Monday, September 15, 2014

Guitars and networks


I have noted before that the evolutionary history of musical instruments is likely to be a reticulating network rather than being tree-like (Cornets: from a tree to a network). As another illustration of the pattern, we can consider the evolution over the past few centuries of the Spanish or flamenco guitar (taken from the Origem do nome Violão blog post).


This genealogy (with time proceeding from left to right) shows three basic characteristics that seem to be common in anthropological histories. First, there are multiple roots — in this case, three different instruments from the 16th century have provided input into the modern acoustic guitar. Second, there is an early history of reticulation, with ideas for new instrumentation being taken freely from among the existing instruments, in this case presumably in the search for better sound reproduction. Third, there is simple transformational evolution, with new models replacing the previous ones in popularity — for example, over the past 100 years the Spanish guitar has simply gotten larger (this is Cope's Rule.)

Wednesday, September 10, 2014

The importance of the Amish for reticulate genealogies


I noted in my previous blog post (Charles Darwin and the coalescent) that the multispecies coalescent needs to be based on a network model not a tree model. This is because reticulation processes occur both within species and between species — there is gene flow within genealogies and within phylogenies.

Reticulate genealogies are nothing new, and I have blogged about some of the best-known human genealogies with reticulations due to consanguinity (marriage between close relatives):
King Charles II of Spain
Charles Darwin
Henri Toulouse-Lautrec
Albert Einstein
Pharaoh Tutankhamun
Pharaoh Cleopatra

Importantly, in the modern world there are quite a few genealogical datasets available for study. For example, the Kinsources repository has c. 100 datasets from around the world, covering multi-generational histories for nearly 350,000 individuals. These data are actively used for research (eg. Bailey et al. 2014).

However, the best documented human genealogies are those for the various Anabaptist populations, who moved from Europe to North America during the 18th and 19th centuries. Anabaptists have mostly closed populations (ie. marriages occur solely within a population), and they are thus inbred, and most importantly they maintain detailed written genealogies. These populations include the Mennonites, Hutterites and Amish, the latter being the best known.

As noted by Agarwala et al. (2001):
The term "Anabaptist" literally means "rebaptizer" and is used to refer to a Christian movement that arose in central Europe in the first half of the 16th century. Adherents support adult baptism, pacifism, and separation of church and state. Among the large Anabaptist groups existing today are Mennonites (who were originally followers of Menno Simons), Amish (originally followers of Jakob Ammann who split away from the Mennonites at the end of the 17th century), and Hutterites (originally followers of Jakob Hutter). Amish and Mennonites emigrated to North America in multiple waves in the 18th and 19th centuries. The Hutterites began emigrating to the northern and western parts of North America in the late 1800s.
Distribution of Amish settlements in North America
Note the rapid expansion over the past 25 years.

The Mennonites originated in the Swiss Alps, and diffused northward into Germany and the Netherlands. The Dutch/North German Mennonites began the migration to America in the 1680s, followed by a much larger migration of Swiss/South German Mennonites beginning in 1707. The Amish are an early split from the Swiss/South German group that occurred in 1693. There are now at least 200,000 Amish in the eastern United States and eastern Canada (see the map above, taken from here), with the numbers apparently growing rapidly with recently increasing movement westward. There are various subgroups (eg. Old Order Amish, New Order Amish). There are about 1.7 million Mennonites worldwide, with c. 150,000 in the eastern United States and eastern Canada. The genealogies of 295,000 Mennonite and Amish individuals from the eastern USA have been databased (Agarwala et al. 2001).

The Hutterites originated as an Anabaptist offshoot in the Tyrolean Alps in the 1500s, but now there are c. 135,000 Hutterites living on 1,350 communal farms in the northern United States (principally South Dakota) and western Canada. Genealogical records trace all extant Hutterites to 90 ancestors who lived during the early 1700s to the early 1800s (see Ober et al. 1999).

These Anabaptist groups are frequently used in medical studies, because it is possible to relate disease occurrences to the recorded genealogy, and thus to assess the genetic component of the disease (eg. Dorsten et al. 1999, Hou et al. 2013). So, the literature is replete with figures showing the distribution of different diseases plotted onto the genealogy. I have included some of the Amish ones here, to illustrate the extreme reticulation that results when inbreeding is ongoing over many generations.

This first one is from Georgi et al. (2014). The diseased people are marked in red.


The next one is from Garner et al. (2001).


This one is from Lee et al. (2008).


The final one is from Racette et al. (2002).


Here is one small part of this genealogy, which emphasizes that between-generation marriages are an important component of the consanguinity.


References

Agarwala R, Schaffer A, Tomlin J (2001) Towards a complete North American Anabaptist genealogy II: analysis of inbreeding. Human Biology 73: 533-545.

Bailey DH, Hill KR, Walker RS (2014) Fitness consequences of spousal relatedness in 46 small-scale societies. Biology Letters 10: 20140160.

Dorsten L, Hotchkiss L, King T (1999) The effect of inbreeding on early childhood mortality: twelve generations of an Amish settlement. Demography 36: 263-271.

Garner C, McInnes LA, Service SK, Spesny M, Fournier E, Leon P, Freimer NB (2001) Linkage analysis of a complex pedigree with severe bipolar disorder, using a Markov chain Monte Carlo method. American Journal of Human Genetics 68: 1061-1064.

Georgi B, Craig D, Kember RL, Liu W, Lindquist I, Nasser S, Brown C, Egeland JA, Paul SM, Bućan M (2014) Genomic view of bipolar disorder revealed by whole genome sequencing in a genetic isolate. PLoS Genetics 10: e1004229.

Hou L, Faraci G, Chen DT, Kassem L, Schulze TG, Shugart YY, McMahon FJ (2013) Amish revisited: next-generation sequencing studies of psychiatric disorders among the Plain people. Trends in Genetics 29: 412-418.

Lee SL, Murdock DG, McCauley JL, Bradford Y, Crunk A, McFarland L, Jiang L, Wang T, Schnetz-Boutaud N, Haines JL (2008) A genome-wide scan in an Amish pedigree with parkinsonism. Annals of Human Genetics 72: 621-629.

Ober C, Hyslop T, Hauck WW (1999) Inbreeding effects on fertility in humans: evidence for reproductive compensation. American Journal of Human Genetics 64: 225–231.

Racette BA, Rundle M, Wang JC, Goate A, Saccone NL, Farrer M, Lincoln S, Hussey J, Smemo S, Lin J, Suarez B, Parsian A, Perlmutter JS (2002) A multi-incident, Old-Order Amish family with PD. Neurology2 58: 568-574.