The History And Prehistory Of Human Disease

A new paper in Nature concludes from ancient DNA that while infectious diseases were common in humans since the hunter-gatherer era, that there was a real surge, not at the time of the Neolithic Revolution, but when steppe herders started to invade and conquerer farmers, and hunter-gatherers, possibly because they lived more closely with their animals and because the diseases that they carried helped facilitate their conquests. The New York Times also discusses the paper.

Infectious diseases have had devastating effects on human populations throughout history, but important questions about their origins and past dynamics remain. To create an archaeogenetic-based spatiotemporal map of human pathogens, we screened shotgun-sequencing data from 1,313 ancient humans covering 37,000 years of Eurasian history. We demonstrate the widespread presence of ancient bacterial, viral and parasite DNA, identifying 5,486 individual hits against 492 species from 136 genera. Among those hits, 3,384 involve known human pathogens, many of which had not previously been identified in ancient human remains. Grouping the ancient microbial species according to their likely reservoir and type of transmission, we find that most groups are identified throughout the entire sampling period. Zoonotic pathogens are only detected from around 6,500 years ago, peaking roughly 5,000 years ago, coinciding with the widespread domestication of livestock. Our findings provide direct evidence that this lifestyle change resulted in an increased infectious disease burden. They also indicate that the spread of these pathogens increased substantially during subsequent millennia, coinciding with the pastoralist migrations from the Eurasian Steppe

Martin Sikora, et al., "The spatiotemporal distribution of human pathogens in ancient Eurasia" Nature (July 9, 2025).

Are Oxygen Levels Related To Earth's Magnetic Field?

The strength of Earth’s magnetic field seems to rise and fall in line with the abundance of oxygen in the planet’s atmosphere, a study of geological records spanning the past half a billion years has found.

From the journal Nature. 

Among other things, the overall oxygen levels in the atmosphere impacts how large animals get, with more oxygen favoring larger animals.

It isn't clear what causes drive the correlation, although there probably is a cause.

Why Do We Kiss?

Why do we kiss? Is there an evolutionary advantage to it? This article tries to answer that question.

A kiss has been a signal of special affection across continents and cultures for millennia. Between times and peoples, social norms invariably prescribe kissing to specific affiliations and contexts, implying deeper biological bases. Why the protruding of the lips and slight suction when touching another? 

Capuchin monkeys stick their fingers in their friends' eyes as sign of affection, why have humans developed kissing? 

Here I briefly review proposed hypotheses for the evolution of human kissing. Great ape social behavior suggests that kissing is likely the conserved final mouth-contact stage of a grooming bout when the groomer sucks with protruded lips the fur or skin of the groomed to latch on debris or a parasite. The hygienic relevance of grooming decreased over human evolution due to fur-loss, but shorter sessions would have predictably retained a final “kissing” stage, ultimately, remaining the only vestige of a once ritualistic behavior for signaling and strengthening social and kinship ties in an ancestral ape.

Adriano R. Lameira, "The evolutionary origin of human kissing" Evolutionary Anthropology (October 17, 2024) https://doi.org/10.1002/evan.22050

Birds Down Under

One of the earliest ever bird fossils has been found in Antarctica.

Fossils representing Cretaceous lineages of crown clade birds (Aves) are exceptionally rare but are crucial to elucidating major ecological shifts across early avian divergences. Among the earliest known putative crown birds is Vegavis iaai, a foot-propelled diver from the latest Cretaceous (69.2–68.4 million years ago) of Antarctica with controversial phylogenetic affinities. Initially recovered by phylogenetic analyses as a stem anatid (ducks and closely related species), Vegavis has since been recovered as a stem member of Anseriformes (waterfowl), or outside Aves altogether. 

Here we report a new, nearly complete skull of Vegavis that provides new insight into its feeding ecology and exhibits morphologies that support placement among waterfowl within crown-group birds. Vegavis has an avian beak (absence of teeth and reduced maxilla) and brain shape (hyperinflated cerebrum and ventrally shifted optic lobes). The temporal fossa is well excavated and expansive, indicating that this bird had hypertrophied jaw musculature. The beak is narrow and pointed, and the mandible lacks retroarticular processes. Together, these features comprise a feeding apparatus unlike that of any other known anseriform but like that of other extant birds that capture prey underwater (for example, grebes and loons). The Cretaceous occurrence of Vegavis, with a feeding ecology unique among known Galloanserae (waterfowl and landfowl), is further indication that the earliest anseriform divergences were marked by evolutionary experiments unrepresented in the extant diversity.

