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16 Dec 2022
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Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depression

Pseudo-overdominance: how linkage and selection can interact and oppose to purging of deleterious mutations.

Recommended by based on reviews by Yaniv Brandvain, Lei Zhao and 1 anonymous reviewer

Most mutations affecting fitness are deleterious and they have many evolutionary consequences. The dynamics and consequences of deleterious mutations are a long-standing question in evolutionary biology and a strong theoretical background has already been developed, for example, to predict the mutation load, inbreeding depression or background selection. One of the classical results is that inbreeding helps purge partially recessive deleterious mutations by exposing them to selection in homozygotes. However, this mainly results from single-locus considerations. When interactions among several, more or less linked, deleterious mutations are taken into account, peculiar dynamics can emerge. One of them, called pseudo-overdominance (POD), corresponds to the maintenance in a population of two (or more) haplotype blocks composed of several recessive deleterious mutations in repulsion that mimics overdominance. Indeed, homozygote individuals for one of the haplotype blocks expose many deleterious mutations to selection whereas they are reciprocally masked in heterozygotes, leading to higher fitness of heterozygotes compared to both homozygotes. A related process, called associative overdominance (AOD) is the effect of such deleterious alleles in repulsion on the linked neutral variation that can be increased by AOD. Although this possibility has been recognized for a long time (Otha and Kimura 1969), it has been mainly considered an anecdotal process. Recently, both theoretical (Zhao and Charlesworth 2016) and genomic analyses (Gilbert et al. 2020) have renewed interest in such a process, suggesting that it could be important in weakly recombining regions of a genome. Donald Waller (2021) - one of the co-authors of the current work - also recently proposed that POD could be quantitatively important with broad implications, and could resolve some unexplained observations such as the maintenance of inbreeding depression in highly selfing species. Yet, a proper theoretical framework analysing the effect of inbreeding on POD was lacking.

In this theoretical work, Diala Abu Awad and Donald Waller (2022) addressed this question through an elegant combination of analytical predictions and intensive multilocus simulations. They determined the conditions under which POD can be maintained and how long it could resist erosion by recombination, which removes the negative association between deleterious alleles (repulsion) at the core of the mechanism. They showed that under tight linkage, POD regions can persist for a long time and generate substantial segregating load and inbreeding depression, even under inbreeding, so opposing (for a while) to the purging effect. They also showed that background selection can affect the genomic structure of POD regions by rapidly erasing weak POD regions but maintaining strong POD regions (i.e with many tightly linked deleterious alleles).

These results have several implications. They can explain the maintenance of inbreeding depression despite inbreeding (as anticipated by Waller 2021), which has implications for the evolution of mating systems. If POD can hardly emerge under high selfing, it can persist from an outcrossing ancestor long after the transition towards a higher selfing rate and could explain the maintenance of mixed mating systems(which is possible with true overdominance, see Uyenoyama and Waller 1991). The results also have implications for genomic analyses, pointing to regions of low or no recombination where POD could be maintained, generating both higher diversity and heterozygosity than expected and variance in fitness. As structural variations are likely widespread in genomes with possible effects on suppressing recombination (Mérot et al. 2020), POD regions should be checked more carefully in genomic analyses (see also Gilbert et al. 2020).

Overall, this work should stimulate new theoretical and empirical studies, especially to assess how quantitatively strong and widespread POD can be. It also stresses the importance of properly considering genetic linkage genome-wide, and so the role of recombination landscapes in determining patterns of diversity and fitness effects.

References

Awad DA, Waller D (2022) Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depression. bioRxiv, 2021.12.16.473022, ver. 3 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.12.16.473022

Gilbert KJ, Pouyet F, Excoffier L, Peischl S (2020) Transition from Background Selection to Associative Overdominance Promotes Diversity in Regions of Low Recombination. Current Biology, 30, 101-107.e3. https://doi.org/10.1016/j.cub.2019.11.063

Mérot C, Oomen RA, Tigano A, Wellenreuther M (2020) A Roadmap for Understanding the Evolutionary Significance of Structural Genomic Variation. Trends in Ecology & Evolution, 35, 561–572. https://doi.org/10.1016/j.tree.2020.03.002

Ohta T, Kimura M (1969) Linkage disequilibrium at steady state determined by random genetic drift and recurrent mutation. Genetics, 63, 229–238. https://doi.org/10.1093/genetics/63.1.229

Uyenoyama MK, Waller DM (1991) Coevolution of self-fertilization and inbreeding depression II. Symmetric overdominance in viability. Theoretical Population Biology, 40, 47–77. https://doi.org/10.1016/0040-5809(91)90046-I

Waller DM (2021) Addressing Darwin’s dilemma: Can pseudo-overdominance explain persistent inbreeding depression and load? Evolution, 75, 779–793. https://doi.org/10.1111/evo.14189

Zhao L, Charlesworth B (2016) Resolving the Conflict Between Associative Overdominance and Background Selection. Genetics, 203, 1315–1334. https://doi.org/10.1534/genetics.116.188912

Conditions for maintaining and eroding pseudo-overdominance and its contribution to inbreeding depressionDiala Abu Awad, Donald Waller<p style="text-align: justify;">Classical models that ignore linkage predict that deleterious recessive mutations should purge or fix within inbred populations, yet inbred populations often retain moderate to high segregating load. True overdomina...Evolutionary Dynamics, Evolutionary Theory, Genome Evolution, Hybridization / Introgression, Population Genetics / Genomics, Reproduction and SexSylvain Glémin2022-01-04 12:15:35 View
05 Aug 2020
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Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita

DNA transposons drive genome evolution of the root-knot nematode Meloidogyne incognita

Recommended by ORCID_LOGO based on reviews by Daniel Vitales and 2 anonymous reviewers

