Research Article |
Corresponding author: Jiří Šmíd ( jirismd@gmail.com ) Academic editor: Johannes Penner
© 2023 Jiří Šmíd, Sergio Matilla Fernández, Hassan Sh Abdirahman Elmi, Tomáš Mazuch.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Šmíd J, Fernández SM, Elmi HSA, Mazuch T (2023) Diversity of Sand Snakes (Psammophiidae, Psammophis) in the Horn of Africa, with the description of a new species from Somalia. Zoosystematics and Evolution 99(2): 345-361. https://doi.org/10.3897/zse.99.101943
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The biological diversity of the Horn of Africa is one of the least studied in the world. Yet the Horn supports rich communities of species that are mostly endemic to the region. Here we study the diversity of Sand Snakes (Psammophis) in East Africa, their phylogeny and systematics. Previous studies have unveiled several cryptic and potentially undescribed species of Psammophis that occur in the Horn and their taxonomic status has remained unclear to this day. We used sequence data from two mitochondrial and one nuclear genes to reconstruct the phylogeny of the genus, in which we included newly obtained samples of six different Psammophis species from Somalia, Ethiopia, Eritrea, Sudan, and Egypt. Our aim was to assess the status of some of the undescribed species, examine the level of intraspecific genetic variation within individual species, improve our understanding of the species distributions, and contribute to the taxonomy of the genus. Our results confirm the existence of two undescribed species, one in eastern Somalia, which we formally describe as new, and one in southern Ethiopia that we refer to as Psammophis cf. sudanensis in accordance with previous studies. Further, we provide first genetic data for the nominotypical subspecies of P. punctulatus and confirm the species status for its subspecies P. trivirgatus. In addition, we provide new genetic data for P. tanganicus from Ethiopia and Somalia, and range extension records for P. rukwae from Eritrea and Ethiopia and for P. aegyptius from Somalia. Our findings contribute considerably to our understanding of the diversity and distribution of Psammophis in East Africa.
East Africa, Eritrea, Ethiopia, phylogeny, reptilia, sand racers, Serpentes
The Horn of Africa is the easternmost projection of the African continent that juts into the Indian Ocean. It supports a broad spectrum of habitats, from the Ethiopian Highlands that exceed 4500 m in elevation to the harsh lowland deserts of Somalia with barely any precipitation. The entire territory of the Horn is considered one of the global biodiversity hotspots, which are classified as regions of exceptionally high species richness and endemism while also suffering considerable habitat loss (
Sand Snakes of the genus Psammophis are distributed primarily in Africa where there are 27 out of 33 currently recognized species. Six additional species occur strictly in Asia, and one stretches broadly across both continents (
Thirteen species of Psammophis occur in and around the Horn of Africa. Five range broadly across the Horn; these are P. biseriatus Peters, 1881; P. pulcher Boulenger, 1895; P. punctulatus Duméril, Bibron & Duméril, 1854 with two subspecies - punctulatus and trivirgatus Peters, 1878; P. sibilans (Linnaeus, 1758); and P. tanganicus Loveridge, 1940, although the distribution of P. pulcher is very limited as the species is known only from a handful of specimens. Psammophis aegyptius Marx, 1958 and P. schokari (Forskål, 1775) are distributed by the Red Sea along which they penetrate south to Eritrea and northern Somalia. The more marginal species to the Horn, but otherwise generally widespread in other parts of Africa, are P. angolensis (Bocage, 1872), P. lineatus (Duméril, Bibron & Duméril, 1854), P. mossambicus Peters, 1882, P. orientalis Broadley, 1977, P. rukwae Broadley, 1966, and P. sudanensis Werner, 1919 (Figs
Sand Snakes of the Horn of Africa, part 1. a. P. aegyptius (Berbera, Somaliland); b. P. angolensis (South Africa); c. P. biseriatus (Voi, Kenya); d. P. lineatus (Nigeria); e. P. mossambicus (Baringo, Kenya); f. P. orientalis (Watamu, Kenya); g. P. pulcher (Bisanadi National Reserve, Kenya). Photo credit T. Mazuch (a); WR. Branch (b), S. Spawls (c, e, f, g), G. Dunger (d).
Sand Snakes of the Horn of Africa, part 2. a. P. punctulatus (Gewane, Ethiopia); b. P. trivirgatus (Mwingi, Kenya); c. P. rukwae (Asmara, Eritrea); d. P. schokari (Kasserine, Tunisia); e. P. sibilans (Debre Zeit, Ethiopia); f. P. cf. sudanensis (Yabelo, Ethiopia); g. P. tanganicus (Mado Gashi, Kenya). Photo credit T. Mazuch (a, c, d, f, g), S. Spawls (b, e).
