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Simonov E, Lopatina NV, Titov SV, Ivanova AD, Brandler OV, Surin VL, Matrosova VA, Dvilis AE, Oreshkova NV, Kapustina SY, Golenishchev FN, Ermakov OA. Traditional multilocus phylogeny fails to fully resolve Palearctic ground squirrels (Spermophilus) relationships but reveals a new species endemic to West Siberia. Mol Phylogenet Evol 2024; 195:108057. [PMID: 38471598 DOI: 10.1016/j.ympev.2024.108057] [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: 10/05/2023] [Revised: 02/29/2024] [Accepted: 03/09/2024] [Indexed: 03/14/2024]
Abstract
Previous efforts to reconstruct evolutionary history of Palearctic ground squirrels within the genus Spermophilus have primarily relied on a single mitochondrial marker for phylogenetic data. In this study, we present the first phylogeny with comprehensive taxon sampling of Spermophilus via a conventional multilocus approach utilizing five mitochondrial and five nuclear markers. Through application of the multispecies coalescent model, we constructed a species tree revealing four distinct clades that diverged during the Late Miocene. These clades are 1) S. alaschanicus and S. dauricus from East Asia; 2) S. musicus and S. pygmaeus from East Europe and northwestern Central Asia; 3) the subgenus Colobotis found across Central Asia and its adjacent regions and encompassing S. brevicauda, S. erythrogenys, S. fulvus, S. major, S. pallidicauda, S. ralli, S. relictus, S. selevini, and S. vorontsovi sp. nov.; and 4) a Central/Eastern Europe and Asia Minor clade comprising S. citellus, S. taurensis, S. xanthoprymnus, S. suslicus, and S. odessanus. The latter clade lacked strong support owing to uncertainty of taxonomic placement of S. odessanus and S. suslicus. Resolving relationships within the subgenus Colobotis, which radiated rapidly, remains challenging likely because of incomplete lineage sorting and introgressive hybridization. Most of modern Spermophilus species diversified during the Early-Middle Pleistocene (2.2-1.0 million years ago). We propose a revised taxonomic classification for the genus Spermophilus by recognizing 18 species including a newly identified one (S. vorontsovi sp. nov.), which is found only in a limited area in the southeast of West Siberia. Employing genome-wide single-nucleotide polymorphism genotyping, we substantiated the role of the Ob River as a major barrier ensuring robust isolation of this taxon from S. erythrogenys. Despite its inherent limitations, the traditional multilocus approach remains a valuable tool for resolving relationships and can provide important insights into otherwise poorly understood groups. It is imperative to recognize that additional efforts are needed to definitively determine phylogenetic relationships between certain species of Palearctic ground squirrels.
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Affiliation(s)
- Evgeniy Simonov
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Frunze Str. 11, Novosibirsk 630091, Russia.
| | - Natalia V Lopatina
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Frunze Str. 11, Novosibirsk 630091, Russia
| | - Sergey V Titov
- Department of Zoology and Ecology, Penza State University, Krasnaya Str. 40, Penza 440026, Russia
| | - Anastasiya D Ivanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow 119991, Russia
| | - Oleg V Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Vadim L Surin
- National Medical Research Center for Hematology, Novyy Zykovskiy Pr. 4, Moscow 125167, Russia
| | - Vera A Matrosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova Str. 32, Moscow 119991, Russia
| | - Alisa E Dvilis
- Institute of Systematics and Ecology of Animals, Siberian Branch of Russian Academy of Sciences, Frunze Str. 11, Novosibirsk 630091, Russia
| | - Nataliya V Oreshkova
- Federal Research Center Krasnoyarsk Science Center, Siberian Branch of Russian Academy of Sciences, Akademgorodok Str. 50, Krasnoyarsk 660036, Russia; Laboratory of Forest Genomics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodnyy Ave. 79, Krasnoyarsk 660041, Russia; V. N. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Akademgorodok Str. 50/28, Krasnoyarsk 660036, Russia; Department of Genomics and Bioinformatics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Svobodnyy Ave. 79, Krasnoyarsk 660041, Russia
| | - Svetlana Yu Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Fedor N Golenishchev
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Emb. 1, Saint Petersburg 199034, Russia
| | - Oleg A Ermakov
- Department of Zoology and Ecology, Penza State University, Krasnaya Str. 40, Penza 440026, Russia.
