201
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Tougard C, Vukić J, Ahnelt H, Buj I, Kovačić M, Moro GA, Tutman P, Šanda R. Quaternary climatic cycles promoted (re)colonization and diversification events in Adriatic sand gobies. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Jasna Vukić
- Department of Ecology Faculty of Science Charles University Prague Czech Republic
| | - Harald Ahnelt
- Department of Evolutionary Biology Faculty of Life Sciences University of Vienna Vienna Austria
- First Zoological Department Natural History Museum in Vienna Vienna Austria
| | - Ivana Buj
- Department of Zoology Faculty of Science University of Zagreb Zagreb Croatia
| | | | | | - Pero Tutman
- Laboratory for Ichthyology and Coastal Fisheries Institute of Oceanography and Fisheries Split Croatia
| | - Radek Šanda
- Department of Zoology National Museum Prague Czech Republic
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202
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Mohammadi Z, Ghorbani F, Kami HG, Khajeh A, Olsson U. Molecular Phylogeny of the Subgenus Karstomys Reveals Genetic Signature of Post-Glacial Colonization of Apodemus mystacinus (Rodentia: Muridae) in the Zagros Mountains from Different Refugia. Zoolog Sci 2021; 38:72-81. [PMID: 33639721 DOI: 10.2108/zs200065] [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] [Received: 04/26/2020] [Accepted: 09/10/2020] [Indexed: 11/17/2022]
Abstract
Eastern broad-toothed field mouse, Apodemus mystacinus, is a rocky habitat dwelling rodent distributed in Asia Minor, the Levant, the Caucasus, and the Zagros Mountains. In this study, we investigated the phylogenetic relationship between different populations of A. mystacinus throughout its range, based on the mitochondrial cytb marker. Phylogenetic analyses revealed the existence of five separately evolving lineages within A. mystacinus, of which two previously unrecognized lineages were identified in the Zagros Mountains and the Levant. Divergence between two major clades of the subgenus Karstomys, corresponding to A. mystacinus and Apodemus epimelas, is inferred to coincide with the Messinian Salinity Crisis (Late Miocene), whereas the splits between major lineages of A. mystacinus are inferred to have occurred during the Pleistocene. Colonization of the Zagros may have occurred from different refugia via eastward migration of the Turkish population and then again by a more recent colonization from the Caucasus, after reopening of the land corridor between the Caucasus and the Zagros Mountains during the Holocene drought.
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Affiliation(s)
- Zeinolabedin Mohammadi
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran, .,Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177948974, Iran
| | - Fatemeh Ghorbani
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran
| | - Haji Gholi Kami
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan, 39361-79142, Golestan, Iran
| | - Asghar Khajeh
- Department of Crop Productions Technology, Faculty of Agriculture, Higher Educational Complex of Saravan, Saravan 99516-34145, Iran
| | - Urban Olsson
- University of Gothenburg, Department of Biology and Environmental Sciences, Systematics and Biodiversity, SE-405 30 Göteborg, Sweden.,Gothenburg Global Biodiversity Centre, SE-405 30 Göteborg, Sweden
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203
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Bachmann L, Cabrera AA, Heide-Jørgensen MP, Shpak OV, Lydersen C, Wiig Ø, Kovacs KM. Mitogenomics and the genetic differentiation of contemporary Balaena mysticetus (Cetacea) from Svalbard. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlaa082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Full mitochondrial genomes were assembled for 12 recently sampled animals from the Svalbard bowhead whale (Balaena mysticetus) stock via high-throughput sequencing data, facilitating analysis of the demographic history of the population for the first time. The Svalbard population has retained noticeable amounts of mitochondrial genome diversity despite extreme historical harvest levels. Haplotype and nucleotide diversities were similar to those estimated earlier for other bowhead whale populations. The reconstructed demographic history was in accordance with a boom–bust scenario, combining a slight Pleistocene population growth 25 000–35 000 years ago and a Holocene decline. Employing a mutation rate of 3.418 × 10–8 substitutions per site per year, the time to the most recent common ancestor for the mitochondrial genomes of the contemporary Svalbard bowhead whales was estimated to be 68 782 (54 353–83 216) years before the present. Based on 370 bp fragments of the D-loop region, significant genetic differentiation was detected between all extant bowhead whale populations across the circumpolar Arctic. Thus, the Svalbard bowhead whales can be regarded as a population with its own genetic legacy.
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Affiliation(s)
- Lutz Bachmann
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Blindern, 0318 Oslo, Norway
| | - Andrea A Cabrera
- Marine Evolution and Conservation, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, AG Groningen, The Netherlands
| | | | - Olga V Shpak
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, 33 Leninsky Prospect, Moscow, Russia
| | | | - Øystein Wiig
- Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, Blindern, 0318 Oslo, Norway
| | - Kit M Kovacs
- Norwegian Polar Institute, Fram Centre, Langnes, 9296 Tromsø, Norway
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204
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Montes E, Kraus F, Chergui B, Pleguezuelos JM. Collapse of the endemic lizard Podarcis pityusensis on the island of Ibiza mediated by an invasive snake. Curr Zool 2021; 68:295-303. [PMID: 35592342 PMCID: PMC9113342 DOI: 10.1093/cz/zoab022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/07/2021] [Indexed: 11/24/2022] Open
Abstract
The invasive snake Hemorrhois hippocrepis colonized the island of Ibiza (Balearic Islands) in 2003 as stowaways inside trunks of olive trees imported for gardening. It has quickly spread since 2010, posing a threat to the island’s only remaining endemic vertebrate, the Ibiza wall lizard Podarcis pityusensis. We map the yearly expansion rate of the snake and estimate via transect surveys how severely it affects the distribution and abundance of the endemic lizard. As well, we surveyed 9 of 30 small lizard populations on islets surrounding Ibiza that have been isolated since the Last Glacial Maximum. Snakes had invaded 49% of Ibiza’s land area by 2018, and censuses show a critical contrast in lizard abundance between areas with and without snakes; almost all censuses in areas without snakes show lizard presence whereas nearly all censuses in areas with H. hippocrepis lack lizard sightings. Moreover, at least one subspecies previously thriving on one of the offshore islets has become extinct, and there have been several snakes recorded swimming between Ibiza and the surrounding islets. Therefore, lizard populations have been dramatically reduced or have vanished within the range of the snake, and our results quantitatively support upgrading this species’ threat level for extinction. This study can inform to programs to manage invasive snake populations and to conservation actions to recover the endemic lizard.
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Affiliation(s)
- Elba Montes
- Department of Zoology, Faculty of Biological Sciences, University of Valencia, c/Dr. Moliner, 50, Burjassot, E-46100 Valencia, Spain
| | - Fred Kraus
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brahim Chergui
- Laboratoire Ecologie, Systématique, Conservation de la Biodiversité, Faculté des Sciences de Tétouan, Université Abdelmalek Essaâdi, BP 2121 El M’Hannech, Tétouan, Morocco
| | - Juan M Pleguezuelos
- Department of Zoology, Faculty of Sciences, Granada University, Granada E-18071, Spain
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205
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Gu Z, Pan S, Lin Z, Hu L, Dai X, Chang J, Xue Y, Su H, Long J, Sun M, Ganusevich S, Sokolov V, Sokolov A, Pokrovsky I, Ji F, Bruford MW, Dixon A, Zhan X. Climate-driven flyway changes and memory-based long-distance migration. Nature 2021; 591:259-264. [PMID: 33658718 DOI: 10.1038/s41586-021-03265-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
Millions of migratory birds occupy seasonally favourable breeding grounds in the Arctic1, but we know little about the formation, maintenance and future of the migration routes of Arctic birds and the genetic determinants of migratory distance. Here we established a continental-scale migration system that used satellite tracking to follow 56 peregrine falcons (Falco peregrinus) from 6 populations that breed in the Eurasian Arctic, and resequenced 35 genomes from 4 of these populations. The breeding populations used five migration routes across Eurasia, which were probably formed by longitudinal and latitudinal shifts in their breeding grounds during the transition from the Last Glacial Maximum to the Holocene epoch. Contemporary environmental divergence between the routes appears to maintain their distinctiveness. We found that the gene ADCY8 is associated with population-level differences in migratory distance. We investigated the regulatory mechanism of this gene, and found that long-term memory was the most likely selective agent for divergence in ADCY8 among the peregrine populations. Global warming is predicted to influence migration strategies and diminish the breeding ranges of peregrine populations of the Eurasian Arctic. Harnessing ecological interactions and evolutionary processes to study climate-driven changes in migration can facilitate the conservation of migratory birds.
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Affiliation(s)
- Zhongru Gu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shengkai Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
| | - Zhenzhen Lin
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
| | - Li Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Han Su
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Juan Long
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Mengru Sun
- University of the Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | | | - Vasiliy Sokolov
- Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, Ekaterinburg, Russia
| | - Aleksandr Sokolov
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, Labytnangi, Russia
| | - Ivan Pokrovsky
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, Labytnangi, Russia.,Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Laboratory of Ornithology, Institute of Biological Problems of the North FEB RAS, Magadan, Russia
| | - Fen Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Michael W Bruford
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, UK
| | - Andrew Dixon
- Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China.,Emirates Falconers' Club, Abu Dhabi, United Arab Emirates.,Reneco International Wildlife Consultants, Abu Dhabi, United Arab Emirates.,International Wildlife Consultants, Carmarthen, UK
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China. .,University of the Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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206
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A geo-chemo-mechanical study of a highly polluted marine system (Taranto, Italy) for the enhancement of the conceptual site model. Sci Rep 2021; 11:4017. [PMID: 33597633 PMCID: PMC7889905 DOI: 10.1038/s41598-021-82879-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/21/2021] [Indexed: 11/09/2022] Open
Abstract
The paper presents the results of the analysis of the geo-chemo-mechanical data gathered through an innovative multidisciplinary investigation campaign in the Mar Piccolo basin, a heavily polluted marine bay aside the town of Taranto (Southern Italy). The basin is part of an area declared at high environmental risk by the Italian government. The cutting-edge approach to the environmental characterization of the site was promoted by the Special Commissioner for urgent measures of reclamation, environmental improvements and redevelopment of Taranto and involved experts from several research fields, who cooperated to gather a new insight into the origin, distribution, mobility and fate of the contaminants within the basin. The investigation campaign was designed to implement advanced research methodologies and testing strategies. Differently from traditional investigation campaigns, aimed solely at the assessment of the contamination state within sediments lying in the top layers, the new campaign provided an interpretation of the geo-chemo-mechanical properties and state of the sediments forming the deposit at the seafloor. The integrated, multidisciplinary and holistic approach, that considered geotechnical engineering, electrical and electronical engineering, geological, sedimentological, mineralogical, hydraulic engineering, hydrological, chemical, geochemical, biological fields, supported a comprehensive understanding of the influence of the contamination on the hydro-mechanical properties of the sediments, which need to be accounted for in the selection and design of the risk mitigation measures. The findings of the research represent the input ingredients of the conceptual model of the site, premise to model the evolutionary contamination scenarios within the basin, of guidance for the environmental risk management. The study testifies the importance of the cooperative approach among researchers of different fields to fulfil the interpretation of complex polluted eco-systems.
