Even before the publication of Darwin's Origin of Species, the perception of evolutionary change has been a tree-like pattern of diversification — with divergent branches spreading further and ...further from the trunk. In the only illustration of Darwin's treatise, branches large and small never reconnect. However, it is now evident that this view does not adequately encompass the richness of evolutionary pattern and process. Instead, the evolution of species from microbes to mammals builds like a web that crosses and re-crosses through genetic exchange, even as it grows outward from a point of origin. Some of the avenues for genetic exchange, for example introgression through sexual recombination versus lateral gene transfer mediated by transposable elements, are based on definably different molecular mechanisms. However, even such widely different genetic processes may result in similar effects on adaptations (either new or transferred), genome evolution, population genetics, and the evolutionary/ecological trajectory of organisms. For example, the evolution of novel adaptations (resulting from lateral gene transfer) leading to the flea-borne, deadly, causative agent of plague from a rarely-fatal, orally-transmitted, bacterial species is quite similar to the adaptations accrued from natural hybridization between annual sunflower species resulting in the formation of several new species. Thus, more and more data indicate that evolution has resulted in lineages consisting of mosaics of genes derived from different ancestors. It is therefore becoming increasingly clear that the tree is an inadequate metaphor of evolutionary change. In this book, the author promotes the ‘web-of-life’ metaphor as a more appropriate representation of evolutionary change in all life-forms.
Genetic exchange between divergent evolutionary lineages, from introgressive hybridization between locally adapted populations to insertion of retroviral sequences into eukaryotic genomes, has now ...been documented. The detection of frequent divergence-with-gene-flow contrasts the neo-Darwinian paradigm of largely allopatric diversification. Nevertheless, of even greater significance is the growing wealth of data suggesting that the recipients of the transferred genomic material gain adaptive phenotypes from the donor lineages. This adaptive enrichment is reflected by changes in pathogenicity in viruses and bacteria, the transformation of ecological amplitude in eukaryotes, and adaptive radiations in extremely diverse lineages. Although genetic exchange may produce maladaptive consequences, most of the recently reported examples suggest increases in fitness, and many such adaptive trait transfers have been identified in our own species.
Although the exchange of genetic material between lineages as diverse as viruses and mammals has been recognized for decades, particularly through the analysis of genomic datasets, it has remained an active debate as to whether such exchanges can lead to adaptive evolution.
Recently, the growing wealth of examples of genetic transfer involving organisms from all domains of life has provided the means to test the hypothesis of adaptive genetic exchange. The repeated testing of this hypothesis has revealed not only adaptive effects among viral and prokaryotic lineages but also for plants, animals, and fungi. Indeed, the data now available indicate how profoundly important ancient and more recent gene exchange has been in the evolution of even humans.
Adaptive evolutionary diversification can now be seen as being often facilitated by the addition of standing genetic variation from one divergent lineage to another.
The role of natural hybridization in the evolutionary history of numerous species is well recognized. The impact of introgressive hybridization and hybrid speciation has been documented especially in ...plant and animal assemblages. However, there remain certain areas of investigation for which natural hybridization and its consequences remain under‐studied and under‐appreciated. One such area involves the evolution of organisms that positively or negatively affect human populations. In this review, I highlight exemplars of how natural hybridization has contributed to the evolution of (i) domesticated plants and animals; (ii) pests; (iii) human disease vectors; and (iv) human pathogens. I focus on the effects from genetic exchange that may lead to the acquisition of novel phenotypes and thus increase the beneficial or detrimental (to human populations) aspects of the various taxa.
In 2016, Medicare implemented Comprehensive Care for Joint Replacement (CJR), a national mandatory bundled-payment model for hip or knee replacement in randomly selected metropolitan statistical ...areas. Hospitals in such areas receive bonuses or pay penalties based on Medicare spending per hip- or knee-replacement episode (defined as the hospitalization plus 90 days after discharge).
