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Wang R, Kass JM, Chaudhary C, Economo EP, Guénard B. Global biogeographic regions for ants have complex relationships with those for plants and tetrapods. Nat Commun 2024; 15:5641. [PMID: 38969636 PMCID: PMC11226674 DOI: 10.1038/s41467-024-49918-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/25/2024] [Indexed: 07/07/2024] Open
Abstract
On a global scale, biodiversity is geographically structured into regions of biotic similarity. Delineating these regions has been mostly targeted for tetrapods and plants, but those for hyperdiverse groups such as insects are relatively unknown. Insects may have higher biogeographic congruence with plants than tetrapods due to their tight ecological and evolutionary links with the former, but it remains untested. Here, we develop a global regionalization for a major and widespread insect group, ants, based on the most comprehensive distributional and phylogenetic information to date, and examine its similarity to regionalizations for tetrapods and vascular plants. Our ant regionalization supports the newly proposed Madagascan and Sino-Japanese realms based on tetrapod delineations, and it recovers clusters observed in plants but not in tetrapods, such as the Holarctic and Indo-Pacific realms. Quantitative comparison suggests strong associations among different groups-plants showed a higher congruence with ants than with tetrapods. These results underscore the wide congruence of diverse distribution patterns across the tree of life and the similarities shared by insects and plants that are not captured by tetrapod groups. Our analysis highlights the importance of developing global biogeographic maps for insect groups to obtain a more comprehensive geographic picture of life on Earth.
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Affiliation(s)
- Runxi Wang
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pok Fu Lam Road, Hong Kong SAR, China.
| | - Jamie M Kass
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
- Macroecology Laboratory, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Chhaya Chaudhary
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pok Fu Lam Road, Hong Kong SAR, China
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Benoit Guénard
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pok Fu Lam Road, Hong Kong SAR, China
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2
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Sekhavati Y, Strait D. Estimating ancestral ranges and biogeographical processes in early hominins. J Hum Evol 2024; 191:103547. [PMID: 38781711 DOI: 10.1016/j.jhevol.2024.103547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
Historical biogeography provides crucial insights into understanding the evolutionary history of hominins. We applied maximum-likelihood and biogeographical stochastic mapping to infer the ancestral ranges of hominins and estimate the frequency of biogeographical events. These events were inferred using two time-calibrated phylogenetic trees that differ in the position of Australopithecus sediba. Results suggest that regardless of which phylogeny was selected, Northcentral Africa was the preferred ancestral region for the ancestor of the Homo-Pan clade, as well as the ancestor of Sahelanthropus and later hominins. The northern and middle part of eastern Africa was the preferred ancestral region for several clades originating at subsequent deep nodes of the trees (∼5-4 Ma). The choice of tree topology had one important effect on results: whether hominin ancestors appearing after ∼4 Ma were widespread or endemic. These different patterns highlight the biogeographic significance of the phylogenetic relationships of A. sediba. Overall, the results showed that dispersal, local extinction, and sympatry played vital roles in creating the hominin distribution, whereas vicariance and jump dispersal were not as common. The results suggested symmetry in the directionality of dispersals. Distance probably influenced how rapidly taxa colonized a new region, and dispersals often followed the closest path. These findings are potentially impacted by the imperfection of the fossil record, suggesting that the results should be interpreted cautiously.
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Affiliation(s)
- Yeganeh Sekhavati
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - David Strait
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63130, USA; Palaeo-Research Institute, University of Johannesburg, Cnr Kingsway and University Road Auckland Park, PO Box 524, Auckland Park 2006, South Africa
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3
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Cooper RB, Flannery-Sutherland JT, Silvestro D. DeepDive: estimating global biodiversity patterns through time using deep learning. Nat Commun 2024; 15:4199. [PMID: 38760390 PMCID: PMC11101433 DOI: 10.1038/s41467-024-48434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/30/2024] [Indexed: 05/19/2024] Open
Abstract
Understanding how biodiversity has changed through time is a central goal of evolutionary biology. However, estimates of past biodiversity are challenged by the inherent incompleteness of the fossil record, even when state-of-the-art statistical methods are applied to adjust estimates while correcting for sampling biases. Here we develop an approach based on stochastic simulations of biodiversity and a deep learning model to infer richness at global or regional scales through time while incorporating spatial, temporal and taxonomic sampling variation. Our method outperforms alternative approaches across simulated datasets, especially at large spatial scales, providing robust palaeodiversity estimates under a wide range of preservation scenarios. We apply our method on two empirical datasets of different taxonomic and temporal scope: the Permian-Triassic record of marine animals and the Cenozoic evolution of proboscideans. Our estimates provide a revised quantitative assessment of two mass extinctions in the marine record and reveal rapid diversification of proboscideans following their expansion out of Africa and a >70% diversity drop in the Pleistocene.
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Affiliation(s)
- Rebecca B Cooper
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.
- Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland.
| | | | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.
- Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland.
- Department of Biological and Environmental Sciences, Global Gothenburg Biodiversity Centre, University of Gothenburg, Gothenburg, 413 19, Sweden.
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4
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Wilenzik IV, Barger BB, Pyron RA. Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic. PeerJ 2024; 12:e17277. [PMID: 38708352 PMCID: PMC11067913 DOI: 10.7717/peerj.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Background Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. Methods We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Results Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.
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Affiliation(s)
- Ian V. Wilenzik
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - Benjamin B. Barger
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - R. Alexander Pyron
- Department of Biology, George Washington University, Washington D.C., United States of America
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Vacher JP, Kok PJR, Rodrigues MT, Lima A, Hrbek T, Werneck FP, Manzi S, Thébaud C, Fouquet A. Diversification of the terrestrial frog genus Anomaloglossus (Anura, Aromobatidae) in the Guiana Shield proceeded from highlands to lowlands, with successive loss and reacquisition of endotrophy. Mol Phylogenet Evol 2024; 192:108008. [PMID: 38181828 DOI: 10.1016/j.ympev.2023.108008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 09/23/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
Two main landscapes emerge from the Guiana Shield: the highlands to the west called the Pantepui region and the Amazonian lowlands to the east, both harbouring numerous endemic species. With 32 currently recognized species, the genus Anomaloglossus stands out among Neotropical frogs as one that diversified only within the Guiana Shield both in the highlands and the lowlands. We present a time-calibrated phylogeny obtained by using combined mitogenomic and nuclear DNA, which suggests that the genus originates from Pantepui where extant lineages started diversifying around 21 Ma, and subsequently (ca. 17 Ma) dispersed during the Miocene Climatic Optimum to the lowlands of the eastern Guiana Shield where the ability to produce endotrophic tadpoles evolved. Further diversification within the lowlands in the A. stepheni group notably led to an evolutionary reversal toward exotrophy in one species group during the late Miocene, followed by reacquisition of endotrophy during the Pleistocene. These successive shifts of reproductive mode seem to have accompanied climatic oscillations. Long dry periods might have triggered evolution of exotrophy, whereas wetter climates favoured endotrophic forms, enabling colonization of terrestrial habitats distant from water. Acquisition, loss, and reacquisition of endotrophy makes Anomaloglossus unique among frogs and may largely explain the current species diversity. The micro evolutionary processes involved in these rapid shifts of reproductive mode remain to be revealed.
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Affiliation(s)
- Jean-Pierre Vacher
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France.
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str, Łódź 90-237, Poland; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Miguel Trefaut Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, Caixa Postal 11.461, CEP 05508-090 São Paulo, Brazil
| | - Albertina Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Tomas Hrbek
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, 69080-900 Manaus, AM, Brazil
| | - Fernanda P Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Antoine Fouquet
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
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Leroy B, Bellard C, Dias MS, Hugueny B, Jézéquel C, Leprieur F, Oberdorff T, Robuchon M, Tedesco PA. Major shifts in biogeographic regions of freshwater fishes as evidence of the Anthropocene epoch. SCIENCE ADVANCES 2023; 9:eadi5502. [PMID: 37976358 PMCID: PMC10656075 DOI: 10.1126/sciadv.adi5502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Animals and plants worldwide are structured in global biogeographic regions, which were shaped by major geologic forces during Earth history. Recently, humans have changed the course of events by multiplying global pathways of introduction for nonindigenous species and propagating local species extirpations. Here, we report on how introductions and extirpations have changed the distributions of freshwater fishes worldwide and how it affected their natural biogeographic regions. We found major shifts in natural regions, with the emergence of an intercontinental region arising from the fusion of multiple faunas, which we named Pan-Anthropocenian Global North and East Asia (PAGNEA). The PAGNEA region is evocative of the Pangea supercontinent, as flows of introductions show that dispersal has become possible again across multiple continents, suggesting that human activities have superseded natural geological forces. Our results constitute evidence on the expected modification of biostratigraphic boundaries based on freshwater fish, which are abundant in the fossil record, thereby supporting the concept of the Anthropocene epoch.
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Affiliation(s)
- Boris Leroy
- Unité Biologie des Organismes et Ecosystèmes Aquatiques (BOREA, UMR 8067), Muséum national d’Histoire naturelle, Sorbonne Université, Université de Caen Normandie, CNRS, IRD, Université des Antilles, Paris, France
| | - Céline Bellard
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Gif-sur-Yvette, France
| | - Murilo S. Dias
- Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília-DF, Brazil
| | - Bernard Hugueny
- UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), CNRS, IRD, UPS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Céline Jézéquel
- UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), CNRS, IRD, UPS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Fabien Leprieur
- MARBEC, Univ Montpellier, IRD, CNRS, IFREMER, Montpellier, France
| | - Thierry Oberdorff
- UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), CNRS, IRD, UPS, Université Paul Sabatier, F-31062 Toulouse, France
| | - Marine Robuchon
- Joint Research Centre (JRC) of the European Commission, Directorate for Sustainable Resources, 21027 Ispra (VA), Italy
| | - Pablo A. Tedesco
- UMR5174 EDB (Laboratoire Evolution et Diversité Biologique), CNRS, IRD, UPS, Université Paul Sabatier, F-31062 Toulouse, France
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7
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Brown MJM, Walker BE, Budden AP, Nic Lughadha E. Re-evaluating the importance of threatened species in maintaining global phytoregions. THE NEW PHYTOLOGIST 2023; 240:1673-1686. [PMID: 37798820 DOI: 10.1111/nph.19295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Anthropogenic introductions are known to be changing the structure of global phytogeographical regions (phytoregions), but previous studies have been limited by incomplete or biased data sets that are likely to underestimate the importance of threatened species. In this work, we analyse a comprehensive data set of all known species and their occurrences (at botanical country resolution) to quantify the impact of potential future extinction scenarios. We used Infomap, a network-based community detection algorithm, to generate phytoregional delineations for six species-distribution scenarios (native, introduced and extinctions of species that are either documented as threatened or likely to be threatened, as well as combinations thereof). We compared the numbers and sizes of phytoregions to characterise the amount and spatial distribution of changes in global phytoregions under each scenario. Extinctions of species that are predicted to be threatened had a greater homogenising effect on phytoregions than introductions, and there was some evidence that introductions may even mitigate the homogenisation caused by extinctions, though this interaction is complex. This research provides the first evidence that the loss of threatened species would have significant ramifications for global phytoregions and demonstrates the need to consider extinction processes in studies of anthropogenic effects on biodiversity patterns.
