scholarly journals Genetic Variation Within Two Sympatric Spotted Gum Eucalypts Exceeds Between Taxa Variation

2008 ◽  
Vol 57 (1-6) ◽  
pp. 249-256 ◽  
Author(s):  
J. W. Ochieng ◽  
M. Shepherd ◽  
P. R. Baverstock ◽  
G. Nikles ◽  
D. J. Lee ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Allele Frequency ◽  
Population Stratification ◽  
East Coast ◽  
Population Substructure ◽  
Cherry Tree ◽  
Separate Species ◽  
Intermediate Morphology ◽  
Species Specific ◽  
A Site

AbstractPopulation substructure and hybridization, among other factors, have the potential to cause erroneous associations in linkage disequilibrium (LD) mapping. Two closely related spotted gum eucalypts, Corymbia variegata and C. henryi (Myrtaceae) occur in sympatry in the east coast of Australia and potentially interbreed. They are morphologically similar but are distinguished as separate species based on capsule and foliage size. To determine whether they hybridize in nature and its implications for LD mapping, we investigated the level of molecular divergence between the two species at two sympatric locations separated by 300 kilometres. Very few individuals of intermediate morphology were identified, despite the two species occurring only metres apart. Analysis of genetic structure using 12 microsatellite loci showed that genetic differentiation between populations of the same species at different locations (FST= 0.07 for both species; p = 0.0001) was significantly higher than that observed between species at each location (mean FST= 0.02 and 0.04 for Cherry tree and Bunyaville respectively; p = 0.0001; all Mann-Whitney U-test p ≤ 0.01). No species-specific alleles or significant allele frequency differences were detected within a site, suggesting recurr#ent local gene flow between the two species. The lack of significant allele frequency differences implies no population stratification along taxonomic lines. This suggested that there is little concern for cryptic hybridization when sampling from sites of sympatry for LD mapping.

scholarly journals Genomic variation and population histories of spotted (Strix occidentalis) and barred (S. varia) owls

2020 ◽  
Author(s):  
Naoko T. Fujito ◽  
Zachary R. Hanna ◽  
Michal Levy-Sakin ◽  
Rauri C. K. Bowie ◽  
Pui-Yan Kwok ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Keystone Species ◽  
Genomic Variation ◽  
F1 Hybrids ◽  
Suitable Habitat ◽  
High Coverage ◽  
Strix Occidentalis ◽  
Strix Varia ◽  
Intermediate Morphology ◽  
Species Specific

AbstractSpotted owls (SO, Strix occidentalis) are a keystone species inhabiting old-growth forests in Western North America. In recent decades, their populations have declined due to ongoing reductions in suitable habitat caused by logging, wildfires, and competition with the congeneric barred owl (BO, Strix varia). The northern spotted owl (subspecies S. o. caurina) has been listed as “threatened” under the Endangered Species Act since 1990. Here we present a comprehensive look at genetic variation to elucidate the population histories of SO and invading western BO. Specifically, we present an improved SO genome assembly, based on 10x and Bionano Genomics data, along with 51 high-coverage whole-genome sequences including 11 SO from two subspecies (caurina and occidentalis), 25 BO, 2 confirmed and 13 potential hybrids. We identified potential hybrids based on intermediate morphology and found them to be a mixture of pure BO, F1 hybrids, and F1 x BO backcrosses. Unlike previous studies reporting asymmetries in the species-specific genders of the parents of F1 hybrids, we did not observe any significant asymmetry. Within species, we found that Western BO genetic variation is not simply a subset of the genetic variation in Eastern BO, suggesting that the two groups have been genetically isolated for longer (thousands of years) than previously suspected (80-130 years). Similarly, we found evidence of substantial genetic differentiation between the two SO subspecies. Finally, our analyses suggest that Northern SO experienced a moderate population bottleneck around the end of the last glaciation, while BO population sizes have always been large.

scholarly journals Divergence and Gene Flow Between Fusarium subglutinans and F. temperatum Isolated from Maize in Argentina

