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Molecular Ecology

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https://www.readbyqxmd.com/read/27933683/genetics-and-the-conservation-of-natural-populations-allozymes-to-genomes
#1
Fred W Allendorf
I consider how the study of genetic variation has influenced efforts to conserve natural populations over the last 50 years. Studies with allozymes in the 1970s provided the first estimates of the amount of genetic variation within and between natural populations at multiple loci. These early studies played an important role in developing plans to conserve species. The description of genetic variation in mitochondrial DNA in the early 1980s laid the foundation for the field of phylogeography, which provided a deeper look in time of the relationships and connectivity among populations...
December 9, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27928865/canine-distemper-virus-in-the-serengeti-ecosystem-molecular-adaptation-to-different-carnivore-species
#2
Veljko M Nikolin, Ximena A Olarte-Castillo, Nikolaus Osterrieder, Heribert Hofer, Edward Dubovi, Camila J Mazzoni, Edgar Brunner, Katja V Goller, Robert D Fyumagwa, Patricia D Moehlman, Dagmar Thierer, Marion L East
Was the 1993/1994 fatal canine distemper virus (CDV) epidemic in lions and spotted hyaenas in the Serengeti ecosystem caused by the recent spillover of a virulent domestic dog strain or one well adapted to these noncanids? We examine this question using sequence data from 13 'Serengeti' strains including five complete genomes obtained between 1993 and 2011. Phylogenetic and haplotype network analyses reveal that strains from noncanids during the epidemic were more closely related to each other than to those from domestic or wild canids...
December 7, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27926985/tropical-rainforests-that-persisted-inferences-from-the-quaternary-demographic-history-of-eight-tree-species-in-the-guiana-shield
#3
Stéphanie Barthe, Giorgio Binelli, Bruno Hérault, Caroline Scotti-Saintagne, Daniel Sabatier, Ivan Scotti
How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rain fall and temperature changes during and/or immediately after the Last Glacial Maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes...
December 7, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27914207/demographic-history-of-the-trace-metal-hyperaccumulator-noccaea-caerulescens-j-presl-and-c-presl-f-k-mey-in-western-europe
#4
Cédric Gonneau, Nausicaa Noret, Cécile Godé, Hélène Frérot, Catherine Sirguey, Thibault Sterckeman, Maxime Pauwels
Noccaea caerulescens (Brassicaceae) is a major pseudometallophyte model for the investigation of the genetics and evolution of metal hyperaccumulation in plants. We studied the population genetics and demographic history of this species to advance the understanding of among-population differences in metal hyperaccumulation and tolerance abilities. Sampling of seven to 30 plants was carried out in 62 sites in Western Europe. Genotyping was done using a combination of new chloroplast and nuclear neutral markers...
December 3, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27914205/mitochondrial-genotype-and-phenotypic-plasticity-of-gene-expression-in-response-to-cold-acclimation-in-killifish
#5
Timothy M Healy, Heather J Bryant, Patricia M Schulte
Adjustments of aerobic metabolic processes are critical components of organismal responses to environmental change that require tight co-ordination between the nuclear and mitochondrial genomes. Intraspecific differences in mitochondrial genotype can affect gene transcription in both genomes. Thus, variation in mitochondrial genotype may be associated with differences in the plasticity of gene expression when organisms are faced with changes in environmental conditions. Cold acclimation is known to result in metabolic responses involving increases in mitochondrial amount and capacity, suggesting that low temperatures may pose a particular challenge when co-ordinating the functions of the nuclear and mitochondrial genomes...
December 3, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27914204/the-genetic-architecture-of-tristyly-and-its-breakdown-to-self-fertilization
#6
Ramesh Arunkumar, Wei Wang, Stephen I Wright, Spencer C H Barrett
The floral polymorphism tristyly involves three style morphs with a reciprocal arrangement of stigma and anther heights governed by two diallelic loci (S and M). Tristyly functions to promote cross-pollination, but modifications to stamen position commonly cause transitions to selfing. Here, we integrate whole genome sequencing and genetic mapping to investigate the genetic architecture of the M locus and the genetic basis of independent transitions to selfing in tristylous Eichhornia paniculata. We crossed independently derived semi-homostylous selfing variants of the long- and mid-styled morph fixed for alternate alleles at the M locus (ssmm and ssMM, respectively) and backcrossed the F1 to the parental ssmm genotype...
December 3, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27914203/multiple-processes-drive-genetic-structure-of-humpback-whale-megaptera-novaeangliae-populations-across-spatial-scales
#7
Francine Kershaw, Inês Carvalho, Jacqueline Loo, Cristina Pomilla, Peter B Best, Ken P Findlay, Salvatore Cerchio, Tim Collins, Marcia H Engel, Gianna Minton, Peter Ersts, Jaco Barendse, P G H Kotze, Yvette Razafindrakoto, Solange Ngouessono, Michael Meÿer, Meredith Thorton, Howard C Rosenbaum
Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3,575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample, and males and females separately, we assessed genetic diversity, tested for genetic differentiation between putative populations and isolation by distance, estimated the number of genetic clusters without a priori population information, and estimated rates of gene flow using maximum likelihood and Bayesian approaches...