In this study we analyze new material from the Horn of Africa and adjoining countries to provide further insight into the phylogenetic relationships, distribution, and taxonomy of the Psammophis snakes of the region. The newly analyzed material originated from targeted herpetological fieldtrips to the Horn countries that were carried out between 2010 and 2022. We assembled a genetic dataset of two mitochondrial and one nuclear gene that was based on published data and which included all known Psammophis species, and we supplemented it by 14 newly analyzed specimens, including specimens that could not be determined with certainty on the basis of morphology and which likely represented some of the putative new species. We inferred their phylogenetic position within the genus and investigated genetic variability of all Psammophis species to assess the taxonomic status of the putative new species in the context of a complete Psammophis phylogeny.
We assembled all genetic data that were available for the genus Psammophis on GenBank. To ensure sufficient overlap of loci we included only genes that were available for most of the Horn species. These were cytochrome b (cyt b) and NADH dehydrogenase subunit 4 (ND4) from the mitochondrial DNA, and oocyte maturation factor MOS (c-mos) from the nuclear DNA. Some species are represented in GenBank by many sequenced individuals. We pruned the dataset to contain only up to three samples per species, provided all the pruned species are monophyletic. It should be noted that the ND4 sequence of P. biseriatus (sample BK10724, GenBank accession DQ486284) and the c-mos sequence of P. tanganicus (sample CMRK87, GenBank accession DQ486183) contained too many ambiguous nucleotide positions to allow their inclusion in the dataset. Sequences of Malpolon monspessulanus, Psammophylax variabilis, Psammophylax rhombeatus, and Rhamphiophis rostratus, all of which belong to the Psammophiidae, were used to root the tree.
We de-novo sequenced 14 samples from different localities across the Horn of Africa and neighboring countries and belonging to P. aegyptius (seven samples from Egypt [2], Sudan [1], Somaliland [4]), P. punctulatus punctulatus (one sample from Ethiopia), P. rukwae (two samples from Ethiopia and Eritrea), P. sudanensis (one sample from Ethiopia), P. tanganicus (two samples from Ethiopia and Somaliland), and one sample from northern Somalia (central Somaliland) tentatively identified as P. cf. tanganicus. See Fig.
Genomic DNA was extracted from ethanol-preserved tissue samples using the DNA Mini Kit protocol. We PCR-amplified the three genes using primers and PCR conditions detailed in
The phylogenetic relationships within Psammophis were estimated by means of a Maximum Likelihood (ML) analysis and a Bayesian Inference (BI). The ML analysis was conducted in IQ-Tree (
The BI analysis was conducted in MrBayes v. 3.2 (
We assessed whether the genetic distances that separate the samples of the unidentified species from eastern Somalia from its sister species P. tanganicus are similar to or deviate from distances between other sister species across the Psammophis tree following the method of
We used the method of
For morphological comparisons, we examined the two specimens of P. tanganicus that were used in the genetic analysis (NMP-P6V 76371–2) and three specimens of the undescribed species from Somalia (NMP-P6V 76373, MVZ:Herp:242772, MVZ:Herp:242773), the former two of which were also included in the genetic analysis. Scale counts and color pattern of the P. tanganicus holotype (MCZ R-30380) were obtained from the photographs available at the MCZ collection database (https://mczbase.mcz.harvard.edu/guid/MCZ:Herp:R-30380). General morphological species characteristics of P. biseriatus and P. tanganicus were assembled from the literature (
Due to a rather small number of specimens available for morphological examinations we did not carry out formal statistical analyses to compare the studied taxa. We nonetheless carried out informal comparisons between them to verify whether there are morphological differences consistent with the genetic results.
The ML and BI analyses resulted in identical topologies, although some branches were not statistically supported in either of the analysis (Fig.
Maximum Likelihood phylogeny of the genus Psammophis based on a concatenated alignment of the cyt b, ND4 and c-mos genes (2,149 bp in total). The clade containing P. biseriatus, P. tanganicus and P. cornusafricae sp. nov. is highlighted in pink. Codes of samples newly sequenced for this study are in red. Locality details and original references of all samples are given in Suppl. material
As for the newly analyzed samples, the sample of P. punctulatus punctulatus (JIR513) was recovered as sister to P. punctulatus trivirgatus with a robust branch support (SH-aLRT: 100/UFBoot: 100/Standard bootstrap: 100/MrBayes pp: 1.0; support values are shown in the same order hereafter). The genetic distances between the two taxa are 8.0% in the cytb b and 9.06% in the ND4.