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Calvente A, da Silva APA, Edler D, Carvalho FA, Fantinati MR, Zizka A, Antonelli A. Spiny but photogenic: Amateur sightings complement herbarium specimens to reveal the bioregions of cacti. AMERICAN JOURNAL OF BOTANY 2023; 110:e16235. [PMID: 37661935 DOI: 10.1002/ajb2.16235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/05/2023]
Abstract
PREMISE Cacti are characteristic elements of the Neotropical flora and of major interest for biogeographic, evolutionary, and ecological studies. We tested global biogeographic boundaries for Neotropical Cactaceae using specimen-based occurrences, coupled with data from visual observations, as a means to tackle the known collection biases in the family. METHODS Species richness and record density were assessed for preserved specimens and human observations, and a bioregional scheme tailored to Cactaceae was produced using the interactive web application Infomap Bioregions, based on data from 261,272 point records cleaned through automated and manual steps. RESULTS We found that areas in Mexico and southwestern USA, in eastern Brazil, and along the Andean region have the greatest density of records and the highest species richness. Human observations complement information from preserved specimens substantially, especially along the Andes. We propose 24 cactus bioregions, among which the most species-rich are northern Mexico/southwestern USA, central Mexico, southern central Mexico, Central America, Mexican Pacific coast, central and southern Andes, northwestern Mexico/extreme southwestern USA, southwestern Bolivia, northeastern Brazil, and Mexico/Baja California. CONCLUSIONS The bioregionalization proposed shows biogeographic boundaries specific to cacti and can thereby aid further evolutionary, biogeographic, and ecological studies by providing a validated framework for further analyses. This classification builds upon, and is distinctive from, other expert-derived regionalization schemes for other taxa. Our results showcase how observation data, including citizen-science records, can complement traditional specimen-based data for biogeographic research, particularly for taxa with specific specimen collection and preservation challenges and those that are threatened or internationally protected.
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Affiliation(s)
- Alice Calvente
- Laboratório de Botânica Sistemática, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, 3000, CEP 59078970, Lagoa Nova, Natal, RN, Brazil
| | - Ana Paula Alves da Silva
- Laboratório de Botânica Sistemática, Departamento de Botânica e Zoologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Av. Senador Salgado Filho, 3000, CEP 59078970, Lagoa Nova, Natal, RN, Brazil
| | - Daniel Edler
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30, Gothenburg, Sweden
| | - Fernanda Antunes Carvalho
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Pampulha, CEP 31270-901, Belo Horizonte, MG, Brazil
| | - Mariana Ramos Fantinati
- Departamento de Ciências Biológicas, Universidade Estadual Paulista-câmpus de Assis, Av. Dom Antônio, 2100, Parque Universitário, CEP 19806-900, Assis, SP, Brazil
| | - Alexander Zizka
- Biodiversity of plants, Philipps University Marburg, Marburg, 35043, Germany
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30, Gothenburg, Sweden
- Royal Botanic Gardens Kew, TW9 3AE, Richmond, United Kingdom
- Department of Biology, University of Oxford, Oxford, OX1 3RB, United Kingdom
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Nuñez LP, Gray LN, Weisrock DW, Burbrink FT. The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini). Mol Phylogenet Evol 2023:107844. [PMID: 37301486 DOI: 10.1016/j.ympev.2023.107844] [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: 03/30/2022] [Revised: 06/01/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
North American Thamnophiini (gartersnakes, watersnakes, brownsnakes, and swampsnakes) are an ecologically and phenotypically diverse temperate clade of snakes representing 61 species across 10 genera. In this study, we estimate phylogenetic trees using ∼3,700 ultraconserved elements (UCEs) for 76 specimens representing 75% of all Thamnophiini species. We infer phylogenies using multispecies coalescent methods and time calibrate them using the fossil record. We also conducted ancestral area estimation to identify how major biogeographic boundaries in North America affect broadscale diversification in the group. While most nodes exhibited strong statistical support, analysis of concordant data across gene trees reveals substantial heterogeneity. Ancestral area estimation demonstrated that the genus Thamnophis was the only taxon in this subfamily to cross the Western Continental Divide, even as other taxa dispersed southward toward the tropics. Additionally, levels of gene tree discordance are overall higher in transition zones between bioregions, including the Rocky Mountains. Therefore, the Western Continental Divide may be a significant transition zone structuring the diversification of Thamnophiini during the Neogene and Pleistocene. Here we show that despite high levels of discordance across gene trees, we were able to infer a highly resolved and well-supported phylogeny for Thamnophiini, which allows us to understand broadscale patterns of diversity and biogeography.
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Affiliation(s)
- Leroy P Nuñez
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA.
| | - Levi N Gray
- Fort Collins Science Center, United States Geological Survey, Guam, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY, USA
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Zhao W, Ma J, Liu Q, Song J, Tysklind M, Liu C, Wang D, Qu Y, Wu Y, Wu F. Comparison and application of SOFM, fuzzy c-means and k-means clustering algorithms for natural soil environment regionalization in China. ENVIRONMENTAL RESEARCH 2023; 216:114519. [PMID: 36252833 DOI: 10.1016/j.envres.2022.114519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Soil attributes and their environmental drivers exhibit different patterns in different geographical directions, along with distinct regional characteristics, which may have important effects on substance migration and transformation such as organic matter and soil elements or the environmental impacts of pollutants. Therefore, regional soil characteristics should be considered in the process of regionalization for environmental management. However, no comprehensive evaluation or systematic classification of the natural soil environment has been established for China. Here, we established an index system for natural soil environmental regionalization (NSER) by combining literature data obtained based on bibliometrics with the analytic hierarchy process (AHP). Based on the index system, we collected spatial distribution data for 14 indexes at the national scale. In addition, three clustering algorithms-self-organizing feature mapping (SOFM), fuzzy c-means (FCM) and k-means (KM)-were used to classify and define the natural soil environment. We imported four cluster validity indexes (CVI) to evaluate different models: Davies-Bouldin index (DB), Silhouette index (Sil) and Calinski-Harabasz index (CH) for FCM and KM, clustering quality index (CQI) for SOFM. Analysis and comparison of the results showed that when the number of clusters was 13, the FCM clustering algorithm achieved the optimal clustering results (DB = 1.16, Sil = 0.78, CH = 6.77 × 106), allowing the natural soil environment of China to be divided into 12 regions with distinct characteristics. Our study provides a set of comprehensive scientific research methods for regionalization research based on spatial data, it has important reference value for improving soil environmental management based on local conditions in China.
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Affiliation(s)
- Wenhao Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jin Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Qiyuan Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Jing Song
- State Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Mats Tysklind
- Department of Chemistry, Umeå University, Umeå, 90187, Sweden
| | - Chengshuai Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081, China
| | - Dong Wang
- Department of Chemistry, Umeå University, Umeå, 90187, Sweden
| | - Yajing Qu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Yihang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
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11
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Miranda CL, Farias IP, Da Silva MNF, Antonelli A, Machado AF, Leite RN, Nunes MDS, De Oliveira TG, Pieczarka JC. Diversification of Amazonian spiny tree rats in genus Makalata (Rodentia, Echimyidae): Cryptic diversity, geographic structure and drivers of speciation. PLoS One 2022; 17:e0276475. [PMID: 36520936 PMCID: PMC9754209 DOI: 10.1371/journal.pone.0276475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 10/10/2022] [Indexed: 12/23/2022] Open
Abstract
Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata, whose species are strongly associated with seasonally flooded forests, watercourses and flooded islands. We use a biogeographical approach based on a mitochondrial cytochrome b gene through divergence time estimation and reconstruction of ancestral areas and events. Our findings indicate an ancient origin of Makalata for the Guiana Shield and Eastern Amazonia as ancestral area. A first cladogenetic event led to a phylogeographic break into two broader clades of Makalata through dispersal, implying a pattern of western/Eastern Amazonian clades coinciding with the Purus Arch (middle Miocene). Most of subclades we infer originated between the late Pliocene to the early Pleistocene, with few recent exceptions in the early Pliocene through dispersal and vicariant events. The hypothesis of rivers as dispersal barriers is not corroborated for Makalata, as expected for mammalian species associated with seasonally flooded environments. We identify two key events for the expansion and diversification of Makalata species: the presence of geologically stable areas in the Guiana and Brazilian shields and the transition from lacustrine conditions in western Amazonia (Acre system) to a river system, with the establishment of the Amazon River transcontinental system and its tributaries. Our results are congruent with older geological scenarios for the Amazon basin formation (Miocene), but we do not discard the influence of recent dynamics on some speciation events and, mainly, on phylogeographic structuring processes.
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Affiliation(s)
- Cleuton Lima Miranda
- Postgraduate Program in Zoology of the Museu Paraense Emílio Goeldi, Federal University of Pará, Belém, Pará, Brazil
- Laboratory of Animal Evolution and Genetics, Institute of Biological Sciences, Department of Genetics, Federal University of Amazonas, Manaus, Amazonas, Brazil
| | - Izeni Pires Farias
- Laboratory of Animal Evolution and Genetics, Institute of Biological Sciences, Department of Genetics, Federal University of Amazonas, Manaus, Amazonas, Brazil
| | | | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Arielli Fabrício Machado
- Laboratory of Animal Evolution and Genetics, Institute of Biological Sciences, Department of Genetics, Federal University of Amazonas, Manaus, Amazonas, Brazil
- Postgraduate Program in Ecology, National Amazon Research Institute, Manaus, Amazonas, Brazil
| | - Rafael N. Leite
- Postgraduate Program in Ecology, National Amazon Research Institute, Manaus, Amazonas, Brazil
| | - Mario Da Silva Nunes
- Laboratory of Animal Evolution and Genetics, Institute of Biological Sciences, Department of Genetics, Federal University of Amazonas, Manaus, Amazonas, Brazil
| | | | - Julio Cesar Pieczarka
- Cytogenetics Laboratory, Center for Advanced Biodiversity Studies, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil
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Ferrari A, Janisch Alvares D, Buratto PM, Ribeiro Barão K. Distribution patterns of Triatominae (Hemiptera: Reduviidae) in the Americas: an analysis based on networks and endemicity. Cladistics 2022; 38:563-581. [PMID: 35148437 DOI: 10.1111/cla.12500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 01/31/2023] Open
Abstract
Triatominae, commonly known as kissing bugs, are a group of approximately 150 species of hematophagous reduviids, some of which are vectors of Trypanosoma cruzi, the etiological agent of the Chagas disease. Distributional patterns of triatomines have been studied based on macroecological and historical biogeographic approaches, but the definition of distributional patterns and areas of endemism are yet to be defined based on objective criteria. We used two methods to identify biogeographic units in the Triatominae: the endemicity analysis based on an optimality criterion (NDM/VNDM software) and a network approach aimed to simplify and highlight the underlying structure in species distributions (Infomap Bioregions). Information on species distributions was obtained from a data paper, comprising 21 815 records for 135 triatomine species occurring in the Americas. The resulting areas of each method were clustered using a meta consensus criterion based on dissimilarities and interpreted as recurrent areas. The NDM areas show a nested structure, presenting greater restrictions to the inclusion of species in a given area, requiring broad sympatry. In contrast, bioregions emphasize spatial patterns with better-delimited areas and species occurrences do not need to be highly congruent. When areas were clustered based on their species composition two clear patterns arose from both methods: (i) areas within the southern Amazon and southeast South America, especially in the Chacoan subregion, formed a cluster, and (ii) areas north of the Amazon, Pacific, Mesoamerica, Mexican transition zone and Nearctic formed another cluster. Moreover, within each of these two clusters, there was a latitudinal gradient of the areas in the Americas showing spatial similarity between the areas found in both methods. Results of both methods show well-bound areas separating the triatomine fauna in the Brazilian subregions, resulting in the recognition of areas corresponding to the biomes Chaco, Pampa, Cerrado, and Caatinga, and, to a lesser extent, the Atlantic Forest.
