journal
https://read.qxmd.com/read/38597332/genetic-insight-into-a-polygenic-trait-using-a-novel-genome-wide-association-approach-in-a-wild-amphibian-population
#41
JOURNAL ARTICLE
Elisavet-Aspasia Toli, Petri Kemppainen, Anastasios Bounas, Konstantinos Sotiropoulos
Body size variation is central in the evolution of life-history traits in amphibians, but the underlying genetic architecture of this complex trait is still largely unknown. Herein, we studied the genetic basis of body size and fecundity of the alternative morphotypes in a wild population of the Greek smooth newt (Lissotriton graecus). By combining a genome-wide association approach with linkage disequilibrium network analysis, we were able to identify clusters of highly correlated loci thus maximizing sequence data for downstream analysis...
April 10, 2024: Molecular Ecology
https://read.qxmd.com/read/38597329/a-time-course-analysis-through-diapause-reveals-dynamic-temporal-patterns-of-micrornas-associated-with-endocrine-regulation-in-the-butterfly-pieris-napi
#42
JOURNAL ARTICLE
Kevin T Roberts, Rachel A Steward, Philip Süess, Philipp Lehmann, Christopher W Wheat
Organisms inhabiting highly seasonal environments must cope with a wide range of environmentally induced challenges. Many seasonal challenges require extensive physiological modification to survive. In winter, to survive extreme cold and limited resources, insects commonly enter diapause, which is an endogenously derived dormant state associated with minimized cellular processes and low energetic expenditure. Due to the high degree of complexity involved in diapause, substantial cellular regulation is required, of which our understanding primarily derives from the transcriptome via messenger RNA expression dynamics...
April 10, 2024: Molecular Ecology
https://read.qxmd.com/read/38596873/survival-in-nunatak-and-peripheral-glacial-refugia-of-three-alpine-plant-species-is-partly-predicted-by-altitudinal-segregation
#43
JOURNAL ARTICLE
Francesco Rota, Pau Carnicero, Gabriele Casazza, Juri Nascimbene, Peter Schönswetter, Camilla Wellstein
Mountain biota survived the Quaternary cold stages most probably in peripheral refugia and/or ice-free peaks within ice-sheets (nunataks). While survival in peripheral refugia has been broadly demonstrated, evidence for nunatak refugia is still scarce. We generated RADseq data from three mountain plant species occurring at different elevations in the southeastern European Alps to investigate the role of different glacial refugia during the Last Glacial Maximum (LGM). We tested the following hypotheses. (i) The deep Piave Valley forms the deepest genetic split in the species distributed across it, delimiting two peripheral refugia...
April 10, 2024: Molecular Ecology
https://read.qxmd.com/read/38591817/rapid-evolutionary-adaptation-potential-and-constraints
#44
EDITORIAL
Aurélien Tellier, Kathryn Hodgins, Wolfgang Stephan, Eva Stukenbrock
No abstract text is available yet for this article.
April 9, 2024: Molecular Ecology
https://read.qxmd.com/read/38584356/symbiodiniaceae-diversity-varies-by-host-and-environment-across-thermally-distinct-reefs
#45
JOURNAL ARTICLE
Magena R Marzonie, Matthew R Nitschke, Line K Bay, David G Bourne, Hugo B Harrison
Endosymbiotic dinoflagellates (Symbiodiniaceae) influence coral thermal tolerance at both local and regional scales. In isolation, the effects of host genetics, environment, and thermal disturbances on symbiont communities are well understood, yet their combined effects remain poorly resolved. Here, we investigate Symbiodiniaceae across 1300 km in Australia's Coral Sea Marine Park to disentangle these interactive effects. We identified Symbiodiniaceae to species-level resolution for three coral species (Acropora cf humilis, Pocillopora verrucosa, and Pocillopora meandrina) by sequencing two genetic markers of the symbiont (ITS2 and psbAncr ), paired with genotype-by-sequencing of the coral host (DArT-seq)...
April 7, 2024: Molecular Ecology
https://read.qxmd.com/read/38581173/the-influence-of-gene-flow-on-population-viability-in-an-isolated-urban-caracal-population
#46
JOURNAL ARTICLE
Christopher C Kyriazis, Laurel E K Serieys, Jacqueline M Bishop, Marine Drouilly, Storme Viljoen, Robert K Wayne, Kirk E Lohmueller
Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1...
