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Rincón-Barrado M, Villaverde T, Perez MF, Sanmartín I, Riina R. The sweet tabaiba or there and back again: phylogeographical history of the Macaronesian Euphorbia balsamifera. ANNALS OF BOTANY 2024; 133:883-904. [PMID: 38197716 PMCID: PMC11082519 DOI: 10.1093/aob/mcae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/01/2024] [Indexed: 01/11/2024]
Abstract
BACKGROUND AND AIMS Biogeographical relationships between the Canary Islands and north-west Africa are often explained by oceanic dispersal and geographical proximity. Sister-group relationships between Canarian and eastern African/Arabian taxa, the 'Rand Flora' pattern, are rare among plants and have been attributed to the extinction of north-western African populations. Euphorbia balsamifera is the only representative species of this pattern that is distributed in the Canary Islands and north-west Africa; it is also one of few species present in all seven islands. Previous studies placed African populations of E. balsamifera as sister to the Canarian populations, but this relationship was based on herbarium samples with highly degraded DNA. Here, we test the extinction hypothesis by sampling new continental populations; we also expand the Canarian sampling to examine the dynamics of island colonization and diversification. METHODS Using target enrichment with genome skimming, we reconstructed phylogenetic relationships within E. balsamifera and between this species and its disjunct relatives. A single nucleotide polymorphism dataset obtained from the target sequences was used to infer population genetic diversity patterns. We used convolutional neural networks to discriminate among alternative Canary Islands colonization scenarios. KEY RESULTS The results confirmed the Rand Flora sister-group relationship between western E. balsamifera and Euphorbia adenensis in the Eritreo-Arabian region and recovered an eastern-western geographical structure among E. balsamifera Canarian populations. Convolutional neural networks supported a scenario of east-to-west island colonization, followed by population extinctions in Lanzarote and Fuerteventura and recolonization from Tenerife and Gran Canaria; a signal of admixture between the eastern island and north-west African populations was recovered. CONCLUSIONS Our findings support the Surfing Syngameon Hypothesis for the colonization of the Canary Islands by E. balsamifera, but also a recent back-colonization to the continent. Populations of E. balsamifera from northwest Africa are not the remnants of an ancestral continental stock, but originated from migration events from Lanzarote and Fuerteventura. This is further evidence that oceanic archipelagos are not a sink for biodiversity, but may be a source of new genetic variability.
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Affiliation(s)
- Mario Rincón-Barrado
- Real Jardín Botánico (RJB), CSIC, Madrid, 28014, Spain
- Centro Nacional de Biotecnología (CNB), CSIC, Madrid, 28049, Spain
| | - Tamara Villaverde
- Universidad Rey Juan Carlos (URJC), Área de Biodiversidad y Conservación, Móstoles, 28933, Spain
| | - Manolo F Perez
- Institut de Systématique, Evolution, Biodiversité (ISYEB – URM 7205 CNRS), Muséum National d’Histoire Naturelle, SU, EPHE & UA, Paris, France
| | | | - Ricarda Riina
- Real Jardín Botánico (RJB), CSIC, Madrid, 28014, Spain
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Briatico G, Bocherens H, Geraads D, Melis RT, Mussi M. The Pleistocene high-elevation environments between 2.02 and 0.6 Ma at Melka Kunture (Upper Awash Valley, Ethiopia) based upon stable isotope analysis. Sci Rep 2024; 14:6619. [PMID: 38503829 PMCID: PMC10950861 DOI: 10.1038/s41598-024-56768-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Pleistocene environments are among the most studied issues in paleoecology and human evolution research in eastern Africa. Many data have been recorded from archaeological sites located at low and medium elevations (≤ 1500 m), whereas few contexts are known at 2000 m and above. Here, we present a substantial isotopic study from Melka Kunture, a complex of prehistoric sites located at 2000-2200 m above sea level in the central Ethiopian highlands. We analyzed the stable carbon and oxygen isotopic composition of 308 faunal tooth enamel samples from sites dated between 2.02 and 0.6 Ma to investigate the animal diets and habitats. The carbon isotopic results indicate that the analyzed taxa had C4-dominated and mixed C3-C4 diets with no significant diachronic changes in feeding behavior with time. This is consistent with faunal and phytolith analyses, which suggested environments characterized by open grasslands (with both C3 and C4 grasses), patches of bushes and thickets, and aquatic vegetation. However, palynological data previously documented mountain forests, woodlands, and high-elevation grasslands. Additionally, the carbon isotopic comparison with other eastern African localities shows that differences in elevation did not influence animal feeding strategies and habitat partitioning, even though plant species vary according to altitudinal gradients. In contrast, the oxygen isotopic comparison suggests significant differences consistent with the altitude effect. Our approach allows us to detect diverse aspects of animal behavior, habitat, and vegetation that should be considered when reconstructing past environments.
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Affiliation(s)
- Giuseppe Briatico
- Dipartimento Di Scienze Dell'Antichità, Sapienza Università Di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy.
- Department of Geosciences, Eberhard Karls University of Tübingen, Hölderlinstrasse 12, 72074, Tübingen, Germany.
- Italo-Spanish Archaeological Mission at Melka Kunture and Balchit, Melka Kunture, Ethiopia.
| | - Hervé Bocherens
- Department of Geosciences, Eberhard Karls University of Tübingen, Hölderlinstrasse 12, 72074, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Sigwartstrasse 10, 72076, Tübingen, Germany
| | - Denis Geraads
- CR2P, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, CP 38, 8 Rue Buffon, 75231, Paris cedex 05, France
| | - Rita T Melis
- Italo-Spanish Archaeological Mission at Melka Kunture and Balchit, Melka Kunture, Ethiopia
- Dipartimento Di Scienze Chimiche E Geologiche, Università Di Cagliari, 09042, Cittadella Di Monserrato, Italy
- CNR-IGAG, Piazzale Aldo Moro 7, 00185, Rome, Italy
| | - Margherita Mussi
- Dipartimento Di Scienze Dell'Antichità, Sapienza Università Di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Italo-Spanish Archaeological Mission at Melka Kunture and Balchit, Melka Kunture, Ethiopia
- ISMEO, Corso Vittorio Emanuele II 244, 00186, Rome, Italy
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Montgelard C, Muller T, Arnal V, Maree S, Taylor PJ, Sands AF, Robinson TJ, Matthee CA. Diversification and evolutionary history of the African laminated-toothed rats (Rodentia, Otomyini). Mol Phylogenet Evol 2023; 183:107779. [PMID: 37019420 DOI: 10.1016/j.ympev.2023.107779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/23/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
The African continent was subjected to periodic climatic shifts during the Pliocene and Pleistocene. These habitat changes greatly affected the evolutionary processes and tempo of diversification in numerous, widely distributed mammals. The Otomyini (Family Muridae) comprises three African rodent genera, Parotomys, Otomys and Myotomys, characterized by unique laminated-shaped molars. Species within this tribe generally prefer open-habitat and show low dispersal capabilities, with previous studies suggesting that their diversification was closely associated with climatic oscillations over the last four million years. Our phylogenetic reconstructions, based on three mitochondrial (mtDNA) genes (Cytb, COI and 12S) and four nuclear introns (EF, SPTBN, MGF and THY), identified eight major genetic clades that are distributed across southern, eastern and western Africa. Our data permit the re-examination of the taxonomic status of the three genera as well as the previously proposed mesic-arid dichotomy of the 10 South African species. Moreover, multiple mtDNA species delimitation methods incorporating 168 specimens estimated the number of Otomyini species to be substantially higher than the ∼30 recognized, suggesting that the current taxonomy will necessitate an integrative approach to delimit extant species diversity within the Otomyini. The data suggests that the origin of the tribe can be dated back to ∼5.7 million years ago (Ma) in southern Africa. The distribution and phylogenetic associations among the eight major otomyine evolutionary lineages can best be explained by several waves of northward colonization from southern Africa, complemented by independent reversed dispersals from eastern back to southern Africa at different time periods. There is strong support for the hypothesis that the radiation, dispersion, and diversification of the otomyine rodents is closely linked to recent Plio-Pleistocene climatic oscillations.
