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Molecular Ecology

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https://www.readbyqxmd.com/read/30240539/going-under-down-under-lineage-ages-argue-for-extensive-survival-of-the-oligocene-marine-transgression-on-zealandia
#1
Graham P Wallis, Fátima Jorge
25 years ago, it was suggested that current-day New Zealand, part of the largely sunken continent of Zealandia, could have been completely inundated during the Oligocene Marine Transgression (OMT) some 25-23 million years ago. Such an event would, of necessity, imply that all terrestrial, freshwater, and maybe coastal marine species must have dispersed there since. This idea has generated heated debate, on which geological, palaeontological and molecular data are being brought to bear. Here we review the phylogeographic literature in the form of molecular estimates of divergence times between New Zealand lineages and their closest overseas sister groups...
September 21, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30240506/a-functional-transcriptomics-analysis-in-the-relict-marsupial-dromiciops-gliroides-reveals-adaptive-regulation-of-protective-functions-during-hibernation
#2
Roberto F Nespolo, Juan Diego Gaitan-Espitia, Julian F Quintero-Galvis, Fernanda V Fernandez, Andrea X Silva, Cristian Molina, Kenneth B Storey, Francisco Bozinovic
The small South American marsupial, Dromiciops gliroides, known as the missing link between the American and the Australian marsupials, is one of the few South American mammals known to hibernate. Expressing both daily torpor and seasonal hibernation, this species may provide crucial information about the mechanisms and the evolutionary origins of marsupial hibernation. Here we compared torpid and active individuals, applying high-throughput sequencing technologies (RNA-seq) to profile gene expression in three D...
September 21, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30230092/sex-chromosome-inversions-enforce-reproductive-isolation-across-an-avian-hybrid-zone
#3
Daniel M Hooper, Simon C Griffith, Trevor D Price
Across hybrid zones, the sex chromosomes are often more strongly differentiated than the autosomes. This is regularly attributed to the greater frequency of reproductive incompatibilities accumulating on sex chromosomes and their exposure in the heterogametic sex. Working within an avian hybrid zone, we explore the possibility that chromosome inversions differentially accumulate on the Z chromosome compared to the autosomes and thereby contribute to Z chromosome differentiation. We analyze the northern Australian hybrid zone between two subspecies of the long-tailed finch (Poephila acuticauda), first described based on differences in bill color, using reduced representation genomic sequencing for 293 individuals over a 1530 km transect...
September 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30230081/lineage-specific-duplication-and-adaptive-evolution-of-bitter-taste-receptor-genes-in-bats
#4
Hengwu Jiao, Yi Wang, Libiao Zhang, Peihua Jiang, Huabin Zhao
By generating raw genetic material and diverse biological functions, gene duplication represents a major evolutionary mechanism that is of fundamental importance in ecological adaptation. The lineage-specific duplication events of bitter taste receptor genes (Tas2rs) have been identified in a number of vertebrates, but functional evolution of new Tas2r copies after duplication remains largely unknown. Here we present the largest data set of bat Tas2rs to date, identified from existing genome sequences of 15 bat species and newly sequenced from 17 bat species, and demonstrate lineage-specific duplications of Tas2r16, Tas2r18 and Tas2r41 that only occurred in Myotis bats...
September 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30230076/the-adaptive-significance-of-chromosomal-inversion-polymorphisms-in-drosophila-melanogaster
#5
Martin Kapun, Thomas Flatt
Chromosomal inversions, structural mutations that reverse a segment of a chromosome, cause suppression of recombination in the heterozygous state. Several studies have shown that inversion polymorphisms can form clines or fluctuate predictably in frequency over seasonal time spans. These observations prompted the hypothesis that chromosomal rearrangements might be subject to spatially and/or temporally varying selection. Here we review what has been learned about the adaptive significance of inversion polymorphisms in the vinegar fly Drosophila melanogaster, the species in which they were first discovered by Sturtevant in 1917...
September 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30230073/assessing-changes-in-arthropod-predator-prey-interactions-through-dna-based-gut-content-analysis-variable-environment-stable-diet
#6
Bernhard Eitzinger, Nerea Abrego, Dominique Gravel, Tea Huotari, Eero J Vesterinen, Tomas Roslin
Analyzing the structure and dynamics of biotic interaction networks and the processes shaping them is currently one of the key fields in ecology. In this paper, we develop a novel approach to gut content analysis, thereby deriving a new perspective on community interactions and their responses to environment. For this, we use an elevational gradient in the High Arctic, asking how the environment and species traits interact in shaping predator-prey interactions involving the wolf spider Pardosa glacialis. To characterize the community of potential prey available to this predator, we used pitfall trapping and vacuum sampling...
September 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30226013/radseq-data-reveal-ancient-but-not-pervasive-introgression-between-californian-tree-and-scrub-oak-species-quercus-sect-quercus-fagaceae
#7
Bernard Y Kim, Wei Xinzeng, Sorel Fitz-Gibbon, Kirk E Lohmueller, Joaquín Ortego, Paul F Gugger, Victoria L Sork
A long-term debate in evolutionary biology is the extent to which reproductive isolation is a necessary element of speciation. Hybridizing plants in general are cited as evidence against this notion and oaks specifically have been used as the classic example of species maintenance without reproductive isolation. Here, we use thousands of SNPs generated by RAD sequencing to describe the phylogeny of a set of sympatric white oak species in California and then test whether these species exhibit pervasive interspecific gene exchange...
