Table Of Contents Page, PNAS Volume 122, Number 31
Special Feature
Monitoring and restoring gene flow in the increasingly fragmented ecosystems of the Anthropocene
Reticulate evolution has long been recognized as a key mechanism that contributes
to genetic and trait diversity. With the widespread availability of genomic data,
investigating historical reticulate evolution across taxa has gained significant attention,
...
Conservation science and policy are geared primarily toward the preservation of species
and habitats, with priority often given to the rarest, most vulnerable or most charismatic
forms. This pattern-based approach has broad appeal and offers a pragmatic ...
Under an accelerating biodiversity crisis, increased urbanization, habitat fragmentation,
and climate change require new approaches to assess conservation impact. We argue
that animal biologging is a cost-effective method for monitoring biodiversity at ...
Implementing ecological connectivity conservation in large landscapes requires cutting-edge
science combined with consideration of ecological, socioeconomic, and cultural factors
that collectively shape the outcomes of conservation efforts. We outline a ...
Genomic sequence data harbor valuable information concerning the history of species
divergence and interspecific gene flow and may offer important insights into conservation
of endangered species. However, extracting such information from genomic data ...
Pumas (Puma concolor) occupy a vast geographical range spanning from Canada to Argentina. Due to urbanization
and unregulated hunting, pumas in Florida, known as panthers, are the only breeding
population east of the Mississippi River. In the 1990s, ...
Anthropogenic destruction and fragmentation of habitat restrict many species to small,
isolated populations, which often experience high extirpation risk. Restoring connectivity
through translocations is one approach for mitigating the demographic and ...
The cytoplasmic genomes of plants and animals often fail to track species boundaries.
However, the mechanisms responsible for such patterns are poorly understood, in part
because few studies have linked cytoplasmic variation to phenotypic traits or ...
Many widespread plant taxa of western North America have diversified into phenotypically
and genetically divergent lineages due to complex biogeographic histories across heterogeneous
landscapes. Mosaic hybrid zones can form when geographically co-...
A central question in evolutionary biology is what drives the diversification of lineages.
Rapid, recent radiations are ideal systems for this question because they still show
key morphological and ecological adaptations associated with speciation. While ...
Natural habitats have undergone drastic changes in quality, continuity, and extent
during the Pleistocene, influencing the distribution of many species. More recently,
human activities have converted continuous habitats into fragmented and isolated ...
This Week in PNAS
Opinion
QnAs
Retrospective
Brian Larkins died in January 2025 at the age of 78 leaving a legacy of seminal scientific
contributions that were fundamental to the establishment of the field of plant molecular
biology. He elucidated the key processes in maize endosperm development and ...
Profile
Evolutionary ecologist Sharon Y. Strauss, an early proponent of unifying the fields
of ecology and evolution, helped advance both disciplines. Now a distinguished emeritus
professor at the University of California, Davis, Strauss remains active in ...
Commentaries
Perspective
Cancer is the origin of a novel tissue that attracts resources, spreads beyond boundaries,
avoids normal controls, and escapes immunity. How does a novel tissue arise? The puzzle
is that two seemingly different processes appear to be the primary driving ...
Brief Reports
How human brain function is established through protracted trajectories of development
is not yet fully understood. Maturation of γ-aminobutyric acid (GABA) circuits drives
critical periods of cortical development in animal models. Whether early ...
Epigenetic clocks based on DNA methylation provide robust biomarkers of biological
age, yet the mechanistic basis and functional significance of slowing these clocks
remain unclear. Progress has been limited by the lack of short-lived, genetically
...
Physical Sciences
Applied Physical Sciences
We present a simple physical model that recapitulates several features of biological
evolution, while being based only on thermally driven attachment and detachment of
elementary building blocks. Through its dynamics, this model samples a large and ...
Biophysics and Computational Biology
With the goal of accelerating the discovery of small molecule–protein complexes, we
leverage fast, low-dose, event-based electron counting microcrystal electron diffraction
(MicroED) data collection and native mass spectrometry. This approach, which we ...
Computer Sciences
Are large language models (LLMs) biased in favor of communications produced by LLMs,
leading to possible antihuman discrimination? Using a classical experimental design
inspired by employment discrimination studies, we tested widely used LLMs, including
...
A central question in the study of language change is whether or not such change is
generational. If a language changes over time generation-by-generation, the process
looks as follows: New generations of speakers introduce innovations, while older ...
Earth, Atmospheric, and Planetary Sciences
The fossil record of functional diversity is increasingly used to study ecosystem
evolution, extinction recovery, and factors affecting long-term trends in biodiversity.
In addition, the youngest fossil record (late Quaternary) can provide insights into
...
