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Wednesday, March 7, 2018

The House Snake Mess for Dummies

This article will soon be available in Spanish

Inspired by Mike Van Valen's "The Ratsnake Mess for Dummies"
Please note that the information in this article is current as of March 2018 (no later)
Please contact me or leave a comment if you spot an error

Arguably House Snakes are much more of a mess than ratsnakes, which makes sense when you consider that they are they distributed over an area almost 7 times larger, including areas as diverse as the Sahara Desert, Congo Rainforest, Great Rift Valley, East African Savannah, Ethiopian Highlands, Okavango Delta, and Southern African Great Escarpment, and occur in a total of 46 countries, many of which have perennially turbulent political climates. It's no surprise that the number of herpetologists working in Africa is dwarfed by the number working in North America, and the vast majority of these people have not been of African descent (although that is beginning to slowly change).

African House Snake (Boaedon fuliginosus) from the
northernmost part of the range in Morocco.
Like everywhere in Africa, there are probably multiple
undescribed cryptic species within this lineage
What is surprising is that African House Snakes are popular in the pet trade and are important model organisms for studies of development, behavior, hormones and reproductive biology, yet we still know almost nothing about them in the wild, even though they are common and tolerant of anthropogenically-disturbed environments.

When most people think of African House Snakes, the scientific name that probably comes to mind is Lamprophis fuliginosus. In this article, I'll try to explain why this well-known species had to be moved into the genus Boaedon in 2011, and why it will probably be split up into multiple species sometime in the (hopefully-not-too-distant) future. The correct scientific name of many African House Snakes in captive breeding colonies may be difficult or impossible to determine, especially because most people don't know which part of Africa their House Snakes originally came from (and they may have since been bred with House Snakes from other parts of Africa).

Simplified phylogenetic tree of Lamprophiinae, with
focus on "house snakes" (genera Boaedon & Lamprophis).
There's enough uncertainty about the structure within Boaedon
that I didn't try to represent much of what's known.
For more detailed trees, see the KellyGreenbaum, & Trape papers.
Green are species lacking genetic data that can't be placed yet.
Red stars are multiple cryptic species (there could be more).

Click here for a larger version
To start, let's get a little taxonomic perspective. Pyron et al.'s 2011 article firmly established the family Lamprophiidae for a large group of mostly African snakes (321 species) formerly classified as colubrids but actually more closely-related to elapids (more detail here and here). They also found support for seven subfamilies of lamprophiids, of which only one, Lamprophiinae, concerns us today. There are currently 78 species placed in Lamprophiinae1, of which 25 are or have been at some point commonly called "House Snakes" and/or placed in the genus Lamprophis. Only one of these is Boaedon (formerly Lamprophis) fuliginosus, but in order to understand it, we'll need to take a closer look at the others.

A great deal of clarity was gained from the taxonomic actions of Chris Kelly & co-authors in 2011, who split the species in the genus Lamprophis up into several genera, depending on their relationships to other genera of lamprophiines. Even this study was only able to include data on ~40% of the species of lamprophiine snakes, so it's probable that surprises and new discoveries still await us.

Swazi Rock Snakes, Inyoka swazicus, are endemic to rocky
outcrops in Swaziland and adjacent provinces of South Africa
There are currently 12 genera of lamprophiines. Two of these, Chamaelycus (4 species) and Dendrolycus (1 species), have not been included in any molecular phylogenetic trees, so we're going to ignore them for now. The general relationships of the other 10 genera have been sketched out, and they're divided into two groups of roughly equal diversity. The first includes the African Wolf Snakes (Lycophidion; 20 species) and the African File Snakes (Gonionotophis, including the former genus Mehelya; 15 species), as well as two monotypic genera: Hormonotus modestus (Uganda House Snake or Yellow Forest Snake) and Inyoka swazicus (Swaziland House Snake or Swazi Rock Snake). Both of these were originally described as species of LamprophisHormonotus left the genus in the 19th century, and Inyoka was created for swazicus by Kelly et al. 2011 (it means ‘snake’ in the Nguni language group, the main language group in Swaziland). When it was originally described in 1970, swazicus was thought to be intermediate between Lamprophis and Boaedon, both of which were in use at the time, but it turns out that the resemblance is superficial and it's closely related to neither. That takes care of the first two of our 25 House Snake species, which aren't really House Snakes at all.

