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Garcia-Jacas N, López-Pujol J, Nualart N, Herrando-Moraira S, Romaschenko K, Ren MX, Susanna A. Centaurea Subsect. Phalolepis (Compositae, Cardueae): A Case Study of Mountain-Driven Allopatric Speciation in the Mediterranean Peninsulas. PLANTS (BASEL, SWITZERLAND) 2022; 12:11. [PMID: 36616140 PMCID: PMC9823864 DOI: 10.3390/plants12010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Centaurea subsection Phalolepis has been thoroughly analyzed in previous studies using microsatellites in four centers of speciation: Anatolia, Greece, the Italian Peninsula and the Iberian Peninsula. Evidence suggests a correlation between taxon diversity and mountains. This group constituted a good case study for examining the mountain-geobiodiversity hypothesis (MGH), which explains the possible reasons for the many radiations occurring in mountains across the world. We combined all the datasets and carried out analyses of their genetic structure to confirm the species of subsect. Phalolepis are grouped according to a geographic pattern. We then checked whether climatic fluctuations favored the "species pump" hypothesis in the mountains by using the Climatic Stability Index (CSI). Finally, the relief of the terrain was tested against the rate of allopatric speciation by region by means of Terrain Ruggedness Index and environmental gradients through our new Climate Niche Breadth Index. Our results supported the MGH hypothesis and confirmed that the main triggers, namely altitudinal zonation, climatic oscillations and rugged terrain, must be present for the development of a radiation.
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Affiliation(s)
- Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. Migdia, s/n, 08038 Barcelona, Spain
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. Migdia, s/n, 08038 Barcelona, Spain
- Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Neus Nualart
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. Migdia, s/n, 08038 Barcelona, Spain
| | - Sonia Herrando-Moraira
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. Migdia, s/n, 08038 Barcelona, Spain
| | - Konstantin Romaschenko
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
- M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, 01601 Kyiv, Ukraine
| | - Ming-Xun Ren
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Hainan University), Ministry of Education, Haikou 570228, China
- Center for Terrestrial Biodiversity of the South China Sea, Hainan University, Haikou 570228, China
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB, CSIC-Ajuntament de Barcelona), Pg. Migdia, s/n, 08038 Barcelona, Spain
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Osmolovsky I, Shifrin M, Gamliel I, Belmaker J, Sapir Y. Eco-Geography and Phenology Are the Major Drivers of Reproductive Isolation in the Royal Irises, a Species Complex in the Course of Speciation. PLANTS (BASEL, SWITZERLAND) 2022; 11:3306. [PMID: 36501345 PMCID: PMC9739335 DOI: 10.3390/plants11233306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/30/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
The continuous nature of speciation implies that different species are found at different stages of divergence, from no- to complete reproductive isolation. This process and its underlying mechanisms are best viewed in incipient species. Moreover, the species complex can offer unique insight into how reproductive isolation (RI) has evolved. The royal irises (Iris section Oncocyclus) are a young group of species in the course of speciation, providing an ideal system for speciation study. We quantified pre- and post-zygotic reproductive barriers between the eight Israeli species of this complex and estimated the total RI among them. We tested for both pre-pollination and post-pollination reproductive barriers. Pre-pollination barriers, i.e., eco-geographic divergence and phenological differentiation were the major contributors to RI among the Iris species. On the other hand, post-pollination barriers, namely pollen-stigma interactions, fruit set, and seed viability had negligible contributions to total RI. The strength of RI was not uniform across the species complex, suggesting that species may have diverged at different rates. Overall, this study in a young, recently diverged group of species provides insight into the first steps of speciation, suggesting a crucial role of the pre-zygotic barriers.