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Affiliation(s)
- Augusto Ferrari
- Programa de Pós-Graduação em Biologia Animal - PPG-BAN, Universidade Federal do Rio Grande Sul, UFRGS, Av. Bento Gonçalves 9500, Porto Alegre, 91540-000, Brazil.,Laboratório de Entomologia, Sistemática e Biogeografia - LESB, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália, km 8, Rio Grande, Rio Grande do Sul, 96203-900, Brazil
| | - Diego Janisch Alvares
- Programa de Pós-Graduação em Biologia Animal - PPG-BAN, Universidade Federal do Rio Grande Sul, UFRGS, Av. Bento Gonçalves 9500, Porto Alegre, 91540-000, Brazil.,Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul (GEMARS), Rua Bento Gonçalves, 165/1002, Torres, 95560-000, Brazil
| | - Patrícia Maria Buratto
- Laboratório de Entomologia, Sistemática e Biogeografia - LESB, Instituto de Ciências Biológicas, Universidade Federal do Rio Grande - FURG, Av. Itália, km 8, Rio Grande, Rio Grande do Sul, 96203-900, Brazil
| | - Kim Ribeiro Barão
- Laboratório de Sistemática e Diversidade de Artrópodes, Unidade Educacional Penedo, Universidade Federal de Alagoas, Av. Beira Rio, s/n, Penedo, 57200-00, Brazil
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13
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Neuman M. PISA data clusters reveal student and school inequality that affects results. PLoS One 2022; 17:e0267040. [PMID: 35544465 PMCID: PMC9094565 DOI: 10.1371/journal.pone.0267040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/31/2022] [Indexed: 11/19/2022] Open
Abstract
The data from the PISA survey show that student performance correlates with socio-economic background, that private schools have higher results and more privileged students, and that this varies between countries. We explore this further and analyze the PISA data using methods from network theory and find clusters of countries whose students have similar performance and socio-economic background. Interestingly, we find a cluster of countries, including China, Spain and Portugal, characterized by less privileged students performing well. When considering private schools only, some countries, such as Portugal and Brazil, are in a cluster with mostly wealthy countries characterized by privileged students. Swedish grades are compared to PISA results, and we see that the higher grades in private schools are in line with the PISA results, suggesting that there is no grade inflation in this case, but differences in socio-economic background suggest that this is due to school segregation.
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Affiliation(s)
- Magnus Neuman
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
- * E-mail:
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Valle D, Jameel Y, Betancourt B, Azeria ET, Attias N, Cullen J. Automatic selection of the number of clusters using Bayesian clustering and sparsity-inducing priors. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2524. [PMID: 34918421 DOI: 10.1002/eap.2524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/14/2021] [Accepted: 07/09/2021] [Indexed: 06/14/2023]
Abstract
Clustering is a ubiquitous task in ecological and environmental sciences and multiple methods have been developed for this purpose. Because these clustering methods typically require users to a priori specify the number of groups, the standard approach is to run the algorithm for different numbers of groups and then choose the optimal number using a criterion (e.g., AIC or BIC). The problem with this approach is that it can be computationally expensive to run these clustering algorithms multiple times (i.e., for different numbers of groups) and some of these information criteria can lead to an overestimation of the number of groups. To address these concerns, we advocate for the use of sparsity-inducing priors within a Bayesian clustering framework. In particular, we highlight how the truncated stick-breaking (TSB) prior, a prior commonly adopted in Bayesian nonparametrics, can be used to simultaneously determine the number of groups and estimate model parameters for a wide range of Bayesian clustering models without requiring the fitting of multiple models. We illustrate the ability of this prior to successfully recover the true number of groups for three clustering models (two types of mixture models, applied to GPS movement data and species occurrence data, as well as the species archetype model) using simulated data in the context of movement ecology and community ecology. We then apply these models to armadillo movement data in Brazil, plant occurrence data from Alberta (Canada), and bird occurrence data from North America. We believe that many ecological and environmental sciences applications will benefit from Bayesian clustering methods with sparsity-inducing priors given the ubiquity of clustering and the associated challenge of determining the number of groups. Two R packages, EcoCluster and bayesmove, are provided that enable the straightforward fitting of these models with the TSB prior.
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Affiliation(s)
- Denis Valle
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, USA
| | - Yusuf Jameel
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, USA
| | - Brenda Betancourt
- Department of Statistics, University of Florida, Gainesville, Florida, USA
| | - Ermias T Azeria
- Alberta Biodiversity Monitoring Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Nina Attias
- Ecology and Conservation Graduate Program, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Joshua Cullen
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, USA
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15
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Cardoso D, Moonlight PW, Ramos G, Oatley G, Dudley C, Gagnon E, Queiroz LPD, Pennington RT, Särkinen TE. Defining Biologically Meaningful Biomes Through Floristic, Functional, and Phylogenetic Data. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.723558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While we have largely improved our understanding on what biomes are and their utility in global change ecology, conservation planning, and evolutionary biology is clear, there is no consensus on how biomes should be delimited or mapped. Existing methods emphasize different aspects of biomes, with different strengths and limitations. We introduce a novel approach to biome delimitation and mapping, based upon combining individual regionalizations derived from floristic, functional, and phylogenetic data linked to environmentally trained species distribution models. We define “core Biomes” as areas where independent regionalizations agree and “transition zones” as those whose biome identity is not corroborated by all analyses. We apply this approach to delimiting the neglected Caatinga seasonally dry tropical forest biome in northeast Brazil. We delimit the “core Caatinga” as a smaller and more climatically limited area than previous definitions, and argue it represents a floristically, functionally, and phylogenetically coherent unit within the driest parts of northeast Brazil. “Caatinga transition zones” represent a large and biologically important area, highlighting that ecological and evolutionary processes work across environmental gradients and that biomes are not categorical variables. We discuss the differences among individual regionalizations in an ecological and evolutionary context and the potential limitations and utility of individual and combined biome delimitations. Our integrated ecological and evolutionary definition of the Caatinga and associated transition zones are argued to best describe and map biologically meaningful biomes.
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16
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Li Q, Sun H, Boufford DE, Bartholomew B, Fritsch PW, Chen J, Deng T, Ree RH. Grade of Membership models reveal geographical and environmental correlates of floristic structure in a temperate biodiversity hotspot. THE NEW PHYTOLOGIST 2021; 232:1424-1435. [PMID: 33932292 DOI: 10.1111/nph.17443] [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] [Received: 11/03/2020] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Identifying the contours and correlates of species turnover is central to understanding the nature of biogeographical regions. The Hengduan Mountains region of south-central China (HMR) is well known for its high diversity of plants, but its boundaries and internal floristic structure are poorly understood, especially in relation to geographical and environmental factors. With data on occurrences and elevational ranges of seed plants across the HMR and adjacent areas of the greater Qinghai-Tibet Plateau, we identified motifs (distinct species assemblages) by Grade of Membership models, and characterized relative contributions of geography, elevation, and climate to their spatial patterns. Motifs segregate primarily by latitude, elevation, and correlated environmental variables, most sharply across the tropical-temperate divide. Secondarily, they segregate by longitude and geographical features, and reveal a novel divide across the Jinsha River. A core set of motifs corresponds to previous delineations of the HMR. The HMR biodiversity hotspot is more a mosaic of floristic elements than a cohesive entity. Grade of Membership models effectively reveal the geographical contours of biotic structure, and are a valuable new tool for biogeographical analysis.
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Affiliation(s)
- Qin Li
- Department of Science and Education, Field Museum, Chicago, IL, 60605, USA
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | | | - Bruce Bartholomew
- Department of Botany, California Academy of Sciences, Golden Gate Park, San Francisco, CA, 94118, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, Fort Worth, TX, 76017, USA
| | - Jiahui Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Richard H Ree
- Department of Science and Education, Field Museum, Chicago, IL, 60605, USA
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17
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Benson RBJ, Butler R, Close RA, Saupe E, Rabosky DL. Biodiversity across space and time in the fossil record. Curr Biol 2021; 31:R1225-R1236. [PMID: 34637736 DOI: 10.1016/j.cub.2021.07.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fossil record is the primary source of information on how biodiversity has varied in deep time, providing unique insight on the long-term dynamics of diversification and their drivers. However, interpretations of fossil record diversity patterns have been much debated, with a traditional focus on global diversity through time. Problems arise because the fossil record is spatially and temporally patchy, so 'global' diversity estimates actually represent the summed diversity across a set of geographically and environmentally distinct regions that vary substantially in number and identity through time. Furthermore, a focus on global diversity lumps the signal of ecological drivers at local and regional scales with the signal of global-scale processes, including variation in the distribution of environments and in provincialism (the extent of subdivision into distinct biogeographic regions). These signals cannot be untangled by studying global diversity measures alone. These conceptual and empirical concerns necessitate a shift away from the study of 'biodiversity through time' and towards the study of 'biodiversity across time and space'. Spatially explicit investigations, including analyses of local- and regional-scale datasets, are central to achieving this and allow analysis of geographic scale, location and the environmental parameters directly experienced by organisms. So far, research in this area has revealed the stability of species richness variation among environments through time, and the potential climatic and Earth-system drivers of changing biodiversity. Ultimately, this research program promises to address key questions regarding the assembly of biodiversity, and the contributions of local-, regional- and global-scale processes to the diversification of life on Earth.
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Affiliation(s)
- Roger B J Benson
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK.
| | - Richard Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roger A Close
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Erin Saupe
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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18
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Kocsis ÁT, Reddin CJ, Scotese CR, Valdes PJ, Kiessling W. Increase in marine provinciality over the last 250 million years governed more by climate change than plate tectonics. Proc Biol Sci 2021; 288:20211342. [PMID: 34403638 PMCID: PMC8370804 DOI: 10.1098/rspb.2021.1342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 07/26/2021] [Indexed: 11/12/2022] Open
Abstract
Amidst long-term fluctuations of the abiotic environment, the degree to which life organizes into distinct biogeographic provinces (provinciality) can reveal the fundamental drivers of global biodiversity. Our understanding of present-day biogeography implies that changes in the distribution of continents across climatic zones have predictable effects on habitat distribution, dispersal barriers and the evolution of provinciality. To assess marine provinciality through the Phanerozoic, here we (a) simulate provinces based on palaeogeographic reconstructions and global climate models and (b) contrast them with empirically derived provinces that we define using network analysis of fossil occurrences. Simulated and empirical patterns match reasonably well and consistently suggest a greater than 15% increase in provinciality since the Mesozoic era. Although both factors played a role, the simulations imply that the effect of the latitudinal temperature gradient has been twice as important in determining marine provinciality as continental configuration.
