For anyone seeking to understand how, "from (a) simple beginning, endless forms most beautiful and most wonderful have been, and are being, evolved" [Darwin, 1859], the relatively simple rules of template-based DNA synthesis, mutation and vertical inheritance offer powerful lenses into the past, provided selection and drift are taken into account. These principles allow us to read genomic similarity as a record of shared ancestry, giving rise to phylogenetics and its tree-like reconstructions of evolutionary history, commonly referred to as phylogenetic trees. 

One striking observation when zeroing on specific lineages is that the community composition of microrganisms that live in and on them are more similar to one another than to the microbial communties of other hosts sharing the same environments or the same diets (the two factors more obviously linked to the microbial communities). Relationships between community compositions in these cases also generate tree-like branching patterns, more precisely called dendrograms, sometimes uncannily mirroring the phylogenetic relationships among the organisms who serve as their hosts. This sort of phylogenetic signal of microbial communities associated with related hosts is called phylosymbiosis [Brucker & Bordenstein, 2013]. While diverse ecological and evolutionary processes can generate mirrored host-microbiome 'trees' [Kohl, 2020], rigorous quantification is required to understand them. DuBose [2025] tackles this methodological challenge by evaluating how different tree-congruence metrics and null models perform when detecting phylosymbiotic signals.

At least three approaches have been used to quantify phylosymbiosis [Lim & Bordenstein, 2020]. Matrix-correlation methods compare host phylogenetic distances with microbiome beta-diversity distances (quantified by Bray-Curtis, Jaccard or UniFrac methods), typically using Mantel [Groussin et al., 2017] or Procrustes tests [Qin et al., 2021]. Phylogenetic comparative methods, though less common in this context, evaluate phylogenetic signal through measures such as Blomberg's K and Pagel's lambda [Donohue et al., 2022] or process-based models like multivariate Brownian motion [Perez-Lamarque et al., 2023]. Topological congruence methods, the most widely used, assess whether a host phylogeny and a microbiome dendrogram are more topologically similar than expected by chance. But the "devil is in the details" regarding what constitutes "chance" and whether different topological congruence metrics agree on the strength of the signal. 

DuBose offers a thorough study of both aspects. First, the author implements a clever neutral community assembly model (following reviewer suggestions) to compare against standard random tree sampling, validating the approach as a robust reference for testing null hypotheses. Second, the study evaluates a large range of congruence metrics available in the widely used TreeDist and phangorn packages. The reproducibility of this method was assessed by a PCI data editor and this recommender; users interested in testing the full range of metrics can easily modify the provided scripts.

While one may miss alternative model trees to represent more biologically grounded processes and most results align with theoretical expectations (e.g. signal is more evident in larger trees), random tree sampling remains common yet under-benchmarked, reference in the literature [Brooks et al., 2016; Travelline et al., 2020; Graham et al.,  2025]. DuBose provides the first systematic exploration of its properties, demonstrating that Monte Carlo sampling across tree space serves as a meaningful null framework. This work clearly outlines key caveats and implementation choices researchers must consider, making it a necessary methodological resource for the field.

References

Andrew W. Brooks, Kevin D. Kohl, Robert M Brucker, Edward J van Opstal, Seth R Bordenstein (2016) Phylosymbiosis: relationships and functional effects of microbial communities across host evolutionary history. PLoS Biol. 14(11):e2000225. https://doi.org/10.1371/journal.pbio.2000225 

Robert M. Brucker, Seth R. Bordenstein (2013) The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science. 341(6146):667-9.  https://doi.org/10.1126/science.1240659

Charles Darwin (1859) On the origin of species by means of natural selection. John Murray, London.

Mariah E. Donohue, Amanda K. Rowe, Eric Kowalewski, Zoe L. Hert, Carly E. Karrick, Lovasoa J. Randriamanandaza, Francois Zakamanana, Stela Nomenjanahary, Rostant Y. Andriamalala, Kathryn M. Everson, Audrey D. Law, Luke Moe, Patricia C. Wright, David W. Weisrock (2022) Significant effects of host dietary guild and phylogeny in wild lemur gut microbiomes. ISME Commun. 2(1):33.  https://doi.org/10.1038/s43705-022-00115-6

James G. DuBose (2025) The effects of host phylogenetic coverage and congruence metric on Monte Carlo-based null models of phylosymbiosis. bioRxiv, ver.4 peer-reviewed and recommended by PCI Evolutionary Biology https://doi.org/10.1101/2025.02.07.637028