2020 ◽  
pp. PHYTO-09-20-043
Author(s):  
M. Veronica Fumero ◽  
Wei Yue ◽  
María L. Chiotta ◽  
Sofía N. Chulze ◽  
John F. Leslie ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Sexual Reproduction ◽  
Fusarium Species ◽  
Population Substructure ◽  
Reverse Direction ◽  
Selective Sweeps ◽  
Fusarium Subglutinans ◽  
Separate Species ◽  
Maize Varieties

Fusarium subglutinans and F. temperatum are two important fungal pathogens of maize whose distinctness as separate species has been difficult to assess. We isolated strains of these species from commercial and native maize varieties in Argentina and sequenced >28,000 loci to estimate genetic variation in the sample. Our objectives were to measure genetic divergence between the species, infer demographic parameters related to their split, and describe the population structure of the sample. When analyzed together, over 30% of each species’ polymorphic sites (>2,500 sites) segregate as polymorphisms in the other. Demographic modeling confirmed the species split predated maize domestication, but subsequent between-species gene flow has occurred, with gene flow from F. subglutinans into F. temperatum greater than gene flow in the reverse direction. In F. subglutinans, little evidence exists for substructure or recent selective sweeps, but there is evidence for limited sexual reproduction. In F. temperatum, there is clear evidence for population substructure and signals of abundant recent selective sweeps, with sexual reproduction probably less common than in F. subglutinans. Both genetic variation and the relative number of polymorphisms shared between species increase near the telomeres of all 12 chromosomes, where genes related to plant−pathogen interactions often are located. Our results suggest that species boundaries between closely related Fusarium species can be semipermeable and merit further study. Such semipermeability could facilitate unanticipated genetic exchange between species and enable quicker permanent responses to changes in the agro-ecosystem, e.g., pathogen-resistant host varieties, new chemical and biological control agents, and agronomic practices.

scholarly journals The distribution of mutational effects on fitness in Caenorhabditis elegans inferred from standing genetic variation

2020 ◽  
Author(s):  
Kimberly J. Gilbert ◽  
Stefan Zdraljevic ◽  
Daniel E. Cook ◽  
Asher D. Cutter ◽  
Erik C. Andersen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Caenorhabditis Elegans ◽  
Population Size ◽  
Genomic Structure ◽  
Random Mating ◽  
Population Substructure ◽  
C Elegans ◽  
Fitness Effects ◽  
Self Fertilization ◽  
New Mutations

ABSTRACTThe distribution of fitness effects for new mutations is one of the most theoretically important but difficult to estimate properties in population genetics. A crucial challenge to inferring the distribution of fitness effects (DFE) from natural genetic variation is the sensitivity of the site frequency spectrum to factors like population size change, population substructure, and non-random mating. Although inference methods aim to control for population size changes, the influence of non-random mating remains incompletely understood, despite being a common feature of many species. We report the distribution of fitness effects estimated from 326 genomes of Caenorhabditis elegans, a nematode roundworm with a high rate of self-fertilization. We evaluate the robustness of DFE inferences using simulated data that mimics the genomic structure and reproductive life history of C. elegans. Our observations demonstrate how the combined influence of self-fertilization, genome structure, and natural selection can conspire to compromise estimates of the DFE from extant polymorphisms. These factors together tend to bias inferences towards weakly deleterious mutations, making it challenging to have full confidence in the inferred DFE of new mutations as deduced from standing genetic variation in species like C. elegans. Improved methods for inferring the distribution of fitness effects are needed to appropriately handle strong linked selection and selfing. These results highlight the importance of understanding the combined effects of processes that can bias our interpretations of evolution in natural populations.

scholarly journals Geographic patterns of human allele frequency variation: a variant-centric perspective

2020 ◽  
Author(s):  
Arjun Biddanda ◽  
Daniel P. Rice ◽  
John Novembre
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Allele Frequency ◽  
Human Genetics ◽  
Geographic Region ◽  
Frequency Variation ◽  
Human Genetic Variation ◽  
Alternative Representation ◽  
Geographic Patterns

AbstractA key challenge in human genetics is to describe and understand the distribution of human genetic variation. Often genetic variation is described by showing relationships among populations or individuals, in each case drawing inferences over a large number of variants. Here, we present an alternative representation of human genetic variation that reveals the relative abundance of different allele frequency patterns across populations. This approach allows viewers to easily see several features of human genetic structure: (1) most variants are rare and geographically localized, (2) variants that are common in a single geographic region are more likely to be shared across the globe than to be private to that region, and (3) where two individuals differ, it is most often due to variants that are common globally, regardless of whether the individuals are from the same region or different regions. To guide interpretation of the results, we also apply the visualization to contrasting theoretical scenarios with varying levels of divergence and gene flow. Our variant-centric visualization clarifies the major geographic patterns of human variation and can be used to help correct potential misconceptions about the extent and nature of genetic differentiation among populations.

scholarly journals Why and how might genetic and phylogenetic diversity be reflected in the identification of key biodiversity areas?