Perchlorate is a toxic, regulated contaminant in drinking water. According to previous
isotopic studies, much of the perchlorate deposited to the Earth’s surface is formed
in the atmosphere, with 36Cl suggesting a large contribution from the stratosphere. ...
The Eoarchean quartz-pyroxene rock from Akilia Island in Greenland has been proposed
as one of Earth’s oldest banded iron formations (BIF) and a potential host for the
earliest biosignatures. However, the origin of its protolith, whether it metamorphosed
...
Engineering
Analyzing cellular health and metabolism without compromising cell integrity is a
major challenge. We present a noninvasive technique using micro magnetic resonance
spectroscopy (micro MRS) for nondestructive metabolic fingerprinting at the single-cell
...
Ocular adnexal lymphoma (OAL) is the most common orbital malignancy in adults. Advanced
tools for precise diagnosis and prognosis of OAL are in demand. Here, the nanoparticle-enhanced
laser desorption/ionization mass spectrometry was applied for the ...
Physics
Atoms and molecules usually hybridize and form bonds when they come in very close
proximity of each other. In this work, we show that molecules can hybridize even through
far-field electromagnetic interactions mediated by the shared mode of an optical ...
Dusty plasma is a mixture of ions, electrons, and macroscopic charged particles that
is commonly found in space and planetary environments. The particles interact through
Coulomb forces mediated by the surrounding plasma, and as a result, the effective
...
Suspensions of self-propelled objects represent a novel paradigm in colloidal science.
In such “active baths,” traditional concepts such as Brownian motion, fluctuation–dissipation
relations, and work extraction from heat reservoirs, must be extended ...
Kagome metals have emerged as a frontier in condensed matter physics due to their
potential to host exotic quantum states. Among these, CsV3Sb5 has attracted significant attention for the unusual coexistence of charge density
wave (CDW) order and ...
Self-assembly (SA) plays a pivotal role in nanotechnology, offering cost-effective
methods for bottom–up fabrication and providing versatile model systems for investigating
fundamental interactions in various bioinspired systems. However, current methods
...
Social Sciences
Economic Sciences
Are large language models (LLMs) biased in favor of communications produced by LLMs,
leading to possible antihuman discrimination? Using a classical experimental design
inspired by employment discrimination studies, we tested widely used LLMs, including
...
Psychological and Cognitive Sciences
A central question in the study of language change is whether or not such change is
generational. If a language changes over time generation-by-generation, the process
looks as follows: New generations of speakers introduce innovations, while older ...
Computational models of reinforcement learning (RL) have significantly contributed
to our understanding of human behavior and decision-making. Traditional RL models,
however, often adopt a linear approach to updating reward expectations, potentially
...
Past traumatic experiences shape neural responses to future stress, but the mechanisms
underlying this dynamic interaction remain unclear. Here, we assessed how trauma-related
brain networks respond to current acute stress in real time. Using a machine ...
Biological Sciences
Biochemistry
With the goal of accelerating the discovery of small molecule–protein complexes, we
leverage fast, low-dose, event-based electron counting microcrystal electron diffraction
(MicroED) data collection and native mass spectrometry. This approach, which we ...
Excretion of L-xylulose is the hallmark of pentosuria, the fourth of Garrod’s inborn
errors of metabolism, yet the molecular basis for L-xylulose formation remains unknown.
Here, by projecting coevolutionary data for 511,114 orthogroups across 1,929 ...
Effective immune therapy against cancer ideally should target a cancer-specific antigen,
an antigen that is present exclusively in cancer cells. However, there is a paucity
of cancer-specific antigens that are endogenously produced. HapImmune™ technology
...
Influenza represents a significant threat with seasonal epidemics that can transition
to global pandemics, and cross-species infection presenting a continuous challenge.
While vaccines and several antiviral drugs are available, constant genetic changes
...
Indole-3-acetic acid (IAA), the major form of auxin, is essential for plant growth.
Auxin resistant 1 (AUX1), the first identified auxin importer, plays a crucial role
in polar auxin transport (PAT). Here, we present cryo-EM structures of Arabidopsis ...
A previous study found that a bacterial group II intron–like reverse transcriptase
(G2L4 RT) evolved to function in double-strand break repair (DSBR) via microhomology-mediated
end-joining (MMEJ) and that a mobile group II intron-encoded RT has a basal ...
How RAG1/2 evolved from ancestral transposases to initiate V(D)J recombination without transposition
The recombination activating genes 1 and 2 (RAG1/2) recombinase, which initiates V(D)J
recombination in jawed vertebrates, evolved from RNaseH-like transposases such as
Transib and ProtoRAG. However, its postcleavage transposase activity is strictly ...
In mammalian genomes, cytosine modifications form a layer of regulatory information
alongside the genetic code. Decoding this information is crucial to our understanding
of biology and disease. Established sequencing methods cannot simultaneously resolve
...
