Museum DNA reveals a new, potentially extinct species of rinkhals (Serpentes: Elapidae: Hemachatus) from the Eastern Highlands of Zimbabwe.

Acknowledgements: We thank the late Tony Phelps for his contribution to this research. For permission to sample specimens of Hemachatus in their care, we thank Thea Litschka Koen and Clifton David Koen, Mark Marshall, Arno Naude, Mike Perry, and Moshe Kahn. Krystal Tolley kindly provided access to laboratory facilities in Cape Town, as well as insightful reviews of two earlier drafts of this manuscript, which greatly improved the final version.Genetic information plays a pivotal role in species recognition and delimitation, but rare or extinct animals can be difficult to obtain genetic samples from. While natural history wet collections have proven invaluable in the description of novel species, the use of these historical samples in genetic studies has been greatly impeded by DNA degradation, especially because of formalin-fixation prior to preservation. Here, we use recently developed museum genomics approaches to determine the status of an isolated population of the elapid snake genus Hemachatus from Zimbabwe. We used multiple digestion phases followed by single strand sequencing library construction and hybridisation capture to obtain 12S and 16S rDNA sequences from a poorly preserved tissue sample of this population. Phylogenetic and morphological analyses in an integrated taxonomic framework demonstrate that the Zimbabwean rinkhals population represents an old and highly distinct lineage, which we describe as a new species, Hemachatus nyangensis sp. nov. Our phylogenetic dating analysis is compatible with venom spitting having evolved in response to the threat posed by early hominins, although more data are required for a robust test of this hypothesis. This description demonstrates the power of museum genomics in revealing rare or even extinct species: Hemachatus from Zimbabwe are only known from a small area of the Eastern Highlands known for high endemism. No living specimens have been seen since the 1980s, most likely due to dramatic land-use changes in the Eastern Highlands, suggesting that the species could be extinct. In view of its recognition as a highly distinct lineage, urgent action is required to determine whether any populations survive, and to safeguard remaining habitat

Museum DNA reveals a new, potentially extinct species of rinkhals (Serpentes: Elapidae: Hemachatus) from the Eastern Highlands of Zimbabwe.

Genetic information plays a pivotal role in species recognition and delimitation, but rare or extinct animals can be difficult to obtain genetic samples from. While natural history wet collections have proven invaluable in the description of novel species, the use of these historical samples in genetic studies has been greatly impeded by DNA degradation, especially because of formalin-fixation prior to preservation. Here, we use recently developed museum genomics approaches to determine the status of an isolated population of the elapid snake genus Hemachatus from Zimbabwe. We used multiple digestion phases followed by single strand sequencing library construction and hybridisation capture to obtain 12S and 16S rDNA sequences from a poorly preserved tissue sample of this population. Phylogenetic and morphological analyses in an integrated taxonomic framework demonstrate that the Zimbabwean rinkhals population represents an old and highly distinct lineage, which we describe as a new species, Hemachatus nyangensis sp. nov. Our phylogenetic dating analysis is compatible with venom spitting having evolved in response to the threat posed by early hominins, although more data are required for a robust test of this hypothesis. This description demonstrates the power of museum genomics in revealing rare or even extinct species: Hemachatus from Zimbabwe are only known from a small area of the Eastern Highlands known for high endemism. No living specimens have been seen since the 1980s, most likely due to dramatic land-use changes in the Eastern Highlands, suggesting that the species could be extinct. In view of its recognition as a highly distinct lineage, urgent action is required to determine whether any populations survive, and to safeguard remaining habitat

Fig 3 -

Bar plots showing the number of dorsal scale rows snakes possessed at the nape (A) and at midbody (B).</p

Results of statistical tests comparing the morphological characters of South African and Zimbabwean <i>Hemachatus</i>.

ANOVA, chi-squared tests, and Fisher’s exact tests were used where appropriate. In the P column, asterisks highlight significant differences or interactions (P < 0.001 ***, < 0.01 **, < 0.05 *).</p

Fig 5 -

(A and B) Hemachatus nyangensis sp. nov. specimen in life, displaying defensive hooding posture. (C and D) Miombo woodland and grassland habitat of H. nyangensis sp. nov.</p

Dated Bayesian phylogenetic tree of the cobra group of elapids.

Grey bars denote 95% HPD confidence intervals for divergence times; nodes lacking grey error bars were used as calibration points. Node labels represent Bayesian posterior probabilities (BPP), with black dots denoting BPP ≥ 0.95. The clade representing Hemachatus individuals from South Africa and Eswatini is highlighted in salmon pink, and the divergent Zimbabwe lineage in blue-green.</p

Eigenvector coefficients for each scaled variable from the principal component analysis, eigenvalues, and the total variance explained by each principal component.

The variables that contributed most to each principal component are in bold.</p

Comparison of standard scale counts between <i>Hemachatus</i> from South Africa and Zimbabwe.

Shown are the mean and standard deviation, with range in brackets, and sample size. Sexually dimorphic characters are divided by sex.</p