Long-read mitogenomes reveal hidden control-region architecture in Smeringurus mesaensis with implications for vaejovid systematics

 

Matt Simon (https://instagram.com/crawly.creepy) made me recently aware of a new article from Matthew Graham and co-workers on the mitochondrial genome for the genus Smeringurus Haradon, 1983 (Vajeovidae). This stuff is way over my head and I had planned to not blog about it, but it turns out that the results have implications for vaejovid systematics and should be mentioned in the blog. 

Fortunately, I have been allowed to use Matt's review of the papers content and bring them to you in this post. And those interested can check out the article to see if you understand more than I do. :)

The researchers of the study set out to recover the first mitochondrial genome for the genus Smeringurus. However, one part of the genome was persistently difficult to recover. "What first appeared to be an incomplete or problematic portion of the genome gradually resolved...into a large and remarkably orderly tandem-repeat array in the control region" of the mitochondrial genome.

This is a new finding. It is significant because it shows "the control region as a structured and, potentially, an evolutionarily informative component of scorpion mitogenomes." The authors believe that this finding brings clarity to a difficult mitogenomic region that in the past was under-recognized because researchers were unable to make sense of it.

However, it's complicated. The researchers observe that this repeat array in the mitogenomic control region occurs in some other scorpion taxa, but it does not occur in all scorpion groups.

Lastly, the authors note that their study has implications for vaejovid systematics. "Within the limits of currently available mitogenomic sampling, S. mesaensis was recovered as sister to the remaining sampled vaejovids. That placement is notable because it is broadly consistent with earlier studies that also placed Smeringurus or Smeringurinae near the base of Vaejovidae."

However, the researchers note, prior work by Santibáñez-López et al. with phylogenomic data "recovered Smeringurinae...not as sister to the remaining vaejovids, but as a long branch nested within the family." That means the two techniques led to different systematic pictures. "That contrast suggests that the placement of Smeringurinae may remain sensitive to character sampling and analytical scale."

Abstract:
Repetitive regions of animal mitochondrial genomes are biologically informative but often difficult to assemble, raising the possibility that structured variation in mitochondrial control regions may be overlooked, especially in short-read datasets. We used Oxford Nanopore long-read sequencing to assemble five complete mitochondrial genomes of the dune scorpion Smeringurus mesaensis and resolve and validate the structure of the mitochondrial control region. In all five individuals, the 1598–1600 bp control region contained six complete 202 bp tandem repeats and one 92 bp terminal partial repeat. Mean control-region coverage ranged from 15.9× to 49.8×, with 10–33 reads spanning the 5′ repeat-array boundary, 14–25 spanning a central repeat junction, and three reads spanning the complete repeat array. Despite this repetitive architecture, the arrays were highly organized: repeats R2–R6 were identical within individuals, whereas R1 and the terminal partial repeat retained consistent positional differences. The 5′ non-repeat region showed significant local similarity to the control regions of Vaejovis mexicanus and V. smithi (72.8% and 69.6% identity), whereas the 202 bp repeat produced only short, nonsignificant matches. This pattern suggests that replication slippage and sequence homogenization have jointly shaped control-region evolution. A comparative survey of published scorpion mitogenomes further indicated that tandem repeats are more widespread and structurally diverse than generally reported. These results demonstrate the value of long reads for direct validation of repeat-rich mitochondrial architecture and highlight control-region structure as an underappreciated feature of scorpion mitogenome evolution.

Reference:
Graham MR, Santibáñez-López CE, Murdoch B. Long-Read Mitogenomes Reveal Hidden Control-Region Architecture in Smeringurus mesaensis and Overlooked Tandem Repeats in Scorpions. Arthropoda. 2026;4(4):16. [Open Access]

Thanks to Matt Simon for informing me about the article and for allowing me to use his review of it!

Family Vaejovidae

A new species of Compsobuthus from Iraq

 

Frantisek Kovarik and Frantisek Stahlavsky have recently published the description of a new species of Compsobuthus Vachon, 1949 (Buthidae) from Iraq.

