Wednesday, January 29, 2014

More datasets for validating network algorithms


Four more datasets have been added to the Datasets blog page. These are:
  • 1 stemmatology study where the manuscript history is known from experimentation
  • 2 stemmatology studies where the manuscript history is known from experimentation, and where there is reticulation caused by contamination
  • 1 plant study where recombination is known.

These are the first three studies to be added from the social sciences, all of them from experimental manipulation of text copying.

Unfortunately, it is unlikely that suitable datasets will be found from other parts of the social sciences, such as linguistics; but please tell us if you know of any relevant studies, where the phylogenetic history is known or inferred independently of the dataset itself.

Monday, January 27, 2014

Network of magicians


In 1965, Christopher Alexander published a classic paper called A City is Not a Tree, in which he pointed out to town planners that human beings naturally arrange themselves spatially in networks, not in the neatly ordered tree-like arrangements then in favour. So, road and rail systems, for example, should be inter-connected networks rather than bifurcating trees leading to / from a single root (e.g. a Central Station). The classic image of a rail system as a network is the one produced by Harry Beck in 1931-1933 that illustrates the London underground as a circuit diagram, which is now widely imitated.

Part of the 1933 map

This image has inspired other network makers, including Tom Crosbie, a professional magician from the UK. He has recently produced the following diagram, which illustrates some of the characteristics shared by a large number of the world's magicians. Note that much of the complexity comes from trying to illustrate each characteristic separately.


Some parts of the diagram do not make sense. Why, for example, are Apollo Robbins and Ava Do apparently at the same point? And also Mike Caveney and Tina Lenert? Why do only Penn & Teller have four intersecting lines, and no-one else?

It is, of course, easy to recognize the limitations of the sampling, since it is heavily biased towards English-language magicians. In particular, in spite of the existence of a "Competitions" category, even a cursory look at the Fédération Internationale des Sociétés Magiques (FISM) World Championships of Magic winners, shows that many recent Grand Prix recipients are missing, including Ivan Necheporenko (Russia), Vladimir Danilin (Russia), Franklin (Germany), Norbert Ferré (France), Jason Latimer (USA) and Rick Merrill (USA). From the German collective known as The Flicking Fingers, only Pit Hartling is included, but not Nicolai Friedrich, Manuel Muerte or Gaston, each of whom has two FISM titles, nor Thomas Fraps or Jörg Alexander, both of whom have one. The absent Arsene Lupin (Poland) has also been a consistent title winner (three times).

Recent UK magicians such as Young & Strange are included but Brynolf & Ljung (Sweden) are not. Very few Asian magicians are included, who have dominated much of the recent talk about magic; notably absent are Han Seol Hui and Kim Hyun Joon. Also, absent is Xavier Mortimer (France), the most prominent on the practitioners who see magic as a performance art (he combines mime, music and illusion). You can add your own list of favourite absentees.

This is not an example of a phylogenetic network, of course, since the people are directly connected rather than connected via inferred ancestors.

Wednesday, January 22, 2014

Blogs about phylogenetics


I have occasionally been asked about what blogs currently exist in phylogenetics, because there seem to be very few. There are blogs in related areas, such as phyloinformatics, evolutionary biology, and systematics, but very few blogs dedicated primarily to phylogenetics (not just occasionally mentioning it).

Below is a list of the current and former blogs that I know about. In each case I have provided basic information taken from the blog itself. Please let me know about any suitable blogs that have been missed. [Updated 15 October 2014]


Current General Blogs


The Genealogical World of Phylogenetic Networks

Biology, computational science, and networks in phylogenetic analysis. This blog is about the use of networks in phylogenetic analysis, as a replacement for (or an adjunct to) the usual use of trees. This topic has received considerable attention in the biological literature, not least in microbiology (where horizontal gene transfer is often considered to be rampant) and botany (where hybridization has always been considered to be common). It has also received increasing attention in the computational sciences.

Contributors: David Morrison, Steven Kelk, Leo van Iersel, Mike Charleston, Jesper Jansson
Started: 25 February 2012


TreeThinkers

TreeThinkers is a blog devoted to phylogenetic and phylogeny-based inference. We aim to use it as a place to discuss recent research and methods; to ask and answer questions; and serve as a general resource for news and trivia in phylogenetics. Although the blog is associated with the Bodega workshop, we welcome posts and participation from the entire phylogenetics community.