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Affiliation(s)
- Ádám T Kocsis
- GeoZentrum Nordbayern, Universität Erlangen-Nürnberg, Loewenichstraße 28, 91054 Erlangen, Germany
- MTA-MTM-ELTE Research Group for Paleontology, PO box 137, 1431 Budapest, Hungary
| | - Carl J Reddin
- GeoZentrum Nordbayern, Universität Erlangen-Nürnberg, Loewenichstraße 28, 91054 Erlangen, Germany
- Museum für Naturkunde, Invalidenstraße 43, 10115 Berlin, Germany
| | - Christopher R Scotese
- Earth and Planetary Sciences, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3130, USA
| | - Paul J Valdes
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK
| | - Wolfgang Kiessling
- GeoZentrum Nordbayern, Universität Erlangen-Nürnberg, Loewenichstraße 28, 91054 Erlangen, Germany
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19
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Noroozi J, Khalvati S, Nafisi H, Kaveh A, Nazari B, Zare G, Minaei M, Vitek E, Schneeweiss GM. Endemics determine bioregionalization in the alpine zone of the Irano-Anatolian biodiversity hotspot (South-West Asia). ALPINE BOTANY 2021; 131:177-186. [PMID: 34721248 PMCID: PMC8549998 DOI: 10.1007/s00035-021-00266-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Alpine habitats are characterized by a high rate of range restricted species compared to those of lower elevations. This is also the case for the Irano-Anatolian global biodiversity hotspot in South-West Asia, which is a mountainous area harbouring a high amount of endemic species. Using two quantitative approaches, Endemicity Analysis and Network-Clustering, we want to identify areas of concordant species distribution patterns in the alpine zone of this region as well as to test the hypothesis that, given the high proportion of endemics among alpine species, delimitation of these areas is determined mainly by endemic alpine species, i.e., areas of concordant species distribution patterns are congruent with areas of endemism. Endemicity Analysis identified six areas of concordant species distribution patterns irrespective of dataset (total alpine species versus endemic alpine species), whereas the Network-Clustering approach identified five and four Bioregions from total alpine species and endemic alpine species, respectively. Most of these areas have been previously identified using the endemic flora of different elevational zones. The identified units using both methods and both datasets are strongly congruent, proposing that they reveal meaningful distribution patterns. Bioregionalization in the Irano-Anatolian biodiversity hotspot appears to be strongly influenced by the endemic alpine species, a pattern likely to hold in alpine regions outside the Irano-Anatolian hotspot. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s00035-021-00266-7.
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Affiliation(s)
- Jalil Noroozi
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Sina Khalvati
- Department of Biology, Bu-Ali Sina University, Hamedan, Iran
| | - Haniyeh Nafisi
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Akram Kaveh
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behnaz Nazari
- Department of Plant Biology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Golshan Zare
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Masoud Minaei
- Department of Geography, Ferdowsi University of Mashhad, Mashhad, Iran
- Geographic Information Science/System and Remote Sensing Laboratory (GISSRS: lab), Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ernst Vitek
- Natural History Museum of Vienna, Vienna, Austria
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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20
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Flores-Tolentino M, Beltrán-Rodríguez L, Morales-Linares J, Ramírez Rodríguez JR, Ibarra-Manríquez G, Dorado Ó, Villaseñor JL. Biogeographic regionalization by spatial and environmental components: Numerical proposal. PLoS One 2021; 16:e0253152. [PMID: 34129612 PMCID: PMC8205180 DOI: 10.1371/journal.pone.0253152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/29/2021] [Indexed: 11/19/2022] Open
Abstract
Regionalization through the analysis of species groups offers important advantages in conservation biology, compared to the single taxon approach in areas of high species richness. We use a systematic framework for biogeographic regionalization at a regional scale based on species turnover and environmental drivers (climate variables and soil properties) mainly of herbaceous plant species richness. To identify phytogeographic regions in the Balsas Depression (BD), we use Asteraceae species, a family widely distributed in Seasonally Dry Tropical Forest (SDTF) and the most diverse of the vascular plants in Mexico. Occurrence records of 571 species were used to apply a quantitative analysis based on the species turnover, the rate of changes in their composition between sites (β-Simpson index) and the analysis of the identified environmental drivers. Also, the environmental predictors that influence species richness in the SDTF were determined with a redundancy analysis. We identified and named two phytogeographic districts within the SDTF of the BD (Upper Balsas and Lower Balsas). According to the multi-response permutation procedure, floristic composition of the two districts differs significantly, and the richness of exclusive species in Upper Balsas was higher (292 species) than in the Lower Balsas (32 species). The proportion of Mg and Ca in the soil and the precipitation of the driest three-month period were the environmental factors with greatest positive influence on species richness. The division of geographic districts subordinated to the province level, based on diverse families such as Asteraceae, proved to be appropriate to set up strategies for the conservation of the regional flora, since at this scale, variation in species richness is more evident. Our findings are consistent with a growing body of biogeographic literature that indicates that the identification of smaller biotic districts is more efficient for the conservation of biodiversity, particularly of endemic or rare plants, whose distribution responds more to microhabitats variation.
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Affiliation(s)
- Mayra Flores-Tolentino
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Leonardo Beltrán-Rodríguez
- Jardín Botánico–Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México, Mexico
| | - Jonas Morales-Linares
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - J. Rolando Ramírez Rodríguez
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Guillermo Ibarra-Manríquez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico
| | - Óscar Dorado
- Centro de Educación Ambiental e Investigación Sierra de Huautla, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - José Luis Villaseñor
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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21
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Folk RA, Siniscalchi CM. Biodiversity at the global scale: the synthesis continues. AMERICAN JOURNAL OF BOTANY 2021; 108:912-924. [PMID: 34181762 DOI: 10.1002/ajb2.1694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/14/2021] [Indexed: 06/13/2023]
Abstract
Traditionally, the generation and use of biodiversity data and their associated specimen objects have been primarily the purview of individuals and small research groups. While deposition of data and specimens in herbaria and other repositories has long been the norm, throughout most of their history, these resources have been accessible only to a small community of specialists. Through recent concerted efforts, primarily at the level of national and international governmental agencies over the last two decades, the pace of biodiversity data accumulation has accelerated, and a wider array of biodiversity scientists has gained access to this massive accumulation of resources, applying them to an ever-widening compass of research pursuits. We review how these new resources and increasing access to them are affecting the landscape of biodiversity research in plants today, focusing on new applications across evolution, ecology, and other fields that have been enabled specifically by the availability of these data and the global scope that was previously beyond the reach of individual investigators. We give an overview of recent advances organized along three lines: broad-scale analyses of distributional data and spatial information, phylogenetic research circumscribing large clades with comprehensive taxon sampling, and data sets derived from improved accessibility of biodiversity literature. We also review synergies between large data resources and more traditional data collection paradigms, describe shortfalls and how to overcome them, and reflect on the future of plant biodiversity analyses in light of increasing linkages between data types and scientists in our field.
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
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Gatto CAFR, Cohn-Haft M. Spatial Congruence Analysis (SCAN): A method for detecting biogeographical patterns based on species range congruences. PLoS One 2021; 16:e0245818. [PMID: 34014918 PMCID: PMC8136640 DOI: 10.1371/journal.pone.0245818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/10/2021] [Indexed: 11/19/2022] Open
Abstract
Species with congruent geographical distributions, potentially caused by common historical and ecological spatial processes, constitute biogeographical units called chorotypes. Nevertheless, the degree of spatial range congruence characterizing these groups of species is rarely used as an explicit parameter. Methods conceived for the identification of patterns of shared ranges often suffer from scale bias associated with the use of grids, or the incapacity to describe the full complexity of patterns, from core areas of high spatial congruence, to long gradients of range distributions expanding from these core areas. Here, we propose a simple analytical method, Spatial Congruence Analysis (SCAN), which identifies chorotypes by mapping direct and indirect spatial relationships among species. Assessments are made under a referential value of congruence as an explicit numerical parameter. A one-layered network connects species (vertices) using pairwise spatial congruence estimates (edges). This network is then analyzed for each species, separately, by an algorithm which searches for spatial relationships to the reference species. The method was applied to two datasets: a simulated gradient of ranges and real distributions of birds. The simulated dataset showed that SCAN can describe gradients of distribution with a high level of detail. The bird dataset showed that only a small portion of range overlaps is biogeographically meaningful, and that there is a large variation in types of patterns that can be found with real distributions. Species analyzed separately may converge on similar or identical groups, may be nested in larger chorotypes, or may even generate overlapped patterns with no species in common. Chorotypes can vary from simple ones, composed by few highly congruent species, to complex, with numerous alternative component species and spatial configurations, which offer insights about possible processes driving these patterns in distinct degrees of spatial congruence. Metrics such as congruence, depth, richness, and ratio between common and total areas can be used to describe chorotypes in detail, allowing comparisons between patterns across regions and taxa.
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Affiliation(s)
- Cassiano A. F. R. Gatto
- Pós Graduação em Ecologia—PPG-ECO, Instituto Nacional de Pesquisas da Amazônia—INPA, Manaus, Brazil
| | - Mario Cohn-Haft
- Coleção de Aves, Coordenação de Pesquisas em Biodiversidade, Instituto Nacional de Pesquisas da Amazônia–INPA, Manaus, Brazil
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23
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Matos-Maraví P, Wahlberg N, Freitas AVL, Devries P, Antonelli A, Penz CM. Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Regional species diversity is explained ultimately by speciation, extinction and dispersal. Here, we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for the distribution and diversity of extant species. We focused on the tribe Brassolini (owl butterflies and allies), a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We inferred a robust species tree using the multispecies coalescent framework and a dataset including molecular and morphological characters. This formed the basis for three changes in Brassolini classification: (1) Naropina syn. nov. is subsumed within Brassolina; (2) Aponarope syn. nov. is subsumed within Narope; and (3) Selenophanes orgetorix comb. nov. is reassigned from Catoblepia to Selenophanes. By applying biogeographical stochastic mapping, we found contrasting species diversification and dispersal dynamics across rainforest biomes, which might be explained, in part, by the geological and environmental history of each bioregion. Our results revealed a mosaic of biome-specific evolutionary histories within the Neotropics, where butterfly species have diversified rapidly (cradles: Mesoamerica), have accumulated gradually (museums: Atlantic Forest) or have diversified and accumulated alternately (Amazonia). Our study contributes evidence from a major butterfly lineage that the Neotropics are a museum and a cradle of species diversity.
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Affiliation(s)
- Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, Branišovská 1160/31, 37005 České Budějovice, Czech Republic
| | - Niklas Wahlberg
- Department of Biology, Lund University, Sölvegatan 37, 22362 Lund, Sweden
| | - André V L Freitas
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, CEP 13.083-862 Campinas, São Paulo, Brazil
| | - Phil Devries
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
- Courtesy Curators of Lepidoptera, Florida Museum of Natural History, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Carl Skottsbergs gata 22B, 41319 Gothenburg, Sweden
- Royal Botanical Gardens Kew, Richmond TW9 3AE, UK
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Carla M Penz
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA
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Daru BH. Exploring a new way to think about climate regions. eLife 2021; 10:67422. [PMID: 33722341 PMCID: PMC7963472 DOI: 10.7554/elife.67422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 11/13/2022] Open
Abstract
A new system for classifying climates emerges from modeling the environmental conditions that 26,000 species of tetrapods experience in their home range.