Compsobuthus hadeki Kovarik & Stahlavsky, 2026

Abstract:
A new species, Compsobuthus hadeki sp. n. from Iraq is described and fully complemented with color photographs and compared with morphologically the most similar species, C. matthiesseni (Birula, 1905). The two species can be unequivocally separated by the following morphological features: in C. hadeki sp. n., movable finger of pedipalp bears 9 rows of granules; telson with aculeus shorter than vesicle, and metasoma III with 10 carinae. Cytogenetic analysis was performed, revealing a diploid chromosome count of 22 in C. hadeki sp. n.

Reference:
Kovarik F, Stahlavsky F. Compsobuthus hadeki sp. n. from Iraq (Scorpiones, Buthidae). Euscorpius. 2026(432):1–8. [Open Access]

Family Buthidae 

The first chromosome study of genera in the family Iuridae

 

Cytogenetic analysis can be important in understanding scorpion taxonomy and evolution. So far, most studies have been on taxa in the family Buthidae. Ersen Yagmur and co-workers have now published a study on the chromosomes in the iurid genera Calchas Birula, 1899 and Neocalchas Yağmur, Soleglad, Fet & Kovařík, 2013. This is the first chromosome study of taxa in the family Iuridae.

Abstract:
The chromosomes of two species belonging to the scorpion family Iuridae are studied for the first time. Both analysed species displayed achiasmatic meiosis and no morphologically differentiated sex chromosomes; these features are typical for all scorpions. Both species possessed monocentric chromosomes, a characteristic specific to the entire parvorder Iurida. The karyotype of Calchas nordmanni Birula, 1899 is composed of 82 chromosomes, and the diploid number of chromosomes in Neocalchas gruberi is 40. Despite this conspicuous difference in 2n chromosome morphology is mainly acrocentric. Both species possess two pairs of the 18S rDNA clusters identified by FISH. A higher number of rDNA loci may represent an ancestral state for the parvorder Iurida.

Reference:
Aydın Yağmur E, Koç H, Yeşílyurt F, Šťáhlavský F. The first chromosome study of the genera Calchas Birula, 1899 and Neocalchas Yağmur, Soleglad, Fet & Kovařík, 2013 (Scorpiones: Iuridae). Zoology in the Middle East. 2023:1-7. [Subscription required for full text]

Thanks to Ersen for sending me this article!

Family Iuridae

A new study of the genetics of the buthid genus Gint, endemic to the Horn of Africa

 

The genus Gint Kovarik, Lowe, Pliskova & Stahlavsky, 2013 (Buthidae) is endemic to the Horn of Africa with 12 species. Pavel Just and co-workers have recently published a study trying determinate the mechanisms of karyotype differentiation in this genus.

Their results showed that the Gint species exhibited substantial karyotype diversity and a high incidence of chromosome heterozygosity. This stuff is way over my head and I have to refer to the abstract and the article for further details on the study and its implications.

Abstract:
To determine the mechanisms of karyotype differentiation in scorpions of the genus Gint, we employed an integrative approach, combining cytogenetic data and sequence-based phylogeny. We cytogenetically examined six species with emphasis on multivalent meiotic configurations, 18S rDNA and (TTAGG)n distribution and compared chromosomal data with genetic divergence based on analysis of 16S rRNA and COI gene markers. Our results show that Gint species exhibit substantial karyotype diversity (2n = 18–45) and a high incidence of chromosome heterozygosity. Meiotic chromosome chains formed by up to six elements were found in 85% of analysed individuals, causing intraspecific chromosome variation in three species. Fluorescence in situ hybridization revealed that the 18S rDNA distribution pattern differed in Gint species, including at the intrapopulation level, but the chromosomal localization of (TTAGG)n motif was stable across species. Conspicuous interspecific differences in chromosome counts broadly corresponded with genetic divergence among Gint species. Our findings indicate that Gint karyotypes have undergone dynamic reorganization through independent fusions, fissions and reciprocal translocations. Owing to present chromosomal polymorphism, such structural changes shaping the genome architecture appear to be still ongoing in the populations of some Gint species.