We conducted difference-in-differences analyses using Medicare claims from 2015 through 2017, encompassing the first 2 years of bundled payments in the CJR program. We evaluated hip- or knee-replacement episodes in 75 metropolitan statistical areas randomly assigned to mandatory participation in the CJR program (bundled-payment metropolitan statistical areas, hereafter referred to as "treatment" areas) as compared with those in 121 control areas, before and after implementation of the CJR model. The primary outcomes were institutional spending per hip- or knee-replacement episode (i.e., Medicare payments to institutions, primarily to hospitals and post-acute care facilities), rates of postsurgical complications, and the percentage of "high-risk" patients (i.e., patients for whom there was an elevated risk of spending - a measure of patient selection). Analyses were adjusted for the hospital and characteristics of the patients and procedures.
From 2015 through 2017, there were 280,161 hip- or knee-replacement procedures in 803 hospitals in treatment areas and 377,278 procedures in 962 hospitals in control areas. After the initiation of the CJR model, there were greater decreases in institutional spending per joint-replacement episode in treatment areas than in control areas (differential change i.e., the between-group difference in the change from the period before the CJR model, -$812, or a -3.1% differential decrease relative to the treatment-group baseline; P<0.001). The differential reduction was driven largely by a 5.9% relative decrease in the percentage of episodes in which patients were discharged to post-acute care facilities. The CJR program did not have a significant differential effect on the composite rate of complications (P=0.67) or on the percentage of joint-replacement procedures performed in high-risk patients (P=0.81).
In the first 2 years of the CJR program, there was a modest reduction in spending per hip- or knee-replacement episode, without an increase in rates of complications. (Funded by the Commonwealth Fund and the National Institute on Aging of the National Institutes of Health.).
At the start of the 2019-2020 influenza season, concern arose that circulating B/Victoria viruses of the globally emerging clade V1A.3 were antigenically drifted from the strain included in the ...vaccine. Intense B/Victoria activity was followed by circulation of genetically diverse A(H1N1)pdm09 viruses that were also antigenically drifted. We measured vaccine effectiveness (VE) in the United States against illness from these emerging viruses.
We enrolled outpatients aged ≥6 months with acute respiratory illness at 5 sites. Respiratory specimens were tested for influenza by reverse-transcriptase polymerase chain reaction (RT-PCR). Using the test-negative design, we determined influenza VE by virus subtype/lineage and genetic subclades by comparing odds of vaccination in influenza cases versus test-negative controls.
Among 8845 enrollees, 2722 (31%) tested positive for influenza, including 1209 (44%) for B/Victoria and 1405 (51%) for A(H1N1)pdm09. Effectiveness against any influenza illness was 39% (95% confidence interval CI: 32-44), 45% (95% CI: 37-52) against B/Victoria and 30% (95% CI: 21-39) against A(H1N1)pdm09-associated illness. Vaccination offered no protection against A(H1N1)pdm09 viruses with antigenically drifted clade 6B.1A 183P-5A+156K HA genes (VE 7%; 95% CI: -14 to 23%) which predominated after January.
Vaccination provided protection against influenza illness, mainly due to infections from B/Victoria viruses. Vaccine protection against illness from A(H1N1)pdm09 was lower than historically observed effectiveness of 40%-60%, due to late-season vaccine mismatch following emergence of antigenically drifted viruses. The effect of drift on vaccine protection is not easy to predict and, even in drifted years, significant protection can be observed.
While antibody titers and neutralization are considered the gold standard for the selection of successful vaccines, these parameters are often inadequate predictors of protective immunity. As ...antibodies mediate an array of extra-neutralizing Fc functions, when neutralization fails to predict protection, investigating Fc-mediated activity may help identify immunological correlates and mechanism(s) of humoral protection. Here, we used an integrative approach termed Systems Serology to analyze relationships among humoral responses elicited in four HIV vaccine trials. Each vaccine regimen induced a unique humoral “Fc fingerprint.” Moreover, analysis of case:control data from the first moderately protective HIV vaccine trial, RV144, pointed to mechanistic insights into immune complex composition that may underlie protective immunity to HIV. Thus, multi-dimensional relational comparisons of vaccine humoral fingerprints offer a unique approach for the evaluation and design of novel vaccines against pathogens for which correlates of protection remain elusive.