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Love SJ, Schweitzer JA, Bailey JK. Climate-driven convergent evolution in riparian ecosystems on sky islands. Sci Rep 2023; 13:2817. [PMID: 36797341 PMCID: PMC9935884 DOI: 10.1038/s41598-023-29564-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
Climate-induced evolution will determine population persistence in a changing world. However, finding natural systems in which to study these responses has been a barrier to estimating the impact of global change on a broad scale. We propose that isolated sky islands (SI) and adjacent mountain chains (MC) are natural laboratories for studying long-term and contemporary climatic pressures on natural populations. We used greenhouse common garden trees to test whether populations on SI exposed to hot and dry climates since the end of the Pleistocene have phenotypically diverged from populations on MC, and if SI populations have converged in these traits. We show: (1) populations of Populus angustifolia from SI have diverged from MC, and converged across SI, in reproductive and productivity traits, (2) these traits (cloning and aboveground biomass, respectively) are significantly correlated, suggesting a genetic linkage between them, and (3) the trait variation is driven by both natural selection and genetic drift. These shifts represent potentially beneficial phenotypes for population persistence in a changing world. These results suggest that the SI-MC comparison is a natural laboratory, as well as a predictive framework, for studying long-term responses to climate change across the globe.
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Affiliation(s)
- S J Love
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Dabney Hall, 1416 Circle Dr, Knoxville, TN, 37996, USA.
| | - J A Schweitzer
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Dabney Hall, 1416 Circle Dr, Knoxville, TN, 37996, USA
| | - J K Bailey
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Dabney Hall, 1416 Circle Dr, Knoxville, TN, 37996, USA
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Hartley R, Clemann N, Atkins Z, Scheele BC, Lindenmayer DB, Amor MD. Isolated on sky islands: genetic diversity and population structure of an endangered mountain lizard. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01495-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Steger C, Boone RB, Dullo BW, Evangelista P, Alemu S, Gebrehiwot K, Klein JA. Collaborative agent-based modeling for managing shrub encroachment in an Afroalpine grassland. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 316:115040. [PMID: 35594826 DOI: 10.1016/j.jenvman.2022.115040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
We co-designed an agent-based model of an Afroalpine grassland in Ethiopia that is experiencing unwanted shrub encroachment. The goal was to enable managers of a community conservation area to better understand the drivers of shrub encroachment and to test possible management actions for controlling shrubs. Due to limited site-specific data, we parameterized this model using insights from published literature, remote sensing, and expert opinion from scientists and local managers. We therefore sought to explore potential future scenarios rather than make highly accurate predictions, focusing on facilitating discussions and learning among the diverse co-management team. We evaluated three social-ecological scenarios with our model, examining: (1) the impact of changing precipitation regimes on vegetation, (2) whether changing the frequency of guassa grass harvests would improve the long-term sustainability of the grassland, and (3) whether the combination of grass harvest and shrub removal would affect shrub encroachment. We found that the model was highly sensitive to the amount of grass harvested each year for local use. Our results indicate that the guassa grass was more resilient than shrubs during persistent dry climatic conditions, whereas a reduction in only the early spring rains (known as the "belg") resulted in considerable loss of grass biomass. While our modeling results lacked the quantitative specificity desired by managers, participants in the collaborative modeling process learned new approaches to planning and management of the conservation area and expanded their knowledge of the ecological complexity of the system. Several participants used the model as a boundary object, interpreting it in ways that reinforced their cultural values and goals for the conservation area. Our work highlights the lack of detailed scientific knowledge of Afroalpine ecosystems, and urges managers to reconnect with traditional ecological management of the conservation area in their pursuit of shrub encroachment solutions. The decline or absence of the belg rains is becoming increasingly common in the Ethiopian highlands, and our results underscore the need for more widespread understanding of how this changing climatic regime impacts local environmental management. This work lays a foundation for social-ecological research to improve both understanding and management of these highly threatened ecosystems.
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Affiliation(s)
- Cara Steger
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14850, USA.
| | - Randall B Boone
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, 80523, USA
| | - Bikila Warkineh Dullo
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Ethiopia
| | - Paul Evangelista
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, CO, 80523, USA
| | - Shambel Alemu
- Department of Plant Biology and Biodiversity Management, Addis Ababa University, Ethiopia
| | | | - Julia A Klein
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, 80523, USA
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Wambulwa MC, Luo YH, Zhu GF, Milne R, Wachira FN, Wu ZY, Wang H, Gao LM, Li DZ, Liu J. Determinants of Genetic Structure in a Highly Heterogeneous Landscape in Southwest China. FRONTIERS IN PLANT SCIENCE 2022; 13:779989. [PMID: 35574120 PMCID: PMC9097793 DOI: 10.3389/fpls.2022.779989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Intra-specific genetic diversity is a fundamental component of biodiversity, and is key to species adaptation and persistence. However, significant knowledge gaps still exist in our understanding of the patterns of genetic diversity and their key determinants. Most previous investigations mainly utilized single-species and/or a limited number of explanatory variables; so here we mapped the patterns of plastid genetic diversity within 15 plant species, and explored the key determinants shaping these patterns using a wide range of variables. Population-level cpDNA sequence data for 15 plant species from the Longitudinal Range Gorge Region (LRGR), southwest China, were retrieved from literature and used to estimate haplotype diversity (H D) and population pairwise genetic differentiation (F ST) indices. Genetic diversity and divergence landscape surfaces were then generated based on the H D and F ST, respectively, to clarify the patterns of genetic structure in the region. Subsequently, we analyzed the relationships between plastid genetic diversity and 16 explanatory variables (classified as anthropogenic, climatic, and topographic). We found that the highest genetic diversity occurred in the Yulong Mountain region, with a significant proportion (~74.81%) of the high diversity land area being located outside of protected areas. The highest genetic divergence was observed approximately along the 25°N latitudinal line, with notable peaks in the western and eastern edges of the LRGR. Genetic diversity (H D) was weakly but significantly positively correlated with both Latitude (lat) and Annual Mean Wet Day Frequency (wet), yet significantly negatively correlated with all of Longitude (long), Annual Mean Cloud Cover Percent (cld), Annual Mean Anthropogenic Flux (ahf), and Human Footprint Index (hfp). A combination of climatic, topographic, and anthropogenic factors explained a significant proportion (78%) of genetic variation, with topographic factors (lat and long) being the best predictors. Our analysis identified areas of high genetic diversity (genetic diversity "hotspots") and divergence in the region, and these should be prioritized for conservation. This study contributes to a better understanding of the features that shape the distribution of plastid genetic diversity in the LRGR and thus would inform conservation management efforts in this species-rich, but vulnerable region.