April 5, 2024: Molecular Ecology
https://read.qxmd.com/read/38576177/genetic-legacies-of-mega-landslides-cycles-of-isolation-and-contact-across-flank-collapses-in-an-oceanic-island
#47
JOURNAL ARTICLE
Víctor Noguerales, Yurena Arjona, Víctor García-Olivares, Antonio Machado, Heriberto López, Jairo Patiño, Brent C Emerson
Catastrophic flank collapses are recognized as important drivers of insular biodiversity dynamics, through the disruption of species ranges and subsequent allopatric divergence. However, little empirical data supports this conjecture, with their evolutionary consequences remaining poorly understood. Using genome-wide data within a population genomics and phylogenomics framework, we evaluate how mega-landslides have impacted evolutionary and demographic history within a species complex of weevils (Curculionidae) within the Canary Island of Tenerife...
April 4, 2024: Molecular Ecology
https://read.qxmd.com/read/38572696/the-role-of-historical-biogeography-in-shaping-colour-morph-diversity-in-the-common-wall-lizard
#48
JOURNAL ARTICLE
Prem Aguilar, Guillem Pérez I de Lanuza, Miguel Carneiro, Pedro Andrade, Catarina Pinho
The maintenance of polymorphisms often depends on multiple selective forces, but less is known on the role of stochastic or historical processes in maintaining variation. The common wall lizard (Podarcis muralis) is a colour polymorphic species in which local colour morph frequencies are thought to be modulated by natural and sexual selection. Here, we used genome-wide single-nucleotide polymorphism data to investigate the relationships between morph composition and population biogeography at a regional scale, by comparing morph composition with patterns of genetic variation of 54 populations sampled across the Pyrenees...
April 4, 2024: Molecular Ecology
https://read.qxmd.com/read/38561950/epigenetic-age-estimation-of-wild-mice-using-faecal-samples
#49
JOURNAL ARTICLE
Eveliina Hanski, Susan Joseph, Aura Raulo, Klara M Wanelik, Áine O'Toole, Sarah C L Knowles, Tom J Little
Age is a key parameter in population ecology, with a myriad of biological processes changing with age as organisms develop in early life then later senesce. As age is often hard to accurately measure with non-lethal methods, epigenetic methods of age estimation (epigenetic clocks) have become a popular tool in animal ecology and are often developed or calibrated using captive animals of known age. However, studies typically rely on invasive blood or tissue samples, which limit their application in more sensitive or elusive species...
April 1, 2024: Molecular Ecology
https://read.qxmd.com/read/38558465/environmental-dna-unveils-deep-phylogeographic-structure-of-a-freshwater-fish
#50
JOURNAL ARTICLE
Tetsu Yatsuyanagi, Takashi Kanbe, Kazuya Fujii, Shouko Inoue, Hitoshi Araki
Phylogeography bears an important part in ecology and evolution. However, current phylogeographic studies are largely constrained by limited numbers of individual samples. Using an environmental DNA (eDNA) assay for phylogeographic analyses, this study provides detailed information regarding the history of Siberian stone loach Barbatula toni, a primary freshwater fish across the whole range of Hokkaido, Japan. Based on an eDNA metabarcoding on 293 river water samples, we detected eDNA from B. toni in 189 rivers...
April 1, 2024: Molecular Ecology
https://read.qxmd.com/read/38558454/retraction-the-genomics-of-mimicry-gene-expression-throughout-development-provides-insights-into-convergent-and-divergent-phenotypes-in-a-m%C3%A3-llerian-mimicry-system
#51
(no author information available yet)
Retraction: Stuckert, A. M. M., Chouteau, M., McClure, M., LaPolice, T. M., Linderoth, T., Nielsen, R., Summers, K., MacManes, M. D. (2021). The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system. Molecular Ecology, 30: 4039-4061. https://doi.org/10.1111/mec.16024. The above article, published online on 19 June 2021 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal Editor in Chief, Loren Rieseberg and John Wiley and Sons Ltd...
April 1, 2024: Molecular Ecology
https://read.qxmd.com/read/38556927/the-prevalence-of-copy-number-increase-at-multiallelic-copy-number-variants-associated-with-cave-colonization
#52
JOURNAL ARTICLE
Ivan Pokrovac, Nicolas Rohner, Željka Pezer
Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred...
March 31, 2024: Molecular Ecology
https://read.qxmd.com/read/38553993/signals-of-selection-and-ancestry-in-independently-feral-gallus-gallus-populations
#53
JOURNAL ARTICLE
E Gering, M Johnsson, D Theunissen, M L Martin Cerezo, A Steep, T Getty, R Henriksen, D Wright
Recent work indicates that feralisation is not a simple reversal of domestication, and therefore raises questions about the predictability of evolution across replicated feral populations. In the present study we compare genes and traits of two independently established feral populations of chickens (Gallus gallus) that inhabit archipelagos within the Pacific and Atlantic regions to test for evolutionary parallelism and/or divergence. We find that feral populations from each region are genetically closer to one another than other domestic breeds, despite their geographical isolation and divergent colonisation histories...
