Does Protein-coding Occur at a Steady-state?

Interesting Article;

Abstract:

The evolutionary rates of protein-coding genes in an organism
span, approximately, 3 orders of magnitude and show a universal,
approximately log-normal distribution in a broad variety of species
from prokaryotes to mammals. This universal distribution implies
a steady-state process, with identical distributions of evolutionary
rates among genes that are gained and genes that are lost. A
mathematical model of such process is developed under the single
assumption of the constancy of the distributions of the propensities
for gene loss (PGL). This model predicts that genes of different
ages, that is, genes with homologs detectable at different phylogenetic
depths, substantially differ in those variables that correlate
with PGL. We computationally partition protein-coding genes from
humans, flies, and Aspergillus fungus into age classes, and show
that genes of different ages retain the universal log-normal distribution
of evolutionary rates, with a shift toward higher rates in
‘‘younger’’ classes but also with a substantial overlap. The only
exception involves human primate-specific genes that show a
heavy tail of rapidly evolving genes, probably owing to gene
annotation artifacts. As predicted, the gene age classes differ in
characteristics correlated with PGL. Compared with ‘‘young’’ genes
(e.g., mammal-specific human ones), ‘‘old’’ genes (e.g., eukaryotespecific),
on average, are longer, are expressed at a higher level,
possess a higher intron density, evolve slower on the short time
scale, and are subject to stronger purifying selection. Thus, genome
evolution fits a simple model with approximately uniform rates of
gene gain and loss, without major bursts of genomic innovation.

Read the rest here;
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

Street Smart Birds

Omnivorous Pleistocene Bears Give Clues to Adaptation

By comparing the morphological features of Pleistocene bear fossils (Arctodus simus and Ursus spelaeus) with that of modern bears, scientists report that analogous cranio-mandibular structures indicate that even the prehistoric hyper carnivores had omnivorous tendencies.

These and other findings provide clues as to the niche plasticity and the ability of mammals to adapt to fluctuating climates.



'Knowing what the extinct bears ate is of utmost relevance to finding out about the evolution of carnivore niches in the Pleistocene when climatic conditions were changing', explains Borja Figueirido, lead author of the study and researcher for the Ecology and Geology Department of the Faculty of Sciences at the University of Málaga.



Figure Above: Landmarks used for describing cranial and mandibular shape. Cranium: (1) most postero-dorsal border of the canine alveolus, (2) most antero-dorsal border of the canine alveolus, (3) most antero-dorsal border of the I3, (4) most anterior edge of the nasal bones, (5) dorsal outline directly superior to post-orbital process, (6) dorsal outline directly superior to the end of the zygomatic arch, (7) most postero-ventral point of the occipital crest, (8) intersection between the occipital condyle and the occiput, (9) intersection between the occipital condyle and the paraoccipital process, (10) ventral tip of postglenoid process, (11) posterior edge of the upper tooth row, (12) point between the upper carnassial and the first upper molar, (13) anterior edge of the upper tooth row, (14) postero-dorsal border of the zygomatic arch, (15) dorsal tip of the frontal process of the zygomatic arch, (16) orbit midheigth, (17) ventral tip of the post-orbital process, (18) ventral intersection between the zygomatic arch and the axilla.Mandible: (1) antero-dorsal border of the incisive alveolus, (2) postero-dorsal border of the canine alveolus, (3) intersection between the trigonid/talonid notch of the lower carnassial and the dorsal border of the alveolus of this tooth, (4) posterior edge of the lower tooth row, (5) posterior edge of the coronoid process, (6) most posterior edge of the articular surface condyle, (7) tip of angular process, (8) ventral outline below the mesial end of the tooth row, (9) ventral outline below the trigonid/talonid notch of the lower carnassial, (10) most ventral point of the symphyseal region. Scale bar equals 5 cm. Deviations of the specimens analyzed from the consensus configuration of landmarks are shown.



Read the research article published in the Journal of Zoology - HERE.



Figueirido, B., Palmqvist, P., & Pérez-Claros, J. (2009). Ecomorphological correlates of craniodental variation in bears and paleobiological implications for extinct taxa: an approach based on geometric morphometrics Journal of Zoology, 277 (1), 70-80 DOI: 10.1111/j.1469-7998.2008.00511.x

Wetland Plant of the Week #12

Sphagnum spp.

“Sphagnum Moss”

Small (1-10cm), obligate, non-vascular plant with tightly arranged clusters of branch fascicles, usually found growing as a dense mat (Picture 2).

Neither flowers nor seeds are present in this Bryophyte with reproduction occurring by fragmentation.