Christopher R. Torres, et al., "Cretaceous Antarctic bird skull elucidates early avian ecological diversity." 638(8049) Nature 146 (2025) DOI: 10.1038/s41586-024-08390-0

Hat tip to Science Daily which provides additional explanation in a somewhat less jargon heavy way. It begins by stating:

Sixty-six million years ago, at the end of the Cretaceous Period, an asteroid impact near the Yucatán Peninsula of Mexico triggered the extinction of all known non-bird dinosaurs. But for the early ancestors of today's waterfowl, surviving that mass extinction event was like…water off a duck's back. Location matters, as Antarctica may have served as a refuge, protected by its distance from the turmoil taking place elsewhere on the planet. Fossil evidence suggests a temperate climate with lush vegetation, possibly serving as an incubator for the earliest members of the group that now includes ducks and geese.

Dingo Origins

The dingo came from East Asia via Melanesia.

the new study, published in Nature Scientific Reports, uses sophisticated 3D scanning and geometric morphometrics on ancient dingo specimens to show clearly that they are most similar to Japanese dogs, as well as the 'singing dogs' of New Guinea and the highland wild dog of Irian Jaya.

The remains studied were over 3,000 years old. 

From this source, citing:

Koungoulos, L.G., Hulme-Beaman, A., Fillios, M. et al., "Phenotypic diversity in early Australian dingoes revealed by traditional and 3D geometric morphometric analysis." Sci Rep (2024) DOI: 10.1038/s41598-024-65729-3

Origin Of Dinosaur Killing Object Located

It is pretty stunning that this 66 million year old mystery can be solved at all. 

The key was the chemical composition of the impactor, which contained Ruthenium. This is almost completely absent on Earth apart from rare extraterrestrial impactors, and is also absent in other impactor candidates, including comets and "siliceous asteroids, a class that formed closer to the sun than carbonaceous asteroids and that are concentrated in the asteroid belt between Mars and Jupiter. Most meteorites that end up on Earth’s surface are from this siliceous family."

Unusual Origin Found for Asteroid That Killed the Dinosaurs

A study adds strong evidence to the hypothesis that the deadly rock came from a family of objects that originally formed well beyond the orbit of the planet Jupiter. . . .

The nature of this apocalyptic object, known as the Chicxulub impactor, has inspired intense debates, including a long-running dispute over whether it was a comet or an asteroid. But evidence has been mounting in recent years that the roughly six-mile-wide impactor belonged to a family of asteroids that formed beyond the orbit of Jupiter, and that rarely impact Earth.

Now, a team led by Mario Fischer-Gödde, a research scientist at the University of Cologne in Germany, has bolstered that case with the help of the rare element ruthenium. Ruthenium is abundant in asteroids but extremely scarce in Earth’s crust, making it a handy bellwether of past impacts by space rocks. The team searched for isotopes of ruthenium in the geological remnants of the Chicxulub impact.

The results revealed a uniform signature across the global layer of debris left by the impact, which is known as the Cretaceous-Paleogene (K-Pg) boundary. And that signature neatly matches the makeup of a group of space rocks known as carbonaceous asteroids because of their high-carbon content, according to a study published on Thursday in Science.

From the New York Times. 

Jurassic Mammals Lived Longer But Matured Later

In the Jurassic era early mammals lived much longer, but matured much later, impairing their ability to overcome threats to their respective species by reproducing early and often. Evolutionary fitness favored the modern pattern.

Researchers were able to image tiny growth rings in fossilized root cement -- the bone tissue that attaches the teeth to the jaw. "The rings are similar to those in trees, but on a microscopic level," explains Professor Thomas Martin of the Vertebrates -- Mammals working group at the University of Bonn Institute of Organismic Biology, who is a senior author of the study. "Counting the rings and analyzing their thickness and texture enabled us to reconstruct the growth patterns and lifespans of these extinct animals."

The researchers determined that the first signs of the growth patterns characteristic of modern mammals, such as a puberty growth spurt, started emerging roughly 150 million years ago. Early mammals grew much more slowly but lived substantially longer than today's small mammals, with lifespans of eight to fourteen years instead of just one or two as in modern mice, for example. However, it took early mammals years to reach sexual maturity, again in contrast to their modern descendants which reach sexual maturity in just a few months.

From Science Daily citing Elis Newham, et al., "The origins of mammal growth patterns during the Jurassic mammalian radiation." 10(32) Science Advances (2024) DOI: 10.1126/sciadv.ado4555

A Global Map Of The Last Glacial Maximum (And Dingos)

The Last Glacial Maximum land bridge in Southeast Asia (ca. 18,000-20,000 years ago) was not the source of dingos in Australia, although this land bridge may have facilitated the migration of modern humans who led to the extinction of relict archaic hominins to the west of the Wallace Line in what is now island Southeast Asia.

The Sahul Shelf and the Sunda Shelf during the past 12,000 years: Tasmania separated from the mainland 12,000 ybp, and New Guinea separated from the mainland 6,500–8,500 ybp.

