Evolutionary Applications最新文献

{"title":"Genomic Diversity as a Key Conservation Criterion: Proof-of-Concept From Mammalian Whole-Genome Resequencing Data","authors":"Jong Yoon Jeon,&nbsp;Andrew N. Black,&nbsp;Erangi J. Heenkenda,&nbsp;Andrew J. Mularo,&nbsp;Gina F. Lamka,&nbsp;Safia Janjua,&nbsp;Anna Brüniche-Olsen,&nbsp;John W. Bickham,&nbsp;Janna R. Willoughby,&nbsp;J. Andrew DeWoody","doi":"10.1111/eva.70000","DOIUrl":"https://doi.org/10.1111/eva.70000","url":null,"abstract":"<p>Many international, national, state, and local organizations prioritize the ranking of threatened and endangered species to help direct conservation efforts. For example, the International Union for Conservation of Nature (IUCN) assesses the Green Status of species and publishes the influential Red List of threatened species. Unfortunately, such conservation yardsticks do not explicitly consider genetic or genomic diversity (GD), even though GD is positively associated with contemporary evolutionary fitness, individual viability, and with future evolutionary potential. To test whether populations of genome sequences could help improve conservation assessments, we estimated GD metrics from 82 publicly available mammalian datasets and examined their statistical association with attributes related to conservation. We also considered intrinsic biological factors, including trophic level and body mass, that could impact GD and quantified their relative influences. Our results identify key population GD metrics that are both reflective and predictive of IUCN conservation categories. Specifically, our analyses revealed that Watterson's theta (the population mutation rate) and autozygosity (a product of inbreeding) are associated with the current Red List categorization, likely because demographic declines that lead to “listing” decisions also reduce levels of standing genetic variation. We argue that by virtue of this relationship, conservation organizations like IUCN could leverage emerging genome sequence data to help categorize Red List threat rankings (especially in otherwise data-deficient species) and/or enhance Green Status assessments to establish a baseline for future population monitoring. Thus, our paper (1) outlines the theoretical and empirical justification for a new GD-based assessment criterion, (2) provides a bioinformatic pipeline for estimating GD from population genomic data, and (3) suggests an analytical framework that can be used to measure baseline GD while providing quantitative GD context for consideration by conservation authorities.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70000","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Demographic History and Inbreeding in Two Declining Sea Duck Species Inferred From Whole-Genome Sequence Data","authors":"María I. Cádiz,&nbsp;Aja Noersgaard Buur Tengstedt,&nbsp;Iben Hove Sørensen,&nbsp;Emma Skindbjerg Pedersen,&nbsp;Anthony David Fox,&nbsp;Michael M. Hansen","doi":"10.1111/eva.70008","DOIUrl":"https://doi.org/10.1111/eva.70008","url":null,"abstract":"<p>Anthropogenic impact has transitioned from threatening already rare species to causing significant declines in once numerous organisms. Long-tailed duck (<i>Clangula hyemalis</i>) and velvet scoter (<i>Melanitta fusca</i>) were once important quarry sea duck species in NW Europe, but recent declines resulted in their reclassification as vulnerable on the IUCN Red List. We sequenced and assembled genomes for both species and resequenced 15 individuals of each. Using analyses based on site frequency spectra and sequential Markovian coalescence, we found <i>C</i>. <i>hyemalis</i> to show more historical demographic stability, whereas <i>M. fusca</i> was affected particularly by the Last (Weichselian) Glaciation. This likely reflects <i>C</i>. <i>hyemalis</i> breeding continuously across the Arctic, with cycles of glaciation primarily shifting breeding areas south or north without major population declines, whereas the more restricted southern range of <i>M. fusca</i> would lead to significant range contraction during glaciations. Both species showed evidence of declines over the past thousands of years, potentially reflecting anthropogenic pressures with the recent decline indicating an accelerated process. Analysis of runs of homozygosity (ROH) showed low but nontrivial inbreeding, with <i>F</i>_ROH from 0.012 to 0.063 in <i>C</i>. <i>hyemalis</i> and ranging from 0 to 0.047 in <i>M. fusca</i>. Lengths of ROH suggested that this was due to ongoing background inbreeding rather than recent declines. Overall, despite demographically important declines, this has not yet led to strong inbreeding and genetic erosion, and the most pressing conservation concern may be the risk of density-dependent (Allee) effects. We recommend monitoring of inbreeding using ROH analysis as a cost-efficient method to track future developments to support effective conservation of these species.