Contributors: Bastien Boussau, Gideon Bradburd, Jeremy Brown, Rich Glor, Tracy Heath, David Hillis, Sebastian Höhna, Luke Mahler, Mike May, Brian Moore, Samantha Price, Peter Wainwright
Editor: Bob Thomson
Started: 2 October 2012


Open Tree of Life

The tree of life links all biodiversity through a shared evolutionary history. This project will produce the first online, comprehensive first-draft tree of all 1.8 million named species, accessible to both the public and scientific communities. Assembly of the tree will incorporate previously-published results, with strong collaborations between computational and empirical biologists to develop, test and improve methods of data synthesis. This initial tree of life will not be static; instead, we will develop tools for scientists to update and revise the tree as new data come in.

Contributors: Robin Blom, Karen Cranston, Karl Gude, Mark Holder, Rosemary Keane, Rick Ree
Started: April 8, 2012


EvoPhylo

Evolution, phylogenetics, bioinformatics, stuff.

Contributor: Dave Lunt
Started: 30 January 2008


The Bayesian Kitchen

Statistical inference and evolutionary biology. Undoubtedly, since its introduction in phylogenetics in the late 90's, Bayesian inference has become an essential part of current applied statistical work in evolutionary sciences. However, there are still many problems, computational, theoretical and even foundational. After ten years of applied Bayesian work in phylogenetics and in evolutionary genetics, I feel the need to step back and re-think the whole thing.

Contributor: Nicolas Lartillot
Started: 24 December 2013


Phylogenetics...

Musings on eukaryote evolution.

Contributor: Marko Prous
Started: 31 December 2013



Current Program Blogs


Phylogenetic Tools for Comparative Biology

This web-log chronicles the development of new tools for phylogenetic analyses in the phytools R package. Unless you are reading a very recent page of the blog, I recommend that you install the latest CRAN version of phytools (or latest beta release) before attempting to replicate any of the analyses of this site. That is because the linked functions may be archived, and very likely have been replaced by newer versions.

Contributor: Liam Revell
Started: 11 December 2010 (at Blogspot)


Osiris Phylogenetics

Accessible and reproducible phylogenetics using the Galaxy workflow system.

Contributor: Todd Oakley
Started: 7 September 2012



Announces the introduction of new tools for phylogenetic analyses in the Beast 2 package, as well as discussing usage issues with the current version, along with tips and tricks.

Contributor: Remco Bouckaert
Started: 18 March 2014



Blogs Currently in Limbo


Dechronization

Dechronization is authored by evolutionary biologists interested in the development and application of methods for estimating phylogeny and making phylogeny-based inferences. The goal of the blog is to provide a forum for discussion of the latest research and methods, while also providing anecdotes, tidbits of natural history, and other related information.

Contributors: Rich Glor, Luke Harmon, Brian Moore, Tom Near, Dan Rabosky, Liam Revell
Started: 29 April 2008      Last post: 6 June 2011


CYPHY - Cybertaxonomy and Phylogenetics

Mostly harmless pointing at things pertaining to cybertaxonomy and phylogenetics.

Contributor: Matt Yoder
Started: 6 November 2007      Last post: 23 February 2011


Phylogeny etc.

Meditations on phylogenetic inference.

Contributor: Bruce Rannala
Started: 6 March 2014      Last post: 6 March 2014


Fish Phylogenetics

I created this new blog to share thoughts on work from my research group on the phylogenetics and evolutionary biology of fishes. This will provide a forum to share insight about the studies that we publish, discuss important scientific aspects of fish diversity, reflect on my experiences teaching ichthyology (the study of fishes), and to comment and review contributions by other researchers.

Contributor: Tom Near
Started: 23 August 2012      Last post: 15 September 2012


Taxonomy Phylogeny

Taxonomies group organisms according to phenotype, while phylogenetic systems groups organisms according to shared evolutionary heritage.

Contributor: ???
Started: 1 January 2008      Last post: 31 December 2010


Phylogenetic Geek

A bag of info on phylogenetics.

Contributor: ???
Started: 5 August 2011      Last post: 16 September 2011

Monday, January 20, 2014

Faux phylogenies II


It is possible to produce a phylogeny of any group of objects that vary in their intrinsic characteristics, and where those characteristics can be inferred to vary through time. I have previously reported some examples of a Tree of LIfe where "life" has been interpreted very broadly, to include legendary figures, cartoon animals, pokémon, and dragons (see Faux phylogenies). Here, I broaden the scope even further.

Phylogeny of taste

This first example comes from the July-August 1998 edition of the Annals of Improbable Research (vol. 4, no. 4), in which Joe Staton published an article entitled Tastes like chicken? It contains the following tetrapod phylogeny onto which has been mapped what they taste like. Note that Homo sapiens is included.


Phylogeny of breakfast

Following the taste theme, Nash Turley works on community phylogenetics, and this has lead him to contemplate the phylogenetics of his own breakfast. This vegetarian feast contains 15 species in 11 families.


