Saudi Journal of Biological Sciences 28 (2021) 3511–3516

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Saudi Journal of Biological Sciences

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Original article Small and overlooked: Phylogeny of the genus Trigonodactylus (: ), with the first record of Trigonodactylus arabicus from ⇑ Lukáš Pola a, , Vojteˇch Hejduk b, Aleš Zíka c, Tomáš Winkelhöfer c, Jirˇí Šmíd a,d, Salvador Carranza e, Mohammed Shobrak f,g, Mohammad Abu Baker h, Zuhair Sami Amr i a Department of Zoology, Faculty of Science, Charles University, Vinicˇná 7, 12844 Prague, Czech Republic b Otovická 268, 403 39 Chlumec, Czech Republic c Zoological and Botanical, Garden in Pilsen, Pod Vinicemi 9, 30116 Pilsen, Czech Republic d Department of Zoology, National Museum, Cirkusová 1740, 19300 Prague, Czech Republic e Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37–49, Barcelona, Spain f Biology Department, Science College, Taif University, P.O. Box 11099, Taif 21944, g Saudi Wildlife Authority, Prince Saud Al Faisal Research Center, Taif, Saudi Arabia h Department of Biology, The University of Jordan, Amman, Jordan i Department of Biology, Jordan University of Science and Technology, Irbid, Jordan article info abstract

Article history: of the genus Trigonodactylus are widely distributed in the sand deserts of the Arabian Peninsula. Received 16 July 2020 Three species of this genus are currently recognized, with a fourth one, Stenodactylus pulcher, which Revised 6 March 2021 placement within Trigonodactylus has been tentatively suggested, but not yet confirmed. We present a Accepted 7 March 2021 phylogenetic analysis of the genus Trigonodactylus with new specimens collected in central Saudi Available online 23 March 2021 Arabia and southern Jordan. New genetic data has been generated from three mitochondrial markers to investigate the phylogenetic relationships of all species of the genus and to assess the putative generic Keywords: assignment of S. pulcher. Our results confirm that S. pulcher indeed belongs within Trigonodactylus, Range extension branching as a sister lineage to all other species of the genus. The new samples cluster within Palearctic naked-toed geckos Stenodactylus Trigonodactylus arabicus, thus confirming the genetic homogeneity of the species across its large and Mitochondrial DNA seemingly inhospitable range. The new specimen collected in southern Jordan represents the first record Middle East for the country and a considerable range extension to the northwest from all previously reported local- ities. Our findings and discovery of a new species for Jordan highlight the need of more field surveys to be carried out in the underexplored parts of Jordan and northern Saudi Arabia, as these places still hold a potential for new discoveries and are crucial for understating the biogeography of the Arabian herpetofauna. Ó 2021 The Authors. Published by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