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Affiliation(s)
- Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, United States
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25
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A multiscale view of the Phanerozoic fossil record reveals the three major biotic transitions. Commun Biol 2021; 4:309. [PMID: 33686149 PMCID: PMC7977041 DOI: 10.1038/s42003-021-01805-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 02/03/2021] [Indexed: 11/14/2022] Open
Abstract
The hypothesis of the Great Evolutionary Faunas is a foundational concept of macroevolutionary research postulating that three global mega-assemblages have dominated Phanerozoic oceans following abrupt biotic transitions. Empirical estimates of this large-scale pattern depend on several methodological decisions and are based on approaches unable to capture multiscale dynamics of the underlying Earth-Life System. Combining a multilayer network representation of fossil data with a multilevel clustering that eliminates the subjectivity inherent to distance-based approaches, we demonstrate that Phanerozoic oceans sequentially harbored four global benthic mega-assemblages. Shifts in dominance patterns among these global marine mega-assemblages were abrupt (end-Cambrian 494 Ma; end-Permian 252 Ma) or protracted (mid-Cretaceous 129 Ma), and represent the three major biotic transitions in Earth’s history. Our findings suggest that gradual ecological changes associated with the Mesozoic Marine Revolution triggered a protracted biotic transition comparable in magnitude to the end-Permian transition initiated by the most severe biotic crisis of the past 500 million years. Overall, our study supports the notion that both long-term ecological changes and major geological events have played crucial roles in shaping the mega-assemblages that dominated Phanerozoic oceans. Rojas et al. present a new multi-scale model that reveals the three major biotic transitions of the Phanerozoic fossil record. This new model supports the hypothesis that both long-term ecological changes and major geological events played crucial roles in shaping ocean mega-assemblages through the Phanerozoic.
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Rivera JA, Rich HN, Michelle Lawing A, Rosenberg MS, Martins EP. Occurrence data uncover patterns of allopatric divergence and interspecies interactions in the evolutionary history of Sceloporus lizards. Ecol Evol 2021; 11:2796-2813. [PMID: 33767837 PMCID: PMC7981219 DOI: 10.1002/ece3.7237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 11/06/2022] Open
Abstract
As shown from several long-term and time-intensive studies, closely related, sympatric species can impose strong selection on one another, leading to dramatic examples of phenotypic evolution. Here, we use occurrence data to identify clusters of sympatric Sceloporus lizard species and to test whether Sceloporus species tend to coexist with other species that differ in body size, as we would expect when there is competition between sympatric congeners. We found that Sceloporus species can be grouped into 16 unique bioregions. Bioregions that are located at higher latitudes tend to be larger and have fewer species, following Rapoport's rule and the latitudinal diversity gradient. Species richness was positively correlated with the number of biomes and elevation heterogeneity of each bioregion. Additionally, most bioregions show signs of phylogenetic underdispersion, meaning closely related species tend to occur in close geographic proximity. Finally, we found that although Sceloporus species that are similar in body size tend to cluster geographically, small-bodied Sceloporus species are more often in sympatry with larger-bodied Sceloporus species than expected by chance alone, whereas large-bodied species cluster with each other geographically and phylogenetically. These results suggest that community composition in extant Sceloporus species is the result of allopatric evolution, as closely related species move into different biomes, and interspecies interactions, with sympatry between species of different body sizes. Our phyloinformatic approach offers unique and detailed insights into how a clade composed of ecologically and morphologically disparate species are distributed over large geographic space and evolutionary time.
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Affiliation(s)
| | | | - A. Michelle Lawing
- Department of Ecosystem and Science ManagementTexas A&M UniversityCollege StationTXUSA
| | - Michael S. Rosenberg
- Center for the Study of Biological ComplexityVirginia Commonwealth UniversityRichmondVAUSA
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White AE, Dey KK, Stephens M, Price TD. Dispersal syndromes drive the formation of biogeographical regions, illustrated by the case of Wallace's Line. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2021; 30:685-696. [PMID: 33776580 PMCID: PMC7986858 DOI: 10.1111/geb.13250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/10/2020] [Accepted: 12/01/2020] [Indexed: 06/07/2023]
Abstract
AIM Biogeographical regions (realms) reflect patterns of co-distributed species (biotas) across space. Their boundaries are set by dispersal barriers and difficulties of establishment in new locations. We extend new methods to assess these two contributions by quantifying the degree to which realms intergrade across geographical space and the contributions of individual species to the delineation of those realms. As our example, we focus on Wallace's Line, the most enigmatic partitioning of the world's faunas, where climate is thought to have little effect and the majority of dispersal barriers are short water gaps. LOCATION Indo-Pacific. TIME PERIOD Present day. MAJOR TAXA STUDIED Birds and mammals. METHODS Terrestrial bird and mammal assemblages were established in 1-degree map cells using range maps. Assemblage structure was modelled using latent Dirichlet allocation, a continuous clustering method that simultaneously establishes the likely partitioning of species into biotas and the contribution of biotas to each map cell. Phylogenetic trees were used to assess the contribution of deep historical processes. Spatial segregation between biotas was evaluated across time and space in comparison with numerous hard realm boundaries drawn by various workers. RESULTS We demonstrate that the strong turnover between biotas coincides with the north-western extent of the region not connected to the mainland during the Pleistocene, although the Philippines contains mixed contributions. At deeper taxonomic levels, Sulawesi and the Philippines shift to primarily Asian affinities, resulting from transgressions of a few Asian-derived lineages across the line. The partitioning of biotas sometimes produces fragmented regions that reflect habitat. Differences in partitions between birds and mammals reflect differences in dispersal ability. MAIN CONCLUSIONS Permanent water barriers have selected for a dispersive archipelago fauna, excluded by an incumbent continental fauna on the Sunda shelf. Deep history, such as plate movements, is relatively unimportant in setting boundaries. The analysis implies a temporally dynamic interaction between a species' intrinsic dispersal ability, physiographic barriers, and recent climate change in the genesis of Earth's biotas.
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Affiliation(s)
- Alexander E. White
- Office of the Chief Information OfficerSmithsonian InstitutionWashingtonDCUSA
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Department of Ecology and EvolutionUniversity of ChicagoChicagoILUSA
| | - Kushal K. Dey
- Department of EpidemiologyHarvard T. H. Chan School of Public HealthBostonMAUSA
- Department of StatisticsUniversity of ChicagoChicagoILUSA
| | | | - Trevor D. Price
- Department of Ecology and EvolutionUniversity of ChicagoChicagoILUSA
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Calatayud J, Neuman M, Rojas A, Eriksson A, Rosvall M. Regularities in species' niches reveal the world's climate regions. eLife 2021; 10:58397. [PMID: 33554863 PMCID: PMC7963475 DOI: 10.7554/elife.58397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 02/07/2021] [Indexed: 11/13/2022] Open
Abstract
Climate regions form the basis of many ecological, evolutionary, and conservation studies. However, our understanding of climate regions is limited to how they shape vegetation: they do not account for the distribution of animals. Here, we develop a network-based framework to identify important climates worldwide based on regularities in realized niches of about 26,000 tetrapods. We show that high-energy climates, including deserts, tropical savannas, and steppes, are consistent across animal- and plant-derived classifications, indicating similar underlying climatic determinants. Conversely, temperate climates differ across all groups, suggesting that these climates allow for idiosyncratic adaptations. Finally, we show how the integration of niche classifications with geographical information enables the detection of climatic transition zones and the signal of geographic and historical processes. Our results identify the climates shaping the distribution of tetrapods and call for caution when using general climate classifications to study the ecology, evolution, or conservation of specific taxa.
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Affiliation(s)
- Joaquín Calatayud
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden.,Departamento de Biología, Geología, Física y Química inorgánica, Universidad Rey Juan Carlos, Madrid, Spain
| | - Magnus Neuman
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | - Alexis Rojas
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | - Anton Eriksson
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | - Martin Rosvall
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
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29
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Abstract
The evolution of long-term sustainable societies is closely connected to the transformation of the physical built environment in which those societies operate. In this paper, we present a comprehensive set of narratives for the built environment in Japan, consistent with the shared socio-economic pathways (SSPs) framework, to assess the future evolution of the adaptation and mitigation challenges. We focus on the linkage between sustainability factors and human living environments including urban form, buildings, and basic infrastructures. We introduce a new, sixth narrative to the SSPs, an alternative interpretation of SSP1. Whereas the original SSP1 assumes high societal and environmental sustainability combined with relatively high economic growth, the SSP1 variant does not highly rely on economic growth and is oriented towards a lower and more locally oriented consumption lifestyle. Nature-based solutions are integrated and examined in the new SSP1 narrative, which is aligned with the adaptation to the digital era with freedom of location. Recent global crises such as climate change and the COVID-19 pandemic may accelerate the transformation of societies. Therefore, this study attempts to imply the benefits and trade-offs of alternative pathways for the built environment.
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30
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Koutsikos N, Vardakas L, Vavalidis T, Kalogianni E, Dimitriou E, Kalantzi OI, Zogaris S. Defining non-indigenous fish assemblage types in Mediterranean rivers: Network analysis and management implications. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 278:111551. [PMID: 33157462 DOI: 10.1016/j.jenvman.2020.111551] [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] [Received: 05/20/2020] [Revised: 09/25/2020] [Accepted: 10/18/2020] [Indexed: 06/11/2023]
Abstract
The design and implementation of appropriate management actions to tackle the spread and negative impacts of non-indigenous fish species (NIFS) in freshwater ecosystems still remains a complex task. In an effort to address the limitations of current managerial approaches, our study develops and applies a classification framework to define non-indigenous fish assemblage types (FATs) in Mediterranean riverine ecosystems and identifies the linkage with various regional, local, biotic and abiotic environmental factors. This framework contributes to a pre-invasion stage screening and to the design of effective type-specific post-invasion management actions dealing with specific NIFS assemblages. A network analysis was applied in order to extract NIFS community level information from 393 samples obtained from 51 river basins of Greece, while a multivariate ordination analysis was conducted to detect the factors best explaining the structure and distribution of FATs. The association patterns of the study's inputs and outcomes are illustrated through an alluvial diagram, providing insights across different spatial scales. In total, five FATs were generated where the major NIFS contributors of average similarity within each modularity class revealed the key indicator species (Gambusia-FAT; Carassius/Lepomis-FAT; Pseudorasbora-FAT; Salmonids-FAT and Carp-FAT). Overall, the identified FATs varied spatially, indicating different community structure, mainly based on the diverse habitat preferences and life-history traits of indicator species. Alien FATs were mainly distributed within large and transboundary rivers, while Translocated and Salmonids FATs mostly occupied ecoregions with relatively depauperate faunas and often in biodiversity hotspots. The results of this study can identify conservation priorities within FATs, inform specific-type post-invasion management actions tackling NIFS, while in addition may provide valuable information for protecting high-priority water bodies before invasion.
