Evolution LettersPub Date : 2024-06-19eCollection Date: 2024-09-01DOI: 10.1093/evlett/qrae025
Jan Brabec, Jérémy Gauthier, Oliver M Selz, Rune Knudsen, Julia Bilat, Nadir Alvarez, Ole Seehausen, Philine G D Feulner, Kim Præbel, Isabel Blasco-Costa
{"title":"Testing the radiation cascade in postglacial radiations of whitefish and their parasites: founder events and host ecology drive parasite evolution.","authors":"Jan Brabec, Jérémy Gauthier, Oliver M Selz, Rune Knudsen, Julia Bilat, Nadir Alvarez, Ole Seehausen, Philine G D Feulner, Kim Præbel, Isabel Blasco-Costa","doi":"10.1093/evlett/qrae025","DOIUrl":"https://doi.org/10.1093/evlett/qrae025","url":null,"abstract":"<p><p>Reciprocal effects of adaptive radiations on the evolution of interspecific interactions, like parasitism, remain barely explored. We test whether the recent radiations of European whitefish (<i>Coregonus</i> spp.) across and within perialpine and subarctic lakes promote its parasite <i>Proteocephalus fallax</i> (Platyhelminthes: Cestoda) to undergo host repertoire expansion via opportunity and ecological fitting, or adaptive radiation by specialization. Using de novo genomic data, we examined <i>P. fallax</i> differentiation across lakes, within lakes across sympatric host species, and the contributions of host genetics versus host habitat use and trophic preferences. Whitefish intralake radiations prompted parasite host repertoire expansion in all lakes, whereas <i>P. fallax</i> differentiation remains incipient among sympatric fish hosts. Whitefish genetic differentiation per se did not explain the genetic differentiation among its parasite populations, ruling out codivergence with the host. Instead, incipient parasite differentiation was driven by whitefish phenotypic radiation in trophic preferences and habitat use in an arena of parasite opportunity and ecological fitting to utilize resources from emerging hosts. Whilst the whitefish radiation provides a substrate for the parasite to differentiate along the same water-depth ecological axis as <i>Coregonus</i> spp., the role of the intermediate hosts in parasite speciation may be overlooked. Parasite multiple-level ecological fitting to both fish and crustacean intermediate hosts resources may be responsible for parasite population substructure in <i>Coregonus</i> spp. We propose parasites' delayed arrival was key to the initial burst of postglacial intralake whitefish diversification, followed by opportunistic tapeworm host repertoire expansion and a delayed nonadaptive radiation cascade of incipient tapeworm differentiation. At the geographical scale, dispersal, founder events, and genetic drift following colonization of spatially heterogeneous landscapes drove strong parasite differentiation. We argue that these microevolutionary processes result in the mirroring of host-parasite phylogenies through phylogenetic tracking at macroevolutionary and geographical scales.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 5","pages":"706-718"},"PeriodicalIF":3.4,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11424076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142356507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evolution LettersPub Date : 2024-06-14eCollection Date: 2024-10-01DOI: 10.1093/evlett/qrae024
Rozenn M Pineau, Penelope C Kahn, Dung T Lac, Tom E R Belpaire, Mia G Denning, Whitney Wong, William C Ratcliff, G Ozan Bozdag
{"title":"Experimental evolution of multicellularity via cuboidal cell packing in fission yeast.","authors":"Rozenn M Pineau, Penelope C Kahn, Dung T Lac, Tom E R Belpaire, Mia G Denning, Whitney Wong, William C Ratcliff, G Ozan Bozdag","doi":"10.1093/evlett/qrae024","DOIUrl":"10.1093/evlett/qrae024","url":null,"abstract":"<p><p>The evolution of multicellularity represents a major transition in life's history, enabling the rise of complex organisms. Multicellular groups can evolve through multiple developmental modes, but a common step is the formation of permanent cell-cell attachments after division. The characteristics of the multicellular morphology that emerges have profound consequences for the subsequent evolution of a nascent multicellular lineage, but little prior work has investigated these dynamics directly. Here, we examine a widespread yet understudied emergent multicellular morphology: cuboidal packing. Extinct and extant multicellular organisms across the tree of life have evolved to form groups in which spherical cells divide but remain attached, forming approximately cubic subunits. To experimentally investigate the evolution of