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Creating insect neopolyploid lines to study animal polyploid evolution","authors":"Saminathan Sivaprakasham Murugesan,&nbsp;Leo W. Beukeboom,&nbsp;Eveline C. Verhulst,&nbsp;Kelley Leung","doi":"10.1111/eva.13706","DOIUrl":"https://doi.org/10.1111/eva.13706","url":null,"abstract":"<p>Whole-genome duplication (polyploidy) poses many complications but is an important driver for eukaryotic evolution. To experimentally study how many challenges from the cellular (including gene expression) to the life history levels are overcome in polyploid evolution, a system in which polyploidy can be reliably induced and sustained over generations is crucial. Until now, this has not been possible with animals, as polyploidy notoriously causes first-generation lethality. The parasitoid wasp <i>Nasonia vitripennis</i> emerges as a stunningly well-suited model. Polyploidy can be induced in this haplodiploid system through (1) silencing genes in the sex determination cascade and (2) by colchicine injection to induce meiotic segregation failure. <i>Nasonia</i> polyploids produce many generations in a short time, making them a powerful tool for experimental evolution studies. The strong variation observed in <i>Nasonia</i> polyploid phenotypes aids the identification of polyploid mechanisms that are the difference between evolutionary dead ends and successes. Polyploid evolution research benefits from decades of <i>Nasonia</i> research that produced extensive reference—omics data sets, facilitating the advanced studies of polyploid effects on the genome and transcriptome. It is also possible to create both inbred lines (to control for genetic background effects) and outbred lines (to conduct polyploid selection regimes). The option of interspecific crossing further allows to directly contrast autopolyploidy (intraspecific polyploidy) to allopolyploidy (hybrid polyploidy). <i>Nasonia</i> can also be used to investigate the nascent field of using polyploidy in biological control to improve field performance and lower ecological risk. In short, <i>Nasonia</i> polyploids are an exceptional tool for researching various biological paradigms.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.13706","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142165218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Transcriptomic Reveals Greater Similarities in Response to Temperature Than to Invasive Alien Predator in the Damselfly Ischnura elegans Across Different Geographic Scales","authors":"Guillaume Wos,&nbsp;Gemma Palomar,&nbsp;Marzena Marszałek,&nbsp;Szymon Sniegula","doi":"10.1111/eva.70002","DOIUrl":"10.1111/eva.70002","url":null,"abstract":"<p>The impact of global changes on populations may not be necessarily uniform across a species' range. Here, we aim at comparing the phenotypic and transcriptomic response to warming and an invasive predator cue in populations across different geographic scales in the damselfly <i>Ischnura elegans</i>. We collected adult females in two ponds in southern Poland (central latitude) and two ponds in southern Sweden (high latitude). We raised their larvae in growth chambers and exposed them to combination of temperature and a predator cue released by the crayfish <i>Orconectes limosus</i>. When larvae reached the prefinal larval stage, they were phenotyped for traits related to growth and size and collected for a gene expression analysis. High-latitude populations exhibited greater phenotypic and transcriptomic variation than central-latitude populations. Across latitudes and ponds, temperature generally increased growth rate and the predator cue decreased mass, but the effects of temperature were also pond-specific. Comparison of the transcriptomic profiles revealed a greater overlap in the response to temperature across latitudes and ponds, especially for pathway-related oxidative stress and sugar and lipid metabolism. The transcriptomic response to a predator cue and to the interaction temperature × predator cue was more pond-specific and overlapped only for few genes and pathways related to cuticle, development and signal transduction. We demonstrated that central- and high-latitude populations may partially respond through similar mechanisms to warming and, to a lower extent to a predator cue and to the interaction temperature × predator cue. For the predator cue and the interaction, the large fraction of ponds-specific genes suggests local adaptation. We show that high-latitude populations were generally more plastic at the phenotypic and transcriptomic level and may be more capable to cope with environmental changes than their central-latitude counterparts.