The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa. However, the irreversible post-mortem degradation of ancient DNA has so far limited its recovery—outside permafrost areas— to specimens that are not older than approximately 0.5 million years (Myr). By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I, and suggested the presence of protein residues in fossils of the Cretaceous period—although with limited phylogenetic use. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia). Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck’s rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel—which is the hardest tissue in vertebrates, and is highly abundant in the fossil record—can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.
Every year, a committee of experts sits down with a tough job to do: from among all ICREA publications, they must find a handful that stand out from all the others. This is indeed a challenge. The debates are sometimes heated and always difficult but, in the end, a shortlist of 24 publications is produced. No prize is awarded, and the only additional acknowledge is the honour of being chosen and highlighted by ICREA. Each piece has something unique about it, whether it be a particularly elegant solution, the huge impact it has in the media or the sheer fascination it generates as a truly new idea. For whatever the reason, these are the best of the best and, as such, we are proud to share them here.
LIST OF SCIENTIFIC HIGHLIGHTS
Proteomeic investigation of ancient dental enamel resolves Early Pleistocene rhino evolution (2019)
Agustí Ballester, Jordi (IPHES)view details
Martínez Navarro, Bienvenido (IPHES)
A new type of urban climate injustice: green climate gentrification (2019)
Anguelovski, Isabelle (ICTA-UAB)view details
My recent research led in collaboration with researchers from the BCNUEJ lab and colleagues from the United States highlights that urban climate resilience planning produces a new type of urban climate injustice: green climate gentrification.
Our studies find that low-income, working class, and minority residents are among the social groups most likely to experience residential and social displacement—in the short and mid-term—from green climate infrastructure. Although green roofs, resilient parks and greenways, rain gardens, or detention basins and canals are increasingly hailed as win-win infrastructure to protect cities against climate change impacts, we argue that such interventions overlook or minimize negative impacts for socially vulnerable groups. At the same time, those projects sell the image of a green and resilient 21st-century city to investors, real estate developers, and new sustainability-class residents who are those most benefiting from green interventions.
The research we conducted in Boston (on greening and resilience planning in East Boston) and Philadelphia (on green stormwater management infrastructure throughout the city) reveals that vulnerable populations—many of whom have already been exposed to hazardous conditions in their neighborhoods—now stand to benefit least from greening initiatives. For instance, in Philaldephia, we find a negative association between the siting of green infrastructure and increased minority population, and a strong positive association between green infrastructure siting, gentrification, and reduced minority and low-income population. In Boston, we find that the Boston real estate industry is building resilient properties for elites and displacing lower-income residents in East Boston, while advocating for the City of Boston to create new protection zones for future investments.
In sum, improvement of marginalized neighborhoods through green infrastructure may cause these vulnerable populations to lose their neighborhoods altogether.
Tissues have independent clocks (2019)
Aznar Benitah, Salvador (IRB Barcelona)view details
Circadian rhythms control organismal physiology throughout the day. At the cellular level, clock regulation is established by a self-sustained transcriptional oscillator network. However, it is still unclear how different tissues achieve a synchronized rhythmic physiology. That is, do they respond independently to environmental signals, or require interactions with each other to do so? These are important issues since deregulation of the clock is causative of accelerated aging and several diseases such as metabolic disorders and a higher predisposition to cancer.
In this work, we showed that unexpectedly, light synchronizes the circadian machinery in single tissues in the absence of clocks in all other tissues. Importantly, tissue-autonomous clocks partially sustain homeostasis in otherwise arrhythmic and prematurely aging animals. Our results therefore support a two-branched model for the daily synchronization of tissues: an autonomous clock that directly responds to light without any commitment of other tissue clocks, and a memory branch using other tissue clocks to "remember" time in the absence of external cues. This new model of the timed synchronization of our clocks nicely explains jetlag, while raising concerns regarding the ¨social jetlag¨ to which we are currently exposing our tissues on a daily basis due to the unnatural exposure to light at night. In addition, our results indicate that tissues have a minimal functional independence which probably ensures a certain degree of tissue fitness even when the functionality of other tissues might be compromised. Overall this would extend organismal fitness even when some component (for instance a specific tissue or organ) is damaged.