Reference:
Just P, Šťáhlavský F, Kovařík F, Štundlová J. Tracking the trends of karyotype differentiation in the phylogenetic context of Gint, a scorpion genus endemic to the Horn of Africa (Scorpiones: Buthidae). Zoological Journal of the Linnean Society. 2022. [Subscription required for full text]

Thanks to Frantisek Kovarik for sending me their article!

Family Buthidae

Genetic diversity among different species of the genus Leiurus in Saudi Arabia and the Middle East

 

 Abdulaziz Alqahtani and Ahmed Badry published this Fall an article on the genetic diversity among different species of the genus Leiurus Ehrenberg, 1828 (Buthidae) in Saudi Arabia and the Middle East. They conclude that there is a clear genetic splitting between Leirus from Egypt and those from Arabia and Turkey. In addition, the results support the taxonomic status of Arabian Leiurus species.

Abstract:
The molecular phylogenetic relationship among two species of genus Leiurus, from Saudi Arabia with additional comparative sequence data available from Egypt, Oman and Turkey is presented. The molecular phylogeny was performed using maximum parsimony, neighbor joining and bayesian inference. Our results indicate a clear deep splitting between the Western clade, which represented by L. quinuestriatus sequences from Egypt and those from the Eastern clade which encompassing different Leiurus species from Saudi Arabia, Oman and Turkey was shown. Also, the phylogenetic relationship represents additional support for the taxonomic status of Arabian Leiurus species.

Reference:
Alqahtani AR, Badry A. Genetic diversity among different species of the genus Leiurus (Scorpiones: Buthidae) in Saudi Arabia and the Middle East. Saudi J Biol Sci. 2020;27(12):3348-53.[Open Access]

Thanks to Dr. Badry for sending me their article!

Family Buthidae

Karyotype evolution and preliminary molecular assessment of genera in the family Scorpiopidae

 

I have stolen the title in this post from the latest article from Frantisek Stahlavsky and co-workers of the moelcular genetics and phylogeny of the family Scorpiopidae. As previously mentioned, I'm not very good at molecular genetics and I leave it up to you readers to checkout this paper to learn more about the details of the results.

The main findings of the article is that their results support the monophyly of the family Scorpiopidae, but most genera were recovered as para- or polyphyletic. This makes the authors questioning the utility of the morphological characteristics currently used in scorpion taxonomy for generic delimitation in this family. I guess these results are the basis for the Scorpiopidae revision published in November by Kovarik et al.

Abstract:
The scorpions represent an ancient and morphologically conserved order of arachnids. Despite that, their karyotypes may differ considerably even among closely related species. In this study, we identify the trends of the karyotype evolution in the family Scorpiopidae based on integrating cytogenetic data and multi-locus molecular phylogenetic approaches. We detected considerable variability in diploid numbers of chromosomes (from 48 to 147), 18S rRNA gene cluster positions (from terminal to pericentromeric) at the interspecific level. Moreover, we identified independent fusions, fissions and inversions in the evolution of the family Scorpiopidae, leading to a remarkable diversification of the karyotypes. The dynamic system of the karyotype changes in this group is further documented by the presence of interstitial telomeric sequences (ITS) in two species. The cytogenetic differences observed among the analyzed species highlight the potential of this type of data for species-level taxonomy in scorpion lineages with monocentric chromosomes. Additionally, the results of our phylogenetic analyses support the monophyly of the family Scorpiopidae, but rendered several genera para- or polyphyletic.

Reference:
Stahlavsky F, Kovarik F, Stockmann M, Opatova V. Karyotype evolution and preliminary molecular assessment of genera in the family Scorpiopidae (Arachnida: Scorpiones). Zoology. 2021;144:125882. [Subscription required for full text]

Thanks to Frantisek Kovarik for sending me their article!

