with hunting seals on sea ice and a soft, lipid-rich diet of blubber and meat. With significant declines in sea ice, it is unclear if and how polar bears may be altering their diets. Read More

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Climatic effects on niche evolution in a passerine bird clade depend on paleoclimate reconstruction method.

Evolution 2021 Mar 16. Epub 2021 Mar 16.

Senckenberg Biodiversity and Climate Research Centre, Frankfurt, 60325, Germany.

Climatic niches describe the climatic conditions in which species can persist. Shifts in climatic niches have been observed to coincide with major climatic change, suggesting that species adapt to new conditions. We test the relationship between rates of climatic niche evolution and paleoclimatic conditions through time for 65 Old-World flycatcher species (Aves: Muscicapidae). Read More

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Effect of Ocean Acidification on Bacterial Metabolic Activity and Community Composition in Oligotrophic Oceans, Inferred From Short-Term Bioassays.

Front Microbiol 2021 26;12:583982. Epub 2021 Feb 26.

State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.

Increasing anthropogenic CO emissions in recent decades cause ocean acidification (OA), affecting carbon cycling in oceans by regulating eco-physiological processes of plankton. Heterotrophic bacteria play an important role in carbon cycling in oceans. However, the effect of OA on bacteria in oceans, especially in oligotrophic regions, was not well understood. Read More

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February 2021

: An Automated Workflow to Account for Isotopologue-Related Interferences in Electrospray Ionization High-Resolution Mass Spectra of Phospholipids.

J Am Soc Mass Spectrom 2021 Apr 11;32(4):1008-1019. Epub 2021 Mar 11.

In the past decade, hydrophilic interaction liquid chromatography (HILIC) has emerged as an efficient alternative to reversed-phase chromatography (RPC) for the analysis of phospholipid (PL) mixtures based on mass spectrometric detection. Since the separation of PL by HILIC is chiefly based on their headgroup, the mass spectrum of each class can be obtained by spectral averaging under the corresponding HILIC band. Using experimental / values resulting from high mass resolution/accuracy instruments, the sum compositions of PL in a specific class can be thus inferred but partial overlapping may occur between signals related to the M + 0 isotopologue of one species and the M + 2/M + 4 isotopologues of species having one/two more C═C bonds in their chemical structures. Read More

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Identifying functional metabolic shifts in heart failure with the integration of omics data and a heart-specific, genome-scale model.

Cell Rep 2021 Mar;34(10):108836

Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA; Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA. Electronic address:

In diseased states, the heart can shift to use different carbon substrates, measured through changes in uptake of metabolites by imaging methods or blood metabolomics. However, it is not known whether these measured changes are a result of transcriptional changes or external factors. Here, we explore transcriptional changes in late-stage heart failure using publicly available data integrated with a model of heart metabolism. Read More

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Composition and distribution of fish environmental DNA in an Adirondack watershed.

PeerJ 2021 26;9:e10539. Epub 2021 Feb 26.

U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA.

Background: Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration.

Methods: We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Read More

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February 2021

Starvation Alters Gut Microbiome in Black Soldier Fly (Diptera: Stratiomyidae) Larvae.

Front Microbiol 2021 16;12:601253. Epub 2021 Feb 16.

Department of Biological Sciences, Mississippi State University, Starkville, MS, United States.

Unlike for vertebrates, the impact of starvation on the gut microbiome of invertebrates is poorly studied. Deciphering shifts in metabolically active associated bacterial communities in vertebrates has led to determining the role of the associated microbiome in the sensation of hunger and discoveries of associated regulatory mechanisms. From an invertebrate perspective, such as the black soldier fly, such information could lead to enhanced processes for optimized biomass production and waste conversion. Read More

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February 2021

Multilocus phylogeny and historical biogeography of Hypostomus shed light on the processes of fish diversification in La Plata Basin.

Sci Rep 2021 Mar 3;11(1):5073. Epub 2021 Mar 3.

Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva 4, Switzerland.

Distribution history of the widespread Neotropical genus Hypostomus was studied to shed light on the processes that shaped species diversity. We inferred a calibrated phylogeny, ancestral habitat preference, ancestral areas distribution, and the history of dispersal and vicariance events of this genus. The phylogenetic and distribution analyses indicate that Hypostomus species inhabiting La Plata Basin do not form a monophyletic clade, suggesting that several unrelated ancestral species colonized this basin in the Miocene. Read More

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Quaternary climatic fluctuations influence the demographic history of two species of sky-island endemic amphibians in the Neotropics.

Mol Phylogenet Evol 2021 Jul 19;160:107113. Epub 2021 Feb 19.

Department of Herpetology, American Museum of Natural History, New York, NY, USA.

We evaluated the role of Quaternary climatic fluctuations on the demographic history and population structure of amphibian species endemic to the 'campo rupestre' in the Neotropics, evaluating their distributional shifts, demographic changes, and lineage formation from the end of Pleistocene to present. We chose two anurans endemic to the high-elevation 'campo rupestre' in the Espinhaço Range (ER) in northeastern and southeastern Brazil (Bokermannohyla alvarengai and Bokermannohyla oxente), as models to test the role of Quaternary climatic fluctuations over their distribution range in this region. We collected tissue samples throughout their distribution range and used statistical phylogeography to examine processes of divergence and population demography. Read More

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Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterised by multiple karyotypic shifts under major environmental instability.