The Olive Water Snake, Lycodonomorphus inornatus,
was formerly thought to be a Lamprophis
The second group of lamprophiines contains six genera. Three of these are rather small and pretty straightforward, if obscure: Ethiopian Mountain Snakes (Pseudoboodon; 4 species), Günther's Black Snake (Bothrolycus ater), and Red-Black Striped Snakes (Bothrophthalmus; 2 species). None of these have ever been called House Snakes or placed in Lamprophis2, and they are clearly morphologically distinct. A fourth genus, African Water Snakes (Lycodonomorphus; 9 species), includes two species that were formerly thought of as House Snakes: Ly. inornatus and Ly. rufulus (the second only briefly). Ly. inornatus is interesting because it's terrestrial, unlike the other species of Lycodonomorphus, which is part of why it was classified in Lamprophis for so long.

Fisk's House Snake, Lamprophis fiskii, is found in
rocky & sandy areas in the western part of South Africa
The really important finding of Kelly et al. 2011 was that Lycodonomorphus split up the remaining members of Lamprophis into two groups. The southern African group containing Lamprophis aurora got to keep the name Lamprophis, because L. aurora was the first species to be placed in Lamprophis (it is the "type species" of the genus). It got to bring along its close relatives L. fiskii, L. fuscus, and L. guttatus, all of which are small house snakes with attractive patterns, sometimes referred to as "dwarf house snakes", that are popular in the pet trade despite being relatively poorly known in the wild.

Olive House Snakes, Boaedon olivaceus
are found in forests rather than savannah
& grassland habitats
The other group needed a new name. Fortunately, Boaedon had already been used to refer to this group for a long time, from the 1850s to the 1980s. Four species in Kelly's study got "new" names: B. olivaceus, B. virgatusB. lineatus, and B. fuliginosus. Additionally, Kelly included B. maculatus in this group, because its morphology is similar to the other four species, but since we have no DNA evidence yet, this could change. These are sometimes informally called the "brown house snakes", in reference to their generally drabber patterns compared with the "dwarf house snakes". Morphological differences between these two genera include that Boaedon have enlarged anterior teeth on both the upper & lower jaw, and that the dorsal scales of Boaedon have apical pits, whereas those of Lamprophis do not.

Three other species get to stick around in Lamprophis for now: "L." abyssinicus and "L." erlangeri from the Ethiopian highlands, and "L." geometricus from the Seychelles. Probably once we get genetic data from these they will be moved into another genus, possibly Boaedon.

Most of the tree from Greenbaum et al. 2015, showing
the paraphyly of B. fuliginosus with respect to other
Boaedon species, and the geographic diversity of the samples.
Now, the problems aren't over. The thing is that, in Kelly's study, Boaedon "fuliginosus" was split up by B. olivaceus, which is clearly a good species and it makes no sense to sink it into fuliginosus, as well as by B. lineatus, which has a more complex relationship with B. "fuliginosus"3. There are at least seven lineages of Boaedon "fuliginosus" (probably more than 10), thus we can expect that at least 7-10 cryptic species are waiting to be described within this species complex. To quote Kelly et al.: "There have been several attempts to make sense of the intricate patterns of morphological variation in this complex, generally with only limited success."4. A handful of subspecies have been named based on morphology (e.g. mentalis in Namibia, angolensis from southeastern Angola to the southern DRC, arabicus in Yemen, bedriagae on the islands of São Tomé and Príncipe), some of which will probably eventually turn out to be used for full species.

Which, if any, of these future species will get to keep the name fuliginosus is not clear, because these decisions are made based on the location of the original specimen, called the "type locality". The type locality for L. fuliginosus was originally and incorrectly reported in 1827 as "Java". People were more careless back then. There is also no clear type specimen; at one point, one was designated, but it was lost by 1965. The type locality was subsequently corrected to the more accurate but still completely unhelpful "Africa" in 1962, and further restricted to either South Africa or Ghana, but which one isn't clear.