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207
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Climate change, not human population growth, correlates with Late Quaternary megafauna declines in North America. Nat Commun 2021; 12:965. [PMID: 33594059 PMCID: PMC7886903 DOI: 10.1038/s41467-021-21201-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
The disappearance of many North American megafauna at the end of the Pleistocene is a contentious topic. While the proposed causes for megafaunal extinction are varied, most researchers fall into three broad camps emphasizing human overhunting, climate change, or some combination of the two. Understanding the cause of megafaunal extinctions requires the analysis of through-time relationships between climate change and megafauna and human population dynamics. To do so, many researchers have used summed probability density functions (SPDFs) as a proxy for through-time fluctuations in human and megafauna population sizes. SPDFs, however, conflate process variation with the chronological uncertainty inherent in radiocarbon dates. Recently, a new Bayesian regression technique was developed that overcomes this problem-Radiocarbon-dated Event-Count (REC) Modelling. Here we employ REC models to test whether declines in North American megafauna species could be best explained by climate changes, increases in human population densities, or both, using the largest available database of megafauna and human radiocarbon dates. Our results suggest that there is currently no evidence for a persistent through-time relationship between human and megafauna population levels in North America. There is, however, evidence that decreases in global temperature correlated with megafauna population declines.
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208
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Hsu MH, Lin JW, Liao CP, Hsu JY, Huang WS. Trans-marine dispersal inferred from the saltwater tolerance of lizards from Taiwan. PLoS One 2021; 16:e0247009. [PMID: 33577597 PMCID: PMC7880474 DOI: 10.1371/journal.pone.0247009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/01/2021] [Indexed: 11/19/2022] Open
Abstract
Dehydration and hypersalinity challenge non-marine organisms crossing the ocean. The rate of water loss and saltwater tolerance thus determine the ability to disperse over sea and further influence species distribution. Surprisingly, this association between physiology and ecology is rarely investigated in terrestrial vertebrates. Here we conducted immersion experiments to individuals and eggs of six lizard species differently distributed across Taiwan and the adjacent islands to understand if the physiological responses reflect the geographical distribution. We found that Plestiodon elegans had the highest rate of water loss and the lowest saltwater tolerance, whereas Eutropis longicaudata and E. multifasciata showed the lowest rate of water loss and the highest saltwater tolerance. Diploderma swinhonis, Hemidactylus frenatus, and Anolis sagrei had medium measurements. For the eggs, only the rigid-shelled eggs of H. frenatus were incubated successfully after treatments. While, the parchment-shelled eggs of E. longicaudata and D. swinhonis lost or gained water dramatically in the immersions without any successful incubation. Combined with the historical geology of the islands and the origin areas of each species, the inferences of the results largely explain the current distribution of these lizards across Taiwan and the adjacent islands, pioneerly showing the association between physiological capability and species distribution.
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Affiliation(s)
- Min-Hao Hsu
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Jhan-Wei Lin
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Chen-Pan Liao
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
- Department of Life Science, Tunghai University, Taichung, Taiwan
| | - Jung-Ya Hsu
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
| | - Wen-San Huang
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Department of Life Science, Tunghai University, Taichung, Taiwan
- * E-mail:
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209
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Ecological and spatial patterns associated with diversification of South American Physaria (Brassicaceae) through the general concept of species. ORG DIVERS EVOL 2021. [DOI: 10.1007/s13127-021-00486-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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210
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Avila-Cervantes J, Arias C, Venegas-Anaya M, Vargas M, Larsson HCE, McMillan WO. Effect of the Central American Isthmus on gene flow and divergence of the American crocodile (Crocodylus acutus). Evolution 2021; 75:245-259. [PMID: 33314048 DOI: 10.1111/evo.14139] [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] [Received: 03/06/2020] [Revised: 11/13/2020] [Accepted: 11/25/2020] [Indexed: 01/22/2023]
Abstract
The final formation of the Central American Isthmus (CAI) about 3.5 million years ago altered global ocean circulation, connected North and South America terrestrial biotas, and established the Caribbean Sea. The nature of this event creates a natural scenario to test vicariance, divergence, and speciation by allopatry. Studies have shown the effect of the CAI on marine and terrestrial species, but none have examined a large-bodied amphibious taxon. We used RAD sequencing on populations of the American crocodile (Crocodylus acutus) to study the genomic variation of C. acutus on both sides of the CAI, infer its demographic history, and measure the effect of the opening of the Panama Canal. Our results showed three genomic clusters: (1) Caribbean and the Panama Canal, (2) Pacific coast, and (3) Coiba island. The estimated divergence times between the Caribbean and Pacific populations are about 20,000 years ago, which is younger than the formation of the CAI, coinciding with the Last Glacial Maximum. We hypothesize the glacial/interglacial cycles facilitated gene flow between the Caribbean and Pacific crocodile populations after the formation of the CAI, masking any genomic divergence the CAI may have caused. There is no evidence of gene flow associated with the opening of the Panama Canal.
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Affiliation(s)
- Jose Avila-Cervantes
- McGill University, Redpath Museum 859 Sherbrooke Street West, Montreal, Quebec, H3A 0C4, Canada
| | - Carlos Arias
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
| | - Miryam Venegas-Anaya
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
| | - Marta Vargas
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
| | - Hans C E Larsson
- McGill University, Redpath Museum 859 Sherbrooke Street West, Montreal, Quebec, H3A 0C4, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Roosevelt Ave. Tupper Bldg. 401, Panama, Rep. of Panama
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211
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Impact of Past and Future Climate Change on the Potential Distribution of an Endangered Montane Shrub Lonicera oblata and Its Conservation Implications. FORESTS 2021. [DOI: 10.3390/f12020125] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Climate change is an important driver of biodiversity patterns and species distributions, understanding how organisms respond to climate change will shed light on the conservation of endangered species. In this study, we modeled the distributional dynamics of a critically endangered montane shrub Lonicera oblata in response to climate change under different periods by building a comprehensive habitat suitability model considering the effects of soil and vegetation conditions. Our results indicated that the current suitable habitats for L. oblata are located scarcely in North China. Historical modeling indicated that L. oblata achieved its maximum potential distribution in the last interglacial period which covered southwest China, while its distribution area decreased for almost 50% during the last glacial maximum. It further contracted during the middle Holocene to a distribution resembling the current pattern. Future modeling showed that the suitable habitats of L. oblata contracted dramatically, and populations were fragmentedly distributed in these areas. As a whole, the distribution of L. oblata showed significant migration northward in latitude but no altitudinal shift. Several mountains in North China may provide future stable climatic areas for L. oblata, particularly, the intersections between the Taihang and Yan mountains. Our study strongly suggested that the endangered montane shrub L. oblata are sensitive to climate change, and the results provide new insights into the conservation of it and other endangered species.
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212
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Silva CNS, Murphy NP, Bell JJ, Green BS, Duhamel G, Cockcroft AC, Hernández CE, Strugnell JM. Global drivers of recent diversification in a marine species complex. Mol Ecol 2021; 30:1223-1236. [PMID: 33342039 DOI: 10.1111/mec.15780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 11/03/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Investigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence during speciation. The processes influencing species diversification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome-wide divergence, introgression patterns and inferred demographic history between species pairs of all six extant rock lobster species (Jasus spp.), which have a long larval duration of up to two years and have populated continental shelf and seamount habitats around the globe at approximately 40o S. Genetic differentiation patterns reflected geographic isolation and the environment (i.e. habitat structure). Eastern Pacific species (J. caveorum and J. frontalis) were geographically more distant and genetically more differentiated from the remaining four species. Species associated with continental shelf habitats shared a common ancestry, but are geographically distant from one another. Similarly, species associated with island/seamount habitats in the Atlantic and Indian Oceans shared a common ancestry, but are also geographically distant. Benthic temperature was the environmental variable that explained most of the genetic differentiation (FST ), while controlling for the effects of geographic distance. Eastern Pacific species retained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa, and seamounts in the Indian and Atlantic oceans, included events of introgression after secondary contact. Our results reveal important effects of habitat and demographic processes on the recent divergence of species within the genus Jasus, providing one of the first empirical studies of genome-wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.
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Affiliation(s)
- Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Nicholas P Murphy
- Department of Ecology, Environment & Evolution, La Trobe University, Melbourne, Vic, Australia
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Bridget S Green
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Guy Duhamel
- Département Adaptations du Vivant, BOREA, MNHN, Paris, France
| | - Andrew C Cockcroft
- Department of Agriculture, Forestry and Fisheries, Cape Town, South Africa
| | - Cristián E Hernández
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Universidad Católica de Santa María, Arequipa, Perú
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Department of Ecology, Environment & Evolution, La Trobe University, Melbourne, Vic, Australia
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213
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Gebbie G. Combining Modern and Paleoceanographic Perspectives on Ocean Heat Uptake. ANNUAL REVIEW OF MARINE SCIENCE 2021; 13:255-281. [PMID: 32928022 DOI: 10.1146/annurev-marine-010419-010844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Monitoring Earth's energy imbalance requires monitoring changes in the heat content of the ocean. Recent observational estimates indicate that ocean heat uptake is accelerating in the twenty-first century. Examination of estimates of ocean heat uptake over the industrial era, the Common Era of the last 2,000 years, and the period since the Last Glacial Maximum, 20,000 years ago, permits a wide perspective on modern-day warming rates. In addition, this longer-term focus illustrates how the dynamics of the deep ocean and the cryosphere were active in the past and are still active today. The large climatic shifts that started with the melting of the great ice sheets have involved significant ocean heat uptake that was sustained over centuries and millennia, and modern-ocean heat content changes are small by comparison.
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Affiliation(s)
- Geoffrey Gebbie
- Department of Physical Oceanography, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA;
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214
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Ledford J, Derkarabetian S, Ribera C, Starrett J, Bond JE, Griswold C, Hedin M. Phylogenomics and biogeography of leptonetid spiders (Araneae:Leptonetidae). INVERTEBR SYST 2021. [DOI: 10.1071/is20065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Leptonetidae are rarely encountered spiders, usually associated with caves and mesic habitats, and are disjunctly distributed across the Holarctic. Data from ultraconserved elements (UCEs) were used in concatenated and coalescent-based analyses to estimate the phylogenetic history of the family. Our taxon sample included close outgroups, and 90% of described leptonetid genera, with denser sampling in North America and Mediterranean Europe. Two data matrices were assembled and analysed; the first ‘relaxed’ matrix includes the maximum number of loci and the second ‘strict’ matrix is limited to the same set of core orthologs but with flanking introns mostly removed. A molecular dating analysis incorporating fossil and geological calibration points was used to estimate divergence times, and dispersal–extinction–cladogenesis analysis (DEC) was used to infer ancestral distributions. Analysis of both data matrices using maximum likelihood and coalescent-based methods supports the monophyly of Archoleptonetinae and Leptonetinae. However, relationships among Archoleptonetinae, Leptonetinae, and Austrochiloidea are poorly supported and remain unresolved. Archoleptonetinae is elevated to family rank Archoleptonetidae (new rank) and Leptonetidae (new status) is restricted to include only members of the subfamily Leptonetinae; a taxonomic review with morphological diagnoses is provided for both families. Four well supported lineages within Leptonetidae (new status) are recovered: (1) the Calileptoneta group, (2) the Leptoneta group, (3) the Paraleptoneta group, and (4) the Protoleptoneta group. Most genera within Leptonetidae are monophyletic, although Barusia, Cataleptoneta, and Leptoneta include misplaced species and require taxonomic revision. The origin of Archoleptonetidae (new rank), Leptonetidae, and the four main lineages within Leptonetidae date to the Cretaceous. DEC analysis infers the Leptoneta and Paraleptoneta groups to have ancestral distributions restricted to Mediterranean Europe, whereas the Calileptoneta and Protoleptoneta groups include genera with ancestral distributions spanning eastern and western North America, Mediterranean Europe, and east Asia. Based on a combination of biology, estimated divergence times, and inferred ancestral distributions we hypothesise that Leptonetidae was once widespread across the Holarctic and their present distributions are largely the result of vicariance. Given the wide disjunctions between taxa, we broadly interpret the family as a Holarctic relict fauna and hypothesise that they were once part of the Boreotropical forest ecosystem.
