Category Archives: Evolution and paleontology

Evolution and paleontology

Xing Xu

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Chinese Academy of Sciences, Beijing

A palaeontologist considers the evolution of birds’ mechanism of breathing.

During both inhalation and exhalation, the air in birds’ lungs moves in just one direction, through small tubes. This is unusual: most animals move air tidally, in and out of dead-end gas-exchange structures. The question of when and how the avian breathing mechanism evolved is interesting to palaeontologists like me who study these unusual features.

Traditionally, the avian pattern of one-way breathing has been thought to depend on special accessory air sacs that work similarly to bellows. Largely because they don’t have these air sacs, alligators have always been presumed to be tidal breathers. However, this has now been questioned by Colleen Farmer and Kent Sanders at the University of Utah in Salt Lake City, who suggest that alligators actually breathe like birds (C. G. Farmer & K. Sanders Science 327, 338–340; 2010).

By measuring air and water flows in the lungs of anaesthetized and dead alligators, respectively, the authors demonstrate unidirectional flow. They draw the reasonable inference that this bird-like breathing is characteristic of the archosaurs, a broad group that includes both alligators and birds.

The finding is leading to changes in the direction of palaeontological research. Farmer and Sanders’ results imply that air sacs are not essential for unidirectional breathing. The function of these sacs in extinct ancestors of birds — dinosaurs such as theropods — should thus be reconsidered.

Unidirectional breathing probably appeared among ancestral archosaurs during the Early Triassic period, some 250 million years ago, a time of low oxygen levels that might have encouraged evolutionary experimentation with improved ventilation. This raises the question of whether the drastic conditions led to other notable changes in Triassic animals.

Matt Friedman

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University of Oxford, UK

A palaeontologist ponders how biodiversity is spread across the vertebrate tree of life.

Why do some biological groups burst at the seams with many different species, whereas others, despite their deep evolutionary heritage, contain only a handful of members? Many of my old vertebrate-biology textbooks are rife with qualitative scenarios, peddled with surprising degrees of confidence, that explain how species-rich branches can chalk up their success to key evolutionary ‘innovations’ and how less-diverse ones haven’t kept up with changing conditions. What you won’t find are details of how these exceptional groups might be identified in the first place.

Michael Alfaro of the University of California, Los Angeles, and his colleagues have now quantified this black art (Proc. Natl Acad. Sci. USA 106, 13410–13414; 2009). They marry statistically explicit models with fossil-calibrated evolutionary trees and counts of living species to ask a basic, but surprisingly unanswered question: precisely which branches of the vertebrate family tree are more or less species-rich than expected given their age?

The authors identify nine groups that show substantial changes from the background tempo of vertebrate evolution: ‘living fossils’ such as lungfishes are characterized by lower-than-predicted diversity, whereas other branches, such as the perch-like fishes and a subset of mammals, contain vastly more species than expected.

As a palaeontologist, I am intrigued that three of the exceptionally diverse radiations are thought (although not without controversy) to have proliferated following the mass extinction that killed off the dinosaurs, hinting at the far-reaching consequences of this event in structuring the modern vertebrate fauna. Most importantly, these authors establish a clear quantitative framework that can be used to test all those textbook stories. I’m confident that in a few years, my students will learn a much more nuanced picture of vertebrate diversification than I ever did, one that will trace its own roots back to studies such as this.

Manyuan Long

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University of Chicago, Illinois, USA

An evolutionary geneticist is surprised by genes of unknown origin.

I once thought that, like us, every gene must have a mother. But recent work has identified some genes that seem to have no genetic ancestry. These ‘motherless’ genes pose a new challenge to understanding the molecular mechanisms and evolutionary forces that shape our DNA. This isn’t the first time we’ve had to revise our ideas about gene evolution.

About 40 years ago, geneticist Susumu Ohno proposed that new genes originate when an existing gene duplicates, then one of the copies evolves a new function. Working with Chuck Langley in the early 1990s, I had the luck to discover a gene in flies that added another strand to Ohno’s story. The gene, named Jingwei, is a chimaera that formed through the combination of two existing genes.

Since then, researchers have identified many other ‘new’ genes assembled from unrelated genes and mobile DNA elements. Often the sequences’ origins can be identified. When they can’t, researchers have simply assumed that subsequent evolution has masked the relationship of the gene to its ancestral sequences.

But this is unlikely to be the case for hydra, a gene found recently in Drosophila melanogaster and closely related species (S.-T. Chen et al. PLoS Genet. 3, e107; 2007). No homologous sequences are found in a species that diverged from those carrying hydra only 13 million years ago — too recently for mutations to have obscured any related sequences. This implies that hydra arose de novo.

Another group has found a further 16 de novo genes in flies, which they propose evolved from non-coding DNA (D. J. Begun et al. Genetics 176, 1131–1137; 2007 and M. T. Levine et al. Proc. Natl Acad. Sci. USA 103, 9935–9939; 2006). These genes beg further study: what initiated their formation?

