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Molecular Ecology

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https://www.readbyqxmd.com/read/30003608/the-impact-of-transposable-elements-in-adaptive-evolution
#1
Lukas Schrader, Jürgen Schmitz
The growing knowledge about the influence of transposable elements (TEs) on (1) long-term genome and transcriptome evolution, (2) genomic, transcriptomic and epigenetic variation within populations, and (3) patterns of somatic genetic differences in individuals continues to spur the interest of evolutionary biologists in the role of TEs in adaptive evolution. As TEs can trigger a broad range of molecular variation in a population with potentially severe fitness and phenotypic consequences for individuals, different mechanisms evolved to keep TE activity in check, allowing for a dynamic interplay between the host, its TEs and the environment in evolution...
July 13, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30003603/asymmetric-assortative-mating-and-queen-polyandry-are-linked-to-a-supergene-controlling-ant-social-organization
#2
Amaury Avril, Jessica Purcell, Alan Brelsford, Michel Chapuisat
Non-recombining genomic variants underlie spectacular social polymorphisms, from bird mating systems to ant social organization. Because these "social supergenes" affect multiple phenotypic traits linked to survival and reproduction, explaining their persistence remains a substantial challenge. Here, we investigate how large non-recombining genomic variants relate to colony social organization, mating system and dispersal in the Alpine silver ant, Formica selysi. The species has colonies headed by a single queen (monogynous) and colonies headed by multiple queens (polygynous)...
July 13, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29989297/monitoring-age-related-trends-in-genomic-diversity-of-australian-lungfish
#3
Daniel J Schmidt, Stewart Fallon, David T Roberts, Thomas Espinoza, Andrew McDougall, Steven G Brooks, Peter K Kind, Nick R Bond, Mark J Kennard, Jane M Hughes
An important challenge for conservation science is to detect declines in intraspecific diversity so that management action can be guided towards populations or species at risk. The lifespan of Australian lungfish (Neoceratodus forsteri) exceeds 80 years, and human impacts on breeding habitat over the last half century may have impeded recruitment, leaving populations dominated by old post-reproductive individuals, potentially resulting in a small and declining breeding population. Here we conduct a "single-sample" evaluation of genetic erosion within contemporary populations of the Australian lungfish...
July 10, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29987880/these-aren-t-the-loci-you-re-looking-for-principles-of-effective-snp-filtering-for-molecular-ecologists
#4
Shannon J O'Leary, Jonathan B Puritz, Stuart C Willis, Christopher M Hollenbeck, David S Portnoy
Sequencing reduced-representation libraries of restriction-site associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming a standard methodology for molecular ecologists. Because of the scale of RADseq data sets, putative loci cannot be assessed individually, making the process of filtering noise and correctly identifying biologically meaningful signal more difficult. Artifacts introduced during library preparation and/ bioinformatic processing of SNP data can create patterns that are incorrectly interpreted as indicative of population structure or natural selection...
July 10, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29972891/-two-rules-of-speciation-revisited
#5
Jerry A Coyne
In the famous last paragraph of On the Origin of Species, Darwin compared the "fixed law of gravity", which causes the Earth to orbit the Sun, with the evolution of species by natural selection. This may be the first recorded case in biology of "physics envy": the view that the proper task of the life sciences-in Darwin's case, evolutionary biology-is to emulate physics by establishing general laws and working out their consequences. Although we don't speak of "laws" in biology, we do have lawlike generalizations, including the near-universality of the genetic code and the mechanism for translating DNA and RNA into proteins...
July 4, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29972881/inferring-selection-in-instances-of-long-range-colonisation-the-aleppo-pine-pinus-halepensis-in-the-mediterranean-basin
#6
R Ruiz Daniels, R S Taylor, M J Serra-Varela, G G Vendramin, S C González-Martínez, D Grivet
Teasing apart the effects of natural selection and demography on current allele frequencies is challenging, due to both processes leaving a similar molecular footprint. In particular, when attempting to identify selection in species that have undergone a recent range expansion, the increase of genetic drift at the edges of range expansions ("allele surfing") can be a confounded factor. To address this potential issue, we first assess the long-range colonisation history of the Aleppo pine across the Mediterranean Basin, using molecular markers...
July 4, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29972880/genomic-parallelism-and-lack-thereof-in-contrasting-systems-of-three-spine-sticklebacks
#7
Shenglin Liu, Anne-Laure Ferchaud, Peter Grønkjaer, Rasmus Nygaard, Michael M Hansen
Parallel evolution and the extent to which it involves gene reuse has attracted much interest. Whereas it has theoretically been predicted under which circumstances gene reuse is expected, empirical studies that directly compare systems showing high and low parallelism are rare. Three-spine stickleback (Gasterosteus aculeatus), where freshwater populations have been independently founded by ancestral marine populations, represent prime examples of phenotypic and genomic parallelism, but cases exist where parallelism is low...
