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R A Coleman, B Gauffre, A Pavlova, L B Beheregaray, J Kearns, J Lyon, M Sasaki, R Leblois, C Sgro, P Sunnucks
Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species...
January 12, 2018: Heredity
Diana A Pazmiño, Gregory E Maes, Madeline E Green, Colin A Simpfendorfer, E Mauricio Hoyos-Padilla, Clinton J A Duffy, Carl G Meyer, Sven E Kerwath, Pelayo Salinas-de-León, Lynne van Herwerden
The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals...
January 11, 2018: Heredity
Mattias L Johansson, Bradley A Dufour, Kyle W Wellband, Lynda D Corkum, Hugh J MacIsaac, Daniel D Heath
The globally invasive Round Goby (Neogobius melanostomus) was introduced to the Great Lakes around 1990, spreading widely and becoming the dominant benthic fish in many areas. The speed and scope of this invasion is remarkable and calls into question conventional secondary spread models and scenarios. We utilized nine microsatellites to identify large-scale genetic structure in Round Goby populations in the eastern Great Lakes, and assessed the role of colonization vs. secondary transport and dispersal in developing this structure...
January 10, 2018: Heredity
Nicolas Navarro, A Murat Maga
Molar size in Mammals shows considerable disparity and exhibits variation similar to that predicted by the Inhibitory Cascade model. The importance of such developmental systems in favoring evolutionary trajectories is also underlined by the fact that this model can predict macroevolutionary patterns. Using backcross mice, we mapped QTL for molar sizes controlling for their sequential development. Genetic controls for upper and lower molars appear somewhat similar, and regions containing genes implied in dental defects drive this variation...
January 5, 2018: Heredity
Takahiro Segawa, Nozomu Takeuchi, Koji Fujita, Vladimir B Aizen, Eske Willerslev, Takahiro Yonezawa
Despite the crucial role of cyanobacteria in various ecosystems, little is known about their evolutionary histories, especially microevolutionary dynamics, because of the lack of knowledge regarding their mutation rates. Here we directly estimated cyanobacterial mutation rates based on ancient DNA analyses of ice core samples collected from Kyrgyz Republic that dates back to ~12,500 cal years before present. We successfully sequenced the 16S rRNA and 16S-23S internal transcribed spacer (ITS) region. Two cyanobacterial operational taxonomic units (OTUs) were detected from the ancient ice core samples, and these OTUs are shared with those from the modern glacier surface...
January 5, 2018: Heredity
Molly Schumer, Gil G Rosenthal, Peter Andolfatto
No abstract text is available yet for this article.
January 5, 2018: Heredity
Xiao-Long Jiang, Miao An, Si-Si Zheng, Min Deng, Zhi-Hao Su
Southwest China is one of the major global biodiversity hotspots. The Tanaka line, extending within southwestern China from its northwest to its southeast, is an important biogeographical boundary between the Sino-Japanese and Sino-Himalayan floristic regions. Understanding the evolutionary history of the regional keystone species would assist with both reconstructing historical vegetation dynamics and ongoing biodiversity management. In this research, we combined phylogeographic methodologies and species distribution models (SDMs) to investigate the spatial genetic patterns and distribution dynamics of Quercus kerrii, a dominant evergreen oak inhabiting southwest China lowland evergreen-broadleaved forests (EBLFs)...
December 27, 2017: Heredity
Boris B Demenou, Jean-Louis Doucet, Olivier J Hardy
Paleo-environmental reconstructions show that the distribution of tropical African rain forests was affected by Quaternary climate changes. They suggest that the Dahomey Gap (DG)-the savanna corridor that currently separates Upper Guinean (UG, West Africa) and Lower Guinean (LG, western Central Africa) rain forest blocks-was forested during the African Humid Holocene period (from at least 9 ka till 4.5 ka), and possibly during other interglacial periods, while an open vegetation developed in the DG under drier conditions, notably during glacial maxima...
December 27, 2017: Heredity
Schyler O Nunziata, David W Weisrock
Large genomic data sets generated with restriction site-associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of species. We used a simulation approach to examine the potential for RADseq data sets to accurately estimate effective population size (N e) over the course of stable and declining population trends, and we compare the ability of two methods of analysis to accurately distinguish stable from steadily declining populations over a contemporary time scale (20 generations)...
December 22, 2017: Heredity
Elizabeth Heppenheimer, Daniela S Cosio, Kristin E Brzeski, Danny Caudill, Kyle Van Why, Michael J Chamberlain, Joseph W Hinton, Bridgett vonHoldt
Human-mediated range expansions have increased in recent decades and represent unique opportunities to evaluate genetic outcomes of establishing peripheral populations across broad expansion fronts. Over the past century, coyotes (Canis latrans) have undergone a pervasive range expansion and now inhabit every state in the continental United States. Coyote expansion into eastern North America was facilitated by anthropogenic landscape changes and followed two broad expansion fronts. The northern expansion extended through the Great Lakes region and southern Canada, where hybridization with remnant wolf populations was common...
December 22, 2017: Heredity
Sara J Oppenheim, Fred Gould, Keith R Hopper
Intraspecific variation in ecologically important traits is a cornerstone of Darwin's theory of evolution by natural selection. The evolution and maintenance of this variation depends on genetic architecture, which in turn determines responses to natural selection. Some models suggest that traits with complex architectures are less likely to respond to selection than those with simple architectures, yet rapid divergence has been observed in such traits. The simultaneous evolutionary lability and genetic complexity of host plant use in the Lepidopteran subfamily Heliothinae suggest that architecture may not constrain ecological adaptation in this group...