1. Introduction odactylus arabicus from Abqaiq, Saudi Arabia (Haas, 1957). Later on, Kluge (1967) synonymized Trigonodactylus with Stenodactylus Trigonodactylus are small, nocturnal and psammophilous based on the morphological similarity of the two genera. For about geckos. The genus was originally described for the species Trigon- 50 years, this taxonomic conclusion was generally followed (e.g. Fujita and Papenfuss, 2011; Metallinou et al., 2012; Metallinou and Carranza, 2013) until recently, when Nazarov et al. (2018) ⇑ Corresponding author. resurrected Trigonodactylus for a clade comprising four species E-mail address: [email protected] (L. Pola). (Stenodactylus arabicus, S. sharqiyahensis, S. persicus, and tentatively Peer review under responsibility of King Saud University. S. pulcher). The latter was, however, missing in the phylogenetic analysis of Nazarov et al. (2018) and is still listed under its former generic name Stenodactylus in the Database (Uetz et al., 2021), despite that morphological and genetic evidence indicate Production and hosting by Elsevier https://doi.org/10.1016/j.sjbs.2021.03.019 1319-562X/Ó 2021 The Authors. Published by Elsevier B.V. on behalf of King Saud University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Lukáš Pola, Vojteˇch Hejduk, Aleš Zíka et al. Saudi Journal of Biological Sciences 28 (2021) 3511–3516 a close relationship to T. arabicus and T. sharqiyahensis (see Arnold, was collected in Jordan ca. 2 km E of Mudawwara (Fig. 2; sample 1980; Metallinou et al., 2012). JIR446, collected on 17.9.2019 at 29.32N 36.01E, 717 m a.s.l., and Members of the genera Stenodactylus and Trigonodactylus deposited in the National Museum Prague [voucher code NMP6V belong to one of the most characteristic and abundant herpetofau- 76022], Czech Republic) and two specimens were collected in nal elements of North African and Arabian deserts, showing a clear Saudi Arabia ca. 100 km NE of Riyadh (sample CN15785, collected Saharo-Arabian distribution pattern (Arnold, 1980; Sindaco and at 25.21N 47.70E, 649 m a.s.l., and deposited at the Institute of Evo- Jeremcˇenko, 2008; Metallinou et al., 2012). The four species of lutionary Biology [IBECN15785], Barcelona, Spain; sample Trigonodactylus are, however, restricted only to the Arabian Penin- CN15789, collected at 25.147N, 47.56E, 665 m a.s.l., deposited at sula, with T. persicus reaching Mesopotamia (Metallinou and Taif University, Taif, Saudi Arabia). The specimens were stored in Carranza, 2013; Nazarov et al., 2018). Trigonodactylus arabicus is 96% ethanol. widely distributed in the deserts of the Arabian Peninsula (Fig. 1). Besides central and eastern Saudi Arabia, from where it 2.2. DNA extractions, PCR and sequence alignment was described, it has been reported from , Bahrain, Qatar, the , , and Yemen (Delima and Al- Genomic DNA was extracted using the Tissue Genomic DNA Nasser, 2007; Gallagher, 1971; Arnold, 1980; Sindaco and Mini Kit (Geneaid, Taiwan). To be able to combine our results with Jeremcˇenko, 2008; Metallinou et al., 2012; Gardner, 2013; previously published sequence data, we PCR-amplified and Carranza et al., 2018; Burriel-Carranza et al., 2019). It was recently sequenced in both directions three mitochondrial markers: 12S reported from Khuzestan province in southwestern (Fathinia rRNA (12S), 16S rRNA (16S), and cytochrome oxidase I (COI). Pri- et al., 2014), however this record very likely represents T. persicus mers, their sequences, amplicon sizes and PCR conditions, and (Nazarov, pers. comm.; Fathinia, pers. comm.). original references for all markers are provided in Table S1. Apart Herein, we produce new genetic data for Trigonodactylus species from sequencing the newly obtained samples, we also generated to infer a complete phylogeny of the genus with the aim to finally 17 new COI sequences for samples used in the study by confirming the generic assignment of T. pulcher. Alongside that, we Metallinou and Carranza (2013) and downloaded available provide a considerable range extension for T. arabicus that we report sequences of all Trigonodactylus species from GenBank for the first time from the Hashemite Kingdom of Jordan and demon- (Metallinou et al., 2012; Metallinou and Carranza, 2013; Nazarov strate the genetic homogeneity of this species across the largest et al., 2018). Five Stenodactylus species were used as outgroups. sand-dune deserts of Arabia, suggesting the presence of high levels All samples and GenBank accessions used in this study are listed of gene-flow across this extreme and inhospitable habitat. in Table S2. Geneious v.11 (Kearse et al., 2012) was used to edit and assemble the chromatograms. Sequences of COI were trans- 2. Material and methods lated into amino acids and no stop codons were revealed, suggest- ing that no pseudogene was amplified. Each gene was aligned 2.1. New material independently using the online version of MAFFT v.7 (Katoh et al., 2019). We applied the Q-INS-i strategy for the 12S and 16S Field work was carried out in Saudi Arabia and Jordan in June genes because it considers the secondary structure of the RNA, and September 2019, respectively. One Trigonodactylus specimen while COI was aligned using default settings.

Fig. 1. Distribution of the four Trigonodactylus species. Numbers in the map indicate localities of the new material: 1 - vicinity of Mudawwara, southern Jordan; 2 and 3 - vicinity of Riyadh, central Saudi Arabia. Black dots inside circles indicate origin of the material used in the phylogenetic analyses. Stars denote type localities of all species. Colors of species correspond to those in Fig. 3. The phylogenetic tree in the inset is a result of the Bayesian analysis and shows the relationships between the Trigonodactylus species.