Insect blog phylogenetics

Moving on to cultural evolution, Morgan Jackson has investigated how insect blogs are related to each other. His phylogenetic analysis of entomology blogs was based on blog morphology, physiology, geography, ecology and behaviour. It produced the following tree, onto which has been plotted the insect families concerned.


Evolution blog phylogenetics

In a similar vein, when the blogger known as Psi Wavefunction hosted the 20th Carnival of Evolution, this was summarized as a phylogenetic tree. The tree was produced by the simple expedient of aligning the URL addresses of the Carnival submissions and performing a parsimony analysis, based on treating the letters as amino acid codes. I can't believe that it worked.


Android bubble shooter games

Finally, Megafouna Software has produced a phylogeny of Android bubble shooter games, based on a small set of their features.


Wednesday, January 15, 2014

Pacific rock art - ordinations and networks


I have written previously about the use of phylogenetic networks as multivariate data displays instead of traditional techniques such as ordination (Networks can outperform PCA ordinations in phylogenetic analysis), and I have provided many empirical examples where I have used networks as heuristics to explore multivariate data. Here, I present a direct comparison between an ordination and a network.

Meredith Wilson (2004. Rethinking regional analyses of western Pacific rock-art. Records of the Australian Museum, Supplement 29: 173-186) has provided an interesting example of a difficult multivartiate dataset. She collated data (published and unpublished) concerning rock-art motifs (ie. engravings and paintings) for various locations in the western Pacific Ocean, including Papua - New Guinea, Solomon Islands, Fiji, Tonga, Micronesia and New Caledonia.


There were data for 614 figurative and non-figurative motifs, from 103 rock-art sites. However, this dataset is problematic to analyze because it contains a high proportion of unique motifs. This means that there is very little information about the art relationships among the sites, and the data summary is therefore uninformative. Wilson solved this problem by performing a series of analyses in which either (i) the motifs were aggregated into classes, or (ii) the sites were aggregated into geographical regions. Both strategies seemed to produce informative data summaries. In all cases, the data summaries were provided by ordinations, although some of these analyses used Multi-Dimensional Scaling while others used Correspondence Analysis.

For one of her analyses (the one discussed here) she kept the 614 individual motifs but aggregated the sites into 10 regions, and then analyzed the data matrix using Correspondence Analysis. The data consisted of counts of the motifs in each of the regions, and the multivariate distances among the regions were measured using the chi-square metric.


Wilson presented two ordination diagrams, with different subsets of the data, as shown above. Two diagrams were necessary because several of the regions were super-imposed in the initial analysis, and so a second analysis was performed with some of the regions omitted, to explore the patterns among the super-imposed regions. As with all ordinations diagrams, it is the proximity of the regions in the graph that expresses their multivariate similarity — nearby regions in the graph have similar rock-art motifs.

For comparison, I have used a NeighborNet network, based on the same chi-square metric distances, as shown below. As usual, regions that are linked by short connections in the network are similar based on their rock-art motifs.


This diagram suffers from the same problem as do the ordination diagrams — it is difficult to see the relationships among the regions. In this case it is because the network structure occupies only a small part of the diagram, with very long terminal edges, indicating that most of the motifs are unique to particular regions. This issue can be dealt with by instead drawing the diagram with uninformative edge lengths (ie. they are all the same length), as shown in the next figure.


The relationships among the regions are now clear in the network. These relationships are the same as shown in the two ordination diagrams, except for Bougainville. The network associates the Bougainville rock art with that of East New Britain, whereas the ordination analyses associate it with the art of Northwest Guadalcanal and Morobe. I have been unable to explain this discrepancy.

This dataset is a difficult one to deal with, because the data matrix is sparse. This necessitates multiple ordination analyses, or a network with uninformative branch lengths. The network may be the simpler data summary in this case, because it requires only one analysis and graph, rather than the two separate analyses needed for the ordination. However, the analysis highlights the fact that any dataset that presents difficulties for one multivariate summary technique is likely to be difficult for all of them.

Monday, January 13, 2014

Bioinformatics and inter-disciplinary work


Bioinformaticians are sometimes seen as multi-disciplinary workers (see the previous post on Results of some bioinformatics polls). If so, then the results of a recent study may be of interest:
Kevin M. Kniffin and Andrew S. Hanks (2013) Boundary spanning in academia: antecedents and near-term consequences of academic entrepreneurialism. Cornell Higher Education Research Institute Working Paper 158.
Kniffin and Hanks used data from the Survey of Earned Doctorates (conducted by the National Science Foundation), based on data from all people who earned PhDs in the U.S.A. between July 1 2009 and June 30 2010 (c. 43,000 people). Apparently, 14,000 people (32.5 %) reported that their doctoral work spanned academic boundaries

Two of their main findings are: (i) individuals who complete an interdisciplinary dissertation display short-term income risk, since they tend to earn nearly $1,700 less in the year after graduation; and (ii) the probability that non-citizens pursue interdisciplinary dissertation work is 4.7% higher when compared with U.S. citizens. Sadly, but not unexpectedly, women tend to earn less compared to men upon completion of the doctorate. Perhaps less expectedly, European American individuals also earn less in their first year after graduation than those in other racial groups.