Duplications, mutations and recombination may be considered the main sources of genomic variation and evolution. In addition, sexual recombination is essential in purging deleterious mutations and allowing advantageous allelic combinations to occur (Glémin et al. 2019). However, in parthenogenetic asexual organisms, variation cannot be explained by sexual recombination, and other mechanisms must account for it. Although it is known that transposable elements (TE) may influence on genome structure and gene expression patterns, their role as a primary source of genomic variation and rapid adaptability has received less attention. An important role of TE on adaptive genome evolution has been documented for fungal phytopathogens (Faino et al. 2016), suggesting that TE activity might explain the evolutionary dynamics of this type of organisms.
The phytopathogen nematode Meloidogyne incognita is one of the worst agricultural pests in warm climates (Savary et al. 2019). This species, as well as other root-knot nematodes (RKN), shows a wide geographical distribution range infecting diverse groups of plants. Although allopolyploidy may have played an important role on the wide adaptation of this phytopathogen, it may not explain by itself the rapid changes required to overcome plant resistance in a few generations. Paradoxically, M. incognita reproduces asexually via mitotic parthenogenesis (Trudgill and Blok 2001; Castagnone-Sereno and Danchin 2014) and only few single nucleotide variations were identified between different host races isolates (Koutsovoulos et al. 2020). Therefore, this is an interesting model to explore other sources of genomic variation such the TE activity and its role on the success and adaptability of this phytopathogen.
To address these questions, Kozlowski et al. (2020) estimated the TE mobility across 12 geographical isolates that presented phenotypic variations in Meloidogyne incognita, concluding that recent activity of TE in both genic and regulatory regions might have given rise to relevant functional differences between genomes. This was the first estimation of TE activity as a mechanism probably involved in genome plasticity of this root-knot nematode. This study also shed light on evolutionary mechanisms of asexual organisms with an allopolyploid origin. These authors re-annotated the 185 Mb triploid genome of M. incognita for TE content analysis using stringent filters (Kozlowski 2020a), and estimated activity by their distribution using a population genomics approach including isolates from different crops and locations. Canonical TE represented around 4.7% of the M. incognita genome of which mostly correspond to TIR (Terminal Inverted Repeats) and MITEs (Miniature Inverted repeat Transposable Elements) followed by Maverick DNA transposons and LTR (Long Terminal Repeats) retrotransposons. The result that most TE found were represented by DNA transposons is similar to the previous studies with the nematode species model Caenorhabditis elegans (Bessereau 2006; Kozlowski 2020b) and other nematodes as well. Canonical TE annotations were highly similar to their consensus sequences containing transposition machinery when TE are autonomous, whereas no genes involved in transposition were found in non-autonomous ones. These findings suggest recent activity of TE in the M. incognita genome. Other relevant result was the significant variation in TE presence frequencies found in more than 3,500 loci across isolates, following a bimodal distribution within isolates. However, variation in TE frequencies was low to moderate between isolates recapitulating the phylogenetic signal of isolates DNA sequences polymorphisms. A detailed analysis of TE frequencies across isolates allowed identifying polymorphic TE loci, some of which might be neo-insertions mostly of TIRs and MITEs (Kozlowski 2020c). Interestingly, the two thirds of the fixed neo-insertions were located in coding regions or in regulatory regions impacting expression of specific genes in M. incognita. Future research on proteomics is needed to evaluate the functional impact that these insertions have on adaptive evolution in M. incognita. In this line, this pioneer research of Kozlowski et al. (2020) is a first step that is also relevant to remark the role that allopolyploidy and reproduction have had on shaping nematode genomes.

References

[1] Bessereau J-L. 2006. Transposons in C. elegans. WormBook. 10.1895/wormbook.1.70.1
[2] Castagnone-Sereno P, Danchin EGJ. 2014. Parasitic success without sex - the nematode experience. J. Evol. Biol. 27:1323-1333. 10.1111/jeb.12337
[3] Faino L, Seidl MF, Shi-Kunne X, Pauper M, Berg GCM van den, Wittenberg AHJ, Thomma BPHJ. 2016. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res. 26:1091-1100. 10.1101/gr.204974.116
[4] Glémin S, François CM, Galtier N. 2019. Genome Evolution in Outcrossing vs. Selfing vs. Asexual Species. In: Anisimova M, editor. Evolutionary Genomics: Statistical and Computational Methods. Methods in Molecular Biology. New York, NY: Springer. p. 331-369. 10.1007/978-1-4939-9074-0_11
[5] Koutsovoulos GD, Marques E, Arguel M-J, Duret L, Machado ACZ, Carneiro RMDG, Kozlowski DK, Bailly-Bechet M, Castagnone-Sereno P, Albuquerque EVS, et al. 2020. Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest. Evol. Appl. 13:442-457. 10.1111/eva.12881
[6] Kozlowski D. 2020a. Transposable Elements prediction and annotation in the M. incognita genome. Portail Data INRAE. 10.15454/EPTDOS
[7] Kozlowski D. 2020b. Transposable Elements prediction and annotation in the C. elegans genome. Portail Data INRAE. 10.15454/LQCIW0
[8] Kozlowski D. 2020c. TE polymorphisms detection and analysis with PopoolationTE2. Portail Data INRAE. 10.15454/EWJCT8
[9] Kozlowski DK, Hassanaly-Goulamhoussen R, Da Rocha M, Koutsovoulos GD, Bailly-Bechet M, Danchin EG (2020) Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita. bioRxiv, 2020.04.30.069948, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. 10.1101/2020.04.30.069948
[10] Savary S, Willocquet L, Pethybridge SJ, Esker P, McRoberts N, Nelson A. 2019. The global burden of pathogens and pests on major food crops. Nat. Ecol. Evol. 3:430-439. 10.1038/s41559-018-0793-y
[11] Trudgill DL, Blok VC. 2001. Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens. Annu Rev Phytopathol 39:53-77. 10.1146/annurev.phyto.39.1.53

Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognitaDjampa KL Kozlowski, Rahim Hassanaly-Goulamhoussen, Martine Da Rocha, Georgios D Koutsovoulos, Marc Bailly-Bechet, Etienne GJ Danchin<p>Despite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant ...Adaptation, Bioinformatics & Computational Biology, Genome Evolution, Molecular Evolution, Population Genetics / Genomics, Reproduction and SexInes Alvarez2020-05-04 11:43:14 View
16 Mar 2017
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Correlated paternity measures mate monopolization and scales with the magnitude of sexual selection

Measurement of sexual selection in plants made easier

Recommended by and

Sexual selection occurs in flowering plants too. However it tends to be understudied in comparison to animal sexual selection, in part because the minuscule size and long dispersal distances of the individuals producing male gametes (pollen grains) seriously complicate the estimation of male siring success and thereby the measurement of sexual selection. Dorken and Perry [1] introduce a novel and clever approach to estimate sexual selection in plants, which bypasses the need for a direct quantification of absolute male mating success. This approach builds on the fact that the strength of sexual selection is directly related to the ability of individuals to monopolize mates [2]. In plants, mate monopolization can be assessed by examining the proportion of seeds produced by a given plant that are full-sibs, i.e. that share the same father. A nice feature of this proportion of full-sib seeds per maternal parent is it equals the coefficient of correlated paternity of Ritland [3], which can be readily obtained from the hundreds of plant mating system studies using genetic markers. A less desirable feature of the proportion of full sibs per maternal plant is that it is inversely related to population size, an effect that should be corrected for. The resulting index of mate monopolization is a simple product: (coefficient of correlated paternity)x(population size – 1). The authors test whether their index of mate monopolization is a good correlate of sexual selection, measured more traditionally as the selection differential on a trait influencing mating success, using a combination of theoretical and experimental approaches. Both approaches confirm that the two quantities are positively correlated, which suggests that the index of mate monopolization could be a convenient way to estimate the relative strength of sexual selection in flowering plants. These results call for further investigation, e.g. to verify that the effect of population size is well controlled for, or to assess the effects of non-random mating and inbreeding depression; however, this work paves the way for an expansion of sexual selection studies in flowering plants.

References

[1] Dorken ME and Perry LE. 2017. Correlated paternity measures mate monopolization and scales with the magnitude of sexual selection. Journal of Evolutionary Biology 30: 377-387 doi: 10.1111/jeb.13013

[2] Klug H, Heuschele J, Jennions M and Kokko H. 2010. The mismeasurement of sexual selection. Journal of Evolutionary Biology 23:447-462. doi: 10.1111/j.1420-9101.2009.01921.x

[3] Ritland K. 1989. Correlated matings in the partial selfer Mimulus guttatus. Evolution 43:848-859. doi: 10.2307/2409312

Correlated paternity measures mate monopolization and scales with the magnitude of sexual selectionDorken, ME and Perry LEIndirect measures of sexual selection have been criticized because they can overestimate the magnitude of selection. In particular, they do not account for the degree to which mating opportunities can be monopolized by individuals of the sex that ...Sexual SelectionEmmanuelle Porcher2017-03-13 23:22:26 View
06 Oct 2022
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Evolution of sperm morphology in a crustacean genus with fertilization inside an open brood pouch.

Evolution of sperm morphology in Daphnia within a phyologenetic context

Recommended by based on reviews by Renate Matzke-Karasz and 1 anonymous reviewer

In this study sperm morphology is studied in 15 Daphnia species and the morphological data are mapped on a Daphnia phylogeny. The authors found that despite the internal fertilization mode, Daphnia have among the smallest sperm recorded, as would be expected with external fertilization. The authors also conclude that increase in sperm length has evolved twice, that sperm encapsulation has been lost in a clade, and that this clade has very polymorphic sperm with long, and often numerous, filopodia.

Daphnia is an interesting model to study sperm morphology because the biology of sexual reproduction is often ignored in (cyclical) parthenogenetic species. Daphnia is part of the very diverse and successful group of cladocerans with cyclical parthenogenetic reproduction. The success of this reproduction mode is reflected in the known 620 species that radiated within this order, this is more than half of the known Branchiopod species diversity and the estimated number of cladoceran species is even two to four times higher (Forró et al. 2008). Looking at this particular model with a good phylogeny and some particularity in the mode of fertilization/reproduction, has thus a large value. Most Daphnia species are cyclical parthenogenetic and switch between sexual and asexual reproduction depending on the environmental conditions. Within the genus Daphnia, evolution to obligate asexuality has evolved in at least four independent occasions by three different mechanisms: (i) obligate parthenogenesis through hybridisation with or without polyploidy, (ii) asexuality has been acquired de novo in some populations and (iii) in certain lineages females reproduce by obligate parthenogenesis, whereas the clonally propagated males produce functional haploid sperm that allows them to breed with sexual females of normal cyclically parthenogenetic lineages (more on this in Decaestecker et al. 2009).