It also turns out that recent discoveries have estimated that the arrival of the dingo (Australia's native dogs) in Australia may have been much more recently than previously estimated, since the oldest dingo remains in Australia were previously misdated. The current dates are consistent with an arrival of dingos in Australia via Austronesian mariners. Wikipedia explains that:

The earliest known dingo remains, found in Western Australia, date to 3,450 years ago. Based on a comparison of modern dingoes with these early remains, dingo morphology has not changed over thousands of years. This suggests that no artificial selection has been applied over this period and that the dingo represents an early form of dog. They have lived, bred, and undergone natural selection in the wild, isolated from other dogs until the arrival of European settlers, resulting in a unique breed.

In 2020, an MDNA study of ancient dog remains from the Yellow River and Yangtze River basins of southern China showed that most of the ancient dogs fell within haplogroup A1b, as do the Australian dingoes and the pre-colonial dogs of the Pacific, but in low frequency in China today. The specimen from the Tianluoshan archaeological site, Zhejiang province dates to 7,000 YBP (years before present) and is basal to the entire haplogroup A1b lineage. The dogs belonging to this haplogroup were once widely distributed in southern China, then dispersed through Southeast Asia into New Guinea and Oceania, but were replaced in China by dogs of other lineages 2,000 YBP.

The oldest reliable date for dog remains found in mainland Southeast Asia is from Vietnam at 4,000 YBP, and in Island Southeast Asia from Timor-Leste at 3,000 YBP. In New Guinea, the earliest dog remains date to 2,500–2,300 YBP from Caution Bay near Port Moresby, but no ancient New Guinea singing dog remains have been found. The earliest dingo remains in the Torres Straits date to 2,100 YBP. 

The earliest dingo skeletal remains in Australia are estimated at 3,450 YBP from the Mandura Caves on the Nullarbor Plain, south-eastern Western Australia; 3,320 YBP from Woombah Midden near Woombah, New South Wales; and 3,170 YBP from Fromme's Landing on the Murray River near Mannum, South Australia. 

Dingo bone fragments were found in a rock shelter located at Mount Burr, South Australia, in a layer that was originally dated 7,000-8,500 YBP. Excavations later indicated that the levels had been disturbed, and the dingo remains "probably moved to an earlier level." 

The dating of these early Australian dingo fossils led to the widely held belief that dingoes first arrived in Australia 4,000 YBP and then took 500 years to disperse around the continent. However, the timing of these skeletal remains was based on the dating of the sediments in which they were discovered, and not the specimens themselves.

In 2018, the oldest skeletal bones from the Madura Caves were directly carbon dated between 3,348 and 3,081 YBP, providing firm evidence of the earliest dingo and that dingoes arrived later than had previously been proposed. The next-most reliable timing is based on desiccated flesh dated 2,200 YBP from Thylacine Hole, 110 km west of Eucla on the Nullarbor Plain, southeastern Western Australia. When dingoes first arrived, they would have been taken up by indigenous Australians, who then provided a network for their swift transfer around the continent. Based on the recorded distribution time for dogs across Tasmania and cats across Australia once indigenous Australians had acquired them, the dispersal of dingoes from their point of landing until they occupied continental Australia is proposed to have taken only 70 years. The red fox is estimated to have dispersed across the continent in only 60–80 years.

At the end of the last glacial maximum and the associated rise in sea levels, Tasmania became separated from the Australian mainland 12,000 YBP, and New Guinea 6,500–8,500 YBP by the inundation of the Sahul Shelf. Fossil remains in Australia date to around 3,500 YBP and no dingo remains have been uncovered in Tasmania, so the dingo is estimated to have arrived in Australia at a time between 3,500 and 12,000 YBP. To reach Australia through Island Southeast Asia even at the lowest sea level of the last glacial maximum, a journey of at least 50 kilometres (31 mi) over open sea between ancient Sunda and Sahul was necessary, so they must have accompanied humans on boats.

Some best estimates of Austronesian migration are as follows:

Suggested early migration route of early Austronesians into and out of Taiwan based on ancient and modern mtDNA data. This hypothesis assumes the Sino-Austronesian grouping, a minority view among linguists. (Ko et al., 2014).

Map showing the migration of the Austronesians from Taiwan. Indonesia is reached ca. 3500 years BP, and Papua New Guinea is reached ca. 3300 years BP.

There is no direct evidence of the involvement of Austronesian mariners bringing dingos to Australia, but they were the only sea faring people in the region at the time who could have made the trip beyond the line of sight over deep waters in that era, were engaged in seafaring in the region at just about the right time, had ties to Southern China where dingos probably originated, and dingos pretty much had to have arrived in Australia with people by boat, as opposed to without human intervention. 

The timing and location of the earliest Australian dingo remains also suggests an introduction from someplace in Indonesia to someplace west of Cape York in Australia, rather than from Papua New Guinea to Cape York, which would have involved the shortest overwater journey. This was a trip well within the maritime capabilities of the Austronesians of 3500 BP to 3300 BP.

