The preprint by Pratlong et al. [1] is a well thought quest for genomic regions involved in local adaptation to depth in a species a red coral living the Mediterranean Sea. It first describes a pattern of structuration and then attempts to find candidate genes involved in local adaptation by contrasting deep with shallow populations. Although the pattern of structuration is clear and meaningful, the candidate genomic regions involved in local adaptation remain to be confirmed. Two external reviewers and myself found this preprint particularly interesting regarding the right-mindedness of the authors in front of the difficulties they encounter during their experiments. The discussions on the pros and cons of the approach are very sound and can be easily exported to a large number of studies that hunt for local adaptation. In this sense, the lessons one can learn by reading this well documented manuscript are certainly valuable for a wide range of evolutionary biologists.
More precisely, the authors RAD-sequenced 6 pairs of 'shallow vs deep' samples located in 3 geographical sea areas (Banyuls, Corsica and Marseilles). They were hoping to detect genes involved in the adaptation to depth, if there were any. They start by assessing the patterns of structuration of the 6 samples using PCA and AMOVA [2] and also applied the STRUCTURE [3] assignment software. They show clearly that the samples were mostly differentiated between geographical areas and that only 1 out the 3 areas shows a pattern of isolation by depth (i.e. Marseille). They nevertheless went on and scanned for variants that are highly differentiated in the deep samples when compared to the shallow paired samples in Marseilles, using an Fst outliers approach [4] implemented in the BayeScEnv software [5]. No clear functional signal was in the end detected among the highly differentiated SNPs, leaving a list of candidates begging for complementary data.
The scan for local adaptation using signatures of highly divergent regions is a classical problem of population genetics. It has been applied on many species with various degrees of success. This study is a beautiful example of a well-designed study that did not give full satisfactory answers. Readers will especially appreciate the honesty and the in-depth discussions of the authors while exposing their results and their conclusions step by step.

References

[1] Pratlong, M., Haguenauer, A., Brener, K., Mitta, G., Toulza, E., Garrabou, J., Bensoussan, N., Pontarotti P., & Aurelle, D. (2018). Separate the wheat from the chaff: genomic scan for local adaptation in the red coral Corallium rubrum. bioRxiv, 306456, ver. 3 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/306456
[2] Excoffier, L., Smouse, P. E. & Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131(2), 479-491.
[3] Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.
[4] Lewontin, R. C., & Krakauer, J. (1973). Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics, 74(1), 175-195.
[5] de Villemereuil, P., & Gaggiotti, O. E. (2015). A new FST‐based method to uncover local adaptation using environmental variables. Methods in Ecology and Evolution, 6(11), 1248-1258. doi: 10.1111/2041-210X.12418

Evolution is usually studied via two distinct approaches: by inferring evolutionary processes from relatedness patterns among living species or by observing evolution in action in the laboratory or field. A recent study by Baym and colleagues in Science [1] has now combined these approaches by taking advantage of the pattern left behind by spatially evolving bacterial populations.

Evolution is often considered too slow to see, and can only be inferred by studying patterns of relatedness using phylogenetic trees. Increasingly, however, researchers are moving nature into the lab and watching as evolution unfolds under their noses. The field of experimental evolution follows evolutionary change in the laboratory over 10s to 1000s of generations, yielding insights into bacterial, viral, plant, or fly evolution (among many other species) that are simply not possible in the field. Yet, as powerful as experimental evolution is, it lacks a posterchild. There is no Galapagos finch radiation, nor a stunning series of cichlids to showcase to our students to pique their interests. Let’s face it, E. coli is no stickleback! And while practitioners of experimental evolution can explain the virtues of examining 60,000 generations of bacterial evolution in action, appreciating this nevertheless requires a level of insight and imagination that often eludes students, who need to see “it” to get it.