cuboidal cell packing, we used settling selection to favor the evolution of simple multicellularity in unicellular, spherical <i>Schizosaccharomyces pombe</i> yeast. Multicellular clusters with cuboidal organization rapidly evolved, displacing the unicellular ancestor. These clusters displayed key hallmarks of an evolutionary transition in individuality: groups possess an emergent life cycle driven by physical fracture, group size is heritable, and they respond to group-level selection via multicellular adaptation. In 2 out of 5 lineages, group formation was driven by mutations in the <i>ace2</i> gene, preventing daughter cell separation after division. Remarkably, <i>ace2</i> mutations also underlie the transition to multicellularity in <i>Saccharomyces cerevisiae</i> and <i>Candida glabrata</i>, lineages that last shared a common ancestor <math><mo>></mo></math> 300 million years ago. Our results provide insight into the evolution of cuboidal cell packing, an understudied multicellular morphology, and highlight the deeply convergent potential for a transition to multicellular individuality within fungi.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 5","pages":"695-704"},"PeriodicalIF":3.4,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11827335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evolution LettersPub Date : 2024-05-11eCollection Date: 2024-09-01DOI: 10.1093/evlett/qrae019
Xueling Yi, Dandan Wang, Kerry Reid, Xueyun Feng, Ari Löytynoja, Juha Merilä
{"title":"Sex chromosome turnover in hybridizing stickleback lineages.","authors":"Xueling Yi, Dandan Wang, Kerry Reid, Xueyun Feng, Ari Löytynoja, Juha Merilä","doi":"10.1093/evlett/qrae019","DOIUrl":"https://doi.org/10.1093/evlett/qrae019","url":null,"abstract":"<p><p>Recent discoveries of sex chromosome diversity across the tree of life have challenged the canonical model of conserved sex chromosome evolution and evoked new theories on labile sex chromosomes that maintain less differentiation and undergo frequent turnover. However, theories of labile sex chromosome evolution lack direct empirical support due to the paucity of case studies demonstrating ongoing sex chromosome turnover in nature. Two divergent lineages (viz. WL & EL) of nine-spined sticklebacks (<i>Pungitius pungitius</i>) with different sex chromosomes (linkage group [LG] 12 in the EL, unknown in the WL) hybridize in a natural secondary contact zone in the Baltic Sea, providing an opportunity to study ongoing turnover between coexisting sex chromosomes. In this study, we first identify an 80 kbp genomic region on LG3 as the sex-determining region (SDR) using whole-genome resequencing data of family crosses of a WL population. We then verify this region as the SDR in most other WL populations and demonstrate a potentially ongoing sex chromosome turnover in admixed marine populations where the evolutionarily younger and homomorphic LG3 sex chromosome replaces the older and heteromorphic LG12 sex chromosome. The results provide a rare glimpse of sex chromosome turnover in the wild and indicate the possible existence of additional yet undiscovered sex chromosome diversity in <i>Pungitius</i> sticklebacks.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 5","pages":"658-668"},"PeriodicalIF":3.4,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11424075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142356506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evolution LettersPub Date : 2024-05-06eCollection Date: 2024-10-01DOI: 10.1093/evlett/qrae018
Stefano Giaimo, Arne Traulsen
{"title":"Juvenile mortality and sibling replacement: a kin selection approach.","authors":"Stefano Giaimo, Arne Traulsen","doi":"10.1093/evlett/qrae018","DOIUrl":"10.1093/evlett/qrae018","url":null,"abstract":"<p><p>Mortality generally is higher around birth and then progressively declines through the juvenile stage. In species where offspring depend upon their parents during maturation, a factor behind this mortality decline could be sibling replacement: offspring sacrifice their survival to benefit future or present siblings as early as possible in order to minimize losses in parental investment. Here, we propose a kin-selection model of sibling replacement. Theoretical analysis of the model and its application to demographic data of mammals suggest that sibling replacement consistently generates a selective incentive for increasing juvenile mortality at early ages when this mortality increment is the result of positive selection for juvenile altruism within the nuclear family. The model highlights how sibling replacement goes beyond optimal allocation of parental resources into dependents and can provoke greater mortality closer to birth also in response to a more favorable ratio of actors to recipients of altruism among siblings.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 5","pages":"647-657"},"PeriodicalIF":3.4,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11827334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143434120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evolution LettersPub Date : 2024-04-27eCollection Date: 2024-08-01DOI: 10.1093/evlett/qrae016