Ancient Giant Sharks Were Warm-Blooded

Being warm-blooded can support larger body size and ancient giant sharks called megalodons were among them. Most fish and reptiles are cold blooded.

Otodus megalodon (center in this illustration, preying on a seal) was warmer-blooded than the great white shark (top left). That warm-bloodedness may have helped it grow so large, but also ultimately spelled its doom as food sources dwindled.

Massive, megatoothed Otodus megalodon ran hot — the ancient shark was at least somewhat warm-blooded, new evidence shows.

Chemical measurements from fossil O. megalodon teeth suggest the sharks had higher body temperatures than their surrounding waters, researchers report June 26 in Proceedings of the National Academy of Sciences. Analyses of carbon and oxygen in the teeth of these and other sharks, both living and extinct, revealed that the giant shark’s body temperature was about 7 degrees Celsius warmer than estimated seawater temperatures at the time.

From Science News citing three papers:

* M. Griffiths et al., Endothermic physiology of extinct megatooth sharks. Proceedings of the National Academy of Sciences (June 26, 2023). doi: 10.1073/pnas.2218153120.

* J. A. Cooper et al. The extinct shark Otodus megalodon was a transoceanic superpredator: Inferences from 3D modeling. Science Advances (August 17, 2022). doi: 10.1126/sciadv.abm9424.

* H. Ferrón. Regional endothermy as a trigger for gigantism in some extinct macropredatory sharks. PLOS ONE (September 22, 2017). doi: 10.1371/journal.pone.0185185.

Brain Size v. Body Size In Mammals

It turns out that the relationship between brain size and body size in mammals is pretty simple and universal if you don't insist on linear relationships.

Despite decades of comparative studies, fundamental questions remain about how brain and body size co-evolved. Divergent explanations exist concurrently in the literature for phenomena such as variation in brain relative to body size, variability in the scaling relationship across taxonomic levels and between taxonomic groups, and purported evolutionary trends. Here we resolve these issues using a comprehensive dataset of brain and body masses across the mammal radiation, and a method enabling us to study brain relative to body mass evolution while estimating their evolutionary rates along the branches of a phylogeny. 

Contrary to the rarely questioned assumption of a log-linear relationship, we find that a curvilinear model best describes the evolutionary relationship between log brain mass and log body mass. This model greatly simplifies our understanding of mammalian brain-body co-evolution: it can simultaneously explain both the much-discussed taxon-level effect and variation in slopes and intercepts previously attributed to complex scaling patterns. 

We also document substantial variation in rates of relative brain mass evolution, with bursts of change scattered through the tree. General trends for increasing relative brain size over time are found in only three mammalian orders, with the most extreme case being primates, setting the stage for the uniquely rapid directional increase that ultimately produced the computational powers of the human brain.

Chris Venditti, Joanna Baker, Robert A. Barton, "Co-evolutionary dynamics of mammalian brain and body size" bioRxiv (June 9, 2023) https://doi.org/10.1101/2023.06.08.544206

Story Of Human Evolution Not Actually Rewritten

Deep inside a South African cave, researchers say they have discovered graves dug by our ancient, small-brained relatives more than 100,000 years before the oldest known human burials, a claim that would revise the story of our evolution.

From the Washington Post.

Yes, this story about Homo naledi is cool.

Does it revise our story of evolution? 

No.

Does it spark debate among people who knew the existing story prior to this discovery? 

Not really, beyond the fine details of interpretation of the site.

This is a side story about a dead end hominin species that existed contemporaneously in Africa with the most direct ancestors of modern humans. It is basically a story from The Silmarillion of hominin evolution. It is entertaining, especially for hard core human evolution fans, but it doesn't really advance the plot.

Meanwhile, John Hawks discusses another recent paper he has co-authored on Homo Naledi from ten years after the original find about H. Naledi teeth.

More than 150 hominin teeth, dated to ∼330–241 thousand years ago, were recovered during the 2013–2015 excavations of the Dinaledi Chamber of the Rising Star cave system, South Africa. These fossils comprise the first large single-site sample of hominin teeth from the Middle Pleistocene of Africa. Though scattered remains attributable to Homo sapiens, or their possible lineal ancestors, are known from older and younger sites across the continent, the distinctive morphological feature set of the Dinaledi teeth supports the recognition of a novel hominin species, Homo naledi. This material provides evidence of African Homo lineage diversity that lasts until at least the Middle Pleistocene. Here, a catalog, anatomical descriptions, and details of preservation and taphonomic alteration are provided for the Dinaledi teeth. Where possible, provisional associations among teeth are also proposed. To facilitate future research, we also provide access to a catalog of surface files of the Rising Star jaws and teeth.

