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Molecular Ecology

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https://read.qxmd.com/read/30770610/the-genomic-pool-of-standing-structural-variation-outnumbers-single-nucleotide-polymorphism-by-three-fold-in-the-marine-teleost-chrysophrys-auratus
#1
Andrew Catanach, Ross Crowhurst, Cecilia Deng, Charles David, Louis Bernatchez, Maren Wellenreuther
Recent studies have highlighted an important role of structural variation (SV) in ecological and evolutionary processes, but few have studied non-model species in the wild. As part of our long-term research programme on the non-model teleost fish Australasian snapper (Chrysophrys auratus) we aim to build one of the first catalogues of genomic variants (SNPs and indels, and deletions, duplications and inversions) in fishes, and evaluate overlap of genomic variants with regions under putative selection (Tajima's D and π), and coding sequences (genes)...
February 15, 2019: Molecular Ecology
https://read.qxmd.com/read/30770604/differential-responses-to-ocean-acidification-between-populations-of-balanophyllia-elegans-corals-from-high-and-low-upwelling-environments
#2
Joanna S Griffiths, Francis T-C Pan, Morgan W Kelly
Ocean acidification (OA), the global decrease in surface water pH from absorption of anthropogenic CO2 , may put many marine taxa at risk. However, populations that experience extreme localized conditions, and are adapted to these conditions predicted in the global ocean in 2100, may be more tolerant to future OA. By identifying locally adapted populations, researchers can examine the mechanisms used to cope with decreasing pH. One oceanographic process that influences pH, is wind driven upwelling. Here we compare two Californian populations of the coral Balanophyllia elegans from distinct upwelling regimes, and test their physiological and transcriptomic responses to experimental seawater acidification...
February 15, 2019: Molecular Ecology
https://read.qxmd.com/read/30770598/divergent-mitochondrial-lineages-arose-within-a-large-panmictic-population-of-the-savannah-sparrow-passerculus-sandwichensis
#3
Phred M Benham, Zachary A Cheviron
Unusual patterns of mtDNA diversity can reveal interesting aspects of a species' biology. However, making such inferences requires discerning among the many alternative scenarios that could underlie any given mtDNA pattern. Next-generation sequencing methods provide large, multi-locus datasets with increased power to resolve unusual mtDNA patterns. A mtDNA-based phylogeography of the Savannah sparrow (Passerculus sandwichensis) previously identified two sympatric, but divergent (~2%) clades within the nominate subspecies group and a third clade that consisted of birds sampled from northwest Mexico...
February 15, 2019: Molecular Ecology
https://read.qxmd.com/read/30768810/deep-segregation-in-the-open-ocean-macaronesia-as-an-evolutionary-hotspot-for-low-dispersal-marine-invertebrates
#4
Pedro E Vieira, Andrea Desiderato, David M Holdich, Pedro Soares, Simon Creer, Gary R Carvalho, Filipe O Costa, Henrique Queiroga
Diversification and speciation of terrestrial organisms is anticipated in oceanic islands such as Macaronesia, a group of Atlantic islands that have remained unconnected to continental landmasses. Hitherto, the diversification of marine organisms in oceanic islands, especially those with low vagility, has received little direct empirical analysis using molecular markers. Here, we focus on such a case study, through applying a multi-locus molecular approach to investigate the diversity and evolution of a group that lacks a planktonic larval stage, the isopod genus Dynamene, in Macaronesia and Northeast Atlantic...
February 15, 2019: Molecular Ecology
https://read.qxmd.com/read/30767303/phototactic-tails-evolution-and-molecular-basis-of-a-novel-sensory-trait-in-sea-snakes
#5
Jenna M Crowe-Riddell, Bruno F Simões, Julian C Partridge, David M Hunt, Steven Delean, Julian G Schwerdt, James Breen, Alastair Ludington, David J Gower, Kate L Sanders
Dermal phototaxis has been reported in a few aquatic vertebrate lineages spanning fish, amphibians and reptiles. These taxa respond to light on the skin of their elongate hind-bodies and tails by withdrawing under cover to avoid detection by predators. Here, we investigated tail phototaxis in sea snakes (Hydrophiinae), the only reptiles reported to exhibit this sensory behaviour. We conducted behavioural tests in 17 wild-caught sea snakes of eight species by illuminating the dorsal surface of the tail and midbody skin using cold white, violet, blue, green and red light...