Sphagnum mat, between grasses

Photographed last week in Volusia County, Florida

Copulating for Carrion

Found this personal ad on Craigslist:

The ad reads:

Copulating for Carrion,
Currently unattached chimp with a passion for Tarzan swings and coprophagia seeks mutually compatible primate for reciprocal grooming, marking territory with urine and hanging around with the troop. Must have own carrion and be willing to share. No weirdoes need respond!

Unprofessional - I know – but couldn’t resist…

But in all seriousnessness (or at least in relative seriousness), check out this article on PLoS One;

Wild Chimpanzees Exchange Meat for Sex on a Long-Term Basis

From the Abstract

"Humans and chimpanzees are unusual among primates in that they frequently perform group hunts of mammalian prey and share meat with conspecifics. Especially interesting are cases in which males give meat to unrelated females. The meat-for-sex hypothesis aims at explaining these cases by proposing that males and females exchange meat for sex, which would result in males increasing their mating success and females increasing their caloric intake without suffering the energetic costs and potential risk of injury related to hunting. Although chimpanzees have been shown to share meat extensively with females, there has not been much direct evidence in this species to support the meat-for-sex hypothesis. Here we show that female wild chimpanzees copulate more frequently with those males who, over a period of 22 months, share meat with them. We excluded other alternative hypotheses to exchanging meat for sex, by statistically controlling for rank of the male, age, rank and gregariousness of the female, association patterns of each male-female dyad and meat begging frequency of each female. Although males were more likely to share meat with estrous than anestrous females given their proportional representation in hunting parties, the relationship between mating success and sharing meat remained significant after excluding from the analysis sharing episodes with estrous females. These results strongly suggest that wild chimpanzees exchange meat for sex, and do so on a long-term basis. Similar studies on humans will determine if the direct nutritional benefits that women receive from hunters in foraging societies could also be driving the relationship between reproductive success and good hunting skills."

The Hand of God Photographed!

Or, a nebula...


From Cosmic Hand Reaches for the Light:





In a new image from NASA's Chandra X-ray Observatory, high-energy X-rays emanating from the nebula around PSR B1509-58 have been colored blue to reveal a structure resembling a hand reaching for some eternal red cosmic light.

Classic Attenborough Video - 1979

"Invasion of the Land"

FROM: Life on Earth: A Natural History by David Attenborough (1979)

Holotomography of a Carboniferous Chimaeroid

Impressive brain imagery of a 300 million year old fish…


“This application of holotomography confirms the rapidly growing possibilities of X-ray synchrotron phase imaging techniques in palaeontology, especially when dealing with the exceptional soft-tissue preservations. It imposes synchrotron radiation as a powerful tool for nondestructive imaging of fossils.”

From Abstract: “Living cartilaginous fishes, or chondrichthyans, include numerous elasmobranch (sharks and rays) species but only few chimaeroid (ratfish) species. The early history of chimaeroids, or holocephalans, and the modalities of their divergence from elasmobranches are much debated. During Carboniferous times, 358–300 million years (Myr) ago, they underwent a remarkable evolutionary radiation, with some odd and poorly understood forms, including the enigmatic iniopterygians that were known until now from poorly informative flattened impressions. Here, we report iniopterygian skulls found preserved in 3 dimensions in _300-Myr-old concretions from Oklahoma and Kansas…”

[Click Link Below to Continue]

Figure 1

Fig. 1. The anatomy of iniopterygians. (A) Reconstruction of Sibyrhynchus denisoni (based on ref. 5, not to scale). (B and C) Part (B) and counterpart (C) of a phosphatic nodule from the Pennsylvanian of Oklahoma (AMNH OKM38) containing the braincase and shoulder girdle of Sibyrhynchus sp. (D–F) Threedimensional reconstruction of the same specimen, obtained from conventional X-ray _CT images, showing the braincase in dorsal (D), ventral (E), and lateral (F) view, with associated teeth. (G–I) Three-dimensional reconstruction of the braincase, shoulder girdle, and pectoral fin elements of a sibyrhynchid iniopterygian from the Pennsylvanian of Kansas (KUNHM 21894), based on SR-_CT images. Braincase in dorsal (G), posterior (H), and ventral views, with articulated shoulder girdles and pectoral fin radials (I). Scale bar, 5 mm; f.IX and f.X, foramina for glossopharyngeus and vagus nerves).

