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evolutionary genetics

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https://www.readbyqxmd.com/read/29668016/genetic-and-ecological-niche-modeling-of-calydorea-crocoides-iridaceae-an-endemic-species-of-subtropical-highland-grasslands
#1
Juliana Lustosa Matos de Alencar, Eliane Kaltchuk-Santos, Juliana Fachinetto, Luana Olinda Tacuatiá, Eliana Regina Forni-Martins, Eudes Maria Stiehl-Alves, Tatiana Teixeira de Souza-Chies
Evolutionary analyses have been widely used for evaluation of genetic diversity of natural populations and correlate these data to the fitness of the species, especially in the case of threatened species. Calydorea crocoides occurs in a restricted area at altitudes from 800 to 1500 m in southern Brazil and is considered endangered. A study assessing genetic diversity, cytogenetic features and ecological niche was performed aiming to characterize C. crocoides by multidisciplinary approaches. Molecular data highlighted that most of the total variation (76%; p < 0...
2018: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29667780/variability-in-vertebral-numbers-does-not-contribute-to-sexual-size-dimorphism-interspecific-variability-or-phenotypic-plasticity-in-body-size-in-geckos-squamata-gekkota-paroedura
#2
Lukáš Kratochvíl, Lukáš Kubička, Martin Vohralík, Zuzana Starostová
Body size is a fundamental trait correlated with nearly every aspect of animal life. It is influenced by numerous genetic and non-genetic factors. Despite its central importance, proximate mechanisms of intra- and interspecific variability in body size are still not well understood even in such a largely studied group as reptiles. For our study, we concentrated on the gecko species Paroedura picta. We investigated whether differences in sexual size dimorphism and in final and asymptotic snout-vent length (induced by a range of incubation and rearing temperatures) are correlated with differences in the number of presacral vertebrae...
April 18, 2018: Journal of Experimental Zoology. Part A, Ecological and Integrative Physiology
https://www.readbyqxmd.com/read/29667323/clades-a-classification-based-machine-learning-method-for-species-delimitation-from-population-genetic-data
#3
Jingwen Pei, Chong Chu, Xin Li, Bin Lu, Yufeng Wu
Species are considered to be the basic unit of ecological and evolutionary studies. Since multi-locus genomic data are increasingly available there has been considerable interests in the use of DNA sequence data to delimit species. In this paper, we show that machine learning can be used for species delimitation. Our method treats the species delimitation problem as a classification problem for identifying the category of a new observation on the basis of training data. Extensive simulation is first conducted over a broad range of evolutionary parameters for training purposes...
April 18, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29666707/realm-of-thermoalkaline-lipases-in-bioprocess-commodities
#4
REVIEW
Ahmad Firdaus B Lajis
For decades, microbial lipases are notably used as biocatalysts and efficiently catalyze various processes in many important industries. Biocatalysts are less corrosive to industrial equipment and due to their substrate specificity and regioselectivity they produced less harmful waste which promotes environmental sustainability. At present, thermostable and alkaline tolerant lipases have gained enormous interest as biocatalyst due to their stability and robustness under high temperature and alkaline environment operation...
2018: Journal of Lipids
https://www.readbyqxmd.com/read/29666616/stem-cell-transcription-factor-foxo-controls-microbiome-resilience-in-hydra
#5
Benedikt M Mortzfeld, Jan Taubenheim, Sebastian Fraune, Alexander V Klimovich, Thomas C G Bosch
The aging process is considered to be the result of accumulating cellular deterioration in an individual organism over time. It can be affected by the combined influence of genetic, epigenetic, and environmental factors including life-style-associated events. In the non-senescent freshwater polyp Hydra , one of the classical model systems for evolutionary developmental biology and regeneration, transcription factor FoxO modulates both stem cell proliferation and innate immunity. This provides strong support for the role of FoxO as a critical rate-of-aging regulator...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29666331/isolation-and-characterization-of-the-major-histocompatibility-complex-dqa1-and-dqa2-genes-in-gayal-bos-frontalis
#6
Sameeullah Memon, Liping Wang, Guozhi Li, Xiangying Liu, Weidong Deng, Dongmei Xi
The species origin of Yunnan gayal has been controversial since many years. However, few recent genetic studies have suggested that it has perhaps originated from the hybridization between male Bos frontalis and female B. taurus or B. indicus. Being an important semi-wild bovid species, this has also been listed under the red list of International Union of Conservation of Nature and Natural Resources. However, there is limited information available about the immunogenicity of this precarious species of Bos...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29665772/evolutionary-history-of-mexican-domesticated-and-wild-meleagris-gallopavo
#7
Gabriela Padilla-Jacobo, Horacio Cano-Camacho, Rigoberto López-Zavala, María E Cornejo-Pérez, María G Zavala-Páramo
BACKGROUND: The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological characteristics and/or geographical variations in wild and domesticated populations. In this paper, based on DNA sequence data from the mitochondrial D-loop, we investigated the genetic diversity and structure, genealogical relationships, divergence time and demographic history of M...