March 30, 2024: Molecular Ecology
https://read.qxmd.com/read/38549143/genetic-architecture-of-inbreeding-depression-may-explain-its-persistence-in-a-population-of-wild-red-deer
#54
JOURNAL ARTICLE
Anna M Hewett, Susan E Johnston, Alison Morris, Sean Morris, Josephine M Pemberton
Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH , we use chromosome-specific inbreeding coefficients (FROHChr ) to explore whether the effect of inbreeding varies between chromosomes...
March 28, 2024: Molecular Ecology
https://read.qxmd.com/read/38533805/genotype-environment-associations-reveal-genes-potentially-linked-to-avian-malaria-infection-in-populations-of-an-endemic-island-bird
#55
JOURNAL ARTICLE
Eleanor C Sheppard, Claudia A Martin, Claire Armstrong, Catalina González-Quevedo, Juan Carlos Illera, Alexander Suh, Lewis G Spurgin, David S Richardson
Patterns of pathogen prevalence are, at least partially, the result of coevolutionary host-pathogen interactions. Thus, exploring the distribution of host genetic variation in relation to infection by a pathogen within and across populations can provide important insights into mechanisms of host defence and adaptation. Here, we use a landscape genomics approach (Bayenv) in conjunction with genome-wide data (ddRADseq) to test for associations between avian malaria (Plasmodium) prevalence and host genetic variation across 13 populations of the island endemic Berthelot's pipit (Anthus berthelotii)...
March 27, 2024: Molecular Ecology
https://read.qxmd.com/read/38533629/nematodes-alter-the-taxonomic-and-functional-profiles-of-benthic-bacterial-communities-a-metatranscriptomic-approach
#56
JOURNAL ARTICLE
Rodgee Mae Guden, Annelies Haegeman, Tom Ruttink, Tom Moens, Sofie Derycke
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities...
March 27, 2024: Molecular Ecology
https://read.qxmd.com/read/38529738/non-concordant-epigenetic-and-transcriptional-responses-to-acute-thermal-stress-in-western-mosquitofish-gambusia-affinis
#57
JOURNAL ARTICLE
Xingyue Ren, Junjie Zhao, Juntao Hu
Climate change is intensifying the frequency and severity of extreme temperatures. Understanding the molecular mechanisms underlying the ability to cope with acute thermal stress is key for predicting species' responses to extreme temperature events. While many studies have focused on the individual roles of gene expression, post-transcriptional processes and epigenetic modifications in response to acute thermal stress, the relative contribution of these molecular mechanisms remains unclear. The wide range of thermal limits of western mosquitofish (Gambusia affinis) provides an opportunity to explore this interplay...
March 26, 2024: Molecular Ecology
https://read.qxmd.com/read/38529721/phylosymbiosis-and-metabolomics-resolve-phenotypically-plastic-and-cryptic-sponge-species-in-the-genus-agelas-across-the-caribbean-basin
#58
JOURNAL ARTICLE
M S Pankey, D J Gochfeld, M Gastaldi, K J Macartney, A Clayshulte Abraham, M Slattery, M P Lesser
Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses...
March 26, 2024: Molecular Ecology
https://read.qxmd.com/read/38520127/matching-maternal-and-paternal-experiences-underpin-molecular-thermal-acclimation
#59
JOURNAL ARTICLE
L C Bonzi, J M Donelson, R K Spinks, P L Munday, T Ravasi, C Schunter
The environment experienced by one generation has the potential to affect the subsequent one through non-genetic inheritance of parental effects. Since both mothers and fathers can influence their offspring, questions arise regarding how the maternal, paternal and offspring experiences integrate into the resulting phenotype. We aimed to disentangle the maternal and paternal contributions to transgenerational thermal acclimation in a reef fish, Acanthochromis polyacanthus, by exposing two generations to elevated temperature (+1...
March 23, 2024: Molecular Ecology
https://read.qxmd.com/read/38515231/patterns-of-genetic-variation-and-local-adaptation-of-a-native-herbivore-to-a-lethal-invasive-plant
#60
JOURNAL ARTICLE
Nitin Ravikanthachari, Rachel A Steward, Carol L Boggs
Understanding the evolutionary processes that influence fitness is critical to predicting species' responses to selection. Interactions among evolutionary processes including gene flow, drift and the strength of selection can lead to either local adaptation or maladaptation, especially in heterogenous landscapes. Populations experiencing novel environments or resources are ideal for understanding the mechanisms underlying adaptation or maladaptation, specifically in locally co-evolved interactions. We used the interaction between a native herbivore that oviposits on a patchily distributed introduced plant that in turn causes significant mortality to the larvae to test for signatures of local adaptation in areas where the two co-occurred...
March 21, 2024: Molecular Ecology
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