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215
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Sarabia C, vonHoldt B, Larrasoaña JC, Uríos V, Leonard JA. Pleistocene climate fluctuations drove demographic history of African golden wolves (Canis lupaster). Mol Ecol 2020; 30:6101-6120. [PMID: 33372365 DOI: 10.1111/mec.15784] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022]
Abstract
Pleistocene climate change impacted entire ecosystems throughout the world. In the northern hemisphere, the distribution of Arctic species expanded during glacial periods, while more temperate and mesic species contracted into climatic refugia, where isolation drove genetic divergence. Cycles of local cooling and warming in the Sahara region of northern Africa caused repeated contractions and expansions of savannah-like environments which connected mesic species isolated in refugia during interglacial times, possibly driving population expansions and contractions; divergence and geneflow in the associated fauna. Here, we use whole genome sequences of African golden wolves (Canis lupaster), a generalist mesopredator with a wide distribution in northern Africa to estimate their demographic history and past episodes of geneflow. We detect a correlation between divergence times and cycles of increased aridity-associated Pleistocene glacial cycles. A complex demographic history with responses to local climate change in different lineages was found, including a relict lineage north of the High Atlas Mountains of Morocco that has been isolated for more than 18,000 years, possibly a distinct ecotype.
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Affiliation(s)
- Carlos Sarabia
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC, Seville, Spain
| | - Bridgett vonHoldt
- Faculty of Ecology and Evolutionary Biology, University of Princeton, Princeton, NJ, USA
| | | | - Vicente Uríos
- Vertebrate Zoology Research Group, University of Alicante, Alicante, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC, Seville, Spain
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216
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Doellman MM, Saint Jean G, Egan SP, Powell THQ, Hood GR, Schuler H, Bruzzese DJ, Glover MM, Smith JJ, Yee WL, Goughnour R, Rull J, Aluja M, Feder JL. Evidence for spatial clines and mixed geographic modes of speciation for North American cherry-infesting Rhagoletis (Diptera: Tephritidae) flies. Ecol Evol 2020; 10:12727-12744. [PMID: 33304490 PMCID: PMC7713972 DOI: 10.1002/ece3.6667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/11/2020] [Accepted: 07/20/2020] [Indexed: 01/23/2023] Open
Abstract
An important criterion for understanding speciation is the geographic context of population divergence. Three major modes of allopatric, parapatric, and sympatric speciation define the extent of spatial overlap and gene flow between diverging populations. However, mixed modes of speciation are also possible, whereby populations experience periods of allopatry, parapatry, and/or sympatry at different times as they diverge. Here, we report clinal patterns of variation for 21 nuclear-encoded microsatellites and a wing spot phenotype for cherry-infesting Rhagoletis (Diptera: Tephritidae) across North America consistent with these flies having initially diverged in parapatry followed by a period of allopatric differentiation in the early Holocene. However, mitochondrial DNA (mtDNA) displays a different pattern; cherry flies at the ends of the clines in the eastern USA and Pacific Northwest share identical haplotypes, while centrally located populations in the southwestern USA and Mexico possess a different haplotype. We hypothesize that the mitochondrial difference could be due to lineage sorting but more likely reflects a selective sweep of a favorable mtDNA variant or the spread of an endosymbiont. The estimated divergence time for mtDNA suggests possible past allopatry, secondary contact, and subsequent isolation between USA and Mexican fly populations initiated before the Wisconsin glaciation. Thus, the current genetics of cherry flies may involve different mixed modes of divergence occurring in different portions of the fly's range. We discuss the need for additional DNA sequencing and quantification of prezygotic and postzygotic reproductive isolation to verify the multiple mixed-mode hypothesis for cherry flies and draw parallels from other systems to assess the generality that speciation may commonly involve complex biogeographies of varying combinations of allopatric, parapatric, and sympatric divergence.
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Affiliation(s)
- Meredith M. Doellman
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
- Present address:
Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
| | - Gilbert Saint Jean
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Scott P. Egan
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
- Advanced Diagnostics & TherapeuticsUniversity of Notre DameNotre DameIndianaUSA
- Department of BioSciencesRice UniversityHoustonTexasUSA
| | - Thomas H. Q. Powell
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
- Department of Biological SciencesBinghamton UniversityBinghamtonNew YorkUSA
| | - Glen R. Hood
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
- Department of Biological SciencesWayne State UniversityDetroitMichiganUSA
| | - Hannes Schuler
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
- Faculty of Science and TechnologyFree University of Bozen‐BolzanoBozenItaly
| | - Daniel J. Bruzzese
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - Mary M. Glover
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
| | - James J. Smith
- Department of EntomologyLyman Briggs CollegeMichigan State UniversityEast LansingMichiganUSA
| | - Wee L. Yee
- Temperate Tree Fruit & Vegetable Research UnitUnited States Department of Agriculture, Agricultural Research ServiceWapatoWashingtonUSA
| | | | - Juan Rull
- Instituto de Ecología, A.C.XalapaMéxico
- LIEMEN‐División Control Biológico de PlagasPROIMI Biotecnología‐CONICETTucumánArgentina
| | | | - Jeffrey L. Feder
- Department of Biological SciencesUniversity of Notre DameNotre DameIndianaUSA
- Advanced Diagnostics & TherapeuticsUniversity of Notre DameNotre DameIndianaUSA
- Environmental Change InitiativeUniversity of Notre DameNotre DameIndianaUSA
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217
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Antarctic ice dynamics amplified by Northern Hemisphere sea-level forcing. Nature 2020; 587:600-604. [PMID: 33239798 DOI: 10.1038/s41586-020-2916-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 09/16/2020] [Indexed: 11/09/2022]
Abstract
Sea-level rise due to ice loss in the Northern Hemisphere in response to insolation and greenhouse gas forcing is thought to have caused grounding-line retreat of marine-based sectors of the Antarctic Ice Sheet (AIS)1-3. Such interhemispheric sea-level forcing may explain the synchronous evolution of global ice sheets over ice-age cycles. Recent studies that indicate that the AIS experienced substantial millennial-scale variability during and after the last deglaciation4-7 (roughly 20,000 to 9,000 years ago) provide further evidence of this sea-level forcing. However, global sea-level change as a result of mass loss from ice sheets is strongly nonuniform, owing to gravitational, deformational and Earth rotational effects8, suggesting that the response of AIS grounding lines to Northern Hemisphere sea-level forcing is more complicated than previously modelled1,2,6. Here, using an ice-sheet model coupled to a global sea-level model, we show that AIS dynamics are amplified by Northern Hemisphere sea-level forcing. As a result of this interhemispheric interaction, a large or rapid Northern Hemisphere sea-level forcing enhances grounding-line advance and associated mass gain of the AIS during glaciation, and grounding-line retreat and mass loss during deglaciation. Relative to models without these interactions, the inclusion of Northern Hemisphere sea-level forcing in our model increases the volume of the AIS during the Last Glacial Maximum (about 26,000 to 20,000 years ago), triggers an earlier retreat of the grounding line and leads to millennial-scale variability throughout the last deglaciation. These findings are consistent with geologic reconstructions of the extent of the AIS during the Last Glacial Maximum and subsequent ice-sheet retreat, and with relative sea-level change in Antarctica3-7,9,10.
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218
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Kirchner S, Sattmann H, Haring E, Victor R, Kruckenhauser L. Hidden diversity—Delimitation of cryptic species and phylogeography of the cyprinid
Garra
species complex in Northern Oman. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Sandra Kirchner
- Department of Evolutionary Biology University of Vienna Vienna Austria
- Central Research Laboratories Natural History Museum Vienna Vienna Austria
| | - Helmut Sattmann
- Third Zoological Department Natural History Museum Vienna Vienna Austria
| | - Elisabeth Haring
- Department of Evolutionary Biology University of Vienna Vienna Austria
- Central Research Laboratories Natural History Museum Vienna Vienna Austria
| | | | - Luise Kruckenhauser
- Department of Evolutionary Biology University of Vienna Vienna Austria
- Central Research Laboratories Natural History Museum Vienna Vienna Austria
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219
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Matthews T, Perry LB, Lane TP, Elmore AC, Khadka A, Aryal D, Shrestha D, Tuladhar S, Baidya SK, Gajurel A, Potocki M, Mayewski PA. Into Thick(er) Air? Oxygen Availability at Humans' Physiological Frontier on Mount Everest. iScience 2020; 23:101718. [PMID: 33376965 PMCID: PMC7756134 DOI: 10.1016/j.isci.2020.101718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 11/25/2022] Open
Abstract
Global audiences are captivated by climbers pushing themselves to the limits in the hypoxic environment of Mount Everest. However, air pressure sets oxygen abundance, meaning it varies with the weather and climate warming. This presents safety issues for mountaineers but also an opportunity for public engagement around climate change. Here we blend new observations from Everest with ERA5 reanalysis (1979-2019) and climate model results to address both perspectives. We find that plausible warming could generate subtle but physiologically relevant changes in summit oxygen availability, including an almost 5% increase in annual minimum VO2 max for 2°C warming since pre-industrial. In the current climate we find evidence of swings in pressure sufficient to change Everest's apparent elevation by almost 750 m. Winter pressures can also plunge lower than previously reported, highlighting the importance of air pressure forecasts for the safety of those trying to push the physiological frontier on Mt. Everest.