December 3, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27891694/genetic-variation-in-blue-whales-in-the-eastern-pacific-implication-for-taxonomy-and-use-of-common-wintering-grounds
#8
R G LeDuc, E I Archer, A R Lang, K K Martien, B Hancock-Hanser, J PTorres-Florez, R Hucke-Gaete, H R Rosenbaum, K van Waerebeek, R L Brownell, B L Taylor
Many aspects of blue whale biology are poorly understood. Some of the gaps in our knowledge, such as those regarding their basic taxonomy and seasonal movements, directly affect our ability to monitor and manage blue whale populations. As a step towards filling in some of these gaps, microsatellite and mtDNA sequence analyses were conducted on blue whale samples from the Southern Hemisphere, the eastern tropical Pacific (ETP), and the northeast Pacific. The results indicate that the ETP is differentially used by blue whales from the northern and southern eastern Pacific, with the former showing stronger affinity to the region off Central America known as the Costa Rican Dome, and the latter favoring the waters of Peru and Ecuador...
November 27, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27886423/an-approach-for-identifying-cryptic-barriers-to-gene-flow-that-limit-species-geographic-ranges
#9
Steven J Micheletti, Andrew Storfer
Species' geographic range limits are most often not demarcated by obvious dispersal barriers. Poor quality habitat at the edge of a species' range can prevent range expansion by preventing outward migration or through reducing adaptive potential resulting from decreased genetic diversity. We identified habitat variables that constrain gene flow across the entire geographic range of an endemic salamander (Ambystoma barbouri) in the eastern United States, and we tested whether increased resistance resulting from these variables provides cryptic dispersal barriers at the range edges...
November 25, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27882647/host-and-tissue-variation-overshadow-the-response-of-boreal-moss-associated-fungal-communities-to-increased-nitrogen-load
#10
Marie L Davey, Marte J Skogen, Einar Heegaard, Rune Halvorsen, Håvard Kauserud, Mikael Ohlson
Human activity has more than doubled the amount of nitrogen entering the global nitrogen cycle, and the boreal forest biome is a nitrogen-limited ecosystem sensitive to nitrogen load perturbation. Although bryophyte-associated microbes contribute significantly to boreal forest ecosystem function, particularly in carbon and nitrogen cycling, little is known about their responses to anthropogenic global change. Amplicon pyrosequencing of the ITS2 region of rDNA was used to investigate how fungal communities associated with three bryophyte species responded to increased nitrogen loads in a long-term fertilization experiment in a boreal Picea abies forest in southern Norway...
November 24, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27873385/introgression-and-selection-shaped-the-evolutionary-history-of-sympatric-sister-species-of-coral-reef-fishes-genus-haemulon
#11
Moisés A Bernal, Michelle R Gaither, W Brian Simison, Luiz A Rocha
Closely related marine species with large sympatric ranges provide opportunities to study the mechanisms of speciation, particularly when there is evidence of gene flow between the lineages. Here we focus on a case of hybridization between the sympatric sister-species Haemulon maculicauda and H. flaviguttatum, using Sanger sequencing of mitochondrial and nuclear loci, as well as 2422 single nucleotide polymorphisms (SNPs) obtained via Restriction-site Associated DNA Sequencing (RADSeq). Mitochondrial markers revealed a shared haplotype for COI and low divergence for CytB and CR between the sister species...
November 22, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27873369/the-genetic-architecture-of-novel-trophic-specialists-higher-effect-sizes-are-associated-with-exceptional-oral-jaw-diversification-in-a-pupfish-adaptive-radiation
#12
Christopher H Martin, Priscilla A Erickson, Craig T Miller
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining the origins of ecological novelty: a sympatric radiation of pupfishes endemic to San Salvador Island, Bahamas containing a large-jawed scale-eater and a short-jawed molluscivore with a skeletal nasal protrusion...
November 22, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27864914/the-lek-mating-system-of-the-worm-pipefish-nerophis-lumbriciformis-a-molecular-maternity-analysis-and-test-of-the-phenotype-linked-fertility-hypothesis
#13
N M Monteiro, D Carneiro, A Antunes, N Queiroz, M N Vieira, A G Jones
The origin and maintenance of mating preferences continues to be an important and controversial topic in sexual selection research. Leks and lek-like mating systems, where individuals gather in particular spots for the sole purpose of mate choice, are particularly puzzling, because the strong directional selection imposed by mate choice should erode genetic variation among competing individuals and negate any benefit for the choosing sex. Here, we take advantage of the lek-like mating system of the worm pipefish (Nerophis lumbriciformis) to test the phenotype-linked fertility hypothesis for the maintenance of mating preferences...