Biophysics and Computational Biology
Voltage-sensing phosphatase (VSP) comprises a voltage sensor domain (VSD) and a cytoplasmic
catalytic region (CCR), achieving a unique electrochemical signal conversion. Previous
studies suggest that phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), a ...
Our current understanding of protein folding is based predominantly on studies of
small (<150 aa) proteins that refold reversibly from a chemically denatured state.
However, as protein length increases so does the competition between off-pathway ...
Diverse extracellular filaments present on the surface of archaea mediate multiple
key processes, such as motility, adhesion, and biofilm formation. Although several
archaeal filament types have been characterized in considerable detail, many remain
...
Cell Biology
Clinically, compromised fracture healing often occurs at sites with less muscle coverage
and muscle flaps can provide the necessary healing environment for appropriate healing
in severe bone loss. However, the underlying mechanisms are largely unknown. ...
Parkinson’s disease is characterized by loss of dopamine neurons that project to the
dorsal striatum, and mutations in LRRK2 and GBA1 are the most common genetic causes of familial Parkinson’s disease. Previously, we
showed that pathogenic LRRK2 mutations ...
Proteins that transmit molecules and signals across the plasma membrane are crucial
in cell biology because they enable cells to sense and respond to their surroundings.
A major challenge for studying cell surface proteins is that often they do not fold
...
Defective mitochondrial quality control in response to loss of mitochondrial membrane
polarization is implicated in Parkinson’s disease by mutations in PINK1 and PRKN. Parkin-expressing U2 osteosarcoma (U2OS) cells were treated with the depolarizing
...
Developmental Biology
Analyzing cellular health and metabolism without compromising cell integrity is a
major challenge. We present a noninvasive technique using micro magnetic resonance
spectroscopy (micro MRS) for nondestructive metabolic fingerprinting at the single-cell
...
The acrosome is a crucial organelle essential for sperm function and male fertility.
During acrosome biogenesis, numerous proacrosomal vesicles (PAVs) are transported
to the concave region of the nuclear membrane and fuse to form the acrosome. However,
...
Ecology
The fossil record of functional diversity is increasingly used to study ecosystem
evolution, extinction recovery, and factors affecting long-term trends in biodiversity.
In addition, the youngest fossil record (late Quaternary) can provide insights into
...
Ecosystem connectivity—the uninterrupted flow of natural processes within and among
ecosystems—is critical for maintaining healthy ecosystem functions. However, in the
Amazon drainage basin, multiple anthropogenic activities are rapidly disrupting ...
Bacteria and phages have been in an ongoing arms race for billions of years. To resist
phages bacteria have evolved numerous defense systems, which nevertheless are still
overcome by counterdefense mechanisms of specific phages. These defense/...
Liquid brains conceptualize living systems that operate without central control, where
collective outcomes emerge from local and dynamic interactions. This concept extends
beyond ants and other social insects to include immune systems, slime molds, and ...
Environmental Sciences
Oxygenic photosynthesis requires excitation energy transfer from light-harvesting
complexes (LHCs) to reaction centers (RCs) to drive photochemical redox chemistry.
The effective absorption cross section of RCs dynamically responds to the light ...
Evolution
We present a simple physical model that recapitulates several features of biological
evolution, while being based only on thermally driven attachment and detachment of
elementary building blocks. Through its dynamics, this model samples a large and ...
Predicting the ability of bacteria to develop antibiotic resistance is challenging,
especially for the vast majority of species for which no experimental data are available.
Here, we investigated the evolvability and intrinsic presence of rifampicin ...
The standard model of sex chromosome evolution is based on ancient XY or ZW systems.
Young neo-sex chromosomes that form via the translocation of autosomal material to
preexisting sex chromosomes provide materials to study early events in sex chromosome
...
Genetic variation underpins evolutionary change, but mutation accumulation increases
genetic load. Various factors affect the extent of load, such as population size and
breeding system, but other important determinants remain unexplored. In particular,
...
Morphological change occurs over macroevolutionary timescales under the action of
natural selection and genetic drift combined with developmental processes shaping
organogenesis. Although determining their relative weight is made difficult by ...
Genetics
Plant–microbe symbioses such as the legume–rhizobium mutualism are vital in the web
of ecological relationships within both natural and managed ecosystems, influencing
primary productivity, crop yield, and ecosystem services. The outcome of these ...
Establishment of correct chromatin configuration in male meiosis is essential for
sperm formation and male fertility. However, how chromatin remodeling contributes
to meiotic progression in male germ cells is not well understood. Here, we find that
the ...