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Affiliation(s)
- Moses C. Wambulwa
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Guang-Fu Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Richard Milne
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Francis N. Wachira
- Department of Life Sciences, School of Science and Computing, South Eastern Kenya University, Kitui, Kenya
| | - Zeng-Yuan Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Krásová J, Mikula O, Lavrenchenko LA, Šumbera R, Meheretu Y, Bryja J. A new rodent species of the genus Mus (Rodentia: Muridae) confirms the biogeographical uniqueness of the isolated forests of southern Ethiopia. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00539-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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9
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Cuypers LN, Sabuni C, Šumbera R, Aghová T, Lišková E, Leirs H, Baird SJE, Goüy de Bellocq J, Bryja J. Biogeographical Importance of the Livingstone Mountains in Southern Tanzania: Comparative Genetic Structure of Small Non-volant Mammals. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.742851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Livingstone Mountains (LM; also known as the Kipengere Range) found in south-western Tanzania at the northern end of Lake Nyasa are an important region for understanding the biogeography of Eastern Africa. The two branches of the East African Rift Valley meet here and the mountains might represent stepping stones for colonization and migration between different parts of the Eastern Afromontane Biodiversity Hotspot (especially the link between the Eastern Arc Mountains, EAM, and the Southern Rift Mountains, SRM), as well as an efficient barrier to gene flow for taxa living in drier savannahs in lower elevations. Here we combine new mitochondrial sequence data from 610 recently sampled rodents and shrews with available georeferenced genetic data (3538 specimens) from southern Tanzania, northern Malawi/Zambia and northern Mozambique and compare the spatial genetic structure among different taxa. There is no universal phylogeographic pattern in taxa preferring humid montane habitats. For some of them, the Makambako Gap acts as a barrier between the SRM and the EAM, but other taxa can bridge this gap. Barriers within the EAM (frequently) and within the SRM (sometimes) appear more important. The Rukwa rift between the SRM and the ARM is an important barrier that perhaps can only be crossed by taxa that are not that strictly tied to humid montane environments. For mammals living in lower-elevation savannah-like habitats, the LM can act as a strict barrier to gene flow, and together with the Ufipa Plateau, Lake Nyasa and the EAM create a very similar phylogeographic pattern with three recognizable genetic groups in most savannah-dwellers. The Livingstone Mountains thus appear to be one of the most important biogeographic crossroads in Eastern Africa.
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Clewing C, Geertz T, Rassam H, Woldekiros TH, Albrecht C. Freshwater diversity at a biogeographic edge zone: the high-mountain pea-clams of Ethiopia. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2021.2005706] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Catharina Clewing
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26 (IFZ), Giessen, 35390 Germany
| | - Thies Geertz
- International Foundation for Environment and Nature, Global Nature Fund (GNF), Radolfzell, Germany
| | - Hanane Rassam
- Muséum d’Histoire Naturelle de Marrakech, Laboratoire Hydrobiologie, Ecotoxicologie, Assainissement et Changements globaux, Université Cadi Ayyad, Marrakech, Morocco
| | | | - Christian Albrecht
- Department of Animal Ecology and Systematics, Justus Liebig University Giessen, Heinrich-Buff-Ring 26 (IFZ), Giessen, 35390 Germany
- Department of Biology, Mbarara University of Science and Technology, Mbarara, Uganda
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Pérez‐Pérez MA, Yu W. Pleistocene origin and colonization history of Lobelia columnaris Hook. f. (Campanulaceae: Lobelioideae) across sky islands of West Central Africa. Ecol Evol 2021; 11:15860-15873. [PMID: 34824795 PMCID: PMC8601881 DOI: 10.1002/ece3.8256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 11/08/2022] Open
Abstract
We aimed to infer ancestral area and historical colonization of Lobelia columnaris in the sky islands of Bioko and Cameroon through dated phylogeny using chloroplast genomes. Specifically, we aim to answer the following questions: (1) What are the phylogenetic relationships among Bioko Island and Cameroon populations? (2) Are the older populations found in the older sky islands? We assembled novel plastomes from 20 individuals of L. columnaris from 5 mountain systems. The plastome data were explored with phylogenetic analyses using Maximum Likelihood and Bayesian Inference. The populations of L. columnaris have a monophyletic origin, subdivided into three plastomes-geographic clades. The plastid phylogenomic results and age of the sky islands indicate that L. columnaris colonized first along with the Cameroon Volcanic Line's young sky islands of Bioko. The crown group (1.54 Ma) split the population in Bioko and mainland Cameroon. It is possible that Bioko was the ancestral area and likely isolated during cold and dry conditions in forest refugia. Presumably, the colonization history occurred during the middle-late Pleistocene from South Bioko's young sky island to North Bioko and the northern old sky islands in Cameroon. Furthermore, the central depression with lowland forest between North and South Bioko is a current geographic barrier that keeps separating the populations of Bioko from each other. Also, the shallow sea channel keeps isolated the populations of Bioko and the mainland populations. The Pleistocene climatic oscillations led to the divergence of the Cameroon and Bioko populations into three clades. L. columnaris colonized the older sky islands in mainland Cameroon after establishment in Bioko's younger sky islands. Contrary to expectations, the biogeography history was an inverse progression with respect to the age of the Afromontane sky islands.
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Affiliation(s)
- Miguel A. Pérez‐Pérez
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
- Department of Biodiversity, Earth & Environmental ScienceDrexel UniversityPhiladelphiaPennsylvaniaUSA
| | - Wen‐Bin Yu
- Center for Integrative ConservationXishuangbanna Tropical Botanical GardenMenglaChina
- Center of Conservation Biology, Core Botanical GardensChinese Academy of SciencesMenglaChina
- Southeast Asia Biodiversity Research InstituteChinese Academy of ScienceYezinMyanmar
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12
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Yang W, Feiner N, Salvi D, Laakkonen H, Jablonski D, Pinho C, Carretero MA, Sacchi R, Zuffi MAL, Scali S, Plavos K, Pafilis P, Poulakakis N, Lymberakis P, Jandzik D, Schulte U, Aubret F, Badiane A, Perez I de Lanuza G, Abalos J, While GM, Uller T. Population genomics of wall lizards reflects the dynamic history of the Mediterranean Basin. Mol Biol Evol 2021; 39:6413643. [PMID: 34718699 PMCID: PMC8760935 DOI: 10.1093/molbev/msab311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan Peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an “Out-of-Italy” expansion following the Messinian salinity crisis (∼5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian, and Balkan Peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flows have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.
