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Journal of Heredity

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https://www.readbyqxmd.com/read/29140441/the-complete-phylogeny-of-pangolins-scaling-up-resources-for-the-molecular-tracing-of-the-most-trafficked-mammals-on-earth
#1
Philippe Gaubert, Agostinho Antunes, Hao Meng, Lin Miao, Stéphane Peigné, Fabienne Justy, Flobert Njiokou, Sylvain Dufour, Emmanuel Danquah, Jayanthi Alahakoon, Erik Verheyen, William T Stanley, Stephen J O'Brien, Warren E Johnson, Shu-Jin Luo
Pangolins, considered the most-trafficked mammals on Earth, are rapidly heading to extinction. Eight extant species of these African and Asian scale-bodied anteaters are commonly recognized, but their evolutionary relationships remain largely unexplored. Here we present the most comprehensive phylogenetic assessment of pangolins, based on genetic variation of complete mitogenomes and nine nuclear genes. We confirm deep divergence among Asian and African pangolins occurring not later than the Oligocene-Miocene boundary ca...
November 13, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29136171/mating-system-and-effective-population-size-of-the-overexploited-neotropical-tree-myroxylon-peruiferum-l-f-and-their-impact-on-seedling-production
#2
Ellida de Aguiar Silvestre, Kaiser Dias Schwarcz, Carolina Grando, Jaqueline Bueno de Campos, Patricia Sanae Sujii, Evandro Vagner Tambarussi, Camila Menezes Trindade Macrini, José Baldin Pinheiro, Pedro Henrique Santin Brancalion, Maria Imaculada Zucchi
The reproductive system of a tree species has substantial impact on genetic diversity and structure within and among natural populations. Such information, should be considered when planning tree planting for forest restoration. Here, we describe the mating system and genetic diversity of an overexploited Neotropical tree, Myroxylon peruiferum L.f. (Fabaceae) sampled from a forest remnant (10 seed trees and 200 seeds) and assess whether the effective population size of nursery-grown seedlings (148 seedlings) is sufficient to prevent inbreeding depression in reintroduced populations...
November 10, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29136178/identification-of-genomic-regions-associated-with-sex-in-pacific-halibut
#3
Daniel P Drinan, Timothy Loher, Lorenz Hauser
Understanding and identifying the genetic mechanisms responsible for sex-determination are important for species management, particularly in exploited fishes where sex biased harvest could have implications on population dynamics and long-term persistence. The Pacific halibut (Hippoglossus stenolepis) supports important fisheries in the North Pacific Ocean. The proportion of each sex in the annual harvest is currently estimated using growth curves, but genetic techniques may provide a more accurate method. We used restriction-site associated DNA (RAD) sequencing to identify RAD-tags that were linked to genetic sex, based on differentiation (FST) between the sexes...
November 9, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29136164/habitat-heterogeneity-host-population-structure-and-parasite-local-adaptation
#4
Curtis M Lively
Reciprocal-transplant experiments have proven to be a powerful tool for detecting local adaptation (LA). More recently, reciprocal cross-inoculation experiments have been used to evaluate adaptation by parasites to their local host populations. These experiments are conceptually similar to reciprocal-transplant experiments, except that the "environment" (the host population) may have evolved in response to changes in the parasite population. Here, I use analytical tools and computer simulations to determine when parasites would be expected to be more infective to their local host populations than to allopatric host populations...
November 9, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29126208/influence-of-range-position-on-locally-adaptive-gene-environment-associations-in-populus-flowering-time-genes
#5
Stephen R Keller, Vikram E Chhatre, Matthew C Fitzpatrick
Local adaptation is pervasive in forest trees, which are characterized by large effective population sizes spanning broad climatic gradients. In addition to having relatively contiguous populations, many species also form isolated populations along the rear edge of their range. These rear-edge populations may contain unique adaptive diversity reflecting a history of selection in marginal environments. Thus, discovering genomic regions conferring local adaptation in rear edge populations is a key priority for landscape genomics to ensure conservation of genetic resources under climate change...
November 8, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29126134/the-study-of-local-adaptation-a-thriving-field-of-research
#6
Lynda F Delph
No abstract text is available yet for this article.
November 8, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29099936/genomic-analysis-suggests-kitlg-is-responsible-for-a-roan-pattern-in-two-pakistani-goat-breeds
#7
Andrea Talenti, Francesca Bertolini, Jamie Williams, Muhammad Moaeen-Ud-Din, Stefano Frattini, Beatrice Coizet, Giulio Pagnacco, James Reecy, Max F Rothschild, Paola Crepaldi
The roan coat color pattern is described as the presence of white hairs intermixed with pigmented hairs. This kind of pigmentation pattern has been observed in many domestic species, including the goat. The molecular mechanisms and inheritance that underlie this pattern are known for some species and the KITLG gene has been shown associated with this phenotype. To date, no research effort has been done to find the gene(s) that controls roan coat color pattern in goats. In the present study, after genotyping with the GoatSNP50 BeadChip, 35 goats that showed a roan pattern and that belonged to two Pakistan breeds (Group A) were analyzed and then compared to 740 goats of 39 Italian and Pakistan goats breeds that did not have the same coat color pattern (Group B)...
