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Heine HLA, Derkarabetian S, Morisawa R, Fu PA, Moyes NHW, Boyer SL. Machine learning approaches delimit cryptic taxa in a previously intractable species complex. Mol Phylogenet Evol 2024; 195:108061. [PMID: 38485107 DOI: 10.1016/j.ympev.2024.108061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024]
Abstract
Cryptic species are not diagnosable via morphological criteria, but can be detected through analysis of DNA sequences. A number of methods have been developed for identifying species based on genetic data; however, these methods are prone to over-splitting taxa with extreme population structure, such as dispersal-limited organisms. Machine learning methodologies have the potential to overcome this challenge. Here, we apply such approaches, using a large dataset generated through hybrid target enrichment of ultraconserved elements (UCEs). Our study taxon is the Aoraki denticulata species complex, a lineage of extremely low-dispersal arachnids endemic to the South Island of Aotearoa New Zealand. This group of mite harvesters has been the subject of previous species delimitation studies using smaller datasets generated through Sanger sequencing and analytical approaches that rely on multispecies coalescent models and barcoding gap discovery. Those analyses yielded a number of putative cryptic species that seems unrealistic and extreme, based on what we know about species' geographic ranges and genetic diversity in non-cryptic mite harvesters. We find that machine learning approaches, on the other hand, identify cryptic species with geographic ranges that are similar to those seen in other morphologically diagnosable mite harvesters in Aotearoa New Zealand's South Island. We performed both unsupervised and supervised machine learning analyses, the latter with training data drawn either from animals broadly (vagile and non-vagile) or from a custom training dataset from dispersal-limited harvesters. We conclude that applying machine learning approaches to the analysis of UCE-derived genetic data is an effective method for delimiting species in complexes of low-vagility cryptic species, and that the incorporation of training data from biologically relevant analogues can be critically informative.
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Affiliation(s)
- Haley L A Heine
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Shahan Derkarabetian
- Museum of Comparative Zoology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.
| | - Rina Morisawa
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Phoebe A Fu
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Nathaniel H W Moyes
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
| | - Sarah L Boyer
- Biology Department, Macalester College, 1600 Grand Ave., St. Paul, MN 55105, USA.
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2
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Shi CM, Zhang XS, Liu L, Ji YJ, Zhang DX. Phylogeography of the desert scorpion illuminates a route out of Central Asia. Curr Zool 2023; 69:442-455. [PMID: 37614924 PMCID: PMC10443618 DOI: 10.1093/cz/zoac061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/27/2022] [Indexed: 08/25/2023] Open
Abstract
A comprehensive understanding of phylogeography requires the integration of knowledge across different organisms, ecosystems, and geographic regions. However, a critical knowledge gap exists in the arid biota of the vast Asian drylands. To narrow this gap, here we test an "out-of-Central Asia" hypothesis for the desert scorpion Mesobuthus mongolicus by combining Bayesian phylogeographic reconstruction and ecological niche modeling. Phylogenetic analyses of one mitochondrial and three nuclear loci and molecular dating revealed that M. mongolicus represents a coherent lineage that diverged from its most closely related lineage in Central Asia about 1.36 Ma and underwent radiation ever since. Bayesian phylogeographic reconstruction indicated that the ancestral population dispersed from Central Asia gradually eastward to the Gobi region via the Junggar Basin, suggesting that the Junggar Basin has severed as a corridor for Quaternary faunal exchange between Central Asia and East Asia. Two major dispersal events occurred probably during interglacial periods (around 0.8 and 0.4 Ma, respectively) when climatic conditions were analogous to present-day status, under which the scorpion achieved its maximum distributional range. M. mongolicus underwent demographic expansion during the Last Glacial Maximum, although the predicted distributional areas were smaller than those at present and during the Last Interglacial. Development of desert ecosystems in northwest China incurred by intensified aridification might have opened up empty habitats that sustained population expansion. Our results extend the spatiotemporal dimensions of trans-Eurasia faunal exchange and suggest that species' adaptation is an important determinant of their phylogeographic and demographic responses to climate changes.