Mol Phylogenet Evol 2021 Jun 16;159:107105. Epub 2021 Feb 16.

Herbarium and Library of African Botany, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, Belgium; Missouri Botanical Garden, Africa and Madagascar Department, 4344 Shaw Blvd., St. Louis, MO 63110, USA; Meise Botanic Garden, Domein van Bouchout, Nieuwelaan 38, B-1860 Meise, Belgium.

Angraecoid orchids present a remarkable diversity of chromosome numbers, which makes them a highly suitable system for exploring the impact of karyotypic changes on cladogenesis, diversification and morphological differentiation. We compiled an annotated cytotaxonomic checklist for 126 species of Angraecinae, which was utilised to reconstruct chromosomal evolution using a newly-produced, near-comprehensive phylogenetic tree that includes 245 angraecoid taxa. In tandem with this improved phylogenetic framework, using combined Bayesian, maximum likelihood and parsimony approaches on ITS-1 and five plastid markers, we propose a new cladistic nomenclature for the angraecoids, and we estimate a new timeframe for angraecoid radiation based on a secondary calibration, and calculate diversification rates using a Bayesian approach. Read More

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Climate and Nutrient-Driven Regime Shifts of Cyanobacterial Communities in Low-Latitude Plateau Lakes.

Environ Sci Technol 2021 03 15;55(5):3408-3418. Epub 2021 Feb 15.

State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.

Cyanobacterial blooms that form in response to climate warming and nutrient enrichment in freshwater lakes have become a global environmental challenge. Historical legacy effects and the mechanisms underlying cyanobacterial community succession are not well understood, especially for plateau lakes that are important global freshwater resources. This study investigated the temporal dynamics of cyanobacterial communities over centuries in response to nutrient enrichment and climate warming in low-latitude plateau lakes using high-throughput DNA sequencing of sedimentary DNA combined with traditional paleolimnological analyses. Read More

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Dietary Diversification and Specialisation in New World Bats Facilitated by Early Molecular Evolution.

Mol Biol Evol 2021 Feb 15. Epub 2021 Feb 15.

School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.

Dietary adaptation is a major feature of phenotypic and ecological diversification, yet the genetic basis of dietary shifts is poorly understood. Among mammals, Neotropical leaf-nosed bats (family Phyllostomidae) show unmatched diversity in diet; from a putative insectivorous ancestor, phyllostomids have radiated to specialize on diverse food sources, including blood, nectar, and fruit. To assess whether dietary diversification in this group was accompanied by molecular adaptations for changing metabolic demands, we sequenced 89 transcriptomes across 58 species, and combined these with published data to compare ∼13,000 protein coding genes across 66 species. Read More

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February 2021

The landscape of gene-CDS-haplotype diversity in rice: Properties, population organization, footprints of domestication and breeding, and implications for genetic improvement.

Mol Plant 2021 May 10;14(5):787-804. Epub 2021 Feb 10.

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Agronomy, Anhui Agricultural University, Hefei, Anhui, 230036, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China. Electronic address:

Polymorphisms within gene coding regions represent the most important part of the overall genetic diversity of rice. We characterized the gene-coding sequence-haplotype (gcHap) diversity of 45 963 rice genes in 3010 rice accessions. With an average of 226 ± 390 gcHaps per gene in rice populations, rice genes could be classified into three main categories: 12 865 conserved genes, 10 254 subspecific differentiating genes, and 22 844 remaining genes. Read More

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Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front.

Sci Rep 2021 Jan 29;11(1):2682. Epub 2021 Jan 29.

Ifremer-Centre de Brest, DYNECO/Pelagos, Technopôle Brest Iroise, 29280, Plouzané, France.

Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. Read More

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January 2021

A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses.

Syst Biol 2021 Jan 28. Epub 2021 Jan 28.

Department of the Geophysical Sciences, University of Chicago, Chicago, USA.

Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species-rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Read More

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January 2021

Speaking with an alien voice: Flexible sense of agency during vocal production.

J Exp Psychol Hum Percept Perform 2021 Jan 25. Epub 2021 Jan 25.

Department of Philosophy, Lund University Cognitive Science, Lund University.

Speakers monitor auditory feedback during speech production in order to correct for speech errors. The comparator model proposes that this process is supported by comparing sensory feedback to internal predictions of the sensory consequences of articulation. Additionally, this comparison process is proposed to support the sense of agency over vocal output. Read More

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January 2021

Menopausal status and observed differences in the gut microbiome in women with and without HIV infection.

Menopause 2021 Jan 11;28(5):491-501. Epub 2021 Jan 11.

Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY.