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The European Ground Squirrel’s Genetic Diversity in Its Ancestral Land: Landscape Insights and Conservation Implications. DIVERSITY 2023. [DOI: 10.3390/d15030365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
The European ground squirrel is an endangered rodent whose populations are declining throughout its range. Only in Bulgaria, the genetic hotspot of the species, are some abundant populations still present. We employed 12 microsatellite loci in ten Bulgarian populations to look at population structure, gene flow and recent bottlenecks. We found that the populations are in good condition in terms of heterozygosity, where values ranged from 0.55 to 0.78. However, the inbreeding index (FIS) was significant for most populations. A recent bottleneck was detected in only one population. Based on Bayesian clustering methods, the populations in Bulgaria were attributed to two groups, northern and southern, with admixture in the northern one. The AMOVA test between these groups showed no differentiation in genetic diversity. The mean value of FST was 0.184, which shows strong diversification among all populations. Hence, gene flow is probably limited. All these results indicate that Bulgaria is the main area to focus the efforts for conservation of the species by ensuring that the complex and rich genetic structure of Bulgarian populations is preserved.
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Conservation of Host, Translocation of Parasites—Monitoring of Helminths during Population Reinforcement of the European Ground Squirrel (Spermophilus citellus). DIVERSITY 2023. [DOI: 10.3390/d15020266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Gastrointestinal helminth parasites can be transferred during conservation translocations and impact their outcome. The current study applied non-invasive coprological sampling to investigate the helminth infection rates and dynamics in translocated and resident European ground squirrels, during and after a population reinforcement. The FLOTAC method was calibrated and applied for the first time for the target species. In the studied coprological samples, helminth eggs belonging to Acanthocephala and Nematoda were found; the latter were morphologically identified as belonging to the families Capillariidae (Enoplida) and Trichostrongylidae (Strongylida) and superfamily Spiruroidea (Spirurida). The overall helminth prevalence and their diversity were higher in the donor colony compared to the resident one before the reinforcement. Pronounced seasonal dynamics in the parasite prevalence and diversity were observed, and their values were considerably lower in spring than in summer in both translocated and resident hosts. A year after the start of the translocation, the helminth prevalence and number of species detected in the reinforced colony had increased significantly. This is in accordance with epidemiological models and other empirical studies that predict a positive relationship between the population density of a host and the prevalence and species richness of parasites.
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Kachamakova M, Koshev Y, Rammou DL, Spasov S. Rise and fall: Results of a multidisciplinary study and 5-year long monitoring of conservation translocation of the European ground squirrel. Biodivers Data J 2022; 10:e83321. [PMID: 36761644 PMCID: PMC9848502 DOI: 10.3897/bdj.10.e83321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/01/2022] [Indexed: 11/12/2022] Open
Abstract
The current publication gives a detailed assessment of the results from a population reinforcement of a European ground squirrel's (Spermophiluscitellus) colony in south-eastern Bulgaria. The reinforcement was planned and implemented along with multidisciplinary research of the adaptation process (including radiotelemetry, parasitological study and assessment of the stress in the animals) and regular monitoring (yearly burrow counting). Although the donor and recipient populations were genetically similar, morphometrical data indicated variations in the body size probably due to the difference in population densities in the two sites. The monitoring revealed that the burrows were aggregated and there was a positive correlation in the spatial distribution of the ground squirrels' burrow holes and the colonies of Harting's vole (Microtushartingi) - another social ground-digging rodent that co-inhabits the study area. The first results showed successful reinforcement according to the three classical evaluation criteria: the individuals survived the translocation process, they successfully reproduced and an initial population growth was observed, based on the burrow entrances' count - from 36 in 2017 to 280 in 2020. In 2021, however, a considerable decline in the abundance of the population was recorded - 58.5% decline in the burrow number and 36% decline in the colony area. A decrease was also observed in the abundance of the Harting's voles' colonies. A review of all the collected information suggests it is unlikely that the decrease is due to helminth parasites, translocation stress or other behaviour issues. The most probable explanation is the bad weather conditions - unusually high rainfalls combined with relatively high temperatures in January 2021. In conclusion, we strongly emphasise the need for detailed and long-term monitoring after conservation translocation and careful evaluation of all the influencing factors before, during and after such actions.