Enter MEGA, an idea and a film that could become the new face of experimental evolution. It replaces big numbers of generations or images of scientists, with an actual picture of the scientific result. MEGA, or Microbial Evolution and Growth Arena, is essentially an enormous petri dish and is the brainchild of Michael Baym, Tami Leiberman and their colleagues in Roy Kishony’s lab at Technion Israel Institute of Technology and Harvard Medical School. The idea of MEGA is to allow bacteria to swim over a spatially defined landscape while adapting to the local conditions, in this case antibiotics. When bacteria are inoculated onto one end of the plate they consume resources while swarming forward from the plate edge. In a few days, the bacteria grow into an area with antibiotics to which they are susceptible. This stops growth until a mutation arises that permits the bacteria to jump this hurdle, after which growth proceeds until the next hurdle of a 10-fold higher antibiotic concentration, and so on. By this simple approach, Baym et al. [1] evolved E. coli that were nearly 105-fold more resistant to two different antibiotics in just over 10 days. In addition, they identified the mutations that were required for these changes, showed that mutations conferring smaller benefits were required before bacteria could evolve maximal resistance, observed changes to the mutation rate, and demonstrated the importance of spatial structure in constraining adaptation.

For one thing, the rate of resistance evolution is impressive, and also quite scary given the mounting threat of antibiotic-resistant pathogens. However, MEGA also offers a uniquely visual insight into evolutionary change. By taking successive images of the MEGA plate, the group was able to watch the bacteria move, get trapped because of their susceptibility to the antibiotic, and then get past these traps as new mutations emerged that increased resistance. Each transition showcases evolution in real time. In addition, by leaving a spatial pattern of evolutionary steps behind, the MEGA plate offers unique opportunities to thoroughly investigate these steps when the experiment is finished. For instance, subsequent steps in mutational pathways can be characterized, but also their effects on fitness can be quantified in situ by measuring changes in survival and reproduction. This new method is undoubtedly a boon to the field of experimental evolution and offers endless opportunities for experimental elaboration. Perhaps of equal importance, MEGA is a tool that is portable to the classroom and to the public at large. Don’t believe in evolution? Watch this. You only have time for a short internship or lab practical? No problem. Don’t worry much about antibiotic resistance? Check this out. Like the best experimental tools, MEGA is simple but allows for complicated insights. And even if it is less charismatic than a finch, it still allows for the kinds of “gee-whiz” insights that will get students hooked on evolutionary biology.

Reference

[1] Baym M, Lieberman TD, Kelsic ED, Chait R, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science 353:1147-1151. doi: 10.1126/science.aag0822

Despite a vast array of ways in which organisms can reproduce (Bell, 1982), most animals engage in sexual reproduction (Otto & Lenormand, 2002). A fascinating alternative to sex is parthenogenesis, where offspring are produced asexually from a gamete, typically the egg, without receiving genetic material from another gamete (Simon, Delmotte, Rispe, & Crease, 2003). One of the long-standing questions in the field is why parthenogenesis is not more widespread, given the costs associated with sex (Otto & Lenormand, 2002).  Natural populations of most species appear to be reproducing either sexually or parthenogenetically, even if a species can employ both reproductive modes (Larose et al 2023). Larose et al (2023) highlight the conundrum in this pattern, as organisms that are capable of employing parthenogenesis facultatively would be able to gain the benefits of both modes of reproduction. Why then, is facultative parthenogenesis not more common?

Larose et al (2023) propose that constraints on being efficient in both sexual and asexual reproduction could cause a trade-off between reproductive modes that favours an obligate strategy of either sex or no sex. This would provide an explanation for why facultative parthenogenesis is rare. Timema stick insects provide an excellent system to investigate reproductive strategies, as some species have parthenogenetic females, while other species are sexual, and they show repeated transitions from sexual reproduction to obligate parthenogenesis (Schwander & Crespi, 2009). The authors performed comprehensive and complementary studies in a recently discovered species T. douglasi, in which populations show both modes of reproduction, with some populations consisting only of females and others showing equal proportions of males and females. The sex ratio varied significantly, with the proportion of females ranging between 43-100% across 29 populations. These populations form a monophyletic clade with clustering into three genetic lineages and only a few cases of admixture. Females from all populations were capable of producing unfertilized eggs, but the hatching success varied hugely among populations and lineages (3-100%). Parthenogenetically produced offspring were homozygous, showing that parthenogenesis causes a complete loss of heterozygosity in a single generation. After producing eggs as virgins, females were mated to assess the capacity to also reproduce sexually, and fertilization increased the hatching success of eggs in two lineages. In one lineage, in which the hatching success of unfertilized eggs is similar to that of other sexually reproducing Timema species, fertilization reduced egg-hatching success, indicating a trade-off between reproductive modes with parthenogenetic reproduction performing best. Approximately 58% of the offspring produced after mating were fertilized, demonstrating the capacity of females to reproduce parthenogenetically also after mating has occurred, however with huge variation among individuals.

