Wednesday, April 29, 2015

Consanguinity and incest can produce the same effects


I have noted before that Pedigrees and phylogenies are networks not trees. For example, a human family "tree" is a tree only if it includes one sex alone. Otherwise, it must be a network when traced backwards from any single individual through both parents, because the lineages must eventually coalesce in a pair of shared common ancestors.

This potentially creates a problem for maintaining genetic diversity within species. If a pedigree is tree-like, then each person would, for example, have 32 great-great-great grand-parents. These 32 people's genes are mixed more-or-less randomly (depending on recombination and assortment) to produce the great-great-great grand-child. This heterozygosity is a good thing, evolutionarily, because there is then genetic diversity within that person.

However, inbreeding turns a tree into a network. This increases the probability that identical alleles will be paired in any one individual. If deleterious recessive alleles are thereby expressed, then genetic problems can ensue, which is called inbreeding depression. However, this situation is not inevitable, but depends on the probability of alleles becoming paired. Indeed, for domesticated organisms, inbreeding is the norm (see Thoroughbred horses and reticulate pedigrees).

I have discussed examples of well-known historical figures who have encountered the unfortunate effects of inbreeding, including Charles Darwin (Charles Darwin's family pedigree network) and Henri Toulouse-Lautrec (Toulouse-Lautrec: family trees and networks). In both cases the problems arose because of consanguineous relationships, which involve people who are first cousins or more closely related.

I have also discussed the extreme case of consanguinity, incest. In particular, royalty have often been exempt from taboos against sibling and parent-child couplings, as noted in Tutankhamun and extreme consanguinity and also in Cleopatra, ambition and family networks. At least for Tutankhamun there is evidence of genetic problems (an accumulation of malformations is evident), but apparently not in Cleopatra's case (there is no convincing evidence of infertility, infant mortality or genetic defects, for example). Royalty have not been the only exceptions to the incest taboo (see Evolutionary fitness and incest).

In Tutankhamun's case it has been suggested that his mother was his father's (Akhenaten) sister (name not known), which is surprising, because only two wives of Akhenaten, Nefertiti and Kiya, are known to have had the title of Great Royal Wife, which the father of the royal heir should bear. As a way out of this dilemma, Marc Gabolde has suggested that the apparent genetic closeness of Tutankhamun's parents is because his mother was his father's first cousin, Nefertiti. The apparent genetic closeness is then not the result of a single brother-sister mating but instead is due to three successive instances of marriage between first cousins.

To explain this idea we can look at an actual example. An historical example of how consanguinity can produce the same genetic effects as incest is provided by the Spanish branch of the Habsburg dynasty in 1700, as discussed in Family trees, pedigrees and hybridization networks.

This example can be explained using inbreeding F values. For any specified offspring, these indicate the probability of paired alleles being identical by descent (ie. due to the close relationship of the parents). For close family relationships the F values are:
self
parent-offspring
siblings
uncle-niece = aunt-nephew
double first cousins
first cousins
first cousins once removed
second cousins
0.500
0.250
0.250
0.125
0.125
0.063
0.031
0.016
Note that incest produces F values of 0.250 while consanguinity values are 0.063 or greater.

If we consider the case of King Charles II of Spain (1661-1700), then his inbreeding F = 0.254, which was achieved entirely without incestuous relationships. His pedigree is shown in the post Family trees, pedigrees and hybridization networks.

This pedigree shows that the parents of each person had the following relationships:

himself = uncle-niece [ie. his parents were uncle and niece]

father = first cousins once removed [ie. his father's parents were first cousins once removed]
mother = first cousins

father's father = (a) = uncle-niece
father's mother = (b) = uncle-niece
mother's father = first cousins
mother's mother = first cousins once removed

father's father's father = not closely related
father's father's mother = first cousins
father's mother's father = not closely related
father's mother's mother = not closely related
mother's father's father = uncle-niece
mother's father's mother = second cousins
mother's mother's father = see person (a)
mother's mother's mother = see person (b)

Thus, on his father's side he was the third generation of consecutive consanguinity, and on his mother's side he was the fourth generation of consecutive consanguinity. This is simply an accumulating series of probabilities — consanguinity potentially produces problems and consecutive consanguinity simply increases the probability.

It is not surprising, then, that Charles suffered genetic problems (he was disfigured, physically disabled and mentally retarded) to such an extent that his royal lineage came to an end, and the Spanish branch of the Habsburg dynasty ceased to rule.

Incidentally, the scientist who devised the quantity F, Sewall Wright, himself had a rather high amount of inbreeding — his parents were first cousins.