Figure 2

Fig. 2. Braincase anatomy and exceptional brain preservation in a sibyrhynchid iniopterygian from the Pennsylvanian of Kansas. (A and B) articulated skull preserved in a nodule (KUNHM 22060) (see also Fig. S1) in dorsal (A) and anterior (B) view (arrow points forward). (C–Q), three-dimensional reconstructions and putative preserved brain structures of the same specimen, obtained from SR-_CT images (and holotomography for brain details). (C–H), Braincase, teeth, and lower jaw in lateral (C), anterior (D), ventral (E), posterior (F), and dorsal (G) view, showing by transparency the outline of the endocranial cavity and labyrinth (H). (I–K), Selected transverse (I and J), and horizontal (K) SR-_CT (holotomography) slices through the calcite-filled endocranial cavity, showing the probably phosphatized brain at the level of the rhombencephalon (I), hypophysis (J), and roof of the optic tectum and cerebellum (K). (L–N) Reconstruction of the endocranial cavity and otic capsule in dorsal (L andM) and lateral (N) view, showing the putative brain by transparency (Mand N). (O–Q), reconstruction of the putative phosphatized brain in dorsal (O), ventral (P), and lateral (Q) view. (Scale bar, 5mmfor A–N and 1mmfor I—K and O–Q. Asc, anterior semicircular canal; Cer, cerebellum; Ed, endolymphatic duct; Hsc, horizontal semicircular canal; Hyp, hypophysis; Olftr, canals for olfactory tracts; Opch, optic chiasm; Optec, optic tectum; Psc, posterior semicircular canal; II, optic nerve; III?, oculomotorius nerve?; IV?, trochlear nerve?; X?, roots of vagus nerve?).


Check out the article HERE.


Pradel, A., Langer, M., Maisey, J., Geffard-Kuriyama, D., Cloetens, P., Janvier, P., & Tafforeau, P. (2009). Skull and brain of a 300-million-year-old chimaeroid fish revealed by synchrotron holotomography Proceedings of the National Academy of Sciences, 106 (13), 5224-5228 DOI: 10.1073/pnas.0807047106

Astrobiology and the Origins of Life

Recorded April 3, 2009 @ NPR Science Friday
Is the appearance of life on Earth a fluke, or is the universe teeming with alien life? In a special broadcast from the Origins Symposium at Arizona State University, leading astrobiologists debate the origin of life on this planet and talk about the best places to look for other life in the universe.

Guests:
Ariel Anbar, principal investigator, NASA Astrobiology Institute team, professor, Arizona State University, Tempe , Ariz.

Barry Blumberg, M.D., winner, 1976 Nobel Prize in Physiology or Medicine, founding director, NASA Astrobiology Institute, senior advisor to the President, Fox Chase Cancer Center, Philadelphia, Penn.

Paul Davies, cosmologist, physicist, astrobiologist, director, The Beyond Center, Arizona State University, Tempe, Ariz.

Peter Ward, professor, department of biology, The Astrobiology Program, The University of Washington, Seattle, Wash.

CLICK HERE TO LISTEN TO THE PODCAST

Caution: Wide Turns - Shell in Tow

If one were to draw a line depicting the rate of average global speciation or evolutionary novelty produced over the last billion years, this linear representation would certainly have a spike near the geologic time of the Cambrian Explosion. By about 500 million years ago, all present day phyla (i.e. body-plans, or animal “designs”) had representative species on the planet (with the exception of Bryozoa), including that of the most abundant animal and second-most abundant organism overall found on earth today (following only bacteria) - the arthropods. The challenges these arthropods overcame in their journey from the sea to a terrestrial existence were both immense and varied. In a recent article published in Geology, James W. Hagadorn and Adolf Seilacher find clues to one arthropod’s strategy to overcome the obstacles of dehydration and desiccation as it makes the transition landward. Within the Orthoquartzites of the Elk Mound Group in central Wisconsin, a type of ichnofossils called Protichnites tell a tale of behavioral adaptation and evolution.

Protichnites are trace fossils that display two parallel lines of tracks with a linear depression at the center. The parallel lines are essentially rows of footprints aligned towards the animal’s direction of travel. Carefully examined, these lines can be used to translate and interpret gait. In the case of the currently examined Elk Mound fossils, “the deeper impressions made by the rear pair of walking legs (i.e., the “pushers”) repeat symmetrically, in the same rhythm as the shell marks. This suggests synchronous movement of leg pairs, similar to modern Limulus and eurypterids, rather than the alternating gait reflected in tracks of crustaceans, scorpions, and insects.”

Photos from Referenced Article

The linear depression at the center of the Protichnites fossils is thought to be remnant drag marks from a tail. When turning, the arthropod’s tail swings outward from the direction of the turn, like a pendulum; these “wide turns” can provide biomechanical clues describing the gait of the animal.