This study is made in the context of a body of research on the evolution of one of the most fundamental and taxonomically diverse cell types. There is surprisingly little known about the adaptive value underlying their morphology because it is very difficult to test this experimentally.  Studying sperm morphology across species is interesting to study evolution itself because it is a "simple trait". As the authors state: The understanding of the adaptive value of sperm morphology, such as length and shape, remains largely incomplete (Lüpold & Pitnick, 2018). Based on phylogenetic analyses across the animal kingdom, the general rule seems to be that fertilization mode (i.e. whether eggs are fertilized within or outside the female) is a key predictor of sperm length (Kahrl et al., 2021). There is a trade-off between sperm number and length (Immler et al., 2011). This study reports on one of the smallest sperm recorded despite the fertilization being internal. The brood pouch in Daphnia is an interesting particularity as fertilisation occurs internally, but it is not disconnected from the environment. It is also remarkable that there are two independent evolution lines of sperm size in this group. It suggests that those traits have an adaptive value. 

References

Decaestecker E, De Meester L, Mergeay J (2009) Cyclical Parthenogenesis in Daphnia: Sexual Versus Asexual Reproduction. In: Lost Sex: The Evolutionary Biology of Parthenogenesis (eds Schön I, Martens K, Dijk P), pp. 295–316. Springer Netherlands, Dordrecht. https://doi.org/10.1007/978-90-481-2770-2_15

Duneau David, Möst M, Ebert D (2022) Evolution of sperm morphology in a crustacean genus with fertilization inside an open brood pouch. bioRxiv, 2020.01.31.929414, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2020.01.31.929414

Forró L, Korovchinsky NM, Kotov AA, Petrusek A (2008) Global diversity of cladocerans (Cladocera; Crustacea) in freshwater. Hydrobiologia, 595, 177–184. https://doi.org/10.1007/s10750-007-9013-5

Immler S, Pitnick S, Parker GA, Durrant KL, Lüpold S, Calhim S, Birkhead TR (2011) Resolving variation in the reproductive tradeoff between sperm size and number. Proceedings of the National Academy of Sciences, 108, 5325–5330. https://doi.org/10.1073/pnas.1009059108

Kahrl AF, Snook RR, Fitzpatrick JL (2021) Fertilization mode drives sperm length evolution across the animal tree of life. Nature Ecology & Evolution, 5, 1153–1164. https://doi.org/10.1038/s41559-021-01488-y

Lüpold S, Pitnick S (2018) Sperm form and function: what do we know about the role of sexual selection? Reproduction, 155, R229–R243. https://doi.org/10.1530/REP-17-0536

Evolution of sperm morphology in a crustacean genus with fertilization inside an open brood pouch.Duneau, David; Moest, Markus; Ebert, Dieter<p style="text-align: justify;">Sperm is the most fundamental male reproductive feature. It serves the fertilization of eggs and evolves under sexual selection. Two components of sperm are of particular interest, their number and their morphology....Evolutionary Ecology, Morphological Evolution, Reproduction and Sex, Sexual SelectionEllen Decaestecker2020-05-30 22:54:15 View
07 Jul 2017
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Negative frequency-dependent selection is frequently confounding

Unmasking the delusive appearance of negative frequency-dependent selection

Recommended by based on reviews by David Baltrus and 2 anonymous reviewers

Explaining the processes that maintain polymorphisms in a population has been a fundamental line of research in evolutionary biology. One of the main mechanisms identified that preserves genetic diversity is negative frequency-dependent selection (NFDS), which constitutes a powerful framework for interpreting the presence of persistent polymorphisms. Nevertheless, a number of patterns that are often explained by invoking NFDS may also be compatible with, and possibly more easily explained by, different processes.
In the present manuscript [1], Brisson acknowledges first that genuine NFDS has been instrumental for our understanding on the dynamics that perpetuate polymorphisms, and that the power and importance of NFDS cannot be disregarded. Second, the author aims at identifying certain of the processes that may result in maintenance of genetic diversity, and whose outcome may be mistaken for NFDS, namely directional selection in changing environments, density-dependent fitness, multiple niche selection and community diversity. The author claims that systematic resort to NFDS as explanatory device may have lead to its application to systems where it does not apply or that do not fulfil the basic assumptions of NFDS. The author struggles in the text to provide with a precise, verbal definition of NFDS, and the exchanges with the reviewers during the recommendation process show that agreeing on such a verbal definition of NFDS is not trivial. Probably a profound mathematical formulation of the varying value of a genotype’s fitness relative to other competing ones as a function of their frequency (developing further the synthesis by Heino [2]) may still be wanting. Indeed, the text is intended for a broad audience of evolutionary biologists with operational mathematical knowledge and interest in models, rather than for modellers or biomathematicians. Nevertheless, the manuscript is rich in references to original literature, elaborates on interesting lines of thought and discussion and will hopefully trigger novel experimental and formal research to clarify the role of NFDS and to discern between alternative mechanisms that may render similar patterns of maintenance of genetic diversity.

References

[1] Brisson D. 2017. Negative frequency-dependent selection is frequently confounding. bioRxiv 113324, ver. 3 of 20th June 2017. doi: 10.1101/113324

[2] Heino M, Metz JAJ and Kaitala V. 1998. The enigma of frequency-dependent selection. Trends in Ecology & Evolution 13: 367-370. doi: 1016/S0169-5347(98)01380-9

Negative frequency-dependent selection is frequently confoundingDustin BrissonThe existence of persistent genetic variation within natural populations presents an evolutionary problem as natural selection and genetic drift tend to erode genetic diversity. Models of balancing selection were developed to account for the high ...Evolutionary Applications, Evolutionary Theory, Population Genetics / GenomicsIgnacio Bravo2017-03-03 18:46:42 View
21 Nov 2022
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Artisanal and farmers bread making practices differently shape fungal species community composition in French sourdoughs

The variety of bread-making practices promotes diversity conservation in food microbial communities

Recommended by and based on reviews by 2 anonymous reviewers

Domesticated organisms are excellent models for understanding ecology and evolution and they are important for our food production and safety. While less studied than plants and animals, micro-organisms have also been domesticated, in particular for food fermentation [1]. The most studied domesticated micro-organism is the yeast used to make wine, beer and bread, Saccharomyces cerevisiae [2, 3, 4].

