Strong Selective Pressure Research Articles

2020 Hindsight: Should evolutionary virologists have expected the unexpected during a pandemic?

2020 Hindsight: Should evolutionary virologists have expected the unexpected during a pandemic?

Ecogenomics and Adaptation Strategies of Southern Ocean Viral Communities.

ABSTRACTThe Southern Ocean (SO) represents up to one-fifth of the total carbon drawdown worldwide. Intense selective pressures (low temperature, high UV radiation, and strong seasonality) and physical isolation characterize the SO, serving as a “natural” laboratory for the study of ecogenomics and unique adaptations of endemic viral populations. Here, we report 2,416 novel viral genomes from the SO, obtained from newly sequenced viral metagenomes in combination with mining of publicly available data sets, which represents a 25% increase in the SO viral genomes reported to date. They comprised 567 viral clusters (defined as approximately genus-level groups), with 186 genera endemic to the SO, demonstrating that the SO viral community is predominantly constituted by a large pool of genetically divergent viral species from widespread viral families. The predicted proteome from SO viruses revealed that several protein clusters related to cold-shock-event responses and quorum-sensing mechanisms involved in the lysogenic-lytic cycle shift decision were under positive selection, which is ultimately important for fine adaptation of viral populations in response to the strong selective pressures of the SO. Finally, changes in the hydrophobicity patterns and amino acid frequencies suggested marked temperature-driven genetic selection of the SO viral proteome. Our data provide valuable insights into how viruses adapt and remain successful in this extreme polar marine environment.IMPORTANCE Viruses are the most abundant biologic entities in marine systems and strongly influence the microbial community composition and diversity. However, little is known about viral communities’ adaptation and diversification in the ocean. In this work, we take advantage of the geographical isolation and the intense selective pressures of the SO, to which viruses are exposed, to identify potential viral adaptations due to positive environmental selection and dispersal limitation. To that end, we recovered more than two thousand novel viral genomes, revealing a high degree of divergence in these SO endemic communities. Furthermore, we describe remarkable viral adaptations in amino acid frequencies and accessory proteins related to cold shock response and quorum sensing that allow them to thrive at lower temperatures. Consequently, our work greatly expands the understanding of the diversification of the viral communities of the SO and their particular adaptations to low temperatures.

Search for Selection Signatures Related to Trypanosomosis Tolerance in African Goats.

Livestock is heavily affected by trypanosomosis in Africa. Through strong selective pressure, several African indigenous breeds of cattle and small ruminants have acquired varying degrees of tolerance against this disease. In this study, we combined LFMM and PCAdapt for analyzing two datasets of goats from West-Central Africa and East Africa, respectively, both comprising breeds with different assumed levels of trypanotolerance. The objectives were (i) to identify molecular signatures of selection related to trypanotolerance; and (ii) to guide an optimal sampling for subsequent studies. From 33 identified signatures, 18 had been detected previously in the literature as being mainly associated with climatic adaptations. The most plausible signatures of trypanotolerance indicate the genes DIS3L2, COPS7B, PD5A, UBE2K, and UBR1. The last gene is of particular interest since previous literature has already identified E3-ubiquitin ligases as playing a decisive role in the immune response. For following-up on these findings, the West-Central African area appears particularly relevant because of (i) a clear parasitic load gradient related to a humidity gradient, and (ii) still restricted admixture levels between goat breeds. This study illustrates the importance of protecting local breeds, which have retained unique allelic combinations conferring their remarkable adaptations.

Antimicrobial Activity of Metals and Metalloids.

Competition shapes evolution. Toxic metals and metalloids have exerted selective pressure on life since the rise of the first organisms on the Earth, which has led to the evolution and acquisition of resistance mechanisms against them, as well as mechanisms to weaponize them. Microorganisms exploit antimicrobial metals and metalloids to gain competitive advantage over other members of microbial communities. This exerts a strong selective pressure that drives evolution of resistance. This review describes, with a focus on arsenic and copper, how microorganisms exploit metals and metalloids for predation and how metal- and metalloid-dependent predation may have been a driving force for evolution of microbial resistance against metals and metalloids.