This wonderful and meticulously performed study produces strong and complementary evidence for facultative parthenogenesis in T. douglasi populations. The study shows large variation in how reproductive mode is employed, supporting the existence of a trade-off between sexual and parthenogenetic reproduction. This might be an example of an ongoing transition from sexual to asexual reproduction, which indicates that obligate parthenogenesis may derive via transient facultative parthenogenesis. 

REFERENCES

Bell, G. (1982) The Masterpiece of Nature: The Evolution and Genetics of Sexuality. University of California Press. 635 p.

Otto, S. P., & Lenormand, T. (2002). Resolving the paradox of sex and recombination. Nature Reviews Genetics, 3(4), 252-261. https://doi.org/10.1038/nrg761

Schwander, T., & Crespi, B. J. (2009). Multiple direct transitions from sexual reproduction to apomictic parthenogenesis in Timema stick insects. Evolution, 63(1), 84-103. 
https://doi.org/10.1111/j.1558-5646.2008.00524.x

Simon, J.-C., Delmotte, F., Rispe, C., & Crease, T. (2003). Phylogenetic relationships between parthenogens and their sexual relatives: the possible routes to parthenogenesis in animals. Biological Journal of the Linnean Society, 79(1), 151-163. https://doi.org/10.1046/j.1095-8312.2003.00175.x

Larose, C., Lavanchy,  G., Freitas, S., Parker, D.J., Schwander, T. (2023) Facultative parthenogenesis: a transient state in transitions between sex and obligate asexuality in stick insects? bioRxiv, 2022.03.25.485836, ver. 4 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2022.03.25.485836