February 15, 2019: Molecular Ecology
https://read.qxmd.com/read/30753744/multiple-parapatric-pollinators-have-radiated-across-a-continental-fig-tree-displaying-clinal-genetic-variation
#6
Hui Yu, Enwei Tian, Linna Zheng, Xiaoxia Deng, Yufen Cheng, Lianfu Chen, Wei Wu, Wattana Tanming, Dayong Zhang, Stephen G Compton, Finn Kjellberg
The ways that plant-feeding insects have diversified is central to our understanding of terrestrial ecosystems. Obligate nursery pollination mutualisms provide highly relevant model systems of how plants and their insect associates have diversified and the over 800 species of fig trees (Ficus) allow comparative studies. Fig trees can have one or more pollinating fig wasp species (Agaonidae) that breed within their figs, but factors influencing their number remain to be established. In some widely distributed fig trees, the plants form populations isolated by large swathes of sea, and the different populations are pollinated by different wasp species...
February 12, 2019: Molecular Ecology
https://read.qxmd.com/read/30742734/isolation-by-instability-historical-climate-change-shapes-population-structure-and-genomic-divergence-of-treefrogs-in-the-neotropical-cerrado-savanna
#7
Mariana M Vasconcellos, Guarino R Colli, Jesse N Weber, Edgardo M Ortiz, Miguel T Rodrigues, David C Cannatella
Although the impact of Pleistocene glacial cycles on the diversification of the tropical biota was once dismissed, increasing evidence suggests that Pleistocene climatic fluctuations greatly affected the distribution and population divergence of tropical organisms. Landscape genomic analyses coupled with paleoclimatic distribution models provide a powerful way to understand the consequences of past climate changes on the present-day tropical biota. Using genome-wide SNP data and mitochondrial DNA, combined with projections of the species distribution across the late Quaternary until the present, we evaluate the effect of paleoclimatic shifts on the genetic structure and population differentiation of Hypsiboas lundii, a treefrog endemic to the South American Cerrado savanna...
February 11, 2019: Molecular Ecology
https://read.qxmd.com/read/30739378/dispersal-of-a-nearshore-marine-fish-connects-marine-reserves-and-adjacent-fished-areas-along-an-open-coast
#8
Diana S Baetscher, Eric C Anderson, Elizabeth A Gilbert-Horvath, Daniel P Malone, Emily T Saarman, Mark H Carr, John Carlos Garza
Marine species with pelagic larvae typically exhibit little population structure, suggesting long distance dispersal and high gene flow. Directly quantifying dispersal of marine fishes is challenging but important, particularly for design of marine protected areas (MPAs). Here, we studied kelp rockfish (Sebastes atrovirens) sampled along ~25 km of coastline in a boundary current-dominated ecosystem and used genetic parentage analysis to identify dispersal events and characterize them, since the distance between sedentary parents and their settled offspring is the lifetime dispersal distance...
February 9, 2019: Molecular Ecology
https://read.qxmd.com/read/30739375/is-genomic-diversity-a-useful-proxy-for-census-population-size-evidence-from-a-species-rich-community-of-desert-lizards
#9
Maggie R Grundler, Sonal Singhal, Mark A Cowan, Daniel L Rabosky
Species abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long-term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome-wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long-term estimates of abundance, occupancy, and degree of ecological specialization in a diverse lizard community from arid Australia...
February 9, 2019: Molecular Ecology
https://read.qxmd.com/read/30739372/phenotypic-and-genetic-introgression-across-a-moving-woodpecker-hybrid-zone
#10
Shawn M Billerman, Carla Cicero, Rauri C K Bowie, Matthew D Carling
In hybrid zones in which two divergent taxa come into secondary contact and interbreed, selection can maintain phenotypic diversity despite widespread genetic introgression. Red-breasted (Sphyrapicus ruber) and Red-naped (S. nuchalis) sapsuckers meet and hybridize along a narrow contact zone that stretches from northern California to southern British Columbia. We found strong evidence for changes in the structure of this hybrid zone across time, with significant temporal shifts in allele frequencies and in the proportions of parental phenotypes across the landscape...