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Affiliation(s)
- Nicholas Koutsikos
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, 19013, Attica, Greece; Department of Environment, University of the Aegean, Mytilene, 81100, Greece.
| | - Leonidas Vardakas
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, 19013, Attica, Greece
| | - Theocharis Vavalidis
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, 19013, Attica, Greece
| | - Eleni Kalogianni
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, 19013, Attica, Greece
| | - Elias Dimitriou
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, 19013, Attica, Greece
| | | | - Stamatis Zogaris
- Hellenic Centre for Marine Research, Institute of Marine Biological Resources and Inland Waters, Anavissos, 19013, Attica, Greece
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31
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Alves FVS, Loeuille BFP. Geographic distribution patterns of species of the subtribe Lychnophorinae (Asteraceae: Vernonieae). RODRIGUÉSIA 2021. [DOI: 10.1590/2175-7860202172072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract With 119 species distributed in 19 genera, most species of the subtribe Lychnophorinae are endemic to the Espinhaço Range in central eastern Brazil. This region is characterized especially by the campos rupestres, a grassland mosaic associated with vegetation on rock outcrops, which display a high level of endemism. The present work aims to identify distribution patterns, collection density, species richness and research bias in collections. Ten geographic distribution patterns were identified: Chapada Diamantina, Chapada dos Veadeiros and adjacent mountains, Pico da Aliança, Extension of the Espinhaço Range, Central-South Arc of Minas Gerais, Espinhaço Range and Brasília Arc, Campos Rupestres and Restinga, Chapada Diamantina and Caatinga, Northwest-Southeast Diagonal and East Triangle. Other Angiosperm families present similar distribution, mainly in the Espinhaço Meridional, where higher collecting efforts are present. Species richness is higher in sites with higher collection intensity, however, the northeast of Goiás shows the opposite pattern. Spearman correlation analysis shows a strong correlation between collection density and species richness, with an exponential asymptotic model that is quite significant for the total variation of species richness. The cluster analysis presented five clusters correlated with five distribution patterns in Lychnophorinae.
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Resende RT, Piepho HP, Rosa GJM, Silva-Junior OB, E Silva FF, de Resende MDV, Grattapaglia D. Enviromics in breeding: applications and perspectives on envirotypic-assisted selection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:95-112. [PMID: 32964262 DOI: 10.1007/s00122-020-03684-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/10/2020] [Indexed: 05/18/2023]
Abstract
We propose the application of enviromics to breeding practice, by which the similarity among sites assessed on an "omics" scale of environmental attributes drives the prediction of unobserved genotype performances. Genotype by environment interaction (GEI) studies in plant breeding have focused mainly on estimating genetic parameters over a limited number of experimental trials. However, recent geographic information system (GIS) techniques have opened new frontiers for better understanding and dealing with GEI. These advances allow increasing selection accuracy across all sites of interest, including those where experimental trials have not yet been deployed. Here, we introduce the term enviromics, within an envirotypic-assisted breeding framework. In summary, likewise genotypes at DNA markers, any particular site is characterized by a set of "envirotypes" at multiple "enviromic" markers corresponding to environmental variables that may interact with the genetic background, thus providing informative breeding re-rankings for optimized decisions over different environments. Based on simulated data, we illustrate an index-based enviromics method (the "GIS-GEI") which, due to its higher granular resolution than standard methods, allows for: (1) accurate matching of sites to their most appropriate genotypes; (2) better definition of breeding areas that have high genetic correlation to ensure selection gains across environments; and (3) efficient determination of the best sites to carry out experiments for further analyses. Environmental scenarios can also be optimized for productivity improvement and genetic resources management, especially in the current outlook of dynamic climate change. Envirotyping provides a new class of markers for genetic studies, which are fairly inexpensive, increasingly available and transferable across species. We envision a promising future for the integration of enviromics approaches into plant breeding when coupled with next-generation genotyping/phenotyping and powerful statistical modeling of genetic diversity.
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Affiliation(s)
- Rafael T Resende
- School of Agronomy, University of Goiás (UFG), Goiânia, GO, 74690-900, Brazil.
| | - Hans-Peter Piepho
- Biostatistics Unit, University of Hohenheim, 70593, Stuttgart, Germany
| | - Guilherme J M Rosa
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 53706, Madison, USA
| | | | - Fabyano F E Silva
- Department of Animal Science, University of Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Marcos Deon V de Resende
- Department of Statistics, University of Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
- EMBRAPA Coffee Research, Brasília, DF, 70770-901, Brazil
| | - Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology - EPqB, Brasília, DF, 70770-910, Brazil.
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Brasília, DF, 70790-160, Brazil.
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Munguía-Ortega KK, López-Reyes E, Ceccarelli FS. Testing the Accuracy of Vegetation-Based Ecoregions for Predicting the Species Composition of Blow Flies (Diptera: Calliphoridae). JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:6. [PMID: 33428743 PMCID: PMC7799434 DOI: 10.1093/jisesa/ieaa144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 06/12/2023]
Abstract
To properly define ecoregions, specific criteria such as geology, climate, or species composition (e.g., the presence of endemic species) must be taken into account to understand distribution patterns and resolve ecological biogeography questions. Since the studies on insects in Baja California are scarce, and no fine-scale ecoregions based on the region's entomofauna is available, this study was designed to test whether the ecoregions based on vegetation can be used for insects, such as Calliphoridae. Nine collecting sites distributed along five ecoregions were selected, between latitudes 29.6° and 32.0°N. In each site, three baited traps were used to collect blow flies from August 2017 to June 2019 during summer, winter, and spring. A total of 30,307 individuals of blow flies distributed in six genera and 13 species were collected. The most abundant species were Cochliomyia macellaria (Fabricius), Phormia regina (Meigen), and Chrysomya rufifacies (Macquart). The composition of the Calliphoridae community was different between the localities and three general groups have been distinguished, based on the species composition similarity (ANOSIM) results: Gulf-Desert, Mountains, and Pacific-Center. The vegetation-based ecoregions only reflect the blow fly species' distributions to a certain extent, meaning that care must be taken when undertaking ecological biogeographical studies using regionalization based on organisms other than the focal taxa because vegetation does not always reflect fauna species composition.
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Affiliation(s)
- K Ketzaly Munguía-Ortega
- Museo de Artrópodos, Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Eulogio López-Reyes
- Museo de Artrópodos, Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - F Sara Ceccarelli
- Museo de Artrópodos, Departamento de Biología de la Conservación, CONACYT-Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
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34
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Maestri R, Duarte L. Evoregions: Mapping shifts in phylogenetic turnover across biogeographic regions. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Renan Maestri
- Departamento de Ecologia Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Leandro Duarte
- Departamento de Ecologia Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
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35
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Jung S, Cho Y. Redefining floristic zones in the Korean Peninsula using high-resolution georeferenced specimen data and self-organizing maps. Ecol Evol 2020; 10:11549-11564. [PMID: 33144983 PMCID: PMC7593177 DOI: 10.1002/ece3.6790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 11/15/2022] Open
Abstract
The use of biota to analyze the distribution pattern of biogeographic regions is essential to gain a better understanding of the ecological processes that cause biotic differentiation and biodiversity at multiple spatiotemporal scales. Recently, the collection of high-resolution biological distribution data (e.g., specimens) and advances in analytical theory have led to the quantitative analysis and more refined spatial delineation of biogeographic regions. This study was conducted to redefine floristic zones in the southern part of the Korean Peninsula and to better understand the eco-evolutionary significance of the spatial distribution patterns. Based on 309,333 distribution data of 2,954 vascular plant species in the Korean Peninsula, we derived floristic zones using self-organizing maps. We compared the characteristics of the derived regions with those of historical floristic zones and ecologically important environmental factors (climate, geology, and geography). In the clustering analysis of the floristic assemblages, four distinct regions were identified, namely, the cold floristic zone (Zone I) in high-altitude regions at the center of the Korean Peninsula, cool floristic zone (Zone II) in high-altitude regions in the south of the Korean Peninsula, warm floristic zone (Zone III) in low-altitude regions in the central and southern parts of the Korean Peninsula, and maritime warm floristic zone (Zone IV) including the volcanic islands Jejudo and Ulleungdo. Totally, 1,099 taxa were common to the four floristic zones. Zone IV showed the highest abundance of specific plants (those found in only one zone), with 404 taxa. Our study improves floristic zone definitions using high-resolution regional biological distribution data. It will help better understand and re-establish regional species diversity. In addition, our study provides key data for hotspot analysis required for the conservation of plant diversity.
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Affiliation(s)
- Songhie Jung
- Gwangneung Forest Conservation CenterKorea National ArboretumPocheonKorea
| | - Yong‐chan Cho
- Gwangneung Forest Conservation CenterKorea National ArboretumPocheonKorea
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Daru BH, Karunarathne P, Schliep K. phyloregion: R package for biogeographical regionalization and macroecology. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13478] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Barnabas H. Daru
- Department of Life Sciences Texas A&M University‐Corpus Christi, Corpus Christi TX USA
| | - Piyal Karunarathne
- Department of Life Sciences Texas A&M University‐Corpus Christi, Corpus Christi TX USA
| | - Klaus Schliep
- Institute of Computational Biotechnology Graz University of Technology Graz Styria Austria
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Plant Diversity and Composition Changes along an Altitudinal Gradient in the Isolated Volcano Sumaco in the Ecuadorian Amazon. DIVERSITY 2020. [DOI: 10.3390/d12060229] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The paramo is a unique and severely threatened ecosystem scattered in the high northern Andes of South America. However, several further, extra-Andean paramos exist, of which a particular case is situated on the active volcano Sumaco, in the northwestern Amazon Basin of Ecuador. We have set an elevational gradient of 600 m (3200–3800 m a.s.l.) and sampled a total of 21 vegetation plots, using the phytosociological method. All vascular plants encountered were typified by their taxonomy, life form and phytogeographic origin. In order to determine if plots may be ensembled into vegetation units and understand what the main environmental factors shaping this pattern are, a non-metric multidimensional scaling (NMDS) analysis was performed. In addition, species turnover was quantified in order to appreciate the quantity and sort of species which are responsible for the similarity or dissimilarity between vegetation units. Therefore, a SIMPER similarity percentage analysis was conducted. We encountered 68 plant species belonging to 54 genera and 31 families, of which three are Ecuadorian endemics. The most frequent life forms were erect herbs, rosette and tussocks, whereas the least were cushions. At genus level, 44% of the Sumaco paramo flora was of tropical origin, followed by temperate (33%) and finally cosmopolitan (22%). The neotropical montane element was the most represented with 15 species, followed by the Austral-Antarctic with ten, wide temperate with another ten and cosmopolitan with seven. Regarding vegetation, four floristically distinct groups were segregated being lower gradient (3250–3500 m a.s.l.) and high altitude (3500–3800 m a.s.l.)
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Peixoto MA, Guedes TB, Silva ETD, Feio RN, Romano PSR. Biogeographic tools help to assess the effectiveness of protected areas for the conservation of anurans in the Mantiqueira mountain range, Southeastern Brazil. J Nat Conserv 2020. [DOI: 10.1016/j.jnc.2020.125799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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39
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Ecological Niche Models Reveal Climate Change Effect on Biogeographical Regions: The Iberian Peninsula as a Case Study. CLIMATE 2020. [DOI: 10.3390/cli8030042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
How species are distributed on Earth depends largely on climate factors. Whenever these environmental conditions change, species tend to shift their distributions to reach more favourable conditions. Distinct sets of species similarly distributed (i.e., chorotypes) occur in biogeographical regions with homogeneous environmental conditions. Here, we analysed whether biogeographical regions are unstable over time (from the past to the future). We modelled the realised niche of amphibians and reptiles in the Iberian Peninsula in the present, and several past and future climate scenarios. Then, we used Jaccard’s index and the unweighted pair group method (UPGMA) to define the biogeographical regions. Our results suggest that the biogeographical regions of Iberian amphibians and reptiles changed greatly over time, due to the climatic changes between periods. Biogeographical regions composed of species with Atlantic affinities changed particularly, overall gaining suitable areas in past colder periods and losing suitable areas in warmer periods. The areas of refugia for amphibians over time corresponded to the most humid regions (north-west of the peninsula), while the most important areas for reptiles occur in the south and on the Atlantic coast. The identification of biogeographical patterns considering past climate changes is essential to better apply conservation measures.