Fungicide sensitivity of Clarireedia spp. isolates from golf courses in China

Dollar spot, caused by Clarireedia spp. (formerly Sclerotinia homoeocarpa), is a devastating turfgrass disease worldwide. Strong selection pressure imposed by continuous fungicide applications has caused the emergence of fungicide resistance in fungal populations. In this context, a total of 358 isolates of Clarireedia spp., collected from 25 locations in the north, east and south regions of China, were assayed for in vitro sensitivities to thiophanate-methyl, iprodione, propiconazole, and boscalid using discriminatory concentrations of 10 μg/mL, 1 μg/mL, 0.1 μg/mL and 10 μg/mL, respectively. Relative mycelial growth (RMG) was used to determine sensitivity or resistance based on comparison with baseline populations. A total of 18, 11 and 14 of the 25 locations exhibited significantly reduced sensitivity (P < 0.05) to propiconazole, boscalid and iprodione, respectively. Thirteen locations had isolates resistant to thiophanate-methyl while 81%, 67%, 63% and 62% of the isolates had reduced sensitivity to propiconazole, boscalid, iprodione and thiophanate-methy1, respectively. Of the 328 isolates with the history of fungicide use screened, 94% had reduced sensitivity to at least two fungicides. Isolates resistant to thiophanate-methyl had significantly higher EC50 values than sensitive isolates for propiconazole but not for boscalid. Low to highly significant correlations were observed between fungicide sensitivities for isolates from the 25 locations, the three regions, and for all isolates in total. Our findings suggest wide-spread cross-resistance to commonly employed fungicides to manage Clarireedia spp. throughout China and underscore the challenges for managing dollar spot.

Fluctuation and Re-Establishment of Aerobic Granules Properties during the Long-Term Operation Period with Low-Strength and Low C/N Ratio Wastewater

Long-term structure stability of aerobic granules is critical to maintaining stable wastewater treatment performance. In this study, granulation and long-term stability of sludge-treating synthetic wastewater with a low chemical oxygen demand to nitrogen (COD/N) ratio of 4:1 and COD concentration of 400 mg/L in anoxic-oxic conditions were investigated for over 300 days. Inoculated suspended sludge gradually transformed into granules-dominant sludge on day 80. Due to the improved sludge volume index after 30 min settling (SVI30), mixed liquor suspended solids (MLSS) reached 5.2 g/L on day 140. Without any external intervention or disturbance, aerobic granules started to disintegrate from day 140, causing the increase in SVI and the decrease in biomass concentration until day 210, with the average sludge size reduced to 243 µm. From day 210, granular sludge started to be re-established by re-granulation, and the average granule size increased to 500 µm on day 302. During these disintegration and re-granulation periods, there was no obvious difference in terms of COD removal and nitrification, but microbial species were found more diverse after the re-granulation, with Thauera and Sphingomonas dominant. Although there was no external intervention, the food to microorganisms ratio (F/M) varied significantly due to the changes in biomass concentration caused by strong selective pressure and the change of sludge-settling ability in the reactor. F/M ratios should be controlled between 0.3 and 1.0 gCOD/gSS·d to maintain the stable structure of granules to minimize the fluctuation of sludge properties under the conditions used in this study. Although aerobic granular sludge is able to re-establish itself after disintegration, controlling F/M ratios in a certain range would benefit long-term stability. The findings in this study are significant to deepen the understanding of granule stability with low-strength and low COD ratio wastewater and, thus, provide guidance for maintaining the long-term stability of granules.

Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice

WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identified prevalence of Group III WRKYs despite differences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that finely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversification of an important gene family under strong selective pressure for biotechnological improvements of the world’s most valued food crop.

Genomic Evolution of the Marine Bacterium Phaeobacter inhibens during Biofilm Growth.