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Affiliation(s)
- Maria Kachamakova
- Institute of Biodiversity and Ecosystem Research at the Bulgarian Academy of Sciences, Sofia, BulgariaInstitute of Biodiversity and Ecosystem Research at the Bulgarian Academy of SciencesSofiaBulgaria
| | - Yordan Koshev
- Institute of Biodiversity and Ecosystem Research at the Bulgarian Academy of Sciences, Sofia, BulgariaInstitute of Biodiversity and Ecosystem Research at the Bulgarian Academy of SciencesSofiaBulgaria
| | - Dimitra-Lida Rammou
- Aristotle University of Thessaloniki, Thessaloniki, GreeceAristotle University of ThessalonikiThessalonikiGreece
| | - Svetoslav Spasov
- Bulgarian Society for the Protection of Birds, Sofia, BulgariaBulgarian Society for the Protection of BirdsSofiaBulgaria
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Guo R, Zhang YH, Zhang HJ, Landis JB, Zhang X, Wang HC, Yao XH. Molecular phylogeography and species distribution modelling evidence of 'oceanic' adaptation for Actinidia eriantha with a refugium along the oceanic-continental gradient in a biodiversity hotspot. BMC PLANT BIOLOGY 2022; 22:89. [PMID: 35227218 PMCID: PMC8883688 DOI: 10.1186/s12870-022-03464-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Refugia is considered to be critical for maintaining biodiversity; while discerning the type and pattern of refugia is pivotal for our understanding of evolutionary processes in the context of conservation. Interglacial and glacial refugia have been studied throughout subtropical China. However, studies on refugia along the oceanic-continental gradient have largely been ignored. We used a liana Actinidia eriantha, which occurs across the eastern moist evergreen broad-leaved forests of subtropical China, as a case study to test hypotheses of refugia along the oceanic-continental gradient and 'oceanic' adaptation. RESULTS The phylogeographic pattern of A. eriantha was explored using a combination of three cpDNA markers and 38 nuclear microsatellite loci, Species distribution modelling and dispersal corridors analysis. Our data showed intermediate levels of genetic diversity [haplotype diversity (hT) = 0.498; unbiased expected heterozygosity (UHE) = 0.510] both at the species and population level. Microsatellite loci revealed five clusters largely corresponding to geographic regions. Coalescent time of cpDNA lineages was dated to the middle Pliocene (ca. 4.03 Ma). Both geographic distance and climate difference have important roles for intraspecific divergence of the species. The Zhejiang-Fujian Hilly Region was demonstrated to be a refugium along the oceanic-continental gradient of the species and fit the 'refugia in refugia' pattern. Species distribution modelling analysis indicated that Precipitation of Coldest Quarter (importance of 44%), Temperature Seasonality (29%) and Mean Temperature of Wettest Quarter (25%) contributed the most to model development. By checking the isolines in the three climate layers, we found that A. eriantha prefer higher precipitation during the coldest quarter, lower seasonal temperature difference and lower mean temperature during the wettest quarter, which correspond to 'oceanic' adaptation. Actinidia eriantha expanded to its western distribution range along the dispersal corridor repeatedly during the glacial periods. CONCLUSIONS Overall, our results provide integrated evidence demonstrating that the Zhejiang-Fujian Hilly Region is a refugium along the oceanic-continental gradient of Actinidia eriantha in subtropical China and that speciation is attributed to 'oceanic' adaptation. This study gives a deeper understanding of the refugia in subtropical China and will contribute to the conservation and utilization of kiwifruit wild resources in the context of climate change.
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Affiliation(s)
- Rui Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Plant Sciences, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EA, UK
| | - Yong-Hua Zhang
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, 325035, China
| | - Hua-Jie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, 14853, USA
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Heng-Chang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Xiao-Hong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China.