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40
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Biogeographical patterns and areas of endemism for the Magellan region based on the distribution of crustacean species (Amphipoda, Copepoda, and Euphausiacea). Polar Biol 2020. [DOI: 10.1007/s00300-020-02626-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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41
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Kubo T. Biogeographical Network Analysis of Cretaceous Terrestrial Tetrapods: A Phylogeny-Based Approach. Syst Biol 2020; 68:1034-1051. [PMID: 31135923 DOI: 10.1093/sysbio/syz024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 03/13/2019] [Accepted: 04/09/2019] [Indexed: 11/13/2022] Open
Abstract
Network methods are widely used to represent and analyze biogeography. It is difficult, however, to convert occurrence data of fossil vertebrates to a biogeographical network, as most species were known from a single locality. A new method for creating a biogeographical network that can incorporate phylogenetic information is proposed in this study, which increases the number of edges in the network of fossil vertebrates and enables the application of various network methods. Using ancestral state reconstruction via maximum parsimony, the method first estimates the biogeographical regions of all internal nodes of a given phylogeny using biogeographical information on the terminal taxa. Then, each internal node in the phylogenetic tree is converted to an edge in the biogeographical network that connects the region(s), if unambiguously estimated, of its two descendants. The new method was applied to phylogenetic trees generated by a birth-death model. Under all conditions tested, an average of $CDATA[$CDATA[$>$$70% of the internal nodes in phylogenetic trees were converted into edges. Three network indices-link density, average link weight, and endemism index (EI)-were evaluated for their usefulness in comparing different biogeographical networks. The EI reflects the rate of dispersal; the other indices reflect nonbiogeographical parameters, the number of taxa and regions, which highlights the importance of evaluating network indices before applying them to biogeographical studies. Multiple Cretaceous biogeographical networks were constructed from the phylogenies of five tetrapod taxa: terrestrial crocodyliforms, terrestrial turtles, nonavian dinosaurs, avians, and pterosaurs. The networks of avians and pterosaurs showed similar topologies and a strong correlation, and unexpectedly high endemism indices. These similarities were probably a result of shared taphonomic biases (i.e., the Lagerstätten effect) for volant taxa with fragile skeletons. The crocodyliform network was partitioned into the Gondwanan and Laurasian continents. The dinosaur network was partitioned into three groups of continents: 1) North America, Asia, and Australia; 2) Europe and Africa; and 3) India, Madagascar, and South America. When Early and Late Cretaceous dinosaurs were analyzed separately, the dinosaur networks were divided into 1) North America, Asia, and Australia; and 2) Europe, Africa, India, and South America for the Early Cretaceous and 1) North America, Asia, and Europe; and 2) India, Madagascar, and South America for the Late Cretaceous. This partitioning of dinosaur and crocodyliform networks corroborates the results of previous biogeographical studies and indicates that the method introduced here can retrieve biogeographical signals from a source phylogeny when sufficient data are available for most targeted biogeographical regions.
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Affiliation(s)
- Tai Kubo
- The University Museum, The University of Tokyo, 7-3-1 Hongo, Bunkyou-ku, Tokyo 113-0033, Japan
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Beger M, Wendt H, Sullivan J, Mason C, LeGrand J, Davey K, Jupiter S, Ceccarelli DM, Dempsey A, Edgar G, Feary DA, Fenner D, Gauna M, Grice H, Kirmani SN, Mangubhai S, Purkis S, Richards ZT, Rotjan R, Stuart-Smith R, Sykes H, Yakub N, Bauman AG, Hughes A, Raubani J, Lewis A, Fernandes L. National-scale marine bioregions for the Southwest Pacific. MARINE POLLUTION BULLETIN 2020; 150:110710. [PMID: 31753567 DOI: 10.1016/j.marpolbul.2019.110710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/29/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
Existing marine bioregions covering the Pacific Ocean are conceptualised at spatial scales that are too broad for national marine spatial planning. Here, we developed the first combined oceanic and coastal marine bioregionalisation at national scales, delineating 262 deep-water and 103 reef-associated bioregions across the southwest Pacific. The deep-water bioregions were informed by thirty biophysical environmental variables. For reef-associated environments, records for 806 taxa at 7369 sites were used to predict the probability of observing taxa based on environmental variables. Both deep-water and reef-associated bioregions were defined with cluster analysis applied to the environmental variables and predicted species observation probabilities, respectively to classify areas with high taxonomic similarity. Local experts further refined the delineation of the bioregions at national scales for four countries. This work provides marine bioregions that enable the design of ecologically representative national systems of marine protected areas within offshore and inshore environments in the Pacific.
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Affiliation(s)
- Maria Beger
- School of Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Centre for Biodiversity and Conservation Science, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Hans Wendt
- Oceania Regional Office, IUCN (International Union for Conservation of Nature), 5 Ma'afu Street, Private Mail Bag, Suva, Fiji
| | - Jonah Sullivan
- Oceania Regional Office, IUCN (International Union for Conservation of Nature), 5 Ma'afu Street, Private Mail Bag, Suva, Fiji; Geoscience Australia, Environmental Geoscience Division, 101 Jerrabomberra Ave, Symonston, ACT, 2609, Australia
| | - Claire Mason
- Centre for Biodiversity and Conservation Science, School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia; Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, TAS, 7004, Australia
| | - Jimaima LeGrand
- Oceania Regional Office, IUCN (International Union for Conservation of Nature), 5 Ma'afu Street, Private Mail Bag, Suva, Fiji; Department of Transport and Main Roads, 131 Sugar Rd, Maroochydore, Queensland, Australia
| | - Kate Davey
- Oceania Regional Office, IUCN (International Union for Conservation of Nature), 5 Ma'afu Street, Private Mail Bag, Suva, Fiji
| | - Stacy Jupiter
- Wildlife Conservation Society, Melanesia Program, 11 Ma'afu Street, Suva, Fiji
| | - Daniela M Ceccarelli
- Marine Ecology Consultant, 36 Barton Street, Magnetic Island QLD, 4819, Australia
| | - Alex Dempsey
- Khaled bin Sultan Living Oceans Foundation, Annapolis, MD, 21403, USA
| | - Graham Edgar
- Institute for Marine and Antarctic Studies, University of Tasmania, Nubeena Crescent, Taroona, 7053, Australia
| | | | | | - Marian Gauna
- Oceania Regional Office, IUCN (International Union for Conservation of Nature), 5 Ma'afu Street, Private Mail Bag, Suva, Fiji
| | - Hannah Grice
- School of Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Sahar Noor Kirmani
- Oceania Regional Office, IUCN (International Union for Conservation of Nature), 5 Ma'afu Street, Private Mail Bag, Suva, Fiji
| | - Sangeeta Mangubhai
- Wildlife Conservation Society, Melanesia Program, 11 Ma'afu Street, Suva, Fiji
| | - Sam Purkis
- Khaled bin Sultan Living Oceans Foundation, Annapolis, MD, 21403, USA; Department of Marine Geosciences, Rosenstiel School of Marine and Atmospheric Science, University of Miami, USA
| | - Zoe T Richards
- Coral Conservation and Research Group, School of Molecular and Life Science, Curtin University, Bentley WA, 6102, Australia; Aquatic Zoology Department, Western Australian Museum, Welshpool, WA, Australia
| | - Randi Rotjan
- Department of Biology, Boston University. 5 Cummington Mall, Boston, MA, 02215, USA
| | - Rick Stuart-Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, Nubeena Crescent, Taroona, 7053, Australia
| | - Helen Sykes
- Marine Ecology Consulting, PO Box 2558, Government Buildings, Suva, Fiji Islands
| | - Naushad Yakub
- Oceania Regional Office, IUCN (International Union for Conservation of Nature), 5 Ma'afu Street, Private Mail Bag, Suva, Fiji
| | - Andrew G Bauman
- Experimental Marine Ecology Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Alec Hughes
- Wildlife Conservation Society, Solomon Islands, P.O. Box 98, Munda, Western Province, Solomon Islands
| | - Jason Raubani
- The Pacific Community, 95 Promenade Roger Laroque, BP D5, 98848, Noumea, New Caledonia
| | - Adam Lewis
- Geoscience Australia, Environmental Geoscience Division, 101 Jerrabomberra Ave, Symonston, ACT, 2609, Australia
| | - Leanne Fernandes
- Oceania Regional Office, IUCN (International Union for Conservation of Nature), 5 Ma'afu Street, Private Mail Bag, Suva, Fiji.
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Pérez-Escobar OA, Lucas E, Jaramillo C, Monro A, Morris SK, Bogarín D, Greer D, Dodsworth S, Aguilar-Cano J, Sanchez Meseguer A, Antonelli A. The Origin and Diversification of the Hyperdiverse Flora in the Chocó Biogeographic Region. FRONTIERS IN PLANT SCIENCE 2019; 10:1328. [PMID: 31867022 PMCID: PMC6910151 DOI: 10.3389/fpls.2019.01328] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Extremely high levels of plant diversity in the American tropics are derived from multiple interactions between biotic and abiotic factors. Previous studies have focused on macro-evolutionary dynamics of the Tropical Andes, Amazonia, and Brazil's Cerrado and Atlantic forests during the last decade. Yet, other equally important Neotropical biodiversity hotspots have been severely neglected. This is particularly true for the Chocó region on the north-western coast of South and Central America. This geologically complex region is Earth's ninth most biodiverse hotspot, hosting approximately 3% of all known plant species. Here, we test Gentry's [1982a,b] hypothesis of a northern Andean-Central American Pleistocene origin of the Chocoan flora using phylogenetic reconstructions of representative plant lineages in the American tropics. We show that plant diversity in the Chocó is derived mostly from Andean immigrants. Contributions from more distant biogeographical areas also exist but are fewer. We also identify a strong floristic connection between the Chocó and Central America, revealed by multiple migrations into the Chocó during the last 5 Ma. The dated phylogenetic reconstructions suggest a Plio-Pleistocene onset of the extant Chocó flora. Taken together, these results support to a limited extend Gentry's hypothesis of a Pleistocene origin and of a compound assembly of the Chocoan biodiversity hotspot. Strong Central American-Chocoan floristic affinity may be partly explained by the accretion of a land mass derived from the Caribbean plate to north-western South America. Additional densely sampled phylogenies of Chocoan lineages also well represented across the Neotropics could enlighten the role of land mass movements through time in the assembly of floras in Neotropical biodiversity hotspots.
