scholarly journals Speciation and introgression between Mimulus nasutus and Mimulus guttatus

2013 ◽  
Author(s):  
Yaniv Brandvain ◽  
Amanda M Kenney ◽  
Lex Fagel ◽  
Graham Coop ◽  
Andrea L Sweigart
Keyword(s):  
Ecological Model ◽  
Negative Relationship ◽  
Genomic Data ◽  
Mimulus Guttatus ◽  
Species Pair ◽  
Data Set ◽  
Genomic Signatures ◽  
Population Genomic ◽  
History Of ◽  
Biological Differentiation

Mimulus guttatus and M. nasutus are an evolutionary and ecological model sister species pair differentiated by ecology, mating system, and partial reproductive isolation. Despite extensive research on this system, the history of divergence and differentiation in this sister pair is unclear. We present and analyze a novel population genomic data set which shows that M. nasutus "budded" off of a central Californian M. guttatus population within the last 200 to 500 thousand years. In this time, the M. nasutus genome has accrued numerous genomic signatures of the transition to predominant selfing. Despite clear biological differentiation, we document ongoing, bidirectional introgression. We observe a negative relationship between the recombination rate and divergence between M. nasutus and sympatric M. guttatus samples, suggesting that selection acts against M. nasutus ancestry in M. guttatus.

scholarly journals Identifying loci under positive selection in complex population histories

2018 ◽  
Author(s):  
Alba Refoyo-Martínez ◽  
Rute R. da Fonseca ◽  
Katrín Halldórsdóttir ◽  
Einar Árnason ◽  
Thomas Mailund ◽  
...  
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Human Population ◽  
Genomic Data ◽  
Human Populations ◽  
Selective Sweeps ◽  
Population Genomic ◽  
Complex Population ◽  
History Of ◽  
Over Time

AbstractDetailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called Graph-aware Retrieval of Selective Sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish and human population genomic data containing multiple population panels related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in under-studied human populations, as well as muscle mass, milk production and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation due to inversions in the history of Atlantic codfish.

scholarly journals Flexible Mixture Model Approaches That Accommodate Footprint Size Variability for Robust Detection of Balancing Selection

2020 ◽  
Vol 37 (11) ◽  
pp. 3267-3291 ◽  
Author(s):  
Xiaoheng Cheng ◽  
Michael DeGiorgio
Keyword(s):  
Pain Perception ◽  
Balancing Selection ◽  
Genomic Data ◽  
Composite Likelihood ◽  
Ratio Test ◽  
Data Set ◽  
Robust Detection ◽  
Population Genomic ◽  
Genomic Regions

Abstract Long-term balancing selection typically leaves narrow footprints of increased genetic diversity, and therefore most detection approaches only achieve optimal performances when sufficiently small genomic regions (i.e., windows) are examined. Such methods are sensitive to window sizes and suffer substantial losses in power when windows are large. Here, we employ mixture models to construct a set of five composite likelihood ratio test statistics, which we collectively term B statistics. These statistics are agnostic to window sizes and can operate on diverse forms of input data. Through simulations, we show that they exhibit comparable power to the best-performing current methods, and retain substantially high power regardless of window sizes. They also display considerable robustness to high mutation rates and uneven recombination landscapes, as well as an array of other common confounding scenarios. Moreover, we applied a specific version of the B statistics, termed B2, to a human population-genomic data set and recovered many top candidates from prior studies, including the then-uncharacterized STPG2 and CCDC169–SOHLH2, both of which are related to gamete functions. We further applied B2 on a bonobo population-genomic data set. In addition to the MHC-DQ genes, we uncovered several novel candidate genes, such as KLRD1, involved in viral defense, and SCN9A, associated with pain perception. Finally, we show that our methods can be extended to account for multiallelic balancing selection and integrated the set of statistics into open-source software named BalLeRMix for future applications by the scientific community.

scholarly journals Phylogenomics With Hyb-Seq Unravels Korean Hosta Evolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Mi-Jeong Yoo ◽  
Byoung-Yoon Lee ◽  
Sangtae Kim ◽  
Chae Eun Lim
Keyword(s):  
Phylogenetic Analyses ◽  
Ornamental Plants ◽  
Introgressive Hybridization ◽  
Nuclear Gene ◽  
Genomic Data ◽  
Data Set ◽  
History Of ◽  
Large Genome Size ◽  
Taxonomic Confusion ◽  
Do So

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.

scholarly journals Population genomic data in spider mites point to a role for local adaptation in shaping range shifts

2020 ◽  
Vol 13 (10) ◽  
pp. 2821-2835
Author(s):  
Lei Chen ◽  
Jing‐Tao Sun ◽  
Peng‐Yu Jin ◽  
Ary A. Hoffmann ◽  
Xiao‐Li Bing ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Genomic Data ◽  
Spider Mites ◽  
Range Shifts ◽  
Population Genomic

Economics of respiratory disease in dairy replacement heifers

2020 ◽  
Vol 21 (2) ◽  
pp. 143-148
Author(s):  
Michael W. Overton
Keyword(s):  
Respiratory Disease ◽  
Milk Production ◽  
Incident Case ◽  
Data Set ◽  
Dairy Heifers ◽  
The Usa ◽  
History Of ◽  
On Farm ◽  
The Impact ◽  
Selective Culling