Map of the species currently in Boaedon Lamprophis
Question marks indicate areas where the species range
is uncertain (pink=lineatus complex, green=olivaceus,
brown="fuliginosus"/"capensis" complex)
Click here for larger version
Finally, there is the issue of Boaedon "capensis", a putative species described in 1997 by Hughes and occurring east of a hazy and ill-defined zone angling northeast-southwest from the Gulf of Aden along the Great Rift Valley, then turning east and extending to the Atlantic Ocean possibly near the Angola-Namibia border, but potentially as far north as the mouth of the Congo River and thus also including three of the largest and most poorly-surveyed countries in Africa: Angola, the Democratic Republic of the Congo, and Sudan (including the still relatively new country of South Sudan). This name effectively replaces fuliginosus in eastern and southern Africa, but the exact boundaries are not remotely known, and it will probably turn out that both species are non-mutually-exclusive complexes of cryptic species. Because of the type locality confusion of fuliginosus, it could even turn out that both names (fuliginosus and capensis) are the same southern African species5, and that the western and central African species will need new names.

Boaedon radfordi, a new species from the Uganda-DRC
border region. From Greenbaum et al. 2015
Recent discoveries have begun the process of adding to the number of species of Boaedon: in 2015, Eli Greenbaum and colleagues named a new species, B. radfordi, from the Albertine Rift in the eastern DRC and Uganda (which was formerly confused with B. olivaceus), and also unexpectedly found that a subspecies of Lycodonomorphus subtaeniatus was actually an undescribed species of Boaedon from a lake in south-central DRC, named B. upembae, that is most closely related to B. virgatus. They wisely refrained from making premature splits to the fuliginosus/capensis complex, stating that "Given the complicated taxonomic history and nebulous type locality for B. fuliginosus, substantial additional sampling and morphometric analyses are needed to assign...B. fuliginosus lineages to available names and to describe new species." They did, however, show that divergence among the various lineages currently referred to as B. fuliginosus could have happened as long as 21 million years ago.

Boaedon longilineatus, a new species from Chad
From Trape & Mediannikov 2016
In 2016, Trape & Mediannikov examined 1,370 specimens from eight countries and described 5 new species of Boaedon from central Africa, bringing the total number of species to 13 (including capensis and the certainly paraphyletic "fuliginosus"). Together, two of these, B. perisilvestris and B. subflavus, seem to effectively separate fuliginosus (western Cameroon and west) and capensis (Angola-DRC-S.Sudan and east), having been split from the middle of the species complex's geographic range; but many sources still use fuliginosus for populations east of the distribution of perisilvestris and subflavus. Trape & Mediannikov seem comfortable with the idea of restricting B. fuliginosus to West Africa, and suggest that a blackish color without clear lines on the head could distinguish the species there, despite the absence of any consistent scale characteristics6. Right now, it's impossible to say how the 5 species described by Trape & Mediannikov fit with those described by Greenbaum or with the clades outlines in Kelly, because they used the 16S RNA gene, whereas the other two studies used three different genes (cyt-b, ND4, and c-mos).

Boaedon capensis from South Africa
So, we seem to be approaching stability, but the most problematic one remaining is the one everybody's heard of, knows and loves. Trape's latest definition notwithstanding, between fuliginosus and capensis, African House Snakes in the strictest sense occur in every country in Africa except for Algeria, Tunisia, Libya, Egypt, Sudan, and offshore countries like Madagascar, the Comoros, and the Seychelles7. At the moment, the L. "fuliginosus" complex is still one of the most widespread snake species in the world.