One set of fossils studied by the authors, later named Protichnites eremite (eremite = Hermit), displayed a medial depression with irregular characteristics. “Instead of following the midline, its markings consist of oblique impressions that are always offset and shingled to the left side. It is unlikely that this represents an individual or population of individuals characterized by a malformed tail, because similar trackways of different widths occur on the same bedding plane and because such trackways occur on more than one horizon. Because there are no pushback hills on the rear sides of the oblique ‘tail’ impressions, it is also unlikely that this asymmetry reflects a behavioral strategy, in which the tail was bent sideways in order to assist in locomotion.”

If the irregular tail marks don’t represent a morphological malformation or provide evidence for locomotion, then what do they indicate, what’s the diagnosis? According to Hagadorn and Seilacher, “the impressions resemble the touch marks of a high-spired, dextrally coiled shell” similar to that carried by modern day hermit crabs.

The conclusion reached by the researchers is that the arthropods, while in transition to a terrestrial existence, probably “still left the water only for short durations, crawling around on the wet sand flats during low tides.” These intertidal sand flats proved ideal for promoting the growth of thin microbial films on which the light-footed arthropods left tracks and trails that later fossilized.

Using modern hermit crabs as an analog, the authors surmised that, “with their cuticular exoskeletons and stiff appendages, arthropods were particularly well preconditioned for terrestrialization. Nevertheless their early pioneers still required special adaptations, such as large body sizes and the use of foreign shells, to minimize water loss.” Transporting a shell on their back buffered the arthropods from arid conditions, but at the same time altered their gait to such an extent that we can read it in the fossils today.

Hagadorn, J., & Seilacher, A. (2009). Hermit arthropods 500 million years ago? Geology, 37 (4), 295-298 DOI: 10.1130/G25181A.1

Capturing the Superorganism or Reviving a Monster?

"The beauty of the dream vanished, and breathless horror and disgust filled my heart," so said Victor, a well established scientist from the upper east side of Transylvania Switzerland as he witnessed life cross the threshold of the lifeless and into his newly created monster – Frankenstein!

Well, OK – maybe quoting from Mary Shelly’s Frankenstein is a bit over-the-top, but a recent article published in the Journal of Evolutionary Biology has made me question whether or not Andy Gardner and Alan Grafen have created a monster of their own – one that they may eventually come to regret.

In a recent article (available as a PDF Here) titled “Capturing the superorganism: a formal theory of group adaptation,” Gardner, a Royal Society University Research Fellow, and Grafen, a Professor at Oxford University widely known for his work in statistics (most memorable to me for his mathematical modeling of Zahavian Handicaps), define, describe and quantify group adaptation and group selection as functional modes of natural selection.

On one hand the article is innovative in that it takes steps to cleanly differentiate between often befuddled concepts, like “kin selection” versus “group selection” and various interpretations of “fitness;” it also empirically formalizes (and limits) the group adaptation theory - indeed it lifts the theory to new heights. However, on the other side of the coin, the article (antagonistically in my mind) compounds any preexisting misunderstanding of these concepts by arguing for even greater expansion of analogy.

For example, the article tediously - though accurately - makes distinctions between various measures of fitness, including inclusive fitness, relative fitness, within-group fitness, personal fitness, between-group fitness, individual fitness and indirect fitness; but then, rather than provide simplicity and clarity to this dizzying collection of measurement methodologies, the article uses them as a foundation in support of further artificial constructs – namely groups as individual units or actors in natural selection.

The superorganism enters… [As a side note, there is a good E.O. Wilson interview (audio file) at NPR’s Science Friday website from last December in which he discusses the superorganism concept and his book of the same title – HERE]

Through their delineations, Capturing the Superorganism’s authors intentionally reveal that both the individual organism and the “group” as focal points of adaptation are only ‘maximizing agent’ analogies and that both are only intermediaries to ever fluctuating gene frequencies. Unfortunately, rather than arguing for a more reductive measure of selection, an all encompassing fitness-model or perhaps even a gene-centered perspective, they instead suggest viewing the process at a greater scale and wider focus.

Ironically, the article opens with a quote from Richard Dawkins’ Extended Phenotype;

“I have characterized inclusive fitness as ‘that property of an individual organism which will appear to be maximized when what is really being maximized is gene survival’... One might generalize this principle to other ‘vehicles’. A group selectionist might define his own version of inclusive fitness as ‘that property of a group which will appear to be maximized when what is really being maximized is gene survival’!