Natalie J. Graham, Nicola J. Day, Gancho Slavov, Peter Ritchie, Steve A. Wakelin (2025) Evidence of phylosymbiosis in the microbiome of conifer roots. Phytobiomes J. 9(4):541-57. https://doi.org/10.1094/PBIOMES-03-25-0022-R

Mathieu Groussin, Florent Mazel, Jon G Sanders, Chris S Smillie, Sebastien Lavergne, Wilfried Thuiller, Eric J Alm (2017) Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun. 8:14319. https://doi.org/10.1038/ncomms14319

Kevin D. Kohl (2020) Ecological and evolutionary mechanisms underlying patterns of phylosymbiosis in host-associated microbial communities. Philos Trans R Soc Lond B Biol Sci. 375(1798):20190251. https://doi.org/10.1098/rstb.2019.0251

Shen J. Lim, Seth R Bordenstein (2020) An introduction to phylosymbiosis. Proc Biol Sci. 287(1922):20192900. https://doi.org/10.1098/rspb.2019.2900

Benoit Perez-Lamarque, Guilhem Sommeria-Klein, Lorena Duret, Helene Morlon (2023) Phylogenetic comparative approach reveals evolutionary conservatism, ancestral composition, and integration of vertebrate gut microbiota. Mol Biol Evol. 40(7):msad144. https://doi.org/10.1093/molbev/msad144

Man Qin, Jing Chen, Shifen Xu, Liyun Jiang, Gexia Qiao (2021) Microbiota associated with Mollitrichosiphum aphids (Hemiptera: Aphididae: Greenideinae): diversity, host species specificity and phylosymbiosis. Environ Microbiol. 23(4):2184-2198. https://doi.org/10.1111/1462-2920.15391

Brian K. Trevelline, Jahree Sosa, Barry K Hartup, Kevin D Kohl (2020) A bird's-eye view of phylosymbiosis: weak signatures of phylosymbiosis among all 15 species of cranes. Proc Biol Sci. 287(1923):20192988. https://doi.org/10.1098/rspb.2019.2988

The cause of isolation between species is often very difficult to determine, because multiple phenomena and layers usually come together in a given situation. Different species can live in different habitats, which limits their opportunity to meet (ecological premating isolation). They can also exhibit different sexual traits and preferences, which limit their opportunity to mate (sexual premating isolation). Furthermore, their offspring can suffer from lower viability and fertility, which limits further genetic exchanges (postmating isolation). The genetic basis of these phenomena has been under scrutiny for decades, but when ecology matters, depends on difficult field studies in a few model systems.

In the 1950s–1970s, the intertidal marine isopods from the Jaera albifrons complex were a useful model for systematicians and cytogeneticists studying speciation and the role of chromosomal rearrangements (1–3). J. albifrons and J. praehirsuta, two species of that complex, are characterised by ecological and sexual isolation, but little postzygotic isolation, as can be concluded from the limited number of laboratory cross-breeding experiments conducted (4). In the field, however, these species sometimes share the same pebble habitat (notably in Normandy), while at other times they live in different algal versus pebble habitats (notably in Brittany). This system therefore allows contrasting two interesting situations in which both ecological and sexual premating isolation occur between the two species in Brittany, while only sexual premating isolation occurs in Normandy. Could this contrast reveal the contribution of ecological versus sexual isolation mechanisms? Can it reveal the genetic basis of sexual isolation? Can it reveal the role of chromosomal rearrangements in these contrasted cases?

In this study, Ambre Ribardière and colleagues embark on this comparison using a remarkable variety of genomic approaches, careful analyses and extensive data. Their first major finding is that genomic differentiation between species indeed is lower when only sexual isolation is operating than when both ecological and sexual isolation are operating. Second, they found that this differentiation is highly heterogeneous across the genome with only a subset of regions found highly differentiated in Normandy compared to Brittany. Third, most of these regions involve regions with low recombination, notably on sex chromosomes, but also on a few rearranged autosomes. Fourth, QTL loci for male sexual traits colocalise in these regions.

With these findings, they demonstrate elegantly that in the absence of ecological isolation, many genomic regions become homogenized by gene flow, while some regions resist its eroding effect, being likely involved in sexual isolation. This study also prompts new questions: what explains the important role of sex chromosomes in this context? The large X/Z effect is usually understood in the context of post-mating, not sexual, isolation (5, 6). Is there absolutely no post-mating isolation in these hybrids, with some Haldane rule pattern? Is the overrepresentation of low recombination regions merely a consequence of QTL detection bias? Are there other field locations where different or parallel contrasts can be made? Undoubtedly, however, with this landmark study, the Jaera albifrons complex (re)emerges as a new and fascinating model system for speciation research in the genomic era.

