Institute of Evolutionary Biology

Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (> 18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.

Public health researchers employ quasi-experimental methods (QEM) to evaluate the effects of policies. Whilst some policies are designed to improve (health) equity, others may intentionally or unintentionally have detrimental effects on disadvantaged populations. We thus sought to investigate how health equity is addressed in policy evaluations which employ QEM. We conducted a content analysis on studies sourced from a scoping review. We drew a random sample of 350 records identified in systematic database searches in Medline, EMBASE, and EconLit (December 2022). Studies that employed QEM labels and examined public policies implemented in the WHO European region were included. We extracted data on study design, policies, and populations; assessed whether outcomes were examined in population sub-groups (as defined by PROGRESS-Plus criteria); and analysed discussion sections for equity-related conclusions. We included 59 studies, of which 39 (66.1%) studies considered health equity—albeit to variable depth. Twenty-five studies were focused exclusively on examining policy outcomes in a disadvantaged population (42.4%), of which 19 studies evaluated policies that targeted disadvantaged groups (e.g. minimum wage, social housing policies). Outcomes were stratified for one or more sub-populations in 22 studies (37.3%), most commonly for gender (n = 15, 25.4%) and a measure of socio-economic status (n = 13, 22%), particularly income and employment. Equity-related results and implications were discussed in 24 studies. While policy evaluations employing QEM have considerable value for informing decision-making in public health and other sectors that influence health, their potential to investigate equity impacts is currently not harnessed.

Genome-wide premortem DNA methylation patterns can be computationally reconstructed from high-coverage DNA sequences of ancient samples. Because DNA methylation is more conserved across species than across tissues, and ancient DNA is typically extracted from bones and teeth, previous works utilizing ancient DNA methylation maps focused on studying evolutionary changes in the skeletal system. Here we suggest that DNA methylation patterns in one tissue may, under certain conditions, be informative on DNA methylation patterns in other tissues of the same individual. Using the fact that tissue-specific DNA methylation builds up during embryonic development, we identified the conditions that allow for such cross-tissue inference and devised an algorithm that carries it out. We trained the algorithm on methylation data from extant species and reached high precisions of up to 0.92 for validation datasets. We then used the algorithm on archaic humans, and identified more than 1,850 positions for which we were able to observe differential DNA methylation in prefrontal cortex neurons. These positions are linked to hundreds of genes, many of which are involved in neural functions such as structural and developmental processes. Six positions are located in the neuroblastoma breaking point family (NBPF) gene family, which probably played a role in human brain evolution. The algorithm we present here allows for the examination of epigenetic changes in tissues and cell types that are absent from the palaeontological record, and therefore provides new ways to study the evolutionary impacts of epigenetic changes.

The symbiosis between corals and dinoflagellate algae is disrupted by heat stress, leading to bleaching. Recurring bleaching events, driven by the climate crisis, are causing massive coral mortality and threatening reefs worldwide. Despite its planetary scale impact, bleaching occurs at the cellular level. While much is known about the physiological and genomic responses of corals to bleaching, our understanding of it at the cellular level remains limited. Using single-cell transcriptomics, we show that individual coral and symbiont cells respond differently to thermal stress. In heat stress experiments with the coral Orbicella faveolata , hosting two co-dominant algal symbionts, we found that calicoblastic cells and cnidocytes were particularly susceptible, with nitrogen metabolism disrupted across all cell types. We also provide the first evidence of differing transcriptomic responses between symbionts with varying heat tolerances within the same coral host. Furthermore, we discovered that symbionts suppress the expression of heat stress related genes of their host cells. These findings reveal that coral cellular responses to bleaching are more complex and varied than previously thought. This study marks a starting point toward understanding the cellular dynamics of coral holobionts, shedding light on the mechanisms behind symbiosis breakdown, coral mortality, and ultimately, reef decline.

Multiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution‐based screens to facilitate gene function prediction. Several PhyKIT functions that streamline multiple sequence alignment and phylogenetic processing—such as renaming FASTA entries or tree tips—are also discussed. These protocols demonstrate how simple command‐line operations in the unified framework of PhyKIT facilitate diverse phylogenomic data analysis and processing, from supermatrix construction and diagnosis to gaining clues about gene function. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1 : Installing PhyKIT and syntax for usage Basic Protocol 2 : Constructing a phylogenomic supermatrix Basic Protocol 3 : Detecting anomalies in orthology relationships Basic Protocol 4 : Quantifying biases in phylogenomic data matrices and related measures Basic Protocol 5 : Identifying polytomies Basic Protocol 6 : Assessing gene‐gene coevolution as a genetic screen

Reverse-transcribing animal DNA viruses include the hepadnaviruses, a well-characterized family of small enveloped viruses that infect vertebrates but also a sister group of nonenveloped viruses more recently discovered in fish and termed the nackednaviruses. Here, we describe the complete sequence of a virus found in the feces of an insectivorous bat, which encodes a core protein and a reverse transcriptase but no envelope protein. A database search identified a viral sequence from a permafrost sample as its closest relative. The two viruses form a cluster that occupies a basal phylogenetic position relative to hepadnaviruses and nackednaviruses, with an estimated divergence time of 500 My. These findings may lead to the definition of a “proto-nackednavirus” family and support the hypothesis that the ancestors of hepadnaviruses were nonenveloped.

Objectives To assess the short term temporal variations in suicide risk related to the day of the week and national holidays in multiple countries. Design Multicountry, two stage, time series design. Setting Data from 740 locations in 26 countries and territories, with overlapping periods between 1971 and 2019, collected from the Multi-city Multi-country Collaborative Research Network database. Participants All suicides were registered in these locations during the study period (overall 1 701 286 cases). Main outcome measures Daily suicide mortality. Results Mondays had peak suicide risk during weekdays (Monday-Friday) across all countries, with relative risks (reference: Wednesday) ranging from 1.02 (95% confidence interval (CI) 0.95 to 1.10) in Costa Rica to 1.17 (1.09 to 1.25) in Chile. Suicide risks were lowest on Saturdays or Sundays in many countries in North America, Asia, and Europe. However, the risk increased during weekends in South and Central American countries, Finland, and South Africa. Additionally, evidence suggested strong increases in suicide risk on New Year’s day in most countries with relative risks ranging from 0.93 (95% CI 0.75 to 1.14) in Japan to 1.93 (1.31 to 2.85) in Chile, whereas the evidence on Christmas day was weak. Suicide risk was associated with a weak decrease on other national holidays, except for Central and South American countries, where the risk generally increased one or two days after these holidays. Conclusions Suicide risk was highest on Mondays and increased on New Year’s day in most countries. However, the risk of suicide on weekends and Christmas varied by country and territory. The results of this study can help to better understand the short term variations in suicide risks and define suicide prevention action plans and awareness campaigns.

Recognizing the influence of pathogen diversity on infection dynamics is crucial for mitigating emerging infectious diseases. Characterising such diversity is often complex, for instance when multiple pathogen variants exist that interact differently with the environment and host. Here, we explore genotypic and phenotypic variation of Batrachochytrium salamandrivorans (Bsal), an emerging fungal pathogen that is driving declines among an increasing number of European amphibian species. For thirteen isolates, spanning most of the known temporal and geographical Bsal range in Europe, we mapped phenotypic diversity through numerous measurements that describe varying reproductive rates in vitro across a range of temperatures. Bsal isolates are revealed to have different thermal optima and tolerances, with phenotypic variation correlating with genomic diversity. Using a mechanistic niche model of the fire salamander (Salamandra salamandra) as an example, we illustrate how host steady-state body temperature and Bsal thermal range variation may influence pathogen growth through space and time across Europe. Our combined findings show how the identity of emergent pathogen variants may strongly influence when and which host populations are most at risk.

Understanding the evolution of chromatin conformation among species is fundamental to elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly distant loci regulate gene function in species-specific patterns, affecting genome function, evolution, and, ultimately, speciation. Yet, data from nonmodel organisms are scarce. To capture the macroevolutionary diversity of vertebrate chromatin conformation, here we generate de novo genome assemblies for two cryptodiran (hidden-neck) turtles via Illumina sequencing, chromosome conformation capture, and RNA-seq: Apalone spinifera (ZZ/ZW, 2 n = 66) and Staurotypus triporcatus (XX/XY, 2 n = 54). We detected differences in the three-dimensional (3D) chromatin structure in turtles compared to other amniotes beyond the fusion/fission events detected in the linear genomes. Namely, whole-genome comparisons revealed distinct trends of chromosome rearrangements in turtles: (1) a low rate of genome reshuffling in Apalone (Trionychidae) whose karyotype is highly conserved when compared to chicken (likely ancestral for turtles), and (2) a moderate rate of fusions/fissions in Staurotypus (Kinosternidae) and Trachemys scripta (Emydidae). Furthermore, we identified a chromosome folding pattern that enables “centromere–telomere interactions” previously undetected in turtles. The combined turtle pattern of “centromere–telomere interactions” (discovered here) plus “centromere clustering” (previously reported in sauropsids) is novel for amniotes and it counters previous hypotheses about amniote 3D chromatin structure. We hypothesize that the divergent pattern found in turtles originated from an amniote ancestral state defined by a nuclear configuration with extensive associations among microchromosomes that were preserved upon the reshuffling of the linear genome.

Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam’s famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.

Background Substantial discoveries during the past century have revealed that transposable elements (TEs) can play a crucial role in genome evolution by affecting gene expression and inducing genetic rearrangements, among other molecular and structural effects. Yet, our knowledge on the role of TEs in adaptation to extreme climates is still at its infancy. The availability of long-read sequencing has opened up the possibility to identify and study potential functional effects of TEs with higher precision. In this work, we used Drosophila montana as a model for cold-adapted organisms to study the association between TEs and adaptation to harsh climates. Results Using the PacBio long-read sequencing technique, we de novo identified and manually curated TE sequences in five Drosophila montana genomes from eco-geographically distinct populations. We identified 489 new TE consensus sequences which represented 92% of the total TE consensus in D. montana. Overall, 11–13% of the D. montana genome is occupied by TEs, which as expected are non-randomly distributed across the genome. We identified five potentially active TE families, most of them from the retrotransposon class of TEs. Additionally, we found TEs present in the five analyzed genomes that were located nearby previously identified cold tolerant genes. Some of these TEs contain promoter elements and transcription binding sites. Finally, we detected TEs nearby fixed and polymorphic inversion breakpoints. Conclusions Our research revealed a significant number of newly identified TE consensus sequences in the genome of D. montana, suggesting that non-model species should be studied to get a comprehensive view of the TE repertoire in Drosophila species and beyond. Genome annotations with the new D. montana library allowed us to identify TEs located nearby cold tolerant genes, and present at high population frequencies, that contain regulatory regions and are thus good candidates to play a role in D. montana cold stress response. Finally, our annotations also allow us to identify for the first time TEs present in the breakpoints of three D. montana inversions.

The Diphyllatea (CRuMs) are heterotrophic protists currently divided into three distinct clades (Diphy I–III). Diphy I are biflagellates in the genus Diphylleia , whereas Diphy II and III represent cryptic clades comprising Collodictyon ‐type quadriflagellates that were recently distinguished based on rRNA gene phylogenies. Here, we isolated Diphyllatea from freshwater crater lakes on two South Pacific islands and generated high‐quality transcriptomes from species representing each clade, including the first transcriptomic data from Diphy III. Phylogenomic analyses support the separation of Diphy II and III, while transcriptome completeness highlights the utility of these data for future studies. Lastly, we discuss the biogeography and ecology of Diphyllatea on these remote islands.

Modification of guanosine to N⁷-methylguanosine (m⁷G) in the variable loop region of tRNA is catalyzed by the METTL1/WDR4 heterodimer and stabilizes target tRNA. Here, we reveal essential functions of Mettl1 in Drosophila fertility. Knockout of Mettl1 (Mettl1-KO) causes no major effect on the development of non-gonadal tissues, but abolishes the production of elongated spermatids and mature sperm, which is fully rescued by expression of a Mettl1-transgene, but not a catalytic-dead Mettl1 transgene. This demonstrates that Mettl1-dependent m⁷G is required for spermatogenesis. Mettl1-KO results in a loss of m⁷G modification on a subset of tRNAs and decreased tRNA abundance. Ribosome profiling shows that Mettl1-KO led to ribosomes stalling at codons decoded by tRNAs that were reduced in abundance. Mettl1-KO also significantly reduces the translation efficiency of genes involved in elongated spermatid formation and sperm stability. Germ cell-specific expression of Mettl1 rescues disrupted m⁷G tRNA modification and tRNA abundance in Mettl1-KO testes but not in non-gonadal tissues. Ribosome stalling is much less detectable in non-gonadal tissues than in Mettl1-KO testes. These findings reveal a developmental role for m⁷G tRNA modification and indicate that m⁷G modification-dependent tRNA abundance differs among tissues.