Fanny Touchard, Frédérique Cerqueira, Nicolas Bierne, Frédérique Viard
{"title":"Adaptive alien genes are maintained amid a vanishing introgression footprint in a sea squirt.","authors":"Fanny Touchard, Frédérique Cerqueira, Nicolas Bierne, Frédérique Viard","doi":"10.1093/evlett/qrae016","DOIUrl":"10.1093/evlett/qrae016","url":null,"abstract":"<p><p>Human transport of species across oceans disrupts natural dispersal barriers and facilitates hybridization between previously allopatric species. The recent introduction of the North Pacific sea squirt, <i>Ciona robusta</i>, into the native range of the North Atlantic sea squirt, <i>Ciona intestinalis</i>, is a good example of this outcome. Recent studies have revealed an adaptive introgression in a single chromosomal region from the introduced into the native species. Here, we monitored this adaptive introgression over time, examining both the frequency of adaptive alleles at the core and the hitchhiking footprint in the shoulders of the introgression island by studying a thousand <i>Ciona</i> spp. individuals collected in 22 ports of the contact zone, 14 of which were sampled 20 generations apart. For that purpose, we developed a KASP multiplex genotyping approach, which proved effective in identifying native, nonindigenous and hybrid individuals and in detecting introgressed haplotypes. We found no early generation hybrids in the entire sample, and field observations suggest a decline in the introduced species. At the core region of the introgression sweep, where the frequency of <i>C. robusta</i> alleles is the highest and local adaptation genes must be, we observed stable frequencies of adaptive alien alleles in both space and time. In contrast, we observed erosion of <i>C. robusta</i> ancestry tracts in flanking chromosomal shoulders on the edges of the core, consistent with the second phase of a local sweep and a purge of hitchhiked incompatible mutations. We hypothesize that adaptive introgression may have modified the competition relationships between the native and invasive species in human-altered environments.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 4","pages":"600-609"},"PeriodicalIF":3.4,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291672/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evolution LettersPub Date : 2024-03-17eCollection Date: 2024-08-01DOI: 10.1093/evlett/qrae011
Tianlin Duan, Zebin Zhang, Mathieu Genete, Céline Poux, Adrien Sicard, Martin Lascoux, Vincent Castric, Xavier Vekemans
{"title":"Dominance between self-incompatibility alleles determines the mating system of <i>Capsella</i> allopolyploids.","authors":"Tianlin Duan, Zebin Zhang, Mathieu Genete, Céline Poux, Adrien Sicard, Martin Lascoux, Vincent Castric, Xavier Vekemans","doi":"10.1093/evlett/qrae011","DOIUrl":"10.1093/evlett/qrae011","url":null,"abstract":"<p><p>The shift from outcrossing to self-fertilization is one of the main evolutionary transitions in plants and has broad effects on evolutionary trajectories. In Brassicaceae, the ability to inhibit self-fertilization is controlled by 2 genes, <i>SCR</i> and <i>SRK</i>, tightly linked within the <i>S</i>-locus. A series of small non-coding RNAs also encoded within the <i>S</i>-locus regulates the transcriptional activity of <i>SCR</i> alleles, resulting in a linear dominance hierarchy between them. In Brassicaceae, natural allopolyploid species are often self-compatible (SC) even when one of the progenitor species is self-incompatible, but the reason why polyploid lineages tend to lose self-incompatibility (SI) and the timing of the loss of SI (immediately after ancestral hybridization between the progenitor species, or at a later stage after the formation of allopolyploid lineages) have generally remained elusive. We used a series of synthetic diploid and tetraploid hybrids obtained between self-fertilizing <i>Capsella orientalis</i> and outcrossing <i>Capsella grandiflora</i> to test whether the breakdown