Objective: Gut microbiota respond to host physiological phenomena, yet little is known regarding shifts in the gut microbiome due to menopausal hormonal and metabolic changes in women. HIV infection impacts menopause and may also cause gut dysbiosis. We therefore sought to determine the association between menopausal status and gut microbiome composition in women with and without HIV. Read More

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January 2021

Wolbachia infection in wild mosquitoes (Diptera: Culicidae): implications for transmission modes and host-endosymbiont associations in Singapore.

Parasit Vectors 2020 Dec 9;13(1):612. Epub 2020 Dec 9.

Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.

Background: Wolbachia are intracellular bacterial endosymbionts found in most insect lineages. In mosquitoes, the influence of these endosymbionts on host reproduction and arboviral transmission has spurred numerous studies aimed at using Wolbachia infection as a vector control technique. However, there are several knowledge gaps in the literature and little is known about natural Wolbachia infection across species, their transmission modes, or associations between various Wolbachia lineages and their hosts. Read More

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December 2020

Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation.

Elife 2020 12 2;9. Epub 2020 Dec 2.

Department of Biology, Stanford University, Stanford, United States.

Building a genotype-phenotype-fitness map of adaptation is a central goal in evolutionary biology. It is difficult even when adaptive mutations are known because it is hard to enumerate which phenotypes make these mutations adaptive. We address this problem by first quantifying how the fitness of hundreds of adaptive yeast mutants responds to subtle environmental shifts. Read More

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December 2020

Expression Partitioning of Duplicate Genes at Single Cell Resolution in Roots.

Front Genet 2020 3;11:596150. Epub 2020 Nov 3.

School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, United States.

Gene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralog pairs rapidly return to single copy status whereas, in other pairs, both paralogs are retained and may diverge in expression pattern or function. The effect of a gene - its site of expression and thus the initial locus of its function - occurs at the level of a cell comprising a single cell type at a given state of the cell's development. Read More

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November 2020

Weak founder effects but significant spatial genetic imprint of recent contraction and expansion of European beech populations.

Heredity (Edinb) 2021 Mar 23;126(3):491-504. Epub 2020 Nov 23.

URFM, INRAE, 84 000, Avignon, France.

Understanding the ecological and evolutionary processes occurring during species range shifts is important in the current context of global change. Here, we investigate the interplay between recent expansion, gene flow and genetic drift, and their consequences for genetic diversity and structure at landscape and local scales in European beech (Fagus sylvatica L.) On Mont Ventoux, South-Eastern France, we located beech forest refugia at the time of the most recent population minimum, ~150 years ago, and sampled 71 populations (2042 trees) in both refugia and expanding populations over an area of 15,000 ha. Read More

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Soil carbon and associated bacterial community shifts driven by fine root traits along a chronosequence of Moso bamboo (Phyllostachys edulis) plantations in subtropical China.

Sci Total Environ 2021 Jan 9;752:142333. Epub 2020 Sep 9.

China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou 310012, PR China. Electronic address:

Moso bamboo (Phyllostachys edulis) is widely considered to be effective in capturing and sequestering atmospheric C, but the long-term effects of extensive management strategies on soil organic carbon (SOC), bacterial communities, fine root (FR, ø ≤ 2 mm) traits, and their inherent connection remain unclear. In this study, we simultaneously measured the SOC content of the bulk and rhizosphere soil fractions, the aggregate stability, the chemical composition of SOC (solid-state C nuclear magnetic resonance [NMR]), the bacterial community structure in the rhizosphere, and the FR morphological traits including biomass, specific root length (SRL), and root length density (RLD) along a chronosequence (stand age of 19, 37, and 64 years) of extensively managed Moso bamboo plantations and in an adjacent secondary forest as a control. The organic C content in both the rhizosphere and bulk soil increased rapidly with plantation age in the 0-20- and 20-40-cm soil layers, accompanied by an increase in the aggregate stability. Read More

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January 2021

A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs.

J Mol Evol 2020 12 29;88(10):720-730. Epub 2020 Oct 29.

Department of Biological Sciences, Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.

Heterotachy-the change in sequence evolutionary rate over time-is a common feature of protein molecular evolution. Decades of studies have shed light on the conditions under which heterotachy occurs, and there is evidence that site-specific evolutionary rate shifts are correlated with changes in protein function. Here, we present a large-scale, computational analysis using thousands of protein sequence alignments from animal and plant proteomes, representing genes related either by orthology (speciation events) or paralogy (gene duplication), to compare sequence divergence patterns in orthologous vs. Read More

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December 2020

Predicting Thermal Adaptation by Looking Into Populations' Genomic Past.

Front Genet 2020 25;11:564515. Epub 2020 Sep 25.

Division of Geological and Planetary Sciences, California Institute of Technology (Caltech), Pasadena, CA, United States.

Molecular evolution offers an insightful theory to interpret the genomic consequences of thermal adaptation to previous events of climate change beyond range shifts. However, disentangling often mixed footprints of selective and demographic processes from those due to lineage sorting, recombination rate variation, and genomic constrains is not trivial. Therefore, here we condense current and historical population genomic tools to study thermal adaptation and outline key developments (genomic prediction, machine learning) that might assist their utilization for improving forecasts of populations' responses to thermal variation. Read More

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September 2020