Delezene, L. K., Skinner, M. M., Bailey, S. E., Brophy, J. K., Elliott, M. C., Gurtov, A., Irish, J. D., Moggi-Cecchi, J., de Ruiter, D. J., Hawks, J., & Berger, L. R., "Descriptive catalog of Homo naledi dental remains from the 2013 to 2015 excavations of the Dinaledi Chamber, site U.W. 101, within the Rising Star cave system, South Africa." 180  Journal of Human Evolution 103372 (2023) 

https://doi.org/10.1016/j.jhevol.2023.103372

The Plague Was In Britain In 2000 BCE

We know that the plague was in Britain around 2000 BCE (the earliest known cases in Britain) based upon ancient plague DNA from that time period, according to the press release for the journal article: Pooja Swali, et al., "Yersinia pestis genomes reveal plague in Britain 4000 years ago." 14(1) Nature Communications (2023) DOI: 10.1038/s41467-023-38393-w

Biodiversity By Organism Size And Aggregate Biomass On Earth

Life on Earth is disproportionately made up of tiny organisms and large organisms, as measured by the aggregate biomass of organisms of each size.

A. Median carbon biomass (log scale) per log size as a function of body size with 95% confidence bounds (black dotted curves) cumulated across biological groups from 1000 bootstraps over within-group biomass and body size error distributions. Groups were organized from the least massive at the bottom to the most massive at the top for visibility on the log scale (ordered from top left to bottom right in color legend for group identity). Group biomasses are stacked so each group’s biomass is represented by its upper y-axis location minus its lower y-axis location (not by the upper y-axis location alone).

 

B. Median biomass in linear biomass scale. Confidence bounds are not shown here because they are so large as to obscure the median patterns on the linear scale.

Recent research has revealed the diversity and biomass of life across ecosystems, but how that biomass is distributed across body sizes of all living things remains unclear. We compile the present-day global body size-biomass spectra for the terrestrial, marine, and subterranean realms. To achieve this compilation, we pair existing and updated biomass estimates with previously uncatalogued body size ranges across all free-living biological groups. These data show that many biological groups share similar ranges of body sizes, and no single group dominates size ranges where cumulative biomass is highest. We then propagate biomass and size uncertainties and provide statistical descriptions of body size-biomass spectra across and within major habitat realms. 

Power laws show exponentially decreasing abundance (exponent -0.9±0.02 S.D., R^2 = 0.97) and nearly equal biomass (exponent 0.09±0.01, R^2 = 0.56) across log size bins, which resemble previous aquatic size spectra results but with greater organismal inclusivity and global coverage. In contrast, a bimodal Gaussian mixture model describes the biomass pattern better (R2 = 0.86) and suggests small (~10^−15 g) and large (~10^7 g) organisms outweigh other sizes by one order magnitude (15 and 65 Gt versus ~1 Gt per log size). The results suggest that the global body size-biomass relationships is bimodal, but substantial one-to-two orders-of-magnitude uncertainty mean that additional data will be needed to clarify whether global-scale universal constraints or local forces shape these patterns.

Eden W. Tekwa, Katrina A. Catalano, Anna L. Bazzicalupo, Mary I. O’Connor, Malin L. Pinsky. "The sizes of life." 18(3) PLOS ONE e0283020 (2023). DOI: 10.1371/journal.pone.0283020 via Science Daily. 

Comb Jellies Have Weird Nervous System

No other animal has a nervous system like a comb jelly, which suggests that they are in a very basal position in the animal kingdom's evolution.

Shimmering, gelatinous comb jellies wouldn’t appear to have much to hide. But their mostly see-through bodies cloak a nervous system unlike that of any other known animal, researchers report in the April 21 Science.

In the nervous systems of everything from anemones to aardvarks, electrical impulses pass between nerve cells, allowing for signals to move from one cell to the next. But the ctenophores’ cobweb of neurons, called a nerve net, is missing these distinct connection spots, or synapses. Instead, the nerve net is fused together, with long, stringy neurons sharing a cell membrane, a new 3-D map of its structure shows.

From Science News citing P. Burkhardt et al., "Syncytial nerve net in a ctenophore adds insights on the evolution of nervous systems" 380 Science 293 (April 21, 2023). doi: 10.1126/science.ade5645 

and 

A. Sebé-Pedrós et al., "Early metazoan cell type diversity and the evolution of multicellular gene regulation" Nature Ecology & Evolution (June 25, 2018) (published online) doi: 10.1038/s41559-018-0575-6

Planets With Weird Orbits And White Dwarfs Can Be Well Suited For Life

Improved astrophysics and climate modeling, and better telescopes, are allowing us to better understand where there are conditions best suited to life in our galaxy.

It appears that planets with high levels of axial title that have highly elongated orbits may actually be better suited to creating habitable conditions for life than planets with little axial tilt and near circular orbits. 

Obliquity means having an axil tilt relative to the plane in which a planet is rotating.

