The evolution of differences among females and males or sexual dimorphism (SD) is very common in animals but rare in plants. These differences emerge because there is a conflict of interests between sexes to maximize their reproductive success. Thus, moving genes of reproductive traits to low recombining regions such as the sex chromosomes might be one way to solve this conflict at the genomic level. Closely related species with young sex chromosomes, which differ in the degree of SD, are ideal systems to explore the underlining genetic architecture of SD. We have crossed a female from Silene latifolia with marked SD with a male from S. dioica with less SD. We performed a QTL analysis of reproductive and vegetative traits in the F2 hybrids to find out if sexually dimorphic traits are located on the sex chromosomes, and how they contribute to species differences. Our results support that evolutionary young sex chromosomes are important for the expression of both SD and species differences. Moreover, transgressive segregation (traits with extreme values) and a reversal of SD in the F2s indicated that SD is constrained within the species but not in the recombinant hybrids. Sexual selection can, thus, contribute to speciation.
Full article: Baena-Díaz F, Zemp N, Widmar A. 2019. Insights into the genetic architecture of sexual dimorphism from an interspecific cross between two diverging Silene (Caryophyllaceae) species. Molecular ecology. https://doi.org/10.1111/mec.15271
Whilst urbanisation poses a major threat to many species, there is growing evidence to suggest that some species, labelled ‘urban adapters’, are thriving within the urban landscape. Urban landscapes differ drastically from native habitats, where urban adapters are often exposed to a more diverse range of novel food items compared to their rural counterparts, which frequently includes human subsidised resources. Diet is one of the most important factors influencing the gut microbiome, an extremely influential symbiotic community that plays a critical role in many processes affecting host health and fitness, including metabolism, nutrition, immunology and development. Here, using populations of the eastern water dragon in Queensland, Australia, we explore the link between urbanisation, diet and gut microbial changes. We show that city dragons exhibit a more diverse gut microbiome than their rural counterparts, and display microbial signatures of a diet that is richer in plant-material and higher in fat. Elevated levels of the Nitrogen-15 isotope in the blood of city dragons also suggests their diet may be richer in protein. These results highlight that urbanisation can have pronounced effects on the gut microbial communities of wild animals, but we do not yet know the possible repercussions of these microbial changes.
Full article: Littleford‐Colquhoun BL, Weyrich LS, Kent N, Frere CH. City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii). Mol Ecol. 2019;28:4592–4607. https://doi.org/10.1111/mec.15240
In this study, we wanted to know how geography and ecology predicted population genetic structure among 58 populations of the gall wasp Belonocnema treatae, which exhibits regional specialization on three host plant species across the U.S. Gulf Coast. We combined range-wide sampling with a genotype-by-sequencing approach for 40,699 SNPs across 1,217 individuals. Disentangling the processes underlying geographic and environmental patterns of biodiversity is challenging, as such patterns emerge from eco‐evolutionary processes confounded by spatial autocorrelation among sample units. We evaluated this question using a hierarchical Bayesian model (ENTROPY) to assign individuals to genetic clusters and estimate admixture proportions. Using distance-based Moran’s eigenvector mapping, we generated regression variables that represent varying degrees of spatial autocorrelation in genetic variation among sample sites. These spatial variables, along with host association, were incorporated in distance-based redundancy analysis (dbRDA) to partition the relative contributions of host plant and spatial autocorrelation. This novel approach of combining ENTROPY results with dbRDA to analyze SNP data unveiled a complex mosaic of diversification within and among insect populations forming discrete host associated lineages coupled with geographic variation. This demonstrates that geography and ecology play significant roles in explaining patterns of genomic variation in B. treatae – an emerging model of ecological speciation.
Full article: Driscoe AL, Nice CC, Busbee RW,Hood GR, Egan SP, Ott JR. Host plant associations and geography interact to shape diversification in a specialist insect herbivore. Mol Ecol. 2019;28:4197–4211. https://doi.org/10.1111/mec.15220
The Lake Whitefish (Coregonus clupeaformis) is found in Nearctic post-glacial freshwater lakes, and diverged about 500,000 years ago from its sister species, the European Whitefish (Coregonus lavaretus) found throughout Northern Europe, European Alpine lakes and Russia. These two lineages underwent an adaptive radiation following the last glaciation, resulting in the sympatric occurrence of limnetic and benthic species-pairs. Decades of research has aimed to decipher the process of adaptive divergence and ecological speciation in the Whitefish species complex. Here, we compared independent diverging species-pairs from the two continents to elucidate the genomic and transcriptomic bases associated with the benthic-limnetic diversification. We used a statistical framework to detect polygenic targets of selection associated with phenotypic diversification. We identified a subset of genes that showed convergent patterns of differential expression between limnetic and benthic species across both continents. Those adaptive divergent genes retained a higher degree of shared polymorphism among species-pairs, most likely due to balancing selection, and this genetic variation was associated with changes in levels of gene expression between species. As such, our results indicate that standing genetic variation underlying phenotypes involved in the ecological speciation of the whitefish species-pairs has been partly maintained in parallel across both continents for at least half a million years.