Through international gene-matching efforts, we identified 10 individuals with ultrarare
heterozygous variants, including 5 de novo variants, in BMAL1, a core component of the molecular clock. Instead of an isolated circadian phenotype
seen with disease-...
Immunology and Inflammation
Neonates and infants are distinct in their clinical and cellular responses to viral
infections, with neonatal CD8+ T cells displaying innate-like characteristics and a low threshold for T cell receptor
activation. However, specific molecular programs that ...
Aging is a risk factor for severe COVID-19, characterized by vascular endothelial
dysfunction. Although possible susceptibility of vascular endothelial cells (ECs)
to SARS-CoV-2 infection has been suggested, the details of entry into cells have not
been ...
Medical Sciences
Ocular adnexal lymphoma (OAL) is the most common orbital malignancy in adults. Advanced
tools for precise diagnosis and prognosis of OAL are in demand. Here, the nanoparticle-enhanced
laser desorption/ionization mass spectrometry was applied for the ...
Microbiology
Granulomas play a crucial role in the pathology of tuberculosis, but the immune environment
governing their formation remains largely unknown. To explore the dynamic changes
in the immune microenvironment during the formation of tuberculous granulomas, we
...
The polar-growing Corynebacteriales have a complex cell envelope architecture characterized by the presence of a specialized
outer membrane composed of mycolic acids. In some Corynebacteriales, this mycomembrane is further supported by a proteinaceous ...
Neuroscience
Past traumatic experiences shape neural responses to future stress, but the mechanisms
underlying this dynamic interaction remain unclear. Here, we assessed how trauma-related
brain networks respond to current acute stress in real time. Using a machine ...
What are the principles that govern the responses of cortical networks to their inputs
and the emergence of these responses from recurrent connectivity? Recent experiments
have probed these questions by measuring cortical responses to two-photon ...
The stress axis is always active, even in the absence of any threat. This manifests
as hourly pulses of corticosteroid stress hormone secretion over the day. Corticotropin-releasing
hormone (CRH) neurons in the paraventricular nucleus of the hypothalamus (...
Sleep promotes cerebrospinal fluid (CSF) to interstitial fluid (ISF) exchange in the
brain facilitated by brain pulsations. Especially brain vasomotion and arterial pulsations
modulated by noradrenaline drive the intracranial fluid dynamics. Narcolepsy ...
Weakening of synaptic transmission at the Drosophila larval neuromuscular junction triggers two forms of homeostatic compensation, one
that increases the probability of glutamate release per action potential (Pr) and another that increases motoneuron (MN) ...
As the serial section community transitions to volume electron microscopy, tools are
needed to balance rapid segmentation efforts with documenting the fine detail of structures
that support cell function. New annotation applications should be accessible ...
Neurons rely on spatial and temporal control of protein synthesis to respond rapidly
and locally to external stimuli, a process facilitated by the dynamic localization
and modification of ribosomes. While previous research has shown that neuronal activity
...
Physiology
Carbamazepine (CBZ) is a widely used antiepileptic drug effective in managing partial
and generalized tonic-clonic seizures. Despite its established therapeutic efficacy,
CBZ has been reported to worsen seizures in another form of epilepsy, generalized
...
Plant Biology
Reproductive, male-enriched small RNAs are present in flowering plants and animals,
yet their role in plants remains underexplored. We generated dicer-like 5 (dcl5) mutants in durum wheat (Triticum turgidum ssp. durum 2n = 4× = 28; AABB), revealing ...
View related content:
Methods for fast and inexpensive gene synthesis from oligonucleotide pools enable
rapid iteration of genetic designs. Here, we describe iggypop (indexed Golden Gate gene assembly from PCR-amplified oligonucleotide pools), a simple
computational–...
Sustainability Science
Ecosystem connectivity—the uninterrupted flow of natural processes within and among
ecosystems—is critical for maintaining healthy ecosystem functions. However, in the
Amazon drainage basin, multiple anthropogenic activities are rapidly disrupting ...
Systems Biology
Metabolic crosstalk among diverse cellular populations contributes to shaping a competitive
and symbiotic tumor microenvironment (TME) to influence cancer progression and immune
responses, highlighting vulnerabilities that can be exploited for cancer ...
Corrections
Cover image: Pictured is an artistic illustration of forest habitats interrupted by deforested land, with a double-strand helix representing restored gene flow between fragmented ecosystems. A collection of articles in the Monitoring and Restoring Gene Flow in the Increasingly Fragmented Ecosystems of the Anthropocene Special Feature highlights the challenges of measuring, monitoring, and maintaining the exchange of genetic material between fragmented wildlife populations. Together, the articles emphasize the synergistic potential of research into the origins and processes of speciation to inform innovations and applications in conservation biology. See the Introduction to the Special Feature, e2500713122. Image credit: Silu Wang.
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