Editor’s Note, the entry previously misspelled the name of the author’s institution. Nature regrets the error.

Eörs Szathmáry

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Collegium Budapest, Hungary, and The Parmenides Foundation for the Study of Thinking, Munich, Germany

A theoretical biologist recommends thought-provoking reading on the origin of translation and the genetic code.

As Francis Crick and his co-workers once noted, “the origin of protein synthesis is a notoriously difficult problem”. Our best hopes of resolving this problem begin, in my opinion, in an RNA world.

The RNA-world hypothesis holds that RNA emerged before DNA and proteins, neatly separating the origin of life from that of the genetic code and its translation. The question then becomes: how did RNA evolve to make proteins?

In a recent paper, Yuri Wolf and Eugene Koonin of the National Institutes of Health in Bethesda, Maryland, present one scenario (Biol. Direct 2, 14; 2007).

They rightly call attention to studies that suggest that protein-based aminoacyl-tRNA synthetases, which are involved in the first steps of assembling amino acids into proteins, are relatively late evolutionary inventions. This forces us to accept the idea that protein synthesis is older than such synthetases.

Before the evolution of synthetases, the only agents that could conceivably have marshalled amino acids are RNA enzymes, or ribozymes. Wolf and Koonin share my view that the recruitment of amino acids was driven by selection for enhanced catalytic activity, and that the ancestor of the large ribosomal RNA that catalyses protein synthesis in today’s cells — a molecular ‘fossil’ — was a catalyst that linked only two amino acids.

I am less happy with these authors’ suggestion of a relatively late switch from peptide-specific proto-ribosomes to those that could use an external template such as mRNA to synthesize peptides with arbitrary sequence — but they may well be right.

They lay out an evolutionary sequence that is more complete than the scenario I once proposed. I highly recommend this well-written, thought-provoking paper.

Michael Purugganan

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New York University, USA

An evolutionary geneticist wonders why certain crops were ‘invented’ not once but multiple times.

Crop species have always captured my imagination — perhaps because Darwin saw domestication as a model for the evolutionary process, or maybe because I am an inveterate foodie. Whatever the reason, I work on the evolution of crop species as diverse as rice, barley and cauliflower, using genomic methods to trace their origins.

I was struck by two recent molecular studies that indicate that key crops may have evolved more than once in association with different cultures, after Neolithic farmers began to cultivate various wild plants and select desirable traits 12,000 years ago.

Rice seems to have originated from the wild rice Oryza rufipogon separately in China and in India and southeast Asia (J. P. Londo et al. Proc. Natl Acad. Sci. USA 103, 9578–9583; 2006). Meanwhile, barley, which originated once in the Fertile Crescent — a region defined by an arc through Lebanon, Syria, Turkey and Iraq, and home to the oldest archaeological evidence for agriculture — may also have had a second origin in present-day eastern Iran (P. L. Morrell and M. T. Clegg Proc. Natl Acad. Sci. USA 104, 3289–3294; 2007).

Previous genetic mapping studies of the loss of seed shattering in rice and barley suggests that the trait is controlled by different genes in different lineages of these crops. This makes sense in the light of a multiple-origins scenario.

The pattern is not unique — cattle, sheep and goats were also domesticated multiple times. So did different cultures learn how to go about domesticating wild plants and animals from each other, or did they arrive at the same evolutionary solutions independently when faced with similar challenges? Hopefully the genetic data will motivate archaeologists to dig for evidence of how groups of people went about developing these crops.

Paul Kenrick

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The Natural History Museum, London, UK

A palaeobotanist finds answers to the origin of roots in the genes of a living moss.

Roots have been called the hidden half of plant diversity. Confined mainly to the subterranean, their unseen influence extends well beyond the plant that they sustain to form an integral component of soil ecosystems and a significant link in the carbon cycle.

In my research, I use fossils to piece together how the fundamental organs and basic lifecycles of plants evolved, and roots are one of the key systems. The fossil record shows that roots were an early innovation in the colonization of the land, and that they evolved remarkably rapidly, developing a diversity of forms comparable to those of the aerial shoots, stems and leaves. Comparative morphology is good for documenting how roots evolved, but are there any underlying molecular developmental similarities among the rooting structures of early plants?

An elegant piece of recent research shows that a similar transcription factor encoded by the gene ROOT HAIR DEFECTIVE 6 regulates root-hair development in the flowering plant Arabidopsis thaliana and rhizoid development in the moss Physcomitrella patens (B. Menand et al. Science 316, 1477–1480; 2007). Because flowering plants and mosses diverged more than 400 million years ago, this surprising result implies that the cells with a key role in nutrient acquisition and anchorage in most land plants share a molecular developmental pathway that is very ancient indeed.