Family Scorpiopidae

Evolutionary dynamics of rDNA clusters on chromosomes of buthid scorpions

I have stolen the original title from this article for this post as I must admit that the topic is beyond my knowledge. I do have a master in zoology, but back then we learned very little about genetics. 

Anyway, Frantisek Stahlavsky and several other co-workers have recently published a study on the evolutionary dynamics of rDNA clusters on chromosomes of buthid scorpions. The study provides the first analysis of karyotype evolution within a phylogenetic context for the whole of the family Buthidae. For more information you can check out the abstract or the article.

Abstract:
We examined the distribution of genes for major ribosomal RNAs (rDNA) on holokinetic chromosomes of 74 species belonging to 19 genera of scorpions from the family Buthidae using fluorescence in situ hybridization (FISH). Our analysis revealed differences between the two main evolutionary lineages within the family. The genera belonging to the ‘Buthus group’, with a proposed Laurasian origin, possess one pair of rDNA mainly in an interstitial position, with the only exceptions being the terminal location found in some Hottentotta and Buthacus species, possibly as a result of chromosome fissions. All the remaining buthid ‘groups’ possess rDNA found strictly in a terminal position. However, the number of signals may increase from an ancestral state of one pair of rDNA loci to up to seven signals in Reddyanus ceylonensis Kovařík et al., 2016. Despite the differences in evolutionary dynamics of the rDNA clusters between the ‘Buthus group’ and other lineages investigated, we found a high incidence of reciprocal translocations and presence of multivalent associations during meiosis in the majority of the genera studied. These phenomena seem to be typical for the whole family Buthidae.

Reference:
Šťáhlavský F, Nguyen P, Sadílek D, Štundlová J, Just P, Haddad CR, et al. Evolutionary dynamics of rDNA clusters on chromosomes of buthid scorpions (Chelicerata: Arachnida). Biological Journal of the Linnean Society. 2020;Online first:1-19. [Subscription required for full text]

Thanks to Frantisek Kovarik for sending me their article!

Family Buthidae

 

 

A comparative cytogenetic study of a three Hadogenes species results in a new species from South Africa

Frantisek Stahlavsky and co-workers have recently published the first comparative cytogenetic study in Hadogenes species (Hormuridae) using both standard and molecular cytogenetic approaches. A new species from South Africa is also described.

Hadogenes weygoldti Stahlavsky, Stundlova, Lowe, Stockmann & Kovarik, 2018

Abstract:
In the present study, we performed the first comparative cytogenetic study in Hadogenes species using both standard and molecular cytogenetic approaches. Information about the diploid set, number and distribution of 18S rDNA and telomeric sequences was obtained from three South African species, Hadogenes trichiurus (Gervais, 1843), H. zuluanus Lawrence, 1937 and H. weygoldti sp. n. All species analysed differ considerably in the number of chromosomes (H. trichiurus 2n=48, H. zuluanus 2n=80, H. weygoldti sp. n. 2n=113). In contrast, the number of 18S rDNA clusters and distribution of telomeric sequences represent rather stable cytogenetic characters in Hadogenes. Within all karyotypes, we identified one pair of 18S rDNA clusters. The telomeric signals were exclusively on the terminal chromosomal regions. Interestingly, the chromosomal location of 18S rDNA clusters varied from terminal to interstitial in species karyotypes, indicating the presence of hidden structural chromosomal changes. Additionally, the present comparative study is complemented by the description of a new species, H. weygoldti sp. n., based on specific karyotype features and morphological characters. Finally, our cytogenetic results are compared with known chromosomal data of other Hadogenes species, and the use of cytogenetic approaches in the taxonomy of scorpions is discussed.

Reference:
Šťáhlavský F, Štundlová J, Lowe G, Stockmann M, Kovařík F. Application of cytogenetic markers in the taxonomy of flat rock scorpions (Scorpiones: Hormuridae), with the description of Hadogenes weygoldti sp. n. Zoologischer Anzeiger. 2018;Accepted Manuscript. [Subscritpion required for full text]

Family Hormuridae