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Tuesday, February 23, 2016

Dragonsnakes and Filesnakes Revisited

I've written about both filesnakes (family Acrochordidae) and dragonsnakes (part of the family Xenodermidae1) before. Traditional snake taxonomy suggests that, although they branch off from the main stem of the snake family tree at about the same time, they're not very closely related. But, new evidence emphasizes the uniqueness of dragonsnakes and thickens the plot in the unfolding story of the evolution of snakes.

Two hypotheses about the relationships of the major groups of snakes.
Left: tree based on nuclear genes, showing Acrochordidae and Xenodermidae
as successive outgroups to core Colubroidea
Right: tree based on mitochondrial genes, showing a sister relationship
between Acrochordidae and Xenodermidae
From Oguiura et al. 2009
Most phylogenetic analyses are pretty consistent in classifying both filesnakes and dragonsnakes as caenophidians, or "advanced" snakes. But, they differ in their placement of dragonsnakes and other xenodermids, including the truly strange and obscure odd-scaled snakes (Achalinus), bearded snakes (Fimbrios), stream, earth, or red snakes (Stoliczkia2), wood, mountain, or narrow-headed snakes (Xylophis), and a new genus, just described in 2015 and still without a common name, Parafimbrios. Most analyses group xenodermids with the colubroids (pareids1, vipers, homalopsids, colubrids, lamprophiids, and elapids), albeit as the most basal branch. Many textbooks actually define Caenophidia as Colubroidea + Acrochordidae (aka Acrochordoidea), distinctly separating the colubroids from the filesnakes on the basis of shared, derived characteristics such as wide ventral scales, as well as features of the skull, hemipenes, and the muscles, cartilages, and arteries between the ribs. However, several recent trees based on DNA sequences suggest instead that filesnakes and dragonsnakes might be one another's closest living relatives.

Study
Acrochordid-Xenodermid Relationship
Support
How many species?
What data were used?
X&A
-
-
Morphology
X+A
8%
37
ND4
X+A
98%
98
4 mitochondrial genes
A,X
not reported
25
7 nuclear genes
A,X
>95%
50
20 nuclear genes
A,X*
100%
30
12 nuclear genes
A,X
94%
131
2 mitochondrial genes + 1 nuclear gene
A,X
97-100%
761
3 mitochondrial genes + 2 nuclear genes
X,A
95-100%
141 extant +
51 extinct
610 morphological characters
A,X
100%
161
44 nuclear genes
X+A
95%
4,161
5 mitochondrial genes + 7 nuclear genes
A,X*
99%
32
333 nuclear loci
with 100% coverage
A,X
91%
4,162
5 mitochondrial genes + 47 nuclear genes
A selection of studies that have examined the relationship between acrochordids and xenodermids.
X+A means that the two are each other's closest relatives; A,X means that acrochordids are more distantly
related to colubroids than xenodermids; X,A means that xenodermids are more distant
*Relationships differed depending on which methods were used


Arafura Filesnake (Acrochordus arafurae)
For example, the first study to use DNA to examine the relationships of these two groups of snakes found some support for each hypothesis, concluding that the "potential sister-taxon relationship of acrochordids and xenodermines [is] a reasonable hypothesis requiring future testing." In 2003, data from three more mitochondrial genes resulted in the same relationship, causing the authors to suggest that xenodermids should be excluded from Colubroidea. However, since that time, numerous studies have not repeated this result. In 2009, one research group predicted that "these differences...are due to taxonomic sampling issues", predicting that as DNA was collected from more species of snakes, the basal position of Acrochordus would be confirmed.

Dragonsnake (Xenodermus javanicus)
So, it was a real surprise when a 2013 analysis, the largest yet, including samples from 80% of all snake genera, placed Acrochordidae and Xenodermidae as sister groups. Neither a follow-up analysis combining that dataset with one containing data from many more genes nor an analysis using only the most complete data have settled the issue. The latter study compared several methods for generating phylogenetic trees and found that the relationship between acrochordids and xenodermids depended a lot on which methods were used. Part of the problem is that, even if they are each others' closest relatives, they still diverged between 70 and 80 million years ago, making them susceptible to a problem in phylogenetics known as long-branch attraction, which happens when the amount of evolutionary change within a lineage causes that lineage to appear similar (and thus closely related) to another long-branched lineage, solely because they have both undergone a lot of change, rather than because they are actually related.

Bearded Snake (Fimbrios klossi)
The truth is that both acrochordids and xenodermids are obscure snakes, and we don't have that much data on either one of them. They are both found in areas of the world that are hard to get to. Morphologically, they appear superficially similar, and an association between them was first hypothesized in 1893But, even the most comprehensive morphological trait database for snakes is missing crucial data on their anatomy, such as whether or not their hemipenial spines are mineralized. This would be helpful to know because  the hemipenial spines of basal snakes such as boas and pythons are not mineralized, whereas those of definitive colubroids are heavily mineralized.

Parafimbrios lao
From Teynié et al. 2015
Within the past year, two new studies on the chromosomes of dragonsnakes (Xenodermus javanicus) have been published. In the first, the karyotype (the number of chromosomes and their shape) of dragonsnakes was reported for the first time. In humans, each cell normally contains 23 pairs of chromosomes, for a total of 46. In most snakes, each cell normally contains 18 pairs of chromosomes, for a total of 36. Usually, eight of these pairs are relatively large (called macrochromosomes), and the other ten are somewhat small (called microchromosomes). Dragonsnakes have 16 pairs of chromosomes, for a total of 32, of which seven are large and nine are small. The dragonsnake karyotype probably evolved by two fusion events, one of two macrochromosomes and the other between a macrochromosome with a microchromosome. There are some other exceptions to the 18-pair pattern; some snakes have as few as 12 or as many as 25 pairs, including the only other xenodermid to have been karyotyped, the Sichuan Odd-scaled Snake (Achalinus meiguensis), which has just 12 pairs of chromosomes.