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Affiliation(s)
- Inna Osmolovsky
- The Botanical Garden, School of Plant Science and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Mariana Shifrin
- The Botanical Garden, School of Plant Science and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Inbal Gamliel
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jonathan Belmaker
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yuval Sapir
- The Botanical Garden, School of Plant Science and Food Security, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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The evolutionary history of the relict scorpion family Iuridae of the eastern Mediterranean. Mol Phylogenet Evol 2022; 177:107622. [PMID: 36058510 DOI: 10.1016/j.ympev.2022.107622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/10/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022]
Abstract
Iuridae is a family of scorpions that exhibits a highly complex biogeographic and taxonomic history. Iuridae taxa are mainly found in Turkey and Greece, whereas a single species is found in northern Iraq. Several taxonomic revisions have been conducted on this family that initially comprised two genera. The latest taxonomic review, based on morphological and anatomical features, raised the number of Iuridae genera to four, and the number of species to 14. Sequence data from three molecular markers (COX1, 16S rDNA, ITS1) originating from numerous Iuridae taxa were analyzed within a phylogenetic framework. Divergence time-estimate analyses, species delimitation approaches and estimation of ancestral areas were implemented in order to: 1) reconstruct the phylogenetic relationships of the Iuridae taxa, 2) evaluate the morphological classifications, and 3) obtain insights into the biogeographic history of the family in the East Mediterranean. The multi-locus phylogeny clearly confirms an ancient division into two clades, Calchinae and Iurinae. Ancient patterns of isolation and dispersal are revealed. Both subfamilies are largely confined to the Anatolian peninsula and its few coastal islands; only the most derived genus Iurus has dispersed westward to Crete and Peloponnese. Based on our findings, three new genera of Iurinae (Metaiurus, Anatoliurus, and Letoiurus) are established. The genus Neocalchas emerges as one of the most ancient scorpion clades, with divergence time about 27 mya.
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Shao YZ, Yuan ZL, Liu YY, Liu FQ, Xiang RC, Zhang YY, Ye YZ, Chen Y, Wen Q. Glacial Expansion or Interglacial Expansion? Contrasting Demographic Models of Four Cold-Adapted Fir Species in North America and East Asia. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding and forecasting species’ response to climate change is a critical need for future conservation and management. Two expansion hypotheses, the glacial expansion versus the interglacial expansion, have been proposed to interpret how cold-adapted organisms in the northern hemisphere respond to Quaternary climatic fluctuations. To test these two hypotheses, we originally used two pairs of high-low elevation firs from North America (Abies lasiocarpa and Abies balsamea) and East Asia (Abies chensiensis and Abies nephrolepis). Abies lasiocarpa and Abies chensiensis are widely distributed in high-elevation regions of western North America and central China. Abies balsamea and Abies nephrolepis occur in central North America and northeast China, with much lower elevations. These fir species are typical cold-adapted species and sensitive to climate fluctuations. Here, we integrated the mtDNA and cpDNA polymorphisms involving 44 populations and 585 individuals. Based on phylogeographic analyses, recent historical range expansions were indicated in two high-elevation firs (Abies lasiocarpa and Abies chensiensis) during the last glaciation (43.8–28.4 or 21.9–14.2 kya, 53.1–34.5 or 26.6–17.2 kya). Such glacial expansions in high-elevation firs were further confirmed by the evidence of species distribution modelling, geographic-driven genetic patterns, palynological records, and current distribution patterns. Unlike the north American firs, the SDM models indicated unremarkable expansion or contraction in East Asia firs for its much more stable conditions during different historical periods. Taken together, our findings highly supported that high-elevation firs experienced glacial expansion during the Quaternary climate change in East Asia and North America, as interglacial expansion within low-elevation firs. Under this situation, the critically endangered fir species distributed in high elevation would have no enough higher elevational space to migrate. Facing the increasing global warming, thus we proposed ex-situ conservation of defining conservation units as the most meaningful strategy.