November 19, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27864912/inferring-contemporary-and-historical-genetic-connectivity-from-juveniles
#14
Pierre Feutry, Oliver Berry, Peter M Kyne, Richard D Pillans, Rich Hillary, Peter M Grewe, James R Marthick, Grant Johnson, Rasanthi M Gunasekera, Nicholas J Bax, Mark Bravington
Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river sharks found only in tropical northern Australia and southern Papua New Guinea...
November 19, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27864911/spatio-temporal-variation-in-parasite-communities-maintains-diversity-at-the-major-histocompatibility-complex-class-ii%C3%AE-in-the-endangered-rio-grande-silvery-minnow
#15
Megan J Osborne, Tyler J Pilger, Joel D Lusk, Thomas F Turner
Climate change will strongly impact aquatic ecosystems particularly in arid and semi-arid regions. Fish-parasite interactions will also be affected by predicted altered flow and temperature regimes, and other environmental stressors. Hence, identifying environmental and genetic factors associated with maintaining diversity at immune genes is critical for understanding species' adaptive capacity. Here we combine genetic (MHC Class IIβ and microsatellites), parasitological and ecological data to explore the relationship between these factors in the remnant wild Rio Grande silvery minnow (Hybognathus amarus) population, an endangered species found in the southwestern United States...
November 19, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27864910/genomic-islands-of-divergence-linked-to-ecotypic-variation-in-sockeye-salmon
#16
Wesley A Larson, Morten T Limborg, Garrett J McKinney, Daniel E Schindler, James E Seeb, Lisa W Seeb
Regions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka) from a single drainage in southwestern Alaska...
November 19, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27864907/stimulation-effects-of-ciprofloxacin-and-sulfamethoxazole-in-microcystis-aeruginosa-and-itraq-based-screening-of-antibiotic-targets
#17
Ying Liu, Shi Chen, Jian Zhang, Xuewen Li, Baoyu Gao
Antibiotics are normally regarded as safe to aquatic ecosystems when their contamination concentrations are lower than the toxic threshold. This study observed the hazard of ciprofloxacin, sulfamethoxazole and their binary mixture to the aquatic environment at environmentally relevant concentrations lower than the toxic threshold, due to the stimulation on the bloom of Microcystis aeruginosa. The enhanced growth of M. aeruginosa, coupled with elevated photosynthesis activity, was exerted by 50 - 200 ng/L of ciprofloxacin, 100 - 200 ng/L of sulfamethoxazole and 20 - 100 ng/L of the binary antibiotic mixture...
November 19, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27864900/recombination-rate-variation-in-mice-from-an-isolated-island
#18
Richard J Wang, Melissa M Gray, Michelle D Parmenter, Karl W Broman, Bret A Payseur
Recombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1,212 meioses, from a unique population of wild house mice (Mus musculus domesticus) that recently colonized remote Gough Island. Crosses to a mainland reference strain (WSB/EiJ) reveal pervasive variation in recombination rate among Gough Island mice, including sub-chromosomal intervals spanning up to 28% of the genome...
November 19, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27864892/introgression-of-mtdna-in-urosaurus-lizards-historical-and-ecological-processes
#19
Gregory J Haenel
Introgression of mtDNA appears common in animals but the implications of acquiring a novel mitochondrial genome are not well known. This study investigates mito-genome introgression between the lizard species Urosaurus graciosus, a thermal specialist, and U. ornatus, a species that occupies a wider range of thermal environments. As ectotherms, their metabolic rate is strongly influenced by the thermal environment; with mitochondria being linked to metabolic rates, overall energy budgets could be impacted by introgression...
November 19, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27859915/transcriptome-based-phylogeny-of-endemic-lake-baikal-amphipod-species-flock-fast-speciation-accompanied-by-frequent-episodes-of-positive-selection
#20
Sergey A Naumenko, Maria D Logacheva, Nina V Popova, Anna V Klepikova, Aleksey A Penin, Georgii A Bazykin, Anna E Etingova, Nikolai S Mugue, Alexey S Kondrashov, Lev Y Yampolsky
Endemic species flocks inhabiting ancient lakes, oceanic islands and other long-lived isolated habitats are often interpreted as adaptive radiations. Yet molecular evidence for directional selection during species flocks radiation is scarce. Using partial transcriptomes of 64 species of Lake Baikal (Siberia, Russia) endemic amphipods and two non-endemic outgroups, we report a revised phylogeny of this species flock, and analyze evidence for positive selection within the endemic lineages. We confirm two independent invasions of amphipods into Baikal and demonstrate that several morphological features of Baikal amphipods, such as body armor and reduction of appendages and sensory organs, evolved in several lineages in parallel...
November 17, 2016: Molecular Ecology
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