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Affiliation(s)
- Weizhao Yang
- Department of Biology, Lund University, Lund, 223 62, Sweden
| | - Nathalie Feiner
- Department of Biology, Lund University, Lund, 223 62, Sweden
| | - Daniele Salvi
- Department of Health, Life and Environmental Sciences, University of L'Aquila, 67100, Italy Coppito L'Aquila
| | - Hanna Laakkonen
- Department of Biology, Lund University, Lund, 223 62, Sweden
| | - Daniel Jablonski
- Department of Zoology, Comenius University, Ilkovičova 6, 842 15, Slovakia in Bratislava, Bratislava
| | - Catarina Pinho
- CIBIO/InBIO Research Centre in Biodiversity and Genetic Resources, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Miguel A Carretero
- CIBIO/InBIO Research Centre in Biodiversity and Genetic Resources, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre, s/n, Porto, 4169 - 007, Portugal
| | - Roberto Sacchi
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, 27100, Italy
| | - Marco A L Zuffi
- Museum Natural History, University of Pisa, Pisa, 56011, Italy
| | - Stefano Scali
- Museum of Natural History of Milan, Milano, 20121, Italy
| | | | - Panayiotis Pafilis
- National & Kapodistrian University of Athens, School of Science, Faculty of Biology, Panepistimiopolis 15701, Athens, Greece
| | - Nikos Poulakakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion, 71409, Greece.,Biology Department, School of Sciences and Engineering, University of Crete, Voutes University Campus, Heraklion, 70013, Greece.,Institute of Molecular Biology and Biotechnology (IMBB), Heraklion, 70013, GreeceFoundation for Research and Technology-Hellas (FORTH)
| | - Petros Lymberakis
- Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, Heraklion, 71409, Greece
| | - David Jandzik
- Department of Zoology, Comenius University, Ilkovičova 6, 842 15, Slovakia in Bratislava, Bratislava
| | - Ulrich Schulte
- Büro für Faunistische Gutachten-Dr. Ulrich Schulte, Kaiserstraße 2, Borgholzhausen, 33829, Germany
| | - Fabien Aubret
- Station d'Ecologie Théorique et Expérimentale, CNRS, 09200, Moulis, France.,School of Molecular and Life Sciences, Curtin University, WA, 6102, Australia
| | - Arnaud Badiane
- IMBE, Aix-Marseille Université, Avignon Université, CNRS, IRD, Marseille, France
| | - Guillem Perez I de Lanuza
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, APT. 22085, 46071, Spain
| | - Javier Abalos
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Valencia, APT. 22085, 46071, Spain
| | - Geoffrey M While
- School of Natural Sciences, University of Tasmania, Sandy Bay, Tasmania, 7005, Australia
| | - Tobias Uller
- Department of Biology, Lund University, Lund, 223 62, Sweden
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13
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Tonzo V, Ortego J. Glacial connectivity and current population fragmentation in sky islands explain the contemporary distribution of genomic variation in two narrow‐endemic montane grasshoppers from a biodiversity hotspot. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13306] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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14
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Grímsson F, Ulrich S, Coiro M, Graham SA, Jacobs BF, Currano ED, Xafis A, Zetter R. Hagenia from the early Miocene of Ethiopia: Evidence for possible niche evolution? Ecol Evol 2021; 11:5164-5186. [PMID: 34025999 PMCID: PMC8131786 DOI: 10.1002/ece3.7408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/10/2021] [Accepted: 02/22/2021] [Indexed: 11/21/2022] Open
Abstract
Fossil pollen believed to be related to extant Hagenia abyssinica were discovered in the early Miocene (21.73 Ma) Mush Valley paleoflora, Ethiopia, Africa. Both the fossil and extant pollen grains of H. abyssinica were examined with combined light microscopy, scanning electron microscopy, and transmission electron microscopy to compare the pollen and establish their relationships. Based on this, the fossil pollen grains were attributed to Hagenia. The presence of Hagenia in the fossil assemblage raises the questions if its habitat has changed over time, and if the plants are/were wind pollinated. To shed light on these questions, the morphology of extant anthers was also studied, revealing specialized hairs inside the anthers, believed to aid in insect pollination. Pollen and anther morphology are discussed in relation to the age and origin of the genus within a molecular dated phylogenetic framework, the establishment of complex topography in East Africa, other evidence regarding pollination modes, and the palynological record. The evidence presented herein, and compiled from the literature, suggests that Hagenia was an insect-pollinated lowland rainforest element during the early Miocene of the Mush Valley. The current Afromontane habitat and ambophilous (insect and wind) pollination must have evolved in post-mid-Miocene times.
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Affiliation(s)
- Friðgeir Grímsson
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Silvia Ulrich
- Department of Botany and Biodiversity ResearchUniversity of ViennaViennaAustria
| | - Mario Coiro
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | | | - Bonnie F. Jacobs
- Roy M. Huffington Department of Earth SciencesSouthern Methodist UniversityDallasTXUSA
| | - Ellen D. Currano
- Departments of Botany and Geology & GeophysicsUniversity of WyomingLaramieWYUSA
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15
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Elfekih S, Tay WT, Polaszek A, Gordon KHJ, Kunz D, Macfadyen S, Walsh TK, Vyskočilová S, Colvin J, De Barro PJ. On species delimitation, hybridization and population structure of cassava whitefly in Africa. Sci Rep 2021; 11:7923. [PMID: 33846476 PMCID: PMC8041820 DOI: 10.1038/s41598-021-87107-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 03/17/2021] [Indexed: 01/03/2023] Open
Abstract
The Bemisia cassava whitefly complex includes species that cause severe crop damage through vectoring cassava viruses in eastern Africa. Currently, this whitefly complex is divided into species and subgroups (SG) based on very limited molecular markers that do not allow clear definition of species and population structure. Based on 14,358 genome-wide SNPs from 62 Bemisia cassava whitefly individuals belonging to sub-Saharan African species (SSA1, SSA2 and SSA4), and using a well-curated mtCOI gene database, we show clear incongruities in previous taxonomic approaches underpinned by effects from pseudogenes. We show that the SSA4 species is nested within SSA2, and that populations of the SSA1 species comprise well-defined south-eastern (Madagascar, Tanzania) and north-western (Nigeria, Democratic Republic of Congo, Burundi) putative sub-species. Signatures of allopatric incipient speciation, and the presence of a 'hybrid zone' separating the two putative sub-species were also detected. These findings provide insights into the evolution and molecular ecology of a highly cryptic hemipteran insect complex in African, and allow the systematic use of genomic data to be incorporated in the development of management strategies for this cassava pest.
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Affiliation(s)
- S Elfekih
- Australian Centre for Disease Preparedness, CSIRO, Geelong, VIC, Australia
| | - W T Tay
- Black Mountain Laboratories, CSIRO, Canberra, ACT, Australia.
| | - A Polaszek
- Department of Life Sciences, Natural History Museum, London, UK
| | - K H J Gordon
- Black Mountain Laboratories, CSIRO, Canberra, ACT, Australia
| | - D Kunz
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - S Macfadyen
- Black Mountain Laboratories, CSIRO, Canberra, ACT, Australia
| | - T K Walsh
- Black Mountain Laboratories, CSIRO, Canberra, ACT, Australia
| | - S Vyskočilová
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - J Colvin
- Natural Resources Institute, University of Greenwich, Kent, UK
| | - P J De Barro
- CSIRO, Ecosciences Precinct, Brisbane, Australia
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16
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Komarova VA, Kostin DS, Bryja J, Mikula O, Bryjová A, Čížková D, Šumbera R, Meheretu Y, Lavrenchenko LA. Complex reticulate evolution of speckled brush-furred rats (Lophuromys) in the Ethiopian centre of endemism. Mol Ecol 2021; 30:2349-2365. [PMID: 33738874 DOI: 10.1111/mec.15891] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/04/2023]
Abstract
The Ethiopian highlands represent a remarkable biodiversity 'hot spot' with a very high number of endemic species, even among vertebrates. Ethiopian representatives of a species complex of speckled brush-furred rats (Lophuromys flavopunctatus sensu lato) inhabit highland habitats ranging from low-elevation forests to Afroalpine grasslands. These may serve as a suitable model for understanding evolutionary processes leading to high genetic and ecological diversity in montane biodiversity hot spots. Here, we analyse the most comprehensive genetic data set of this group, comprising 315 specimens (all nine putative Ethiopian Lophuromys taxa sampled across most of their distribution ranges) genotyped at one mitochondrial and four nuclear markers, and thousands of SNPs from ddRAD sequencing. We performed phylogenetic analyses, delimited species and mapped their distribution and estimated divergence time between species (under the species-tree framework) and mitochondrial lineages. We found significant incongruence between mitochondrial and nuclear phylogenies, most probably caused by multiple interspecific introgression events. We discuss alternative scenarios of Ethiopian Lophuromys evolution, from retention of ancestral polymorphism to hybridization upon secondary contact of partially reproductively isolated lineages leading to reticulate evolution. Finally, we use the diversity of the speckled brush-furred rats for the description of the main biogeographic patterns in the fauna of the Ethiopian highlands.