Phaeobacter inhibens 2.10 is an effective biofilm former on marine surfaces and has the ability to outcompete other microorganisms, possibly due to the production of the plasmid-encoded secondary metabolite tropodithietic acid (TDA). P. inhibens 2.10 biofilms produce phenotypic variants with reduced competitiveness compared to the wild type. In the present study, we used longitudinal, genome-wide deep sequencing to uncover the genetic foundation that contributes to the emergent phenotypic diversity in P. inhibens 2.10 biofilm dispersants. Our results show that phenotypic variation is not due to the loss of the plasmid that carries the genes for TDA synthesis but instead show that P. inhibens 2.10 biofilm populations become rapidly enriched in single nucleotide variations in genes involved in the synthesis of TDA. While variants in genes previously linked to other phenotypes, such as lipopolysaccharide production (i.e., rfbA) and cellular persistence (i.e., metG), also appear to be selected for during biofilm dispersal, the number and consistency of variations found for genes involved in TDA production suggest that this metabolite imposes a burden on P. inhibens 2.10 cells. Our results indicate a strong selection pressure for the loss of TDA in monospecies biofilm populations and provide insight into how competition (or a lack thereof) in biofilms might shape genome evolution in bacteria. IMPORTANCE Biofilm formation and dispersal are important survival strategies for environmental bacteria. During biofilm dispersal, cells often display stable and heritable variants from the parental biofilm. Phaeobacter inhibens is an effective colonizer of marine surfaces, in which a subpopulation of its biofilm dispersal cells displays a noncompetitive phenotype. This study aimed to elucidate the genetic basis of these phenotypic changes. Despite the progress made to date in characterizing the dispersal variants in P. inhibens, little is understood about the underlying genetic changes that result in the development of the specific variants. Here, P. inhibens phenotypic variation was linked to single nucleotide polymorphisms (SNPs), in particular in genes affecting the competitive ability of P. inhibens, including genes related to the production of the antibiotic tropodithietic acid (TDA) and bacterial cell-cell communication (e.g., quorum sensing). This work is significant as it reveals how the biofilm lifestyle might shape genome evolution in a cosmopolitan bacterium.

Acoustic and visual stimuli combined promote stronger responses to aerial predation in fish.

Bird predation poses a strong selection pressure on fish. Since birds must enter the water to catch fish, a combination of visual and mechano-acoustic cues (multimodal) characterize an immediate attack, while single cues (unimodal) may represent less dangerous disturbances. We investigated whether fish could use this information to distinguish between non-threatening and dangerous events and adjust their antipredator response to the perceived level of risk. To do so, we investigated the antipredator behavior of the sulphur molly (Poecilia sulphuraria), a small freshwater fish which is almost exclusively preyed on by piscivorous birds in its endemic sulfide spring habitat. In a field survey, we confirmed that these fish frequently have to distinguish between disturbances stemming from attacking birds (multimodal) and those which pose no (immediate) threat such as bird overflights (unimodal). In a laboratory experiment, we then exposed fish to artificial visual and/or acoustic stimuli presented separately or combined. Sensitivity was high regardless of stimulus type and number (more than 96% of fish initiated diving), but fish dove deeper, faster, and for longer when both stimuli were available simultaneously. Based on the system’s high rates of bird activity, we argue that such an unselective dive initiation with subsequent fine-tuning of diving parameters in accordance to cue modality represents an optimal strategy for these fish to save energy necessary to respond to future attacks. Ultimately, our study shows that fish anticipate the imminent risk posed by disturbances linked to bird predation through integrating information from both visual and acoustic cues.

Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia

We lack a thorough understanding of the origin and maintenance of standing genetic variation that enables rapid evolutionary responses of natural populations. Whole genome sequencing of a resurrected Daphnia population shows that standing genetic variation in over 500 genes follows an evolutionary trajectory that parallels the pronounced and rapid adaptive evolution of multiple traits in response to predator-driven natural selection and its subsequent relaxation. Genetic variation carried by only five founding individuals from the regional genotype pool is shown to suffice at enabling the observed evolution. Our results provide insight on how natural populations can acquire the genomic variation, through colonization by a few regional genotypes, that fuels rapid evolution in response to strong selection pressures. While these evolutionary responses in our study population involved hundreds of genes, we observed no evidence of genetic erosion.

Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species.

The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses.

Integrative Studies of Sexual Selection in Manakins, a Clade of Charismatic Tropical Birds.

The neotropical manakins (family Pipridae) provide a great opportunity for integrative studies of sexual selection as nearly all of the 51 species are lek-breeding, an extreme form of polygyny, and highly sexually dimorphic both in appearance and behavior. Male courtship displays are often elaborate and include auditory cues, both vocal and mechanical, as well as visual elements. In addition, the displays are often extremely rapid, highly acrobatic, and, in some species, multiple males perform coordinated displays that form the basis of long-term coalitions. Male manakins also exhibit unique neuroendocrine, physiological, and anatomical adaptations to support the performance of these complex displays and the maintenance of their intricate social systems. The Manakin Genomics Research Coordination Network (Manakin RCN, https://www.manakinsrcn.org) has brought together researchers (many in this symposium and this issue) from across disciplines to address the implications of sexual selection on evolution, ecology, behavior, and physiology in manakins. The objective of this paper is to present some of the most pertinent and integrative manakin research as well as introducing the papers presented in this issue. The results discussed at the manakin symposium, part of the 2021 Society for Integrative and Comparative Biology Conference, highlight the remarkable genomic, behavioral, and physiological adaptations as well as the evolutionary causes and consequences of strong sexual selection pressures that are evident in manakins.

Optimizing long-acting acaricide use for integrated tick management of Rhipicephalus australis-infesting cattle in New Caledonia.

The tick Rhipicephalus australis, formerly known as Rhipicephalus microplus, is the most economically important ectoparasite of livestock in New Caledonia, affecting cattle health and production. Decades of control attempts based on the application of chemical acaricides have exerted a strong selective pressure on R. australis populations, some of which have evolved resistance to these treatments. Research to develop integrated tick control programs is now focused on decreasing applications of chemicals. This study reports the implementation of a method of pasture and herd management involving minimal strategic use of long-acting acaricides, here defined as those having substantial efficacy against larvae for several weeks. Diverse parameters concerning the utilization of long-acting acaricides in association with pasture and herd management on 21 New Caledonian farms over a 5-year period were analyzed to optimize their strategic use. Longer larval acaricidal effect was achieved with a commercial pour-on formulation of fluazuron than with a commercial injectable (subcutaneous) formulation containing 3.15% ivermectin. Pasture and herd management allowed an increase in the delay between a long-lasting acaricide application and the subsequent acaricide treatment from 11.0weeks to 17.7weeks. However, if ticks were detected and reported by producers on the day of a long-acting acaricide application, the delay to the following treatment was reduced from 18.5weeks to 11.2weeks. The impact of a long-acting acaricide treatment on larval populations in pastures was greatest with a stocking rate of 5 animals per hectare grazing during 1week. These results provide science-based evidence to cattle producers for adaptive integrated tick management in order to delay the development of acaricide resistance.

The future of immune checkpoint combinations with tumor-targeted small molecule drugs.

Immune-checkpoint blockade (ICB) has transformed the landscape of cancer treatment. However, there is much to understand around refractory or acquired resistance in patients in order to utilize ICB therapy to its full potential. In this perspective article, we discuss the opportunities and challenges that are emerging as our understanding of immuno-oncology resistance matures. Firstly, there has been remarkable progress made to understand the exquisite overlap between oncogenic and immune signaling pathways. Several cancer-signaling pathways are constitutively active in oncogenic settings and also play physiological roles in immune cell function. A growing number of precision oncology tumor-targeted drugs show remarkable immunogenic properties that might be harnessed with rational combination strategies. Secondly, we now understand that the immune system confers a strong selective pressure on tumors. Whilst this pressure can lead to novel tumor evolution and immune escape, there is a growing recognition of tumor-intrinsic dependencies that arise in immune pressured environments. Such dependencies provide a roadmap for novel tumor-intrinsic drug targets to alleviate ICB resistance. We anticipate that rational combinations with existing oncology drugs and a next wave of tumor-intrinsic drugs that specifically target immunological resistance will represent the next frontier of therapeutic opportunity.