References

1. C. Bocquet, Recherches Sur Le Polymorphisme Naturel Des Jaera Marina (Fabr.) (Isopodes Asellotes). Essai de Systématique Évolutive (CNRS, 1953).

2. P. Lecher, Cytogénétique de l’hybridisation expérimentale et naturelle chez l’isopode Jaera (albifrons) syei Bocquet. Archives de Zoologie Expérimentale et Générale 108, 633–698 (1967).

3. M. Solignac, Isolating mechanisms and modalities of speciation in the Jaera albifrons species complex (Crustacea, Isopoda). Syst. Zool. 30, 387–405 (1981). https://doi.org/10.1093/sysbio/30.4.387

4. A. Ribardière, E. Pabion, J. Coudret, C. Daguin‐Thiébaut, C. Houbin, S. Loisel, S. Henry, T. Broquet, Sexual isolation with and without ecological isolation in marine isopods Jaera albifrons and J. praehirsuta. J. Evol. Biol. 34, 33–48 (2021). https://doi.org/10.1111/jeb.13559

5. A. Ribardière, C. Daguin-Thiébaut, J. Coudret, G. Le Corguillé, K. Avia, C. Houbin, S. Loisel, P.-A. Gagnaire, T. Broquet. Sex chromosomes and chromosomal rearrangements are key to behavioural sexual isolation in Jaera albifrons marine isopods. bioRxiv, ver.3 (2025) peer-reviewed and recommended by PCI Evolutionary Biology. https://doi.org/10.1101/2025.01.08.631900

6. J. A. Coyne, H. A. Orr, “Two rules of speciation” in Speciation and Its Consequences (Sinauer, Sunderland, MA, D Otte; J Endler., 1989), pp. 180–207.

7. J. A. Coyne, “Two rules of speciation” revisited. Molecular Ecology 27, 3749–3752 (2018). https://doi.org/10.1111/mec.14790

This study provides an interesting contribution to our understanding of reproductive strategies and genetic diversity in Arctic marine invertebrates. 

The authors investigate the reproductive modes of the circumpolar sea anemone Aulactinia stella across a broad geographic range, from the northern Pacific to the Atlantic, combining population genetic analyses with observations of reproductive structures. Their results reveal a geographic pattern in reproductive strategies, with predominantly clonal populations in the Atlantic and more sexually reproducing populations in the Pacific. The identification of parthenogenesis as a reproductive mode in A. stella, along with strong clonality in several Arctic populations, has important implications for understanding how sessile organisms persist and disperse in extreme and rapidly changing environments. 

The strength of this work lies in the extensive sampling carried out across the entire range of the species. The study also has some limitations, which are adequately discussed in the text, mainly the use of microsatellites that may display mutational patterns difficult to interpret (Ellegren, 2004). 

Overall, this work is methodologically sound, clearly presented, and provides valuable data for understanding the evolution and connectivity of Arctic species. It will be of broad interest to researchers studying reproductive evolution, population genetics, and biogeography in polar ecosystems.

References

Ekaterina Bocharova, Alexander Volkov, Solenn Stoeckel (2025) Increased clonality, decreased allele diversity and high genetic structure in tetraploid sea anemone Aulactinia stella populations from North Pacific to Atlantic across the Arctic Ocean. bioRxiv, ver.3 peer-reviewed and recommended by PCI Evolutionary Biology https://doi.org/10.1101/2025.04.24.650399

Ellegren, H. (2004) Microsatellites: simple sequences with complex evolution. Nature Reviews Genetics, 5, 435–445. https://doi.org/10.1038/nrg1348

Hybridisation, the interbreeding between distinct species or populations, can act as a powerful mechanism of evolutionary innovation. Hybridization has been demonstrated to play a role in range expansion and biological invasions (Verhoeven et al., 2011). When gene pools that have evolved in isolation come into secondary contact, their combination can generate novel phenotypes that extend beyond parental variation, providing the raw material for rapid adaptation in new or changing environments. Hybridisation can produce a wide range of outcomes, from hybrid vigour (heterosis) to hybrid depression. In cases of heterosis, hybrids outperform their parents thanks to overdominance or because deleterious recessive alleles are masked in heterozygotes. Conversely, hybrid depression can arise when the co-adapted gene complexes of the parents are disrupted, or when hybrids are less well adapted to parental environment. The direction and magnitude of these effects depend on the specific genetic combinations involved, as well as the ecological context in which hybridisation occurs.