of SI could be observed immediately after hybridization, and whether the occurrence of SC phenotypes could be explained by the dominance interactions between <i>S</i>-haplotypes inherited from the parental lineages. We used RNA-sequencing data from young inflorescences to measure allele-specific expression of the <i>SCR</i> gene and infer dominance interactions in the synthetic hybrids. We then evaluated the seed set from autonomous self-pollination in the synthetic hybrids. Our results demonstrate that self-compatibility of the hybrids depends on the relative dominance between <i>S</i>-alleles inherited from the parental species, confirming that SI can be lost instantaneously upon formation of the ancestral allopolyploid lineage. They also confirm that the epigenetic regulation that controls dominance interactions between <i>S</i>-alleles can function between subgenomes in allopolyploids. Together, our results illustrate how a detailed knowledge of the mechanisms controlling SI can illuminate our understanding of the patterns of co-variation between the mating system and changes in ploidy.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 4","pages":"550-560"},"PeriodicalIF":3.4,"publicationDate":"2024-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evolution LettersPub Date : 2024-03-16eCollection Date: 2024-08-01DOI: 10.1093/evlett/qrae010
Robert J Knell, Jonathan M Parrett
{"title":"Alternative reproductive tactics and evolutionary rescue.","authors":"Robert J Knell, Jonathan M Parrett","doi":"10.1093/evlett/qrae010","DOIUrl":"10.1093/evlett/qrae010","url":null,"abstract":"<p><p>Almost all life on earth is facing environmental change, and understanding how populations will respond to these changes is of urgent importance. One factor that is known to affect the speed by which a population can evolve when faced with changes in the environment is strong sexual selection. This increases the adaptive capacity of a population by increasing reproductive skew toward well-adapted (usually) males who will, on average, be best able to compete for matings. This effect could potentially be disrupted when males pursue alternative reproductive tactics (ARTs), whereby males within a species exhibit qualitatively different behaviors in their pursuit of matings. ARTs are diverse, but one common class is those expressed through condition-dependent polyphenism such that high-quality, well-adapted males compete aggressively for mates and low-quality, poorly adapted males attempt to acquire matings via other, nonaggressive behaviors. Here, using an individual-based modeling approach, we consider the possible impacts of ARTs on adaptation and evolutionary rescue. When the ART is simultaneous, meaning that low-quality males not only engage in contests but also pursue other tactics, adaptive capacity is reduced and evolutionary rescue, where a population avoids extinction by adapting to a changing environment, becomes less likely. This is because the use of the ART allows low-quality males to contribute more maladaptive genes to the population than would happen otherwise. When the ART is fixed, however, such that low-quality males will only use the alternative tactic and do not engage in contests, we find the opposite: adaptation happens more quickly and evolutionary rescue when the environment changes is more likely. This surprising effect is caused by an increase in the mating success of the highest quality males who face many fewer competitors in this scenario-counterintuitively, the presence of males pursuing the ART increases reproductive skew toward those males in the best condition.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 4","pages":"539-549"},"PeriodicalIF":3.4,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evolution LettersPub Date : 2024-03-08eCollection Date: 2024-08-01DOI: 10.1093/evlett/qrae008
Mohammadali Dashtbali, Xiaoyan Long, Jonathan M Henshaw
