Top 10 Biorxiv Papers Today in Evolutionary Biology


2.031 Mikeys
#1. The role of recombination on genome-wide patterns of local ancestry exemplified by supplemented Brook Charr populations
Maeva Leitwein, Hugo Cayuela, Anne-Laure Ferchaud, Eric Normandeau, Pierre-Alexandre Gagnaire, Louis Bernatchez
Assessing the immediate and long-term evolutionary consequences of human-mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome-wide scale, but few have considered the dynamics of this process within and between chromosomes. Here, we used an exploited freshwater fish, the Brook Charr (Salvelinus fontinalis) for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped SNPs genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early and late-generation hybrids using admixture tracts information. To assess the selective outcomes following admixture we then evaluated the relationship between recombination...
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biorxivpreprint: The role of recombination on genome-wide patterns of local ancestry exemplified by supplemented Brook Charr populations https://t.co/Y9BgFVUuA1 #bioRxiv
biorxiv_evobio: The role of recombination on genome-wide patterns of local ancestry exemplified by supplemented Brook Charr populations https://t.co/TgGnuBvHeJ #biorxiv_evobio
Github

Pipeline for local ancestry inference - in progress...

Repository: local_ancestry_inference_with_ELAI
User: mleitwein
Language: R
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Sample Sizes : [177, 177]
Authors: 6
Total Words: 13014
Unqiue Words: 3633

2.023 Mikeys
#2. Enhanced leaky sex expression is an adaptive plastic response to pollen limitation in the dioecious plant Mercurialis annua
Guillaume Cossard, John R. Pannell
Phenotypic plasticity is all but ubiquitous across the tree of life, but clear demonstrations that it is adaptive are rare. In dioecious plants, males and females frequently show 'leaky' sex expression, with individuals occasionally producing flowers of the opposite sex. Here, we ask whether leaky sex expression in the wind-pollinated dioecious herb Mercurialis annua is plastically responsive to its mating context, and whether such plasticity is adaptive. We compared experimental populations of females growing either with or without males. Females growing in the absence of males were leakier in their sex expression than controls with males, producing more than twice as many male flowers, and they enjoy much greater fitness. We discuss differences in the degree of plasticity between ploidal races of annua Mercurialis in terms of likely differences in the reliability of the signal plants may perceive for the presence of males in their populations. Our results provide a striking instance of adaptive plasticity in the reproductive...
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biorxivpreprint: Enhanced leaky sex expression is an adaptive plastic response to pollen limitation in the dioecious plant Mercurialis annua https://t.co/dyEQI7Eylg #bioRxiv
biorxiv_evobio: Enhanced leaky sex expression is an adaptive plastic response to pollen limitation in the dioecious plant Mercurialis annua https://t.co/S33e3S7um8 #biorxiv_evobio
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Sample Sizes : None.
Authors: 2
Total Words: 5654
Unqiue Words: 1901

2.016 Mikeys
#3. Maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure
Hillary Koch, Michael DeGiorgio
Though large multilocus genomic datasets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI, that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI's performance in the four-taxon setting, and demonstrate the application of TASTI on a six-species Afrotropical mosquito dataset. Finally, we have implemented TASTI in an open-source software...
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biorxivpreprint: Maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure https://t.co/JJyXzpL5mA #bioRxiv
biorxiv_evobio: Maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure https://t.co/wdEJHhER1e #biorxiv_evobio
JoshPenalba: Maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure [NEW RESULTS] https://t.co/caeRooXbdp
Github

Taxa with Ancestral structure Species Tree Inference

Repository: TASTI
User: hillarykoch
Language: R
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Sample Sizes : None.
Authors: 2
Total Words: 15593
Unqiue Words: 3563