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Affiliation(s)
- Tom Matthews
- Department of Geography & Environment, Loughborough University, Loughborough, UK
| | - L Baker Perry
- Department of Geography & Planning, Appalachian State University, Boone, NC, USA
| | - Timothy P Lane
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | | | - Arbindra Khadka
- Central Department of Hydrology & Meteorology, Tribhuvan University, Kathmandu, Nepal.,International Centre for Integrated Mountain Development, Lalitpur, Nepal
| | - Deepak Aryal
- Central Department of Hydrology & Meteorology, Tribhuvan University, Kathmandu, Nepal
| | - Dibas Shrestha
- Central Department of Hydrology & Meteorology, Tribhuvan University, Kathmandu, Nepal
| | | | | | - Ananta Gajurel
- Department of Geology, Tribhuvan University, Kathmandu, Nepal
| | - Mariusz Potocki
- Climate Change Institute, University of Maine, Orono, ME, USA.,School of Earth and Climate Sciences, University of Maine, Orono, ME, USA
| | - Paul A Mayewski
- Climate Change Institute, University of Maine, Orono, ME, USA
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220
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Hartmann FE, Rodríguez de la Vega RC, Gladieux P, Ma WJ, Hood ME, Giraud T. Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence. Mol Biol Evol 2020; 37:668-682. [PMID: 31651949 PMCID: PMC7038665 DOI: 10.1093/molbev/msz252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nonrecombining sex chromosomes are widely found to be more differentiated than autosomes among closely related species, due to smaller effective population size and/or to a disproportionally large-X effect in reproductive isolation. Although fungal mating-type chromosomes can also display large nonrecombining regions, their levels of differentiation compared with autosomes have been little studied. Anther-smut fungi from the Microbotryum genus are castrating pathogens of Caryophyllaceae plants with largely nonrecombining mating-type chromosomes. Using whole genome sequences of 40 fungal strains, we quantified genetic differentiation among strains isolated from the geographically overlapping North American species and subspecies of Silene virginica and S. caroliniana. We inferred that gene flow likely occurred at the early stages of divergence and then completely stopped. We identified large autosomal genomic regions with chromosomal inversions, with higher genetic divergence than the rest of the genomes and highly enriched in selective sweeps, supporting a role of rearrangements in preventing gene flow in genomic regions involved in ecological divergence. Unexpectedly, the nonrecombining mating-type chromosomes showed lower divergence than autosomes due to higher gene flow, which may be promoted by adaptive introgressions of less degenerated mating-type chromosomes. The fact that both mating-type chromosomes are always heterozygous and nonrecombining may explain such patterns that oppose to those found for XY or ZW sex chromosomes. The specific features of mating-type chromosomes may also apply to the UV sex chromosomes determining sexes at the haploid stage in algae and bryophytes and may help test general hypotheses on the evolutionary specificities of sex-related chromosomes.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Wen-Juan Ma
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Michael E Hood
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
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221
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Willi Y, Fracassetti M, Bachmann O, Van Buskirk J. Demographic Processes Linked to Genetic Diversity and Positive Selection across a Species' Range. PLANT COMMUNICATIONS 2020; 1:100111. [PMID: 33367266 PMCID: PMC7747977 DOI: 10.1016/j.xplc.2020.100111] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/27/2020] [Accepted: 09/09/2020] [Indexed: 06/12/2023]
Abstract
Demography determines the strength of genetic drift, which generally reduces genetic variation and the efficacy of selection. Here, we disentangled the importance of demographic processes at a local scale (census size and mating system) and at a species-range scale (old split between population clusters, recolonization after the last glaciation cycle, and admixture) in determining within-population genomic diversity and genomic signatures of positive selection. Analyses were based on re-sequence data from 52 populations of North American Arabidopsis lyrata collected across its entire distribution. The mating system and range dynamics since the last glaciation cycle explained around 60% of the variation in genomic diversity among populations and 52% of the variation in the signature of positive selection. Diversity was lowest in selfing compared with outcrossing populations and in areas further away from glacial refugia. In parallel, reduced positive selection was found in selfing populations and in populations with a longer route of postglacial range expansion. The signature of positive selection was also reduced in populations without admixture. We conclude that recent range expansion can have a profound influence on diversity in coding and non-coding DNA, similar in magnitude to the shift toward selfing. Distribution limits may in fact be caused by reduced effective population size and compromised positive selection in recently colonized parts of the range.
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Affiliation(s)
- Yvonne Willi
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056 Basel, Switzerland
| | - Marco Fracassetti
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056 Basel, Switzerland
| | - Olivier Bachmann
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056 Basel, Switzerland
| | - Josh Van Buskirk
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, CH-8057 Zürich, Switzerland
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222
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Teschler-Nicola M, Fernandes D, Händel M, Einwögerer T, Simon U, Neugebauer-Maresch C, Tangl S, Heimel P, Dobsak T, Retzmann A, Prohaska T, Irrgeher J, Kennett DJ, Olalde I, Reich D, Pinhasi R. Ancient DNA reveals monozygotic newborn twins from the Upper Palaeolithic. Commun Biol 2020; 3:650. [PMID: 33159107 PMCID: PMC7648643 DOI: 10.1038/s42003-020-01372-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/01/2020] [Indexed: 01/29/2023] Open
Abstract
The Upper Palaeolithic double burial of newborns and the single burial of a ca. 3-month-old infant uncovered at the Gravettian site of Krems-Wachtberg, Austria, are of paramount importance given the rarity of immature human remains from this time. Genome-wide ancient DNA shows that the male infants of the double grave are the earliest reported case of monozygotic twins, while the single grave´s individual was their 3rd-degree male relative. We assessed the individuals´ age at death by applying histological and µCT inspection of the maxillary second incisors (i2) in conjunction with C- and N-isotope ratios and Barium (Ba) intake as biomarker for breastfeeding. The results show that the twins were full-term newborns, and that while individual 2 died at birth, individual 1 survived for about 50 days. The findings show that Gravettian mortuary behaviour also included re-opening of a grave and manipulation of its layout and content.
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Affiliation(s)
- Maria Teschler-Nicola
- Department of Anthropology, Natural History Museum Vienna, A-1010, Vienna, Austria.
- Department of Evolutionary Anthropology, University of Vienna, A-1090, Vienna, Austria.
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, A-1090, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Marc Händel
- Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria
| | - Thomas Einwögerer
- Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria
| | - Ulrich Simon
- Institute for Oriental and European Archaeology, Austrian Academy of Sciences, A-1020, Vienna, Austria
| | | | - Stefan Tangl
- Karl Donath Laboratory for Hard Tissue and Biomaterial Research, University Clinic of Dentistry Vienna, Medical University of Vienna, A-1090, Vienna, Austria
- Austrian Cluster for Tissue Regeneration, A-1200, Vienna, Austria
| | - Patrick Heimel
- Karl Donath Laboratory for Hard Tissue and Biomaterial Research, University Clinic of Dentistry Vienna, Medical University of Vienna, A-1090, Vienna, Austria
- Austrian Cluster for Tissue Regeneration, A-1200, Vienna, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, A-1200, Vienna, Austria
| | - Toni Dobsak
- Karl Donath Laboratory for Hard Tissue and Biomaterial Research, University Clinic of Dentistry Vienna, Medical University of Vienna, A-1090, Vienna, Austria
- Austrian Cluster for Tissue Regeneration, A-1200, Vienna, Austria
| | - Anika Retzmann
- Chair of General and Analytical Chemistry, Montanuniversität Leoben, A-8700, Leoben, Austria
| | - Thomas Prohaska
- Chair of General and Analytical Chemistry, Montanuniversität Leoben, A-8700, Leoben, Austria
| | - Johanna Irrgeher
- Chair of General and Analytical Chemistry, Montanuniversität Leoben, A-8700, Leoben, Austria
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, A-1090, Vienna, Austria.
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223
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Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication. Nat Genet 2020; 52:1423-1432. [PMID: 33139952 PMCID: PMC7728601 DOI: 10.1038/s41588-020-00723-9] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/22/2020] [Indexed: 12/20/2022]
Abstract
Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality. Phased diploid genomes of the cultivated apple Malus domestica cv. Gala and its two major wild progenitors M. sieversii and M. sylvestris, as well as pan-genome analyses, provide insights into the genetic history of apple domestication.
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224
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Beier J, Anthes N, Wahl J, Harvati K. Prevalence of cranial trauma in Eurasian Upper Paleolithic humans. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 174:268-284. [PMID: 33107025 DOI: 10.1002/ajpa.24163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 08/11/2020] [Accepted: 10/02/2020] [Indexed: 01/14/2023]
Abstract
OBJECTIVES This study characterizes patterns of cranial trauma prevalence in a large sample of Upper Paleolithic (UP) fossil specimens (40,000-10,000 BP). MATERIALS AND METHODS Our sample comprised 234 individual crania (specimens), representing 1,285 cranial bones (skeletal elements), from 101 Eurasian UP sites. We used generalized linear mixed models (GLMMs) to assess trauma prevalence in relation to age-at-death, sex, anatomical distribution, and between pre- and post-Last Glacial Maximum (LGM) samples, while accounting for skeletal preservation. RESULTS Models predicted a mean cranial trauma prevalence of 0.07 (95% CI 0.003-0.19) at the level of skeletal elements, and of 0.26 (95% CI 0.08-0.48) at the level of specimens, each when 76-100% complete. Trauma prevalence increased with skeletal preservation. Across specimen and skeletal element datasets, trauma prevalence tended to be higher for males, and was consistently higher in the old age group. We found no time-specific trauma prevalence patterns for the two sexes or age cohorts when comparing samples from before and after the LGM. Samples showed higher trauma prevalence in the vault than in the face, with vault remains being affected predominantly in males. DISCUSSION Cranial trauma prevalence in UP humans falls within the variation described for Mesolithic and Neolithic samples. According to our current dataset, UP males and females were exposed to slightly different injury risks and trauma distributions, potentially due to different activities or behaviors, yet both sexes exhibit more trauma among the old. Environmental stressors associated with climatic changes of the LGM are not reflected in cranial trauma prevalence. To analyze trauma in incomplete skeletal remains we propose GLMMs as an informative alternative to crude frequency calculations.
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Affiliation(s)
- Judith Beier
- Paleoanthropology, Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Nils Anthes
- Animal Evolutionary Ecology Group, Institute of Evolution and Ecology, University of Tübingen, Tübingen, Germany
| | - Joachim Wahl
- Paleoanthropology, Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Katerina Harvati
- Paleoanthropology, Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools", University of Tübingen, Tübingen, Germany
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225
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Lynch LM, Felice R, O'Brien HD. Appendicular skeletal morphology of North American Martes reflect independent modes of evolution in conjunction with Pleistocene glacial cycles. Anat Rec (Hoboken) 2020; 304:1439-1462. [PMID: 33099887 DOI: 10.1002/ar.24545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 11/12/2022]
Abstract
Pleistocene glacial cycles are thought to have driven ecological niche shifts, including novel niche formation. North American pine martens, Martes americana and M. caurina, are exemplar taxa thought to have diverged molecularly and morphologically during Pleistocene glaciation. Previous research found correlations between Martes limb morphology with biome and climate, suggesting that appendicular evolution may have occurred via adaptation to selective pressures imposed by novel and shifting habitats. Such variation can also be achieved through non-adaptive means such as genetic drift. Here, we evaluate whether regional genetic differences reflect limb morphology differences among populations of M. americana and M. caurina by analyzing evolutionary tempo and mode of six limb elements. Our comparative phylogenetic models indicate that genetic structure predicts limb shape better than size. Marten limb size has low phylogenetic signal, and the best supported model of evolution is punctuational (kappa), with morphological and genetic divergence occurring simultaneously. Disparity through time analysis suggests that the tempo of limb evolution in Martes tracks Pleistocene glacial cycles, such that limb size may be responding to shifting climates rather than population genetic structure. Contrarily, we find that limb shape is strongly tied to genetic relationships, with high phylogenetic signal and a lambda mode of evolution. Overall, this pattern of limb size and shape variation may be the result of geographic isolation during Pleistocene glacial advance, while declines in disparity suggest hybridization during interglacial periods. Future inclusion of extinct populations of Martes, which were more morphologically and ecologically diverse, may further clarify Martes phenotypic evolution.