Eccentricity is the extent to which an elliptical orbit of a planet deviations from being circular.

Planetary obliquity and eccentricity influence climate by shaping the spatial and temporal patterns of stellar energy incident at a planet's surface, affecting both the annual mean climate and magnitude of seasonal variability. 

Previous work has demonstrated the importance of both planetary obliquity and eccentricity for climate and habitability, but most studies have not explicitly modeled the response of life to these parameters. While exaggerated seasons may be stressful to some types of life, a recent study found an increase in marine biological activity for moderately high obliquities <45∘ assuming an Earth-like eccentricity. However, it is unclear how life might respond to obliquities >45∘, eccentricities much larger than Earth's, or the combination of both. 

To address this gap, we use cGENIE-PlaSim, a 3-D marine biogeochemical model coupled to an atmospheric general circulation model, to investigate the response of Earth-like marine life to a large range of obliquities (0-90∘) and eccentricities (0-0.4). 

We find that marine biological activity increases with both increasing obliquity and eccentricity across the parameter space we considered, including the combination of high obliquity and high eccentricity. We discuss these results in the context of remote biosignatures, and we argue that planets with high obliquity and/or eccentricity may be superhabitable worlds that are particularly favorable for exoplanet life detection.

Jonathan Jernigan, Émilie Laflèche, Angela Burke, Stephanie Olson, "Superhabitability of High-Obliquity and High-Eccentricity Planets" arXiv:2303.02188 (March 3, 2023) (published at 944 ApJ 205). https://doi.org/10.3847/1538-4357/acb81c

Another potentially attractive place for life outside Earth is on planets with short period orbits around white dwarf stars - these planets are heated by both the sunlight from its star and by the tidal tug and release on the planet itself (presumably giving rise to geothermal heating) caused by the gravitational interactions of the star and the planet with each other. 

In recent years, there have been a growing number of observations indicating the presence of rocky material in short-period orbits around white dwarfs. 

In this Letter, we revisit the prospects for habitability around these post-main-sequence star systems. In addition to the typically considered radiative input luminosity, potentially habitable planets around white dwarfs are also subjected to significant tidal heating. The combination of these two heating sources can, for a narrow range of planetary properties and orbital parameters, continuously maintain surface temperatures amenable for habitability for planets around white dwarfs over time scales up to 10 Gyr. We show that for a specific locus of orbital parameter space, tidal heating can substantially extend the timescale of continuous habitability for a planet around a white dwarf.

Juliette Becker, Darryl Z. Seligman, Fred C. Adams, Marshall J. Styczinski, "The Influence of Tidal Heating on the Habitability of Planets Orbiting White Dwarfs" arXiv:2303.02217 (March 3, 2023) (Accepted to ApJL).

One factors that makes the existence of life beyond Earth plausible is our detection of complex organic molecules, such as CH₃OH, C₂H₃CN, CH₃OCHO, CH₃COCH₃, aGg'-(CH_2LOH)₂, ¹³CO, CO(2-1), and SiO(5-4), in the matter spewing out of distant galaxies.

This would give the development of life a huge head start if some of those molecules ended up in a place that was otherwise habitable.

A New Branch Of The Tree Of Life

It is not every day that a new branch of organism at a level even higher than that of kingdoms is discovered.

The tree of life is a useful diagram for understanding the relationships between different forms of life, present and extinct. The trunks are made up of three broad groups called domains – Bacteria, Archaea and Eukaryota – which then branch into kingdoms such as animals and fungi. From there the branches become more and more specific until you reach individual species.

The new discovery adds quite a major bough to the tree – Provora. These lifeforms make up a category informally called a “supergroup,” which sits below domains and can contain multiple kingdoms.

“This is an ancient branch of the tree of life that is roughly as diverse as the animal and fungi kingdoms combined, and no one knew it was there,” said Dr. Patrick Keeling, senior author of the study.

Members of the Provora supergroup are tiny organisms that the team describes as the “lions of the microbial world.” That’s because they prey upon other microbes, and within their ecosystem they’re relatively rare. The supergroup is further divided into two clades – the “nibblerids,” which use tooth-like structures to nibble chunks off their prey, and the “nebulids,” which engulf their prey whole.

The team discovered this new kind of life in samples taken from around the world, including the coral reefs in Curaçao, sediment from the Black and Red seas and water from the Pacific and Arctic oceans. . . .

“In the taxonomy of living organisms, we often use the gene ‘18S rRNA’ to describe genetic difference,” said Dr. Denis Tikhonenkov, first author of the study. “For example, humans differ from guinea pigs in this gene by only six nucleotides. We were surprised to find that these predatory microbes differ by 170 to 180 nucleotides in the 18S rRNA gene from every other living thing on Earth. It became clear that we had discovered something completely new and amazing.”

From New Atlas.

Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity. The vast majority of newly discovered species fall into a small number of known supergroups. 