AbstractBovine respiratory disease (BRD) is a frequent disease concern in dairy cattle and is most commonly diagnosed in young dairy heifers. The impact of BRD is highly variable, depending on the accuracy and completeness of detection, effectiveness of treatment, and on-farm culling practices. Consequences include decreased rate of weight gain, a higher culling risk either as heifers or as cows, delayed age at first service, delayed age at first calving, and in some cases, lower future milk production. In this data set of 104,100 dairy replacement heifers from across the USA, 36.6% had one or more cases diagnosed within the first 120 days of age with the highest risk of new cases occurring prior to weaning. Comparison of the raising cost for heifers with BRD and those without a recorded history of BRD resulted in an estimated cost per incident case occurring in the first 120 days of age of $252 or $282, depending upon whether anticipated future milk production differences were considered or not. Current market conditions contributed to a cost estimate that is significantly higher than previously published estimates, driven in part by the losses associated with selective culling of a subset of heifers that experienced BRD.

scholarly journals Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 737
Author(s):  
Issiaka Bagayoko ◽  
Marcos Giovanni Celli ◽  
Gustavo Romay ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Sierra Leone ◽  
Evolutionary History ◽  
Molecular Diversity ◽  
Genomic Data ◽  
Gene Recombination ◽  
Necrosis Virus ◽  
History Of ◽  
Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

scholarly journals Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mario Vallejo-Marín ◽  
Jannice Friedman ◽  
Alex D. Twyford ◽  
Olivier Lepais ◽  
Stefanie M. Ickert-Bond ◽  
...  
Keyword(s):  
Biological Invasions ◽  
Historical Analysis ◽  
Historical Records ◽  
British Isles ◽  
Mimulus Guttatus ◽  
Introduced Populations ◽  
Genome Wide ◽  
Starting Point ◽  
History Of ◽  
Global Invasion

AbstractImperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments.

Inverse Relationship Between Serum Bilirubin and Atherosclerosis in Men: A Meta-Analysis of Published Studies

2003 ◽  
Vol 228 (5) ◽  
pp. 568-571 ◽  
Author(s):  
Ladislav Novotný ◽  
Libor Vítek
Keyword(s):  
Inverse Relationship ◽  
Serum Bilirubin ◽  
Linear Trend ◽  
Meta Analysis ◽  
Negative Relationship ◽  
Epidemiological Studies ◽  
Atherosclerotic Disease ◽  
Categorical Variables ◽  
History Of ◽  
Stratified Analysis

Bilirubin, a major intravascular product of heme catabolism, is a potent antioxidant compound. Numerous studies have been published showing the relationship between serum bilirubin levels and atherosclerosis. In the present investigation all the epidemiological studies available on the effect of serum bilirubin levels and atherosclerotic disease were analyzed. Studies on the epidemiology of atherosclerotic diseases in relation to serum bilirubin levels were searched in the MEDLINE database. Selected studies were subdivided according to serum bilirubin levels and severity of atherosclerotic disease. Because of the limited number of females involved in the studies, only males were included into meta-analysis. Associations for ordered categorical variables (bilirubin and natural history of graded atherosclerosis) were assessed to find correlation and linear trend between analyzed variables. A stratified analysis was conducted to compare risks of clinical outcomes. Eleven relevant studies were used for analysis. A close negative relationship was found between serum bilirubin levels and severity of atherosclerosis (Spearman rank coefficient r = −0.31, P < 0.0001). The linear trend was confirmed in analysis of proportions with x2 values for both disease conditions to be very significant ( P < 0.0001). Unambiguous inverse relationship between serum bilirubin levels and atherosclerosis was demonstrated in this preliminary meta-analytic study. These results indicate the importance of hem oxygenase-related products in the prevention of oxidative stress-mediated diseases.

Characteristics and Care of U.S. Nursing Home Residents with a History of Chronic Mental Illness

2000 ◽  
Vol 19 (S2) ◽  
pp. 1-17 ◽  
Author(s):  
Charles D. Phillips ◽  
Kathleen M. Spry
Keyword(s):  
Nursing Home ◽  
Nursing Home Residents ◽  
Minimum Data Set ◽  
Chronic Mental Illness ◽  
Data Set ◽  
Minimum Data ◽  
Troubles Mentaux ◽  
History Of ◽  
Resident Assessment ◽  
Medicaments Psychotropes

RÉSUMÉTrès peu de recherches ont été effectuées sur les pensionnaires des maisons de soins ayant manifestés des troubles mentaux chroniques sans démence avant leur entrée en institution. Les données du Minimum Data Set for Nursing Home Resident Assessment and Care Screening (MDS) de 1993 ont été utilisées pouranalyser les différences dans les caractéristiques et les soins se rapportant à ce type de pensionnaires par rapport aux autres pensionnaires. Cette enquête portait sur 70 000 pensionnaires du Kansas, du Maine, du Mississippi et du Dakota du Sud. Les caractéristiques des pensionnaires qui éprouvaient ce type de troubles mentaux chroniques étaient plus fréquemment les suivantes: sexe masculin, 65 ans et plus, bénéficiaires de Medicaid, moins médicalement inaptes et niveau plus élevé de problèmes de comportements. Ces pensionnaires reçoivent aussi davantage de médicaments psychotropes et suivant une thérapie, la prévalence de la thérapie étant cependant moins éleveé. Les informations recueillies pourraient laisser croire que les soins accordés à ces pensionnaires ne sont pas des plus appropriés.

scholarly journals The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fan Li ◽  
Yunyun Lv ◽  
Zhengyong Wen ◽  
Chao Bian ◽  
Xinhui Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Physiological Activity ◽  
Complete Mitochondrial Genome ◽  
Dynamic Environment ◽  
Data Set ◽  
History Of ◽  
Complete Mitogenome ◽  
Selection Signal ◽  
Positive Selection Signal

Abstract Background Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders. Results We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene. Conclusions Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.

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