For us, some of the more interesting data are:
Discipline
Agricultural & Life Sciences
Biological Sciences
Health Sciences
Computer Sciences & Mathematics
% of all Research Doctorates
2.3
17.6
4.4
7.0
% Interdisciplinary
44.5
41.1
29.9
22.7

In the regression models, adjusting for all other factors, the "influence of interdisciplinary research upon salary" was positive for Computer Sciences & Mathematics as well as for Health Sciences, but was negative for Biological Sciences. However, the "influence of interdisciplinary research upon employment as postdoctoral researcher" was negative for Computer Sciences & Mathematics as well as for Health Sciences, but was positive for Biological Sciences.

Make of this what you will.

Wednesday, January 8, 2014

The dilemma of evolutionary networks and Darwinian trees


I have noted before that Franz Hilgendorf (1839-1904), a German palaeontologist, was apparently the first person to publish a Darwinian tree based on the fossil record, in 1866 (Who published the first phylogenetic tree?). Indeed, among the people who first produced trees inspired by Darwin's work, Hilgendorf seems to have been the only "real" Darwinian — St George Mivart later became a strong anti-Darwinist, Albert Gaudry accepted Darwin's genealogical ideas but rejected the idea of natural selection, and Ernst Haeckel was in practice more of a Lamarckian than a Darwinian. Hilgendorf, on the other hand, continued to pursue Darwinism throughout the rest of his career, even being the first to introduce evolutionary theory into Japan (c. 1873) .


What I wish to point out here is that he was also the first person to face what I will now christen "Hilgendorf's Dilemma", which is a problem that phylogenetics has faced ever since the publication of Darwin's book in 1859. Hilgendorf solved the problem in the same way that later phylogeneticists also did — it is only in the last 2-3 decades that a different solution has been widely adopted.

The problem is this: what do you do when your data are not tree-like but you accept the evolution-as-tree paradigm? The solution of choice has been: publish a tree anyway.

The history of phylogenetic metaphors

I have previously emphasized the important point that the earliest genealogical diagrams were networks, published in 1755 and 1766 by the Frenchmen Buffon and Duchesne, respectively (Networks of genealogy). However, genealogical diagrams were then mostly ignored for the next century, except by Lamarck — most published relationship diagrams were affinity networks rather than representing genealogy (see Affinity networks updated).

One of Darwin's main goals in 1859 was thus to re-introduce genealogy as being the most important relationship concept in biology. However, he chose the tree as his metaphor rather than the previously proposed network. This seems to have been a rhetorical device as much as anything else, alluding to the biblical Tree of Life (Hellström 2011, Penny 2011). Darwin succeeded in his goal, and genealogical trees have been the dominant metaphor since that time, rather than genealogical networks.

Franz Martin Hilgendorf

Hilgendorf knew and apparently accepted Darwin's ideas (Heinrich Bronn's German translation of the Origin had appeared in 1860), and he applied them to his PhD studies in 1862. He was investigating the fossil gastropods of the middle Miocene basin at Steinheim, in southern Germany. He studied the morphological variation, in the different stratigraphic layers, of the various fossil forms of what he referred to as Planorbis multiformis. Importantly, he recognized that the different morphological forms (which he called varieties) occurred exclusively in different stratigraphic layers. Thus, what he saw in the stratigraphy could be translated into a phylogenetic diagram, as shown in this next figure.

Adapted from Rasser (2013).

On the face of it, Hilgendorf's work provides strong support for Darwinism, and in his thesis (Hilgendorf 1863) he explicitly noted the relationship to Darwin's ideas. However, he did not include his phylogenetic diagram, and he did not publish his thesis. The 42-page thesis was hand-written, and he did not even leave a copy behind at the University of Tübingen. The only known copy (presumably the original) is now in the Museum für Naturkunde, Berlin, where Hilgendorf later worked, donated by Hilgendorf's heirs. It was discussed by Reif (1983), and has recently been transcribed by Glaubrecht (2012).

The usual explanation given for Hilgendorf's decision not to publish is the controversial nature of the subject of evolution (eg. Weltner 1906, Reif 1983, Janz 1999, Glaubrecht 2012), which was not even supported by his own supervisor (Friedrich von Quenstedt). However, it seems equally likely that the explanation was Hilgendorf's Dilemma.

