Clan of the cave bear: researching ancient DNA

Reconstruction of a cave bear (Ursus spelaeus)
Uploaded by Sergiodlarosa to Wikimedia Commons (CC)

The proceedings of a Royal Society discussion meeting on ancient DNA have just been published (here). Three reviews in particular captured my interest.

Ancient DNA: the first three decades by Hagelberg, Hofreiter and Keyser (here) is a lucid account of the history of the field (a major advance was shotgun sequencing as applied to the cave bear). It highlights not only high profile papers from Nature and Science (some of them reviewed in my blog), but also gives credit to important follow up studies from specialist journals. A very useful ressource indeed!

Ancient genomics by Der Sarkissian et al. (here) is from the renowned Centre for GeoGenetics in Copenhagen. This review is especially strong on the technical advances in the field and even includes a user's manual. With the techniques initially available it would have required 180 kg of material and 130 million amplicons to generate a first draft of the cave bear genome. A lot has happened since then. They conclude that even "Looking back 5 years, no one could have predicted the current state of current genomics."

Almost 20 years of Neanderthal palaeogenetics by Sánchez-Quinto and Lalueza-Fox (here) does a remarkably good job of surveying what has been learned from the DNA of Neanderthals from various geographical locations. It covers more than just their relations to and interbreeding with Denisovans and modern humans (previous post). A great deal can be inferred about their demographics, population size and ultimate extinction.

ISBN 0-517-54202-1

 The title of this post is of course an homage to the fiction of Jean M. Auel. The clan of the cave bear are Neanderthals who interact (and interbreed) with modern humans. First published in 1980 it far anticipated the scientific evidence given in the above reviews.

Pregnancy-associated malaria research suggests a way to target cancer cells

Anopheles stephensi - a vector for the malaria parasite
Centers for Disease Control and Prevention

The malaria parasite Plasmodium falciparum is spread by mosquitos. It multiplies and resides in the liver and erythrocytes (red blood cells). In areas with heavy infection with Plasmodium most individuals acquire immunity. During pregnancy, however, infected erythrocytes are able to accumulate in the placenta. Pregnancy-associated malaria is an important cause of maternal and fetal morbidity and mortality (reviewed here).



Placenta from a stillbirth due to maternal malaria infection. Normal erythrocytes lack
a nucleus. Thus a nucleus indicates the presence of the malaria parasite.
Wikimedia Commons (CC BY-SA 3.0) uploaded by Nephron

Infected erythrocytes express surface proteins, among them VAR2CSA, which can bind to a placental variant of chondroitin sulphate A (CSA) expressed by syncytiotrophoblast.

A paper just out in Cancer Cell (here) shows that placental CSA is expressed by many types of cancer cell. This knowledge was leveraged to target cancer cells using recombinant VAR2CSA fused to diptheria toxin or conjugated to hemiasterlin. Human cancer cells in vitro were effectively killed by this means. Tumour growth and metastasis in mice could be inhibited by a similar approach.

A. C. Haddon

Mask of turtle shell plates made by Torres Strait Islander and described by A. C. Haddon
Creative Commons (CC BY-NC-SA 4.0) The Trustees of the British Museum

Alfred Cort Haddon was a marine zoologist who  morphed into an eminent ethnologist and anthropologist after joining an expedition to the Torres Strait in 1898.

The Torres Strait Islanders are a Melanesian people distinct from the Aborigines of mainland Australia. Haddon collected their artefacts avidly -- convinced that their culture would soon be repressed by zealous missionaries. I had an opportunity to view some of these artefacts on a recent visit to the Queensland Museum in Brisbane. Haddon donated also to the British Museum, but the bulk of his Collection is now in the Museum of Anthropology and Archaeology at Cambridge University.

Alfred Cort Haddon (1855-1940)
The Wellcome Museum, Wellcome Images (CC BY 4.0)

Haddon's Collection was key to a 2011 study that examined the origin of the Australian Aborigines (here). A genomic sequence was obtained from a hair sample that had been collected in the 1920s as Haddon passed through Golden Ridge, near Kalgoorlie, Western Australia. Ethical concerns about using this material were allayed when it could be shown, with the aid of contemporary newspaper reports, that the sample was donated voluntarily. The main finding was that Aborigines are descendents of a human dispersal out of Africa that was separate and much earlier than that giving rise to present day Asians.



Cambridge University Press 1924 (Second and Revised Edition)

Human genomics has greatly improved our understanding of the migrations that gave rise to modern peoples. Haddon would have been fascinated. He did what he could with the tools then available to him and summarized them in the above book. The title was not as controversial at the time as it might be considered today.

