PaperPlayer biorxiv evolutionary biology

Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.249045v1?rss=1

Authors: Bao, Y.-J., Qiu, J., Rodriguez, F., Qiu, H.-J.

Abstract:

African swine fever virus (ASFV) is a lethal disease agent that causes high mortality in swine population and devastating loss in swine industries. The development of efficacious vaccines has been hindered by the knowledge gap in genetic properties of ASFV and the interface of virus-host interactions. In this study, we performed a genetic study of ASFV aiming to profile the variation landscape and identify genetic factors with signatures of positive selection and relevance to virus-host interactions. To achieve this goal, we developed a new tool "SweepCluster" for systematic identification of selective sweep. Our data reveals a high level of genetic variability of ASFV shaped by both diversifying selection and selective sweep. The selection signatures are widely distributed across the genome with the diversifying selection falling within 29 genes and selection sweep within 25 genes. Further examination of the structure properties reveals the link of the selection signatures with virus-host interactions. Specifically, we discovered a site at 157th of the antigen protein EP402R under diversifying selection located in the cytotoxic T-cell epitope involved in the serotype-specific T-cell response. Moreover, we reported 24 novel candidate genes with relevance to virus-host interactions. By integrating the candidate genes with selection signatures into a unified framework of interactions between ASFV and hosts, we showed that those genes are involved in multiple processes of host immune evasion and virus life cycles, and may play crucial roles in circumventing host defense systems and enhancing adaptive fitness.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.249359v1?rss=1

Authors: Bobay, L.-M., Buton, A. J.

Abstract:

Homologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized in Escherichia coli and analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species: E. coli, Haemophilus influenzae, Bacillus subtilis, Lactococcus lactis and Staphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif of E. coli in 85 species of Proteobacteria. Most Chi motifs were detected in Enterobacteriaceae and this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.249557v1?rss=1

Authors: Chavarie, L., Voelker, S., Hansen, M., Bronte, C., Muir, A., Zimmerman, M., Krueger, c.

Abstract:

Pathways through which phenotypic variation arises among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. To address biological complexity below the species level, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr ecotypes in Rush Lake, USA. We found a rapid phenotypic shift in body and head shape within a decade. The magnitude and direction of the observed phenotypic change was consistent in both ecotypes, which suggests similar pathways caused the temporal variation over time. Over the same time period, annual growth increments declined for both lake charr ecotypes and corresponded with a consistent phenotypic shift of each ecotype. Despite ecotype-specific annual growth changes in response to winter conditions, the observed annual growth shift for both ecotypes was linked, to some degree, with variation in the environment. Particularly, a declining trend in regional cloud cover was associated with an increase of early stage (age 1-3) annual growth for lake charr of Rush Lake. Underlying mechanisms causing reduced growth rates and constrained morphological modulation are not fully understood. An improved knowledge of the biology hidden within the expression of phenotypic variation promises to clarify our understanding of temporal morphological diversity and instability.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.249599v1?rss=1

Authors: Gross, J., Avrani, S., Katz, S., Hershberg, R.

Abstract:

Escherichia coli and many other bacterial species, which are incapable of sporulation, can nevertheless survive within resource exhausted media by entering a state termed long-term stationary phase (LTSP). We have previously shown that E. coli populations adapt genetically under LTSP in an extremely convergent manner. Here we examine how the dynamics of LTSP genetic adaptation are influenced by varying a single parameter of the experiment - culture volume. We find that culture volume affects survival under LTSP, with viable counts decreasing as volumes increase. Across all volumes, mutations accumulate with time, and the majority of mutations accumulated demonstrate signals of being adaptive. However, positive selection appears to affect mutation accumulation more strongly at higher, compared to lower volumes. Finally, we find that several similar genes are likely involved in adaptation across volumes. However, the specific mutations within these genes that contribute to adaptation can vary in a consistent manner. Combined, our results demonstrate how varying a single parameter of an evolutionary experiment can substantially influence the dynamics of observed adaptation.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.249128v1?rss=1

Authors: Amson, E., Bibi, F.

