Lifeboat Foundation

As sponges and ctenophores are such disparate animals¹³, the nature of the first diverging animal lineage has implications for the evolution of fundamental animal characteristics. Adult sponges are generally sessile filter-feeding organisms with body plans organized into reticulated water-filtration channels, structures built out of silica or calcium carbonate, and specialized cell types and tissues used for feeding, reproduction and self-defence, but they lack neuronal and muscle cells¹⁵. By contrast, ctenophores are gelatinous marine predators that move using eight longitudinal ‘comb rows’ of ciliary bundles^16,17; they are superficially similar but unrelated to cnidarian medusae^13,18 and possess multiple nerve nets¹⁹. Thus, whereas the sponge-sister scenario suggests a single origin of neurons on the ctenophore–parahoxozoan stem, the ctenophore-sister scenario implies either that either ancestral metazoan neurons were lost in the sponge lineage, or that there was convergent evolution of neurons in the ctenophore and parahoxozoan lineages^3,6. Similar considerations apply to other metazoan cell types¹⁸, gene regulatory networks, animal development^13,18 and other uniquely metazoan features.

Despite its importance for understanding animal evolution, the relative branching order of sponges, ctenophores and other animals has proven to be difficult to resolve². The fossil record is largely silent on this issue as verified Precambrian sponge fossils are extremely rare²⁰ and putative fossils of the soft-bodied ctenophores are difficult to interpret²¹. Morphological characters of living groups (for example, choanocytes of sponges) are not sufficient to resolve the question because true homology is difficult to assign, and such characters are easily lost or can arise convergently^13,22. The ctenophore-sister hypothesis is supported by a pair of gene duplications shared by sponges, bilaterians, placozoans and cnidarians but not ctenophores²³. Although sophisticated methods for sequence-based phylogenomics have been developed and applied to increasingly large molecular datasets, there is still considerable debate about the relative position of sponges and ctenophores as results are sensitive to how sequence evolution is modelled¹¹, which taxa or sites are included^24,25, and the effects of long-branch artifacts and nucleotide compositional variation²⁶. New approaches are needed.

We reasoned that patterns of synteny, classically defined as chromosomal gene linkage without regard to gene order²⁷, could provide a powerful tool for resolving the ctenophore-sister versus sponge-sister debate. Chromosomal patterns of gene linkage evolve slowly in many lineages^12,28,29,30, probably because it is improbable for interchromosomal translocations to be fixed in populations with large effective population sizes^28,31,32. Notably, some changes in synteny are effectively irreversible. For example, when two distinct ancestral synteny groups are combined onto a single chromosome by translocation, and subsequent intrachromosomal rearrangements mix these two groups of genes, it is very unlikely that the ancestral separated pattern will be restored by further rearrangement and fission, in the same sense that spontaneous reduction in entropy is improbable¹². Such rare and irreversible changes are particularly useful for resolving challenging phylogenetic questions as they give rise to shared derived features that unambiguously unite all descendant lineages^33,34,35. Deeply conserved syntenies observed between animals and their closest unicellular relatives¹² suggest that outgroup comparisons could be used to infer ancestral metazoan states and polarize changes within animals to address the sponge-sister versus ctenophore-sister debate. Yet, chromosome-scale genome sequences of the unicellular or colonial eukaryotic outgroups closest to animals (choanoflagellates, filastereans and ichthyosporeans) have not been reported.

Dr. Steven Gazal, an assistant professor of population and public health sciences at the Keck School of Medicine of USC, is on a mission to answer a perplexing question: Why, despite millions of years of evolution, do humans still suffer from diseases?

As part of an international research team, Gazal has made a groundbreaking discovery. They’ve become the first to accurately pinpoint specific base pairs in the human genome that have remained unaltered throughout millions of years of mammalian evolution. These base pairs play a significant role in human disease. Their findings were published in a special Zoonomia edition of the journal Science.

Gazal and his team analyzed the genomes of 240 mammals, including humans, zooming in with unprecedented resolution to compare DNA.

Scientists with the Human Pangenome Reference Consortium have made groundbreaking progress in characterizing the fraction of human DNA that varies between individuals. They have assembled genomic sequences of 47 people from around the world into a so-called pangenome in which more than 99 percent of each sequence is rendered with high accuracy.

For two decades, scientists have relied on the human reference genome as a standard to compare against other genetic data. Thanks to this reference genome, it was possible to identify genes implicated in specific diseases and trace the evolution of human traits, among other things.