February 9, 2019: Molecular Ecology
https://read.qxmd.com/read/30723959/broadening-the-taxonomic-scope-of-coral-reef-paleoecological-studies-using-ancient-dna
#11
M D C Gomez Cabrera, J M Young, G Roff, T Staples, J C Ortiz, John M Pandolfi, A Cooper
Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), paleoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here we apply DNA metabarcoding and High-Throughput Sequencing of the 18S rDNA gene on paleoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance paleoecological studies by incorporating key soft-bodied taxa, including macroalgae...
February 5, 2019: Molecular Ecology
https://read.qxmd.com/read/30719799/postglacial-ecotype-formation-under-outcrossing-and-self-fertilization-in-arabidopis-lyrata
#12
Kay Lucek, Nora Hohmann, Yvonne Willi
The formation of ecotypes has been invoked as an important driver of postglacial biodiversity, because many species colonized heterogeneous habitats and experienced divergent selection. Ecotype formation has been predominantly studied in outcrossing taxa, while far less attention has been paid to the implications of mating system shifts. Here we addressed whether substrate-related ecotypes exist in selfing and outcrossing populations of Arabidopsis lyrata subsp. lyrata and whether the genomic footprint differs between mating systems...
February 5, 2019: Molecular Ecology
https://read.qxmd.com/read/30714254/retention-of-a-chromosomal-inversion-from-an-anadromous-ancestor-provides-the-genetic-basis-for-alternative-freshwater-ecotypes-in-rainbow-trout
#13
Martin C Arostegui, Thomas P Quinn, Lisa W Seeb, James E Seeb, Garrett J McKinney
Migratory behavior patterns in animals are controlled by a complex genetic architecture. Rainbow trout (Oncorhynchus mykiss) is a salmonid fish that spawns in streams but exhibits three primary life history pathways: stream-resident (fluvial), lake-migrant (adfluvial), and ocean-migrant (anadromous). Previous studies examining fluvial and anadromous O. mykiss have identified several genes associated with life history divergence including the presence of an inversion complex within chromosome 5 (Omy05) that appears to maintain a suite of linked genes controlling migratory behavior...
February 3, 2019: Molecular Ecology
https://read.qxmd.com/read/30714250/comparative-phylogeography-of-trans-andean-freshwater-fishes-based-on-genome-wide-nuclear-and-mitochondrial-markers
#14
Melissa Rincon-Sandoval, Ricardo Betancur-R, Javier A Maldonado-Ocampo
The Neotropical region represents one of the greatest biodiversity hotspots on earth. Despite its unparalleled biodiversity, regional comparative phylogeographic studies are still scarce, with most focusing on model clades (e.g., birds) and typically examining a handful of loci. Here, we apply a genome-wide comparative phylogeographic approach to test hypotheses of co-diversification of freshwater fishes in the trans-Andean region. Using target capture methods, we examined exon data for over 1,000 loci combined with complete mitochondrial genomes to study the phylogeographic history of five primary fish species (>150 individuals) collected from eight major river basins in Northwestern South America and Lower Central America...
February 3, 2019: Molecular Ecology
https://read.qxmd.com/read/30714247/genomics-environment-and-balancing-selection-in-behaviorally-bimodal-populations-the-caribou-case
#15
Maria Cavedon, Chrysoula Goubili, Elizabeth Heppenheimer, Bridgett vonHoldt, Stefano Mariani, Mark Hebblewhite, Troy Hegel, Dave Hervieux, Robert Serrouya, Robin Steenweg, Byron V Weckworth, Marco Musiani
Selection forces that favor different phenotypes in different environments can change frequencies of genes between populations along environmental clines. Clines are also compatible with balancing forces, such as negative frequency-dependent selection (NFDS), which maintains phenotypic polymorphisms within populations. For example, NFDS is hypothesized to maintain partial migration, a dimorphic behavioral trait prominent in species where only a fraction of the population seasonally migrates. Overall, NFDS is believed to be a common phenomenon in nature, yet, a scarcity of studies were published linking naturally occurring allelic variation with bimodal or multimodal phenotypes and balancing selection...