October 28, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29077895/pinniped-diphyly-and-bat-triphyly-more-homology-errors-drive-conflicts-in-the-mammalian-tree
#8
Mark S Springer, John Gatesy
Homology is perhaps the most central concept of phylogenetic biology. At difficult to resolve polytomies that are deep in the Tree of Life, a few homology errors in phylogenomic data can drive spurious phylogenetic results. Feijoo and Parada (2017) assembled three phylogenomic data sets for mammals and reported methodological discrepancies and unexpected results that contradict the monophyly of well-established clades in Pinnipedia and Yangochiroptera. Examination of Feijoo and Parada's (2017) data sets reveals extensive homology errors (paralogous sequences, alignments of different exons to each other) and cross-contamination of sequences from different species...
October 25, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29045702/the-edaphic-environment-mediates-flowering-time-differentiation-between-adjacent-populations-of-leptosiphon-parviflorus
#9
Emily L Dittmar, Douglas W Schemske
Flowering time is an important life history trait in plants that often affects fitness. The optimal time to flower may be influenced by trade-offs between flowering time and growth-related traits, and is thus likely to differ among habitats. Because flowering-time differences between populations can also reduce gene flow, understanding the factors that contribute to variation in flowering time among closely adjacent populations that experience gene flow is of particular interest. Plant adaptation to different edaphic environments provides some of the best examples of adaptive divergence at small spatial scales, and often coincides with flowering-time shifts...
October 17, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29045754/genomic-studies-of-local-adaptation-in-natural-plant-populations
#10
Victoria L Sork
Local adaptation arises as a result of selection by the local environment favoring phenotypes that enhance fitness. Geographic patterns of phenotypic variation are in part due to this selective process. Classically, the genetic basis of those phenotypes has been studied in plant populations using a quantitative genetic approach in which plants from different source populations are grown in common environments, in reciprocal transplant experiments, or in studies across a wide geographic and environmentally heterogeneous area...
October 14, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29040658/fire-does-not-strongly-affect-genetic-diversity-or-structure-of-a-common-treefrog-in-the-endangered-florida-scrub
#11
J M Robertson, S W Fitzpatrick, B B Rothermel, L M Chan
Fire regimes influence natural populations of organisms in diverse ways, via direct effects on population dynamics as well as indirect effects on habitat and ecosystem processes. Although many amphibian species have evolved to persist in fire-dependent ecosystems, the effects of fire on the genetic diversity of amphibian populations remain relatively unexplored. We examined how different aspects of fire history relate to population genetic diversity and structure of an abundant anuran, Hyla femoralis, in a large, intact area of Florida scrub containing hundreds of seasonally inundated ponds...
October 11, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29040605/negative-assortative-mating-in-the-white-throated-sparrow
#12
Philip W Hedrick, Elaina M Tuttle, Rusty A Gonser
Non-random mating based on phenotype has been observed in a number of organisms, but a very high proportion of these examples are of assortative mating. The strongest example of negative-assortative mating is for white-striped versus tan-striped crown in the white-throated sparrow, where about 98% of the observed pairings (mated pairs or social pairs) are between mates with different phenotypes and the correlation between mating types is -0.964. Although non-random mating has been explored theoretically for decades, these models have generally not focused on specific well-documented examples...
October 10, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29040588/glyphosate-resistance-and-epsps-gene-duplication-convergent-evolution-in-multiple-plant-species
#13
Eric L Patterson, Dean J Pettinga, Karl Ravet, Paul Neve, Todd A Gaines
One of the increasingly widespread mechanisms of resistance to the herbicide glyphosate is copy number variation (CNV) of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. EPSPS gene duplication has been reported in eight weed species, ranging from 3-5 extra copies to more than 150 extra copies. In the case of Palmer amaranth (Amaranthus palmeri), a section of >300 kb containing EPSPS and many other genes has been replicated and inserted at new loci throughout the genome, resulting in significant increase in total genome size...
October 10, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036657/genomic-admixture-between-locally-adapted-populations-of-arabidopsis-thaliana-mouse-ear-cress-evidence-of-optimal-genetic-outcrossing-distance
#14
Kattia Palacio-Lopez, Stephen R Keller, Jane Molofsky
Admixture can break up divergent genetic architectures between populations, resulting in phenotypic novelty and generating raw material for environmental selection. The contribution of admixture to progeny trait variation and fitness varies based on the degree of genetic isolation between the parental populations, for which most studies have used geographic distance as a proxy. A novel approach is to estimate optimal crossing distance using the adaptive genetic distance between mates estimated from loci that contribute directly to local adaptation...