-Clément Rougeux – Postdoctoral Researcher, University of Calgary
Full article: Rougeux C, Gagnaire P‐A, Praebel K, Seehausen O, Bernatchez L. Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex. Mol Ecol. 2019;28:4388–4403. https://doi.org/10.1111/mec.15226
We were challenged to design and build a simple and rapid species monitoring system. Why do we need such a system? Biodiversity loss is at an all-time high and such a system would help to support the management and conservation of fish species within aquatic environments by acquiring knowledge of species distribution that traditionally is gained through visual detection and counting. These methods are expensive, time consuming and can lead to harm of the species of interest. We decided that environmental DNA (eDNA) was the way to go but we had to solve the ‘PCR problem’ i.e., avoid having to do cyclical high temperatures as that would see us ending up with a costly, once-off device that would likely not be applied outside our lab. This got us brainstorming and led us to a novel isothermal detection method, combining Recombinase Polymerase Amplification with CRISPR-Cas detection, which simplifies the adaptation of nucleic acid detection on to a biosensor device.
This innovative methodology utilises the collateral cleavage activity of Cas12a, a ribonuclease guided by a highly specific single CRISPR RNA, to detect specific species from eDNA. We proved it could work for eDNA by applying the technology to the detection of Salmo salar from eDNA samples collected in Irish rivers, where presence or absence had been previously confirmed using conventional field sampling. The beauty of this advance is that it can be applied to any species in the environment. Not only does this assay solve the ‘PCR problem’, it is also is a better approach for distinguishing very closely related species. We look forward to others in the field adapting it to their own favourite species of interest.
Citation: Williams, M‐A, O’Grady, J, Ball, B, et al. The application of CRISPR‐Cas for single species identification from environmental DNA. Mol Ecol Resour. 2019; 19: 1106– 1114. https://doi.org/10.1111/1755-0998.13045
The study of species and where they live is of particular interest to biologists, because it not only allows us to gain insight into genetic diversity, but also into how different populations interact. Animals with widespread distributions are often assumed to be of least concern. This can be misleading, as it does not take into account the possibility of fragmentation and population disjunction. The Stripey fish Microcanthus strigatus is one example, as it is listed as being of least concern on the IUCN Red List. Although it spans a wide distribution across the western Pacific and eastern Indian Oceans, our study suggests that populations in Western Australia, the southwest Pacific (including eastern Australia), Hawaii and East Asia are very genetically divergent. Several of these populations have been isolated since the last glacial cycle in the Pleistocene epoch, and are currently so fragmented that no contemporary genetic exchange occurs. This is of significant conservation concern as a once widespread population is revealed to consist of four cryptic groups, especially in light of evidence suggesting that the Hawaiian population is currently in decline and that the southwest Pacific population is distinct enough to warrant recognition as a different species.
Read the full article: Tea Y‐K, Van Der Wal C, Ludt WB, Gill AC, Lo N, Ho SYW. Boomeranging around Australia: Historical biogeography and population genomics of the anti‐equatorial fish Microcanthus strigatus (Teleostei: Microcanthidae). Mol Ecol. 2019;28:3771–3785. https://doi.org/10.1111/mec.15172
Plant pathogens are a major factor in farming and forestry, and also play a key role in ecosystem health. Understanding pathogens at national scales is critical for appropriate prevention and management strategies and for a sustainable provision of future ecosystem services and agroecosystem productivity. Despite this, at present we have little knowledge of the diversity patterns of plant pathogens and how they change with land use at a broad scale.
In our study we show how land uses such as farming and plantation forestry affected the variety of plant pathogens in soil, roots and on plant leaves – and we show there are many more species of plant pathogens in land that’s been modified by pasture, cropping, and plantation forestry than there are in natural forest. The patterns of pathogen diversity are distinct from other microbes.