September 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30225945/how-bacterioplankton-community-can-go-with-cascade-damming-in-the-highly-regulated-lancang-mekong-river-basin
#8
Xun Wang, Chao Wang, Peifang Wang, Juan Chen, Lingzhan Miao, Tao Feng, Qiusheng Yuan, Sheng Liu
Rivers make vital contributions to the transport of water, sediment and nutrients from terrestrial to marine ecosystems. However, many large rivers worldwide are suffering from dam regulation. Increasing attention has been paid to bacterioplankton communities since they are highly responsive to river alterations and may influence biogeochemical processes. Here, a comprehensive study was conducted in the highly regulated Lancang-Mekong River Basin to address the question of how bacterioplankton communities respond to cascade damming...
September 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30225943/a-modified-dna-barcode-approach-to-define-trophic-interactions-between-native-and-exotic-pentatomids-and-their-parasitoids
#9
T D Gariepy, A Bruin, J Konopka, C Scott-Dupree, H Fraser, M-C Bon, E Talamas
The establishment of invasive Halyomorpha halys (Stål) outside of its native range may impact native species assemblages, including other pentatomids and their scelionid parasitoids. This has generated interest in defining species diversity and host-parasitoid associations in this system to better understand the impact of invasive alien species on trophic interactions in invaded regions. Information on scelionid-pentatomid associations in natural habitats is lacking, and species-level identification of these associations can be tenuous using rearing and dissection techniques...
September 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30222228/apparent-inbreeding-preference-despite-inbreeding-depression-in-the-american-crow
#10
Andrea K Townsend, Conor C Taff, Melissa L Jones, Katherine H Getman, Sarah S Wheeler, Mitch G Hinton, Ryane M Logsdon
Although matings between relatives can have negative effects on offspring fitness, apparent inbreeding preference has been reported in a growing number of systems, including those with documented inbreeding depression. Here, we examined evidence for inbreeding depression and inbreeding preference in two populations (Clinton, New York and Davis, California, USA) of the cooperatively breeding American crow (Corvus brachyrhynchos). We then compared observed inbreeding strategies with theoretical expectations for optimal, adaptive levels of inbreeding, given the inclusive fitness benefits and population-specific magnitude of inbreeding depression...
September 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30222226/species-complex-diversification-and-host-plant-associations-in-bemisia-tabaci-a-plant-defense-detoxification-perspective-revealed-by-rnaseq-analyses
#11
Osnat Malka, Diego Santos-Garcia, Ester Feldmesser, Elad Sharon, Renate Krause-Sakate, Hélène Delatte, Sharon van Brunschot, Mitulkumar Patel, Paul Visendi Muhindira, Habibu Mugerwa, Susan Seal, John Colvin, Shai Morin
Insect-plant associations and their role in diversification are mostly studied in specialists. Here, we aimed to identify macroevolution patterns in the relationships between generalists and their host plants that have the potential to promote diversification. We focused on the Bemisia tabaci species complex containing more than 35 cryptic species. Mechanisms for explaining this impressive diversification have focused so far on allopatric forces that assume a common, broad, host range. We conducted a literature survey which indicated that species in the complex differ in their host range, with only few showing a truly broad one...
September 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30222225/disentangling-protist-communities-identified-from-dna-and-rna-surveys-in-the-pearl-river-south-china-sea-continuum-during-the-wet-and-dry-seasons
#12
Wenxue Wu, Hongbin Liu
Little is known about the mechanisms that regulate the assembly of microbial communities in the river-sea continuum. Here, we performed HiSeq paired-end sequencing of the V4 region of 18S rRNA gene, using both DNA and RNA extracts, to identify protist communities in the surface and bottom water layers along a transect of the Pearl River-South China Sea Continuum (PSC) during the wet (summer) and dry (winter) seasons. We found that during the summer but not during the winter, protist communities, identified from their DNA or RNA signatures, could be better explained by mass effects and species sorting, respectively...
September 17, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30194888/neutral-variation-does-not-predict-immunogenetic-variation-in-the-european-grayling-thymallus-thymallus-implications-for-management
#13
J V Huml, M I Taylor, W Edwin Harris, R Sen, J S Ellis
Preservation of genetic diversity is critical to successful conservation and there is increasing demand for the inclusion of ecologically meaningful genetic information in management decisions. Supportive breeding programmes are increasingly implemented to combat declines in many species, yet their effect on adaptive genetic variation is understudied. This is despite the fact that supportive breeding may interfere with natural evolutionary processes. Here, we assessed the performance of neutral and adaptive markers (Major Histocompatibility Complex; MHC) to inform management of European grayling (Thymallus thymallus), which routinely involves supplementation of natural populations with hatchery-reared fish (stocking)...