EGG: A tool to simulate language emergence in deep networks. (2019)
Baroni, Marco (UPF)view details
Deep artificial neural networks are increasingly pervasive in our daily lives, helping us in everyday tasks such as tagging pictures or translating from one language to the other. However, these computational systems are not endowed with the ability to communicate with each other and with us, which makes them rather inflexible and opaque tools. Marco Baroni and his colleagues are interested in the question: what happens if we let a community of artificial deep network "invent" their own language in order to solve a task together. In order to encourage research in this interdisciplinary area, involving artificial intelligence, linguistics and cognitive science, in 2020 the team open-sourced the EGG toolkit. Using the toolkit (currently starred more than 100 times on GitHub, and presented at the prestigious EMNLP conference) Baroni and colleagues were able to highlight several interesting properties of the emergent system developed by deep networks to communicate. For example, the networks are not subject to the same energy saving constraints that shape the communication systems of humans and animals. Consequently, they might associate very long forms, such as "fjksjkgjrgjkrgksfkeeeeeeff", to very frequent words (e.g., those meaning "the" or "it"). Conversely, neural networks can invent very clever ways to communicate about the world (e.g., by referring to the relative intensity of different pixels) that lead to languages that are completely obscure for us, but allow extremely efficient information transmission. The research goal set for 2020 is to find a common ground between the language spoken by deep networks and the one spoken by people!
Reducing Child Deaths in Low-Income Countries. (2019)
Bassat Orellana, Quique (ISGlobal)view details
A simple algorithm could contribute to reducing the high mortality among newborns and babies in the month following their hospital discharge.
In the last 25 years, the reduction in mortality of children under five years of age has been remarkable but insufficient. In low-income countries, children are at increased risk of dying following hospitalization, regardless of their illness, with an estimated risk ranging between 3 and 13% in the month following discharge. The challenge, therefore, is to identify those children at higher risk in order to follow them up closely after discharge, and thereby avoid a considerable number of pediatric deaths.
We conducted a retrospective study analyzing data from more than 20,000 pediatric hospital admissions over almost 20 years, in the district hospital of Manhiça, a semi-rural area in Southern Mozambique where almost half of the population is under 15 years of age. We determined mortality during the first, second and third month after hospital discharge, and looked for indicators that would allow to identify and eventually target children at higher risk of dying.
The results show that the average mortality after discharge is high (3.6%), a figure even higher than the documented intra-hospital mortality. Half of the post-discharge deaths occur within the first 30 days. The risk is highest in babies under 3 months of age and decreases progressively with age. The study also identifies a series of clinical parameters (malnutrition, diarrhea, clinical pneumonia, etc.) that allow to identify those children at highest mortality risk. Using all or some of these variables, the team used a series of predictive models capable of identifying up to 80% of children at risk of dying after discharge.
The children thus identified could benefit from a close follow-up during the first 30 days by community health workers, or receive preventive antimicrobial therapies. If these simple models, based on easy-to-obtain parameters like those used in this study, are validated in other contexts, they could represent a valuable tool to save neonatal and infant lives in countries with a high burden of child mortality.
Freshwater biodiversity is declining at an alarming rate in Europe and Central Asia (2019)
Brucet, Sandra (UVIC)view details
Freshwater systems are the most threatened ecosystem type in Europe and Central Asia region, with the quantity and quality of habitats and abundance of many species rapidly declining. This is the conclusion from our review paper which is part of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) report on Europe and Central Asia.
In the study we also show that only about half of the EU’s rivers and lakes achieved good ecological status in 2015 (as defined by the Water Framework Directive in terms of the quality of the biological community), and many lakes, ponds, and streams are disappearing as a consequence of agricultural intensification and ineffective irrigation and urbanisation, combined with climate change. The situation regarding freshwater biodiversity remains highly critical in Europe and Central Asia as many species remain threatened with extinction, including >50% of known species for some groups (e.g. molluscs, amphibians).
The reasons for the decline in freshwater biodiversity are the destruction or modification of their habitat, including water abstraction, which affects ∼89% of all amphibian threatened species and ∼26% of threatened freshwater invertebrate species. Of particular concern is the lack of data for freshwater invertebrates. Current status is available for only a minority of species, and the impact of alien invasive species is often unknown, especially in Central Asia.
Based on current freshwater biodiversity trends, it is highly unlikely that Europe and Central Asia will achieve either the respective Aichi biodiversity targets by 2020 (i.e., targets, 2–4,6–12,14) or Target 1 of the Biodiversity Strategy.