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Publications in Evolutionary Biology by NOMIS researchers

Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment

NOMIS Researcher(s)

Published in

January 30, 2025

Human accelerated regions (HARs) have been implicated in human brain evolution. However, insight into the genes and pathways they control is lacking, hindering the understanding of their function. Here, we identify 2,963 conserved gene targets for 1,590 HARs and their orthologs in human and chimpanzee neural stem cells (NSCs). Conserved gene targets are enriched for neurodevelopmental functions and are overrepresented among differentially expressed genes (DEGs) identified in human NSCs (hNSCs) and chimpanzee NSCs (cNSCs) as well as in human versus non-human primate brains. Species-specific gene targets do not converge on any function and are not enriched among DEGs. HAR targets also show cell-type-specific expression in the human fetal brain, including in outer radial glia, which are linked to cortical expansion. Our findings support that HARs influence brain evolution by altering the expression of ancestral gene targets shared between human and chimpanzee rather than by gaining new targets in human and facilitate hypothesis-directed studies of HAR biology.

Research field(s)
Bioinformatics, Developmental Biology, Evolutionary Biology

DOI
10.1016/j.cell.2025.01.007

Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome

NOMIS Researcher(s)

Published in

January 2, 2025

Glacier-fed streams (GFS) feature among Earth’s most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change.

Research field(s)
Biology, Evolutionary Biology

DOI
10.1038/s41564-024-01874-9

Diversity and biogeography of the bacterial microbiome in glacier-fed streams

NOMIS Researcher(s)

Published in

January 1, 2025

The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change1,2. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms2,3. However, current knowledge on the GFS microbiome is scarce4,5, precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth’s major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.

Research field(s)
Biology, Evolutionary Biology

DOI
10.1038/s41586-024-08313-z

If you please, draw me a neuron — linking evolutionary tinkering with human neuron evolution

NOMIS Researcher(s)

Published in

October 1, 2024

Animal speciation often involves novel behavioral features that rely on nervous system evolution. Human-specific brain features have been proposed to underlie specialized cognitive functions and to be linked, at least in part, to the evolution of synapses, neurons, and circuits of the cerebral cortex. Here, we review recent results showing that, while the human cortex is composed of a repertoire of cells that appears to be largely similar to the one found in other mammals, human cortical neurons do display specialized features at many levels, from gene expression to intrinsic physiological properties. The molecular mechanisms underlying human species-specific neuronal features remain largely unknown but implicate hominid-specific gene duplicates that encode novel molecular modifiers of neuronal function. The identification of human-specific genetic modifiers of neuronal function brings novel insights on brain evolution and function and, could also provide new insights on human species-specific vulnerabilities to brain disorders.

Research field(s)
Genetics & Heredity, Evolutionary Biology

DOI
10.1016/j.gde.2024.102260

A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis

NOMIS Researcher(s)

Published in

March 14, 2024

Genome-wide association studies (GWAS) identified thousands of genetic variants linked to phenotypic traits and disease risk. However, mechanistic understanding of how GWAS variants influence complex morphological traits and can, in certain cases, simultaneously confer normal-range phenotypic variation and disease predisposition, is still largely lacking. Here, we focus on rs6740960, a single nucleotide polymorphism (SNP) at the 2p21 locus, which in GWAS studies has been associated both with normal-range variation in jaw shape and with an increased risk of non-syndromic orofacial clefting. Using in vitro derived embryonic cell types relevant for human facial morphogenesis, we show that this SNP resides in an enhancer that regulates chondrocytic expression of PKDCC – a gene encoding a tyrosine kinase involved in chondrogenesis and skeletal development. In agreement, we demonstrate that the rs6740960 SNP is sufficient to confer chondrocyte-specific differences in PKDCC expression. By deploying dense landmark morphometric analysis of skull elements in mice, we show that changes in Pkdcc dosage are associated with quantitative changes in the maxilla, mandible, and palatine bone shape that are concordant with the facial phenotypes and disease predisposition seen in humans. We further demonstrate that the frequency of the rs6740960 variant strongly deviated among different human populations, and that the activity of its cognate enhancer diverged in hominids. Our study provides a mechanistic explanation of how a common SNP can mediate normal-range and disease-associated morphological variation, with implications for the evolution of human facial features.

