New species of river dolphin

The Araguaian boto (C) Nicole Dutra

The boto, Inia geoffrensis, popularly known as the pink dolphin, is widely distributed in the rivers of the Amazon basin. It is also found in the Araguaia-Tocantins river basin. Since the two basins became disconnected at the Pliocene-Pleistocene boundary, Tomas Hrbek and colleagues (here) asked if this really was the same species. They analysed morphological and molecular data (including mitochondrial genes), concluded that the Araguaian boto was a distinct species and named it Inia araguaiaensis. In addition they proposed that the boto found in the Bolivian sub-basin be raised from subspecies to species status as Inia boliviensis.     

Distribution map of species and subspecies of Inia
From Hrbek et al. PLoS ONE 2014: 9: e83623
(c) Hrbek et al. (Creative Commons)

Some time ago Dr. Vera da Silva, a co-author of the new study, afforded me the opportunity to study placentation in the boto and also the tucuxi (Sotalia fluviatilis), another dolphin found in the Amazon (here).


Placenta of the boto
From da Silva et al. RBE 2007; 5: 26

For more about these creatures including their place in folklore I recommend Journey of the Pink Dolphins: An Amazon Quest by Sy Montgomery.

More debate on the origin of placentals

The first placental mammal
From O'Leary et al. Science 2013; 339: 662-7
Reprinted with permission from AAAS

Controversy over the timing of the mammalian tree (previous post) continues. The latest contribution, by Mario dos Reis et al. (here), boldly states, "O'Leary et al. seek to reignite a controversy over the age of the placental ancestor that otherwise has been settled." The italics are mine. The references that support this statement are a paper by the same authors and one by Meredith et al. No false modesty here.



Alternative calibrations of the same tree
From dos Reis et al. Biol Lett 2014; 10: 20131003
(c) The authors (Creative Commons)

The problem arises because of different approaches to calibration of the molecular clock. The figure shows trees with identical topology but dated with different sets of fossils. In the first three, many extant orders of mammal can trace their origin to the Late Cretaceous. The problem is that all known fossils of placentals date from after the mass extinction event at the Cretaceous-Paleogene boundary. A literal interpretation of the fossil record, on the other hand, has all orders and even placentals themselves postdating the boundary.
It is not easy to choose appropriate fossils for calibration. Dos Reis and colleagues criticise O'Leary et al. for placing too much weight on Protungulatum donnae. They point out that the fossils of the genus may be found in the Cretaceous, yet the authors they cite (here) are unsure whether or not Protungulatum is a placental.

For a sober discussion of the difficulties in fossil calibration I highly recommend a recent paper by Bibi (here) on the evolution of ruminants. En passant Bibi observes, "The problem stems in part from the opacity of paleontological literature to non-specialists."

The O'Leary paper is co-authored by some of the most eminent specialists in fossil mammals. Arraigned gainst them we have some of the most competent molecular phylogeneticists. There seems little chance of compromise to judge from the acrimonious tone in this latest contribution. Surely the reviewers and editor of Biology Letters could asked the authors to damp things down?
     

Was Homo erectus the fourth hominin?

Skull of Homo erectus (Wikimedia Commons)

The current issue of Nature has a comprehensive analysis of the genome of Neanderthals and comparisons with modern humans and Denisovans (here). The supplementary material alone fills 16 Mb but there is an excellent summary (here) entitled "Four makes a party." As it says, "it does seem that Eurasia during the Late Pleistocene was an interesting place to be a hominin, with individuals of at least four quite divergent groups living, meeting and occasionally having sex."

The fourth hominin was alluded to in a previous post and is inferred from analysis of the Denisovan genome (previous post). The current study estimates that this putative hominin's ancestor diverged from other hominins 0.9-1.4 million years ago. This date is compatible with the unknown hominin being Homo erectus a hominin well known from the fossil record.

Evolution of flowering plants

Amborella trichopoda, basal to all other flowering plants
(Wikimedia Commons)

Amborella is a sprawling shrub endemic to New Caledonia. This monotypic genus is basal to the angiosperms and sister to all other flowering plants. Now its mitochondrial and nuclear genomes have been sequenced and this is the subject of three papers in the current issue of Science (summarized here).