Hilgendorf's Dilemma

Hilgendorf refers to this dilemma in the penultimate paragraph of his thesis. After discussing the Darwinian ideas that species are connected with each other through intermediate stages, and have evolved apart over time, he says:
Eine Beobachtung die, so viel ich weiß, mit den bisher aufgestellten Ansichten nicht stimmt, [wäre], daß früher getrennte Arten sich einander nähern und endlich miteinander Verschmelzen können. Darauf würde das schöne Bild, das Darwin uns vom Zusammenhange der Species in einem Zweige=reichen Baume vorführt, nicht passen; die Zweige eines Baumes wachsen nicht wieder zusammen.
An observation which, as far as I know, contradicts these previously discussed views, [would be], that formerly separate species approach each other and finally merge with each other. This would not fit the beautiful image that Darwin presented about the connection of species in a branch-rich tree; the branches of a tree do not fuse again.
The problem for Hilgendorf was that this is precisely what happened in his reconstructed phylogeny. Among the Hilgendorf artifacts found in the Institut und Museum für Geologie und Paläontologie, Tübingen, as discussed by Reif (1983), is a series of cards attributed to the time of his thesis work. These mostly illustrate some of Hilgendorf's proposed morphological transformation series, but one of them represents a phylogeny. This is shown in the next figure. This phylogeny shows gradual transformation of lineages (anagenesis), splitting of lineages (cladogenesis), and one lineage fusion. The diagram seems to accurately reflect the discussion in Hilgendorf's thesis, and so it is considered to be the phylogeny "missing" from that thesis.


The dilemma for Hilgendorf, then, was that he saw his work as supporting Darwin's evolutionary ideas but not supporting his metaphor. Under these circumstances, he decided not to rush into print. (Why publish on a controversial subject when you are not convinced by your evidence?)

What he did, instead, was return to Steinheim two years later (1865) and collect more data. This time his phylogenetic method produced a tree instead of a network (illustrated in Gastropods on Monday), and he subsequently published the result (Hilgendorf 1866, 1867). This paper makes no mention of Darwin at all. Interestingly, the first version had a subtitle ("an example of morphological change through time") that was not used in the final version, thus expunging all explicit references to evolutionary theory. It was not until Hilgendorf (1879) that he once again placed the Steinheim work into an explicitly Darwinian framework.

Hilgendorf could thus have been the third person to publish a genealogical network. Instead, he became the second person to publish a post-Darwinian phylogenetic tree. (Mivart had published the first tree in 1865, while Hilgendorf was prevaricating.)

Hilgendorf continued to defend his work in print against attacks from a number of people, notably Carl Sandberger, another German (who rejected transmutation entirely), and Alpheus Hyatt, an American (who was a Lamarckian) (see Reif 1983, Janz 1999, Rasser 2013). Ironically, these two anti-Darwinians seem to have convinced Darwin himself that Hilgendorf's work was not worthwhile (see Rasser 2013), and the only comment that Darwin added to later editions of his book was: "Hilgendorf has described a most curious case of ten graduated forms of Planorbis multiformis in the successive beds of a fresh-water formation in Switzerland [sic!]." As a result, Hilgendorf and his work have been ignored by most biologists.

Note that Darwin consistently down-played the importance of fossil evidence for his theory — he seemed to think that biogeographic evidence, for example, would be more convincing (as independently suggested by Alfred Russel Wallace). He thus failed to give due credence to the work of both Hilgendorf and Gaudry (a Frenchman digging in Greece), who each provided the first good examples of Darwinian evolution based on fossil stratigraphy.

The general Dilemma

I see Hilgendorf's personal history as the first example of a dilemma that all subsequent phylogeneticists have potentially faced, and when necessary have usually resolved in a similar manner. Darwin inappropriately changed the phylogenetic metaphor from a network to a tree, even in the face of then-known reticulation processes such as hybridization and introgression. And every time we are confronted with non-tree-like data we face the same dilemma; and most people have resolved it in the same way by publishing a tree instead of a network (see Phylogenetic networks 1900-1990).

It is only in the past couple of decades that we have started to behave in a more rational manner, and have returned to publishing networks instead of trees.

References

Darwin C. (1859) On the Origin of Species by Means of Natural Selection. John Murray, London.

Glaubrecht M. (2012) Franz Hilgendorf's dissertation "Beiträge zur Kenntnis des Süßwasserkalks von Steinheim" from 1863: transcription and description of the first Darwinian interpretation of transmutation. Zoosystematics & Evolution 88: 231-259.

Hellström N.P. (2011) The tree as evolutionary icon: TREE in the Natural History Museum, London. Archives of Natural History 38: 1-17.