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Affiliation(s)
- Valeria A Komarova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Danila S Kostin
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ondřej Mikula
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Anna Bryjová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Dagmar Čížková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Yonas Meheretu
- Department of Biology and Institute of Mountain Research and Development, Mekelle University, Mekelle, Tigray, Ethiopia
| | - Leonid A Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
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17
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Voelker G, Huntley JW, Bryja J, Denys C, Šumbera R, Demos TC, Lavrenchenko L, Nicolas V, Gnoske TP, Kerbis Peterhans JC. Molecular systematics and biogeographic history of the African climbing-mouse complex (Dendromus). Mol Phylogenet Evol 2021; 161:107166. [PMID: 33798668 DOI: 10.1016/j.ympev.2021.107166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/08/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Climbing mice in the genus Dendromus (sensu lato) are widely distributed in Africa, south of the Saharan Desert. The 17 currently recognized species in the genus range from widespread taxa to single-mountain endemics, and there is considerable variation across species with respect to habitats occupied. These habitats range from arid grasslands and savannahs to sub-alpine and alpine vegetation. Using the most comprehensive geographic and genetic survey to date and after reviewing many type specimens, we assess the systematics and biogeography of Dendromus. Given the structure of our molecular phylogenetic hypotheses, in which we recover six major clades, we propose the recognition of three genera within the Dendromus group (sensu lato): in addition to Dendromus (26 lineages), we suggest the retention of Megadendromus (monotypic) and the resurrection of the genus Poemys (six lineages). From our model-based molecular phylogenetic results and morphological comparisons, we suggest that six formerly synonymized taxa should be resurrected, and we highlight 14 previously undescribed lineages. We also constructed time-calibrations on our phylogeny, and performed ancestral area reconstructions using BioGeoBEARS. Based on fossil evidence, Dendromus appears to have had a widespread African distribution dating back to the Late Miocene (8-10 Ma), and our basal ancestral area reconstruction (Ethiopians Highlands + Eastern African Mountains + Zambezian region) supports this. Divergence of the six major clades we recover (Poemys, Megadendromus and four within Dendromus) occurred prior to or at the Miocene-Pliocene boundary 5.3 Ma. Biogeographically, Megadendromus is restricted to the Ethiopian Highlands. The ancestral area for Poemys is reconstructed as the Zambezian region, with species distributions ranging from South Africa to Western Africa. The ancestral area for Dendromus is reconstructed as the Ethiopian Highlands, with the ancestral areas of the four major clades being reconstructed as Ethiopian Highlands, Albertine Rift, South Africa or Western Africa. None of the four Dendromus clades are reciprocally monophyletic with respect to distributional area.
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Affiliation(s)
- G Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, United States.
| | - J W Huntley
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, United States
| | - J Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - C Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - R Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - T C Demos
- Science and Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, United States
| | - L Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - V Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - T P Gnoske
- Science and Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, United States
| | - J C Kerbis Peterhans
- Science and Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, United States; College of Arts & Sciences, Roosevelt University, 430 S. Michigan Avenue, Chicago, IL 60605, United States
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18
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Koppetsch T, Nečas P, Wipfler B. A new chameleon of the Trioceros affinis species complex (Squamata, Chamaeleonidae) from Ethiopia. ZOOSYST EVOL 2021. [DOI: 10.3897/zse.97.57297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A new species of chameleon, Trioceros wolfgangboehmeisp. nov., inhabiting the northern slopes of the Bale Mountains in Ethiopia, is described. It differs from its Ethiopian congeners by a combination of the following features: presence of a prominent dorsal crest with a low number of enlarged conical scales reaching along the anterior half of the tail as a prominent tail crest, a casque raised above the dorsal crest, heterogeneous body scalation, long canthus parietalis, rugose head scalation, high number of flank scales at midbody and unique hemipenial morphology. Based on morphological characteristics, phylogenetic discordances of previous studies and biogeographical patterns, this new species is assigned to the Trioceros affinis (Rüppell, 1845) species complex. An updated comprehensive key to the Trioceros found in Ethiopia is provided.
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19
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Bianconi ME, Dunning LT, Curran EV, Hidalgo O, Powell RF, Mian S, Leitch IJ, Lundgren MR, Manzi S, Vorontsova MS, Besnard G, Osborne CP, Olofsson JK, Christin PA. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species. Proc Biol Sci 2020; 287:20201960. [PMID: 33171085 PMCID: PMC7735283 DOI: 10.1098/rspb.2020.1960] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
C4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C4 and non-C4 populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C4 lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C4 phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C4 physiology away from its region of origin.
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Affiliation(s)
- Matheus E Bianconi
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Emma V Curran
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Oriane Hidalgo
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Robyn F Powell
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Sahr Mian
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Ilia J Leitch
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Marjorie R Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Sophie Manzi
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Maria S Vorontsova
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Guillaume Besnard
- Laboratoire Evolution and Diversité Biologique (EDB UMR5174), Université de Toulouse III - Paul Sabatier, CNRS, IRD, 118 route de Narbonne, 31062 Toulouse, France
| | - Colin P Osborne
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Jill K Olofsson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Pascal-Antoine Christin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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20
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Ghaedi Z, Badri S, Saberi-Pirooz R, Vaissi S, Javidkar M, Ahmadzadeh F. The Zagros Mountains acting as a natural barrier to gene flow in the Middle East: more evidence from the evolutionary history of spiny-tailed lizards (Uromasticinae: Saara). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
We investigated the phylogeographic structure of the genus Saara and studied whether the Zagros Mountain ranges influence the gene flow and dispersal at the landscape scale between the Iranian Saara species, including S. asmussi in the central Iranian plateau and S. loricata in the Mesopotamian lowlands. Phylogenetic analyses clearly show three well-supported species, including S. loricata, S. asmussi and S. hardwickii, that are distinct from Uromastyx species. The S-DIVA and BBM analyses demonstrate that species of Saara originated from an ancestor somewhere in the Iranian Plateau and then dispersed to its current geographical range. Our results indicate that the separation of S. loricata from S. asmussi coincides with the orogenic events of the Zagros Mountains during the Pliocene, and thus it may show a vicariance event. Diversification within populations of S. loricata and S. assmussi are estimated to have occurred during the Pleistocene. The haplotype network indicates one haplogroup for each of the Iranian Saara species. Population genetic analyses shows signals of demographic expansions at the beginning of the Holocene for S. loricata. Our results support the hypothesis that the Zagros Mountains act as a barrier for gene flow and Quaternary climatic oscillations affected intraspecific genetic divergences of S. loricata and S. asmussi.
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Affiliation(s)
- Zeinab Ghaedi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Sahar Badri
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Reihaneh Saberi-Pirooz
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
| | - Somaye Vaissi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
- Department of Biology, Faculty of Science, Baghabrisham, Razi University, Kermanshah, Iran
| | - Mohammad Javidkar
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Faraham Ahmadzadeh
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research Institute, Shahid Beheshti University, G.C., Evin, Tehran, Iran
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21
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Zanin M, Gonzalez-Borrajo N, ChÁvez C, Rubio Y, Harmsen B, Keller C, Villalva P, Srbek-Araujo AC, Costa LP, Palomares F. The differential genetic signatures related to climatic landscapes for jaguars and pumas on a continental scale. Integr Zool 2020; 16:2-18. [PMID: 32929877 DOI: 10.1111/1749-4877.12486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Modern and paleoclimate changes may have altered species dynamics by shifting species' niche suitability over space and time. We analyze whether the current genetic structure and isolation of the two large American felids, jaguar (Panthera onca) and puma (Puma concolor), are mediated by changes in climatic suitability and connection routes over modern and paleoclimatic landscapes. We estimate species distribution under 5 climatic landscapes (modern, Holocene, last maximum glaciations [LMG], average suitability, and climatic instability) and correlate them with individuals' genetic isolation through causal modeling on a resemblance matrix. Both species exhibit genetic isolation patterns correlated with LMG climatic suitability, suggesting that these areas may have worked as "allele refuges." However, the jaguar showed higher vulnerability to climate changes, responding to modern climatic suitability and connection routes, whereas the puma showed a continuous and gradual transition of genetic variation. Despite differential responsiveness to climate change, both species are subjected to the climatic effects on genetic configuration, which may make them susceptible to future climatic changes, since these are progressing faster and with higher intensity than changes in the paleoclimate. Thus, the effects of climatic changes should be considered in the design of conservation strategies to ensure evolutionary and demographic processes mediated by gene flow for both species.