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Affiliation(s)
- Cheng-Min Shi
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding 071001, China
| | - Xue-Shu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ya-Jie Ji
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - De-Xing Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
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3
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Wu N, Wang S, Dujsebayeva TN, Chen D, Ali A, Guo X. Geography and past climate changes have shaped the evolution of a widespread lizard in arid Central Asia. Mol Phylogenet Evol 2023; 184:107781. [PMID: 37044189 DOI: 10.1016/j.ympev.2023.107781] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
The complex orogenic history and structure of Central Asia, coupled with Pleistocene glacial cycles have generated its stepwise aridification. Such events would have significantly influenced the evolution of many mid-latitude species in arid Central Asia (ACA). In this study, we employed two mitochondrial genes (CO1 and ND2) and genome-wide SNPs, coupled with ecological niche modeling, to investigate the lineage diversification and historical demography within a widespread lizard Phrynocepahlus helioscopus, and their associations with geography and past climate change. We obtained themtDNA dataset for 300 individuals from 96 localities within the known range of the lizard, among which 51 individuals from 27 localities were selected for generating the SNP dataset via genotyping-by-sequencing approach. Phylogenetic analyses of the concatenated mtDNA dataset revealed eight geographically correlated lineages that diverged by 4.21-10.41% for the CO1 gene, which were estimated to have coalesced ∼4.47 million years ago. However, we observed mito-nuclear discordance pattern regarding the population of Clade V (P. helioscopus sergeevi) from Tajikistan. Ancestral area estimations suggested that P. helioscopus originated from the Fergana Valley and then dispersed into the adjacent areas in ACA along with a history of multiple allopatric divergence processes, suggesting that Fergana may have been the cradle of diversification of P. helioscopus. The intensification of aridification across Central Asia during the Late Pliocene may have facilitated the rapid radiation of this arid-adapted lizard throughout this vast territory. Subsequently, the geological events (e.g., uplift of the Hissar-Alay, transgressions of the Caspian Sea) and geographic barriers (e.g., Amu Darya River, Zerarshan River) during the Pleistocene triggered the progressive diversification of P. helioscopus. Interestingly, Clade VIII (P. helioscopus varius) experienced rapid population growth coupled with range expansion while Clade IV (P. helioscopus cameranoi) underwent drastic population expansion associated with range contraction during the Last Glacial Maximum. In Clade IV, but not in Clade VIII, environmental turnover contributes more to mitochondrial genetic distinctiveness than geographic distance. Overall, the SNP dataset demonstrates that geographic distance plays a greater role than environmental distance. Both the mtDNA dataset and the SNP dataset suggest local-scale genetic differentiation in Clade IV and Clade VIII, revealing potential geographic barriers in the Ili River Valley and the Junggar Basin, respectively. Twenty-seven outlier SNPs associated with environmental factors (precipitation and temperature) were identified, which supports the signature of local adaptation to the arid desert environment. Finally, our finding suggests taxonomic implications, such as support for full species status for P. saidalievi (Clade II) and P. meridionalis (Clade I). Future analyses based on further evidence and increased taxon and geographic sampling should be carried out to corroborate our findings.
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Affiliation(s)
- Na Wu
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wang
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China
| | - Tatjana N Dujsebayeva
- Laboratory of Ornithology and Herpetology, Institute of Zoology, Ministry of Sciences and High Education of Republic of Kazakhstan, Almaty 050060, Kazakhstan
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Abid Ali
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianguang Guo
- Chengdu Institute of Biology Chinese Academy of Sciences, Chengdu 610041, China.
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4
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Fet V, Kovak F, Gantenbein B, Graham MR. Three new species of Olivierus (Scorpiones: Buthidae) from Kazakhstan and Uzbekistan. Zootaxa 2021; 5006:54-72. [PMID: 34810587 DOI: 10.11646/zootaxa.5006.1.9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Indexed: 11/04/2022]
Abstract
Following Graham et al. (2019), the recently described desert species Olivierus gorelovi (Fet et al., 2018) from Central Asia is herein restricted to Turkmenistan and southern Uzbekistan. In this contribution, we described other populations formerly included in O. gorelovi as three new species: O. mikhailovi sp. n. (southern Kazakhstan, Uzbekistan), O. tarabaevi sp. n. (Kazakhstan) and O. voldemari sp. n. (Uzbekistan: Ferghana Valley).