This excerpt, and the context in which it is constructed, clearly makes an argument against viewing the individual organism as a unit of selection and implies that any unit above that of the gene is so artificial as to be considered arbitrary. Key to this idea is the phrase “will appear to be maximized,” which means that it is not truly being maximized, but rather it is a merely an extension of the gene – a vehicle. A “vehicle” is precisely what a “group” represents, a vehicle composed of multiple smaller vehicles – all of which have a gene behind the wheel.

From the abstract: “Adaptation is conventionally regarded as occurring at the level of the individual organism.”

Perhaps individual organisms are ‘conventionally regarded,’ but not accurately so… Individual organisms may be units of reproduction, but they are not replicators. Genes lay at the core of all phenotypes; morphological, behavioral, social or otherwise - is it really convenient to think of natural selection as occurring at the level of the individual organism? Most successful organisms aren’t replicated in their entirety; rather it’s the successful, or surviving, genes contained within their DNA that are passed on with an increased probability of contributing to the genome of future generations. Genes are passed on, not whole organisms; if the analogy is not “true” for individuals, why up the ante and recommend adopting a level of biological organization that is even higher than an individual?

The authors admit that the Group Maximization Analogy (GMA) does have limitations;

“we find that there is a strong mathematical correspondence between the ynamics of gene frequency change and the GMA analogy in scenarios where groups comprise genetically identical individuals or where within-group competition is repressed. This correspondence reveals that, in such scenarios, natural selection acts to optimize group phenotypes for the purpose of group fitness maximization –i.e. group adaptation.”

According to the authors, group adaptation seems a best fit in those situations in which individual members have identical genomes (i.e. are “cloned”) or in those scenarios where competition is repressed (i.e. is “policed,” or controlled by an external agent). Wouldn’t these situations, one in which like-vehicles “strive” to move like-genes, and one in which a dominant phenotype exhibits some level of control (policing or chemical control via pheromones) over a less-dominant phenotype, also represent strong cases for a gene-centered, or an Individual Maximization Analogy?

Considering that within-group selection (i.e. genes by way of individual organisms) is inevitable, are there any cases, or models for group-selection that take this into account?

“We have found no formal justification for group adaptationism in any scenario in which within-group selection is permitted. Obviously, no real-world species will perfectly embody the ideal of zero within-group selection.”

OK, doesn’t such a finding impair the group model as an inclusive theory?

“…we emphasize that this is not sufficient grounds for abandoning the notion of group adaptation in evolutionary biology.”

Why not?

“The theory of individual-level adaptation is similarly based upon limiting assumptions, such as unbiased genetic transmission, which are not expected to be perfectly realized in any species; yet, it enjoys huge experimental and empirical success.”

True, however the individual-level adaptation model is also a “maximization analogy,” used as a tool, artificially constructed to demonstrate, measure and communicate what in actuality is occurring at a lower level - the level of the gene. Is that the purpose of the GMA, simply an additional tool to be used in exhibiting the effects of genetic frequency, and if so what is the benefit of up-scaling from the level of the organism to that of the group, or extending the phenotype to greater distances, bearing in mind that at the very least the individual is the unit of reproduction and any expansion of analogy is likely to cause even greater confusion?

“Our emphasis has been on formality and not generality – there is much work to be carried out to establish whether other scenarios will admit a group adaptationist view of social evolution. In the meantime, we suggest that it is safer to view social adaptations as occurring at the level of the individual organism, where they function to maximize inclusive fitness.”

Gardner et al. (2009). Capturing the superorganism: a formal theory of group adaptation. Journal of Evolutionary Biology DOI: 10.1111/j.1420-9101.2008.01681.x

Wetland Plant of the Week #11

Utricularia cornuta

"Bladderwort"

Carnivorous, obligate (free floating) plant with small bladders located on stems that trap insects. Flowers can be white yellow, pink or purple.

From Wikipedia: All Utricularia are carnivorous and capture small organisms by means of bladder-like traps.

The traps can range is size from 0.2 mm to 1.2 cm. Aquatic species, such as U. vulgaris (common bladderwort), possess bladders that are usually larger and can feed on more substantial prey such as water fleas (Daphnia), nematodes and even fish fry, mosquito larvae and young tadpoles.

Despite their small size, the traps are extremely sophisticated. In the active traps of the aquatic species, prey brush against trigger hairs connected to the trapdoor. The bladder, when "set", is under negative pressure in relation to its environment so that when the trapdoor is mechanically triggered, the prey, along with the water surrounding it, is swept into the bladder. Once the bladder is full of water, the door closes again, the whole process taking only ten to fifteen thousandths of a second.

Photographed this one earlier today in Volusia County, Florida.