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Affiliation(s)
- Marina Zanin
- Biology Department, Federal University of Maranhão, São Luís, Brazil
| | - Noa Gonzalez-Borrajo
- Departamento de Biologia de la Conservación, Estación Biológica de Doñana, Sevilla, Spain
| | - Cuauhtémoc ChÁvez
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Yamel Rubio
- Escuela de Biologia, Universidad Autónoma de Sinaloa, Culiacán, Mexico
| | | | - Claudia Keller
- Biodiversity Coordination, Amazon Research Institute, Manaus, Brazil
| | - Pablo Villalva
- Departamento de Biologia de la Conservación, Estación Biológica de Doñana, Sevilla, Spain
| | | | - Leonora Pires Costa
- Biological Sciences Department, Federal University of Espírito Santo, Vitória, Brazil
| | - Francisco Palomares
- Departamento de Biologia de la Conservación, Estación Biológica de Doñana, Sevilla, Spain
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22
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Kostin DS, Martynov AA, Komarova VA, Alexandrov DY, Yihune M, Kasso M, Bryja J, Lavrenchenko LA. Rodents of Choke Mountain and surrounding areas (Ethiopia): the Blue Nile gorge as a strong biogeographic barrier. JOURNAL OF VERTEBRATE BIOLOGY 2020. [DOI: 10.25225/jvb.20016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Danila S. Kostin
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
| | - Aleksey A. Martynov
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
| | - Valeria A. Komarova
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
| | - Dmitriy Yu. Alexandrov
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
| | - Mesele Yihune
- Addis Ababa University, Department of Zoological Sciences, Addis Ababa, Ethiopia
| | | | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - Leonid A. Lavrenchenko
- A. N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 119071 Moscow, Russia; e-mail:
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23
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Migliore J, Lézine AM, Hardy OJ. The recent colonization history of the most widespread Podocarpus tree species in Afromontane forests. ANNALS OF BOTANY 2020; 126:73-83. [PMID: 32193530 PMCID: PMC7304463 DOI: 10.1093/aob/mcaa049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/18/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND AIMS Afromontane forests host a unique biodiversity distributed in isolated high-elevation habitats within a matrix of rain forests or savannahs, yet they share a remarkable flora that raises questions about past connectivity between currently isolated forests. Here, we focused on the Podocarpus latifolius-P. milanjianus complex (Podocarpaceae), the most widely distributed conifers throughout sub-Saharan African highlands, to infer its demographic history from genetic data. METHODS We sequenced the whole plastid genome, mitochondrial DNA regions and nuclear ribosomal DNA of 88 samples from Cameroon to Angola in western Central Africa and from Kenya to the Cape region in eastern and southern Africa to reconstruct time-calibrated phylogenies and perform demographic inferences. KEY RESULTS We show that P. latifolius and P. milanjianus form a single species, whose lineages diverged during the Pleistocene, mostly between approx, 200 000 and 300 000 years BP, after which they underwent a wide range expansion leading to their current distributions. Confronting phylogenomic and palaeoecological data, we argue that the species originated in East Africa and reached the highlands of the Atlantic side of Africa through two probable latitudinal migration corridors: a northern one towards the Cameroon volcanic line, and a southern one towards Angola. Although the species is now rare in large parts of its range, no demographic decline was detected, probably because it occurred too recently to have left a genetic signature in our DNA sequences. CONCLUSIONS Despite the ancient and highly fluctuating history of podocarps in Africa revealed by palaeobotanical records, the extended distribution of current P. latifolius/milanjianus lineages is shown to result from a more recent history, mostly during the mid-late Pleistocene, when Afromontane forests were once far more widespread and continuous.
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Affiliation(s)
- Jérémy Migliore
- Sorbonne Université, Laboratoire d’Océanographie et du Climat: Expérimentations et Approches Numériques (LOCEAN/IPSL), CNRS UMR, Paris, France
- Université Libre de Bruxelles, Faculté des Sciences, Service Evolution Biologique et Ecologie, Bruxelles, Belgium
- Muséum départemental du Var, Toulon, France
| | - Anne-Marie Lézine
- Sorbonne Université, Laboratoire d’Océanographie et du Climat: Expérimentations et Approches Numériques (LOCEAN/IPSL), CNRS UMR, Paris, France
| | - Olivier J Hardy
- Université Libre de Bruxelles, Faculté des Sciences, Service Evolution Biologique et Ecologie, Bruxelles, Belgium
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Yang C, Zhu EJ, He QJ, Yi CH, Wang XB, Hu SJ, Wei SJ. Strong genetic differentiation among populations of Cheirotonus gestroi (Coleoptera: Euchiridae) in its native area sheds lights on species conservation. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:108-119. [PMID: 32202195 DOI: 10.1080/24701394.2020.1741565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The long-armed scarab (Cheirotonus gestroi) is an endangered large insect in southwestern China and neighboring countries; however, limited information is available regarding its population genetics, hindering conservation efforts. Therefore, we investigated the population genetic structure and evolutionary history of C. gestroi in southwestern China. Twenty-five haplotypes were obtained from 47 specimens across five populations. The Dawei Mountain (DWS) population differed from other populations by a high genetic distance. Population structure analysis generated three distinct clades, corresponding to Hengduan Mountains (HM), Ailao Mountains (AM), and Dawei Mountains (DM), and high-level genetic diversity was found in two HM populations. Collectively, the strong genetic differentiation among populations might be due to limited gene flow, geographical isolation, and habitat fragmentation. Therefore, while developing a conservation strategy, HM, AM, and DM groups should be defined as separate management units. Additionally, the DWS population should be given priority protection due to its uniqueness and low genetic diversity.
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Affiliation(s)
- Chen Yang
- Key Lab Forest Disaster Warning and Control Yunnan, Southwest Forestry University, Kunming, China.,Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - En-Jiao Zhu
- Key Lab Forest Disaster Warning and Control Yunnan, Southwest Forestry University, Kunming, China.,Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Qiu-Ju He
- Key Lab Forest Disaster Warning and Control Yunnan, Southwest Forestry University, Kunming, China
| | - Chuan-Hui Yi
- Key Lab Forest Disaster Warning and Control Yunnan, Southwest Forestry University, Kunming, China.,Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Xu-Bo Wang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Shao-Ji Hu
- Yunnan Key Laboratory of International Rivers and Transboundary Eco-security, Yunnan University, Kunming, China.,Institute of International Rivers and Eco-security, Yunnan University, Kunming, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Shee ZQ, Frodin DG, Cámara-Leret R, Pokorny L. Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics. FRONTIERS IN PLANT SCIENCE 2020; 11:258. [PMID: 32265950 PMCID: PMC7099051 DOI: 10.3389/fpls.2020.00258] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/19/2020] [Indexed: 05/19/2023]
Abstract
With its large proportion of endemic taxa, complex geological past, and location at the confluence of the highly diverse Malesian and Australian floristic regions, Papuasia - the floristic region comprising the Bismarck Archipelago, New Guinea, and the Solomon Islands - represents an ideal natural experiment in plant biogeography. However, scattered knowledge of its flora and limited representation in herbaria have hindered our understanding of the drivers of its diversity. Focusing on the woody angiosperm genus Schefflera (Araliaceae), we ask whether its morphologically defined infrageneric groupings are monophyletic, when these lineages diverged, and where (within Papuasia or elsewhere) they diversified. To address these questions, we use a high-throughput sequencing approach (Hyb-Seq) which combines target capture (with an angiosperm-wide bait kit targeting 353 single-copy nuclear loci) and genome shotgun sequencing (which allows retrieval of regions in high-copy number, e.g., organellar DNA) of historical herbarium collections. To reconstruct the evolutionary history of the genus we reconstruct molecular phylogenies with Bayesian inference, maximum likelihood, and pseudo-coalescent approaches, and co-estimate divergence times and ancestral areas in a Bayesian framework. We find strong support for most infrageneric morphological groupings, as currently circumscribed, and we show the efficacy of the Angiosperms-353 probe kit in resolving both deep and shallow phylogenetic relationships. We infer a sequence of colonization to explain the present-day distribution of Schefflera in Papuasia: from the Sunda Shelf, Schefflera arrived to the Woodlark plate (present-day eastern New Guinea) in the late Oligocene (when most of New Guinea was submerged) and, subsequently (throughout the Miocene), it migrated westwards (to the Maoke and Bird's Head Plates and thereon) and further diversified, in agreement with previous reconstructions.