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Affiliation(s)
- Victor Fet
- Department of Biological Sciences, Marshall University, Huntington, West Virginia 25755-2510, USA. .
| | | | - Benjamin Gantenbein
- Tissue and Organ Mechanobiology, Institute for Surgical Technology and Biomechanics, University of Bern, Stauffacherstrasse 78, CH-3014 Bern, Switzerland..
| | - Matthew R Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, Connecticut 06226, USA..
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5
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Cain S, Loria SF, Ben-Shlomo R, Prendini L, Gefen E. Dated phylogeny and ancestral range estimation of sand scorpions (Buthidae: Buthacus) reveal Early Miocene divergence across land bridges connecting Africa and Asia. Mol Phylogenet Evol 2021; 164:107212. [PMID: 34029718 DOI: 10.1016/j.ympev.2021.107212] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 11/15/2022]
Abstract
Sand scorpions of the genus Buthacus Birula, 1908 (Buthidae C.L. Koch, 1837) are widespread in the sandy deserts of the Palearctic region, occurring from the Atlantic coast of West Africa across the Sahara, and throughout the Middle East to Central Asia. The limits of Buthacus, its two species groups, and many of its species remain unclear, and in need of revision using modern systematic methods. The study presented here set out to investigate the phylogeny and biogeography of the Buthacus species occurring in the Levant, last studied in 1980. A phylogenetic analysis was performed on 104 terminals, including six species collected from more than thirty localities in Israel and other countries in the region. Three mitochondrial and two nuclear gene loci were sequenced for a total of 2,218 aligned base-pairs. Morphological datasets comprising 22 qualitative and 48 quantitative morphological characters were compiled. Molecular and morphological datasets were analyzed separately and simultaneously with Bayesian Inference, Maximum Likelihood, and parsimony. Divergence time and ancestral range estimation analyses were performed, to understand dispersal and diversification. The results support a revised classification of Levantine Buthacus, and invalidate the traditional species groups of Buthacus, instead recovering two geographically-delimited clades, an African clade and an Asian clade, approximately separated by the Jordan Valley (the Jordan Rift Valley or Syro-African Depression), the northernmost part of the Great Rift Valley. The divergence between these clades occurred in the Early Miocene (ca. 19 Ma) in the Levant, coinciding temporally with the existence of two land bridges, which allowed faunal exchange between Africa and Asia.
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Affiliation(s)
- Shlomo Cain
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Israel
| | - Stephanie F Loria
- Scorpion Systematics Research Group, Arachnology Lab, Division of Invertebrate Zoology, American Museum of Natural History, New York, USA
| | - Rachel Ben-Shlomo
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa - Oranim, Israel
| | - Lorenzo Prendini
- Scorpion Systematics Research Group, Arachnology Lab, Division of Invertebrate Zoology, American Museum of Natural History, New York, USA
| | - Eran Gefen
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa - Oranim, Israel.