April 17, 2018: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/29664344/how-criticality-of-gene-regulatory-networks-affects-the-resulting-morphogenesis-under-genetic-perturbations
#8
Hyobin Kim, Hiroki Sayama
Whereas the relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single-cell level has been vigorously studied, the relationship between the criticality of GRNs and system properties at a higher level has not been fully explored. Here we aim at revealing a potential role of criticality of GRNs in morphogenesis, which is hard to uncover through the single-cell-level studies, especially from an evolutionary viewpoint. Our model simulated the growth of a cell population from a single seed cell...
April 17, 2018: Artificial Life
https://www.readbyqxmd.com/read/29663588/from-transects-to-transcripts-teasing-apart-the-architecture-of-reproductive-isolation
#9
Jill A Hamilton, Joshua M Miller
Understanding the processes underlying speciation has long been a challenge to evolutionary biologists. This spurs from difficulties teasing apart the various mechanisms that contribute to the evolution of barriers to reproduction. The study by Rafati et al. () in this issue of Molecular Ecology combines spatially explicit whole-genome resequencing with evaluation of differential gene expression across individuals with mixed ancestry to associate the genomic architecture of reproductive barriers with expression of reproductive incompatibilities...
March 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29663185/synergy-from-reproductive-division-of-labor-and-genetic-complexity-drive-the-evolution-of-sex
#10
Klaus Jaffe
Computer experiments that mirror the evolutionary dynamics of sexual and asexual organisms as they occur in nature were used to test features proposed to explain the evolution of sexual recombination. Results show that this evolution is better described as a network of interactions between possible sexual forms, including diploidy, thelytoky, facultative sex, assortation, bisexuality, and division of labor between the sexes, rather than a simple transition from parthenogenesis to sexual recombination. Diploidy was shown to be fundamental for the evolution of sex; bisexual reproduction emerged only among anisogamic diploids with a synergistic division of reproductive labor; and facultative sex was more likely to evolve among haploids practicing assortative mating...
April 16, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29660114/molecular-evolution-of-key-metabolic-genes-during-transitions-to-c-4-and-cam-photosynthesis
#11
Eric W Goolsby, Abigail J Moore, Lillian P Hancock, Jurriaan M De Vos, Erika J Edwards
PREMISE OF THE STUDY: Next-generation sequencing facilitates rapid production of well-sampled phylogenies built from very large genetic data sets, which can then be subsequently exploited to examine the molecular evolution of the genes themselves. We present an evolutionary analysis of 83 gene families (19 containing carbon-concentrating mechanism (CCM) genes, 64 containing non-CCM genes) in the portullugo clade (Caryophyllales), a diverse lineage of mostly arid-adapted plants that contains multiple evolutionary origins of all known photosynthesis types in land plants (C3 , C4 , CAM, C4 -CAM, and various intermediates)...
April 16, 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29659893/temporal-mitogenomics-of-the-galapagos-giant-tortoise-from-pinz%C3%A3-n-reveals-potential-biases-in-population-genetic-inference
#12
Evelyn L Jensen, Joshua M Miller, Danielle L Edwards, Ryan C Garrick, Washington Tapia, Adalgisa Caccone, Michael A Russello
Empirical population genetic studies generally rely on sampling subsets of the population(s) of interest and of the nuclear or organellar genome targeted, assuming each are representative of the whole. Violations of these assumptions may impact population-level parameter estimation and lead to spurious inferences. Here we used targeted capture to sequence the full mitochondrial genome from 123 individuals of the Galapagos giant tortoise endemic to Pinzón Island (Chelonoidis duncanensis) sampled at two time points pre- and post-bottleneck (circa 1906 and 2014) to explicitly assess differences in diversity estimates and demographic reconstructions based on subsets of the mitochondrial genome versus the full sequences, and to evaluate potential biases associated with diversity estimates and demographic reconstructions from post-bottlenecked samples alone...
April 6, 2018: Journal of Heredity
https://www.readbyqxmd.com/read/29659810/conservation-of-sex-linked-markers-among-conspecific-populations-of-a-viviparous-skink-niveoscincus-ocellatus-exhibiting-genetic-and-temperature-dependent-sex-determination
#13
Peta L Hill, Christopher P Burridge, Tariq Ezaz, Erik Wapstra
Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile that is polymorphic for sex determination system, the spotted snow skink, Niveoscincus ocellatus, to quantify the genomic differences that have accompanied this transition. In a highland population, sex is determined genetically, whereas in a lowland population, offspring sex ratio is influenced by temperature...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29658841/genetic-structure-of-zymoseptoria-tritici-in-northern-france-at-region-field-plant-and-leaf-layer-scales
#14
Ali Siah, Myriam Bomble, Benoit Tisserant, Thierry Cadalen, Maxime Holvoet, Jean-Louis Hilbert, Patrice Halama, Philippe Lucien Reignault
Population genetic structure of the worldwide-distributed wheat pathogen Zymoseptoria tritici has been extensively studied at large geographical scales, but to a much less extent at small or local spatial scales. A total of 627 single-conidial fungal isolates were sampled from several locations in northern France (Hauts-de-France Region) to assess fungal genetic structure at region, field, plant and leaf layer scales, using highly polymorphic microsatellite markers and mating type idiomorphs. Important and overall similar levels of both gene and genotype diversities (gene diversity values ≥ 0...