Filamentous fungi used for cheese-making have recently gained interest, for example Penicillium roqueforti used to make blue cheeses and P. camemberti to make soft cheeses [5, 6, 7, 8]. As for plants and animals, domestication has led to beneficial traits for food production in fermenting fungi, but also to bottlenecks and degeneration [6, 7, 9]; P. camemberti for example does not produce enough spores any more for optimal culture and inoculation and P. roqueforti has lost sexual fertility [9]. The loss of genetic diversity and of species diversity in our food production system is concerning for multiple reasons : i) it jeopardizes future improvement in the face of global changes ; ii) it causes the loss of evolved diversity during centuries under human selection, and therefore of beneficial characteristics and specificities that we may never be able to recover ; iii) it leads to degeneration in the few cultivated strains; iv) it impoverishes the diversity of our food products and local adaptation of production practices. 

The study of domesticated fungi used for food fermentation has focused so far on the evolution of lineages and on their metabolic specificities. Microbiological assemblages and species diversity have been much less studied, while they likely also have a strong impact on the quality and safety of final products. This study by Elisa Michel and colleagues [10] addresses this question, using an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyse bread-making practices and their impact on microbial communities in sourdough. Elisa Michel and colleagues [10] identified two distinct groups of bread-making practices based on interviews and surveys, with farmer-like practices (low bread production, use of ancient wheat populations, manual kneading, working at ambient temperature, long fermentation periods and no use of commercial baker’s yeast) versus more intensive, artisanal-like practices. Metabarcoding and microbial culture-based analyses showed that the well-known baker’s yeast, Saccharomyces cerevisiae, was, surprisingly, not the most common species in French organic sourdoughs. Kazachstania was the most represented yeast genus over all sourdoughs, both in terms of read abundance and of species diversity. Kazachstania species were also often dominant in individual sourdoughs, but Saccharomyces uvarum or Torulaspora delbrueckii could also be the dominant yeast species.

Metabarcoding analyses further revealed that the composition of the fungal communities differed between the farmer-like and more intensive practices, representing the first evidence of the influence of artisanal practices on microbial communities. The fungal communities were impacted by a combination of bread-making variables including the type of wheat varieties, the length of fermentation, the quantity of bread made per week and the use of commercial yeast. Maintaining on farm less intensive bread-making practices, may allow the preservation of typical species and phenotypic diversity in microbial communities in sourdough. Farmer-like practices did not lead to higher diversity within sourdoughs but, overall, the diversity of bread-making practices allow maintaining a larger diversity in sourdoughs. For example, different Kazachstania species were most abundant in sourdoughs from artisanal-like and farmer-like practices. Interviews with the bakers suggested the role of dispersal of Kazachstania species in shaping sourdough microbial communities, dispersal occurring by seed exchanges, sourdough mixing or gifts, bread-making training in common or working in one another’s bakery. Nikolai Vavilov [11] had already highlighted for crops the importance of isolated cultures and selection in different farms for generating and preserving crop diversity, but also the importance of seed exchange for fostering adaptation. 

Furthermore, one of the yeast frequently found in artisanal sourdoughs, Kazachstania humilis, displayed phenotypic differences between sourdough and non-sourdough strains, suggesting domestication. The sourdough strains exhibited significantly higher CO2 production rate and a lower fermentation latency-phase time. 

The study by Elisa Michel and colleagues [10] is thus novel and inspiring in showing the importance of interdisciplinary studies, combining metabarcoding, microbiology and interviews for assessing the composition and diversity of microbial communities in human-made food, and in revealing the impact of artisanal-like bread-making practices in preserving microbial community diversity.

Interdisciplinary studies are still rare but have already shown the importance of combining ethno-ecology, biology and evolution to decipher the role of human practices on genetic diversity in crops, animals and food microorganisms and to help preserving genetic resources [12]. For example, in the case of the bread wheat Triticum aestivum, such interdisciplinary studies have shown that genetic diversity has been shaped by farmers’ seed diffusion and farming practices [13]. We need more of such interdisciplinary studies on the impact of farmer versus industrial agricultural and food-making practices as we urgently need to preserve the diversity of micro-organisms used in food production that we are losing at a rapid pace [6, 7, 14]. 

References

[1] Dupont J, Dequin S, Giraud T, Le Tacon F, Marsit S, Ropars J, Richard F, Selosse M-A (2017) Fungi as a Source of Food. Microbiology Spectrum, 5, 5.3.09. https://doi.org/10.1128/microbiolspec.FUNK-0030-2016

[2] Legras J-L, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T, Sanchez I, Couloux A, Guy J, Franco-Duarte R, Marcet-Houben M, Gabaldon T, Schuller D, Sampaio JP, Dequin S (2018) Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication. Molecular Biology and Evolution, 35, 1712–1727. https://doi.org/10.1093/molbev/msy066

[3] Bai F-Y, Han D-Y, Duan S-F, Wang Q-M (2022) The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae. Genes, 13, 230. https://doi.org/10.3390/genes13020230

[4] Fay JC, Benavides JA (2005) Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae. PLOS Genetics, 1, e5. https://doi.org/10.1371/journal.pgen.0010005

[5] Ropars J, Rodríguez de la Vega RC, López-Villavicencio M, Gouzy J, Sallet E, Dumas É, Lacoste S, Debuchy R, Dupont J, Branca A, Giraud T (2015) Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi. Current Biology, 25, 2562–2569. https://doi.org/10.1016/j.cub.2015.08.025