July 4, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29972878/pathway-position-constrains-the-evolution-of-an-ecologically-important-pathway-in-aspens-populus-tremula-l
#8
Christopher T Cole, Pär K Ingvarsson
Many ecological interactions of aspens and their relatives (Populus spp.) are affected by products of the phenylpropanoid pathway synthesizing condensed tannins (CTs), whose production involves trade-offs with other ecologically important compounds and with growth. Genes of this pathway are candidates for investigating the role of selection on ecologically important, polygenic traits. We analyzed sequences from 25 genes representing 10 steps of the CT synthesis pathway, which produces CTs used in defense and lignins used for growth, in 12 individuals of European aspen (Populus tremula)...
July 4, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29972877/speciation-in-sympatry-with-ongoing-secondary-gene-flow-and-a-potential-olfactory-trigger-in-a-radiation-of-cameroon-cichlids
#9
Jelmer W Poelstra, Emilie J Richards, Christopher H Martin
The process of sympatric speciation in nature remains a fundamental unsolved problem. Cameroon crater lake cichlid radiations were long regarded as one of the most compelling examples; however, recent work showed that their origins were more complex than a single colonization event followed by isolation. Here, we performed a detailed investigation of the speciation history of a radiation of Coptodon cichlids from Lake Ejagham, Cameroon using whole-genome sequencing data. The existence of the Lake Ejagham Coptodon radiation is remarkable since this 0...
July 4, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29972876/the-cotton-stainer-s-gut-microbiota-suppresses-infection-of-a-co-transmitted-trypanosomatid-parasite
#10
Thomas Ogao Onchuru, Adam Martinez, Martin Kaltenpoth
The evolutionary and ecological success of many insects is attributed to mutualistic partnerships with bacteria that confer hosts with novel traits including food digestion, nutrient supplementation, detoxification of harmful compounds and defense against natural enemies. Dysdercus fasciatus firebugs (Hemiptera: Pyrrhocoridae), commonly known as cotton stainers, possess a simple but distinctive gut bacterial community including B-vitamin supplementing Coriobacteriaceae symbionts. In addition, their guts are often infested with the intestinal trypanosomatid parasite Leptomonas pyrrhocoris (Kinetoplastida: Trypanosomatidae)...
July 4, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29972610/urbanization-as-a-facilitator-of-gene-flow-in-a-human-health-pest
#11
Lindsay S Miles, J Chadwick Johnson, Rodney J Dyer, Brian C Verrelli
Urban fragmentation can reduce gene flow that isolates populations, reduces genetic diversity and increases population differentiation, all of which have negative conservation implications. Alternatively, gene flow may actually be increased among urban areas consistent with an urban facilitation model. In fact, urban adapter pests are able to thrive in the urban environment and may be experiencing human-mediated transport. Here, we used social network theory with a population genetic approach to investigate the impact of urbanization on genetic connectivity in the Western black widow spider, as an urban pest model of human health concern...
July 4, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29957826/pleiotropic-effects-of-regulatory-variation-in-tan-result-in-correlation-of-two-pigmentation-traits-in-drosophila-melanogaster
#12
Lukas Endler, Jean-Michel Gibert, Viola Nolte, Christian Schlötterer
Traits with a common genetic basis frequently display correlated phenotypic responses to selection or environmental conditions. In Drosophila melanogaster pigmentation of the abdomen and a trident-shaped region on the thorax are genetically correlated. Here, we used a pooled replicated genome-wide association approach (Pool-GWAS) to identify the genetic basis of variation in thoracic trident pigmentation in two Drosophila melanogaster populations. We confirmed the previously reported large effect of ebony and the association of the cosmopolitan inversion In(3R)Payne...
June 29, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29953708/dissecting-the-basis-of-novel-trait-evolution-in-a-radiation-with-widespread-phylogenetic-discordance
#13
Meng Wu, Jamie L Kostyun, Matthew W Hahn, Leonie C Moyle
Phylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon-dubbed "hemiplasy"-is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread...
June 28, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29940092/an-association-between-differential-expression-and-genetic-divergence-in-the-patagonian-olive-mouse-abrothrix-olivacea
#14
Facundo M Giorello, Matias Feijoo, Guillermo D'Elía, Daniel E Naya, Lourdes Valdez, Juan C Opazo, Enrique P Lessa
Recent molecular studies have found striking differences between desert-adapted species and model mammals regarding water conservation. In particular, aquaporin 4, a classical gene involved in water regulation of model species, is absent or not expressed in the kidneys of desert-adapted species. To further understand the molecular response to water availability we studied the Patagonian olive mouse Abrothrix olivacea, a species with an unusually broad ecological tolerance that exhibits a great urine concentration capability...