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Affiliation(s)
- Zhi Qiang Shee
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Singapore Botanic Gardens, Singapore, Singapore
| | | | - Rodrigo Cámara-Leret
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Bren School of Environmental Science and Management, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP UPM-INIA), Madrid, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
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The Role of Climate and Topography in Shaping the Diversity of Plant Communities in Cabo Verde Islands. DIVERSITY 2020. [DOI: 10.3390/d12020080] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The flora and vegetation of the archipelago of Cabo Verde is dominated by Macaronesian, Mediterranean, and particularly by African tropical elements, resulting from its southernmost location, when compared to the other islands of the Macaronesia (i.e., Azores, Madeira, Selvagens, and Canary Islands). Very likely, such a geographical position entailed higher susceptibility to extreme climatic fluctuations, namely those associated with the West African Monsoon oscillations. These fluctuations led to a continuous aridification, which is a clear trend shown by most recent studies based on continental shelf cores. Promoting important environmental shifts, such climatic fluctuations are accepted as determinant to explain the current spatial distribution patterns of taxa, as well as the composition of the plant communities. In this paper, we present a comprehensive characterization of the main plant communities in Cabo Verde, and we discuss the role of the climatic and topoclimatic diversity in shaping the vegetation composition and distribution of this archipelago. Our study reveals a strong variation in the diversity of plant communities across elevation gradients and distinct patterns of richness among plant communities. Moreover, we present an overview of the biogeographical relationships of the Cabo Verde flora and vegetation with the other Macaronesian Islands and northwestern Africa. We discuss how the distribution of plant communities and genetic patterns found among most of the endemic lineages can be related to Africa’s ongoing aridification, exploring the impacts of a process that marks northern Africa from the Late Miocene until the present.
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Englmaier GK, Tesfaye G, Bogutskaya NG. A new species of Enteromius (Actinopterygii, Cyprinidae, Smiliogastrinae) from the Awash River, Ethiopia, and the re-establishment of E. akakianus. Zookeys 2020; 902:107-150. [PMID: 31997886 PMCID: PMC6978609 DOI: 10.3897/zookeys.902.39606] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 12/02/2019] [Indexed: 11/23/2022] Open
Abstract
In the present study, populations of small-sized smiliogastrin barbs with a thickened and serrated last simple dorsal-fin ray distributed in the Main Ethiopian Rift were analysed. An integrated approach combining genetic markers and a variety of morphological methods based on a wide set of characters, including osteology and sensory canals, proved to be very productive for taxonomy in this group of fishes. The results showed that Ethiopian Enteromius species with a serrated dorsal-fin ray are distant from the true E. paludinosus (with E. longicauda as a synonym) and the so-called E. paludinosus complex involves several supposedly valid species with two distinct species occurring in the Main Ethiopian Rift area. A new species, Enteromius yardiensis sp. nov., is described from the Afar Depression in the north-eastern part of the Northern Main Ethiopian Rift. Enteromius akakianus is resurrected as a valid species including populations from the Central Main Ethiopian Rift (basins of lakes Langano, Ziway, and Awasa). No genetic data were available for E. akakianus from its type locality. Enteromius yardiensis sp. nov. is clearly distant from E. akakianus from the Central Main Ethiopian Rift by CO1 and cytb barcodes: pairwise distances between the new species and the Ethiopian congeners were 5.4 % to 11.0 %. Morphologically, the new species most clearly differs from all examined Ethiopian congeners by three specialisations which are unique in the group: the absence of the anterior barbel, the absence of the medial branch of the supraorbital sensory canal, and few, 1-3, commonly two, scale rows between the lateral line and the anus.
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Affiliation(s)
- Gernot K. Englmaier
- University of Graz, Institute of Biology, Universitätsplatz 2, A-8010 Graz, AustriaUniversity of GrazGrazAustria
| | - Genanaw Tesfaye
- National Fisheries and Aquatic Life Research Centre, P.O.Box: 64, Sebeta, EthiopiaNational Fisheries and Aquatic Life Research CentreSebetaEthiopia
| | - Nina G. Bogutskaya
- Natural History Museum Vienna, Burgring 7, A-1010 Vienna, AustriaNatural History Museum ViennaViennaAustria
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Mairal M. Una historia de dos bosques: el ocaso de la vegetación subtropical Afro-Macaronésica. CONSERVACIÓN VEGETAL 2019. [DOI: 10.15366/cv2019.23.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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29
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Branca A, Le Ru B, Calatayud PA, Obonyo J, Musyoka B, Capdevielle-Dulac C, Kaiser-Arnauld L, Silvain JF, Gauthier J, Paillusson C, Gayral P, Herniou EA, Dupas S. Relative Influence of Host, Wolbachia, Geography and Climate on the Genetic Structure of the Sub-saharan Parasitic Wasp Cotesia sesamiae. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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30
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Li Y, Song F, Zhang XN, Lv GH. Phylogeography suggest the Yili Valley being the glacial refuge of the genus Ixiolirion (Amaryllidaceae) in China. SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1612966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yan Li
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
| | - Feng Song
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Xue-Ni Zhang
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
| | - Guang-Hui Lv
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, 830046, China
- Key Laboratory of Oasis Ecology, Xinjiang University, Urumqi, 830046, China
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Mairal M, Caujapé-Castells J, Pellissier L, Jaén-Molina R, Álvarez N, Heuertz M, Sanmartín I. A tale of two forests: ongoing aridification drives population decline and genetic diversity loss at continental scale in Afro-Macaronesian evergreen-forest archipelago endemics. ANNALS OF BOTANY 2018; 122:1005-1017. [PMID: 29905771 PMCID: PMC6266103 DOI: 10.1093/aob/mcy107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/25/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Various studies and conservationist reports have warned about the contraction of the last subtropical Afro-Macaronesian forests. These relict vegetation zones have been restricted to a few oceanic and continental islands around the edges of Africa, due to aridification. Previous studies on relict species have generally focused on glacial effects on narrow endemics; however, little is known about the effects of aridification on the fates of previously widespread subtropical lineages. METHODS Nuclear microsatellites and ecological niche modelling were used to understand observed patterns of genetic diversity in two emblematic species, widely distributed in these ecosystems: Canarina eminii (a palaeoendemic of the eastern Afromontane forests) and Canarina canariensis (a palaeoendemic of the Canarian laurel forests). The software DIYABC was used to test alternative demographic scenarios and an ensemble method was employed to model potential distributions of the selected plants from the end of the deglaciation to the present. KEY RESULTS All the populations assessed experienced a strong and recent population decline, revealing that locally widespread endemisms may also be alarmingly threatened. CONCLUSIONS The detected extinction debt, as well as the extinction spiral to which these populations are subjected, demands urgent conservation measures for the unique, biodiversity-rich ecosystems that they inhabit.