The Latitudinal Diversity Gradient (LDG) has fascinated natural historians, ecologists and evolutionary biologists ever since [1] described it about 200 years ago [2]. Despite such interest, agreement on the origin and nature of this gradient has been elusive. Several tens of hypotheses and models have been put forward as explanations for the LDG [2-3], that can be grouped in ecological, evolutionary and historical explanations [4] (see also [5]). These explanations can be reduced to no less than 26 hypotheses, which account for variations in ecological limits for the establishment of progressively larger assemblages, diversification rates, and time for species accumulation [5]. Besides that, although in general the tropics hold more species, different taxa show different shapes and rates of spatial variation [6], and a considerable number of groups show reverse patterns, with richer assemblages in cold temperate regions (see e.g. [7-9]).
Understanding such complexity needs integrating ecological and evolutionary research into the wide temporal and spatial perspectives provided by the burgeoning field of biogeography. This integrative discipline ¬–that traces back to Humboldt himself (e.g. [10])– seeks to put together historical and functional explanations to explain the complex dynamics of Earth’s biodiversity. Different to quantum physicists, biogeographers cannot pursue the ultimate principle behind the patterns we observe in nature due to the interplay of causes and effects, which in fact tell us that there is not such a single principle. Rather, they need to identify an array of basic principles coming from different perspectives, to then integrate them into models that provide realistic –but never simple– explanations to biodiversity gradients such as LDG (see, e.g., [5; 11]). That is, rather than searching for a sole explanation, research on the LDG must aim to identify as many signals hidden in the pattern as possible, and provide hypotheses or models that account for these signals. To later integrate them and, whenever possible, to validate them with empirical data on the organisms’ distribution, ecology and traits, phylogenies, fossils, etc.
Within this context, Meseguer & Condamine [12] provide a novel perspective to LDG research using phylogenetic and fossil evidence on the origin and extinction of taxa within the turtle, crocodile and lizard (i.e. squamate) lineages. By digging into deep time down to the Triassic (about 250 Myr ago) they are able to identify several episodes of flattening and steepening of the LDG for these three clades. Strikingly, their results show similar diversification rates in the northern hemisphere and in the equator during the over 100 Myr long global greenhouse period that extends from the late Jurassic to the Cretaceous and early Neogene. During this period, the LDG for these three groups would have appeared quite even across a mainly tropical Globe, although the equatorial regions were apparently much more evolutionarily dynamic. The equator shows much higher rates of origination and extinction of branches throughout the Cretaceous, but they counteract each other so net diversification is similar to that of the northern hemisphere in all three groups. The transition to a progressively colder Earth in the Paleogene (starting around 50 Myr ago) provokes a mass extinction in the three clades, which is compensated in the equator by the dispersal of many taxa from the areas that currently pertain to the Holarctic biogeographical realm. Finally, during the coldhouse Earth’s climatic conditions of the Neogene only squamates show significant positive diversification rates in extratropical areas, while the diversity of testudines remains, and crocodiles continue declining progressively towards oblivion in the whole world.
Meseguer & Condamine [12] attribute these temporal patterns to the so-called asymmetric gradient of extinction and dispersal (AGED) framework. Here, the dynamics of extinction-at and dispersal-from high latitudes during colder periods increase the steepness of the LDG. Whereas the gradient flattens when Earth warms up as a result of dispersal from the equator followed by increased diversification in extratropical regions. This idea in itself is not new, for the influence of climatic oscillations on diversification rates is well known, at least for the Pleistocene Ice Ages [13], as is the effect of niche conservatism on the LDG [14]. Nevertheless, Meseguer & Condamine’s AGED provides a synthetic verbal model that could allow integrating the three main types of processes behind the LDG into a single framework. To do this it would be necessary to combine AGED’s cycles of dispersal and diversification with realistic models of: (1) the ecological limits to host rich assemblages in the colder and less productive temperate climatic domains; (2) the variations in diversification rates with shifts in temperature and/or energy regimes; and (3) the geographical patterns of climatic oscillation through time that determine the time for species accumulation in each region.
Integrating these models may allow transposing Meseguer & Condamine’s [12] framework into the more mechanistic macroecological models advocated by Pontarp et al. [5]. This type of mechanistic models has been already used to understand the development of biodiversity gradients through the climatic oscillations of the Pleistocene and the Quaternary (e.g. [11]). So the challenge in this case would be to generate a realistic scenario of geographical dynamics that accounts for plate tectonics and long-term climatic oscillations. This is still a major gap and we would benefit from the integrated work by historical geologists and climatologists here. For instance, there is little doubt about the progressive cooling through the Cenozoic based in isotope recording in sea floor sediments [15]. Meseguer & Condamine [12] use this evidence for separating greenhouse, transition and coldhouse world scenarios, which should not be a problem for these rough classes. However, a detailed study of the evolutionary correlation of true climate variables across the tree of life is still pending, as temperature is inferred only for sea water in an ice-free ocean, say earlier half of the Cenozoic [15]. Precipitation regime is even less known. Such scenario would provide a scaffold upon which the temporal dynamics of several aspects of the generation and loss of biodiversity can be modelled. Additionally, one of the great advantages of selecting key clades to study the LDG would be to determine the functional basis of diversification. There are species traits that are well known to affect speciation and extinction probabilities, such as reproductive strategies or life histories (e.g. [16]). Whereas these traits might also be a somewhat redundant effect of climatic causes, they might foster (i.e. “extended reinforcement”, [17]) or slow diversification. Even so, it is unlikely that such a model would account for all the latitudinal variation in species richness. But it will at least provide a baseline for the main latitudinal variations in the diversity of the regional communities (sensu [18]) worldwide. Within this context the effects of recent ecological, evolutionary and historical processes, such as environmental heterogeneity, current diversification rates or glacial cycles, will only modify the general LDG pattern resulting from the main processes contained in Meseguer & Condamine’s AGED, thereby providing a more comprehensive understanding of the geographical gradients of diversity.