Hilgendorf F. (1863) Beiträge zur Kenntniß des Süßwasserkalkes von Steinheim. Unpublished PhD Dissertation. Philosophische Fakultät, Universität Tübingen, 42 pp.

Hilgendorf F. (1866) Planorbis multiformis im Steinheimer Süßwasserkalk: ein beispiel von gestaltveränderung im laufe der zeit. Buchhandlung von W. Weber, Berlin, 36 pp.

Hilgendorf F. (1867) Über Planorbis multiformis im Steinheimer Süsswasserkalk. Monatsberichte der Königliche Preussischen Akademie der Wissenschaften zu Berlin 1866: 474-504.

Hilgendorf F. (1879) Zur Streitfrage des Planorbis multiformis. Kosmos 5: 10-22, 90-99.

Janz H. (1999) Hilgendorf's planorbid tree — the first introduction of Darwin's theory of transmutation into palaeontology. Paleontological Research 3/4: 287-293.

Penny D. (2011) Darwin's theory of descent with modification, versus the biblical Tree of Life. PLoS Biology 9: e1001096.

Rasser M.W. (2013) Darwin's dilemma: the Steinheim snails' point of view. Zoosystematics & Evolution 89: 13-20.

Reif W.-E. (1983) Hilgendorf's (1863) dissertation on the Steinheim planorbids (Gastropoda; Miocene): the development of a phylogenetic research program for paleontology. Paläontologische Zeitschrift 57: 7-20.

Weltner W. (1906) Franz Hilgendorf. 5 Dezember 1839 – 5 Juli 1904. Archiv für Naturgeschichte 72(1): I-XII.

Monday, January 6, 2014

Albert Einstein's consanguineous marriage


In previous blog posts, I have mentioned several well-known people who were involved in consanguineous marriages, which is defined as the union of two people who are related as closer than second cousins. In the first post (Charles Darwin's family pedigree network) I discussed in detail Charles Darwin (who married his first cousin); and in a later post (Toulouse-Lautrec: family trees and networks) I discussed the artist Henri Toulouse-Lautrec, who was the offspring of a marriage between first cousins. Now, it is the turn of Albert Einstein (1879-1955).

Einstein's first marriage (in 1903) was to a former fellow physics student, Mileva Marić (1875-1948). They had three children: Lieserl (1902-?), who was born the year before they married, Hans Albert (1904-1973) and Eduard (1910-1965). Einstein seems to have been far from the ideal husband or father, as detailed in the book by Roger Highfield & Paul Carter (The Private Lives of Albert Einstein, St. Martin's Griffin, 1994). Some brief information is given below.

When the marriage ended, Einstein married (in 1919) Elsa Löwenthal (née Einstein) (1876-1936), who brought with her two daughters from her own first marriage: Ilse (1897-1934) and Margot (1899-1986). As shown in the family pedigree below, Albert and Elsa were first cousins through their mothers (traced in red) and second cousins through their fathers (traced in blue). [NB. This is only part of the family tree.]


The main issue here is that this pedigree is a reticulating hybridization network, rather than a diverging tree, which clearly shows the problems with consanguineous marriages. The genetic diversity of any individual born from such a marriage has a much higher risk of expressing recessive genes in their phenotype, many of which cause serious health problems. For example, several of Darwin's children died young, and several others were apparently infertile. As well, Toulouse-Lautrec is well-known for his short stature and genetic deformities, and his brother died young, and several of his cousins (also the offspring of a consanguineous marriage) had the same genetic problem's as himself. Consanguineous marriages are not encouraged, if children are an intended outcome (see Bennett et al. 2002. Genetic counseling and screening of consanguineous couples and their offspring: recommendations of the National Society of Genetic Counselors. Journal of Genetic Counseling 11: 97-119).

Elsa and Albert are not known to have had any children (but see the note below), and it has been assumed that they had a relatively platonic relationship. So, this particular story does not have the same sad ending as those of Darwin and Toulouse-Lautrec. It would be interesting to know whether Albert and Elsa's childless state was a deliberate decision (in light of the possible genetic problems for any child), a consequence of age (they were in the 40s when they married, which makes pregnancy risky), or a result of (unreported) miscarriages.

The following note about Einstein as a husband is from The other side of Albert Einstein:
Einstein was far from the ideal husband. A year before they married, Maric gave birth to a daughter, Lieserl, while Einstein was away. The child's fate is unknown – she is presumed to have been given up for adoption, perhaps under pressure from Einstein, who is thought to have never seen his first born. After the marriage, Mileva bore two sons but the family was not to stay together. Einstein began an affair with his cousin Elsa Löwenthal while on a trip to Berlin in 1912, leaving Mileva and his family two years later. Einstein and Mileva finally divorced in 1919 ... Einstein married Elsa soon after the divorce [he had been living with Elsa for nearly five years], but a few years later began an affair with Betty Neumann, the niece of a friend. By one account, Elsa allowed Einstein to carry on with this affair to prevent him sneaking around. That relationship ended in 1924, but Einstein continued to have liaisons with other women until well after Elsa's death in 1936.
For information about a possible child of Albert and Elsa in 1932, see Einstein's son? It's a question of relativity.