2015 ◽  
Vol 370 (1662) ◽  
pp. 20140019 ◽  
Author(s):  
T. M. Brooks ◽  
A. Cuttelod ◽  
D. P. Faith ◽  
J. Garcia-Moreno ◽  
P. Langhammer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Threatened Species ◽  
Phylogenetic Diversity ◽  
Species Population ◽  
Threatened Taxa ◽  
Conservation Actions ◽  
Ecosystem Diversity ◽  
Species Specific ◽  
A Site ◽  
Specific Conservation

‘Key biodiversity areas' are defined as sites contributing significantly to the global persistence of biodiversity. The identification of these sites builds from existing approaches based on measures of species and ecosystem diversity and process. Here, we therefore build from the work of Sgró et al. (2011 Evol. Appl. 4 , 326–337. ( doi:10.1111/j.1752-4571.2010.00157.x )) to extend a framework for how components of genetic diversity might be considered in the identification of key biodiversity areas. We make three recommendations to inform the ongoing process of consolidating a key biodiversity areas standard: (i) thresholds for the threatened species criterion currently consider a site's share of a threatened species' population; expand these to include the proportion of the species' genetic diversity unique to a site; (ii) expand criterion for ‘threatened species' to consider ‘threatened taxa’ and (iii) expand the centre of endemism criterion to identify as key biodiversity areas those sites holding a threshold proportion of the compositional or phylogenetic diversity of species (within a taxonomic group) whose restricted ranges collectively define a centre of endemism. We also recommend consideration of occurrence of EDGE species (i.e. threatened phylogenetic diversity) in key biodiversity areas to prioritize species-specific conservation actions among sites.

scholarly journals Unique Genomic and Phenotypic Responses to Extreme and Variable pH Conditions in Purple Urchin Larvae

2020 ◽  
Vol 60 (2) ◽  
pp. 318-331
Author(s):  
April D Garrett ◽  
Reid S Brennan ◽  
Anya L Steinhart ◽  
Aubrey M Pelletier ◽  
Melissa H Pespeni
Keyword(s):  
Genetic Variation ◽  
Allele Frequency ◽  
Sea Urchin ◽  
Genetic Basis ◽  
Adaptive Genetic Variation ◽  
Protein Coding ◽  
Purple Sea Urchin ◽  
Ph Conditions ◽  
Frequency Changes ◽  
Genetic Responses

Synopsis Environmental variation experienced by a species across space and time can promote the maintenance of genetic diversity that may be adaptive in future global change conditions. Selection experiments have shown that purple sea urchin, Strongylocentrotus purpuratus, populations have adaptive genetic variation for surviving pH conditions at the “edge” (pH 7.5) of conditions experienced in nature. However, little is known about whether populations have genetic variation for surviving low-pH events beyond those currently experienced in nature or how variation in pH conditions affects organismal and genetic responses. Here, we quantified survival, growth, and allele frequency shifts in experimentally selected developing purple sea urchin larvae in static and variable conditions at three pH levels: pH 8.1 (control), pH 7.5 (edge-of-range), and pH 7.0 (extreme). Variable treatments recovered body size relative to static treatments, but resulted in higher mortality, suggesting a potential tradeoff between survival and growth under pH stress. However, within each pH level, allele frequency changes were overlapping between static and variable conditions, suggesting a shared genetic basis underlying survival to mean pH regardless of variability. In contrast, genetic responses to pH 7.5 (edge) versus pH 7.0 (extreme) conditions were distinct, indicating a unique genetic basis of survival. In addition, loci under selection were more likely to be in exonic regions than regulatory, indicating that selection targeted protein-coding variation. Loci under selection in variable pH 7.5 conditions, more similar to conditions periodically experienced in nature, performed functions related to lipid biosynthesis and metabolism, while loci under selection in static pH 7.0 conditions performed functions related to transmembrane and mitochondrial processes. While these results are promising in that purple sea urchin populations possess genetic variation for surviving extreme pH conditions not currently experienced in nature, they caution that increased acidification does not result in a linear response but elicits unique physiological stresses and survival mechanisms.