References
[1] Humboldt, A. v. (1808). Ansichten der Natur, mit wissenschaftlichen Erläuterungen. J. G. Cotta, Tübingen.
[2] Hawkins, B. A. (2001). Ecology's oldest pattern? Trends in Ecology & Evolution, 16, 470. doi: 10.1016/S0169-5347(01)02197-8
[3] Lomolino, M. V., Riddle, B. R. & Whittaker, R. J. (2017). Biogeography. Fifth Edition. Sinauer Associates, Inc., Sunderland, Massachussets.
[4] Mittelbach, G. G., Schemske, D. W., Cornell, H. V., Allen, A. P., Brown, J. M., Bush, M. B., Harrison, S. P., Hurlbert, A. H., Knowlton, N., Lessios, H. A., McCain, C. M., McCune, A. R., McDade, L. A., McPeek, M. A., Near, T. J., Price, T. D., Ricklefs, R. E., Roy, K., Sax, D. F., Schluter, D., Sobel, J. M. & Turelli, M. (2007). Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecology Letters, 10, 315-331. doi: 10.1111/j.1461-0248.2007.01020.x
[5] Pontarp, M., Bunnefeld L., Cabral, J. S., Etienne, R. S., Fritz, S. A., Gillespie, R. Graham, C. H., Hagen, O., Hartig, F., Huang, S., Jansson, R., Maliet, O., Münkemüller, T., Pellissier, L., Rangel, T. F., Storch, D., Wiegand, T. & Hurlbert, A. H. (2019). The latitudinal diversity gradient: novel understanding through mechanistic eco-evolutionary models. Trends in ecology & evolution, 34, 211-223. doi: 10.1016/j.tree.2018.11.009
[6] Hillebrand, H. (2004). On the generality of the latitudinal diversity gradient. The American Naturalist, 163, 192-211. doi: 10.1086/381004
[7] Santos, A. M. C. & Quicke, D. L. J. (2011). Large-scale diversity patterns of parasitoid insects. Entomological Science, 14, 371-382. doi: 10.1111/j.1479-8298.2011.00481.x
[8] Morinière, J., Van Dam, M. H., Hawlitschek, O., Bergsten, J., Michat, M. C., Hendrich, L., Ribera, I., Toussaint, E. F. A. & Balke, M. (2016). Phylogenetic niche conservatism explains an inverse latitudinal diversity gradient in freshwater arthropods. Scientific Reports, 6, 26340. doi: 10.1038/srep26340
[9] Weiser, M. D., Swenson, N. G., Enquist, B. J., Michaletz, S. T., Waide, R. B., Zhou, J. & Kaspari, M. (2018). Taxonomic decomposition of the latitudinal gradient in species diversity of North American floras. Journal of Biogeography, 45, 418-428. doi: 10.1111/jbi.13131
[10] Humboldt, A. v. (1805). Essai sur la geographie des plantes; accompagné d'un tableau physique des régions equinoxiales. Levrault, Paris.
[11] Rangel, T. F., Edwards, N. R., Holden, P. B., Diniz-Filho, J. A. F., Gosling, W. D., Coelho, M. T. P., Cassemiro, F. A. S., Rahbek, C. & Colwell, R. K. (2018). Modeling the ecology and evolution of biodiversity: Biogeographical cradles, museums, and graves. Science, 361, eaar5452. doi: 10.1126/science.aar5452
[12] Meseguer, A. S. & Condamine, F. L. (2019). Ancient tropical extinctions contributed to the latitudinal diversity gradient. bioRxiv, 236646, ver. 4 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/236646
[13] Jansson, R., & Dynesius, M. (2002). The fate of clades in a world of recurrent climatic change: Milankovitch oscillations and evolution. Annual review of ecology and systematics, 33(1), 741-777. doi: 10.1146/annurev.ecolsys.33.010802.150520
[14] Wiens, J. J., & Donoghue, M. J. (2004). Historical biogeography, ecology and species richness. Trends in ecology & evolution, 19, 639-644. doi: 10.1016/j.tree.2004.09.011
[15] Zachos, J. C., Dickens, G. R., & Zeebe, R. E. (2008). An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature, 451, 279-283. doi: 10.1038/nature06588
[16] Zúñiga-Vega, J. J., Fuentes-G, J. A., Ossip-Drahos, A. G., & Martins, E. P. (2016). Repeated evolution of viviparity in phrynosomatid lizards constrained interspecific diversification in some life-history traits. Biology letters, 12, 20160653. doi: 10.1098/rsbl.2016.0653
[17] Butlin, R. K., & Smadja, C. M. (2018). Coupling, reinforcement, and speciation. The American Naturalist, 191, 155-172. doi: 10.1086/695136
[18] Ricklefs, R. E. (2015). Intrinsic dynamics of the regional community. Ecology letters, 18, 497-503. doi: 10.1111/ele.12431