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Affiliation(s)
- Leigha M Lynch
- Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, USA.,Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Ryan Felice
- Cell and Developmental Biology, University College London, London, United Kingdom
| | - Haley D O'Brien
- Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, USA
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226
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Ye Z, Chen D, Yuan J, Zheng C, Yang X, Wang W, Zhang Y, Wang S, Jiang K, Bu W. Are population isolations and declines a threat to island endemic water striders? A lesson from demographic and niche modelling of Metrocoris esakii (Hemiptera: Gerridae). Mol Ecol 2020; 29:4573-4587. [PMID: 33006793 DOI: 10.1111/mec.15669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022]
Abstract
Genetic stochasticity and bottlenecking in the course of Pleistocene glaciations have been identified as threatening the survival of local endemics. However, the mechanisms by which local endemic species balance the influences of these two events remain poorly understood. Here, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) data set, mined mitochondrial sequences and constructed ecological niche models for the island endemic water strider Metrocoris esakii (Hemiptera: Gerridae). We found that M. esakii comprised three divergent lineages (i.e., north, central and south) isolated by geographical barriers and generally experienced population declines with the constriction of suitable areas during the Last Glacial Maximum (LGM). Further demographic model testing and stairway plots revealed a history of recent gene flow among the neighbouring lineages and rapid recovery at the end of the LGM, indicating that M. esakii at least had the potential for an adaptive response to population fragmentation and bottlenecking. The northern lineage did not show genetic bottlenecking during the LGM, which was probably due to its large effective population size (Ne ) from migration, which improved its adaptive potential. Relative to the ddRAD-seq data set, the demographic results based on mitochondrial sequences were less conclusive, showing weak differentiation and oversimplified demographic trajectories for the three genetic lineages. Overall, this study provides some degree of optimism for the survival of island endemic water striders from a demographic perspective, but further evaluation of their extinction risk under the impacts of human activities is required.
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Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Danyang Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Juanjuan Yuan
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xin Yang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenwu Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yaoyao Zhang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Siqi Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Kun Jiang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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227
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Foraminifer and Ostracod Occurrence in a Cool-Water Carbonate Factory of the Cape Adare (Ross Sea, Antarctica): A Key Lecture for the Climatic and Oceanographic Variations in the Last 30,000 Years. GEOSCIENCES 2020. [DOI: 10.3390/geosciences10100413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Foraminifers and ostracods were studied in a gravity-core recovered near Cape Adare (Ross Sea, Antarctica) with the aim of identifying the climatic and oceanographic variations during the last 30 ka. The sedimentary sequence represents conditions of a cool-water carbonate factory, which evidences that during the Marine Isotope Stage 2 (MIS2) the area was ice-free and very productive. The overall preservation of delicate skeletal remains such as bryozoans and molluscs indicated moderate bottom currents. This carbonate factory was interrupted by some terrigenous levels, representing conditions of instability/retreat of the ice shelves southward. The younger levels were referred to the meltwater pulse (MWP)-1A and 1B events. The Holocene sequence comprised more terrigenous sediments, reflecting high bottom-currents similar to the present-day conditions. Very abundant and well preserved foraminifers and ostracods, representative of shelf-upper slope paleoenvironments, were recovered. Epistominella exigua, among the foraminifers, suggested the influence of the Circumpolar Deep Water during some periods of the late Quaternary. Heavy-test taxa, such as Cibicides refulgens, indicated strengthening bottom hydrodynamics. As for the ostracods, peaks in the presence of Australicythere devexa, Bairdoppilata simplex and Pseudocythere aff. caudata together with significant values of Polycope spp. allowed us to identify environments rich in nutrients with the influence of cold and deep water upwelling phenomena.
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228
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Su YC, Su SH, Li HY, Wang HY, Lee SC. Implication of single year seasonal sampling to genetic diversity fluctuation that coordinates with oceanographic dynamics in torpedo scads near Taiwan. Sci Rep 2020; 10:16829. [PMID: 33033371 PMCID: PMC7544891 DOI: 10.1038/s41598-020-74025-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022] Open
Abstract
Many fisheries management and conservation plans are based on the genetic structure of organisms in pelagic ecosystems; however, these structures tend to vary over time, particularly in cyclic ocean currents. We performed genetic analyses on the populations of the pelagic fish, Megalaspis cordyla (Osteichthyes: Carangidae) in the area surrounding Taiwan during 2000–2001. Genotyping was performed on M. cordyla collected seasonally around Taiwan as well as specimens collected from Singapore (Malacca strait) and Indonesia (Banda Sea). Gonadosomatic indices (GSI) revealed that M. cordyla does not spawn near Taiwan. Data related to the mitochondrial control region revealed that the samples from Singapore and Indonesia represented two distinct genetic cohorts. Genotyping revealed that during the summer (June–August 2000), the Indonesian variant was dominant in eastern Taiwan (presumably following the Kuroshio Current) and in the Penghu region (following the Kuroshio Branch Current). During the same period, the Singapore genotype was dominant along the western coast of Taiwan (presumably following the South China Sea Current); however, the number dropped during the winter (December–February 2001) under the effects of the China Coast Current. Divergence time estimates indicate that the two genetic cohorts split during the last glacial maximum. Despite the fact that these results are based on sampling from a single year, they demonstrate the importance of seasonal sampling in unravelling the genetic diversity in pelagic ecosystems.
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Affiliation(s)
- Yong-Chao Su
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Shan-Hui Su
- Kaohsiung Municipal Zhongshan Elementary School, Kaohsiung, 80457, Taiwan
| | - Han-Yun Li
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan
| | - Hurng-Yi Wang
- Institute of Clinical Medicine, National Taiwan University, Taipei, 10617, Taiwan
| | - Sin-Che Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan.
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229
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Nuñez JJ, Suárez-Villota EY, Quercia CA, Olivares AP, Sites JW. Phylogeographic analysis and species distribution modelling of the wood frog Batrachyla leptopus (Batrachylidae) reveal interglacial diversification in south western Patagonia. PeerJ 2020; 8:e9980. [PMID: 33083116 PMCID: PMC7546244 DOI: 10.7717/peerj.9980] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/27/2020] [Indexed: 01/07/2023] Open
Abstract
Background The evolutionary history of southern South American organisms has been strongly influenced by Pleistocene climate oscillations. Amphibians are good models to evaluate hypotheses about the influence of these climate cycles on population structure and diversification of the biota, because they are sensitive to environmental changes and have restricted dispersal capabilities. We test hypotheses regarding putative forest refugia and expansion events associated with past climatic changes in the wood frog Batrachyla leptopus distributed along ∼1,000 km of length including glaciated and non-glaciated areas in southwestern Patagonia. Methods Using three mitochondrial regions (D-loop, cyt b, and coI) and two nuclear loci (pomc and crybA1), we conducted multilocus phylogeographic analyses and species distribution modelling to gain insights of the evolutionary history of this species. Intraspecific genealogy was explored with maximum likelihood, Bayesian, and phylogenetic network approaches. Diversification time was assessed using molecular clock models in a Bayesian framework, and demographic scenarios were evaluated using approximate Bayesian computation (ABC) and extended Bayesian skyline plot (EBSP). Species distribution models (SDM) were reconstructed using climatic and geographic data. Results Population structure and genealogical analyses support the existence of four lineages distributed north to south, with moderate to high phylogenetic support (Bootstrap > 70%; BPP > 0.92). The diversification time of B. leptopus’ populations began at ∼0.107 mya. The divergence between A and B lineages would have occurred by the late Pleistocene, approximately 0.068 mya, and divergence between C and D lineages was approximately 0.065 mya. The ABC simulations indicate that lineages coalesced at two different time periods, suggesting the presence of at least two glacial refugia and a postglacial colonization route that may have generated two southern lineages (p = 0.93, type I error: <0.094, type II error: 0.134). EBSP, mismatch distribution and neutrality indexes suggest sudden population expansion at ∼0.02 mya for all lineages. SDM infers fragmented distributions of B. leptopus associated with Pleistocene glaciations. Although the present populations of B. leptopus are found in zones affected by the last glacial maximum (∼0.023 mya), our analyses recover an older history of interglacial diversification (0.107–0.019 mya). In addition, we hypothesize two glacial refugia and three interglacial colonization routes, one of which gave rise to two expanding lineages in the south.
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Affiliation(s)
- José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Región de Los Ríos, Chile
| | - Elkin Y Suárez-Villota
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Concepción, Región del Bio-Bío, Chile
| | - Camila A Quercia
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Región de Los Ríos, Chile
| | - Angel P Olivares
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Región de Los Ríos, Chile
| | - Jack W Sites
- Department of Biology and M.L. Bean Life Science Museum, Brigham Young University, Provo, UT, United States of America.,Current affiliation: Department of Biology, Austin Peay St University, Clarksville, TN, United States of America
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230
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He Z, Dai X, Beaumont M, Yu F. Estimation of Natural Selection and Allele Age from Time Series Allele Frequency Data Using a Novel Likelihood-Based Approach. Genetics 2020; 216:463-480. [PMID: 32769100 PMCID: PMC7536852 DOI: 10.1534/genetics.120.303400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/29/2020] [Indexed: 11/18/2022] Open
Abstract
Temporally spaced genetic data allow for more accurate inference of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel likelihood-based method for jointly estimating selection coefficient and allele age from time series data of allele frequencies. Our approach is based on a hidden Markov model where the underlying process is a Wright-Fisher diffusion conditioned to survive until the time of the most recent sample. This formulation circumvents the assumption required in existing methods that the allele is created by mutation at a certain low frequency. We calculate the likelihood by numerically solving the resulting Kolmogorov backward equation backward in time while reweighting the solution with the emission probabilities of the observation at each sampling time point. This procedure reduces the two-dimensional numerical search for the maximum of the likelihood surface, for both the selection coefficient and the allele age, to a one-dimensional search over the selection coefficient only. We illustrate through extensive simulations that our method can produce accurate estimates of the selection coefficient and the allele age under both constant and nonconstant demographic histories. We apply our approach to reanalyze ancient DNA data associated with horse base coat colors. We find that ignoring demographic histories or grouping raw samples can significantly bias the inference results.
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Affiliation(s)
- Zhangyi He
- Department of Statistics, University of Oxford, OX1 3LB, United Kingdom
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Feng Yu
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
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231
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Soghigian J, Gloria‐Soria A, Robert V, Le Goff G, Failloux A, Powell JR. Genetic evidence for the origin of Aedes aegypti, the yellow fever mosquito, in the southwestern Indian Ocean. Mol Ecol 2020; 29:3593-3606. [PMID: 33463828 PMCID: PMC7589284 DOI: 10.1111/mec.15590] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/14/2020] [Accepted: 07/23/2020] [Indexed: 01/07/2023]
Abstract
Aedes aegypti is among the best-studied mosquitoes due to its critical role as a vector of human pathogens and ease of laboratory rearing. Until now, this species was thought to have originated in continental Africa, and subsequently colonized much of the world following the establishment of global trade routes. However, populations of this mosquito on the islands in the southwestern Indian Ocean (SWIO), where the species occurs with its nearest relatives referred to as the Aegypti Group, have received little study. We re-evaluated the evolutionary history of Ae. aegypti and these relatives, using three data sets: nucleotide sequence data, 18,489 SNPs and 12 microsatellites. We found that: (a) the Aegypti Group diverged 16 MYA (95% HPD: 7-28 MYA) from its nearest African/Asian ancestor; (b) SWIO populations of Ae. aegypti are basal to continental African populations; (c) after diverging 7 MYA (95% HPD: 4-15 MYA) from its nearest formally described relative (Ae. mascarensis), Ae. aegypti moved to continental Africa less than 85,000 years ago, where it recently (<1,000 years ago) split into two recognized subspecies Ae. aegypti formosus and a human commensal, Ae. aegypti aegypti; (d) the Madagascar samples form a clade more distant from all other Ae. aegypti than the named species Ae. mascarensis, implying that Madagascar may harbour a new cryptic species; and (e) there is evidence of introgression between Ae. mascarensis and Ae. aegypti on Réunion, and between the two subspecies elsewhere in the SWIO, a likely consequence of recent introductions of domestic Ae. aegypti aegypti from Asia.