Background Emerging zoonotic diseases arise from cross-species transmission events between wild or domesticated animals and humans, with bats being one of the major reservoirs of zoonotic viruses. Viral metagenomics has led to the discovery of many viruses, but efforts have mainly been focused on some areas of the world and on certain viral families. Methods We set out to describe full-length genomes of new picorna-like viruses by collecting feces from hundreds of bats captured in different regions of Spain. Viral sequences were obtained by high-throughput Illumina sequencing and analyzed phylogenetically to classify them in the context of known viruses. Linear discriminant analysis (LDA) was performed to infer likely hosts based on genome composition. Results We found five complete or nearly complete genomes belonging to the family Picornaviridae, including a new species of the subfamily Ensavirinae. LDA suggested that these were true vertebrate viruses, rather than viruses from the bat diet. Some of these viruses were related to picornaviruses previously found in other bat species from distant geographical regions. We also found a calhevirus genome that most likely belongs to a proposed new family within the order Picornavirales, and for which genome composition analysis suggested a plant host. Conclusions Our findings describe new picorna-like viral species and variants circulating in the Iberian Peninsula, illustrate the wide geographical distribution and interspecies transmissibility of picornaviruses, and suggest new hosts for calheviruses.

1. Temporary ponds are small-sized limnic systems that dry periodically. The length of the wet phase defines the hydroregime and determines community assembly in temporary ponds. Zooplankton species have adapted to desiccation by adopting some dormant strategies, such as the formation of resting stages. Hatching from resting stages is a source of recolonization after drought events and the composition of hatching taxa is also influenced by hydroregime. We compared metacommunity structures and composition of the dormant sub-community (resting stages); the pioneer active sub-community (fauna present immediately after inundation of ponds); and the cumulative active sub-community (fauna present at the initial, middle and final phases of hydroperiod) in a set of temporary ponds with semipermanent and seasonal hydroregimes in two areas with mediterranean climate: central Chile and eastern Spain. We aimed to determine the influence of hydroregime and identify whether metacommunity patterns are consistent between regions sharing a mediterranean climate. 2. We selected five semipermanent and five seasonal ponds in each region to sample sediments and active zooplankton sub-communities. By combining hatching experiments from the sediments with direct counts of active zooplankton from the field samples, we gathered data on both dormant and active sub-communities to build unweighted bipartite networks of species occurrences in each pond. The obtained networks were analysed to determine seasonal trends in structural features of the metacommunities (diversity, nestedness and modularity) and their relation to hydroregime (semipermanent and seasonal) and geographical location (Chile and Spain). 3. We observed consistent differences in community structure when comparing sub-communities at different successional stages (dormant, pioneer active and cumulative active) and with different hydroregimes (semipermanent vs. seasonal). Both α-and γ-diversity showed a consistent trend, being highest in cumulative active sub-communities and lowest in dormant ones, and were consistently higher in seasonal ponds, regardless of the region. In addition, β-diversity was higher in the pioneer active sub-community in both regions, with no significant differences between hydroregimes. The species composition of cumulative active sub-communities were less heterogeneous than that of the pioneer and dormant ones. No consistent patterns were found in modularity and nestedness values across sub-communities and hydroregimes. 4. In agreement with our hypotheses, we observed a gradual accumulation of taxa as well as community homogenization over time in both regions. Contrary to our expectations, hydroregime did not affect these patterns and, surprisingly, shorter hydroperiods exhibited higher regional diversity. Our results suggest that hydroregime as a single variable does not have a strong explanatory power for metacommunity assembly of temporary ponds. Therefore, a more comprehensive theory is needed to anticipate the effects of the upcoming hydroperiod shortening.