December 14, 2017: Heredity
Boby Mathew, Jens Léon, Mikko J Sillanpää
Single nucleotide polymorphism (SNP)-heritability estimation is an important topic in several research fields, including animal, plant and human genetics, as well as in ecology. Linear mixed model estimation of SNP-heritability uses the structures of genomic relationships between individuals, which is constructed from genome-wide sets of SNP-markers that are generally weighted equally in their contributions. Proposed methods to handle dependence between SNPs include, "thinning" the marker set by linkage disequilibrium (LD)-pruning, the use of haplotype-tagging of SNPs, and LD-weighting of the SNP-contributions...
December 14, 2017: Heredity
Eliana Faria Oliveira, Pablo Ariel Martinez, Vinícius Avelar São-Pedro, Marcelo Gehara, Frank Thomas Burbrink, Daniel Oliveira Mesquita, Adrian Antonio Garda, Guarino Rinaldi Colli, Gabriel Correa Costa
Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera...
December 14, 2017: Heredity
Andrés Eduardo Rodriguez Cubillos, Hao Tong, Saleh Alseekh, Francisco de Abreu E Lima, Jing Yu, Alisdair R Fernie, Zoran Nikoloski, Roosa A E Laitinen
Metabolism is a key determinant of plant growth and modulates plant adaptive responses. Increased metabolic variation due to heterozygosity may be beneficial for highly homozygous plants if their progeny is to respond to sudden changes in the habitat. Here, we investigate the extent to which heterozygosity contributes to the variation in metabolism and size of hybrids of Arabidopsis thaliana whose parents are from a single growth habitat. We created full diallel crosses among seven parents, originating from Southern Germany, and analysed the inheritance patterns in primary and secondary metabolism as well as in rosette size in situ...
December 13, 2017: Heredity
Roman Zug, Peter Hammerstein
Maternally inherited symbionts such as Wolbachia have long been seen mainly as reproductive parasites, with deleterious effects on host fitness. It is becoming clear, however, that, frequently, these symbionts also have beneficial effects on host fitness, either along with reproductive parasitism or not. Using the examples of cytoplasmic incompatibility (CI) and male-killing (MK), we here analyze the effect of direct fitness benefits on the evolution of reproductive parasites. By means of a simple theoretical framework, we synthesize and extend earlier modeling approaches for CI and MK, which usually ignore fitness benefits...
December 13, 2017: Heredity
Wen-Long Ren, Yang-Jun Wen, Jim M Dunwell, Yuan-Ming Zhang
Although nonparametric methods in genome-wide association studies (GWAS) are robust in quantitative trait nucleotide (QTN) detection, the absence of polygenic background control in single-marker association in genome-wide scans results in a high false positive rate. To overcome this issue, we proposed an integrated nonparametric method for multi-locus GWAS. First, a new model transformation was used to whiten the covariance matrix of polygenic matrix K and environmental noise. Using the transferred model, Kruskal-Wallis test along with least angle regression was then used to select all the markers that were potentially associated with the trait...
December 13, 2017: Heredity
Thea V Kristensen, Emily E Puckett, Erin L Landguth, Jerrold L Belant, John T Hast, Colin Carpenter, Jaime L Sajecki, Jeff Beringer, Myron Means, John J Cox, Lori S Eggert, Don White, Kimberly G Smith
Previously, American black bears (Ursus americanus) were thought to follow the pattern of female philopatry and male-biased dispersal. However, recent studies have identified deviations from this pattern. Such flexibility in dispersal patterns can allow individuals greater ability to acclimate to changing environments. We explored dispersal and spatial genetic relatedness patterns across ten black bear populations-including long established (historic), with known reproduction >50 years ago, and newly established (recent) populations, with reproduction recorded <50 years ago-in the Interior Highlands and Southern Appalachian Mountains, United States...
December 13, 2017: Heredity
Ling Lu, Yuanqi Wu, Zhengqiao Liao, Jing Xiong, Fengkai Wu, Jie Xu, Hai Lan, Qiling Tang, Shufeng Zhou, Yaxi Liu, Yanli Lu
ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1)-blue-light photoreceptors-play important roles in regulating the circadian clock and photoperiodic flowering pathway in plants. In this study, phylogenetic analysis revealed that the LOV (Light, Oxygen, or Voltage) and Kelch repeat-containing F-box (LFK) gene family can be classified into two clades, ZTL/LKP2 and FKF1, with clear differentiation between monocots and dicots within each clade. The LFK family genes underwent strong purifying selection; however, signatures of positive selection to adapt to local conditions still existed in 18 specific codons...
December 11, 2017: Heredity
A A Karamanlidis, T Skrbinšek, M de Gabriel Hernando, L Krambokoukis, V Munoz-Fuentes, Z Bailey, C Nowak, A V Stronen
Understanding the mechanisms and patterns involved in population recoveries is challenging and important in shaping conservation strategies. We used a recovering rear-edge population of brown bears at their southernmost European range in Greece as a case study (2007-2010) to explore the recovery genetics at a species' distribution edge. We used 17 microsatellite and a mitochondrial markers to evaluate genetic structure, estimate effective population size and genetic diversity, and infer gene flow between the identified subpopulations...
December 11, 2017: Heredity
G W Low, B Chattopadhyay, K M Garg, M Irestedt, Pgp Ericson, G Yap, Q Tang, S Wu, F E Rheindt
Invasive species exert a serious impact on native fauna and flora and have been the target of many eradication and management efforts worldwide. However, a lack of data on population structure and history, exacerbated by the recency of many species introductions, limits the efficiency with which such species can be kept at bay. In this study we generated a novel genome of high assembly quality and genotyped 4735 genome-wide single nucleotide polymorphic (SNP) markers from 78 individuals of an invasive population of the Javan Myna Acridotheres javanicus across the island of Singapore...
December 11, 2017: Heredity
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