Left High and Dry: Froth Nesting Allows Eggs of the Anuran Amphibian to Complete Embryogenesis in the Absence of Free-Standing Water

For amphibians that oviposit in temporary aquatic systems, there is a high risk of desiccation-induced offspring mortality when water evaporates prior to the completion of embryo or tadpole development. Such a strong selective pressure has led to the evolution of a variety of traits in reproducing females and their offspring to improve the odds of reproductive success when free-standing water is temporarily available. Herein, we describe an adaptive function of froth nesting in the Sandpaper Frog, Lechriodus fletcheri, as a possible maternal strategy for protecting embryos from the immediate risk of desiccating in highly ephemeral pools that frequently dry prior to hatching. Field observations revealed that embryos located near the core of nests remained alive and continued to develop for several days after becoming stranded out of water due to declining water levels, with embryo viability maintained long enough for additional rainfall to recharge pools and support hatching of tadpoles into water in some cases. In laboratory trials, the proportion of embryos surviving in nests exposed to desiccating conditions was positively correlated with nest volume, while the rate of water loss relative to nest mass declined, both of which are likely a function of reduced surface area relative to volume in larger nests. We suggest that the encapsulation of embryos within an aerated mucus shields them from desiccation by trapping moisture around their external surfaces. As embryos of L. fletcheri complete development rapidly, the ability for the froth nest to protect against desiccation for several days may allow embryogenesis to be completed largely out of water despite the larval phase not being terrestrial. These results suggest froth nesting has played an important role in facilitating this species' use of ephemeral habitats that most other amphibians with aquatic reproductive modes are incapable of exploiting.

Delineating the Functional Consequences of CEBPA Mutations in Acute Myeloid Leukaemia