Composers and consanguinity

There are many other people whose names are well-known and who were involved in a consanguineous marriage. Notably, there have been several composers of classical music:
  • Johann Sebastian Bach married his second cousin, Maria Barbara Bach. The pair had seven children together, but only four survived to adulthood.
  • Edvard Grieg married his first cousin, Nina Hagerup. Their only child, a daughter, died at the age of one. Around the same time Nina also had a miscarriage.
  • Sergei Rachmaninoff married his first cousin, Natalya Satina. They had two daughters who survived to adulthood.
  • Igor Stravinsky married his first cousin, Yekaterina Nossenko. They had four children surviving to adulthood – two sons and two daughters.
Note that this type of marriage was very unusual for Rachmaninoff and Stravinsky, because the Russian Orthodox Church explicitly forbids marriage between first cousins (they needed to get permission from the Czar), and so the families involved also opposed their marriages. Apparently, the relevant families also opposed Grieg's marriage. Indeed, it is reported that Edvard and Nina were surprised and disappointed to find out that they were not able to have children together.

Wednesday, January 1, 2014

Carnival of Evolution, No. 67 — Wallace centenary edition


Charles Darwin's Tree of Life metaphor (from 1859) has become world-famous. However, Alfred Russel Wallace, who independently developed the idea of evolution by means of natural selection, had already used a very similar image in 1855, when he noted: "the analogy of a branching tree [is] the best mode of representing the natural arrangement of species ... a complicated branching of the lines of affinity, as intricate as the twigs of a gnarled oak ... we have only fragments of this vast system, the stem and main branches being represented by extinct species of which we have no knowledge, while a vast mass of limbs and boughs and minute twigs and scattered leaves is what we have to place in order, and determine the true position each originally occupied with regard to the others".

This past year has been one in which many people commemorated the death of Wallace (1823-1913), and so it seems appropriate to join them for the final summary of 2013's posts at the Carnival of Evolution.

Wallace spent 1848-1852 collecting in the Amazon, and 1854-1862 doing the same in South-East Asia. He is best known today for his studies of biogeography, but he also worked on what we now call environmental issues, and even what is now known as exobiology. More controversially, he also involved himself in social criticism, and atheistic spiritualism. At his death, he was as well known as any living biologist; but since then he has sadly been eclipsed by Darwin.

This month's blog posts

Wallace was interested in origins, of course, so we can start the list of evolution posts with that topic.

Darren Naish at Tetrapod Zoology discussed a new species of perissodactyl from the Amazon (A new living species of large mammal: hello, Tapirus kabomani) (submitted by Donald Prothero). New mammal species are rather rare these days, but Wallace would not have been surprised to find them in the Amazon.

At the Panda's Thumb, Wilson Sayres asked: Why sequence the manatee genome? (submitted by Ryan Gregory). In spite of being aquatic mammals, manatees are more closely related to elephants than they are to dolphins or whales. Gert Korthof then took us to the origin of life (New Szostak protocell is closest approximation to origin of life and Darwinian evolution so far), discussing the creation of a prebiotically plausible protocell, consisting of a fatty acid vesicle in which RNA replication occurs autonomously without the help of enzymes.

Kathy Orlinsky at The Stochastic Scientist then takes us to the origin of genetic variation, noting that for mitochondria DNA mutations might not be so random after all.

1848

Wallace studied adaptations, among other things, so we can now proceed on to that topic.

GrrlScientist was formerly one of the mainstays of the Carnival of Evolution, but she then drifted off into natural-history blogging, instead. However, this month she reported on a study of hummingbird species living at high altitudes (How do hummingbirds thrive in the Andes?). They have independently evolved hemoglobin with enhanced oxygen-binding properties, so they can thrive in oxygen-poor environments.

Ed Yong at Not Exactly Rocket Science considered the evolution of the two of the oddest mammals, the platypus (How the platypus and a quarter of fishes lost their stomachs) and the koala (Organ helps koalas bellow at elephant pitch).

Tim Eisele at The Backyard Arthropod Project talked about the options available for getting yourself through the winter when you are a living organism (Winter is the enemy).

At Eco-Evo Evo-Eco, Steven Brady contemplated why wood frog populations seem locally maladapted to roads (Homage to the Island of Misfit Toys) (submitted by Ben Haller), and Andrew Hendry considered the question of whether adaptation is driven by many genes of small effect or by a few genes of large effect (Epic wrap battles of Christmas).