However, it has always been a flawed tool: 70% of its data came from a single man of predominantly African-European background whose DNA was sequenced during the Human Genome Project. Hence, it can reveal very little about individuals on this planet who are different from each other, creating an inherent bias in biomedical data believed to be responsible for some of the health disparities affecting patients today.

A spinning plasma ring mimics the rotating structure surrounding a black hole.

Astrophysicists have many questions about the so-called accretion disk that forms from plasma and other matter falling into a black hole. Now researchers have generated a rotating ring of plasma in an unconfined arrangement in the lab, which will enable more realistic studies of plasma in astrophysical disks [1]. The lab plasma also produced a jet perpendicular to the disk, as real black holes do. The experiment could provide a platform for testing theories describing the evolution of astrophysical disks.

According to observations, the matter in a black hole accretion disk spirals inward at a rate that is thousands of times faster than would be expected from turbulence-free rotation. The leading explanation involves turbulence generated in part by the interaction of magnetic fields with the plasma in the disk, but this theory is difficult to test without a lab plasma that rotates rapidly. Such an experimental system would also allow researchers to investigate accretion disks around massive objects other than black holes.

In a major advance, scientists have assembled genomic sequences of 47 people from diverse backgrounds to create a pangenome, which offers a more accurate representation of human genetic diversity than the existing reference genome. This new pangenome will help researchers refine their understanding of the link between genes and diseases, and could ultimately help address health disparities.

For more than 20 years, scientists have relied on the human reference genome, a consensus genetic sequence, as a standard against which to compare other genetic data. Used in countless studies, the reference genome has made it possible to identify genes implicated in specific diseases and trace the evolution of human traits, among other things.

But it has always been a flawed tool. One of its biggest problems is that about 70 percent of its data came from a single man of predominantly African-European background whose DNA.

Exceptionally well-preserved fossils from the Cambrian period have helped fill a gap in our understanding of the origin and evolution of major animal groups alive today.

A new analysis of fossils belonging to an extinct invertebrate called Rotadiscus grandis have helped place this species in the animal tree of life, revealing how some characteristics of living species may have evolved independently rather than originating in a single common ancestor.

Half a billion years ago, an unusual-looking animal crawled over the sea floor, using tentacles to pick up food particles along the way.

A study of the mechanical forces in certain immune cells may give new insights into how organisms deal with ever-evolving pathogens.

To fight disease, many organisms have an adaptive immune system, which learns the molecular shapes of foreign elements (antigens) and remembers them to mount a defense against future infections. In vertebrates, the learning stage involves a remarkable cycle of evolution within an individual animal—a cycle called affinity maturation, which involves a type of immune cell called a B cell (Fig. 1). In this process, B cells are selected to have receptors that bind strongly to specific antigens. However, if these cells become too specialized, they risk becoming unresponsive to slightly mutated pathogens. Fortunately, the immune system can limit affinity maturation to retain a range of specificities for target pathogens. Just how the immune system is able to do that is the subject of a fascinating new study by Hongda Jiang and Shenshen Wang from the University of California, Los Angeles [1].

Mathematicians have uncovered a universal explanatory framework that provides a “window into evolution.” This framework explains how molecules interact with each other in adapting to changing conditions while still maintaining tight control over essential properties that are crucial for survival.

According to Dr. Araujo from the QUT School of Mathematical Sciences, the research results provide a blueprint for the creation of signaling networks that are capable of adapting across all life forms and for the design of synthetic biological systems.

“Our study considers a process called robust perfect adaptation (RPA) whereby biological systems, from individual cells to entire organisms, maintain important molecules within narrow concentration ranges despite continually being bombarded with disturbances to the system,” Dr. Araujo said.

Like treasured recipes passed down from generation to generation, there are just some regions of DNA that evolution doesn’t dare tweak. Mammals far and wide share a variety of such encoded sequences, for example, which have remained untouched for millions of years.

Humans are a strange exception to this club. For some reason, recipes long preserved by our ancient ancestors were suddenly ‘spiced up’ within a short evolutionary period of time.

Because we’re the only species in which these regions have been rewritten so rapidly, they are called ‘human accelerated regions’ (or HARs). What’s more, scientists think at least some HARs could be behind many of the qualities that set humans apart from their close relatives, like chimpanzees and bonobos.