[6] Dumas E, Feurtey A, Rodríguez de la Vega RC, Le Prieur S, Snirc A, Coton M, Thierry A, Coton E, Le Piver M, Roueyre D, Ropars J, Branca A, Giraud T (2020) Independent domestication events in the blue-cheese fungus Penicillium roqueforti. Molecular Ecology, 29, 2639–2660. https://doi.org/10.1111/mec.15359

[7] Ropars J, Didiot E, Rodríguez de la Vega RC, Bennetot B, Coton M, Poirier E, Coton E, Snirc A, Le Prieur S, Giraud T (2020) Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties. Current Biology, 30, 4441-4453.e4. https://doi.org/10.1016/j.cub.2020.08.082

[8] Caron T, Piver ML, Péron A-C, Lieben P, Lavigne R, Brunel S, Roueyre D, Place M, Bonnarme P, Giraud T, Branca A, Landaud S, Chassard C (2021) Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavor and texture in blue cheeses. International Journal of Food Microbiology, 354, 109174. https://doi.org/10.1016/j.ijfoodmicro.2021.109174

[9] Ropars J, Lo Y-C, Dumas E, Snirc A, Begerow D, Rollnik T, Lacoste S, Dupont J, Giraud T, López-Villavicencio M (2016) Fertility depression among cheese-making Penicillium roqueforti strains suggests degeneration during domestication. Evolution, 70, 2099–2109. https://doi.org/10.1111/evo.13015

[10] Michel E, Masson E, Bubbendorf S, Lapicque L, Nidelet T, Segond D, Guézenec S, Marlin T, Devillers H, Rué O, Onno B, Legrand J, Sicard D, Bakers TP (2022) Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs. bioRxiv, 679472, ver. 6 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/679472

[11] Vavilov NI, Vavylov MI, Dorofeev VF (1992) Origin and Geography of Cultivated Plants. Cambridge University Press.

[12] Saslis-Lagoudakis CH, Clarke AC (2013) Ethnobiology: the missing link in ecology and evolution. Trends in Ecology & Evolution, 28, 67–68. https://doi.org/10.1016/j.tree.2012.10.017

[13] Thomas M, Demeulenaere E, Dawson JC, Khan AR, Galic N, Jouanne-Pin S, Remoue C, Bonneuil C, Goldringer I (2012) On-farm dynamic management of genetic diversity: the impact of seed diffusions and seed saving practices on a population-variety of bread wheat. Evolutionary Applications, 5, 779–795. https://doi.org/10.1111/j.1752-4571.2012.00257.x

[14] Demeulenaere É, Lagrola M (2021) Des indicateurs pour accompagner “ les éleveurs de microbes” : Une communauté épistémique face au problème des laits “ paucimicrobiens ” dans la production fromagère au lait cru (1995-2015). Revue d’anthropologie des connaissances, 15. http://journals.openedition.org/rac/24953

Artisanal and farmers bread making practices differently shape fungal species community composition in French sourdoughsElisa Michel, Estelle Masson, Sandrine Bubbendorf, Leocadie Lapicque, Thibault Nidelet, Diego Segond, Stephane Guezenec, Therese Marlin, Hugo deVillers, Olivier Rue, Bernard Onno, Judith Legrand, Delphine Sicard<p style="text-align: justify;">Preserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbia...Adaptation, Evolutionary Applications, Evolutionary EcologyTatiana Giraud2022-01-27 14:53:08 View
14 Dec 2016
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High Rates of Species Accumulation in Animals with Bioluminescent Courtship Displays

Bioluminescent sexually selected traits as an engine for biodiversity across animal species

Recommended by and

In evolutionary biology, sexual selection is hypothesized to increase speciation rates in animals, as theory predicts that sexual selection will contribute to phenotypic diversification and affect rates of species accumulation at macro-evolutionary time scales. However, testing this hypothesis and gathering convincing evidence have proven difficult. Although some studies have shown a strong correlation between proxies of sexual selection and species diversity (mostly in birds), this relationship relies on some assumptions on the link between these proxies and the strength of sexual selection and is not detected in some other taxa, making taxonomically widespread conclusions impossible.

In a recent study published in Current Biology [1], Ellis and Oakley provide strong evidence that bioluminescent sexual displays have driven high species richness in taxonomically diverse animal lineages, providing a crucial link between sexual selection and speciation.
It was known that bioluminescence has evolved independently more than 40 times, with males often using it as a mating signal but with also some other possible adaptive functions including anti-predator defense and predation. Moreover, it has been reported that small marine lanternfishes and sharks that use bioluminescence in mate identification had a greater concentration of species than other deep-sea fishes that use bioluminescence for defensive purposes [2-4]. But no one had ever determined whether this pattern is consistent across diverse and distantly related animal groups living on sea and land.

Ellis and Oakley [1] explored the scientific literature for well-resolved evolutionary trees with branches containing bioluminescent lineages and identified lineages that use light for courtship or camouflage in a wide range of marine and terrestrial taxa including insects, crustaceans, cephalopods, segmented worms, and fishes. The researchers counted the number of species in each bioluminescent clade and found that all groups with light-courtship displays had more species and faster rates of species accumulation than their non-luminous most closely related sister lineages or ancestors. In contrast, those groups that used bioluminescence for predator avoidance had a lower than expected rate of species richness on average.

Nicely encompassing a diversity of taxa and neatly controlling for the rate of species accumulation of the encompassing clade, the results of Ellis and Oakley are clear-cut and provide the most comprehensive evidence to date for the hypothesis that sexual displays can act as drivers of speciation. One question this study incites is what is happening in terms of sexual selection in species displaying defensive bioluminescence or no bioluminescence at all: do those lineages use no mating signals at all or other mating signals that are less apparent, and will those experience lower levels of sexual selection than bioluminescent mating signals, i.e. consistent with Ellis and Oakley results? It would also be interesting to investigate the diversification rates in animal species using other modalities, such as chemical, acoustic or any other type of signals used by males, females or both sexes, to determine what types of sexual signals may be more generally drivers of speciation.