2.01 Mikeys
#4. Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping
Kerry A Geiler-Samerotte, Shuang Li, Charalampos Lazaris, Auston Taylor, Naomi Ziv, Chelsea Ramjeawan, Annalise B Paaby, Mark L Siegal
Pleiotropy - when a single mutation affects multiple traits - is a controversial topic with far-reaching implications. Pleiotropy plays a central role in ongoing debates about how complex traits evolve and whether biological systems tend to be modular or organized such that every gene has the potential to affect many traits. Pleiotropy is also critical to initiatives in evolutionary medicine that seek to trap infectious microbes or tumors by selecting for mutations that encourage growth in some conditions at the expense of others. Research in these fields, and others, would benefit from understanding the extent to which pleiotropy reflects inherent relationships among phenotypes that correlate no matter the perturbation (vertical pleiotropy), versus the action of genetic changes that impose correlations between otherwise independent traits (horizontal pleiotropy). We tackle this question by using high-throughput single-cell phenotyping to measure thousands of pairwise trait correlations across hundreds of thousands of cells...
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biorxivpreprint: Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping https://t.co/XQIbajL4j7 #bioRxiv
biorxiv_evobio: Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping https://t.co/fkUhrohJWi #biorxiv_evobio
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Authors: 8
Total Words: 18867
Unqiue Words: 5293

2.002 Mikeys
#5. Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data
Thibaut Sellinger, Diala Abu-Awad, Markus Moest, Aurelien Tellier
Several methods based on the Sequential Markovian Coalescent (SMC) have been developed to use full genome sequence data to uncover population demographic history, which is of interest in its own right and a key requirement to generate a null model for selection tests. While these methods can be applied to all possible species, the underlying assumptions are sexual reproduction at each generation and no overlap of generations. However, in many plant, invertebrate, fungi and other species, those assumptions are often violated due to different ecological and life history traits, such as self-fertilization or long term dormant structures (seed or egg-banking). We develop a novel SMC-based method to infer 1) the rates of seed/egg-bank and of self-fertilization, and 2) the populations' past demographic history. Using simulated data sets, we demonstrate the accuracy of our method for a wide range of demographic scenarios and for sequence lengths from one to 30 Mb using four sampled genomes. Finally, we apply our method to a Swedish and a...
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Github

Contains all requirement to run eSMC

Repository: eSMC
User: TPPSellinger
Language: R
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Authors: 4
Total Words: 12906
Unqiue Words: 3798

2.0 Mikeys
#6. Cryptic genetic variation underpins rapid adaptation to ocean acidification
Mark C. Bitter, Lydia Kapsenberg, Jean-Pierre Gattuso, Catherine A. Pfister
Global climate change has intensified the need to assess the capacity for natural populations to adapt to abrupt shifts in the environment. Reductions in seawater pH constitute a conspicuous stressor associated with increasing atmospheric carbon dioxide that is affecting marine ecosystems globally. Here, we quantify the phenotypic and genetic modifications associated with rapid adaptation to reduced seawater pH in the marine mussel, Mytilus galloprovincialis . We reared a genetically diverse larval population in ambient and extreme low pH conditions (pHT 8.1 and 7.4) and tracked changes in the larval size and allele frequency distributions through settlement. Additionally, we separated larvae by size to link a fitness-related trait to its underlying genetic background in each treatment. Both phenotypic and genetic data show that M. galloprovincialis can evolve in response to a decrease in seawater pH. This process is polygenic and characterized by genotype-environment interactions, suggesting the role of cryptic genetic variation...
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HenriquesRo: RT @biorxiv_evobio: Cryptic genetic variation underpins rapid adaptation to ocean acidification https://t.co/n4qZKWRHg4 #biorxiv_evobio
EvolPaper: RT @biorxiv_evobio: Cryptic genetic variation underpins rapid adaptation to ocean acidification https://t.co/n4qZKWRHg4 #biorxiv_evobio
TonyBurnetti: RT @biorxiv_evobio: Cryptic genetic variation underpins rapid adaptation to ocean acidification https://t.co/n4qZKWRHg4 #biorxiv_evobio
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Sample Sizes : [6, 3, 3, 3, 3, 2, 3]
Authors: 4
Total Words: 12067
Unqiue Words: 3833