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6
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Loria SF, Prendini L. Out of India, thrice: diversification of Asian forest scorpions reveals three colonizations of Southeast Asia. Sci Rep 2020; 10:22301. [PMID: 33339838 PMCID: PMC7749168 DOI: 10.1038/s41598-020-78183-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 11/04/2020] [Indexed: 11/10/2022] Open
Abstract
The 'Out of India' hypothesis is often invoked to explain patterns of distribution among Southeast Asian taxa. According to this hypothesis, Southeast Asian taxa originated in Gondwana, diverged from their Gondwanan relatives when the Indian subcontinent rifted from Gondwana in the Late Jurassic, and colonized Southeast Asia when it collided with Eurasia in the early Cenozoic. A growing body of evidence suggests these events were far more complex than previously understood, however. The first quantitative reconstruction of the biogeography of Asian forest scorpions (Scorpionidae Latreille, 1802: Heterometrinae Simon, 1879) is presented here. Divergence time estimation, ancestral range estimation, and diversification analyses are used to determine the origins, dispersal and diversification patterns of these scorpions, providing a timeline for their biogeographical history that can be summarized into four major events. (1) Heterometrinae diverged from other Scorpionidae on the African continent after the Indian subcontinent became separated in the Cretaceous. (2) Environmental stresses during the Cretaceous-Tertiary (KT) mass extinction caused range contraction, restricting one clade of Heterometrinae to refugia in southern India (the Western Ghats) and Sri Lanka (the Central Highlands). (3) Heterometrinae dispersed to Southeast Asia three times during India's collision with Eurasia, the first dispersal event occurring as the Indian subcontinent brushed up against the western side of Sumatra, and the other two events occurring as India moved closer to Eurasia. (4) Indian Heterometrinae, confined to southern India and Sri Lanka during the KT mass extinction, recolonized the Deccan Plateau and northern India, diversifying into new, more arid habitats after environmental conditions stabilized. These hypotheses, which are congruent with the geological literature and biogeographical analyses of other taxa from South and Southeast Asia, contribute to an improved understanding of the dispersal and diversification patterns of taxa in this biodiverse and geologically complex region.
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Affiliation(s)
- Stephanie F Loria
- Richard Gilder Graduate School, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024-5192, USA.
- Scorpion Systematics Research Group, Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024-5192, USA.
| | - Lorenzo Prendini
- Scorpion Systematics Research Group, Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th St., New York, NY, 10024-5192, USA
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7
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Karyotype evolution and preliminary molecular assessment of genera in the family Scorpiopidae (Arachnida: Scorpiones). ZOOLOGY 2020; 144:125882. [PMID: 33278760 DOI: 10.1016/j.zool.2020.125882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 11/20/2022]
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.
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8
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Borges A, Rojas de Arias A, de Almeida Lima S, Lomonte B, Díaz C, Chávez-Olórtegui C, Graham MR, Kalapothakis E, Coronel C, de Roodt AR. Genetic and toxinological divergence among populations of Tityus trivittatus Kraepelin, 1898 (Scorpiones: Buthidae) inhabiting Paraguay and Argentina. PLoS Negl Trop Dis 2020; 14:e0008899. [PMID: 33315884 PMCID: PMC7769620 DOI: 10.1371/journal.pntd.0008899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 12/28/2020] [Accepted: 10/20/2020] [Indexed: 11/22/2022] Open
Abstract
Envenoming by scorpions in genus Tityus is a public health problem in Tropical America. One of the most medically significant species is Tityus trivittatus, which is known to occur from southwest Brazil to central-northern and eastern Argentina. In this work, we studied the lethality, composition, antigenicity, and enzymatic activity of venom from a T. trivittatus population found further north in urban areas of eastern Paraguay, where it has caused serious envenomation of children. Our results indicate that the population is of medical importance as it produces a potently toxic venom with an LD50 around 1.19 mg/kg. Venom neutralization in preliminary mouse bioassays was complete when using Brazilian anti-T. serrulatus antivenom but only partial when using Argentinean anti-T. trivittatus antivenom. Venom competitive solid-phase enzyme immunoassays and immunoblotting from Argentinean and Paraguayan T. trivittatus populations indicated that antigenic differences exist across the species range. SDS-PAGE showed variations in type and relative amounts of venom proteins between T. trivitattus samples from Argentina and Paraguay. MALDI-TOF mass spectrometry indicated that while some sodium channel toxins are shared, including β-toxin Tt1g, others are population-specific. Proteolytic activity by zymography and peptide identification through nESI-MS/MS also point out that population-specific proteases may exist in T. trivitattus, which are postulated to be involved in the envenoming process. A time-calibrated molecular phylogeny of mitochondrial COI sequences revealed a significant (8.14%) genetic differentiation between the Argentinean and Paraguayan populations, which appeared to have diverged between the mid Miocene and early Pliocene. Altogether, toxinological and genetic evidence indicate that T. trivitattus populations from Paraguay and Argentina correspond to distinct, unique cryptic species, and suggest that further venom and taxonomic diversity exists in synanthropic southern South American Tityus than previously thought.