April 16, 2018: Phytopathology
https://www.readbyqxmd.com/read/29658173/contrasting-results-from-gwas-and-qtl-mapping-on-wing-length-in-great-reed-warblers
#15
Bengt Hansson, Hanna Sigeman, Martin Stervander, Maja Tarka, Suvi Ponnikas, Maria Strandh, Helena Westerdahl, Dennis Hasselquist
A major goal in evolutionary biology is to understand the genetic basis of adaptive traits. In migratory birds, wing morphology is such a trait. Our previous work on the great reed warbler (Acrocephalus arundinaceus) shows that wing length is highly heritable and under sexually antagonistic selection. Moreover, a quantitative trait locus (QTL) mapping analysis detected a pronounced QTL for wing length on chromosome 2, suggesting that wing morphology is partly controlled by genes with large effects. Here, we re-evaluate the genetic basis of wing length in great reed warblers using a genome-wide association study (GWAS) approach based on restriction site-associated DNA sequencing (RADseq) data...
April 15, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29658161/parallel-evolutionary-forces-influence-the-evolution-of-male-and-female-songs-in-a-tropical-songbird
#16
Brendan A Graham, Daniel D Heath, Ryan P Walter, Melissa M Mark, Daniel J Mennill
Given the important role that animal vocalizations play in mate attraction and resource defence, acoustic signals are expected to play a significant role in speciation. Most studies, however, have focused on the acoustic traits of male animals living in the temperate zone. In contrast to temperate environments, in the tropics it is commonplace for both sexes to produce complex acoustic signals. Therefore tropical birds offer the opportunity to compare the sexes and provide a more comprehensive understanding of the evolution of animal signals...
April 15, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29657963/hologenomics-systems-level-host-biology
#17
Kevin R Theis
The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations...
March 2018: MSystems
https://www.readbyqxmd.com/read/29657837/inter-and-intracontinental-migrations-and-local-differentiation-have-shaped-the-contemporary-epidemiological-landscape-of-canine-parvovirus-in-south-america
#18
Sofía Grecco, Gregorio Iraola, Nicola Decaro, Alice Alfieri, Amauri Alfieri, Marina Gallo Calderón, Ana Paula da Silva, Daniela Name, Jaime Aldaz, Lucía Calleros, Ana Marandino, Gonzalo Tomás, Leticia Maya, Lourdes Francia, Yanina Panzera, Ruben Pérez
Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes one of the most significant infectious diseases of dogs. Although the virus dispersed over long distances in the past, current populations are considered to be spatially confined and with only a few instances of migration between specific localities. It is unclear whether these dynamics occur in South America where global studies have not been performed. The aim of this study is to analyze the patterns of genetic variability in South American CPV populations and explore their evolutionary relationships with global strains...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29657812/resurrected-ancient-daphnia-genotypes-show-reduced-thermal-stress-tolerance-compared-to-modern-descendants
#19
Aime'e M Yousey, Priyanka Roy Chowdhury, Nicole Biddinger, Jennifer H Shaw, Punidan D Jeyasingh, Lawrence J Weider
Understanding how populations adapt to rising temperatures has been a challenge in ecology. Research often evaluates multiple populations to test whether local adaptation to temperature regimes is occurring. Space-for-time substitutions are common, as temporal constraints limit our ability to observe evolutionary responses. We employed a resurrection ecology approach to understand how thermal tolerance has changed in a Daphnia pulicaria population over time. Temperatures experienced by the oldest genotypes were considerably lower than the youngest...
March 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29657123/transcriptome-of-the-bivalve-limecola-balthica-l-from-western-pacific-a-new-resource-for-studies-of-european-populations
#20
Andrey A Yurchenko, Nataliia Katolikova, Dmitrii Polev, Irina Shcherbakova, Petr Strelkov
The Baltic clam Limecola balthica L. (Tellinidae) is broadly used in ecophysiological, toxicological, evolutionary and environmental monitoring studies. However, it is poorly studied in respect of genome and gene functions. We obtained a transcriptome of Limecola b. balthica from Kamchatka (Western Pacific) generated with the use of Illumina high-throughput sequencing. We annotated 11,374 proteins, including 53 from the oxidative phosphorylation pathway and a number of pollution-stress biomarkers, recovered 254,540 single nucleotide variants within two annotated transcriptomes including 25,330 scorable in the previously published European data...
April 12, 2018: Marine Genomics
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