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11377989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142152718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Climate change vulnerability and conservation strategies for tertiary relict tree species: Insights from landscape genomics of Taxus cuspidata","authors":"Yanjun Luo,&nbsp;Wei Qin,&nbsp;Yu Yan,&nbsp;Kangquan Yin,&nbsp;Runguo Zang,&nbsp;Fang K. Du","doi":"10.1111/eva.13686","DOIUrl":"10.1111/eva.13686","url":null,"abstract":"<p>The unprecedented habitat fragmentation or loss has threatened the existence of many species. Therefore, it is essential to understand whether and how these species can pace with the environmental changes. Recent advantages in landscape genomics enabled us to identify molecular signatures of adaptation and predict how populations will respond to changing environments, providing new insights into the conservation of species. Here, we investigated the pattern of neutral and putative adaptive genetic variation and its response to changing environments in a tertiary relict tree species, <i>Taxus cuspidata</i> Sieb. et Zucc, which is distributed in northeast China and adjacent regions. We investigated the pattern of genetic diversity and differentiation using restriction site-associated DNA sequencing (RAD-seq) and seven nuclear microsatellites (nSSRs) datasets. We further explored the endangered mechanism, predicted its vulnerability in the future, and provided guidelines for the conservation and management of this species. RAD-seq identified 16,087 single nucleotide polymorphisms (SNPs) in natural populations. Both the SNPs and nSSRs datasets showed high levels of genetic diversity and low genetic differentiation in <i>T. cuspidata</i>. Outlier detection by <i>F</i>_ST outlier analysis and genotype-environment associations (GEAs) revealed 598 outlier SNPs as putative adaptive SNPs. Linear redundancy analysis (RDA) and nonlinear gradient forest (GF) showed that the contribution of climate to genetic variation was greater than that of geography, and precipitation played an important role in putative adaptive genetic variation. Furthermore, the genetic offset and risk of non-adaptedness (RONA) suggested that the species at the northeast edge may be more vulnerable in the future. These results suggest that although the species has maintained high current genetic diversity in the face of recent habitat loss and fragmentation, future climate change is likely to threaten the survival of the species. Temperature (Bio03) and precipitation (Prec05) variables can be potentially used as predictors of response of <i>T. cuspidata</i> under future climate. Together, this study provides a theoretical framework for conservation and management strategies for wildlife species in the context of future climate change.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11375028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142152717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the Genetic Landscape: Insights Into the Genomic Signatures of Changle Goose","authors":"Hao Chen,&nbsp;Yan Wu,&nbsp;Yihao Zhu,&nbsp;Keyi Luo,&nbsp;Sumei Zheng,&nbsp;Hongbo Tang,&nbsp;Rui Xuan,&nbsp;Yuxuan Huang,&nbsp;Jiawei Li,&nbsp;Rui Xiong,&nbsp;Xinyan Fang,&nbsp;Lei Wang,&nbsp;Yujie Gong,&nbsp;Junjie Miao,&nbsp;Jing Zhou,&nbsp;Hongli Tan,&nbsp;Yanan Wang,&nbsp;Liping Wu,&nbsp;Jing Ouyang,&nbsp;Min Huang,&nbsp;Xueming Yan","doi":"10.1111/eva.13768","DOIUrl":"10.1111/eva.13768","url":null,"abstract":"<p>The Changle goose (CLG), a Chinese indigenous breed, is celebrated for its adaptability, rapid growth, and premium meat quality. Despite its agricultural value, the exploration of its genomic attributes has been scant. Our study entailed whole-genome resequencing of 303 geese across CLG and five other Chinese breeds, revealing distinct genetic diversity metrics. We discovered significant migration events from Xingguo gray goose to CLG and minor gene flow between them. We identified genomic regions through selective sweep analysis, correlating with CLG's unique traits. An elevated inbreeding coefficient in CLG, alongside reduced heterozygosity and rare single nucleotide polymorphisms (R_SNPs), suggests a narrowed genetic diversity. Genomic regions related to reproduction, meat quality, and growth were identified, with the <i>GATA3</i> gene showing strong selection signals for meat quality. A non-synonymous mutation in the <i>Sloc2a1</i> gene, which is associated with reproductive traits in the CLG, exhibited significant differences in allelic frequency. The roles of <i>CD82</i>, <i>CDH8</i>, and <i>PRKAB1</i> in growth and development, alongside <i>FABP4</i>, <i>FAF1</i>, <i>ESR1</i>, and <i>AKAP12</i> in reproduction, were highlighted. Additionally, <i>Cdkal1</i> and <i>Mfsd14a</i> may influence meat quality. This comprehensive genetic analysis underpins the unique genetic makeup of CLG, providing a basis for its conservation and informed breeding strategies.