Wallace's main collecting interest was beetles

Processes were at the heart of Wallace's evidence for evolution, so we should look at this topic, too.

Caroline Tucker at The EEB & Flow looked at an example (Ecological processes may diffuse through evolutionary time: an example from Equidae) of how patterns of trait divergence and adaptive radiation can evolve as a result of diffusion evolution, rather than from a single strong ecological pressure (submitted by Bradly Alicea).

At Synthetic Daisies, Bradly Alicea examined the nonlinear evolutionary dynamics of Mexican cavefish (Dragons, sandpiles, and cavefish: an evolutionary inquiry), considering both the Sandpile and the Dragon King statistical models for the developmental changes that made them eyeless.

Kim Gilbert at The Molecular Ecologist asked the question: How prevalent are non-overlapping generations?, which is of obvious importance for evolutionary modeling, and found that there is no known answer.

At The Genealogical World of Phylogenetic Networks, David Morrison asked a phylogenetic question: Is rate variation among lineages actually due to reticulation? He decided that it might be, but for most studies it is simply an untested assumption that it isn't.

1862

Selection involving groups was a bit out of Wallace's line, but it is prominent these days.

At Evolution in Structured Populations, Charles Goodnight noted that kin selection can be useful for developing an intuitive or qualitative grasp of social evolution, but for many reasons it fails when it is applied to the real world (Now I know I am "El Lobo Solitario"). He then considered the phenotypic view of evolution, by assessing the adaptive role of religion in providing cohesion in societies (Group selection and religion) (submitted by Bjørn Østman).

Wallace's global biogeographical regions

Now we come to those posts about the broad range of applications of evolutionary ideas.

Sarah Bodbyl at the BEACON blog asked about whether plants experiencing rapid loss of their pollinators are able to adapt and maintain viable populations by increasing their ability to reproduce without pollinators (Mating system evolution).

At The Mermaid's Tale, Anne Buchanan noted that genes associated with domestication and diversification have been identified with fine-mapping or genome-wide association studies, thus distinguishing artificial selection from natural selection (What domestication can and can't tell us about evolution). Then, Ken Weiss asked: "Every trait is due to natural selection!" .... often said, but is it true? This is belief in a form of very strong determinism, which he investigates in relation to the human thumb.

Carl Zimmer at The Loom pointed out that one of the best places to survey the sloppy creativity of evolution is inside your own nose (The smell of evolution).

Noah Reid at Nothing in Biology Makes Sense highlighted one of the more popular topics of the news, blog and twitter world in late November, which concerned a proposed phylogeny of the well-known folk tale about Little Red Riding Hood (Learn the origins of fairytales with this one weird trick!). However, The Genealogical World of Phylogenetic Networks has countered with a post about The phylogenetics of Little Red Riding Hood, in which it is shown that studying the evolution of folk tales requires knowledge of the time direction of evolutionary change — and it appears that the proposed phylogeny might be wrong.

1895

Finally, here are some miscellaneous blog posts about evolution and blogging.

PZ Myers, the grumpy old man at Pharyngula, critiqued a paper on the human brain that apparently has no data, or a hypothesis that makes sense (Frugal to the point of vacuity).

At the Tumbld Thoughts microblog, Bradly Alicea looked at the nature of blogosphere academic activity, and its relationship to open-source publishing (Blogosphere review).

Finally, every month has its drinking vessel in which the waters become stormy. Recently in Aeon magazine, science writer David Dobbs published an article (Die, selfish gene, die) in which he noted that: "The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong." This has generated a number of responses (as submitted by Ryan Gregory and Bjørn Østman), including those by PZ Myers from Pharyngula (Higher order thinking), Annalee Newitz from io9 (It's time to get skeptical about "the selfish gene"), and Larry Moran from Sandwalk (Razib Khan doesn't like Gould and doesn't like new-fangled ideas) (all of them arguing in favor of Dobbs, to one extent or another), and from Jerry Coyne from Why Evolution Is True (David Dobbs mucks up evolution, part I; and part II) and Razib Khan from Gene Expression (There is no revolution in genetics; and Evolutionary orthodoxy may be boring, but it is probably true) (who are against). David Dobbs has replied, as has Richard Dawkins.

Coda

Well, that's it for this month. While you wait for the next edition, you will find the Carnival of Evolution on Facebook and Twitter, as well as at the official Carnival of Evolution blog. Past posts and future hosts can be found on the Carnival index page.

The host of next month's Carnival will be Byte Size Biology.

You can submit posts for the next edition using the Carnival submission form (which requires you to log in), by commenting at the Carnival facebook page, or by sending an email to Bjørn Østman.