September 8, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30193406/transcriptomic-responses-to-extreme-low-salinity-among-locally-adapted-populations-of-olympia-oyster-ostrea-lurida
#14
Ashley Maynard, Jillian M Bible, Melissa H Pespeni, Eric Sanford, Tyler G Evans
The Olympia oyster (Ostrea lurida) is a foundation species inhabiting estuaries along the North American west coast. In California estuaries, O. lurida is adapted to local salinity regimes and populations differ in low salinity tolerance. In this study, oysters from three California populations were reared for two generations in a laboratory common garden and subsequently exposed to low salinity seawater. Comparative transcriptomics was then used to understand species-level responses to hyposmotic stress and population-level mechanisms underlying divergent salinity tolerances...
September 7, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30193397/vanishing-refuge-testing-the-forest-refuge-hypothesis-in-coastal-east-africa-using-genome-wide-sequence-data-for-seven-amphibians
#15
Christopher D Barratt, Beryl A Bwong, Robert Jehle, H Christoph Liedtke, Peter Nagel, Renske E Onstein, Daniel M Portik, Jeffrey W Streicher, Simon P Loader
High-throughput sequencing data have greatly improved our ability to understand the processes that contribute to current biodiversity patterns. The "vanishing refuge" diversification model is speculated for the coastal forests of eastern Africa, whereby some taxa have persisted and diversified between forest refugia, while others have switched to becoming generalists also present in non-forest habitats. Complex arrangements of geographical barriers (hydrology and topography) and ecological gradients between forest and non-forest habitats may have further influenced the region's biodiversity, but elucidation of general diversification processes has been limited by lack of suitable data...
September 7, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30192998/genomic-evidence-for-asymmetric-introgression-by-sexual-selection-in-the-common-wall-lizard
#16
Weizhao Yang, Geoffrey M While, Hanna Laakkonen, Roberto Sacchi, Marco A L Zuffi, Stefano Scali, Daniele Salvi, Tobias Uller
Strongly selected characters can be transferred from one lineage to another with limited genetic exchange, resulting in asymmetric introgression and a mosaic genome in the receiving population. However, systems are rarely sufficiently well studied to link the pattern of introgression to its underlying process. Male common wall lizards in western Italy exhibit exaggeration of a suite of sexually selected characters that make them outcompete males from a distantly related lineage that lack these characters. This results in asymmetric hybridization and adaptive introgression of the suite of characters following secondary contact...
September 7, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30187989/venom-gland-size-and-venom-complexity-essential-trophic-adaptations-of-venomous-predators-a-case-study-using-spiders
#17
Stano Pekár, Ondřej Bočánek, Ondřej Michálek, Lenka Petráková, Charles R Haddad, Ondrej Šedo, Zbyněk Zdráhal
Specialised predators possess a variety of adaptations. In venomous predators this may include the size of the venom gland and venom composition. It is expected that due to different foraging strategies, predators with a wide trophic niche (generalists) should possess larger venom glands that contain more diversified components than predators with a narrow niche (specialists). We focused on spiders, as the most diversified group of venomous predators, in which a wide variety of trophic strategies have evolved...
September 6, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30187987/host-derived-population-genomics-data-provides-insights-into-bacterial-and-diatom-composition-of-the-killer-whale-skin
#18
Rebecca Hooper, Jaelle C Brealey, Tom van der Valk, Antton Alberdi, John W Durban, Holly Fearnbach, Kelly M Robertson, Robin W Baird, M Bradley Hanson, Paul Wade, M Thomas P Gilbert, Phillip A Morin, Jochen B W Wolf, Andrew D Foote, Katerina Guschanski
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated microorganisms. Whereas amplicon sequencing has traditionally been used to characterise the microbiome, the increasing number of published population genomics datasets offer an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterise the skin microbiome and investigate how host social and geographic factors influence the microbial community composition...
September 6, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30187980/a-comparison-of-genomic-islands-of-differentiation-across-three-young-avian-species-pairs
#19
Darren E Irwin, Borja Milá, David P L Toews, Alan Brelsford, Haley L Kenyon, Alison N Porter, Christine Grossen, Kira E Delmore, Miguel Alcaide, Jessica H Irwin
Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., "islands of differentiation" in FST ), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's / mourning warblers; Townsend's / black-throated green warblers; and Audubon's / myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone...
September 6, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/30182504/brood-tending-males-in-a-biparental-fish-suffer-high-paternity-losses-but-rarely-cuckold
#20
Aneesh P H Bose, Holger Zimmermann, Jonathan M Henshaw, Karoline Fritzsche, Kristina M Sefc
Extra-pair paternity within socially monogamous mating systems is well-studied in birds and mammals but rather neglected in other animal taxa. In fishes, social monogamy has evolved several times but few studies have investigated the extent to which pair-bonded male fish lose fertilizations to cuckolders and gain extra-pair fertilizations themselves. We address this gap and present genetic paternity data collected from a wild population of Variabilichromis moorii, a socially monogamous African cichlid with biparental care of offspring...
September 4, 2018: Molecular Ecology
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