More surprising still is the notion that these genes are expressed in both haploid and diploid plants — that is, those whose cells have one or two sets of chromosomes, respectively. Many plants cycle between haploid and diploid forms during their lifecycles. Menand et al. propose that genes expressed in early haploid plants were turned on in many tissues during the evolution of plants with diploid phases. Pending further testing, this interesting model is plausible for components of the vascular system, cortex, epidermis, shoot and root.

Axel Kleidon

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Max-Planck Institute for Biogeochemistry, Jena, Germany

A biogeochemist finds inspiration for life on the ocean floor.

My research interests lie in understanding the interplay between the physical and chemical conditions that constrain life, and the feedback processes by which life shapes the Earth’s environment.

I want to understand these interactions in terms of a thermodynamic hypothesis that states that systems dissipate as much energy as possible. Can life be seen as an emergent outcome of this tendency for the whole Earth system? To test this, one would need to show that it is possible to predict the emergence of life from the hypothesis, as well as its impact on Earth’s early environment.

Two articles (M. J. Russell & A. J. Hall GSA Memoir 198, 1–32; 2006, and M. J. Russell Am. Sci. 94, 32–39; 2006) could provide a starting point. The authors give a detailed picture of the thermodynamics of life emerging at hydrothermal mounds on the ocean floor.

One of the earliest metabolic reactions would have involved the conversion of hydrogen, carbon dioxide and sulphur compounds into organic carbon, acetate and water. This would have happened in the hot, mineral-rich spring water seeping into the hollow mound.

But its influence would have been felt more widely. Removing sulphur from the environment would have changed atmospheric composition and cloud cover, affecting the amount of sunlight reaching the ground. And acetate may have served as fuel for methanogens, methane-producing organisms known to live in vents. Increased methane production would have raised its levels in the atmosphere, resulting in higher surface temperatures on Earth.

Quantifying these interactions should help us to understand whether the evolution of our planet emerged from general thermodynamic trends.

David R. Liu

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Harvard University, Cambridge, Massachusetts, USA

Thanks to the discovery of a new catalytic RNA, a chemical biologist can satisfy his student’s curiosity.

An first-year undergraduate recently asked me a remarkable question: are all natural ribozymes, RNA molecules with catalytic activity, simply leftovers from the ‘RNA world’? The RNA-world hypothesis supposes that RNA molecules were precursors to the first primitive forms of life, before the evolution of DNA and proteins.

Unanswered, my student’s question preoccupied me until I encountered a recent paper by Jack Szostak of Massachusetts General Hospital, Boston, and his co-workers (K. Salehi-Ashtiani et al. Science 313, 1788–1792; 2006).

Prior to this work, only two of the known natural ribozymes were associated with mammals. The rarity of catalytic RNAs in more recently evolved, higher-order cells could reflect their attrition on the evolutionary battlefield during the rise of more highly functional protein enzymes.

This paper, however, supports a different conclusion. Szostak’s group designed an ingenious system to isolate self-cleaving RNA molecules from RNA encoded in the human genome. Using this system, they discovered several new ribozymes.

One of these ribozymes, associated with a gene known as CPEB3, is highly conserved among placental mammals and marsupials, but is absent from non-mammalian vertebrates. This observation suggests that it arose relatively recently, around 200 million years ago.

We can therefore infer that some ribozymes have evolved in modern organisms, long after the era of the RNA world. The work elegantly demonstrates a new approach to the study of ancient molecules — and also reminds me that our youngest students can ask some of the best questions.

Michael Sanderson

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University of Arizona, Tucson

A biologist turns his attention to evolution’s neglected radiations.

Evolution’s spectacular adaptive radiations get a lot of press: Darwin’s finches and the Hawaiian silversword plants being textbook examples. These organisms, in adapting to environmental pressures, underwent both rapid speciation and radical morphological change.

Such episodes give rise to easily observable diversity and have stimulated extensive study. But how about those hyperdiverse clades in the tree of life in which many species have little morphological difference between them?

I first pondered this problem when musing about my thesis on the flowering-plant taxon Astragalus. I was cursed with perhaps 2,500 species, many remarkably similar. Their small differences were typically of uncertain adaptive significance.

Alas, I have counted barely ten papers since then that have addressed such radiations, which end up being labelled as ‘non-adaptive’. I hope the most recent will shake things up a bit.

It analyses the speciation rate of North American Plethodon, a clade of salamanders most diverse in the woodlands of the Appalachian mountains (K. H. Kozak et al. Proc. R. Soc. B. 273, 539–546; 2006). This group has an evolutionary history that runs back 28 million years and has spun off about 46 species, many of which are only diagnosable by molecular markers.

Remarkably, the rate of speciation in the group’s early days matched or exceeded rates seen in the textbook adaptive radiations. This suggests that we have a lot to learn about the evolutionary phenomena driving such radiations.

The authors make some interesting suggestions about the role of geography, ecology and adaptation in the salamanders’ evolution. For example, the lineages may have evolved by tracking the ebb and flow of favourable habitats.