scholarly journals Identification of a Novel Genomic Island Associated withvanD-Type Vancomycin Resistance in Six Dutch Vancomycin-ResistantEnterococcus faeciumIsolates

2018 ◽  
Vol 62 (3) ◽  
Author(s):  
Janetta Top ◽  
Jan C. Sinnige ◽  
Ellen C. Brouwer ◽  
Guido Werner ◽  
Jukka Corander ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Enterococcus Faecium ◽  
Genomic Island ◽  
Gene Clusters ◽  
Genomic Comparison ◽  
Variable Size ◽  
Content Type ◽  
Enterococcal Species ◽  
Vancomycin Resistant ◽  
Species Specific

ABSTRACTGenomic comparison of the first six DutchvanD-type vancomycin-resistantEnterococcus faecium(VRE) isolates with fourvanDgene clusters from other enterococcal species and anaerobic gut commensals revealed that thevanDgene cluster was located on a genomic island of variable size. Phylogenetic inferences revealed that the Dutch VRE isolates were genetically not closely related and that genetic variation of thevanD-containing genomic island was not species specific, suggesting that this island is transferred horizontally between enterococci and anaerobic gut commensals.

DIVERSITY AND DISTRIBUTION OF EUPHYLLIDAE CORALS IN TIOMAN ISLAND: EMPHASIS ON THE GENETIC VARIATION OF EUPHYLLIA CRISTATA

2015 ◽  
Vol 77 (24) ◽  
Author(s):  
Mohd Fikri Akmal Khodzori ◽  
Shahbudin Saad ◽  
Noor Faizul Hadry Nordin ◽  
Muhammad Faris Salleh ◽  
Mohd Husaini Rani ◽  
...  
Keyword(s):  
Genetic Variation ◽  
West Coast ◽  
East Coast ◽  
Coastal Development ◽  
Pairwise Distance ◽  
Evolutionary Divergence ◽  
Point Count ◽  
Significant Difference ◽  
Genetic Sequences ◽  
Mitochondrial Cytochrome Oxidase

Euphyllidae corals are among the most beautiful corals that have been exploited for the aquarium trade all over the world. In Malaysia, the information on these coral species particularly on the diversity and genetic variation is not fully documented. Realizing to this matter, the diversity and distribution of Euphylllidae corals were investigated at 13 sampling stations in Tioman Island. The diversity and distribution of Euphyllidae corals were observed and recorded using the Coral Video Transect (CVT) method. The captured images were analyzed using Coral Point Count with Excel extension (CPCe) software. The samples of Euphyllia cristata were collected at three different zones in Tioman Island (East Coast, West Coast and Isolated Island). The samples were extracted and mitochondrial Cytochrome Oxidase 1 gene primer was used to study their genetic variation. A total of six species belong to three genera of Euphyllia, Plerogyra and Physogyra were recorded. Benuang Bay (East Coast) and Bayan Bay (Isolated Island) have shown higher diversity and distribution of Euphyllidae corals among the sampling stations. The Shannon-Weinner index (H’) of Benuang Bay and Bayan Bay were 1.42 and 1.43 respectively. The West Coast zone had the lowest diversity and distribution of Euphyllidae corals due to massive coastal development and loads of human intervention. The genetic sequences from the East Coast and West Coast were closely related. The pairwise distance between these two zones is 0.003. There is a slight difference in the sequence from the Isolated Island. The pairwise distance of West Coast-Isolated and East Coast-Isolated are 0.021 and 0.025 respectively. However, it is relatively low to consider there is evolutionary divergence between the samples. Thus, no genetic variation was observed between all Euphyllia cristata taken at three different zones of Tioman Island. This study has shown that there was a highly significant difference (p<0.01) in the diversity and distribution of Euphyllidae corals with respect to sampling stations.

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