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Pleistocene allopatric differentiation followed by recent range expansion explains the distribution and molecular diversity of two congeneric crustacean species in the Palaearctic. Sci Rep 2021; 11:22866. [PMID: 34819546 PMCID: PMC8613293 DOI: 10.1038/s41598-021-02164-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/03/2021] [Indexed: 11/09/2022] Open
Abstract
Pleistocene glaciations had a tremendous impact on the biota across the Palaearctic, resulting in strong phylogeographic signals of range contraction and rapid postglacial recolonization of the deglaciated areas. Here, we explore the diversity patterns and history of two sibling species of passively dispersing taxa typical of temporary ponds, fairy shrimps (Anostraca). We combine mitochondrial (COI) and nuclear (ITS2 and 18S) markers to conduct a range-wide phylogeographic study including 56 populations of Branchinecta ferox and Branchinecta orientalis in the Palaearctic. Specifically, we investigate whether their largely overlapping ranges in Europe resulted from allopatric differentiation in separate glacial refugia followed by a secondary contact and reconstruct their postglacial recolonization from the inhabited refugia. Our results suggest the existence of distinct refugia for the two species, with genetic divergence among intraspecific lineages consistent with late Pleistocene glacial cycles. While B. ferox lineages originated from Mediterranean refugia, the origin of B. orientalis lineages was possibly located on the Pannonian Plain. We showed that most dispersal events predominantly happened within 100 km, coupled with several recent long-distance events (> 1000 km). Hence the regional habitat density of suitable habitats in Central Europe is possibly a key to the co-existence of the two species. Overall, our study illustrates how isolation in combination with stochastic effects linked to glacial periods are important drivers of the allopatric differentiation of Palaearctic taxa.
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Distribution, Population Size, and Habitat Characteristics of the Endangered European Ground Squirrel (Spermophilus citellus, Rodentia, Mammalia) in Its Southernmost Range. SUSTAINABILITY 2021. [DOI: 10.3390/su13158411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The European ground squirrel (Spermophilus citellus) is an endangered species, endemic to Central and Southeastern Europe, inhabiting burrow colonies in grassland and agricultural ecosystems. In recent years, agricultural land-use changes and increased urbanization have largely contributed to a severe population decline across its range, particularly in its southernmost edge. Assessing the population and habitat status of this species is essential for prioritizing appropriate conservation actions. The present study aims to track population size changes and identify habitat characteristics of the species in Greece via a literature search, questionnaires, and fieldwork for assessing trends in population size as well as spatial K-means analysis for estimating its relation to specific habitat attributes. We found that both distribution size (grid number) and colony numbers of the species decreased in the last decades (by 62.4% and 74.6%, respectively). The remaining colonies are isolated and characterized by low density (mean = 7.4 ± 8.6 ind/ha) and low number of animals (mean = 13 ± 16 individuals). Most of the colonies are situated in lowlands and did not relate to specific habitat attributes. Habitat aspect and system productivity (NDVI) were the main factors contributing mostly to the clustering of the existing colonies. These results demonstrate that the species is confined to small, isolated anthropogenic habitats. Specific conservation actions such as population reinforcement, habitat improvement, and specific common agricultural policy measures could effectively improve agroecological zones that are suitable for the maintenance and protection of existing and potential habitats for populations of the species.
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Resident European ground squirrels exhibit higher stress levels than translocated individuals after conservation reinforcement. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00066-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Recently lost connectivity in the Western Palaearctic steppes: the case of a scarce specialist butterfly. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01271-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Koshev Y, Kachamakova M, Arangelov S, Ragyov D. Translocations of European ground squirrel (Spermophilus citellus) along altitudinal gradient in Bulgaria – an overview. NATURE CONSERVATION 2019. [DOI: 10.3897/natureconservation.35.30911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The European ground squirrel (Spermophiluscitellus) is a vulnerable species (IUCN) living in open habitats of Central and South-eastern Europe. Translocations (introductions, reintroductions and reinforcements) are commonly used as part of the European ground squirrel (EGS) conservation. There are numerous publications for such activities carried out in Central Europe, but data from South-eastern Europe, where translocations have also been implemented, are still scarce.
The present study summarises the methodologies used in the translocations in Bulgaria and analyses the factors impacting their success. Eight translocations of more than 1730 individuals were performed in the period 2010 to 2018. These included 4 reinforcements, 3 reintroductions and 1 introduction. Two of the translocations are still ongoing. Five of the completed six (83%) translocations were successful, although in two cases the number of individuals was critically low. The relatively higher success in Bulgaria than in Central Europe is probably due to using the gained experience. Most of the translocations (6) used a soft release approach. In 6 cases, the animals settled 100 to 720 metres away from the release site, implying management and protection of suitable habitat beyond the translocation area. In 7 of the translocations, the altitude between the donor colony and the release site varied from 470 to 1320 m which could have a hindering effect on the adaptation of animals due to the specific conditions in the mountains. The main reasons for failure are probably poorly selected and maintained habitats and bad climatic conditions (rainy and cool weather) during the translocation action. European funds are of critical importance for translocations, with only two translocations funded by other sources. Based on the gathered data, the current paper also gives some recommendations for improvement in translocation activities.