Abstract:

The skeleton is involved in most aspects of vertebrate life history. Previous macroevolutionary analyses have shown that structural, historical, and functional factors influence the gross morphology of bone. The inner structure of bone has, however, received comparatively little attention. Here we address this gap in our understanding of vertebrate evolution by quantifying bone structure in appendicular and axial elements (humerus and mid-lumbar vertebra) across therian mammals (placentals + marsupials). Our sampling captures all transitions to aerial, fully aquatic, and subterranean lifestyles in extant mammal clades. We found that mammalian inner bone structure is highly disparate. We show that vertebral structure mostly correlates with body size, but not lifestyle, while the opposite is true for humeral structure. The latter also shows a high degree of convergence among the clades that have acquired specialised lifestyles. Our results suggest that radically different extrinsic constraints can apply to bone structure in different skeletal elements.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.248328v1?rss=1

Authors: PAPADOPULOS, A. S. T., Helmstetter, A. J., Osborne, O. G., Comeault, A. A., Wood, D. P., Straw, E. A., Mason, L. D., Fay, M. F., Parker, J., Dunning, L. T., Foote, A. D., Smith, R. J., Lighten, J.

Abstract:

The impact of human mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, species' capacity to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonised isolated, disused mines with phytotoxic, zinc-contaminated soils. Here, we found that rapid parallel adaptation to anthropogenic pollution has taken place without geneflow spreading adaptive alleles between populations of the mine ecotype. Across replicate ecotype pairs, we identified shared targets of selection with functions linked to physiological differences between the ecotypes, although the genetic response is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.13.250415v1?rss=1

Authors: Grant, N. A., Abdel Magid, A., Franklin, J., Dufour, Y. S., Lenski, R.

Abstract:

Bacteria adopt a wide variety of sizes and shapes, with many species exhibiting stereotypical morphologies. How morphology changes, and over what timescales, is less clear. Previous work examining cell morphology in an experiment with Escherichia coli showed that populations evolved larger cells and, in some cases, cells that were less rod-like. That experiment has now run for over two more decades. Meanwhile, genome sequence data are available for these populations, and new computational methods enable high-throughput microscopic analyses. Here, we measured stationary-phase cell volumes for the ancestor and 12 populations at 2,000, 10,000, and 50,000 generations, including measurements during exponential growth at the last timepoint. We measured the distribution of cell volumes for each sample using a Coulter counter and microscopy, the latter of which also provided data on cell shape. Our data confirm the trend toward larger cells, while also revealing substantial variation in size and shape across replicate populations. Most populations first evolved wider cells, but later reverted to the ancestral length-to-width ratio. All but one population evolved mutations in rod-shape maintenance genes. We also observed many ghost-like cells in the only population that evolved the novel ability to grow on citrate, supporting the hypothesis that this lineage struggles with maintaining balanced growth. Lastly, we show that cell size and fitness remain correlated across 50,000 generations. Our results suggest larger cells are beneficial in the experimental environment, while the reversion toward ancestral length-to-width ratios suggests partial compensation for the less favorable surface area-to-volume ratios of the evolved cells.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.246108v1?rss=1

Authors: Lopes, F., Oliveira, L. R., Kessler, A., Crespo, E., Cardenas-Alayza, S., Majluf, P., Sepulveda, M., Brownell, R. L., Franco-Trecu, V., Paez-Rosas, D., Chaves, J., Loch, C., Robertson, B., Acevedo-Whitehouse, K., Elorriaga-Verplancken, F. R., Kirkman, S. P., Peart, C. R., Wolf, J. B. W., Bonatto, S. L.