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Affiliation(s)
- Mario Mairal
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo, Madrid, Spain
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico ‘Viera y Clavijo’ – Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico ‘Viera y Clavijo’ – Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Ruth Jaén-Molina
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico ‘Viera y Clavijo’ – Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Nadir Álvarez
- Department of Ecology and Evolution, Institute of Biology, University of Lausanne, Biophore Dorigny, Lausanne, Switzerland
| | | | - Isabel Sanmartín
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo, Madrid, Spain
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Wang P, Yao H, Gilbert KJ, Lu Q, Hao Y, Zhang Z, Wang N. Glaciation-based isolation contributed to speciation in a Palearctic alpine biodiversity hotspot: Evidence from endemic species. Mol Phylogenet Evol 2018; 129:315-324. [PMID: 30218774 DOI: 10.1016/j.ympev.2018.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 07/31/2018] [Accepted: 09/06/2018] [Indexed: 10/28/2022]
Abstract
Organisms are unevenly distributed on earth and the evolutionary drivers of that have puzzled ecologists and evolutionary biologists for over a century. Even though many studies have focused on the mechanisms of unevenly distributed fauna and flora, there remains much to learn about the evolutionary drivers behind biodiversity hotspots. In the Tibetan Plateau and Hengduan Mountains, a biodiversity hotspot in the Palearctic realm, alpine uplift cannot be the driver for recent speciation (<two million years ago), researchers broadly refer to climatic oscillations driven biodiversity, however, the specific individual roles of glaciation and inter-glaciation periods in promoting biodiversity is unclear. The current study focuses on investigating whether recent speciation between two close-related avian species (White eared pheasant, Crossoptilon crossoptilon and Tibetan eared pheasant, C. harmani) was driven by glaciation-based isolation or by dispersal during inter-glaciation. To answer this question, we combined Sanger sequencing and next-generation sequencing technology to estimate population structure, phylogeny, divergence time, demographic history and potential historical distributions for C. crossoptilon and C. harmani, which are endemic to China. We found that the divergence time between these two species and within C. crossoptilon are both during glaciation periods. During glaciation periods, both C. harmani and C. crossoptilon experienced isolated distributions and extreme bottlenecks. The results of this study suggest that glaciation-based isolation contributed to recent speciation in the Tibetan Plateau and Hengduan Mountains, and sheds light on our understanding of the evolutionary mechanisms that contributed to the formation of Palearctic alpine biodiversity hotspots and unevenly distributed species richness pattern.
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Affiliation(s)
- Pengcheng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Hongyan Yao
- School of Nature Conservation, Beijing Forestry University, Beijing 100083, PR China
| | - Kadeem J Gilbert
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Qi Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Yu Hao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, PR China.
| | - Nan Wang
- School of Nature Conservation, Beijing Forestry University, Beijing 100083, PR China.
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Mekonnen A, Rueness EK, Stenseth NC, Fashing PJ, Bekele A, Hernandez-Aguilar RA, Missbach R, Haus T, Zinner D, Roos C. Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands. BMC Evol Biol 2018; 18:106. [PMID: 29986642 PMCID: PMC6038355 DOI: 10.1186/s12862-018-1217-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
Background Species with a restricted geographic distribution, and highly specialized habitat and dietary requirements, are particularly vulnerable to extinction. The Bale monkey (Chlorocebus djamdjamensis) is a little-known arboreal, bamboo-specialist primate endemic to the southern Ethiopian Highlands. While most Bale monkeys inhabit montane forests dominated by bamboo, some occupy forest fragments where bamboo is much less abundant. We used mitochondrial DNA (mtDNA) sequences to analyse the genetic structure and evolutionary history of Bale monkeys covering the majority of their remaining distribution range. We analysed 119 faecal samples from their two main habitats, continuous forest (CF) and fragmented forests (FF), and sequenced 735 bp of the hypervariable region I (HVI) of the control region. We added 12 orthologous sequences from congeneric vervets (C. pygerythrus) and grivets (C. aethiops) as well as animals identified as hybrids, previously collected in southern Ethiopia. Results We found strong genetic differentiation (with no shared mtDNA haplotypes) between Bale monkey populations from CF and FF. Phylogenetic analyses revealed two distinct and highly diverged clades: a Bale monkey clade containing only Bale monkeys from CF and a green monkey clade where Bale monkeys from FF cluster with grivets and vervets. Analyses of demographic history revealed that Bale monkey populations (CF and FF) have had stable population sizes over an extended period, but have all recently experienced population declines. Conclusions The pronounced genetic structure and deep mtDNA divergence between Bale monkey populations inhabiting CF and FF are likely to be the results of hybridization and introgression of the FF population with parapatric Chlorocebus species, in contrast to the CF population, which was most likely not impacted by hybridization. Hybridization in the FF population was probably enhanced by an alteration of the bamboo forest habitat towards a more open woodland habitat, which enabled the parapatric Chlorocebus species to invade the Bale monkey's range and introgress the FF population. We therefore propose that the CF and FF Bale monkey populations should be managed as separate units when developing conservation strategies for this threatened species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1217-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Addisu Mekonnen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway. .,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia.
| | - Eli K Rueness
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - Peter J Fashing
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Anthropology and Environmental Studies Program, California State University Fullerton, Fullerton, CA, 92834, USA
| | - Afework Bekele
- Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - R Adriana Hernandez-Aguilar
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Rose Missbach
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tanja Haus
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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Alcantara S, Ree RH, Mello-Silva R. Accelerated diversification and functional trait evolution in Velloziaceae reveal new insights into the origins of the campos rupestres' exceptional floristic richness. ANNALS OF BOTANY 2018; 122:165-180. [PMID: 29800276 PMCID: PMC6025242 DOI: 10.1093/aob/mcy063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/12/2018] [Indexed: 05/06/2023]
Abstract
Background and Aims The greater diversity of plant clades in the Neotropics compared to their relatives in Africa is a pervasive pattern in biogeography. To better understand the causes of this imbalance, we studied the diversification dynamics of the monocot family Velloziaceae. In addition to being conspicuously richer in the Neotropics compared to the Palaeotropics, many species of Velloziaceae exhibit extreme desiccation tolerance (i.e. 'resurrection' behaviour), and other ecological specializations to life on rocky outcrops, poor sandy soils, open vegetation and seasonally dry climates. Velloziaceae is also ecologically dominant in the campos rupestres, a habitat having exceptionally high plant diversity and endemism in Brazil. Methods We reconstructed a densely sampled time-calibrated molecular phylogeny and used state-dependent and state-independent models to estimate rates of lineage diversification in relation to continent-scale geographical occurrence and functional traits associated with desiccation tolerance and water storage capacity. Key Results Independent shifts to faster diversification occurred within two Neotropical lineages, Vellozia and Barbacenia. The Vellozia radiation was associated with the presence of conspicuous aerial stems, and was followed by decreasing diversification rates during the Oligocene, a time of rising global temperatures and expanding open areas around the world. The Barbacenia radiation was faster and more recent, occurring during the cooling conditions of the Miocene, and associated with the acquisition of aquiferous parenchyma on the leaves. Conclusions High species richness of Velloziaceae in South America has been driven by faster diversification in lineages predominantly occurring in the campos rupestres, putatively by the evolution of adaptive strategies in response to independent climatic events. The radiation of Vellozia in particular might have played a key role in the assembly of the campos rupestres vegetation.
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Affiliation(s)
- Suzana Alcantara
- Departamento de Botânica, Universidade Federal de Santa Catarina, Centro de Ciências Biológicas, Campus Universitário, Trindade, Florianópolis, SC, Brazil
- Departamento de Botânica, Universidade de São Paulo, São Paulo, SP, Brazil
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Richard H Ree
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Renato Mello-Silva
- Departamento de Botânica, Universidade de São Paulo, São Paulo, SP, Brazil
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Wereszczuk A, Leblois R, Zalewski A. Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats. BMC Ecol 2017; 17:46. [PMID: 29273026 PMCID: PMC5741947 DOI: 10.1186/s12898-017-0156-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/13/2017] [Indexed: 11/10/2022] Open
Abstract
Background Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species’ ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations. Results We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten. Conclusions Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades. Electronic supplementary material The online version of this article (10.1186/s12898-017-0156-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Wereszczuk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland.
| | - Raphaël Leblois
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France.,Institut de Biologie Computationnelle, University Montpellier, Montpellier, France
| | - Andrzej Zalewski
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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