Recently, however, a handful of species with no clear relationship to other supergroups have been described, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration. 

Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators—Nebulidia and Nibbleridia—that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. 

These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.

Denis V. Tikhonenkov, et al., "Microbial predators form a new supergroup of eukaryotes" Nature (December 7, 2022).

Neanderthal Admixture Was Followed By Fitness Based Selection

Neanderthal admixture with modern humans was followed by strong fitness driven natural selection against many Neanderthal genes that made their way into the X chromosome in locations where natural selection also played a strong part in shaping great ape genetics.

We don't yet really understand, however, precisely what phenotypic traits the Neanderthal X chromosome genes selected against governed. 

We would like to know because that would help tell us what genetic traits unique to modern humans, and not found in Neanderthals or Denisovans, helped our species of hominins survive when other hominin species went extinct in the Upper Paleolithic era.

The X chromosome in non-African human populations shows less diversity and less Neanderthal introgression than expected under the standard neutral model. 

We analyzed 162 X chromosomes from human males worldwide and discovered 14 chromosomal regions where haplotypes of several hundred kilobases rapidly rose to high frequencies in non-Africans. These observations cannot be explained by neutral genetic drift in realistic demographic scenarios and are only consistent with partial selective sweeps produced by strong selection. 

Using an approach for inferring individual Neanderthal-derived haplotypes, which do not rely on an archaic reference genome, we further discover that the swept haplotypes are devoid of the archaic ancestry otherwise typical of the affected chromosomal regions. The ancient Ust’-Ishim male carries its expected proportion of these haplotypes, implying that the sweeps must have occurred between 45,000 and 55,000 years ago. 

Finally, we find that the chromosomal positions of sweeps overlap previously reported hotspots of selection in great ape evolution. We propose that this puzzling combination of observations points to a general mechanism of positive selection unique to the X chromosome.

L. Skov, et al., "Extraordinary selection on the human X chromosome associated with archaic admixture" bioRxiv (September 20, 2022).

What Killed The Megafauna?

We've seen a mass extinction of megafauna worldwide since humans started to develop technologies like bows and arrows and make their first forays out of Africa. 

How much was climate responsible for this shift and how much was due to overhunting by modern humans?

A new paper makes the case for overhunting as the dominant cause of megafauna extinction worldwide. But I'm not convinced that there is a single answer. The paper itself observes that there are regional differences and then largely ignores this observation:

Population declines varied across ecological realms, with Australasia and the Neotropics experiencing the least severe declines over the Quaternary period (95% HPDI: [-0.244, 0.044] and [-0.228, -0.070], respectively), compared to Indomalaya and Nearctic (95% HPDI: [-0.458, -0.299] and [-0.410, -0.227], respectively). 

Separation of species according to the biome they occupy resulted in the largest discrepancy of population size decline between polar (95% HPDI: [-0.317, 0.037]) and temperate-adapted species (95% HPDI: [-0.460, -0.296]), while insectivores (95% HPDI: [-0.228, 0.201]) experienced a small and non-significant decrease compared to hypercarnivores (95% HPDI: [-0.394, -0.223]). 

Lastly, species with ranges overlapping regions where Homo sapiens was the first and only hominin present, tend to have the lowest decline (95% HPDI: [-0.269, -0.155]), compared to species in regions where archaic Homo species arrived early (95% HPDI: [-0.380, -0.290]). 

Generally, non-African temperate regions with a relatively long history of hominin activity experienced the largest decrease in megafauna population sizes. In contrast, and with the exception of polar species, warmer biomes with only H. sapiens activity seem to have declined the least. 

However, this observation is most likely driven by an increase of megafauna population sizes in Neotropics and Australasia between 1.25 million and 100,000 years ago, prior to human arrival. Notably, population decline starting at approximately 100,000 years ago, and continuing towards the present, is ubiquitous across realms.

In the Americas and especially in North America, the Younger Dryas climate event appears to have been a powerful driver of species extinction relative to the overhunting that had occurred by then. 

In Australia, we see one wave of mass megafauna extinction when modern humans arrive and a secondary wave when the dingo enters the Australian ecosystem.

In Africa, where modern humans originated and to a lesser extent in tropical Southeast Asia, megafauna extinction was more measured.

In Northern Eurasia, the Last Glacial Maximum ice age surely played some part in extinguishing megafauna and modern humans alike from the region and resulted in a global reduction of modern human effective population size almost everywhere in the world.

This paper's bottom line conclusion may be correct, but I'm not convinced that the story can be completely told at this level of generality.

The worldwide loss of large animal species over the past 100,000 years is evident from the fossil record, with climate and human impact as the most likely causes of megafauna extinctions. To help distinguish between these two scenarios, we analysed whole-genome sequence data of 142 species to infer their population size histories during the Quaternary. 