In case you lost count, a quick recap of species that are or have been in Lamprophis:
  1. Hormonotus modestus (Yellow Forest Snake or "Uganda House Snake"; moved in 1850s)
  2. Inyoka swazicus (Swazi Rock Snake or "Swaziland House Snake"; moved in 2011)
  3. Pseudoboodon lemniscatus (briefly in Lamprophis in 1904, barely counts, see footnote2)
  4. Lycodonomorphus inornatus (originally described as a Lamprophis because it was terrestrial, but always a little weird; moved in 2011)
  5. Lycodonomorphus rufulus (briefly in Lamprophis 1840s-1860s, barely counts)
  6. Lamprophis aurora (type species for the genus, will always be a Lamprophis by definition)
  7. Lamprophis fiskii (gets to stick with aurora)
  8. Lamprophis fuscus (gets to stick with aurora)
  9. Lamprophis guttatus (gets to stick with aurora)
  10. "Lamprophis" abyssinicus (awaiting DNA data; Ethioipian highlands)
  11. "Lamprophis" erlangeri (awaiting DNA data; Ethioipian highlands)
  12. "Lamprophis" geometricus (awaiting DNA data; Seychelles)
  13. Boaedon lineatus (type species for the genus, will always be a Boaedon by definition, although as defined it too is likely a cryptic species complex)
  14. Boaedon virgatus (gets to stick with lineatus)
  15. Boaedon olivaceus (gets to stick with lineatus)
  16. Boaedon maculatus (awaiting DNA data; got to stick with the above 3 because of morphology; Horn of Africa)
  17. Boaedon radfordi (described by Greenbaum et al. 2015, split from olivaceus)
  18. Boaedon upembae (formerly Lycodonomorphus subtaeniatus upembae; moved by Greenbaum et al. 2015; in the B. virgatus group)
  19. Boaedon littoralis (split from B. lineatus by Trape & Mediannikov 2016, but lacks DNA data)
  20. Boaedon longilineatus (split from B. lineatus by Trape & Mediannikov 2016)
  21. Boaedon paralineatus (split from B. lineatus by Trape & Mediannikov 2016)
  22. Boaedon perisilvestris (the first of many cryptic species to be split from B. fuliginosus; by Trape & Mediannikov 2016)
  23. Boaedon subflavus (the 2nd split from B. fuliginosus by Trape & Mediannikov 2016)
  24. Boaedon capensis (replaces fuliginosus in east Africa, could be multiple cryptic species)
  25. Boaedon fuliginosus (definitely at least 7 cryptic species, probably many more, no guarantee that any will be called fuliginosus)
The Aurora House Snake, Lamprophis aurora, is the
type species of the genus Lamprophis, meaning it will always
be in Lamprophis unless that genus goes away completely
Whether fuliginosus goes away completely or remains, it won't be going back to Lamprophis unless Lycodonomorphus does too, or unless new genomic data overwhelm the signals found in the genes used by Kelly's, Greenbaum's, & Trape's studies. There's a recurring debate in taxonomy about whether we should attempt to preserve widely-used and well-known names like fuliginosus, since people are probably going to continue using them anyway, or do away with "the burden of heritage" and adhere strictly to a system that discards 150-year-old names if they prove inconvenient or impossible to keep, at the risk of creating confusion & resentment. Proponents of the second argue that eventually people won't remember the old names, and I think they're right: I was born in the 1980s and didn't realize that Lamprophis fuliginosus was called Boaedon for 130 years beforehand; when I learned its name in ~1999, it was as Lamprophis fuliginosus and that was that. These changes might seem radical, but whenever possible they reinstate older names, like Boaedon, the disuse of which might seem radical to an older generation.

There's further debate about the utility of splitting up cryptic species complexes, especially if it makes it almost impossible to identify which species you're looking at by morphology alone. These same issues are recapitulated in the North American ratsnake taxonomic "mess", North American slimy salamanders, egg-eating snakes, and in countless other species groups around the world. When I was writing this article, I thought more than once that I should just wait for a better time when it's all stabilized, but actually there's never a good time; we're always learning more. Ultimately, fleshing out and revising phylogenies and taxonomies will teach us a lot about biodiversity, evolution, and human nature. My advice is to try to be open-minded rather than bitter and ugly when discussing them. There is no "right" or "wrong", there are just rules we've (mostly) agreed to follow. It's an exciting time.

If this group of snakes interests you, watch the labs of Christopher Kelly, Jakob Hallermann, Aaron Bauer, and Jean-François Trape for future research that should make much of this article obsolete.