Amami Odd-scaled Snake (Achalinus werneri)
From the 1960s to the 1980s, before DNA sequencing became cheap and easy, scientists invested heavily in collecting karyotypes from a diversity of species for comparative purposes, so we can say with pretty good certainty that the ancestral state for all snakes is 36 (18 pairs). That's the number in filesnakes, pareids, most vipers, homalopsids, and many "crown colubroids" (colubrids, lamprophiids, and elapids, although there are lots of exceptions in these three groups).  The fusions in xenodermids emphasize their uniqueness, but unfortunately don't shed any new light on their phylogenetic placement.

Stoliczkia borneensis
The other study focused on the sex chromosomes. In humans, sex is determined by which combination of sex chromosomes a baby receives from its parents: two X chromosomes make a female, whereas an X and a Y chromosome make a male. It's pretty similar in snakes, with a twist: the sex chromosomes are called Z and W instead of X any Y, and females are the heterogametic sex (meaning that a Z and a W chromosome make a female, and two Z chromosomes make a male). Birds and many other reptiles also have ZW sex determination. In many colubroid snakes, the W chromosome is about twice the size of the Z,  and it is often unusual in other ways as well, such as having sections of highly condensed chromatin or a different centromere position. In contrast, filesnakes, boids, and other more basal snakes have morphologically indistinguishable Z and W chromosomes, although they still contain different genes and perform different functions.

Perrotet's Narrow-headed Snake (Xylophis perroteti)
Are members of this genus really xenodermids? Or, like the
former xenodermids Oxyrhabdium and Nothopsis, will they
prove to be more closely related to something else?
One reason the W chromosome looks so different from the Z in colubroids is that it contains repetitive elements called Bkm ('banded krait minorsatellite') repeats, which consist of the sequence "GATA" (sometimes "GACA") repeated thousands of times. Mammalian X chromosomes and avian W chromosomes also have these repeats. Cell biologists think that these repeats function to inactivate all the genes on the W chromosome except for those that determine sex3. Both mammalian X chromosomes and snake W chromosomes become very dense in body cells, so that none of the genes on them can be expressed. They only decondense and plays their brief, female-determining roles, in maturing eggs that are destined to become females. Unlike in mammals, the sex chromosomes of snakes span the gamut from completely identical to markedly differentiated, allowing biologists to study the evolution of chromosomal sex determination. The new study showed that female dragonsnakes have two different-looking sex chromosomes, with many Bkm repeats in the W, whereas the two Z sex chromosomes of male dragonsnakes look similar and lacked Bkm repeats, bolstering the relationship between xenodermids and other colubroids and diminishing the relationship between xenodermids and filesnakes.

The other major finding of the new study is the documentation that at least part of the sex chromosomes are homologous across all families of caenophidian snakes, suggesting that snake sex chromosomes emerged in the common ancestor of Caenophidia some 60-80 million years ago. One gene that is only on the Z chromosome in all caenophidians, including dragonsnakes, is also found on the W chromosome in filesnakes. The Z-chromosome-specific genes in caenophidians were on both the Z and W chromosomes in boas, pythons, and sunbeam snakes (Xenopeltidae), as well as in bearded dragons and anoles. Other toxicoferan lizards with ZW sex chromosomes, including chameleons and monitor lizards, seem to have evolved them independently.



1 A recent article in the journal Herpetological Review pointed out that the grammatical rules for structuring family and subfamily names from genus names have recently been incorrectly applied in two cases involving snakes which concern this article: 1) Xenodermatidae/inae for the family/subfamily containing Xenodermus, the root of which is "dermus", a masculine noun with which the masculine specific epithet javanicus is correctly coupled (not the neuter javanicum; in contrast think of the neuter Heloderma horridum in family Helodermatidae). The correct family or subfamily name is thus Xenodermidae/inae. 2) Pareatidae or Pareatinae for the family containing Pareas, which is also masculine, making the correct family/subfamily name Pareidae/inae.



2 Don't confuse this snake genus (Stoliczkia) with a genus of extinct ammonite (Stoliczkaia), both named for Czech biologist Ferdinand Stoliczka. The extra "a" was added to the original spelling of the snake genus by Boulenger in 1899, probably by accident, and this genus is still widely misspelled today (e.g., on GenBank and on Wikipedia before I fixed it while writing this article).



3 It's also thought that "GATA" is a particularly potent regulatory sequence, with the power to turn nearby genes on and off. In a way, the sex genes have essentially 'hijacked' the W chromosome, turning off all its other genes, and simultaneously creating a concentrated source of mutation-causing elements. Chromosomal sex determination may therefore constitute a unique and potentially very powerful genotypic mechanism for abruptly enhancing evolutionary rates, which might have contributed to the explosive radiations of species in clades with chromosomal sex determination, such as mammals, birds, squamates, and certain groups of insects.

ACKNOWLEDGMENTS

Thanks to Thomas CalameSam HowardKonrad MebertZeeshan MirzaTakehito Sato, and Stephen Zozaya for the use of their photos.

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Life is Short, but Snakes are Long by Andrew M. Durso is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License.