September 27, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036328/phylogeography-and-population-genetic-analyses-in-the-iberian-toothcarp-aphanius-iberus-valenciennes-1846-at-different-time-scales
#15
Elena G Gonzalez, Carina Cunha, Hamid R Ghanavi, Francisco J Oliva-Paterna, Mar Torralva, Ignacio Doadrio
Secondary freshwater fish species inhabiting fluctuating and extreme environments are susceptible to changes in dispersion, effective population size, and genetic structure. The Iberian toothcarp Aphanius iberus is an endemic cyprinodontid of the Iberian Peninsula restricted to brackish water of salt marshes and coastal lagoons on the eastern Spanish Mediterranean coast. In this study we analysed mitochondrial cytochrome b DNA and microsatellite variation to evaluate ways in which the processes of extinction, dispersal, and colonization of A...
September 22, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036614/identification-of-a-candidate-mutation-in-the-col1a2-gene-of-a-chow-chow-with-osteogenesis-imperfecta
#16
E M Quist, R Doan, R R Pool, B F Porter, D L Bannasch, S V Dindot
Osteogenesis imperfecta (OI) is a genetic disease that occurs in humans and animals. Individuals with OI exhibit signs of extreme bone fragility and osteopenia with frequent fractures and perinatal lethality in severe cases. In this study, we report the clinical diagnosis of OI in a dog and the use targeted next-generation sequencing to identify a candidate autosomal dominant mutation in the COL1A2 gene. A five-month old male Chow Chow was examined with a fractured left humerus and resolving, bilateral femoral fractures...
September 19, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28992259/wgssat-a-high-throughput-computational-pipeline-for-mining-and-annotation-of-ssr-markers-from-whole-genomes
#17
Manmohan Pandey, Ravindra Kumar, Prachi Srivastava, Suyash Agarwal, Shreya Srivastava, N S Nagpure, J K Jena, Basdeo Kushwaha
Mining and characterization of SSR markers from whole genomes provide valuable information about biological significance of SSR distribution and also facilitate development of markers for genetic analysis. WGS-SSR Annotation Tool (WGSSAT) is a graphical user interface pipeline developed using Java Netbeans and Perl scripts which facilitates in simplifying the process of SSR mining and characterization. WGSSAT takes input in FASTA format and automates the prediction of genes, ncRNA, core genes, repeats and SSRs from whole genomes followed by mapping of the predicted SSRs onto a genome (classified according to genes, ncRNA, repeats, exonic, intronic and core gene region) along with primer identification and mining of cross-species markers...
September 16, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28992201/progress-toward-rice-seed-omics-in-low-level-gamma-radiation-environment-in-iitate-village-fukushima
#18
Randeep Rakwal, Gohei Hayashi, Junko Shibato, Saligrama A Deepak, Seetaramanjaneyulu Gundimeda, Upendra Simha, Arunkumar Padmanaban, Ravi Gupta, Sang-Ik Han, Sun Tae Kim, Akihiro Kubo, Tetsuji Imanaka, Manabu Fukumoto, Ganesh Kumar Agrawal, Seiji Shioda
Here, we present an update on the next level of experiments studying the impact of the gamma radiation environment, created post-March, 2011 nuclear accident at Fukushima Daiichi nuclear power plant, on rice plant and its next generation - the seed. Japonica-type rice (Oryza sativa L. cv. Koshihikari) plant was exposed to low-level gamma radiation (~4 μSv/h) in the contaminated Iitate Farm field in Iitate village (Fukushima). Seeds were harvested from these plants at maturity, and serve as the treated group...
September 11, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28992200/effects-of-radiation-from-contaminated-soil-and-moss-in-fukushima-on-embryogenesis-and-egg-hatching-of-the-aphid-prociphilus-oriens
#19
Shin-Ichi Akimoto, Yang Li, Tetsuji Imanaka, Hitoshi Sato, Ken Ishida
Radiation contaminated soils are widespread around the Fukushima Daiichi Nuclear Power Plant, and such soils raise concerns over its harmful effect on soil-dwelling organisms. We evaluated the effects of contaminated soil and moss sampled in Fukushima on the embryogenesis and hatching of aphid eggs, along with the measurement of the egg exposure dose. Cs-137 concentration in soil and moss from Fukushima ranged from 2200 to 3300 Bq/g and from 64 to 105 Bq/g, respectively. Eggs of the eriosomatine aphid Prociphilus oriens that were collected from a non-contaminated area were directly placed on the soil and moss for four or three months during diapause and then incubated until hatching...
September 11, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28992108/defining-the-role-of-the-mads-box-gene-zea-agamous-like1-a-target-of-selection-during-maize-domestication
#20
David M Wills, Zhou Fang, Alessandra M York, James B Holland, John F Doebley
Genomic scans for genes that show the signature of past selection have been widely applied to a number of species and have identified a large number of selection candidate genes. In cultivated maize (Zea mays ssp. mays) selection scans have identified several hundred candidate domestication genes by comparing nucleotide diversity and differentiation between maize and its progenitor, teosinte (Z. mays ssp. parviglumis). One of these is a gene called zea agamous-like1 (zagl1), a MADS-box transcription factor, that is known for its function in the control of flowering time...
September 5, 2017: Journal of Heredity
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