1 Note the difference between the endings of the family ("-idae") and subfamily ("-inae") names.



2 Except for Pseudoboodon lemniscatus, but that was only once, in 1904. It counts, but only in the same way as stuff you did once in college. This is complicated enough already.



3 Sources differ on whether B. lineatus is distinct from B. fuliginosis, but it seems to be in western Africa (though both could be multiple cryptic species). Some resources use B. lineatus for house snakes with head stripes in e.g. Uganda, Ethiopia, and Sudan, but increasingly these are referred to as B. capensis. Characteristics used to distinguish B. virgatus & B. olivaceus from B. fuliginosus/capensis/lineatus include undivided subcaudal scales in B. olivaceus and only 23 dorsal scale rows in B. virgatus, as well as the fact that B. virgatus B. olivaceus are found in forests whereas the others are savannah species.



4 The presence or absence of head stripes has been used as a highly visible character, but ultimately this probably won't prove to be closely correlated with genetic variation (and it's complicated by the fact that some Boaedon populations have head stripes as juveniles but lose them as adults). This is also the case in North American ratsnakes, where former subspecies with radically different adult color patterns, like E. o. rossalleni and E. o. quadrivittata turned out to be so genetically similar to the more widespread black phenotype that they are now not recognized. This is part of a move away from the subspecies concept in general, wherein many authors either synonymize subspecies with existing species as "mere variants" or elevate them to full species status using genetic data. I think we can expect this trend to continue with House Snakes.



5 This could happen if South Africa is chosen as the type locality of fuliginosus, because the type locality of capensis is also in South Africa—if South Africa ultimately contains just one species from the fuliginosus complex, then it will get to keep the older name (fuliginosus), and other former members elsewhere should not use the name capensis in order to avoid further confusion. If the type locality of fuliginosus is chosen to be in Ghana instead, then the name will probably continue to be used in western Africa. Let us hope for the 2nd option.



6 This isn't an identification guide, but if you want to see the scale characters for the different species, you can refer to the tables and descriptions in the Kelly, Greenbaum, and Trape papers.



7 "B. fuliginosus" are also found on the Arabian peninsula in Yemen; this could be the most obvious future split if these are shown to be their own lineage, and several sources have already used the name arabicus for them, although just a few individuals are known and additional biological specimens from Yemen are hard to come by. A recent paper used bedriagae as the name of a full species on the islands of São Tomé, with a new species being described from the neighboring island of Príncipe.


ACKNOWLEDGMENTS

Thanks to Peter Uetz for his advice on literature, and to Konrad Mebert, Cliff & Suretha Dorse, and Dan Rosenberg for the use of their photos.

REFERENCES

For map references, see map inset

Bates, M. F., W. Branch, A. Bauer, M. Burger, J. Marais, G. Alexander, and M. De Villiers. 2014. Atlas and red list of the reptiles of South Africa, Lesotho and Swaziland. South African National Biodiversity Institute <full-text>

Bogert, C. M. 1940. Herpetological results of the Vernay Angola Expedition. Part 1. Snakes, including an arrangement of African Colubridae. Bulletin of the American Museum of Natural History 77:1-107 <link>

Branch, W. R. 1984. The House Snakes of southern Africa (genus Lamprophis). Litteratura Serpentium 204:106-120 <link>

Brassine, M. C., C. M. R. Kelly, N. P. Barker, and M. H. Villet. 2008. The phylogenetics of the Lamprophis fuliginosus/capensis species complex in southern Africa. Page 13  Proceedings of the 9th Conference of the Herpetological Association of Africa, Sterkfontein Dam, South Africa.

Broadley, D. G. 1969. The African house snakes—How many genera? The Journal of the Herpetological Association of Africa 5:6-8 <preview>

Ceríaco, L. M., M. P. Marques, and A. M. Bauer. 2018. Miscellanea Herpetologica Sanctithomae, with a provisional checklist of the terrestrial herpetofauna of São Tomé, Príncipe and Annobon islands. Zootaxa 4387:91-108.