CEBPA is a bZIP transcription factor mutated in approximately 10% of sporadic acute myeloid leukaemia (AML). In 50% of cases a single allele of CEBPA is mutated while in the other 50% both alleles are mutated. The majority of dm-CEBPA mutations occur with one allele mutated at the N terminal region (CEBPANterm) resulting in a frame-shift, and the other allele at the C terminus (CEBPACterm), leading to inframe indels in the bZIP/Leucine zipper region of the protein, presumably abrogating DNA binding. In wild-type conditions two CEBPA isoforms are translated; full length p42 in far greater amounts than p30, an N-terminal truncated isoform derived from an in frame internal initiating site.In addition to somatic mutations of CEBPA in AML, several kindreds have been described who carry germline mutations in CEBPANterm. This results in familial predisposition to AML. Such cases highlight a strong selective pressure to acquire CEBPA CEBPACterm, as not only do the vast majority of patients acquire such mutations at presentation with AML, but several have shown distinct CEBPACterm mutations at relapse. CEBPACterm are often considered null with respect to DNA binding capacity, implying that CEBPA functional activity as a transcription factor arises from its p30 isoform in cases with mutations in both alleles.To model the steps leading to leukemia development in CEBPA-mutated AML we used TALENs to generate zebrafish carrying analogous CEBPANterm (K75fs; cebpaNterm) and CEBPACterm (K243del243-246, cebpaCterm). To assess the affect of these mutation (alone or in combination) on developmental myelopoiesis we used Sudan Black (SB) staining at 5 days post fertilization (dpf). cebpaNterm/Nterm mutants, showed a complete absence of SB+ cells by 5dpf, while cebpaNterm/+ mutants had modestly, but statistically significantly reduced numbers (A). To further delineate the stage in myeloid differentiation that the observed defect arose we used flow cytometry of cebpaNterm mutants carrying the Tg(Lys:mCherry) and Tg(pu.1:GFP) transgenes . At 5 dpf we observed that both pu.1 (early myeloid) and lysC (later myeloid) expressing cells could be seen in all genotypes. Nonetheless, we observed that the earliest myeloid cells (pu.1-GFP+/lysC mCherry-) and intermediate differentiation stage populations (pu.1-GFP+/lysC mCherry+) both showed dose dependent reduction in numbers with acquisition of cebpaNterm mutation. This data suggests that cebpaNterm mutation leads to a defect in myeloid differentiation in a allele dependent manner.cebpaCterm mutants notably showed a distinct phenotype. Whilst cebpaCterm/Cterm showed severely reduced numbers of SB+ cells, in contrast to cebpaNterm/Nterm they were not completely absent (B). Furthermore, the cebpaCterm/+ mutants showed a significant increase in SB+ cells, in striking contrast to the reduction in cebpaNterm/+ (B). This suggests secondary CEBPACterm could convey a proliferation advantage to overcome the deficit in mature myeloid numbers induced by an initiating CEBPANterm. Analysis of cebpaCterm/+ and cebpaNterm/+ mutantscarrying Tg(Lys:mCherry) show that the proportion of myeloid cells expressing the brightest mCherry are markedly reduced in cebpaCterm/+ mutants alone compared to WT siblings. Further, SB stains in cebpaCterm/+ and cebpaCterm/Cterm also show qualitative less intense and smaller granules suggesting defective granule formation in these mutants.We then went on to determine the effects of combined mutation of cebpaCterm and cebpaNterm, since this is the most commonly observed genotype in patients. SB staining at 5dpf in cebpaNterm/Cterm showed a spectrum of phenotypes (C). These range from absent (upper) or severely reduced (middle) SB+ cells as in cebpaNterm or cebpaCterm respectively, or a of near normal numbers but with abnormal localization in the caudal haematopoietic tissue (fetal liver equivalent) (lower).In conclusion we have generated zebrafish that model Cebpa N and C terminal mutations observed in AML and demonstrate differential and combined effects on developmental haematopoeisis arising from these 2 alleles. Our data suggest that mechanisms to overcome the myeloid differentiation defect resulting from CebpaNterm/+ may underpin the selective pressure driving mutations in the C term of the other Cebpa allele, which phenotypically compensate for this. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Integrating genetics, physiology and morphology to study desert adaptation in a lizard species.

Integration of multiple approaches is key to understand the evolutionary processes of local adaptation and speciation. Reptiles have successfully colonized desert environments, that is, extreme and arid conditions that constitute a strong selective pressure on organisms. Here, we studied genomic, physiological and morphological variations of the lizard Liolaemus fuscus to detect adaptations to the Atacama Desert. By comparing populations of L. fuscus inhabiting the Atacama Desert with populations from the Mediterranean forests from central Chile, we aimed at characterizing features related to desert adaptation. We combined ddRAD sequencing with physiological (evaporative water loss, metabolic rate and selected temperature) and morphological (linear and geometric morphometrics) measurements. We integrated the genomic and phenotypic data using redundancy analyses. Results showed strong genetic divergence, along with a high number of fixed loci between desert and forest populations. Analyses detected 110 fixed and 30 outlier loci located within genes, from which 43 were in coding regions, and 12 presented non-synonymous mutations. The candidate genes were associated with cellular membrane and development. Desert lizards presented lower evaporative water loss than those from the forest. Morphological data showed that desert lizards had smaller body size, different allometry, larger eyeballs and more dorsoventrally compressed heads. Our results suggest incipient speciation between desert and forest populations. The adaptive signal must be cautiously interpreted since genetic drift could also contribute to the divergence pattern. Nonetheless, we propose water and resource availability, and changes in habitat structure, as the most relevant challenges for desert reptiles. This study provides insights of the mechanisms that allow speciation as well as desert adaptation in reptiles at multiple levels, and highlights the benefit of integrating independent evidence.