Monday, April 27, 2015

A phylogenetic network of late-night US television shows


"Late night" broadcasting on United States network / cable TV starts at about 11:00 or 11:30 pm, and goes for a couple of hours. Many networks broadcast similar shows during this time, which directly compete against each other for the available audience (which is currently estimated to be slightly in excess of 10 million people per night at 11:30 pm). Many of these shows have been on for a long time. Most of them are recorded on several weekday nights in front of a live audience, and they are usually associated with only a very few presenters over time (almost always men!).


For example, since the early 1990s we have had:
NBC Tonight Show



NBC Late Night



CBS Late Show
CBS Late Late Show



ABC Kimmel Live
ABC Nightline

ComedyCentral Daily Show

ComedyCentral Colbert Report
TBS Conan
11:35-12:35



12:35-01:35



11:35-12:35
12:35-01:35



11:35-12:35
12:35-01:05

11:00-11:30

11:30-12:00
11:00-12:00
Jay Leno 1992-2009
Conan O'Brien 2009-2010
Jay Leno 2010-2014
Jimmy Fallon 2014-
David Letterman 1982-1993
Conan O'Brien 1993-2009
Jimmy Fallon 2009-2014
Seth Meyers 2014-
David Letterman 1993-2015
Tom Snyder 1995-1999
Craig Kilborn 1999-2004
Craig Ferguson 2005-2014
James Corden 2015-
Jimmy Kimmel 2003-
Ted Koppel 1980-2005
Three-anchor team 2005-
Craig Kilborn 1996-1998
Jon Stewart 1999-
Stephen Colbert 2005-2014
Conan O'Brien 2010-

Eventually, the presenters retire or move elsewhere, and the other presenters then move around among the shows. This has lead to the so-called "Late night wars", in which the NBC studio executives in charge repeatedly show that their personnel management skills are often lacking. For example, David Letterman was expected to replace Johnny Carson when he retired as the host of the NBC Tonight Show in 1992, but the job was given to Jay Leno, instead. So, Letterman moved to a directly competing show on CBS. When Leno subsequently moved to another show, Conan O'Brien took over. However, Leno then moved back again, and so O'Brien moved to a directly competing show on TBS. The media interest in these shenanigans exceeded their interest in the shows themselves.

Another substantial decision was that by ABC, at the end of 2012, to swap the timelsots of Nightline (which used to run 11:35-12:00) and Kimmel Live (which ran 12:00-13:00). This had a notable effect on the audience numbers, because Nightline was one of the top two shows in its original timeslot whereas Kimmel Live currently gets about 1 million viewers fewer per night in that same slot. On the other hand Nightline in its new timelsot gets about the same audience as Kimmel Live did when it occupied the slot. That seems to be a net loss of audience for ABC.

The Nielsen Media Research viewing data are available online at the TV by the Numbers site. They provide the weekly averages for each show in millions of viewers, based on what is known as "live plus same day" viewing (ie. the audience at the time of broadcast plus same-day viewing of video recordings). The data I have looked at run from early December 2011 to the end of December 2014 (161 weeks). Unfortunately, these data rely on NBC press releases (rather than direct access to Nielsen), so there are some missing data.

The comparison of these shows can be visualized using a phylogenetic network, as a tool for exploratory data analysis. To create the network, I first calculated the similarity of the nine shows using the manhattan distance; and a Neighbor-net analysis was then used to display the between-show similarities as a phylogenetic network. So, shows that are closely connected in the network are similar to each other based on their audience figures across the three years, and those that are further apart are progressively more different from each other.


The network shows a gradient of increasing audience size, from bottom-left to top-right. So, the Tonight Show consistently got a average nightly audience of c. 3.5 million people, while Conan had c. 0.8 million. The two CBS shows both consistently did somewhat worse than their NBC timeslot competitors.

The two ABC shows apparently did well, but this is confounded by the timeslot swap noted above. Nightline did well for the first year (before it was moved) but not for the second two years, while Kimmel Live did the opposite. This is what creates the big reticulation in the middle of the network, as all of the other shows had fairly consistent audiences throughout the three years.

However, there was a steady decrease in the total audience size across the three years, from c. 12 million per night (at 11:30 pm) at the end of 2011 to c. 10 million at the end of 2014. The only major exception to this was at the time when Jimmy Fallon took over from Jay Leno (early 2014). For several weeks the Tonight Show audience increased to >8 million per night, so that the total audience was c. 15.5 million (a 50% increase). This shows just how many people are available to be added to the late-night viewing, compared to how many watch regularly. So, why are they not watching in the other weeks? It seems that Late Night Television is not reaching its full potential.