The wasp spider (Argiope bruennichi) offers a particularly convincing example of how hybridisation can influence adaptation and range expansion. It has been shown that hybridisation between Asian and European populations has occurred in Eastern and Central Europe, and the resulting hybrid population has expanded its distribution northwards (Krehenwinkel et al., 2015). Introgression of Asian alleles into the southern European gene pool may have enabled this hybrid lineage to tolerate colder conditions, facilitating its colonisation of northern latitudes. Furthermore, previous behavioural work revealed that hybridisation is most likely to occur between European females and Asian males (Franke & Schneider, 2025).

Using controlled crosses between females from southern France (representing the European lineage) and males from Japan (the Asian lineage), Franke et al. (2025) mimicked the hybridisation that occurred in the wild. Reciprocal crosses were also made, along with pure parental lines. They compared life history traits of hybrid lines to parental lines under different environmental conditions — varying temperature, day length, and food availability. This experimental design allowed the authors to assess how hybridisation affects offspring fitness and to determine how this process contributes to the species’ northward expansion.

The authors reveal marked differences among crosses based on the performance of 2,868 offspring spiders across treatments. As expected, the most Northern climatic treatment induced faster growth and early mortality  whereas low food availability decreased growth rate. Crosses between French females and Japanese males showed significantly lower hatching success, growth rate and survival rates, under all environmental treatments, consistent with hybrid depression. In contrast, the reciprocal cross (Japanese female × French male) performed comparably to the pure parental lines. This suggests that incompatibility between the two populations is not general but rather specific to cross direction. This asymmetry likely stems from mitonuclear incompatibility, the mismatched interaction between maternally inherited mitochondrial genomes and paternal nuclear genes. 

This study of A. bruennichi highlights the complexity of hybridisation as an evolutionary process. The outcome depends not only on the genetic architecture of the parental populations but also on the direction of hybridisation and on the environmental context.

References

Franke S, Schneider JM (2025) Simulating a hybridization event of a range-expanding sexual cannibal (Argiope bruennichi). Biological Journal of the Linnean Society, 144, blae018. https://doi.org/10.1093/biolinnean/blae018

Franke S, Volquardsen A, Schneider JM (2025) Asymmetric performance in early life stages of hybrid Argiope bruennichi. OSF , ver.2 peer-reviewed and recommended by PCI Evolutionary Biology https://doi.org/10.17605/OSF.IO/3JFM5

Krehenwinkel H, Rödder D, Tautz D (2015) Eco-genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture. Global Change Biology, 21, 4320–4332. https://doi.org/10.1111/gcb.13042

Verhoeven KJF, Macel M, Wolfe LM, Biere A (2011) Population admixture, biological invasions and the balance between local adaptation and inbreeding depression. Proceedings of the Royal Society B: Biological Sciences, 278, 2–8. https://doi.org/10.1098/rspb.2010.1272

Cross-discipline research is an increasing need in modern world just to fit societal expectations or simply to better achieve one critical aim of scientific inquiry, to know the true causes of facts, both proximate and ultimate. This is increasingly notorious in day-to-day life of researchers, as evaluation of research grants and careers considers multi-, inter- and trans-disciplinarity as items to be specifically addressed (Porter et al., 2008; Wagner et al., 2011). Whereas interdisciplinarity is also encouraged by top journals, even by those within classical scientific disciplines, most of papers are not beyond multidisciplinarity, that is, they use methods and/or approach interpretations based on those proper of each field, but results do not surpass a merely additive advance. True interdisciplinarity means that results obtained lay far beyond those obtained by the single disciplines composing the study. Complex questions need also complex approaches. This is a difficult aim since methods should be properly linked (Lynch, 2006). Here we recommend a genuine interdisciplinary paper (Gilabert et al. 2025).
 