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11340016/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142034662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linked Selection and Gene Density Shape Genome-Wide Patterns of Diversification in Peatmosses","authors":"Olena Meleshko,&nbsp;Michael D. Martin,&nbsp;Kjell Ivar Flatberg,&nbsp;Hans K. Stenøien,&nbsp;Thorfinn Sand Korneliussen,&nbsp;Péter Szövényi,&nbsp;Kristian Hassel","doi":"10.1111/eva.13767","DOIUrl":"10.1111/eva.13767","url":null,"abstract":"<p>Genome evolution under speciation is poorly understood in nonmodel and nonvascular plants, such as bryophytes—the largest group of nonvascular land plants. Their genomes are structurally different from angiosperms and likely subjected to stronger linked selection pressure, which may have profound consequences on genome evolution in diversifying lineages, even more so when their genome architecture is conserved. We use the highly diverse, rapidly radiated group of peatmosses (<i>Sphagnum</i>) to characterize the processes affecting genome diversification in bryophytes. Using whole-genome sequencing data from populations of 12 species sampled at different phylogenetic and geographical scales, we describe high correlation of the genomic landscapes of differentiation, divergence, and diversity in <i>Sphagnum</i>. Coupled with evidence from the patterns of covariation among different measures of genetic diversity, phylogenetic discordance, and gene density, this provides strong support that peatmoss genome evolution has been shaped by the long-term effects of linked selection, constrained by distribution of selection targets in the genome. Thus, peatmosses join the growing number of animal and plant groups where functional features of the genome, such as gene density, and linked selection drive genome evolution along predetermined and highly similar routes in different species. Our findings demonstrate the great potential of bryophytes for studying the genomics of speciation and highlight the urgent need to expand the genomic resources in this remarkable group of plants.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11333200/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142007949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing genotype–environment interactions in Atlantic salmon reared in freshwater loch and recirculating systems","authors":"Mette J. Tollervey,&nbsp;Michaël Bekaert,&nbsp;Agustín Barría González,&nbsp;Saif Agha,&nbsp;Ross D. Houston,&nbsp;Andrea Doeschl-Wilson,&nbsp;Ashie Norris,&nbsp;Herve Migaud,&nbsp;Alejandro P. Gutierrez","doi":"10.1111/eva.13751","DOIUrl":"10.1111/eva.13751","url":null,"abstract":"<p>The interest in recirculating aquaculture systems (RAS) is growing due to their benefits such as increased productivity, better control over animal care, reduced environmental effects, and less water consumption. However, in some regions of the world, traditional aquaculture methods remain prevalent, and selective breeding has often been designed for performance within these systems. Therefore, it is important to evaluate how current fish populations fare in RAS to guide future breeding choices. In a commercial setting, we explore the genetic structure of growth characteristics, measure genotype–environment interactions (GxE) in salmon smolts, and examine genetic markers related to growth in freshwater lochs and RAS. Young salmon were raised together until they reached the parr stage, after which they were divided equally between freshwater net-pens and RAS. After an 8-week period, we sampled fish from each environment and genotyped them. Our findings revealed that fish reared in RAS were generally smaller in weight and length but exhibited a higher condition factor and uniformity. We found a notably smaller component of unexplained variance in the RAS, leading to higher heritability estimates. We observed a low GxE effect for length and condition factor, but significant re-ranking for whole-body weight, as well as noticeable differences in trait associations across environments. Specifically, a segment of chromosome 22 was found to be linked with the condition factor in the RAS population only. Results suggests that if the use of RAS continues to expand, the efficiency of existing commercial populations may not reach its full potential unless breeding programs specific to RAS are implemented.