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Affiliation(s)
- John Soghigian
- Yale UniversityNew HavenCTUSA
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Andrea Gloria‐Soria
- Yale UniversityNew HavenCTUSA
- Center for Vector Biology & Zoonotic DiseasesDepartment of Environmental SciencesThe Connecticut Agricultural Experiment StationNew HavenCTUSA
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232
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Modern Northern Domestic Horses Carry Mitochondrial DNA Similar to Przewalski’s Horse. J MAMM EVOL 2020. [DOI: 10.1007/s10914-020-09517-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractSeveral recent studies have suggested past gene flow between the Przewalski’s horse and modern domestic horse and questioned the wild origin of the Przewalski’s horse. Mitochondrial DNA has placed representatives of the Przewalski’s horse into three among the eighteen haplogroups detected from the modern horse. Of these, two haplogroups have so far been found exclusively in the Przewalski’s horse, while the one shared with the domestic horse includes captive individuals that have uncertain pedigrees. We recently found five domestic horse individuals of North European horse breeds to carry a mitochondrial haplogroup that was previously confined only to the Przewalski’s horse. These individuals were sequenced for 6039 bp of mitochondrial DNA and used, together with domestic and Przewalski’s horse sequences presenting all horse haplogroups, to examine the phylogenetic relationships and to date the divergence time between Przewalski’s and domestic horse clusters within this haplogroup. The divergence was dated to have likely occurred about 13,300–11,400 years ago, which coincides with the time of the Younger Dryas.
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233
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Decker SK, Ammerman LK. Phylogeographic analysis reveals mito-nuclear discordance in Dasypterus intermedius. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Abstract
Northern yellow bats (Dasypterus intermedius) are tree-roosting bats in the family Vespertilionidae comprised of two subspecies: D. intermedius intermedius and D. intermedius floridanus. The two subspecies are thought to be geographically separated. Due to their cryptic morphology, this hypothesis has never been tested and can benefit from being examined within a molecular framework. In this study, mitochondrial sequence data from 38 D. intermedius and nuclear sequence data from 14 D. intermedius from across their range were used to test the hypothesis that genetically defined groups correspond geographically with the two morphologically defined subspecies. Although high levels of divergence of the mitochondrial sequence (11.6%) suggest genetically distinct clusters sympatric in southern Texas, no genetic structure was recovered with the nuclear marker. Moreover, the mitochondrial sequence data recovered a paraphyletic relationship between the two subspecies of D. intermedius with the Cuban yellow bat (D. insularis), whereas no such paraphyly was recovered from analysis of the nuclear marker. Divergence time based on analyses of mitochondrial sequence for the two subspecies was approximately 5.5 Ma. The patterns observed are hypothesized to be the result of past isolation of lineages and secondary contact that is currently contributing to gene flow.
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Affiliation(s)
- Sydney K Decker
- Department of Biology, Angelo State University, San Angelo, TX, USA
| | - Loren K Ammerman
- Department of Biology, Angelo State University, San Angelo, TX, USA
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234
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Liesner D, Fouqueau L, Valero M, Roleda MY, Pearson GA, Bischof K, Valentin K, Bartsch I. Heat stress responses and population genetics of the kelp Laminaria digitata (Phaeophyceae) across latitudes reveal differentiation among North Atlantic populations. Ecol Evol 2020; 10:9144-9177. [PMID: 32953052 PMCID: PMC7487260 DOI: 10.1002/ece3.6569] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 12/26/2022] Open
Abstract
To understand the thermal plasticity of a coastal foundation species across its latitudinal distribution, we assess physiological responses to high temperature stress in the kelp Laminaria digitata in combination with population genetic characteristics and relate heat resilience to genetic features and phylogeography. We hypothesize that populations from Arctic and cold-temperate locations are less heat resilient than populations from warm distributional edges. Using meristems of natural L. digitata populations from six locations ranging between Kongsfjorden, Spitsbergen (79°N), and Quiberon, France (47°N), we performed a common-garden heat stress experiment applying 15°C to 23°C over eight days. We assessed growth, photosynthetic quantum yield, carbon and nitrogen storage, and xanthophyll pigment contents as response traits. Population connectivity and genetic diversity were analyzed with microsatellite markers. Results from the heat stress experiment suggest that the upper temperature limit of L. digitata is nearly identical across its distribution range, but subtle differences in growth and stress responses were revealed for three populations from the species' ecological range margins. Two populations at the species' warm distribution limit showed higher temperature tolerance compared to other populations in growth at 19°C and recovery from 21°C (Quiberon, France), and photosynthetic quantum yield and xanthophyll pigment responses at 23°C (Helgoland, Germany). In L. digitata from the northernmost population (Spitsbergen, Norway), quantum yield indicated the highest heat sensitivity. Microsatellite genotyping revealed all sampled populations to be genetically distinct, with a strong hierarchical structure between southern and northern clades. Genetic diversity was lowest in the isolated population of the North Sea island of Helgoland and highest in Roscoff in the English Channel. All together, these results support the hypothesis of moderate local differentiation across L. digitata's European distribution, whereas effects are likely too weak to ameliorate the species' capacity to withstand ocean warming and marine heatwaves at the southern range edge.
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Affiliation(s)
- Daniel Liesner
- Alfred Wegener InstituteHelmholtz Centre for Polar and Marine ResearchBremerhavenGermany
| | - Louise Fouqueau
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRSSorbonne Université, UC, UACH, Station Biologique de RoscoffRoscoff CedexFrance
| | - Myriam Valero
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRSSorbonne Université, UC, UACH, Station Biologique de RoscoffRoscoff CedexFrance
| | - Michael Y. Roleda
- Norwegian Institute of Bioeconomy ResearchBodøNorway
- The Marine Science Institute, College of ScienceUniversity of the Philippines, DilimanQuezon CityPhilippines
| | | | - Kai Bischof
- Marine BotanyUniversity of BremenBremenGermany
| | - Klaus Valentin
- Alfred Wegener InstituteHelmholtz Centre for Polar and Marine ResearchBremerhavenGermany
| | - Inka Bartsch
- Alfred Wegener InstituteHelmholtz Centre for Polar and Marine ResearchBremerhavenGermany
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235
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Epibenthic megafauna communities in Northeast Greenland vary across coastal, continental shelf and slope habitats. Polar Biol 2020. [DOI: 10.1007/s00300-020-02733-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractThe marine area of Northeast Greenland belongs to the largest national park in the world. Biodiversity assessments and tailored conservation measures often target specific physiographic or oceanographic features of an area for which detailed knowledge on their biological communities is incomplete. This study, therefore, characterizes epibenthic megafauna communities in a priori defined seabed habitats (fjord, shelf, shelf break and slope) and their relationship to environmental conditions in Northeast Greenland waters as a basis for conservation and management planning. Megabenthos was sampled from the Bessel Fjord across the shelf to the upper continental slope between latitudes 74.55°N–79.27°N and longitudes 5.22°W–21.72°W by Campelen and Agassiz trawls at 18 locations (total of 33 samples) at depths between 65 and 1011 m in August 2015 and September 2017. A total of 276 taxa were identified. Gross estimates of abundance ranged from 4 to 854 individuals 1000 m−2 and biomass ranged from 65 to 528 g wet weight 1000 m−2 (2017 only). The phyla Arthropoda and Porifera contributed the most to taxon richness, while Mollusca and Echinodermata were the most abundant, and Echinodermata had the highest biomass of all phyla. Fjord, shelf, shelf break and slope seabed habitats revealed different megafaunal communities that were partly explained by gradients in depth, bottom oxygen concentration, temperature, salinity, and turbidity. The present study provides a current baseline of megabenthos across seabed habitats in Northeast Greenlandic waters and reveals putative connections between Arctic and Atlantic biota.
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236
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Rougemont Q, Moore JS, Leroy T, Normandeau E, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon. PLoS Genet 2020; 16:e1008348. [PMID: 32845885 PMCID: PMC7478589 DOI: 10.1371/journal.pgen.1008348] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/08/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded recently, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored. Reconstruction of a species’ past demographic history from genetic data can highlight historical factors that have shaped the distribution of genetic diversity along its genome and its geographic range. Here, we combine genotyping-by-sequencing with demographic modelling to address these issues in the Coho salmon, a Pacific salmon of conservation concern in some parts of its range, notably in the south. Our demographic reconstructions reveal a linear decrease in genetic diversity toward the north of the species range, supporting the hypothesis of a northern route of postglacial recolonization from a single major southern refugium. As predicted by theory, we also observed a higher proportion of deleterious mutations in the most distant populations from this refugium. Beyond this general pattern, among-site variation in the proportion of deleterious mutations is consistent with different local trends in effective population sizes. Our results highlight the potential importance of understanding historical factors that have shaped geographic patterns of the distribution of deleterious mutations in order to implement effective management programs for the conservation of wild populations. Such fundamental knowledge of human historical demography is now having major impacts on health sciences, and we argue it is time to integrate such approaches in conservation science as well.
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Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Thibault Leroy
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B. Rondeau
- Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Ruth E. Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M. Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, United States of America
| | - Penelope A. Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, United States of America
| | - Kerry A. Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
| | - John Carlos Garza
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service and Institute of Marine Sciences, University of California–Santa Cruz, Santa Cruz, California, United States of America
| | - Terry D. Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F. Koop
- Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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238
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Wei S, Li Z, Momigliano P, Fu C, Wu H, Merilä J. The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae). Mol Ecol 2020; 29:3667-3683. [PMID: 32762086 DOI: 10.1111/mec.15584] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/16/2020] [Accepted: 07/28/2020] [Indexed: 01/02/2023]
Abstract
The role of geological events and Pleistocene climatic fluctuations as drivers of current patterns of genetic variation in extant species has been a topic of continued interest among evolutionary biologists. Nevertheless, comprehensive studies of widely distributed species are still rare, especially from Asia. Using geographically extensive sampling of many individuals and a large number of nuclear single nucleotide polymorphisms (SNPs), we studied the phylogeography and historical demography of Hyla annectans populations in southern China. Thirty-five sampled populations were grouped into seven clearly defined genetic clusters that closely match phenotype-based subspecies classification. These lineages diverged 2.32-5.23 million years ago (Ma), a timing that closely aligns with the rapid and drastic uplifting of the Qinghai-Tibet Plateau and adjacent southwest China. Demographic analyses and species distribution models indicate that different populations of this species have responded differently to past climatic changes. In the Hengduan Mountains, most populations experienced a bottleneck, whereas the populations located outside of the Hengduan Mountains have gradually declined in size since the end of the last glaciation. In addition, the levels of phenotypic and genetic divergence were strongly correlated across major clades. These results highlight the combined effects of geological events and past climatic fluctuations, as well as natural selection, as drivers of contemporary patterns of genetic and phenotypic variation in a widely distributed anuran in Asia.