In natural sciences, it should be admitted that interdisciplinarity is more easily adopted in some specific fields which rapidly ask for support from the social sciences. This is for example the case of ecology and evolutionary biology. Serve as already classical and nearly synchronous examples, the interplay between human population genetics and linguistics (Cavalli-Sforza, 1997), or between ecology and history of human societies (Diamond, 1997), which have percolated so profoundly in the social sciences that they are currently established their own research programmes. Gilabert et al. (2025) have managed to use methods from three disciplines (archaeology, linguistics, and crop domestication and expansion by artificial and cultural selection). One can imagine of a similar study using solely modern phylogeographical tools for depicting migration routes of cultivated sorghum and then interpreting results using the available information from other fields. Instead, the authors use also available information on the relationships among languages (closely related in pursuit and methodology to evolutionary biology, with a different target) of societies that use races of this crop, and archaeological remains to date genomic phylogeography, similar to the use of fossils for dating phylogenies. This multiple approach mighty revealed the routes of crop expansion through time and confirmed the geographic origin of the domestication formerly proposed with more classical, archaeological procedures. One of the reviewers suggested the use of another technique for depicting these expansion routes, which apparently produces more resolution and better visualization of the timing and spread of the process, although it relies on additional information on the dates of the process. Not being a molecular phylogenetist myself, it is easy to recognize that this and other tools will throw more light in the near future, due the rapid development of these techniques and the power of the data acquired by the authors. 
 
Despite that authors claim their study as multidisciplinary I think they are very modest as it accomplishes required conditions to be interdisciplinary. As much, a multidisciplinary study would ascertain congruence between the three different approaches (linguistics, archaeology, genomic phylogeography); instead, there is a clear integration of methods and data from these in a single analytical procedure. Thus, the results transcend from single congruence. This paper paves the way for future use of even more data and information from other sources, some of them already mentioned by the authors. These may include (1) the relationship between human groups beyond those ascertained through language relationships, as done by Tao et al. (2023), cited by authors; (2) the effect of changing paleoclimates during the period revealed in this paper within the Holocene using available data and maps (e.g., Joussaume & Taylor, 2000; http://pmip.lsce.ipsl.fr/); and (3) the relationship between current crops and archaeological crop remains with the possible use of ancient DNA (Brown et al. 2015). This will prove the development of the emerging field of phyloculture reconstruction, using crops as a model system.
 
 
References
 
Brown, T. A., Cappellini, E., Kistler, L., Lister, D. L., Oliveira, H. R., Wales, N., & Schlumbaum, A. (2015). Recent advances in ancient DNA research and their implications for archaeobotany. Vegetation History and Archaeobotany, 24(1), 207-214. https://doi.org/10.1007/s00334-014-0489-4

Cavalli-Sforza, L. L. (1997). Genes, peoples, and languages. Proceedings of the National Academy of Sciences, 94(15), 7719-7724. https://doi.org/10.1073/pnas.94.15.7719

Diamond, J. (1997). Guns. Germs and Steel: The Fates of Human Societies, Vintage, 186.

Gilabert A., Deu M., Champion L., Cubry Ph., Donkpegan A. Rami J.F., Pot D., Vigouroux Y., Leclerc Ch. (2025). Integrating ethnolinguistic and archaeobotanical data to uncover the origin and dispersal of cultivated sorghum in Africa: a genomic perspective. bioRxiv, ver.1 peer-reviewed and recommended by PCI Evolutionary Biology. https://doi.org/10.1101/2025.04.16.648676

Joussaume S., Taylor K.E. (2000) The palaeoclimate modeling intercomparison project. Palaeoclimate modelling intercomparison project (PMIP). Proceedings of the Third PMIP Workshop, La Huardiere, Canada, 4–8 October 1999, (ed. by P. Braconnot), pp. 9 – 25. World Meteorological Organization, Geneva, Switzerland.

Lynch, J. (2006). It's not easy being interdisciplinary. International journal of epidemiology, 35(5), 1119-1122. https://doi.org/10.1093/ije/dyl200

Porter, A. L., Roessner, D. J., & Heberger, A. E. (2008). How interdisciplinary is a given body of research?. Research evaluation, 17(4), 273-282. https://doi.org/10.3152/095820208X364553

Tao, L., Yuan, H., Zhu, K., Liu, X., Guo, J., Min, R., He, H., Cao, D., Yang, X., Zhou, Z., Wang, R., Zhao, D., Ma, H., Chen, J., Zhao, J., Li, Y., He, Y., Suo, D., Zhang, R., Li, S., Li, L., Yang, F., Li, H., Zhang, L., Jin, L., Wang, C.-C., 2023. Ancient genomes reveal millet farming-related demic diffusion from the Yellow River into southwest China. Curr. Biol. Volume 33, Issue 22 P4995-5002.E7 https://doi.org/10.1016/j.cub.2023.09.055

Wagner, C. S., Roessner, J. D., Bobb, K., Klein, J. T., Boyack, K. W., Keyton, J., ... & Börner, K. (2011). Approaches to understanding and measuring interdisciplinary scientific research (IDR): A review of the literature. Journal of informetrics, 5(1), 14-26. https://doi.org/10.1016/j.joi.2010.06.004