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Li H, Kong L, Wang K, Zhang S, Motokawa M, Wu Y, Wang W, Li Y. Molecular phylogeographic analyses and species delimitations reveal that Leopoldamys edwardsi (Rodentia: Muridae) is a species complex. Integr Zool 2019; 14:494-505. [PMID: 30688015 DOI: 10.1111/1749-4877.12378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation. We used 2 mitochondrial (Cytb, CO1) and 3 nuclear (GHR, IRBP and RAG1) genes to clarify species phylogeography and geographical differentiation. Maximum likelihood (ML) and Bayesian phylogenetic inference (BI) trees consistently indicated that L. edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter (K2P) divergences (i.e. lineages LN , LS and LHN ) found in the northern and southern China and Hainan Island, respectively. The 3 species delimitation methods, automated barcoding gap discovery, Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography, consistently supported the existence of cryptic species. Divergence times among the main lineages were inferred to be during the Pleistocene, with LHN /LS split at 1.33 Ma and LN /(LHN +LS ) at 2.61 Ma; the diversifications of L. edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau, paleoclimate change and complex topography. The divergence between LHN and LS was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait. Lineages LN and (LS +LHN ) likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier. Our results suggested that L. edwardsi complex contains at least 3 distinct species: LHN represents L. hainanensis, endemic to Hainan Island and previously considered as a subspecies L. e. hainanensis; LS represents a cryptic species distributed throughout the southern Chinese continent; and LN represents the nominotypical species L. edwardsi.
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Affiliation(s)
- Haotian Li
- Marine College, Shandong University, Weihai, China
| | | | - Kaiyun Wang
- Institute of Ecology and Biodiversity, Shandong University, Jinan, China
| | - Shuping Zhang
- Institute of Ecology and Biodiversity, Shandong University, Jinan, China
| | | | - Yi Wu
- College of Life Science, Guangzhou University, Guangzhou, China
| | - Wenquan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yuchun Li
- Marine College, Shandong University, Weihai, China
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Kapustina SY, Adiya Y, Brandler OV. Genetic Differentiation of the Daurian Ground Squirrel Spermophilus dauricus Brandt, 1843 according to Variability of the Mitochondrial DNA Control Region. BIOL BULL+ 2018. [DOI: 10.1134/s1062359018050060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gür H, Perktaş U, Gür MK. Do climate-driven altitudinal range shifts explain the intraspecific diversification of a narrow ranging montane mammal, Taurus ground squirrels? MAMMAL RES 2017. [DOI: 10.1007/s13364-017-0347-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Noguerales V, Cordero PJ, Ortego J. Inferring the demographic history of an oligophagous grasshopper: Effects of climatic niche stability and host-plant distribution. Mol Phylogenet Evol 2017; 118:343-356. [PMID: 29080673 DOI: 10.1016/j.ympev.2017.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/09/2017] [Accepted: 10/22/2017] [Indexed: 11/19/2022]
Abstract
Understanding the consequences of past environmental changes on the abiotic and biotic components of the landscape and deciphering their impacts on the demographic trajectories of species is a major issue in evolutionary biogeography. In this study, we combine nuclear and mitochondrial genetic data to study the phylogeographical structure and lineage-specific demographic histories of the scrub-legume grasshopper (Chorthippus binotatus binotatus), a montane taxon distributed in the Iberian Peninsula and France that exclusively feeds on certain scrub-legume species. Genetic data and paleo-distribution modelling indicate the presence of four main lineages that seem to have diverged in allopatry and long-term persisted in Iberian and French refugia since the Mid Pleistocene. Comparisons of different demographic hypotheses in an Approximate Bayesian Computation (ABC) framework supported a population bottleneck in the northwestern French clade and paleo-distribution modelling indicate that the populations of this lineage have experienced more severe environmental fluctuations during the last 21 000 years than those from the Iberian Peninsula. Accordingly, we found that nuclear genetic diversity of the populations of scrub-legume grasshopper is positively associated with local stability of suitable habitats defined by both Pleistocene climate changes and historical distributional shifts of host-plant species. Overall, our study highlights the importance of integrating the potential effects of abiotic (i.e. climate and geography) and biotic components (i.e. inter-specific interactions) into the study of the evolutionary and demographic history of specialist taxa with narrow ecological requirements.