These are some of the first landscape level insights into these critically important communities including fungal, oomycete and bacterial pathogens in seemingly healthy ecosystems. Our results give scientists new insights into where pathogens exist, and how pathogen communities are structured.
Andreas Makiola and Ian Dickie (Bio-Protection Research Centre, New Zealand)
Arid environments are ecosystems of energetic stringency. Their typical high temperatures, low primary productivity, and unpredictable water availability prove physiologically challenging for birds. How these vertebrates cope with such harshness remains a conundrum in physiological evolutionary biology. While physiological adaptation likely involves energetic metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we developed a intra-specific level framework (Figure 1) that links environmental conditions, phenotypes and genotypes in a passerine bird whose range spans an aridity gradient. We found variation in energetic physiology phenotypes (a measure of energy expenditure) and gut microbiota composition (involved in energy retrieval from food) to be associated with environmental features and identified a small list of candidate adaptive genes. By working at the interface of physiology and genomics, we suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly with contribution of gut microbiota may facilitate adaptation to local conditions. Ultimately, our findings offer a possible explanation to the high avian intra-specific divergence observed in harsh environments, raises awareness that accounting for intra-specific variation is fundamental when modeling physiological responses to climate change, and provides a stepping-stone for further research into the mechanisms of phenotypic adaptation to aridity.
Ribeiro ÂM, Puetz L, Pattinson NB, Dálen L, Deng Y, Zhang G, da Fonseca RR, Smit B, Gilbert MT. (2019). 31° South: The physiology of adaptation to arid conditions in a passerine bird. Molecular Ecology. 2019. 28-16. 3709-3721.
Individuals within a species vary, and this variation can have important implications for the role a species may play within ecosystems. We compared the relative importance of variation within species due to genetic changes within its own genome versus symbiotic interactions between the focal species and its associated bacteria, also called their microbiome. We focused on Microcystis aeruginosa, a globally distributed photosynthetic cyanobacterium, also known as blue-green algae, that often dominates freshwater harmful algal blooms.
These blooms have recently become more common and intense worldwide, causing major economic and ecological damages. We studied Microcystis and their associated microbiomes from lakes in Michigan, USA that vary in phosphorus content, which is the primary limiting nutrient in lakes. We found genomic changes among strains of Microcystis along this phosphorus gradient that indicated increased efficiency in the use of phosphorus and nitrogen. Intriguingly, we found that genotypes adapted to different nutrient environments co-occurred in phosphorus‐rich lakes. This co-occurrence may have critical implications for understanding how Microcystis blooms persist for many months, long after nutrients become depleted within lakes. Similar to previous findings in for example the human microbiome, we uncovered that the bacteria comprising the microbiomes of Microcystis varied in community composition but were more stable at the level of functional contributions to their hosts across the phosphorus gradient. Finally, while our work was mostly focused on unraveling the genomic underpinnings of nutrient adaptation, we also observed consequences of these differences in Microcystis genome and microbiome composition at a physiological level. In particular, when nutrients were provided in abundance, Microcystis (and its microbiome) that had evolved to thrive in low-phosphorus environments could not grow as rapidly as strains from high-phosphorus environments.
– Sara Jackrel, Postdoctoral Fellow, University of Michigan.
The green anole (Anolis carolinensis), also called the American chameleon due to its ability to change color, is a common species in South-East USA. It has been studied for decades to understand how reptiles adapt to their environment. Unlike other species of its genus, its range encompasses territories outside tropical climate, reaching the winter-exposed flanks of the Appalachians. The green anole colonized these colder regions from Florida in the last 300,000 years. We used DNA variation covering the whole genome and contrasted populations having recently colonized colder territories with the ones from tropical Florida. We compared multiple approaches to detect which segments in DNA sequences harbored variation compatible with selection. Since these signatures can also be produced by past demography, we took the latter into account to limit the detection of false positives. We then identified the most likely function of genes overlapping with candidate regions for selection, and observed that many of those were involved in exploratory behavior, immunity and response to cold. This suggests that the success of green anoles may have been due to changes in both physiology and behavioral shifts, a hypothesis that could be further tested experimentally.
– Yann Bourgeois and Stephane Boissinot
Bourgeois, Y., & Boissinot, S. (2019). Selection at behavioral, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer. Molecular Ecology. 2019. 28-15. 3523-3543