{"title":"The evolution of honest and dishonest signals of fighting ability.","authors":"Mohammadali Dashtbali, Xiaoyan Long, Jonathan M Henshaw","doi":"10.1093/evlett/qrae008","DOIUrl":"https://doi.org/10.1093/evlett/qrae008","url":null,"abstract":"<p><p>Competition over resources is often decided via aggressive interactions, which may or may not escalate to all-out fights. Weapons and body size play important roles in such interactions, as they often provide reliable cues of an individual's fighting ability. In contrast, traits like nonfunctional display \"weapons\" may dishonestly exaggerate fighting ability in order to intimidate opponents into retreating. Signals used in the context of aggressive interactions potentially evolve via very different mechanisms than courtship signals, but have received far less theoretical attention. Here, we contrast the evolution of honest and dishonest signals of fighting ability using a game-theoretic model. Contests are assumed to consist of three discrete stages: display from a distance, low-intensity physical contact, and fighting. At each stage, contestants evaluate the fighting ability of their opponents in comparison to their own based on body size and an aggressive signal. After making this evaluation, contestants decide whether to escalate the interaction or cede to their opponent. Our model predicts that both honest and dishonest aggressive signals can exaggerate far beyond their ecological optima, but that exaggeration is more pronounced for honest signals. Equilibrium levels of aggressiveness-as measured by individuals' propensity to escalate aggressive interactions to the next stage-are independent of the honesty of signals. We additionally develop a novel approach, based on causal inference theory, to understand how changes in underlying parameters shape the coevolution of multiple traits. We use this approach to study how aggression coevolves with body and signal size in response to changes in the cost of losing a fight.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 4","pages":"514-525"},"PeriodicalIF":3.4,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142510983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evolution LettersPub Date : 2024-03-05eCollection Date: 2024-08-01DOI: 10.1093/evlett/qrae006
Baosheng Wu, Qingmiao Ren, Xiaoting Yan, Fei Zhao, Tao Qin, Peidong Xin, Xinxin Cui, Kun Wang, Rui Du, Knut H Røed, Steeve D Côté, Glenn Yannic, Zhipeng Li, Qiang Qiu
{"title":"Resequencing of reindeer genomes provides clues to their docile habits.","authors":"Baosheng Wu, Qingmiao Ren, Xiaoting Yan, Fei Zhao, Tao Qin, Peidong Xin, Xinxin Cui, Kun Wang, Rui Du, Knut H Røed, Steeve D Côté, Glenn Yannic, Zhipeng Li, Qiang Qiu","doi":"10.1093/evlett/qrae006","DOIUrl":"10.1093/evlett/qrae006","url":null,"abstract":"<p><p>Reindeer have long been served as vital subsistence resources for inhabitants of Arctic and subarctic regions owing to their domestication. However, the evolutionary relationships and divergence times among different reindeer populations, genetic traits that distinguish domesticated reindeer, and factors that contribute to their relative docility compared with that of other Cervidae specie, remain unclear. In this study, we sequenced the genomes of 32 individuals from wild and domestic reindeer populations that inhabit Arctic and subarctic regions. We found that reindeer experienced 2 or more independent domestication events characterized by weak artificial selection pressure and limited significant differences in genomic parameters between wild and domestic populations. Alterations in conserved noncoding elements in the reindeer genomes, particularly those associated with nervous system development, may have contributed to their domestication by rendering the nervous system less responsive. Together, our results suggest that inherent species-specific traits, rather than intense artificial selection, may have played a significant role in the relatively docile behavior of reindeer and offer valuable insights into the domestication process of these animals.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 4","pages":"494-504"},"PeriodicalIF":3.4,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141890629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Evolution LettersPub Date : 2024-03-05eCollection Date: 2024-08-01DOI: 10.1093/evlett/qrae009
Michał Aleksander Ciach, Julia Pawłowska, Paweł Górecki, Anna Muszewska
{"title":"The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.","authors":"Michał Aleksander Ciach, Julia Pawłowska, Paweł Górecki, Anna Muszewska","doi":"10.1093/evlett/qrae009","DOIUrl":"10.1093/evlett/qrae009","url":null,"abstract":"<p><p>Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from <i>Chytridiomycota</i> to <i>Mucoromycota</i>. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to <i>Mortierellomycota</i>. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.</p>","PeriodicalId":48629,"journal":{"name":"Evolution Letters","volume":"8 4","pages":"526-538"},"PeriodicalIF":3.4,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11291939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141891563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}