Transcriptome of the pregnant male seahorse

Pot-bellied seahorse (Hippocampus abdominalis) from Sketchbook of Fishes
by William Buelow Gould (1801-53)

Viviparity in seahorses involves incubation of the embryos in the brood pouch of the male. A new study (abstract here) analyses the transcriptome of the brood pouch of the pot-bellied seahorse for genes that are upregulated during pregnancy and in transition to the post partum state.

Many of the same genes or their homologs are upregulated during pregnancy in mammals and other viviparous taxa. Placentologists will want to scan the tables for their favourite genes. I found it interesting that genes involved in lipid transport and iron transfer are upregulated.

The authors suggest the possibility that a common toolkit of genes is recruited to support pregnacy in mammals, reptiles and live-bearing fish.

Monotreme fetal membranes

Short-beaked Echidna (Tachyglossus aculeatus) Barossa Valley,
South Australia. It has tucked in its beak at the end by the tuft of grass

The three species of echidna and the duck-billed platypus constitute the order Monotremata. They produce milk and thus are mammals but they lay eggs. The aborigines knew this as reported by Caley in 1803 but their accounts were distrusted. It was not until 1884 that Caldwell could send his famous cable to the British Association: " Monotremes oviparous, ovum meroblastic."

Drawing of the echidna by Charles-Alexandre Lesueur 1802-3

The first description of an echidna, in 1792, was by Captain William Bligh of Bounty fame. The drawing above was made during the French Baudin expedition in 1802-3.

Because they lay eggs, one might suppose monotremes to lack a placenta. Yet two-thirds of embryonic development takes place in the uterus and the embryo is nourished in part by endometrial secretions. These are taken up by the yolk sac through the egg shell membrane, which is porous and able to stretch as the embryo grows in size. This state of affairs is best described as matrotrophy (explained here), although it has been argued that the yolk sac of monotremes ought to be regarded as a placenta (here).

Baltimore: The John Hopkins University Press 2004
ISBN 0-8018-8052-1 (pbk.) 

 For a fascinating and well illustrated account of early work on the embryology of monotremes, the above book can be recommended.

Defining the genus Homo

Reconstruction of Homo erectus georgicus by Élisabeth Daynes
Licensed under CC BY-SA 3.0 via Wikipedia Commons

A thought provoking essay in the current issue of Science (here) asserts definitions of the genus Homo and the species assigned to it remain "as fuzzy as ever." They drive home their point by showing, on the one hand, specimens attributed to Homo with australopithecine features and, on the other, australopithecine fossils with features hitherto claimed to be confined to Homo.

This is a brief but instructive read. The take home message is that hominid systematics needs to be rethought. In the process we may need to scrap "the iconic list of names in which fossil specimens have historically been trapped."

Cover of Third Edition 1956

One name that may have to go is Homo habilis (previous post), the handy man. Louis Leakey, it is suggested, was keen (perhaps too keen) to identify this fossil as the maker of simple tools following the dictum of Man the Toolmaker. It was a pleasant surprise to find Kenneth P. Oakley's booklet cited as an influence on previous and current thinking. My well thumbed copy dates from my schooldays.

Viviparity in extinct reptiles

Mesosaur - an aquatic reptile from the Palaeozoic
Nobu Tamura (CC BY 2.5 via Wikimedia Commons)

Dan Blackburn and Christian Sidor have written an interesting paper (here)summarizing the fossil evidence for viviparity in the Late Palaeozoic and Mesozoic Eras. They document a minimum of six separate evolutionary origins of viviparity. Most are aquatic reptiles including mesosaurs (picture), sauropterygians, ichthyopterygians, choristoderans and mosasauroids. The sixth example is a Cretaceous lizard Yabeinosaurus.



Mosasaurus hoffmannii - an aquatic reptile from the Late Cretaceous
 Nobu Tamura (CC BY 3.0 via Wikimedia Commons)

 It cannot be established with certainty that the fetuses were supported by a placenta, since soft tissues usually do not fossilize. The probability is great, however, given the advanced stage of development at birth and by analogy with present day snakes and lizards. Some have extremely complex placentas an example being the New World lizard Mabuya (here).

Materpiscis attenboroughi - a live-bearing fish from the Late Devonian 
Sularko - Museum Victoria (Licensed under CC BY-SA 3.0 via Wikimedia Commons)


My own article on fossil evidence for viviparity (here) was prompted by the discovery of an extremely well preserved fish with a putative umbilical cord (here).

The chicken or the egg

 As an afterthought it is of interest that the original amniote egg had a leathery shell like many reptiles today. A calcified shell was evolved at least four times (here) including in the dinosaur lineage that led to the birds. The calcified egg came before the chicken!