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Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ronda de Toledo 12, E-13071 Ciudad Real, Spain.
| | - Pedro J Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ronda de Toledo 12, E-13071 Ciudad Real, Spain
| | - Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio 26, E-41092 Seville, Spain
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Mediterranean lineage endemism, cold-adapted palaeodemographic dynamics and recent changes in population size in two solitary bees of the genus Anthophora. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0952-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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16
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Yang Y, Li J, Yang S, Li X, Fang L, Zhong C, Duke NC, Zhou R, Shi S. Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: a lesson from Sonneratia alba. BMC Evol Biol 2017; 17:22. [PMID: 28100168 PMCID: PMC5241957 DOI: 10.1186/s12862-016-0849-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/08/2016] [Indexed: 11/21/2022] Open
Abstract
Background A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation. Results In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods. Extremely small effective population size (Ne) was inferred in populations from both eastern and western Malay Peninsula (44 and 396, respectively), mirroring the fragility of mangrove plants and their paucity of robustness against future climate perturbations and human activity. Two major genetic lineages of high divergence were identified in the two mangrove biodiversity centres: the Indo-Malesia and Australasia regions. The estimated splitting time between these two lineages was 3.153 million year ago (MYA), suggesting a role for pre-Pleistocene events in shaping the major diversity patterns of mangrove species. Within the Indo-Malesia region, a subdivision was implicated between the South China Sea (SCS) and the remaining area with a divergence time of 1.874 MYA, corresponding to glacial vicariance when the emerged Sunda Shelf halted genetic exchange between the western and eastern coasts of the Malay Peninsula during Pleistocene sea-level drops. Notably, genetic admixture was observed in populations at the boundary regions, especially in the two populations near the Malacca Strait, indicating secondary contact between divergent lineages during interglacial periods. These interregional genetic exchanges provided ample opportunity for the re-use of standing genetic variation, which could facilitate mangrove establishment and adaptation in new habitats, especially in the context of global climate changes. Conclusion Phylogeogrpahic analysis in this study reveal that Pleistocene sea-level fluctuations had profound influence on population differentiation of the mangrove tree S. alba. Our study highlights the fragility of mangrove plants and offers a guide for the conservation of coastal mangrove communities experiencing ongoing changes in sea-level. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0849-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuchen Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jianfang Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shuhuan Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xinnian Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Lu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve, Haikou, 571129, China
| | - Norman C Duke
- Trop WATER, James Cook University, Townsville, Quennsland, Australia
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
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Senczuk G, Colangelo P, De Simone E, Aloise G, Castiglia R. A combination of long term fragmentation and glacial persistence drove the evolutionary history of the Italian wall lizard Podarcis siculus. BMC Evol Biol 2017; 17:6. [PMID: 28056768 PMCID: PMC5216540 DOI: 10.1186/s12862-016-0847-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The current distribution of genetic diversity is the result of a vast array of microevolutionary processes, including short-term demographic and ecological mechanisms and long-term allopatric isolation in response to Quaternary climatic fluctuations. We investigated past processes that drove the population differentiation and spatial genetic distribution of the Italian wall lizard Podarcis siculus by means of sequences of mitochondrial cytb (n = 277 from 115 localities) and nuclear mc1r and β-fibint7genes (n = 262 and n = 91, respectively) from all its distribution range. The pattern emerging from the genetic data was compared with current and past (last glacial maximum) species distribution modeling (SDM). RESULTS We identified seven deeply divergent parapatric clades which presumably remained isolated in different refugia scattered mainly throughout the Tyrrhenian coast. Conversely, the Adriatic coast showed only two haplogroups with low genetic variability. These results appear to agree with the SDM prediction at the last glacial maximum (LGM) indicating a narrow area of habitat suitability along the Tyrrhenian coast and much lower suitability along the Adriatic one. However, the considerable land exposure of the Adriatic coastline favored a glacial colonization of the Balkan Peninsula. CONCLUSIONS Our population-level historical demography showed a common trend consistent with glacial expansions and regional persistence during the last glacial maximum. This complex genetic signature appears to be inconsistent with the expectation of the expansion-contraction model and post-LGM (re)colonizations from southern refugia. Hence it is one of an increasing number of cases in which these assumptions are not met, indicating that long-term fragmentation and pre-LGM events such as glacial persistence were more prominent in shaping genetic variation in this temperate species.