June 25, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29940087/evaluating-genomic-signatures-of-the-large-x-effect-during-complex-speciation
#15
Daven C Presgraves
The ubiquity of the "two rules of speciation"- Haldane's rule and the large X-effect- imply a general, special role for sex chromosomes in the evolution of intrinsic postzygotic reproductive isolation. The recent proliferation of genome-scale analyses has revealed two further general observations: (1) complex speciation involving some form of gene flow is not uncommon; and (2) sex chromosomes in male- and in female-heterogametic taxa tend to show elevated differentiation relative to autosomes. Together these observations are consistent with speciation histories in which population genetic differentiation at autosomal loci is reduced by gene flow while natural selection against hybrid incompatibilities renders sex chromosomes relatively refractory to gene flow...
June 25, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29940083/how-much-is-enough-effects-of-technical-and-biological-replication-on-metabarcoding-dietary-analysis
#16
Vanessa A Mata, Hugo Rebelo, Francisco Amorim, Gary F McCracken, Simon Jarman, Pedro Beja
DNA metabarcoding is increasingly used in dietary studies to estimate diversity, composition, and frequency of occurrence of prey items. However, few studies have assessed how technical and biological replication affect the accuracy of diet estimates. This study addresses these issues using the European free-tailed bat Tadarida teniotis, involving high-throughput sequencing of a small fragment of the COI gene in 15 separate faecal pellets and a 15-pellet pool per each of 20 bats. We investigated how diet descriptors were affected by variability among (i) individuals, (ii) pellets of each individual, and (iii) PCRs of each pellet...
June 25, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29939447/the-choice-of-universal-primers-and-the-characteristics-of-the-species-mixture-determines-when-dna-metabarcoding-can-be-quantitative
#17
Josep Piñol, Miquel A Senar, William O C Symondson
DNA metabarcoding is a technique used to survey biodiversity in many ecological settings, but there are doubts about whether it can provide quantitative results, i.e. the proportions of each species in the mixture as opposed to a species list. While there are several experimental studies that report quantitative metabarcoding results, there are a similar number that fail to do so. Here we provide the rationale to understand under what circumstances the technique can be quantitative. Basically, we simulate a mixture of DNA of S species with a defined initial abundance distribution...
June 25, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29927007/the-decline-of-the-turtle-dove-dietary-associations-with-body-condition-and-competition-with-other-columbids-analysed-using-high-throughput-sequencing
#18
Jenny C Dunn, Jennifer E Stockdale, Rosemary J Moorhouse-Gann, Alexandra McCubbin, Helen Hipperson, Antony J Morris, Philip V Grice, William O C Symondson
Dietary changes linked to the availability of anthropogenic food resources can have complex implications for species and ecosystems, especially when species are in decline. Here, we use recently developed primers targeting the ITS2 region of plants to characterise diet from faecal samples of four UK columbids, with particular focus on the European turtle dove (Streptopelia turtur), a rapidly declining obligate granivore. We examine dietary overlap between species (potential competition), associations with body condition in turtle doves, and spatiotemporal variation in diet...
June 21, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29924889/tree-sex-and-size-ecological-determinants-of-male-versus-female-fecundity-in-three-fagus-sylvatica-stands
#19
Sylvie Oddou-Muratorio, Julie Gauzere, Aurore Bontemps, Jean-François Rey, Etienne K Klein
Inter-individual variation in fecundities has major consequences on population evolutionary potential, through genetic drift and selection. Using two spatially explicit mating models that analyze the genotypes of seeds and seedlings, we investigated the variation of male and female fecundities within and among three European beech (Fagus sylvatica) stands situated along an altitudinal gradient. Female and male individual fecundity distributions were both skewed in this monoecious species, and we found a higher variance in female as compared to male fecundities...
June 20, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29924883/kin-discrimination-and-outer-membrane-exchange-in-myxococcus-xanthus-a-comparative-analysis-among-natural-isolates
#20
Sébastien Wielgoss, Francesca Fiegna, Olaya Rendueles, Yuen-Tsu N Yu, Gregory J Velicer
Genetically similar cells of the soil bacterium Myxococcus xanthus cooperate at multiple social behaviours, including motility and multicellular development. Another social interaction in this species is outer-membrane exchange (OME), a behaviour of unknown primary benefit in which cells displaying closely related variants of the outer-membrane protein TraA transiently fuse and exchange membrane contents. Functionally incompatible TraA variants do not mediate OME, which led to the proposal that TraA incompatibilities determine patterns of intercellular cooperation in nature, but how this might occur remains unclear...
June 20, 2018: Molecular Ecology
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