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11310769/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141915599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Niche breadth and divergence in sympatric cryptic coral species (Pocillopora spp.) across habitats within reefs and among algal symbionts","authors":"Scott C. Burgess,&nbsp;Alyssa M. Turner,&nbsp;Erika C. Johnston","doi":"10.1111/eva.13762","DOIUrl":"10.1111/eva.13762","url":null,"abstract":"<p>While the presence of morphologically cryptic species is increasingly recognized, we still lack a useful understanding of what causes and maintains co-occurring cryptic species and its consequences for the ecology, evolution, and conservation of communities. We sampled 724 <i>Pocillopora</i> corals from five habitat zones (the fringing reef, back reef, and fore reef at 5, 10, and 20 m) at four sites around the island of Moorea, French Polynesia. Using validated genetic markers, we identified six sympatric species of <i>Pocillopora</i>, most of which cannot be reliably identified based on morphology: <i>P. meandrina</i> (42.9%), <i>P. tuahiniensis</i> (25.1%), <i>P. verrucosa</i> (12.2%), <i>P. acuta</i> (10.4%), <i>P. grandis</i> (7.73%), and <i>P.</i> cf. <i>effusa</i> (2.76%). For 423 colonies (58% of the genetically identified hosts), we also used <i>psbA</i>^ncr or ITS2 markers to identify symbiont species (Symbiodiniaceae). The relative abundance of <i>Pocillopora</i> species differed across habitats within the reef. Sister taxa <i>P. verrucosa</i> and <i>P. tuahiniensis</i> had similar niche breadths and hosted the same specialist symbiont species (mostly <i>Cladocopium pacificum</i>) but the former was more common in the back reef and the latter more common deeper on the fore reef. In contrast, sister taxa <i>P. meandrina</i> and <i>P. grandis</i> had the highest niche breadths and overlaps and tended to host the same specialist symbiont species (mostly <i>C. latusorum</i>). <i>Pocillopora acuta</i> had the narrowest niche breadth and hosted the generalist, and more thermally tolerant, <i>Durusdinium gynnii</i>. Overall, there was a positive correlation between reef habitat niche breadth and symbiont niche breadth—<i>Pocillopora</i> species with a broader habitat niche also had a broader symbiont niche. Our results show how fine-scale variation within reefs plays an important role in the generation and coexistence of cryptic species. The results also have important implications for how niche differences affect community resilience, and for the success of coral restoration practices, in ways not previously appreciated.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11294925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141887765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The many dimensions of combination therapy: How to combine antibiotics to limit resistance evolution","authors":"Christin Nyhoegen,&nbsp;Sebastian Bonhoeffer,&nbsp;Hildegard Uecker","doi":"10.1111/eva.13764","DOIUrl":"10.1111/eva.13764","url":null,"abstract":"<p>In combination therapy, bacteria are challenged with two or more antibiotics simultaneously. Ideally, separate mutations are required to adapt to each of them, which is a priori expected to hinder the evolution of full resistance. Yet, the success of this strategy ultimately depends on how well the combination controls the growth of bacteria with and without resistance mutations. To design a combination treatment, we need to choose drugs and their doses and decide how many drugs get mixed. Which combinations are good? To answer this question, we set up a stochastic pharmacodynamic model and determine the probability to successfully eradicate a bacterial population. We consider bacteriostatic and two types of bactericidal drugs—those that kill independent of replication and those that kill during replication. To establish results for a null model, we consider non-interacting drugs and implement the two most common models for drug independence—Loewe additivity and Bliss independence. Our results show that combination therapy is almost always better in limiting the evolution of resistance than administering just one drug, even though we keep the total drug dose constant for a ‘fair’ comparison. Yet, exceptions exist for drugs with steep dose–response curves. Combining a bacteriostatic and a bactericidal drug which can kill non-replicating cells is particularly beneficial. Our results suggest that a 50:50 drug ratio—even if not always optimal—is usually a good and safe choice. Applying three or four drugs is beneficial for treatment of strains with large mutation rates but adding more drugs otherwise only provides a marginal benefit or even a disadvantage. By systematically addressing key elements of treatment design, our study provides a basis for future models which take further factors into account. It also highlights conceptual challenges with translating the traditional concepts of drug independence to the single-cell level.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11297101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141887677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}