Conradie, W., R. Bills, and W. Branch. 2016. The herpetofauna of the Cubango, Cuito, and lower Cuando river catchments of south-eastern Angola. Amphibian and Reptile Conservation 10:6-36 <full-text>

de Witte, G. F. 1963. The colubrid snake genera Chamaelycus Boulenger and Oophilositum Parker. Copeia 1963:634-636 <full-text>

Greenbaum, E., F. Portillo, K. Jackson, and C. Kusamba. 2015. A phylogeny of Central African Boaedon (Serpentes: Lamprophiidae), with the description of a new cryptic species from the Albertine Rift. African Journal of Herpetology 64:18-38 <abstract>

Hallermann, J. and A. Schmitz. 2007. First results on the taxonomy of the Lamprophis fuliginosus complex in Africa. 14th European Congress of Herpetology and SEH Ordinary General Meeting <abstract book>

Hughes, B. 1997. Dasypeltis scabra and Lamprophis fuliginosus - two pan-African snakes in the Horn of Africa: a tribute to Don Broadley. African Journal of Herpetology 46:68-77 <abstract>

Kelly, C. M. R., W. R. Branch, D. G. Broadley, N. P. Barker, and M. H. Villet. 2011. Molecular systematics of the African snake family Lamprophiidae Fitzinger, 1843 (Serpentes: Elapoidea), with particular focus on the genera Lamprophis Fitzinger 1843 and Mehelya Csiki 1903. Molecular Phylogenetics and Evolution 58:415-426 <academia.edu>

Pyron, R. A., F. T. Burbrink, G. R. Colli, A. N. M. de Oca, L. J. Vitt, C. A. Kuczynski, and J. J. Wiens. 2011. The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. Molecular Phylogenetics and Evolution 58:329-342 <full-text>

Roux-Estève, R. and J. Guibé. 1965. Contribution a l’étude du genre Boaedon (Serpentes, Colubridae). Bulletin du Muséum National d’Histoire Naturelle, Paris 36:761-774.

Roux-Estève, R. and J. Guibé. 1965. Étude comparée de Boaedon fuliginosus (Boié) et B. lineatus D. et B. (Ophidiens). Bulletin de l’Institut Fondamental d’Afrique Noire, Dakar 27A:397-409.

Schaefer, N. 1970. A new species of house snake from Swaziland, with notes on the status of the two genera Lamprophis and Boaedon. Annals of the Cape provincial Museums 8:205-208 <full-text from BHL>

Schätti, B. 1989. Amphibians and reptiles from the Yemen Arab Republic and Djibouti. Revue Suisse de Zoologie 96:905-937 <full-text from BHL>

Thorpe, R. and C. McCarthy. 1978. A preliminary study, using multivariate analysis, of a species complex of African house snakes (Boaedon fuliginosus). Journal of Zoology 184:489-506 <abstract>

Trape, J.-F. o. and O. Mediannikov. 2016. Cinq serpents nouveaux du genre Boaedon Duméril, Bibron & Duméril, 1854 (Serpentes : Lamprophiidae) en Afrique centrale. Bulletin de la Societe Herpetologique de France 159:61-111 <abstract>

Vidal, N., W. R. Branch, O. S. G. Pauwels, S. B. Hedges, D. Broadley, M. Wink, C. Cruaud, U. Joger, and Z. Nagy. 2008. Dissecting the major African snake radiation: a molecular phylogeny of the Lamprophiidae Fitzinger (Serpentes, Caenophidia). Zootaxa 1945:51-66 <full-text>

Visser, J. 1979. Notes on two rare house snakes – Part 1. Lamprophis fiskii Boulenger (1887) and L. swazicus Schaefer (1970). Journal of the Herpetological Association of Africa 19:10-13.

Visser, J. 1979. Notes on two rare house snakes – Part 2: The generic status of Lamprophis fiskii Boulenger (1887) and Lamprophis swazicus Schaefer (1970). Journal of the Herpetological Association of Africa 21:31-37.

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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.






1 comment:

World of Animals, Inc said...

Thanks for posting. It's amazing how many different kinds of species there are of snakes. Also discovering new species all the time is thrilling in itself. I hope they keep discovering new species so we can see whats new to our world. Have a great day.
World of Animals