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Goëau H, Lorieul T, Heuret P, Joly A, Bonnet P. Can Artificial Intelligence Help in the Study of Vegetative Growth Patterns from Herbarium Collections? An Evaluation of the Tropical Flora of the French Guiana Forest. PLANTS (BASEL, SWITZERLAND) 2022; 11:530. [PMID: 35214863 PMCID: PMC8875713 DOI: 10.3390/plants11040530] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
A better knowledge of tree vegetative growth phenology and its relationship to environmental variables is crucial to understanding forest growth dynamics and how climate change may affect it. Less studied than reproductive structures, vegetative growth phenology focuses primarily on the analysis of growing shoots, from buds to leaf fall. In temperate regions, low winter temperatures impose a cessation of vegetative growth shoots and lead to a well-known annual growth cycle pattern for most species. The humid tropics, on the other hand, have less seasonality and contain many more tree species, leading to a diversity of patterns that is still poorly known and understood. The work in this study aims to advance knowledge in this area, focusing specifically on herbarium scans, as herbariums offer the promise of tracking phenology over long periods of time. However, such a study requires a large number of shoots to be able to draw statistically relevant conclusions. We propose to investigate the extent to which the use of deep learning can help detect and type-classify these relatively rare vegetative structures in herbarium collections. Our results demonstrate the relevance of using herbarium data in vegetative phenology research as well as the potential of deep learning approaches for growing shoot detection.
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Affiliation(s)
- Hervé Goëau
- Botany and Modeling of Plant Architecture and Vegetation (AMAP), French Agricultural Research Centre for International Development (CIRAD), French National Centre for Scientific Research (CNRS), French National Institute for Agriculture, Food and Environment (INRAE), Research Institute for Development (IRD), University of Montpellier, 34398 Montpellier, France; (P.H.); (P.B.)
| | - Titouan Lorieul
- ZENITH Team, Laboratory of Informatics, Robotics and Microelectronics-Joint Research Unit, Institut National de Recherche en Informatique et en Automatique (INRIA) Sophia-Antipolis, CEDEX 5, 34095 Montpellier, France; (T.L.); (A.J.)
| | - Patrick Heuret
- Botany and Modeling of Plant Architecture and Vegetation (AMAP), French Agricultural Research Centre for International Development (CIRAD), French National Centre for Scientific Research (CNRS), French National Institute for Agriculture, Food and Environment (INRAE), Research Institute for Development (IRD), University of Montpellier, 34398 Montpellier, France; (P.H.); (P.B.)
| | - Alexis Joly
- ZENITH Team, Laboratory of Informatics, Robotics and Microelectronics-Joint Research Unit, Institut National de Recherche en Informatique et en Automatique (INRIA) Sophia-Antipolis, CEDEX 5, 34095 Montpellier, France; (T.L.); (A.J.)
| | - Pierre Bonnet
- Botany and Modeling of Plant Architecture and Vegetation (AMAP), French Agricultural Research Centre for International Development (CIRAD), French National Centre for Scientific Research (CNRS), French National Institute for Agriculture, Food and Environment (INRAE), Research Institute for Development (IRD), University of Montpellier, 34398 Montpellier, France; (P.H.); (P.B.)
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Atia MAM, El-Moneim DA, Abdelmoneim TK, Reda EH, Shakour ZTA, El-Halawany AM, El-Kashoury ESA, Shams KA, Abdel-Azim NS, Hegazy MEF. Evaluation of genetic variability and relatedness among eight Centaurea species through CAAT-box derived polymorphism (CBDP) and start codon targeted polymorphism (SCoT) markers. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1960891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Mohamed Atia Mohamed Atia
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental and Agricultural Sciences, Arish University, Arish, Egypt
| | - Taghreed Khaled Abdelmoneim
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Eman Hussein Reda
- Phytochemistry Laboratory, National Organization for Drug Control and Research, Giza, Egypt
| | | | | | | | - Khaled Ahmed Shams
- Chemistry of Medicinal Plants Department, National Research Centre, Giza, Egypt
| | | | - Mohamed-Elamir Fathy Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, Giza, Egypt
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Mainz, Germany
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Özüdoğru B, Özgi̇şi K, Perktaş U, Gür H. The Quaternary range dynamics of Noccaea iberidea(Brassicaceae), a typical representative of subalpine/alpine steppe communities of Anatolian mountains. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractThe responses of Anatolian plants to global climate change have been poorly investigated. In this study, we aimed to understand how climatic oscillation during the Quaternary period helped to shape the current distribution patterns of the Anatolian endemic Noccaea iberidea, a typical representative of tragacanthic (thorny cushion) steppe communities of Anatolia. We used ecological niche modelling combined with statistical phylogeography, based on nuclear ribosomal ITS and plastidic trnL-F and trnS-ycf9 regions. Both the structure of the haplotype networks and the results of the extended Bayesian skyline plot analysis clearly indicated that N. iberidea has been through a recent population expansion. This interpretation was also supported by ecological niche modelling analysis, which showed that the availability of areas of high suitability expanded from the Last Interglacial to the Last Glacial Maximum, suggesting that N. iberidea might have expanded its range during the glacial periods. In conclusion, the study improves our understanding of the demographic history and responses of steppe plant communities of Anatolia to global climate changes through the Late Quaternary glacial–interglacial cycles, which in turn might aid in the development of future conservation strategies.