3512 Lukáš Pola, Vojteˇch Hejduk, Aleš Zíka et al. Saudi Journal of Biological Sciences 28 (2021) 3511–3516

constant population tree prior with a 1/X population size prior (Drummond & Bouckaert, 2017). Gamma priors (alpha = 0.05, beta = 10) were used for all substitution rate parameters. The BI analysis ran three times for 3 Â 107 generations with parameters and trees sampled every 3 Â 104 generations. Convergence of runs, their stationarity and effective sample sizes of all estimated parameters were inspected in Tracer v.1.7.1 (Rambaut et al., 2018). In each run, 10% of posterior trees were discarded as burnin and the remaining trees were combined using LogCombiner. The Maximum clade credibility tree was then identified with TreeAnnotator (both programs are part of the BEAST package). To speed up the computational process, the BI analysis was set up to run through the CIPRES Science Gateway (Miller et al., 2010). Nodes that received UFBoot  95, SH-aLRT  80, and Bayesian pos- terior probability (pp)  0.95 were considered strongly supported. Inter- and intraspecific uncorrected p-distances with pairwise deletion were estimated using MEGA X (Kumar et al., 2018) for the COI marker only, as it is the only overlapping marker for all four species of the genus Trigonodactylus in our dataset. Intraspeci- fic uncorrected p-distances between all samples of Trigonodactylus arabicus were estimated for all three markers.

3. Results

Fig. 2. A: Specimen NMP6V 76022 in life; B: Habitat in the vicinity of Mudawwara, The newly collected specimens from Jordan and Saudi Arabia southern Jordan where the specimen was collected; C: Detail of the interdigital were identified as Trigonodactylus arabicus using available relevant webbing on the front foot. Photos by Lukáš Pola. literature (Arnold, 1980, 1986; Gardner, 2013; Metallinou and Carranza, 2013; Nazarov et al., 2018) based on the following fea- 2.3. Phylogenetic analyses tures: Adults small of up to 40 mm from snout to vent, slender habitus, clearly webbed forefeet, and dark and slightly triangular- We performed Maximum Likelihood (ML) and Bayesian infer- shaped transverse bar in front of the eyes across the snout. This ence (BI) phylogenetic analyses applying a partitioning scheme morphological species assignment was also confirmed by the by gene. For the ML analysis we also tested an alternative parti- genetic results (Fig. 3). tioning of the dataset using PartitionFinder v.2.1.1 (Lanfear et al., The final dataset included 73 specimens sequenced for up to 2016). The input settings were as follows, linked branch lengths, 1603 base pairs (bp; 399 bp of 12S, 547 bp of 16S, and 657 bp of all models, BIC model selection, greedy search algorithm and COI COI). The number of variable and parsimony-informative positions, alignment divided by codon positions. The results suggested that respectively, were as follows: 140 and 104 for 12S, 167 and 123 for 12S, 16S, and the first codon position of COI should be considered 16S, 266 and 215 for COI. as one partition, and the second and third codon position of COI Both phylogenetic analyses resulted in an identical topology at each to be a separate partition. The ML analysis was carried out the deepest nodes. The ML results remained consistent regardless in IQ-TREE (Nguyen et al., 2015) using its online web interface of the partitioning scheme applied, we thus report only those for W-IQ-TREE (Trifinopoulos et al., 2016). The best substitution model the partitioned by genes scheme. According to the trees (Fig. 3), for each gene was selected automatically by ModelFinder the Trigonodactylus clade is strongly supported (UFBoot = 100; (Kalyaanamoorthy et al., 2017) as implemented in IQ-TREE, as well SH-aLRT = 100; BI pp = 1.00, support values are given in this order as the best models for the alternative partitioning. The best model hereafter) and consists of these four species: T. pulcher, T. sharqiya- of nucleotide substitution for the partition by gene scheme was hensis, T. arabicus, and T. persicus. Trigonodactylus pulcher is sup- identified as TPM2u+F+G4 for 12S, GTR+F+G4 for 16S and TPM3 ported as sister to the remaining three species (100; 100; 1.00). +F+I+G4 for COI. For the alternative partitioning scheme, ModelFin- Trigonodactylus sharqiyahensis is supported as a sister taxon to der identified GTR+F+G4 for the first partition (12S, 16S and the the clade formed by T. persicus and T. arabicus (100; 100; 1.00). first codon position of COI), F81+F+I and TN+F+G4 for the second The new samples from Jordan and Saudi Arabia cluster within T. and third partition respectively. Branch support was assessed by arabicus. The two samples from central Saudi Arabia are genetically the ultrafast bootstrap approximation algorithm (UFBoot; Minh close to samples from Qatar and central and southern Oman, albeit et al., 2013) and the Shimodaira-Hasegawa-like approximate like- with low node support (93; 74.1; 0.89). The new sample from Jor- lihood ratio test (SH-aLRT; Guindon et al., 2010), both with 1000 dan clusters with two samples from Kuwait (99; 95.8; 1.00). This replicates. group of samples from Jordan and Kuwait was in the BI analysis BEAST v.2.5.2. (Bouckaert et al., 2014) was used for the BI anal- sister to a strongly supported clade formed by all remaining T. ara- ysis applying a partitioning scheme by gene only. We applied the bicus samples (pp = 1.00). Although the ML analysis resulted in a GTR+G for the 12S and 16S partitions and HKY+G for the COI par- similar topology, the support for the clade of all remaining T. ara- tition, which were selected as the best models of nucleotide substi- bicus samples was not convincing (UFBoot = 84; SH-aLRT = 93.3). tution by jModelTest v.2.1.6. (Darriba et al., 2012). Site and clock Uncorrected p-distances between the new sample from Jordan models were unlinked across partitions. Strict clock model was (JIR 446) and the remaining T. arabicus samples range between used for all partitions with normal prior distributions specified 1.3–2.9% for the 12S, 1.8–2.7% for the 16S and 3.7–7% for the COI for the 16S and COI with the mean = 1 (relative to the clock rate (Table S3). Mean intraspecific genetic variability within T. arabicus of the 12S). Given the character of the dataset that contained mul- is 1.6% for the 12S, 1.8% for the 16S and 4.3% for the COI (Table 1). tiple samples for the four target species we used the coalescent Inter- and intraspecific genetic distances based on the COI gene for all four species are shown in Table 1.