February 3, 2019: Molecular Ecology
https://read.qxmd.com/read/30714238/correlation-and-causation-between-the-microbiome-wolbachia-and-host-functional-traits-in-natural-populations-of-drosophilid-flies
#16
Caroline Fromont, Karen L Adair, Angela E Douglas
Resident microorganisms are known to influence the fitness and traits of animals under controlled laboratory conditions, but, the relevance of these findings to wild animals is uncertain. This study investigated the host functional correlates of microbiota composition in a wild community of three sympatric species of mycophagous drosophilid flies, Drosophila falleni, D. neotestacea and D. putrida. Specifically, we quantified bacterial communities and host transcriptomes by parallel 16S rRNA gene amplicon sequencing and RNA-Seq of individual flies...
February 3, 2019: Molecular Ecology
https://read.qxmd.com/read/30714237/density-dependent-fitness-not-dispersal-movements-drives-temporal-variation-in-spatial-genetic-structure-in-dark-eyed-juncos-junco-hyemalis
#17
Eric B Liebgold, Nicole M Gerlach, Ellen D Ketterson
Some studies have found that dispersal rates and distances increase with density, indicating that density-dependent dispersal likely affects spatial genetic structure. In an 11-year mark-recapture study on a passerine, the dark-eyed junco, we tested whether density affected dispersal distance and/or fine-scale spatial genetic structure. Contrary to expectations, we found no effect of pre-dispersal density on dispersal distance or the proportion of locally-produced juveniles returning to the population from which they hatched...
February 3, 2019: Molecular Ecology
https://read.qxmd.com/read/30712274/seed-traits-are-pleiotropically-regulated-by-the-flowering-time-gene-perpetual-flowering-1-pep1-in-the-perennial-arabis-alpina
#18
P William Hughes, Wim J J Soppe, Maria C Albani
The life cycles of plants are characterized by two major life history transitions-germination and the initiation of flowering-the timing of which are important determinants of fitness. Unlike annuals, which make the transition from the vegetative to reproductive phase only once, perennials iterate reproduction in successive years. The floral repressor PERPETUAL FLOWERING 1 (PEP1), an orthologue of FLOWERING LOCUS C, in the alpine perennial Arabis alpina ensures the continuation of vegetative growth after flowering and thereby restricts the duration of the flowering episode...
February 3, 2019: Molecular Ecology
https://read.qxmd.com/read/30710395/louse-flies-of-eleonora-s-falcons-that-also-feed-on-their-prey-are-evolutionary-dead-end-hosts-for-blood-parasites
#19
L Gangoso, R Gutiérrez-López, J Martínez-de la Puente, J Figuerola
Host shifts are widespread among avian haemosporidians, although the success of transmission depends upon parasite-host and parasite-vector compatibility. Insular avifaunas are typically characterized by a low prevalence and diversity of haemosporidians, although the underlying ecological and evolutionary processes remain unclear. We investigated the parasite transmission network in an insular system formed by Eleonora's falcons (the avian host), louse flies that parasitize the falcons (the potential vector), and haemosporidians (the parasites)...
February 1, 2019: Molecular Ecology
https://read.qxmd.com/read/30697889/antibiotic-disturbance-affects-aquatic-microbial-community-composition-and-foodweb-interactions-but-not-community-resilience
#20
Ester M Eckert, Grazia M Quero, Andrea Di Cesare, Giuliana Manfredini, Francesca Mapelli, Sara Borin, Diego Fontaneto, Gian Marco Luna, Gianluca Corno
Notwithstanding the fundamental role that environmental microbes play for ecosystem functioning, data on how microbes react to disturbances are still scarce, and most factors that confer stability to microbial communities are unknown. In this context, antibiotic discharge into the environment is considered a worldwide threat for ecosystems with potential risks to human health. We therefore tested resilience of microbial communities challenged by the presence of an antibiotic. In a continuous culture experiment we compared the abundance, composition and diversity of microbial communities undisturbed or disturbed by the constant addiction of tetracycline in low (10 μg L-1 ) or intermediate (100 μg L-1 ) concentration (press disturbance)...
January 29, 2019: Molecular Ecology
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