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Affiliation(s)
- Adolfo Borges
- Centro para el Desarrollo de la Investigación Científica (CEDIC), Asunción, Paraguay
- Laboratorio de Biología Molecular de Toxinas y Receptores, Instituto de Medicina Experimental, Facultad de Medicina, Universidad Central de Venezuela, Caracas, Venezuela
| | | | - Sabrina de Almeida Lima
- Laboratorio de Inmunoquimica, Departamento de Bioquímica e Inmunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Cecilia Díaz
- Instituto Clodomiro Picado, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos Chávez-Olórtegui
- Laboratorio de Inmunoquimica, Departamento de Bioquímica e Inmunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | - Matthew R. Graham
- Department of Biology, Eastern Connecticut State University, Willimantic, Connecticut, United States of America
| | - Evanguedes Kalapothakis
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | - Cathia Coronel
- Centro para el Desarrollo de la Investigación Científica (CEDIC), Asunción, Paraguay
| | - Adolfo R. de Roodt
- Instituto Nacional de Producción de Biológicos “Carlos G. Malbrán”, Buenos Aires, Argentina
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9
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Šťáhlavský F, Nguyen P, Sadílek D, Štundlová J, Just P, Haddad CR, Koç H, Ranawana KB, Stockmann M, Yağmur EA, Kovařík F. Evolutionary dynamics of rDNA clusters on chromosomes of buthid scorpions (Chelicerata: Arachnida). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
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.
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Affiliation(s)
- František Šťáhlavský
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Petr Nguyen
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská, České Budějovice, Czech Republic
| | - David Sadílek
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Jana Štundlová
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Pavel Just
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
| | - Charles R Haddad
- Department of Zoology and Entomology, University of the Free State, Bloemfontein, South Africa
| | - Halil Koç
- Department of Biology, Faculty of Arts and Science, Sinop University, Sinop, Turkey
| | - Kithsiri B Ranawana
- Department of Zoology, Faculty of Science, University of Peradeniya, Sri Lanka
| | | | - Ersen Aydin Yağmur
- Alaşehir Vocational School, Celal Bayar University, Alaşehir, Manisa, Turkey
| | - František Kovařík
- Department of Zoology, Faculty of Science, Charles University, Viničná, Prague, Czech Republic
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10
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Cheng J, Xia L, Feijó A, Shenbrot GI, Wen Z, Ge D, Lu L, Yang Q. Phylogeny, taxonomic reassessment and ‘ecomorph’ relationship of the Orientallactaga sibirica complex (Rodentia: Dipodidae: Allactaginae). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The ecological gradient–morphological variation (‘ecomorph’) relationship has long interested ecologists and evolutionary biologists, but it is applied far less frequently than genetic differentiation in cryptic species detection and species identification. With integrative methods, we revise taxonomic uncertainties in the Orientallactaga sibirica complex (OSC), with 298 sequence specimens and 469 voucher specimens from 138 localities covering nearly the entire distribution of the OSC. Phylogenetic relationships are assessed by Bayesian inference and maximum likelihood using two mitochondrial and nine nuclear genes. We use species-delimitation approaches to divide and validate the ‘candidate species’. We evaluate correlations between ecological divergence and phylogenetic splits, and visualize geographical patterns of morphological variation. The OSC is divided into four phylogenetic groups, the Ognevi, Altay, Bogda and Sibirica groups, and the OSC exhibits a significant ecomorph relationship and ecological divergence pattern. Morphological variations not only follow the general regularity under a large gradient of ecological factors, but are also closely related to the local environment/habitat. We suggest considering the comprehensive ecomorph relationship to identify species. Molecular analyses reveal that the OSC more easily forms deeply divergent lineages in the foothills and this differentiation depth may be related to mountain system size.
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Affiliation(s)
- Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Georgy I Shenbrot
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Liang Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Centre for Disease Control and Prevention, Changping District, Beijing, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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