References

[1] Ellis EA, Oakley TH. 2016. High Rates of Species Accumulation in Animals with Bioluminescent Courtship Displays. Current Biology 26:1916–1921. doi: 10.1016/j.cub.2016.05.043

[2] Davis MP, Holcroft NI, Wiley EO, Sparks JS, Smith WL. 2014. Species-specific bioluminescence facilitates speciation in the deep sea. Marine Biology 161:1139­1148. doi: 10.1007/s00227-014-2406-x

[3] Davis MP, Sparks JS, Smith WL. 2016. Repeated and Widespread Evolution of Bioluminescence in Marine Fishes. PLoS One 11:e0155154. doi: 10.1371/journal.pone.0155154

[4] Claes JM, Nilsson D-E, Mallefet J, Straube N. 2015. The presence of lateral photophores correlates with increased speciation in deep-sea bioluminescent sharks. Royal Society Open Science 2:150219. doi: 10.1098/rsos.150219

High Rates of Species Accumulation in Animals with Bioluminescent Courtship DisplaysEllis EA, Oakley THOne of the great mysteries of evolutionary biology is why closely related lineages accumulate species at different rates. Theory predicts that populations undergoing strong sexual selection will more quickly differentiate because of increased pote...Adaptation, Evolutionary Ecology, Sexual Selection, SpeciationAstrid Groot2016-12-14 19:01:59 View
01 Mar 2024
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Rapid life-history evolution reinforces competitive asymmetry between invasive and resident species

The evolution of a hobo snail

Recommended by based on reviews by David Reznick and 2 anonymous reviewers

At the very end of a paper entitled "Copepodology for the ornithologist" Hutchinson (1951) pointed out the possibility of 'fugitive species'.  A fugitive species, said Hutchinson, is one that we would typically think of as competitively inferior.  Wherever it happens to live it will eventually be overwhelmed by competition from another species.  We would expect it to rapidly go extinct but for one reason: it happens to be a much better coloniser than the other species.  Now all we need to explain its persistence is a dose of space and a little disturbance: a world in which there are occasional disturbances that cause local extinction of the dominant species. Now, argued Hutchinson, we have a recipe for persistence, albeit of a harried kind.  As Hutchinson put it, fugitive species "are forever on the move, always becoming extinct in one locality as they succumb to competition, and always surviving as they reestablish themselves in some other locality."

It is a fascinating idea, not just because it points to an interesting strategy, but also because it enriches our idea of competition: competition for space can be just as important as competition for time.

Hutchinson's idea was independently discovered with the advent of metapopulation theory (Levins 1971; Slatkin 1974) and since then, of course, ecologists have gone looking, and they have unearthed many examples of species that could be said to have a fugitive lifestyle.  These fugitive species are out there, but we don't often get to see them evolve.  

In their recent paper, Chapuis et al. (2024) make a convincing case that they have seen the evolution of a fugitive species.  They catalog the arrival of an invasive freshwater snail on Guadeloupe in the Lesser Antilles, and they wonder what impact this snail's arrival might have on a native freshwater snail.  This is a snail invasion, so it has been proceeding at a majestic pace, allowing the researchers to compare populations of the native snail that are completely naive to the invader with those that have been exposed to the invader for either a relatively short period (<20 generations) or longer periods (>20 generations).  They undertook an extensive set of competition assays on these snails to find out which species were competitively superior and how the native species' competitive ability has evolved over time.

Against naive populations of the native, the invasive snail turns out to be unequivocally the stronger competitor.  (This makes sense; it probably wouldn't have been able to invade if it wasn't.)  So what about populations of the native snail that have been exposed for longer, that have had time to adapt?  Surprisingly these populations appear to have evolved to become even weaker competitors than they already were. 

So why is it that the native species has not simply been driven extinct? Drawing on their previous work on this system, the authors can explain this situation.  The native species appears to be the better coloniser of new habitats.  Thus, it appears that the arrival of the invasive species has pushed the native species into a different place along the competition-colonisation axis.  It has sacrificed competitive ability in favour of becoming a better coloniser; it has become a fugitive species in its own backyard.

This is a really nice empirical study.  It is a large lab study, but one that makes careful sampling around a dynamic field situation.  Thus, it is a lab study that informs an earlier body of fieldwork and so reveals a fascinating story about what is happening in the field. We are left not only with a particularly compelling example of character displacement towards a colonising phenotype but also with something a little less scientific: the image of a hobo snail, forever on the run, surviving in the spaces in between.

References

Chapuis E, Jarne P, David P (2024) Rapid life-history evolution reinforces competitive asymmetry between invasive and resident species. bioRxiv, 2023.10.25.563987, ver. 2 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.10.25.563987

Hutchinson, G.E. (1951) Copepodology for the Ornithologist. Ecology 32: 571–77. https://doi.org/10.2307/1931746

Levins, R., and D. Culver. (1971) Regional Coexistence of Species and Competition between Rare Species. Proceedings of the National Academy of Sciences 68, no. 6: 1246–48. https://doi.org/10.1073/pnas.68.6.1246.

Slatkin, Montgomery. (1974) Competition and Regional Coexistence. Ecology 55, no. 1: 128–34. https://doi.org/10.2307/1934625.