The newly analyzed samples of P. rukwae (JIR511, TMHC2012.12.148) clustered within other samples of the species from Chad and Kenya (support 97.4/100/96/1.0), with p-distances within the species ranging between 1.48–5.17% in the cyt b and 0.76–5.74% in the ND4.
The new sample of P. sudanensis from Ethiopia (TMHC2013.07.250) did not cluster with the other samples of the species included in the analyses, but actually with a lineage termed P. cf. sudanensis from Kenya and Tanzania that was first discovered by
The samples of P. aegyptius from Egypt and Sudan clustered with other samples of the species available on GenBank from Egypt and Niger (support 100/100/100/1.0), and the four samples from Somaliland were sister to this clade (support 97.5/99/97/1.0). Mean p-distances between the Somali samples and those from the north (Egypt, Sudan, Niger) were 8.03% in the cyt b (range 4.92–10.42%) and 9.24% in the ND4 (range 8.61–10.27%).
The two samples of P. tanganicus and that from central Somaliland that we tentatively identified as P. cf. tanganicus all clustered in a clade with P. biseriatus that was well supported in all analyses (support 100/100/100/1.0). In this clade, the two samples of P. tanganicus from Ethiopia and Somalia JIR508–509 (vouchers
Mitochondrial genetic distances (uncorrected p-distances in %) between P. biseriatus, P. tanganicus, and P. cornusafricae sp. nov. Below the diagonal are values for the cyt b gene, above the diagonal for the ND4. For each comparison, the mean is shown with the min-max range in brackets.
P. biseriatus | P. tanganicus | P. cornusafricae sp. nov. | |
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P. biseriatus | 10.18 (9.52–10.57) | 12.04 (11.99–12.08) | |
P. tanganicus | 10.78 (10.33–11.04) | 9.74 (9.26–10.77) | |
P. cornusafricae sp. nov. | 9.90 (9.75–10.06) | 7.79 (7.2–8.58) |
The genus showed clear genetic structuring with significant differences in the genetic distances found between the examined categories: within species, between sister species, between non-sister species, and the distance between the P. tanganicus and the undescribed species from Somalia (ANOVA F(3, 5152) = 575.4, p < 0.001). The post hoc tests confirmed pairwise differences between all categories (p < 0.01), except for the comparison between the categories ‘between sister species’ and ‘tanganicus-Somali species’ (p = 0.999; Fig.
Comparison of genetic distances within the Psammophis species, between sister species pairs, between non-sister species. The distances (y axis) are based on the ML tree. Horizontal bars with asterisks on top of the graph indicate significant differences in the observed genetic distances (p < 0.001; tested by the Tukey HSD post hoc test of ANOVA). The average distance between P. tanganicus and P. cornusafricae sp. nov. (0.127 subst. per site) is shown by the dashed line. The animal depicted is specimen
Based on the combined evidence of the genetic and morphological differentiation we recognize the undescribed species from the northeastern Somali regions of Somaliland and Puntland as new and provide its formal description below.
Psammophiidae Bourgeois, 1968
Psammophis Fitzinger, 1826
English name: African Horn Sand Snake Somali name: Subxaanyo [pronounced Subhanyo]; a term in the Somali language that refers to all Psammophis species that occur in the region. All Subxaanyo are believed to be harmless and friendly by the locals and are an important part of their folklore
Psammophis biseriatus in
Psammophis biseriatus tanganicus in
Psammophis tanganicus Largen and Ramussen (1993; in part), Brandstätter (1996; in part),
Psammophis sp. in
Holotype
:
Paratype
:
A Psammophis species sister to P. tanganicus, with the following combination of morphological characters: 11 infralabials; 9 supralabials, three of which are in contact with the eye; nostril pierced between two equal sized nasals; 15 anterior dorsals; 14–15 midbody dorsals; 11 posterior dorsals; 146–158 ventrals; 95–100 subcaudals. Body brown, grey or beige with only a faintly visible pale vertebral stripe but with well pronounced dorsolateral orange stripes on each side of the body. Tail with only a slight trace of or completely lacking any dark vertebral stripe; the posterior half of the tail uniformly pale yellow. Venter white to yellowish with a conspicuous stipple of irregular dark smears. Head dorsally with a symmetrical pattern of brown markings outlined by black margins which contrast with the grey or beige background coloration. Labials white with dark margins forming a black lip. Dark brown temporal stripe outlined by black blotches and stretching from the eye to the posterior end of the head.