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Affiliation(s)
- Shichao Wei
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Zitong Li
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Chao Fu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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239
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Bi C, Lu N, Huang Z, Chen J, He C, Lu Z. Whole-genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations. Ecol Evol 2020; 10:8210-8224. [PMID: 32788973 PMCID: PMC7417228 DOI: 10.1002/ece3.6527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole-genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size (N e) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long-term population dynamics of Branchiostoma. The inferred ancestral N e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10-9) or third glaciation (mutation rate = 9 × 10-9) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long-term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.
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Affiliation(s)
- Changwei Bi
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Na Lu
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic AdministrationCollege of Life SciencesFujian Normal UniversityFuzhouChina
- Key Laboratory of Special Marine Bio‐resources Sustainable Utilization of Fujian ProvinceFuzhouChina
| | - Junyuan Chen
- Nanjing Institute of Paleontology and GeologyChinese Academy of SciencesNanjingChina
| | - Chunpeng He
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Zuhong Lu
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
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240
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Taylor RS, Manseau M, Horn RL, Keobouasone S, Golding GB, Wilson PJ. The role of introgression and ecotypic parallelism in delineating intraspecific conservation units. Mol Ecol 2020; 29:2793-2809. [PMID: 32567754 PMCID: PMC7496186 DOI: 10.1111/mec.15522] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/04/2020] [Accepted: 06/15/2020] [Indexed: 01/03/2023]
Abstract
Parallel evolution can occur through selection on novel mutations, standing genetic variation or adaptive introgression. Uncovering parallelism and introgressed populations can complicate management of threatened species as parallelism may have influenced conservation unit designations and admixed populations are not generally considered under legislations. We examined high coverage whole-genome sequences of 30 caribou (Rangifer tarandus) from across North America and Greenland, representing divergent intraspecific lineages, to investigate parallelism and levels of introgression contributing to the formation of ecotypes. Caribou are split into four subspecies and 11 extant conservation units, known as designatable units (DUs), in Canada. Using genomes from all four subspecies and six DUs, we undertake demographic reconstruction and confirm two previously inferred instances of parallel evolution in the woodland subspecies and uncover an additional instance of parallelism of the eastern migratory ecotype. Detailed investigations reveal introgression in the woodland subspecies, with introgressed regions found spread throughout the genomes encompassing both neutral and functional sites. Our investigations using whole genomes highlight the difficulties in unequivocally demonstrating parallelism through adaptive introgression in nonmodel species with complex demographic histories, with standing variation and introgression both potentially involved. Additionally, the impact of parallelism and introgression on conservation policy for management units needs to be considered in general, and the caribou designations will need amending in light of our results. Uncovering and decoupling parallelism and differential patterns of introgression will become prevalent with the availability of comprehensive genomic data from nonmodel species, and we highlight the need to incorporate this into conservation unit designations.
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Affiliation(s)
| | - Micheline Manseau
- Biology DepartmentTrent UniversityPeterboroughONCanada
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaONCanada
| | - Rebekah L. Horn
- Biology DepartmentTrent UniversityPeterboroughONCanada
- Columbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Sonesinh Keobouasone
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaONCanada
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241
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Li D, Sun G, Zhang M, Cao Y, Zhang C, Fu Y, Li F, Li G, Jiang R, Han R, Li Z, Wang Y, Tian Y, Liu X, Li W, Kang X. Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken. BMC Genomics 2020; 21:511. [PMID: 32703156 PMCID: PMC7376702 DOI: 10.1186/s12864-020-06900-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
Background Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype. Results Principal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds. Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds. The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago. Fst analysis identified a selective sweep that contains genes related to melanogenesis. This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection. A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis. Conclusions These findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals.
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Affiliation(s)
- Donghua Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Guirong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Meng Zhang
- The First Hospital, Jilin University, Changchun, 130062, Jilin, China
| | - Yanfang Cao
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Chenxi Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yawei Fu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Fang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Guoxi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Ruili Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Yanbin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Yadong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Xiangtao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China. .,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450046, China.
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242
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Ardelean CF, Becerra-Valdivia L, Pedersen MW, Schwenninger JL, Oviatt CG, Macías-Quintero JI, Arroyo-Cabrales J, Sikora M, Ocampo-Díaz YZE, Rubio-Cisneros II, Watling JG, de Medeiros VB, De Oliveira PE, Barba-Pingarón L, Ortiz-Butrón A, Blancas-Vázquez J, Rivera-González I, Solís-Rosales C, Rodríguez-Ceja M, Gandy DA, Navarro-Gutierrez Z, De La Rosa-Díaz JJ, Huerta-Arellano V, Marroquín-Fernández MB, Martínez-Riojas LM, López-Jiménez A, Higham T, Willerslev E. Evidence of human occupation in Mexico around the Last Glacial Maximum. Nature 2020; 584:87-92. [PMID: 32699412 DOI: 10.1038/s41586-020-2509-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 06/16/2020] [Indexed: 11/09/2022]
Abstract
The initial colonization of the Americas remains a highly debated topic1, and the exact timing of the first arrivals is unknown. The earliest archaeological record of Mexico-which holds a key geographical position in the Americas-is poorly known and understudied. Historically, the region has remained on the periphery of research focused on the first American populations2. However, recent investigations provide reliable evidence of a human presence in the northwest region of Mexico3,4, the Chiapas Highlands5, Central Mexico6 and the Caribbean coast7-9 during the Late Pleistocene and Early Holocene epochs. Here we present results of recent excavations at Chiquihuite Cave-a high-altitude site in central-northern Mexico-that corroborate previous findings in the Americas10-17of cultural evidence that dates to the Last Glacial Maximum (26,500-19,000 years ago)18, and which push back dates for human dispersal to the region possibly as early as 33,000-31,000 years ago. The site yielded about 1,900 stone artefacts within a 3-m-deep stratified sequence, revealing a previously unknown lithic industry that underwent only minor changes over millennia. More than 50 radiocarbon and luminescence dates provide chronological control, and genetic, palaeoenvironmental and chemical data document the changing environments in which the occupants lived. Our results provide new evidence for the antiquity of humans in the Americas, illustrate the cultural diversity of the earliest dispersal groups (which predate those of the Clovis culture) and open new directions of research.
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Affiliation(s)
- Ciprian F Ardelean
- Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Zacatecas, Mexico. .,Department of Archaeology, University of Exeter, Exeter, UK.
| | - Lorena Becerra-Valdivia
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.,Chronos 14C-Cycle Facility, SSEAU, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Jean-Luc Schwenninger
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Charles G Oviatt
- Department of Geology, Kansas State University, Manhattan, KS, USA
| | - Juan I Macías-Quintero
- Escuela de Arqueología, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoología, Subdirección de Laboratorios y Apoyo Académico, Instituto Nacional de Antropología e Historia, Mexico City, Mexico
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Yam Zul E Ocampo-Díaz
- Facultad de Ingeniería, Universidad Autónoma de San Luís Potosí, San Luis Potosí, Mexico.,Grupo de Geología Exógena y del Sedimentario, San Luis Potosí, Mexico
| | | | - Jennifer G Watling
- Laboratório de Arqueologia dos Trópicos, Museu de Arqueologia e Etnologia, Universidade de São Paulo, São Paulo, Brazil
| | - Vanda B de Medeiros
- Laboratório de Micropaleontologia, Instituto de Geociências, Universidade de São Paulo, São Paulo, Brazil
| | - Paulo E De Oliveira
- Laboratório de Micropaleontologia, Instituto de Geociências, Universidade de São Paulo, São Paulo, Brazil.,Botany Department, The Field Museum of Natural History, Chicago, IL, USA
| | - Luis Barba-Pingarón
- Laboratorio de Prospección Arqueológica, Instituto de Investigaciones Antropológicas (IIA), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Agustín Ortiz-Butrón
- Laboratorio de Prospección Arqueológica, Instituto de Investigaciones Antropológicas (IIA), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Jorge Blancas-Vázquez
- Laboratorio de Prospección Arqueológica, Instituto de Investigaciones Antropológicas (IIA), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Irán Rivera-González
- Laboratorio de Palinología, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Corina Solís-Rosales
- Laboratorio de Espectrometría de Masas con Aceleradores, Instituto de Física, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - María Rodríguez-Ceja
- Laboratorio de Espectrometría de Masas con Aceleradores, Instituto de Física, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Devlin A Gandy
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Alejandro López-Jiménez
- Laboratorio de Arqueozoología, Subdirección de Laboratorios y Apoyo Académico, Instituto Nacional de Antropología e Historia, Mexico City, Mexico
| | - Thomas Higham
- Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, University of Copenhagen, Copenhagen, Denmark. .,Welcome Trust, Sanger Institute, Hinxton, UK. .,The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK.
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243
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The timing and effect of the earliest human arrivals in North America. Nature 2020; 584:93-97. [PMID: 32699413 DOI: 10.1038/s41586-020-2491-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 05/26/2020] [Indexed: 01/01/2023]
Abstract
The peopling of the Americas marks a major expansion of humans across the planet. However, questions regarding the timing and mechanisms of this dispersal remain, and the previously accepted model (termed 'Clovis-first')-suggesting that the first inhabitants of the Americas were linked with the Clovis tradition, a complex marked by distinctive fluted lithic points1-has been effectively refuted. Here we analyse chronometric data from 42 North American and Beringian archaeological sites using a Bayesian age modelling approach, and use the resulting chronological framework to elucidate spatiotemporal patterns of human dispersal. We then integrate these patterns with the available genetic and climatic evidence. The data obtained show that humans were probably present before, during and immediately after the Last Glacial Maximum (about 26.5-19 thousand years ago)2,3 but that more widespread occupation began during a period of abrupt warming, Greenland Interstadial 1 (about 14.7-12.9 thousand years before AD 2000)4. We also identify the near-synchronous commencement of Beringian, Clovis and Western Stemmed cultural traditions, and an overlap of each with the last dates for the appearance of 18 now-extinct faunal genera. Our analysis suggests that the widespread expansion of humans through North America was a key factor in the extinction of large terrestrial mammals.
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244
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Rethinking the Disappearance of Microblade Technology in the Terminal Pleistocene of Hokkaido, Northern Japan: Looking at Archaeological and Palaeoenvironmental Evidence. QUATERNARY 2020. [DOI: 10.3390/quat3030021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Archaeological research, for several decades, has shown that various microblade technologies using obsidian and hard shale appeared and developed from the Last Glacial Maximum to the terminal Pleistocene (Bølling–Allerød–Younger Dryas) in Hokkaido, Northern Japan. It is well accepted that microblade technology was closely related to the high mobility of foragers to adapt to harsh environments. Recent archaeological and palaeoenvironmental evidence from Hokkaido demonstrates that the disappearance of microblade technology occurred during the terminal Pleistocene, influenced by a wide range of factors, including changes in landscape, climate, subsistence and human populations. The goal of this paper is to provide an overview of the current state of research on the process and background of the disappearance of microblade technology and to discuss prospects for future research. This paper will (1) review palaeoenvironmental research in Hokkaido on changes in climate and biological composition from the terminal Pleistocene to the initial Holocene; (2) survey changes in the technological adaptations and resource use of humans based on the archaeological evidence; and (3) discuss how the abrupt fluctuations of climate that occurred in the terminal Pleistocene affected human behaviour and demographics in Hokkaido.