3513 Lukáš Pola, Vojteˇch Hejduk, Aleš Zíka et al. Saudi Journal of Biological Sciences 28 (2021) 3511–3516

Fig. 3. Phylogenetic relationships within Trigonodactylus. The tree is a result of the ML analysis based on the concatenated mitochondrial dataset of 12S, 16S and COI. Black dots at nodes represent UFBoot  95, SH-aLRT  80 and Bayesian posterior probabilities  0.95. New samples from central Saudi Arabia (CN15785, CN15789) and southern Jordan (JIR446) are highlighted in red.

Table 1 Interspecific genetic distances (below diagonal) and intraspecific distances (on diagonal in bold) based on the COI gene for the four recognized species of the genus Trigonodactylus.

T. arabicus T. persicus T. pulcher T. sharqiyahensis T. arabicus 0.043 T. persicus 0.109 0.003 T. pulcher 0.162 0.165 0.003 T. sharqiyahensis 0.126 0.121 0.163 0.017

4. Discussion Gardner, 2013). Among Arabian geckos, it is the only genus with interdigital webbing, an adaptation that allows the to walk Despite several previous attempts to infer the phylogeny of on loose sand. This unique pedal specialization is only known in Trigonodactylus, none of the studies had all species of the genus two other species, both of the genus Pachydactylus from represented (Metallinou et al., 2012; Nazarov et al., 2018). The Namibia (Arnold, 1980; Bauer and Russell, 1991). results of our phylogenetic analyses conclusively confirm T. pulcher Sand deserts and dunes cover vast areas of Arabia. Most of to belong to Trigonodactylus, branching as sister species to the southern Arabia is encompassed by the Rub Al Khali (also termed three remaining taxa (Fig. 3). The close relationship of T. pulcher the Empty Quarter), the largest continuous sand field in the world. and T. arabicus was first found by Metallinou et al. (2012), who also Sand fields extend from there through the Dahna desert, a corridor time-calibrated their tree. Their age estimate of the split between that stretches north-, northwestward from the Rub Al Khali and the two species, which corresponds to the crown node of Trigon- connects it with another large sand field, the Nafud desert, located odactylus as confirmed here, dates back to the Middle Miocene in northwestern Arabia (Edgell, 2006). The range of T. arabicus fol- (17.3 million years ago [Mya], 95% highest posterior density inter- lows tightly this distribution, albeit the interior of the Rub Al Khali val: 11.3–23.6 Mya). This indicates that Trigonodactylus originated lacks, for the time being, records (Šmíd et al., 2021). By sequencing in Arabia at the time when the peninsula was already well sepa- T. arabicus samples from the central part of the species range near rated from Africa (e.g. Šmíd et al., 2013; Tamar et al., 2016). The Riyadh we confirm the genetic homogeneity of the species, sug- subsequent split between T. arabicus and T. sharqiyahensis, which gesting high levels of gene-flow in the interior of the Arabian with our current understanding is the crown split between T. ara- Peninsula. bicus, T. sharqiyahensis and T. persicus, took place 6.4 Mya (3.9–9.3 The new record from Jordan reported here represents a consid- Mya) according to Metallinou et al. (2012). erable range extension (ca. 930 km) to the northwest from all pre- The distribution of all Trigonodactylus species is strongly tied viously reported localities of the species. It is surprising that its with the distribution of sandy habitats as a result of their strict presence in Jordan has remained undetected until now despite psammophilous requirements and adaptations (Arnold, 1980; the fairly extensive herpetological research being done (Sindaco