(Fig.
Head flattened dorsoventrally, separated from the body by a distinct neck; nostril pierced between two nasals, major sector-shaped (‘pac-man’-like shape); eyes large, with a round pupil; rostral roughly heptagonal, with a distinct groove at the base for flicking the tongue out; rostral visible from above and followed dorsally by one pair of internasals, one pair of prefrontals, a long and narrow frontal with nearly equally as long supraoculars to its side; preoculars in narrow contact with the frontal and wedged between the prefrontals and supraoculars; large pair of parietals contacted laterally by large anterior temporals, posterior temporals and enlarged postparietals. The temporal formula of the anterior temporal + posterior temporal scales is 1+3. Laterally, rostral followed by two consecutive nasals, an elongated loreal and a large preocular that forms the anterior margin of the eye. Two postoculars at the posterior eye margin, the upper of which being contacted by the parietal and the lower by the anterior temporal. Nine supralabials, of which the 4th, 5th and 6th are in contact with the eye; 11 infralabials, five of which are in contact with the anterior pair of chin shields. Two pairs of chin shields. Four (right side) and five (left side) gulars in a longitudinal row between chin shields and preventrals. Anterior dorsals 15, midbody dorsals 14, posterior dorsals 11; 158 ventrals; 85 subcaudals.
Coloration in preservation: body brownish beige, dorsum darker than the flanks, with dark sets of three to five dorsolateral scales separated by two to three paler scale rows. The frontal and supraoculars with dark pigment patches at their anterior sides, posterior margins pale. Parietals with dark oblong blotches by the medial line and at the anterior margin of the scales. Internasals and prefrontals dark to the sides and paler medially, which forms a narrow white-yellowish stripe at the nose tip. Supralabials white with contrasting dark brown upper and lower margins. The white of the supralabials continues onto the sides of the neck. Throat with extensive dark spots arranged in longitudinal stripes – one on each side of the mouth on the lower side of the infralabials up to the 6th infralabial, one at the mid-line running through the chin shields and gulars further on the belly.
Psammophis cornusafricae sp. nov. can be differentiated from other congeners that occur in the Horn of Africa as follows: from its sister species P. tanganicus (character in brackets) by having 3–5 gulars in a longitudinal row between chin shields and preventrals (versus 2–3), posterior tip of the frontal moderately pointed (versus rounded), by lacking a clear orange or brownish dorsal stripe along the body and tail (versus orange vertebral stripe present), tail lacking a stripe, or having only a weakly developed dark vertebral stripe (versus tail with a clear dark vertebral stripe), having a clearly demarcated narrow temporal stripe on the head (versus broad stripe without clear demarcation), dark markings on the head dorsum paired and not fused (versus dark marking on the back of the head fused into a ‘W’ shape); from P. biseriatus (character in brackets) by having three supralabials in contact with the eye (versus two), usually one large anterior temporal (versus two), gular region strongly pigmented with dark longitudinal stripes (versus weakly pigmented with small dark spots), head ornately patterned above (versus uniformly colored), tail with absent or only a weakly developed dark vertebral stripe (versus tail with a clear dark vertebral stripe). Further morphological comparisons between P. cornusafricae sp. nov., P. tanganicus, and P. biseriatus are summarized in Table
Morphological comparisons of P. biseriatus, P. tanganicus and P. cornusafricae sp. nov. Superscript letters refer to the original references from which the data was obtained as follows: a -
P. biseriatus | P. tanganicus | P. cornusafricae sp. nov. | ||||||
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General | General |
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Total length (cm) | ~ 50–80 (max 100)a | ~ 50–80 (max 100)a | 63 | 90.8 | NA * | 58.8 | 62.9 | 73.8 |
SVL (cm) | 40.6 | 61.5 | 47.4 | 39.7 | 42.6 | 49.7 | ||
TL (cm) | 22.4 | 29.3 | NA * | 19.1 | 20.3 | 24.1 | ||
SVL/Total length (×100) | 61.7 (56–66)c | 66.7 (64–81) c | 64.4 | 67.7 | 67.5 | 67.7 | 67.3 | |
Infralabials | 10–11c | 9–11 | 11 | 11 | 10 | 10/11 (right/left) | 11 | 10 |
Supralabials | 9c | 9 c | 9 | 9 | 9 | 8 | 9 | 9 |
Supralabial in contact with eye | Two b (5th–6th) | Three (4th–6th) | Three (4th–6th) | Three (4th–6th) | Three (4th–6th) | Three (3rd–5th) | Three (4th–6th) | Three (4th–6th) |
Midbody dorsals | 15a | 15a | 15 | 15 | 15 | 15 | 14 | 15 |
Ventrals | 138–168a | 143–169a | 151 | 159 (+2 preventrals) | 150 (+1 preventral) | 151 (+1 preventral) | 158 | 146 (+1 preventral) |
Subcaudals | 97–134a | 81–123a | 114 | 110 | NA * | 95 | 85 | 100 |
From the other Horn species P. cornusafricae sp. nov. differs by having a lower number of midbody dorsals (14–15 versus 17 or 19 in P. aegyptius, P. lineatus, P. mossambicus, P. orientalis, P. punctulatus, P. rukwae, P. schokari, P. sudanensis a P. cf. sudanensis, P. trivirgatus), or a higher number of midbody dorsals (11 in P. angolensis, 13 in P. pulcher).