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Affiliation(s)
- Bariş Özüdoğru
- Department of Biology, Hacettepe University, Ankara, Turkey
- Biogeography Research Laboratory, Hacettepe University, Ankara, Turkey
| | - Kurtuluş Özgi̇şi
- Department of Biology, Faculty of Science and Letters, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Utku Perktaş
- Department of Biology, Hacettepe University, Ankara, Turkey
- Biogeography Research Laboratory, Hacettepe University, Ankara, Turkey
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | - Hakan Gür
- Anatolian Biogeography Research Group, Kırşehir Ahi Evran University, Kırşehir, Turkey
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Ben-Menni Schuler S, López-Pujol J, Blanca G, Vilatersana R, Garcia-Jacas N, Suárez-Santiago VN. Influence of the Quaternary Glacial Cycles and the Mountains on the Reticulations in the Subsection Willkommia of the Genus Centaurea. FRONTIERS IN PLANT SCIENCE 2019; 10:303. [PMID: 30949188 PMCID: PMC6437100 DOI: 10.3389/fpls.2019.00303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Late Neogene and Quaternary climatic oscillations have greatly shaped the genetic structure of the Mediterranean Basin flora, with mountain plant species tracking warm interglacials/cold glacials by means of altitudinal shifts instead of broad latitudinal ones. Such dynamics may have enhanced population divergence but also secondary contacts. In this paper, we use a case example of subsection Willkommia of Centaurea (comprising three narrowly distributed endemic species, Centaurea gadorensis, C. pulvinata, and C. sagredoi) to test for reticulate evolution and recurrent hybridizations between nearby populations. For this, we combine analyses of genetic diversity and structuring, gene flow and spatial correlation, and ecological niche modeling. Our results support the contention that the current genetic structure of the three species is the result of historical gene flow at sites of secondary contact during the glacial periods, followed by isolation after the retraction of populations to the middle-upper areas of the mountains during the interglacial periods. The extent and direction of the gene flow was determined largely by the location of the populations on mountainsides oriented toward the same valley or toward different valleys, suggesting the intermountain valleys as the areas where secondary contacts occurred.
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Affiliation(s)
| | | | - Gabriel Blanca
- Departamento de Botánica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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Garcia-Jacas N, López-Pujol J, López-Vinyallonga S, Janaćković P, Susanna A. Centaurea subsect. Phalolepis in Southern Italy: ongoing speciation or species overestimation? Genetic evidence based on SSRs analyses. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2018.1549617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Núria Garcia-Jacas
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s. n., Barcelona, 08038, Spain
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s. n., Barcelona, 08038, Spain
| | - Sara López-Vinyallonga
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s. n., Barcelona, 08038, Spain
| | - Pedja Janaćković
- Faculty of Biology, Institute of Botany and Botanical Garden “Jevremovac”, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | - Alfonso Susanna
- Botanic Institute of Barcelona (IBB, CSIC-ICUB), Pg. del Migdia, s. n., Barcelona, 08038, Spain
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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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