Karstic lakes on gypsum are a very peculiar type of ecosystem declared as a Habitat Type of Community Interest (Type 3190) by the European Habitats Directive. They are usually small lakes but often displaying a high relative depth, located in active gypsum karst areas, with a high saturation of Ca2⁺ and SO4²⁻ in its waters. These lakes can usually stratify from spring to early autumn when the depth is high enough, then a sulphide-rich anoxic hypolimnion can develop in deep layers. So far, neither a comprehensive scientific definition of their ecological characteristics nor an exhaustive catalogue of their occurrence in a particular territory are available. This paper delves on their biotic and abiotic features needed for their identification as an ecosystem type. A proper methodology was also designed and applied for the evaluation of their conservation status, with the definition of reference values and assessment methods following the criteria of the Habitats Directive. The Spanish karstic lakes on gypsum (THCI 3190) were here identified, statistically representative sites were selected, and spatial GIS methods and multimetric indices were applied to assess the range, area, structure and function, and future prospects of this Habitat Type, as requested for the reporting according to Article 17 of the Habitats Directive. Results showed a favourable conservation status of this habitat type in the Alpine and Atlantic regions of Spain, but unfavourable-inadequate status in the Mediterranean, due to the pressures and impacts acting on some specific sites. A critical analysis of the methodologies and the values obtained for its conservation status was carried out.

Marine microbial communities differ genetically, metabolically, and ecologically according to their lifestyle, and they may respond differently to environmental changes. In this study, we investigated the seasonal dynamics of bacterial assemblies in the free‐living (FL) and particle‐associated (PA) fractions across a span of 6 years in the Blanes Bay Microbial Observatory in the Northwestern Mediterranean. Both lifestyles showed marked seasonality. The trends in alpha diversity were similar, with lower values in spring–summer than in autumn‐winter. Samples from both fractions were grouped seasonally and the percentage of community variability explained by the measured environmental variables was comparable (32% in FL and 31% in PA). Canonical analyses showed that biotic interactions were determinants of bacterioplankton dynamics and that their relevance varies depending on lifestyles. Time‐decay curves confirmed a high degree of predictability in both fractions. Yet, ‘seasonal’ Amplicon Sequence Variants (ASVs) (as defined by Lomb Scargle time series analysis) in the PA communities represented 46% of the total relative abundance while these accounted for 30% in the FL fraction. These results demonstrate that bacteria inhabiting both fractions exhibit marked seasonality, highlighting the importance of accounting for both lifestyles to fully comprehend the dynamics of marine prokaryotic communities.

Comparable data is essential to understand biodiversity patterns. While assemblage or community inventorying requires comprehensive sampling, monitoring focuses on as few components as possible to detect changes. Quantifying species, their evolutionary history, and the way they interact requires studying changes in taxonomic (TD), phylogenetic (PD) and functional diversity (FD). Here we propose a method for the optimization of sampling protocols for inventorying and monitoring assemblages or communities across these three diversity dimensions taking sampling costs into account. We used Iberian spiders and Amazonian bats as two case-studies. The optimal combination of methods for inventorying and monitoring required optimizing the accumulation curve of α-diversity and minimizing the difference between sampled and estimated β-diversity (bias), respectively. For Iberian spiders, the optimal combination for TD, PD and FD allowed sampling at least 50% of estimated diversity with 24 person-hours of fieldwork. The optimal combination of six person-hours allowed reaching a bias below 8% for all dimensions. For Amazonian bats, surveying all the 12 sites with mist-nets and 0 or 1 acoustic recorders was the optimal combination for almost all diversity types, resulting in >89% of the diversity and <10% bias with roughly a third of the cost. Only for phylogenetic α-diversity, the best solution was less clear and involved surveying both with mist nets and acoustic recorders. The widespread use of optimized and standardized sampling protocols and regular repetition in time will radically improve global inventory and monitoring of biodiversity. We strongly advocate for the global adoption of sampling protocols for both inventory and monitoring of taxonomic, phylogenetic and functional diversity.

The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.

The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing the genome of the >40 000 eukaryotic species estimated to live in the Catalan-speaking territories (Catalan Linguistic Area, CLA). These territories represent a biodiversity hotspot. While covering less than 1% of Europe, they are home to about one fourth of all known European eukaryotic species. These include a high proportion of endemisms, many of which are threatened. This trend is likely to get worse as the effects of global change are expected to be particularly severe across the Mediterranean Basin, particularly in freshwater ecosystems and mountain areas. Following the EBP model, the CBP is a networked organization that has been able to engage many scientific and non-scientific partners. In the pilot phase, the genomes of 52 species are being sequenced. As a case study in biodiversity conservation, we highlight the genome of the Balearic shearwater Puffinus mauretanicus, sequenced under the CBP umbrella.