Amongst other things it addresses Darwin's "abominable mystery" - the question of why flowers suddenly proliferated on earth millions of years ago (discussed in this press release). It confirms, as had previously been suspected, that the evolution of flowering plants was preceded by a genome duplication.

Whole genome duplication has also played a significant role in the evolution of vertebrates (reviewed here). Tandem duplication of genes or groups of genes is common in the mammalian lineage and the basis for the evolution of placental hormones and fetal hemoglobins (my review here).

Footnote: In botany, placentation refers to the manner in which the ovules are attached within the ovary. It is an important taxonomic feature.

Placental gas exchange in ground squirrels

Golden-mantled ground squirrel (Callospermophilus lateralis)

(Wikipedia Commons)

Fetal blood tends to have a higher oxygen affinity than maternal blood. This aids oxygen transfer across the placenta. Some mammals (human, sheep) have a special fetal hemoglobin. In many others, hemoglobin is the same in fetus and mother, but in fetal blood it has increased affinity for oxygen because the red blood cells have a low content of DPG (here). This is the case in the few rodents studied so far.

Ground squirrels cannot use this trick. A new study (here) found that even adults have hemoglobin of high oxygen affinity and there is no effect of raising or lowering DPG.

Placenta of the golden-mantled ground squirrel from Carter and Enders (here)

© Carter and Enders 2004; Licensee Biomed Central Ltd.

So is oxygen transfer across the placenta of ground squirrels likely to be less efficient than, say, in a rat? Probably not. The same study established that an unusually large Bohr effect (defined here) aids unloading of oxygen to the tissues of ground squirrels. In any placenta there is a double Bohr effect because, as fetal blood takes up oxygen, it unloads carbon dioxide, while the opposite occurs in the maternal blood (discussed in detail here).

The new study concerns ground squirrels living at low and high altitude. The authors speculate that hemoglobin evolved to meet the demands of their fossorial life style. This in turn made it easier to expand into mountainous habitats. They did not consider the possible impact on reproduction - but perhaps they should.  

 

Transgenic monkeys

Common marmoset (Callithrix jacchus) Wikipedia Commons

A news article in Nature (here) tells how new gene-editing techniques offer the opportunity to create transgenic primates. The emphasis is on neuroscience and models of brain disease. But if transgenic lines are developed there should be placentas available for study.

Although work on rhesus macaques is mentioned, more progress has been made using marmosets. One advantage might be that marmosets usually carry twins so a colony could be built up quicker. These Neotropical primates have placentas that differ in several ways from human placenta.

Haematopoietic foci in the placenta of a marmoset

(Callithrix jacchus) from Carter and Mess (here)

© Museum für Naturkunde Berlin

As an example, the placenta is an important site of haematopoiesis. The conventional wisdom is that there is little or no trophoblast invasion, but this is one aspect that calls for reexamination. If marmosets begin to emerge as important disease models there will be a need to look more closely at their placentation.

Denisovans crossed the Wallace line

Wallacea is bordered to the west by the Wallace Line

and to the east by the Lydekker Line (Wikimedia Commons)

Denisovans were archaic hominins distinct from Neanderthals and modern humans (previous post). There is evidence for gene flow between all three populations and putatively a fourth. The greatest amount of introgressed Denisovan DNA is found in the aboriginal peoples of New Guinea and Australia (here).

This is remarkable for several reasons. Firstly, it is a long way from Denisova in Siberia to New Guinea. Secondly, there is no trace of Denisovan DNA in modern humans from mainland Asia or from Southeast Asia west of the Wallace Line. As pointed out in a recent essay (here), the most likely explanation is that Denisovans crossed the Wallace Line into Wallacea (see map) and that exchange of genes with modern humans occurred there. Traces of Denisovan DNA do occur in modern populations from Wallacea as well as further east to Polynesia and Fiji.

Does that mean there was no contact between Denisovans and the ancestors of present day Asian populations? Not necessarily. Some Denisovan genes may have been retained east of the Wallace Line because they conferred resistance to disease (purifying selection). Further west Denisovan DNA may have been "overwritten" in the course of time.