Genome Evolution of Two Genetically Homogeneous Infectious Bursal Disease Virus Strains During Passages in vitro and ex vivo in the Presence of a Mutagenic Nucleoside Analog.

The avibirnavirus infectious bursal disease virus (IBDV) is responsible for a highly contagious and sometimes lethal disease of chickens (Gallus gallus). IBDV genetic variation is well-described for both field and live-attenuated vaccine strains, however, the dynamics and selection pressures behind this genetic evolution remain poorly documented. Here, genetically homogeneous virus stocks were generated using reverse genetics for a very virulent strain, rvv, and a vaccine-related strain, rCu-1. These viruses were serially passaged at controlled multiplicities of infection in several biological systems, including primary chickens B cells, the main cell type targeted by IBDV in vivo. Passages were also performed in the absence or presence of a strong selective pressure using the antiviral nucleoside analog 7-deaza-2′-C-methyladenosine (7DMA). Next Generation Sequencing (NGS) of viral genomes after the last passage in each biological system revealed that (i) a higher viral diversity was generated in segment A than in segment B, regardless 7DMA treatment and viral strain, (ii) diversity in segment B was increased by 7DMA treatment in both viruses, (iii) passaging of IBDV in primary chicken B cells, regardless of 7DMA treatment, did not select cell-culture adapted variants of rvv, preserving its capsid protein (VP2) properties, (iv) mutations in coding and non-coding regions of rCu-1 segment A could potentially associate to higher viral fitness, and (v) a specific selection, upon 7DMA addition, of a Thr329Ala substitution occurred in the viral polymerase VP1. The latter change, together with Ala270Thr change in VP2, proved to be associated with viral attenuation in vivo. These results identify genome sequences that are important for IBDV evolution in response to selection pressures. Such information will help tailor better strategies for controlling IBDV infection in chickens.

Validation of predicted anonymous proteins simply using Fisher's exact test.

Genomes sequencing has become the primary (and often the sole) experimental method to characterize newly discovered organisms, in particular from the microbial world (bacteria, archaea, viruses). This generates an ever increasing number of predicted proteins the existence of which is unwarranted, in particular among those without homolog in model organisms. As a last resort, the computation of the selection pressure from pairwise alignments of the corresponding 'Open Reading Frames' (ORFs) can be used to validate their existences. However, this approach is error-prone, as not usually associated with a significance test. We introduce the use of the straightforward Fisher's exact test as a postprocessing of the results provided by the popular CODEML sequence comparison software. The respective rates of nucleotide changes at the nonsynonymous versus synonymous position (as determined by CODEML) are turned into entries into a 2 × 2 contingency table, the probability of which is computed under the Null hypothesis that they should not behave differently if the ORFs do not encode actual proteins. Using the genome sequences of two recently isolated giant viruses, we show that strong negative selection pressures do not always provide a solid argument in favor of the existence of proteins.

Comparative analysis of mite genomes reveals positive selection for diet adaptation

Diet is a powerful evolutionary force for species adaptation and diversification. Acari is one of the most abundant clades of Arachnida, exhibiting diverse dietary types, while the underlying genetic adaptive mechanisms are not fully understood. Based on comparative analyses of 15 Acari genomes, we found genetic bases for three specialized diets. Herbivores experienced stronger selection pressure than other groups; the olfactory genes and gene families involving metabolizing toxins showed strong adaptive signals. Genes and gene families related to anticoagulation, detoxification, and haemoglobin digestion were found to be under strong selection pressure or significantly expanded in the blood-feeding species. Lipid metabolism genes have a faster evolutionary rate and been subjected to greater selection pressures in fat-feeding species; one positively selected site in the fatty-acid amide hydrolases 2 gene was identified. Our research provides a new perspective for the evolution of Acari and offers potential target loci for novel pesticide development.