Ecological specialisation, especially among parasites infecting a set of host species, is ubiquitous in nature. Host specialisation can be understood as resulting from trade-offs in parasite infectivity, virulence and growth. However, it is not well understood how variation in these trade-offs shapes the overall fitness trade-off a parasite faces when adapting to multiple hosts. For instance, it is not clear whether a strong trade-off in one fitness component may sufficiently constrain the evolution of a generalist parasite despite weak trade-offs in other components. A second mechanism explaining variation in specialisation among species is habitat availability and quality. Rare habitats or habitats that act as ecological sinks will not allow a species to persist and adapt, preventing a generalist phenotype to evolve. Understanding the prevalence of those mechanisms in natural systems is crucial to understand the emergence and maintenance of host specialisation, and biodiversity in general.
In their study "Trait-specific trade-offs prevent niche expansion in two parasites", Lievens et al. [1] report the results of an evolution experiment involving two parasitic microsporidians, Anostracospora rigaudi and Enterocytospora artemiae, infecting two sympatric species of brine shrimp, Artemia franciscana and Artemia parthenogenetica. The two parasites were originally specialised on their primary host: A. rigaudi on A. parthenogenetica and E. artemiae on A. franciscana, although they encounter both species in the wild but at different rates. After passaging each parasite on each single host and on both hosts alternatively, Lievens et al. asked how host specialisation evolved. They found no change in specialisation at the fitness level in A. rigaudi in either treatment, while E. artemiae became more of a generalist after having been exposed to its secondary host, A. parthenogenetica. The most interesting part of the study is the decomposition of the fitness trade-off into its underlying trade-offs in spore production, infectivity and virulence. Both species remained specialised for spore production on their primary host, interpreted as caused by a strong trade-off between hosts preventing improvements on the secondary host. A. rigaudi evolved reduced virulence on its primary host without changes in the overall fitness trad-off, while E. artemiae evolved higher infectivity on its secondary host making it a more generalist parasite and revealing a weak trade-off for this trait and for fitness. Nevertheless, both parasites retained higher fitness on their primary host because of the lack of an evolutionary response in spore production.
This study made two important points. First, it showed that despite apparent strong trade-off in spore production, a weak trade-off in infectivity allowed E. artemiae to become less specialised. In contrast, A. rigaudi remained specialised, presumably because the strong trade-off in spore production was the overriding factor. The fitness trade-off that results from the superposition of multiple underlying trade-offs is thus difficult to predict, yet crucial to understand potential evolutionary outcomes. A second insight is related to the ecological context of the evolution of specialisation. The results showed that E. artemiae should be less specialised than observed, which points to a role played by source-sink dynamics on A. parthenogenetica in the wild. The experimental approach of Lievens et al. thus allowed them to nicely disentangle the various sources of constraints on the evolution of host adaptation in the Artemia system.

References

[1] Lievens, E.J.P., Michalakis, Y. and Lenormand, T. (2019). Trait-specific trade-offs prevent niche expansion in two parasites. bioRxiv, 621581, ver. 4 peer-reviewed and recommended by PCI Evolutionary Biology. doi: 10.1101/621581