We modeled differences in population dynamics among species using ecological factors, paleoclimate and human presence as covariates. We report a significant population decline towards the present time in more than 90% of species, with larger megafauna experiencing the strongest decline. We find that population decline became ubiquitous approximately 100,000 years ago, with the majority of species experiencing their lowest population sizes during this period. 

We assessed the relative impact of climate fluctuations and human presence on megafauna dynamics and found that climate has limited explanatory power for late-Quaternary shifts in megafauna population sizes, which are largely explained by Homo sapiens arrival times. 

As a consequence of megafauna decline, total biomass and metabolic input provided by these species has drastically reduced to less than 25% compared to 100,000 years ago. These observations imply that the worldwide expansion of H. sapiens caused a major restructuring of ecosystems at global scale.

Juraj Bergman, et al., "Worldwide late-Quaternary population declines in extant megafauna are due to Homo sapiens rather than climate" bioRxiv (August 15, 2022). doi: https://doi.org/10.1101/2022.08.13.503826

A Long, Long Time Ago, On Earth

 The names are obviously anachronistic.

Borgs

Scientists last year discovered a whole new kind of DNA bearing entity. Whether it is an organism itself isn't entirely clear, and if it is one, it doesn't fit into any of the existing categories of DNA bearing entities.

It's one thing to find a new species or even a new family or organisms, it's another to find a whole new kind of organism which is on a par with being the first person to discover viruses. It is quite an exciting discovery.

In the TV series Star Trek, the Borg are cybernetic aliens that assimilate humans and other creatures as a means of achieving perfection. So when Jill Banfield, a geomicrobiologist at the University of California, Berkeley, sifted through DNA in the mud of her backyard and discovered a strange linear chromosome that included genes from a variety of microbes, her Trekkie son proposed naming it after the sci-fi aliens. The new type of genetic material was a mystery. Maybe it was part of a viral genome. Maybe it was a strange bacterium. Or maybe it was just an independent piece of DNA existing outside of cells. . . .

Banfield . . . and graduate student Basem Al-Shayeb were searching for viruses that infect archaea, a type of microbe often found in places devoid of oxygen. They would dig 1 meter or more below the surface and collect mud samples that might harbor archaea and their viruses. Next, they would sequence every stretch of DNA in the samples and use sophisticated computer programs to scan for sequences that signified a virus, rather than any other organism.

"We started off with a piece of mud and 10 trillion pieces of DNA," Banfield says. One sample, taken from the mud on her property, contained a gene-filled stretch of DNA almost 1 million bases long—and more than half the genes were novel. This linear stretch of DNA also had a particular pattern of bases at its beginning and end, distinct stretches of repetitive DNA between its genes, and two places along the sequence where DNA duplication could begin—which indicated the Borg could make copies of itself. Together, this suggested it was not just a random concoction of genes.

After they identified the first Borg sequence, the researchers began to scan microbial DNA in public databases to see whether they could find anything similar. They found a few variations in groundwater from Colorado—there, the first purported Borg showed up about 1 meter deep and got more abundant deeper down. Other versions showed up in DNA from the discharge of an abandoned mercury mine in Napa, California, and from a shallow riverbed of the East River in Colorado.

Altogether, the researchers isolated 23 sequences they think may be Borgs—and 19 they have identified as having all the characteristics of the first Borg they discovered, they write . . . on the preprint server bioRxiv. Some are almost 1 million bases long. "I don't think anything else that's been discovered is as big as these guys are," among previously known extrachromosomal DNA elements, Doolittle says.

In every place, copies of the Borg co-occurred with DNA linked to a methane-oxidizing archaeon called Methanoperedens. That suggests the Borgs may exist inside the microbe, the researchers say. But because Methanoperedens can't be grown in a lab, the team hasn't been able to confirm this suspicion. Meanwhile, team members have ruled out the possibility that the Borg came from another microbe, as they lack many necessary genes for life, or a virus, which typically have shorter chromosomes.

From Science.

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions, yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetland soil where methane production and oxidation occur, we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins. Four curated, complete genomes are linear, up to ~1 Mbp in length and share genome organization, including replicore structure, long inverted terminal repeats, and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are a new type of archaeal extrachromosomal element with a distinct evolutionary origin. Gene sequence similarity, phylogeny, and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as “Borgs”. We identified at least 19 different Borg types coexisting with Methanoperedens in four distinct ecosystems. Borg genes expand redox and respiratory capacity (e.g., clusters of multiheme cytochromes), ability to respond to changing environmental conditions, and likely augment Methanoperedens capacity for methane oxidation (e.g., methyl coenzyme M reductase). By this process, Borgs could play a previously unrecognized role in controlling greenhouse gas emissions.

Basem Al-Shayeb, "Borgs are giant extrachromosomal elements with the potential to augment methane oxidation" bioRxiv (July 10, 2021).