3514 Lukáš Pola, Vojteˇch Hejduk, Aleš Zíka et al. Saudi Journal of Biological Sciences 28 (2021) 3511–3516 et al., 1995; Disi et al., 2001; Al Quran, 2010; Disi, 2011; Scholz Burriel-Carranza, B., Tarroso, P., Els, J., Garder, A., Soorae, P., Mohammd, A.A., et al., 2013). Delima and Al-Nasser (2007), who discovered T. ara- Tubati, S.R.K., Eltayeb, M.M., Shan, J.N., Tejero-Cicuéndez, H., Simó-Riudalbas, M., Pleguezuelos, J.M., Fernández-Guiberteau, D., Šmíd, J., Carranza, S., 2019. bicus in Kuwait commented that the species might have remained An integrative assesment of th diversity phylogeny, distribution, and unknown from the country for the difficulty of spotting due to its conservation of the terrestrial (Sauropsida, Squamata) of the United small size and pinkish, almost translucent appearance. Its occur- Arab Emirates. PLoS ONE 14 (5), e0216273. https://doi.org/10.1371/journal. pone.0216273. rence in Jordan could have been overlooked for similar reasons, Carranza, S., Xipell, M., Tarroso, P., Gardner, A.S., Arnold, E.N., Robinson, M.D., Simó- or as a result of confusion with the sympatrically occurring Sten- Riudalbas, M., Vasconcelos, R., de Pous, P., Amat, F., Šmíd, J., Sindaco, R., odactylus doriae or S. slevini (pers. obs.), although we find this very Metallinou, M., Els, J., Pleguezuelos, J.M., Machado, L., Donaire, D., Martínez, G., Garcia-Porta, J., Mazuch, T., Wilms, T., Gebhart, J., Aznar, J., Gallego, J., Zwanzig, unlikely for the unique morphology of Trigonodactylus geckos. Its B.M., Fernandez-Guiberteau, D., Papenfuss, T., Al Saadi, S., Alghafri, A., Khalifa, S., discovery is, however, not that surprising in terms of biogeogra- Al Farqani, H., Bilal, S.B., Alazri, I.S., Al Adhoobi, A.S., Al Omairi, Z.S., Al Shariani, phy, as some other Arabian psammophilous squamates reach up M., Al Kiyumi, A., Al Sariri, T., Al Shukaili, A.S., Al Akhzami, S.N., 2018. Diversity, distribution and conservation of the terrestrial reptiles of Oman (Sauropsida, to southern Jordan (e.g. Cerastes gasperettii, Acanthodactylus Squamata). PLoS ONE 13 (2), e0190389. https://doi.org/10.1371/journal. schmidti, arabicus, pone.0190389. (Wittenberg, 1992; Disi et al., 2001). Darriba, D., Taboada, G.L., Doallo, R., Posada, D., 2012. jModelTest 2: more models, Our findings highlight the need for more field surveys to be car- new heuristics and parallel computing. Nat. Methods 9 (772). https://doi.org/ 10.1038/nmeth.2109. ried out in the underexplored deserts of southern Jordan and Delima, E.C., Al-Nasser, A., 2007. New record of the Web-footed Sand Gecko, northern Saudi Arabia, as these difficult-to-access places still hold Stenodactylus arabicus (Haas, 1957) (Sauria: Gekkonidae), from Kuwait. Zool. a potential for new discoveries and are crucial for understanding Middle East 41 (1), 111–112. https://doi.org/10.1080/ 09397140.2007.10638235. the biogeography of the Arabian herpetofauna. Disi, A.M., 2011. Review of the lizard fauna of Jordan. Zool. Middle East 54 (3), 89– 102. https://doi.org/10.1080/09397140.2011.10648900. Declaration of Competing Interest Disi, A.M., Modry´ , D., Necˇas, P., Rifai, L., 2001. The Amphibians and Reptiles of the Hashemite Kingdom of Jordan. An Atlas and Field guide. Edition Chimaira. Drummond, A.J., Bouckaert, R.R., 2017. Bayesian evolutionary analysis with BEAST. The authors declare that they have no known competing finan- Cambridge University Press. cial interests or personal relationships that could have appeared Edgell, H.S., 2006. Arabian deserts: Nature, Origin and Evolution. Springer. Fathinia, B., Gholamifard, A., Rastegar-Pouyani, N., 2014. First record of to influence the work reported in this paper. Stenodactylus arabicus (Haas, 1957) from Iran. Herpetozoa 36 (3/4), 169–173. Fujita, M.K., Papenfuss, T.J., 2011. Molecular systematics of Stenodactylus Acknowledgements (Gekkonidae), an Afro-Arabian gecko species complex. Mol. Phylogenet. Evol. 58 (1), 71–75. https://doi.org/10.1016/j.ympev.2010.10.014. Gallagher, M.D., 1971. The Amphibians and Reptiles of Bahrain. M.D. Gallagher, We would like to thank Royal Society for the Conservation of Bahrain. Nature (RSCN; Jordan) for granting us permission for sample col- Gardner, A.S., 2013. The Amphibians and Reptiles of Oman and the UAE. Edition lection. Field work in Saudi Arabia was supported by Saudi Wildlife Chimaira. Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W., Gascuel, O., 2010. Authority (SWA). We are especially grateful to Dr. Hany Tatwany, New algorithms and methods to estimate maximum-likelihood phylogenies: the vice president of SWA, for his support and encouragement. We assessing the performance of PhyML 3.0. Sys. Biol. 59 (3), 307–321. https://doi. thank the SWA field researchers, namely Ali Al Faqih, Saad Alsub- org/10.1093/sysbio/syq010. Haas, G., 1957. Some amphibians and reptiles from Arabia. Proc. Calif. Acad. Sci. 29, aie, AbdulKarim Alanazi, Raed Al Gethami, and Abdelaziz Al 47–86. Gethami for their support and participation in the field work. We Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K., Von Haeseler, A., Jermiin, L.S., 2017. are thankful to Taif University, Saudi Arabia, for support (under ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14 (6), 587–589. https://doi.org/10.1038/nmeth.4285. Researcher Supporting project number TURSP-2020/06). We would Katoh, K., Rozewicki, J., Yamada, K.D., 2019. MAFFT online service: multiple like to thank R. A. Nazarov and B. Fathinia for providing their help- sequence alignment, interactive sequence choice and visualization. Brief. ful comments. LP, VH, AZ and TW would like to express their grat- Bioinformatics 20 (4), 1160–1166. https://doi.org/10.1093/bib/bbx108. Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., Buxton, S., itude and thanks to the kind and always helpful people of Jordan Cooper, A., Markowitz, S., Duran, Ch., Thierer, T., Ashton, B., Meintjes, P., during their stay. LP was supported by Charles University (SVV Drummond, A., 2012. Geneious Basic: an integrated and extendable desktop 260571/2021). JŠ was funded by the Czech Science Foundation software platform for the organization and analysis of sequence data. 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