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245
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Gregariousness in the giant sloth Lestodon (Xenarthra): multi-proxy approach of a bonebed from the Last Maximum Glacial of Argentine Pampas. Sci Rep 2020; 10:10955. [PMID: 32616813 PMCID: PMC7331707 DOI: 10.1038/s41598-020-67863-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/11/2020] [Indexed: 11/15/2022] Open
Abstract
Megamammals constituted an important component in the Pleistocene faunal communities of South America. Paleobiological and paleoecological studies involving different megamammal taxa have increased significantly in the last years, but there are still several poorly-known issues of its life history. In this work, we analyze an assemblage composed of 13 individuals of different ontogenetic stages, and possibly different sex, belonging to the giant ground sloth Lestodon armatus (Xenarthra, Folivora), recovered from Playa del Barco site (Pampean Region, Argentina). A dating of 19,849 years Cal BP allows assigning this assemblage to a period of the MIS (Marine Isotope Stage) 2 related to the end of the Last Glacial Maximum. Based on multiple lines of research (e.g. taphonomy, paleopathology, osteohistology, isotopy), we interpret the origin of the assemblage and diverse paleobiological and paleoecological aspects (e.g. social behavior, ontogenetic changes, sexual dimorphism, diseases, resource and habitat use, trophic relationships) of L. armatus. Evidence suggests that the assemblage was formed by a local single event of catastrophic mortality, which affected different members of a social group. This record represents the first accurate evidence of gregariousness for this ground sloth, providing new data on a poorly-known behavior among extinct Folivora.
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246
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Branco C, Ray N, Currat M, Arenas M. Influence of Paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia. Mol Ecol 2020; 29:2150-2159. [PMID: 32436243 DOI: 10.1111/mec.15479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/29/2022]
Abstract
Cavalli-Sforza and coauthors originally explored the genetic variation of modern humans throughout the world and observed an overall east-west genetic gradient in Asia. However, the specific environmental and population genetics processes causing this gradient were not formally investigated and promoted discussion in recent studies. Here we studied the influence of diverse environmental and population genetics processes on Asian genetic gradients and identified which could have produced the observed gradient. To do so, we performed extensive spatially-explicit computer simulations of genetic data under the following scenarios: (a) variable levels of admixture between Paleolithic and Neolithic populations, (b) migration through long-distance dispersal (LDD), (c) Paleolithic range contraction induced by the last glacial maximum (LGM), and (d) Neolithic range expansions from one or two geographic origins (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we estimated genetic gradients from the simulated data and we found that they were sensible to the analysed processes, especially to the range contraction induced by LGM and to the number of Neolithic expansions. Some scenarios were compatible with the observed east-west genetic gradient, such as the Paleolithic expansion with a range contraction induced by the LGM or two Neolithic range expansions from both the east and the west. In general, LDD increased the variance of genetic gradients among simulations. We interpreted the obtained gradients as a consequence of both allele surfing caused by range expansions and isolation by distance along the vast east-west geographic axis of this continent.
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Affiliation(s)
- Catarina Branco
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Nicolas Ray
- GeoHealth Group, Institute of Global Health, University of Geneva, Geneva, Switzerland.,Institute for Environmental Sciences, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution - Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.,Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
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247
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Delrieu-Trottin E, Hubert N, Giles EC, Chifflet-Belle P, Suwalski A, Neglia V, Rapu-Edmunds C, Mona S, Saenz-Agudelo P. Coping with Pleistocene climatic fluctuations: Demographic responses in remote endemic reef fishes. Mol Ecol 2020; 29:2218-2233. [PMID: 32428327 DOI: 10.1111/mec.15478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Elucidating demographic history during the settlement of ecological communities is crucial for properly inferring the mechanisms that shape patterns of species diversity and their persistence through time. Here, we used genomic data and coalescent-based approaches to elucidate for the first time the demographic dynamics associated with the settlement by endemic reef fish fauna of one of the most remote peripheral islands of the Pacific Ocean, Rapa Nui (Easter Island). We compared the demographic history of nine endemic species in order to explore their demographic responses to Pleistocene climatic fluctuations. We found that species endemic to Rapa Nui share a common demographic history, as signatures of population expansions were retrieved for almost all of the species studied here, and synchronous demographic expansions initiated during the last glacial period were recovered for more than half of the studied species. These results suggest that eustatic fluctuations associated with Milankovitch cycles have played a central role in species demographic histories and in the final stage of the community assembly of many Rapa Nui reef fishes. Specifically, sea level lowstands resulted in the maximum reef habitat extension for Rapa Nui endemic species; we discuss the potential role of seamounts in allowing endemic species to cope with Pleistocene climatic fluctuations, and we highlight the importance of local historical processes over regional ones. Overall, our results shed light on the mechanisms by which endemism arises and is maintained in peripheral reef fish fauna.
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Affiliation(s)
- Erwan Delrieu-Trottin
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France.,Museum für Naturkunde, Leibniz-Institut für Evolutions-und Biodiversitätsforschung an der, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicolas Hubert
- Institut de Recherche pour le Développement, UMR 5554 (UM-CNRS-IRD-EPHE), ISEM, Montpellier, France
| | - Emily C Giles
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile.,Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Pascaline Chifflet-Belle
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Arnaud Suwalski
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France
| | - Valentina Neglia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | | | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum National d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,EPHE, PSL Research University, Paris, France.,Laboratoire d'Excellence CORAIL, Papetoai, French Polynesia
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
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248
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Cumming RT, Thurman JH, Youngdale S, Tirant SL. Walaphyllium subgen. nov., the dancing leaf insects from Australia and Papua New Guinea with description of a new species (Phasmatodea, Phylliidae). Zookeys 2020; 939:1-28. [PMID: 32577080 PMCID: PMC7297813 DOI: 10.3897/zookeys.939.52071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 04/07/2020] [Indexed: 11/24/2022] Open
Abstract
A new subgenus, Walaphylliumsubgen. nov., is described within Phyllium Illiger, 1798 to accommodate three leaf insect species. One of the species included is newly described herein as Phyllium (Walaphyllium) lelantossp. nov. from Papua New Guinea. This new subgenus of Phyllium can be diagnosed by a following combination of features. This new species is compared to the two additional new subgenus members, Phylliumzomproi Größer, 2001 and Phylliummonteithi Brock & Hasenpusch, 2003. Also for the first time the male morphology of Phylliumzomproi is described and illustrated. To conclude, a brief biogeographical view of the leaf insects on either side of the Torres Strait is presented, as well as a key to species and a distribution map to the known species of Phyllium (Walaphyllium)subgen. nov.
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Affiliation(s)
- Royce T Cumming
- Associate researcher, Montréal Insectarium, 4581 rue Sherbrooke, Montreal, Quebec, H1X 2B2, Canada Montréal Insectarium Quebec Canada.,PhD Student, Richard Gilder Graduate School, American Museum of Natural History, New York, NY 10024, USA American Museum of Natural History New York United States of America.,PhD Student, City University New York, Graduate Center, Ecology and Evolutionary Biology subprogram, New York, NY, USA City University New York United States of America
| | - Jessa H Thurman
- PhD Student, School of Biological Sciences, University of Queensland, St Lucia, Queensland, Australia University of Queensland Queensland Australia
| | - Sam Youngdale
- Los Angeles, California, USA Unaffiliated California United States of America
| | - Stephane Le Tirant
- Collection manager, Montréal Insectarium, 4581 rue Sherbrooke, Montreal, Quebec, H1X 2B2, Canada Collection manager, Montréal Insectarium Quebec Canada
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249
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Late Pleistocene-Holocene vegetation history and anthropogenic activities deduced from pollen spectra and archaeological data at Guxu Lake, eastern China. Sci Rep 2020; 10:9306. [PMID: 32518244 PMCID: PMC7283361 DOI: 10.1038/s41598-020-65834-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/08/2020] [Indexed: 11/21/2022] Open
Abstract
This study presents high-resolution pollen and charcoal records from Guxu Lake in the Taihu Lake Basin, eastern China, spanning the last 23,000 years. The sedimentary sequences revealed dynamic terrestrial and lacustrine environments during 23.0-11.7 cal ka BP, the climate was relatively cold and dry, and the vegetation was dominated by evergreen-deciduous broadleaf and coniferous mixed forest. During 11.7-4.4 cal ka BP, the Quercus- and Castanopsis-dominated evergreen-deciduous broadleaf mixed forest expanded, while the Poaceae and Artemisia were still the major terrestrial herbs under warmer and more humid conditions. After this period, the climate became relatively cool and dry again, and the vegetation landscape was comparatively stable, as it remains today. Wild rice likely grew before Neolithic humans occupied this area. The variations in Oryza-type Poaceae pollen spectra and distributions of Neolithic archaeological sites indicate rice agriculture may have first appeared and developed with human occupation in ca. 7.0-4.4 ka BP. During the historical period, beginning approximately 4 ka BP, a clear signal of intensified anthropogenic disturbance is evident from the clearing of forests, high charcoal concentrations and the presence of rice pollen in large quantities. These results suggest more intensified rice farming was widespread, with increasing human impact on the environment.
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250
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Yannic G, Hagen O, Leugger F, Karger DN, Pellissier L. Harnessing paleo-environmental modeling and genetic data to predict intraspecific genetic structure. Evol Appl 2020; 13:1526-1542. [PMID: 32684974 PMCID: PMC7359836 DOI: 10.1111/eva.12986] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022] Open
Abstract
Spatially explicit simulations of gene flow within complex landscapes could help forecast the responses of populations to global and anthropological changes. Simulating how past climate change shaped intraspecific genetic variation can provide a validation of models in anticipation of their use to predict future changes. We review simulation models that provide inferences on population genetic structure. Existing simulation models generally integrate complex demographic and genetic processes but are less focused on the landscape dynamics. In contrast to previous approaches integrating detailed demographic and genetic processes and only secondarily landscape dynamics, we present a model based on parsimonious biological mechanisms combining habitat suitability and cellular processes, applicable to complex landscapes. The simulation model takes as input (a) the species dispersal capacities as the main biological parameter, (b) the species habitat suitability, and (c) the landscape structure, modulating dispersal. Our model emphasizes the role of landscape features and their temporal dynamics in generating genetic differentiation among populations within species. We illustrate our model on caribou/reindeer populations sampled across the entire species distribution range in the Northern Hemisphere. We show that simulations over the past 21 kyr predict a population genetic structure that matches empirical data. This approach looking at the impact of historical landscape dynamics on intraspecific structure can be used to forecast population structure under climate change scenarios and evaluate how species range shifts might induce erosion of genetic variation within species.
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Affiliation(s)
- Glenn Yannic
- Univ. Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - Oskar Hagen
- Landscape Ecology Department of Environmental Systems Sciensce Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research Birmensdorf Switzerland
| | - Flurin Leugger
- Landscape Ecology Department of Environmental Systems Sciensce Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research Birmensdorf Switzerland
| | - Dirk N Karger
- Swiss Federal Institute for Forest, Snow and Landscape Research Birmensdorf Switzerland
| | - Loïc Pellissier
- Landscape Ecology Department of Environmental Systems Sciensce Institute of Terrestrial Ecosystems ETH Zürich Zürich Switzerland.,Swiss Federal Institute for Forest, Snow and Landscape Research Birmensdorf Switzerland
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