Research field(s)
Developmental Biology, Genetics & Heredity, Evolutionary Biology

DOI
10.7554/eLife.82564

Climatic and soil factors explain the two-dimensional spectrum of global plant trait variation

NOMIS Researcher(s)

Published in

January 1, 2022

Plant functional traits can predict community assembly and ecosystem functioning and are thus widely used in global models of vegetation dynamics and land–climate feedbacks. Still, we lack a global understanding of how land and climate affect plant traits. A previous global analysis of six traits observed two main axes of variation: (1) size variation at the organ and plant level and (2) leaf economics balancing leaf persistence against plant growth potential. The orthogonality of these two axes suggests they are differently influenced by environmental drivers. We find that these axes persist in a global dataset of 17 traits across more than 20,000 species. We find a dominant joint effect of climate and soil on trait variation. Additional independent climate effects are also observed across most traits, whereas independent soil effects are almost exclusively observed for economics traits. Variation in size traits correlates well with a latitudinal gradient related to water or energy limitation. In contrast, variation in economics traits is better explained by interactions of climate with soil fertility. These findings have the potential to improve our understanding of biodiversity patterns and our predictions of climate change impacts on biogeochemical cycles.

Research field(s)
Natural Sciences, Biology, Evolutionary Biology

DOI
10.1038/s41559-021-01616-8

Computational and neurocognitive approaches to the political brain: Key insights and future avenues for political neuroscience

NOMIS Researcher(s)

Published in

April 12, 2021

Although the study of political behaviour has been traditionally restricted to the social sciences, new advances in political neuroscience and computational cognitive science highlight that the biological sciences can offer crucial insights into the roots of ideological thought and action. Echoing the dazzling diversity of human ideologies, this theme issue seeks to reflect the multiplicity of theoretical and methodological approaches to understanding the nature of the political brain. Cutting-edge research along three thematic strands is presented, including (i) computational approaches that zoom in on fine-grained mechanisms underlying political behaviour, (ii) neurocognitive perspectives that harness neuroimaging and psychophysiological techniques to study ideological processes, and (iii) behavioural studies and policy-minded analyses of such understandings across cultures and across ideological domains. Synthesizing these findings together, the issue elucidates core questions regarding the nature of uncertainty in political cognition, the mechanisms of social influence and the cognitive structure of ideological beliefs. This offers key directions for future biologically grounded research as well as a guiding map for citizens, psychologists and policymakers traversing the uneven landscape of modern polarization, misinformation, intolerance and dogmatism. This article is part of the theme issue ‘The political brain: neurocognitive and computational mechanisms’.

Research field(s)
Natural Sciences, Biology, Evolutionary Biology

DOI
10.1098/rstb.2020.0130

Joining a group diverts regret and responsibility away from the individual

NOMIS Researcher(s)

Published in

March 11, 2020

It has recently been proposed that a key motivation for joining groups is the protection from the negative consequences of undesirable outcomes. To test this claim, we investigated how experienced outcomes triggering loss and regret impacted people’s tendency to decide alone or join a group, and how decisions differed when voluntarily made alone versus in group. Replicated across two experiments, participants (n = 125 and n = 496) selected whether to play alone or contribute their vote to a group decision. Next, they chose between two lotteries with different probabilities of winning and losing. The higher the negative outcome, the more participants switched from deciding alone to with others. When joining a group to choose the lottery, choices were less driven by outcome and regret anticipation. Moreover, negative outcomes experienced alone, not part of a group vote, led to worse subsequent choices than positive outcomes. These results suggest that the protective shield of the collective reduces the influence of negative emotions that may help individuals re-evaluate past choices.

Research field(s)
Natural Sciences, Biology, Evolutionary Biology

DOI
10.1098/rspb.2019.2251

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