The studied specimens of P. cornusafricae sp. nov. show some degree of morphological variation (Table
The species epithet indicates the geographic origin of the species and translates as “The Sand Snake of the Africa’s Horn”. It is a noun in the genitive case that is derived from the Latin words for horn (cornu-us) and Africa (Africa-ae).
Our knowledge on the distribution of P. cornusafricae sp. nov. is very limited because it has so far been confirmed only from two localities. They are both located in Somalia; the type locality is at the very tip of the Horn of Africa (Puntland), the locality of specimen
Distribution of P. biseriatus, P. tanganicus and P. cornusafricae sp. nov. in the Horn of Africa. Localities sampled for the genetic analysis are shown along with sample codes. The background layer shows shaded relief and water bodies and drainages and was made with Natural Earth (www.naturalearthdata.com). The species range maps were derived from
Sand Snakes represent an important element of the snake fauna of Africa and Asia. Their diurnal habits, active foraging for prey and a relatively large size make them conspicuous and frequently encountered by naturalists (e.g., 2008 observations on iNaturalist as of April 27, 2023). This may be the reason why tissue samples are not that difficult to obtain for genetic analyses and why our understanding of their phylogenetic relationships is fairly complete, at least from the taxon sampling perspective. Of the 33 currently recognized species (
This study is the first to target the Sand Snakes of the Horn of Africa specifically. We analyze 14 newly obtained samples of six species and provide new insights into their distribution, genetic variability, and taxonomy. The phylogenetic reconstruction of the broader relationships between the Psammophis species confirmed previous findings (
The description of P. cornusafricae sp. nov. adds one more species to the list of snakes endemic to Puntland and eastern Somaliland (e.g., Platyceps brevis and P. messanai (
Besides the description of the new species we also analyzed new specimens of other Horn taxa to shed light on their diversity and distributions. The two newly analyzed samples of P. rukwae from Ethiopia and Eritrea cluster with other samples of the species from Chad and Kenya. This broadly distributed species ranges from Senegal in the West through the Sahel to East Africa (
The existence of the cryptic species referred to as P. cf. sudanensis that morphologically resembles P. sudanensis is well established (
The species with the most newly analyzed samples was P. aegyptius. The new samples from Egypt and Sudan are genetically very similar to other conspecific samples from the same region. The four samples from Somaliland, on the other hand, show marked genetic differences from the North African samples, as well as within themselves. The range of P. aegyptius covers the eastern part of the Sahara and has until now not been known to occur this far south (
Lastly, the sample of P. punctulatus punctulatus included in our analysis is the first of the taxon to have been analyzed. Previous material of the species belonged to the subspecies P. p. trivirgatus (
Sand Snakes rank among the most studied African snakes from the phylogenetic perspective. Yet, as evidenced by the number of cryptic or undescribed species, we are still far from fully comprehending their diversity. With the currently available sampling it is obvious that East Africa, and the Horn of Africa in particular, supports the highest diversity of undescribed species of Psammophis. Once their taxonomy is resolved, the diversity in the Horn may surpass that of the currently richest hotspot of the genus in southern Africa.
We are indebted to C. Spencer, J. Ho, and Natalie Ng (
List of Psammophis species and samples included in the phylogenetic analysis
Data type: Genetic data matrix
Explanation note: List of Psammophis species and samples included in the phylogenetic analysis, with their sample/voucher number, country and locality of origin (datum WGS84), GenBank accession numbers, MorphoBank accessions (MorphoBank Project No. 4527), and original reference. Samples newly sequenced for this study are in bold. The GPS coordinates of P. tanganicus from Tanzania that are marked with asterisks are only approximate.