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•Beyond neutralization, antibodies drive antiviral control via Fc-mediated functions•Distinct vaccines elicit unique antibody Fc-effector profiles•Network analyses comprehensively integrating antibody profiles can compare vaccines•Case:control RV144 analysis points to mechanisms of reduced risk of HIV infection
Systems Serology reveals unique vaccine-induced “fingerprints,” highlighting potential markers of protection against HIV and providing a powerful method for comparing candidate vaccines against pathogens for which correlates of protection remain elusive.
• Understanding the origin and distribution of genetic diversity across landscapes is critical for predicting the future of organisms in changing climates. This study investigated how adaptive and ...demographic forces have shaped diversity and population structure in Pinus densata, a keystone species on Qinghai-Tibetan Plateau (QTP).
• We examined the distribution of genomic diversity across the range of P. densata using exome capture sequencing. We applied spatially explicit tests to dissect the impacts of allele surfing, geographic isolation and environmental gradients on population differentiation and forecasted how this genetic legacy may limit the persistence of P. densata in future climates.
• We found that allele surfing from range expansion could explain the distribution of 39% of the c. 48 000 genotyped single nucleotide polymorphisms (SNPs). Uncorrected, these allele frequency clines severely confounded inferences of selection. After controlling for demographic processes, isolation-by-environment explained 9.2–19.5% of the genetic structure, with c. 4.0% of loci being affected by selection. Allele surfing and genotype–environment associations resulted in genomic mismatch under projected climate scenarios.
• We illustrate that significant local adaptation, when coupled with reduced diversity as a result of demographic history, constrains potential evolutionary response to climate change. The strong signal of genomic vulnerability in P. densata may be representative for other QTP endemics.
Hybrid fitness across time and habitats Arnold, Michael L.; Martin, Noland H.
Trends in ecology & evolution (Amsterdam),
09/2010, Volume:
25, Issue:
9
Journal Article
Peer reviewed
There has been considerable debate about the role of hybrids in the evolutionary process. One question has involved the relative fitness of hybrid versus non-hybrid genotypes. For some, the ...assumption of lower hybrid fitness continues to be integral to their concept of species and speciation. In contrast, numerous workers have suggested that hybrid genotypes might demonstrate higher relative fitness under various environmental settings. Of particular importance in deciding between these opposing hypotheses are long-term analyses coupling ecological and genetic information. Although currently rare, such analyses have provided a test of the fitness of hybrid genotypes across generations and habitats and their role in adaptation and speciation. Here we discuss examples of these analyses applied to viruses, prokaryotes, plants and Darwin's Finches.
Background. Circulating A/H3N2 influenza viruses drifted significantly after strain selection for the 2014-2015 vaccines. Also in 2014-2015, the Advisory committee on Immunization Practices ...recommended preferential use of live attenuated influenza vaccine (LAIV) over inactivated influenza vaccine (IIV) among children aged 2-8 years. Methods. Vaccine effectiveness (VE) across age groups and vaccine types was examined among outpatients with acute respiratory illness at 5 US sites using a test-negative design, that compared the odds of vaccination among reverse transcription polymerase chain reaction-confirmed influenza positives and negatives. Results. Of 9311 enrollees with complete data, 7078 (76%) were influenza negative, 1840 (19.8%) were positive for influenza A (A/H3N2, n=1817), and 395 (4.2%) were positive for influenza B (B/Yamagata, n=340). The overall adjusted VE was 19% (95% confidence interval CI, 10% to 27%) and was statistically significant in all age strata except those aged 18-64 years. The adjusted VE of 6% (95%CI, -5% to 17%) against A/H3N2-associated illness was not statistically significant, unlike VE for influenza B/Yamagata, which was 55% (95%CI, 43% to 65%). Among those aged 2-8 years, VE against A/H3N2 was 15% (95%CI, −16% to 38%) for IIV and -3% (CI, -50% to 29%) for LAIV; VE against B/Yamagata was 40% (95%CI, -20% to 70%) for IIV and 74% (95%CI, 25% to 91%) for LAIV. Conclusions. The 2014-2015 influenza vaccines offered little protection against the predominant influenza A/H3N2 virus but were effective against influenza B. Preferential use of LAIV among young children was not supported.
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