Rapid life-history evolution reinforces competitive asymmetry between invasive and resident speciesElodie Chapuis, Philippe Jarne, Patrice David<p style="text-align: justify;">Biological invasions by phylogenetically and ecologically similar competitors pose an evolutionary challenge to native species. Cases of character displacement following invasions suggest that they can respond to th...Evolutionary Ecology, Life History, Species interactionsBen Phillips2023-10-26 15:49:33 View
05 Dec 2017
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Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data

Predicting small ancestors using contemporary genomes of large mammals

Recommended by based on reviews by Bruce Rannala and 1 anonymous reviewer

Recent methodological developments and increased genome sequencing efforts have introduced the tantalizing possibility of inferring ancestral phenotypes using DNA from contemporary species. One intriguing application of this idea is to exploit the apparent correlation between substitution rates and body size to infer ancestral species' body sizes using the inferred patterns of substitution rate variation among species lineages based on genomes of extant species [1].
The recommended paper by Figuet et al. [2] examines the utility of such approaches by analyzing the Cetartiodactyla, a clade of large mammals that have mostly well resolved phylogenetic relationships and a reasonably good fossil record. This combination of genomic data and fossils allows a direct comparison between body size predictions obtained from the genomic data and empirical evidence from the fossil record. If predictions seem good in groups such as the Cetartiodactyla, where there is independent evidence from the fossil record, this would increase the credibility of predictions made for species with less abundant fossils.
Figuet et al. [2] analyze transcriptome data for 41 species and report a significant effect of body mass on overall substitution rate, synonymous vs. non-synonymous rates, and the dynamics of GC-content, thus allowing a prediction of small ancestral body size in this group despite the fact that the extant species that were analyzed are nearly all large.
A comparative method based solely on morphology and phylogenetic relationships would be very unlikely to make such a prediction. There are many sources of uncertainty in the variables and parameters associated with these types of approaches: phylogenetic uncertainty (topology and branch lengths), uncertainty about inferred substitution rates, and so on. Although the authors do not account for all these sources of uncertainty the fact that their predicted body sizes appear sensible is encouraging and undoubtedly the methods will become more statistically sophisticated over time.

References

[1] Romiguier J, Ranwez V, Douzery EJP and Galtier N. 2013. Genomic evidence for large, long-lived ancestors to placental mammals. Molecular Biology and Evolution 30: 5–13. doi: 10.1093/molbev/mss211

[2] Figuet E, Ballenghien M, Lartillot N and Galtier N. 2017. Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data. bioRxiv, ver. 3 of 4th December 2017. 139147. doi: 10.1101/139147

Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic dataEmeric Figuet, Marion Ballenghien, Nicolas Lartillot, Nicolas Galtier<p>Reconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, it was proposed that ancestral traits...Genome Evolution, Life History, Macroevolution, Molecular Evolution, Phylogenetics / PhylogenomicsBruce Rannala2017-05-18 15:28:58 View
28 Mar 2024
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Gene expression is the main driver of purifying selection in large penguin populations

Purifying selection on highly expressed genes in Penguins

Recommended by based on reviews by Tanja Pyhäjärvi and 1 anonymous reviewer

Given the general importance of protein expression levels, in cells it is widely accepted that gene expression levels are often a target of natural selection and that most mutations affecting gene expression levels are therefore likely to be deleterious [1]. However, it is perhaps less obvious that the strength of selection on the regulated genes themselves may be influenced by their expression levels. This might be due to harmful effects of misfolded proteins, for example, when higher protein concentrations exist in cells [2]. Recent studies have suggested that highly expressed genes accumulate fewer deleterious mutations; thus a positive relationship appears to exist between gene expression levels and the relative strength of purifying selection [3].

The recommended paper by Trucchi et al. [4] examines the relationship between gene expression, purifying selection and a third variable -- effective population size -- in populations of two species of penguin with different population sizes, the Emperor penguin (Aptenodytes forsteri) and the King penguin (A. patagonicus). Using transcriptomic data and computer simulations modeling selection, they examine patterns of nonsynonymous and synonymous segregating polymorphisms (p) across genes in the two populations, concluding that even in relatively small populations purifying selection has an important effect in eliminating deleterious mutations. 

References

1] Gilad Y, Oshlack A, and Rifkin SA. 2006. Natural selection on gene expression. Trends in Genetics 22: 456-461. https://doi.org/10.1016/j.tig.2006.06.002
 
[2] Yang JR, Liao BY, Zhuang SM, and Zhang J. 2012. Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proceedings of the National Academy of Sciences 109: E831-E840. https://doi.org/10.1073/pnas.1117408109
 
[3] Duret L, and Mouchiroud D (2000). Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Molecular Biology and Evolution 17; 68-070. https://doi.org/10.1093/oxfordjournals.molbev.a026239

[4] Trucchi E, Massa P, Giannelli F, Latrille T, Fernandes FAN, Ancona L, Stenseth NC, Obiol JF, Paris J, Bertorelle G, and Le Bohec, C. 2023. Gene expression is the main driver of purifying selection in large penguin populations. bioRxiv 2023.08.08.552445, ver. 2 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2023.08.08.552445

 

Gene expression is the main driver of purifying selection in large penguin populationsEmiliano Trucchi, Piergiorgio Massa, Francesco Giannelli, Thibault Latrille, Flavia A.N. Fernandes, Lorena Ancona, Nils Chr Stenseth, Joan Ferrer Obiol, Josephine Paris, Giorgio Bertorelle, Celine Le Bohec<p style="text-align: justify;">Purifying selection is the most pervasive type of selection, as it constantly removes deleterious mutations arising in populations, directly scaling with population size. Highly expressed genes appear to accumulate ...Bioinformatics & Computational Biology, Evolutionary Dynamics, Evolutionary Theory, Population Genetics / GenomicsBruce Rannala2023-08-09 17:53:03 View