Abstract:

The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance pointing at strong gene-tree species tree discordance. Divergence times in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events occurred. Here we used high-coverage whole genome-wide sequencing for 14 of the 15 species of Otariidae to elucidate the phylogeny of the family and its bearing on the taxonomy and biogeographical history. Despite extreme topological discordance among gene trees, we found a fully supported species tree that agrees with the few well-accepted relationships and establishes monophyly of the genus Arctocephalus. Our data support a relatively recent trans-hemispheric dispersal at the base of a southern clade, which rapidly diversified into six major lineages between 3 to 2.5 Mya. Otaria diverged first, followed by Phocarctos and then four major lineages within Arctocephalus. However, we found Zalophus to be non-monophyletic, with California (Z. californianus) and Steller sea lions (Eumetopias jubatus) grouping closer than the Galapagos sea lion (Z. wollebaeki) with evidence for introgression between the two genera. Overall, the high degree of genealogical discordance was best explained by incomplete lineage sorting resulting from quasi-simultaneous speciation within the southern clade with introgresssion playing a subordinate role in explaining the incongruence among and within prior phylogenetic studies of the family.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.11.247403v1?rss=1

Authors: Singh, B., Kumar, A., Uniyal, V. P., GUPTA, S. K.

Abstract:

We investigated the phylogeographic pattern of red muntjac across its distribution range, intending to address the presence of distinct lineages from Northwest India. The Complete mitogenome analysis revealed that India holds three mitochondrial lineages of red muntjac, whereas four were identified from its entire distribution range: Himalayan red muntjac (M. (m.) aureus), Northern red muntjac (M. vaginalis), Srilankan and Western Ghat India (M. malabaricus) and Southern red muntjac (M. muntjak) from Sundaland. The newly identified Himalayan red muntjac found in the Northwestern part of India, which was previously described based on their morphological differences. Estimates of the divergence dating indicate that the Northwest and Northern lineage split during the late Pleistocene approximately 0.83 Myr (CI95%:0.53 to 1.26), which is the younger lineages, whereas M. malabaricus is the most primitive lineage among all the red muntjac. Microsatellite results also supported the mitochondrial data and evident the presence of three distinct genetic clusters within India. The pronounced climate fluctuation during the Quaternary period was considered as a critical factor influencing the current spatial distribution of forest-dwelling species that restricted themselves in northwest areas. Based on molecular data, this study provided evidence of a new lineage within the red muntjac group from India that required to be managed as an evolutionary significant unit (ESUs). It highlighted a need for the taxonomic revision of Himalayan red muntjac (M. (m.) aureus) and also suggested its conservation status under IUCN Red List.

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Link to bioRxiv paper:

http://biorxiv.org/cgi/content/short/2020.08.12.247718v1?rss=1

Authors: Liu, S., DECROOCQ, S., Harte, E., Tricon, D., Chague, A., Balakishiyeva, G., Kostritsyna, T., Turdiev, T., Fischer Le Saux, M., Dallot, S., GIRAUD, T., DECROOCQ, V.

Abstract:

In-depth characterization of the genetic diversity and population structure of wild relatives of crops is of paramount importance for genetic improvement and biodiversity conservation, and is particularly crucial when the wild relatives of crops are endangered. In this study, we therefore sampled the Alpine plum (Briancon apricot) Prunus brigantina Vill. across its natural distribution in the French Alps, where its populations are severely fragmented and its population size strongly impacted by humans. We analysed 71 wild P. brigantina samples with 34 nuclear markers and studied their genetic diversity and population structure, with the aim to inform in situ conservation measures and build a core collection for long-term ex-situ conservation. We also examined the genetic relationships of P. brigantina with other species in the Prunophora subgenus, encompassing the Prunus (Eurasian plums), Prunocerasus (North-American plums) and Armeniaca (apricots) sections, to check its current taxonomy. We detected a moderate genetic diversity in P. brigantina and a Bayesian model-based clustering approach revealed the existence of three genetically differentiated clusters, endemic to three geographical regions in the Alps, which will be important for in situ conservation measures. Based on genetic diversity and population structure analyses, a subset of 36 accessions were selected for ex-situ conservation in a core collection that encompasses the whole detected P. brigantina allelic diversity. Using a dataset of cultivated apricots and wild cherry plums (P. cerasifera) genotyped with the same markers, we detected gene flow neither with European P. armeniaca cultivars nor with diploid plums. In contrast with previous studies, dendrograms and networks placed P. brigantina closer to Armeniaca species than to Prunus species. Our results thus confirm the classification of P. brigantina within the Armeniaca section; it also illustrates the importance of the sampling size and design in phylogenetic studies

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