1.998 Mikeys
#7. Can the microbiome influence host evolutionary trajectories?
Lucas Henry, Marjolein Bruijning, Simon Forsberg, Julien Ayroles
The microbiome shapes many traits in hosts, but we still do not understand how it influences host evolution. To impact host evolution, the microbiome must be heritable and have phenotypic effects on the host. However, the complex inheritance and context-dependence of the microbiome challenges traditional models of organismal evolution. Here, we take a multifaceted approach to identify conditions in which the microbiome influences host evolutionary trajectories. We explore quantitative genetic models to highlight how microbial inheritance and phenotypic effects can modulate host evolutionary responses to selection. We synthesize the literature across diverse taxa to find common scenarios of microbiome driven host evolution. First, hosts may leverage locally adapted microbes, increasing survivorship in stressful environments. Second, microbial variation may increase host phenotypic variation, enabling exploration of novel fitness landscapes. We further illustrate these effects by performing a meta-analysis of artificial selection in...
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biorxivpreprint: Can the microbiome influence host evolutionary trajectories? https://t.co/mKCA1FYoRn #bioRxiv
biorxiv_evobio: Can the microbiome influence host evolutionary trajectories? https://t.co/PzXSxxjJNH #biorxiv_evobio
Vladimir_Tch: RT @biorxiv_evobio: Can the microbiome influence host evolutionary trajectories? https://t.co/PzXSxxjJNH #biorxiv_evobio
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Authors: 4
Total Words: 0
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1.998 Mikeys
#8. Collapse and rescue of evolutionary food webs under global warming
Youssef Yacine, Korinna Theresa Allhoff, Avril Weinbach, Nicolas Loeuille
Global warming is severely impacting ecosystems and threatening ecosystem services and human well-being. While some species face extinction risk, several studies have demonstrated the possibility that fast evolution may allow species adaptation and survival despite environmental change. We aim to assess how such evolutionary rescue dynamics extend to multitrophic communities and whether evolution systematically preserve biodiversity under global warming. Using a simplified consumer-resource model, we analyze mathematically how evolution of body mass and of foraging strategies affect coexistence. We then extend our analysis to diverse, multi-trophic networks of co-evolving morphs. Our simulations predict that the long-term diversity loss triggered by warming is considerably higher in scenarios where evolution is slowed down or switched off completely, indicating that eco-evolutionary feedbacks indeed help to preserve biodiversity. Evolving webs however experience vast disruptions in their structure and functioning and reversing...
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Authors: 4
Total Words: 17140
Unqiue Words: 4782

1.996 Mikeys
#9. Dinoflagellates with relic endosymbiont nuclei as novel models for elucidating organellogenesis
Chihiro Sarai, Goro Tanifuji, Takuro Nakayama, Ryoma Kamikawa, Kazuya Takahashi, Hideaki Miyashita, Ken-ichiro Ishida, Mitsunori Iwataki, Yuji Inagaki
Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process integrating an endosymbiont alga into be a host-governed plastid (organellogenesis). Nevertheless, past studies suggested that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet to pinpoint the closest free-living relative of the endosymbiotic alga engulfed by the ancestral chlorarachniophyte or cryptophyte, making difficult to infer how organellogenesis altered the endosymbiont genome. To counter the above issues, we need novel nucleomorph-bearing algae, in which from-endosymbiont-to-host DNA transfer is on-going and of which endosymbiont/plastid origins can be inferred at a fine taxonomic scale. Here, we report two previously undescribed dinoflagellates, strains MGD and TGD,...
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Authors: 9
Total Words: 0
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1.996 Mikeys
#10. The relative impact of evolving pleiotropy and mutational correlation on trait divergence
Jobran Chebib, Frederic Guillaume
Both pleiotropic connectivity and mutational correlations can restrict the divergence of traits under directional selection, but it is unknown which is more important in trait evolution. In order to address this question, we create a model that permits within-population variation in both pleiotropic connectivity and mutational correlation, and compare their relative importance to trait evolution. Specifically, we developed an individual-based, stochastic model where mutations can affect whether a locus affects a trait and the extent of mutational correlations in a population, under the corridor selection model (some traits under directional selection and others under stabilizing selection). We find that traits can diverge whether there is evolution in pleiotropic connectivity or mutational correlation but when both can evolve then evolution in pleiotropic connectivity is more likely to allow for divergence to occur. The most common genotype found in this case is characterized by having one locus that maintains connectivity to all...
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Authors: 2
Total Words: 7276
Unqiue Words: 1942

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