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Affiliation(s)
- Gabriele Senczuk
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma LA SAPIENZA, sede di Anatomia comparata, Rome, Italy.
| | - Paolo Colangelo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma LA SAPIENZA, sede di Anatomia comparata, Rome, Italy.,National Research Council, Institute of Ecosystem Study, Largo Tonnoli 50, 28922, Verbania Pallanza, Italy
| | - Emanuela De Simone
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma LA SAPIENZA, sede di Anatomia comparata, Rome, Italy
| | - Gaetano Aloise
- Museo di Storia Naturale della Calabria e Orto Botanico, Università della Calabria, CAP 87036, Rende, Cosenza, Italy
| | - Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università di Roma LA SAPIENZA, sede di Anatomia comparata, Rome, Italy
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Matrosova VA, Rusin MY, Volodina EV, Proyavka SV, Savinetskaya LE, Shekarova ON, Rashevska HV, Volodin IA. Genetic and alarm call diversity across scattered populations of speckled ground squirrels (Spermophilus suslicus). Mamm Biol 2016. [DOI: 10.1016/j.mambio.2016.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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Lv X, Xia L, Ge D, Wen Z, Qu Y, Lu L, Yang Q. Continental Refugium in the Mongolian Plateau during Quaternary Glacial Oscillations: Phylogeography and Niche Modelling of the Endemic Desert Hamster, Phodopus roborovskii. PLoS One 2016; 11:e0148182. [PMID: 26839955 PMCID: PMC4740458 DOI: 10.1371/journal.pone.0148182] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/14/2016] [Indexed: 11/25/2022] Open
Abstract
The Mongolian Plateau (MP), which is situated in the interior of Asia and possesses a typical continental climate, experienced harsh climatic conditions during the Quaternary glacial fluctuations. Although these events likely had huge impacts on the local animal populations, the current effects have hardly been explored. To investigate whether the MP supported a refugium along an oceanic-continental gradient (ROCG), and whether this refugium was glacial or interglacial, we investigated the demographic and phylogeographic history of an endemic mammal species, the desert hamster Phodopus roborovskii. We reconstructed the demographic variation, the phylogeographic diffusion, and modelled the potential habitat during historical periods. The genetic diversity in the MP was the highest among all the localities, and the MP was a suitable habitat throughout the modelled historical periods. A phylogeographic diffusion analysis emphasized the importance of the MP as the centre of origin, preservation and spread for P. roborovskii. The homogeneous landscape provided the opportunity for a wide gene flow, which resulted in low resolution of the phylogenetic relationships. Moreover, P. roborovskii was favoured by the interglacial condition, with both its demographical and geographical ranges expanded within the interglacial periods. The range variation from the Last Glacial Maximum to the current condition reflects a distinct longitudinal shift, while both ranges largely contracted from that of the Last Interglacial. Our results support that the MP served as a refugium and spread centre for P. roborovskii during the Quaternary climate fluctuations. The interglacial expansion and the longitudinal shifts highlighted the important effects of precipitations on the distribution range of species adapted to arid and semi-arid during glacial oscillations.
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Affiliation(s)
- Xue Lv
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Science, University of Chinese Academy of Science, Beijing 100049, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liang Lu
- National Institute for Communicable Disease Control and Prevention, Chinese Centre of Disease Control and Prevention, Beijing 102206, China
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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Chassovnikarova T, Rovatsos M, Atanasov N, Koshev Y. Sex chromosome variability of Spermophilus citellus (Linnaeus, 1766) in the Southeastern part of the Balkan Peninsula. Mamm Biol 2015. [DOI: 10.1016/j.mambio.2014.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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