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Affiliation(s)
- Oscar Alejandro Pérez-Escobar
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Eve Lucas
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Panama, Panama
- ISEM, U. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Alexandre Monro
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Sarah K. Morris
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
| | - Diego Bogarín
- Universidad de Costa Rica, Jardín Botánico Lankester, Cartago, Costa Rica
| | - Deborah Greer
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Department of Environment, Food and Rural Affairs, London, United Kingdom
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, Luton, United Kingdom
| | | | | | - Alexandre Antonelli
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, London, United Kingdom
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
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Chiarucci A, Nascimbene J, Campetella G, Chelli S, Dainese M, Giorgini D, Landi S, Lelli C, Canullo R. Exploring patterns of beta-diversity to test the consistency of biogeographical boundaries: A case study across forest plant communities of Italy. Ecol Evol 2019; 9:11716-11723. [PMID: 31695881 PMCID: PMC6822039 DOI: 10.1002/ece3.5669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 11/23/2022] Open
Abstract
AIM To date, despite their great potential biogeographical regionalization models have been mostly developed on descriptive and empirical bases. This paper aims at applying the beta-diversity framework on a statistically representative data set to analytically test the consistency of the biogeographical regionalization of Italian forests. LOCATION Italy. TAXON Vascular plants. METHODS Forest plant communities were surveyed in 804 plots made in a statistically representative sample of forest communities made by 201 sites of Italian forests across the three biogeographical regions of the country: Alpine, Continental, and Mediterranean. We conducted an ordination analysis and an analysis of beta-diversity, decomposing it into its turnover and nestedness components. RESULTS Our results provide only partial support to the consistency of the biogeographical regionalization of Italy. While the differences in forest plant communities support the distinction between the Alpine and the other two regions, differences between Continental and Mediterranean regions had lower statistical support. Pairwise beta-diversity and its turnover component are higher between- than within-biogeographical regions. This suggests that different regional species pools contribute to assembly of local communities and that spatial distance between-regions has a stronger effect than that within-regions. MAIN CONCLUSIONS Our findings confirm a biogeographical structure of the species pools that is captured by the biogeographical regionalization. However, nonsignificant differences between the Mediterranean and Continental biogeographical regions suggest that this biogeographical regionalization is not consistent for forest plant communities. Our results demonstrate that an analytical evaluation of species composition differences among regions using beta-diversity analysis is a promising approach for testing the consistency of biogeographical regionalization models. This approach is recommended to provide support to the biogeographical regionalization used in some environmental conservation polices adopted by EU.
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Affiliation(s)
- Alessandro Chiarucci
- Department of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Juri Nascimbene
- Department of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Giandiego Campetella
- Plant Diversity and Ecosystems Management UnitSchool of Biosciences and Veterinary MedicineUniversity of CamerinoCamerinoItaly
| | - Stefano Chelli
- Plant Diversity and Ecosystems Management UnitSchool of Biosciences and Veterinary MedicineUniversity of CamerinoCamerinoItaly
| | - Matteo Dainese
- Institute for Alpine EnvironmentEurac ResearchBolzanoItaly
| | - Daniele Giorgini
- Plant Diversity and Ecosystems Management UnitSchool of Biosciences and Veterinary MedicineUniversity of CamerinoCamerinoItaly
| | - Sara Landi
- Department of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
- Department of Natural and Land SciencesUniversity of SassariSassariItaly
| | - Chiara Lelli
- Department of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Roberto Canullo
- Plant Diversity and Ecosystems Management UnitSchool of Biosciences and Veterinary MedicineUniversity of CamerinoCamerinoItaly
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Changes in Fish Taxonomy Affect Freshwater Biogeographical Regionalisations: Insights from Greece. WATER 2019. [DOI: 10.3390/w11091743] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Freshwater fishes are key indicators for delineating biogeographical maps worldwide. However, controversy in regional-scale ichthyogeographic boundaries still persists, especially in areas of high species endemicity, such as in Greece. One problem concerns the taxonomy of the fishes because there have been extensive changes, mainly due to an increased splitting of species in recent years in Europe. Here, we explore why ichthyogeographic boundary disagreements and uncertainties in region-scale biogeographical units persist. We compare cluster analyses of river basin fish fauna in Greece using two taxonomic datasets: the older fish taxonomy (from 1991) and the current taxonomy that now follows the phylogenetic species concept (PSC), which has become widely established in Europe after 2007. Cluster analyses using the older fish taxonomy depicts only two major biogeographical regional divisions, while the current taxonomy defines four major regional divisions in mainland Greece. Interestingly, some older maps from the pre-PSC taxonomy era also similarly show four ichthyogeographic divisions in Greece and we can assume that the older biogeographical work did not solely use numerical taxonomy but followed an expert-guided synthesis; the older regional definitions have persisted quite well despite radical changes in Europe’s fish taxonomy. Through the prism of biodiversity conservation planning, we hope this review may help identify ways to help standardize policy-relevant biogeographical mapping.
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Chomicki G, Weber M, Antonelli A, Bascompte J, Kiers ET. The Impact of Mutualisms on Species Richness. Trends Ecol Evol 2019; 34:698-711. [DOI: 10.1016/j.tree.2019.03.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/11/2019] [Accepted: 03/18/2019] [Indexed: 11/28/2022]
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Oliveira U, Soares-Filho B, Leitão RFM, Rodrigues HO. BioDinamica: a toolkit for analyses of biodiversity and biogeography on the Dinamica-EGO modelling platform. PeerJ 2019; 7:e7213. [PMID: 31338256 PMCID: PMC6628879 DOI: 10.7717/peerj.7213] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/30/2019] [Indexed: 11/28/2022] Open
Abstract
Biogeography and macroecology are at the heart of the debate on ecology and evolution. We have developed the BioDinamica package, a suite of user-friendly graphical programs for analysing spatial patterns of biogeography and macroecology. BioDinamica includes analyses of beta-diversity, species richness, endemicity, phylo-diversity, species distribution models, predictive models of biodiversity patterns, and several tools for spatial biodiversity analysis. BioDinamica consists of a sub-library of Dinamica-EGO operators developed by integrating EGO native functions with R scripts. The BioDinamica operators can be assembled to create complex analytical and simulation models through the EGO graphical programming interface. In addition, we make available “Wizard” tutorials for end users. BioDinamica can be downloaded free of charge from the Dinamica EGO submodel store. The tools made available in BioDinamica not only facilitate complex biodiversity analyses, they also help develop state-of-the-art spatial models for biogeography and macroecology studies.
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Affiliation(s)
- Ubirajara Oliveira
- Centro de Sensoriamento Remoto, Instituto de Geociências, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Britaldo Soares-Filho
- Centro de Sensoriamento Remoto, Instituto de Geociências, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Rômulo Fernandes Machado Leitão
- Centro de Sensoriamento Remoto, Instituto de Geociências, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Hermann O Rodrigues
- Centro de Sensoriamento Remoto, Instituto de Geociências, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, Minas Gerais, Brazil
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Zhou L, Liang T, Shi L. Amphibian and Reptilian Chorotypes in the Arid Land of Central Asia and Their Determinants. Sci Rep 2019; 9:9453. [PMID: 31263271 PMCID: PMC6603035 DOI: 10.1038/s41598-019-45912-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 06/20/2019] [Indexed: 11/08/2022] Open
Abstract
The analysis of the biogeographic distribution of species is the basis for establishing a strategy for land management and responding to climatic change, but research on the distribution of amphibians and reptiles in the arid land in the middle of Asia is extremely limited. After classifying the chorotypes of amphibians and reptiles in the arid land of Central Asia using a clustering analysis, we delineated their distribution characteristics and discovered the ecological determinants for the chorotypes in terms of feature selection and the Akaike information criterion (AIC). We identified 6 chorotypes at the higher level and 16 sub-chorotypes at the lower level. Compared to small-scale or subjective research, which produces unstable results, research characterized by both large scale and clustering methods yields more consistent and stable results. Our results show that the Mean Altitude (MA), Mean Annual Temperature (MAT), and Mean Temperature in the Wettest Quarter (MTWE) are the critical variables determining the higher-level chorotypes. Furthermore, geographical factors appear to have a stronger influence on chorotypes than climatic factors. Several climatic variables and MA were identified as the best fit in the AIC model at the lower level, while the sub-chorotypes are determined more by multiple climatic factors with complex relationships. The research on amphibian and reptilian distribution patterns will shed light on the overall distribution of other species in the same understudied area. Widespread species in the study area are not clearly distinguished due to the cluster analysis computing process. This problem however, appears in studies of the distribution of other organisms thus warrants further research. Our methodology based on the selection of multiple models is effective to explore how the environment determines the distributions of different animal groups.
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Affiliation(s)
- Lu Zhou
- College of Animal Science, Xinjiang Agricultural University, No. 311, Nongda East Road, Urumqi, Xinjiang, 830052, China
- Institute of Hydrobiology of the Chinese Academy of Sciences, 7 South Donghu Road, Wuchang District, Wuhan, 430072, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Tao Liang
- College of Animal Science, Xinjiang Agricultural University, No. 311, Nongda East Road, Urumqi, Xinjiang, 830052, China
| | - Lei Shi
- College of Animal Science, Xinjiang Agricultural University, No. 311, Nongda East Road, Urumqi, Xinjiang, 830052, China.
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White AE, Dey KK, Mohan D, Stephens M, Price TD. Regional influences on community structure across the tropical-temperate divide. Nat Commun 2019; 10:2646. [PMID: 31201312 PMCID: PMC6570764 DOI: 10.1038/s41467-019-10253-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/29/2019] [Indexed: 12/02/2022] Open
Abstract
Many models to explain the differences in the flora and fauna of tropical and temperate regions assume that whole clades are restricted to the tropics. We develop methods to assess the extent to which biotas are geographically discrete, and find that transition zones between regions occupied by tropical-associated or temperate-associated biotas are often narrow, suggesting a role for freezing temperatures in partitioning global biotas. Across the steepest tropical-temperate gradient in the world, that of the Himalaya, bird communities below and above the freezing line are largely populated by different tropical and temperate biotas with links to India and Southeast Asia, or to China respectively. The importance of the freezing line is retained when clades rather than species are considered, reflecting confinement of different clades to one or another climate zone. The reality of the sharp tropical-temperate boundary adds credence to the argument that exceptional species richness in the tropics reflects species accumulation over time, with limited transgressions of species and clades into the temperate.
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Affiliation(s)
- Alexander E White
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA.
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 600 Maryland Avenue SW, Washington, 20024, DC, USA.
- National Museum of Natural History, Smithsonian Institution, MRC 166 PO Box 37012, Washington, DC, 20013, USA.
| | - Kushal K Dey
- Department of Statistics, University of Chicago, 5747 S Ellis Avenue, Chicago, IL, 60637, USA
- Department of Epidemiology, Harvard University, 665 Huntington Avenue, Cambridge, MA, 02115, USA
| | - Dhananjai Mohan
- Wildlife Institute of India, PO Box 18, Chandrabani, Dehradun, 248001, India
| | - Matthew Stephens
- Department of Statistics, University of Chicago, 5747 S Ellis Avenue, Chicago, IL, 60637, USA
- Department of Human Genetics, University of Chicago, 920 E 58th Street, Chicago, IL, 60637, USA
| | - Trevor D Price
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th Street, Chicago, IL, 60637, USA
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Bernardo‐Madrid R, Calatayud J, González‐Suárez M, Rosvall M, Lucas PM, Rueda M, Antonelli A, Revilla E. Human activity is altering the world’s zoogeographical regions. Ecol Lett 2019; 22:1297-1305. [DOI: 10.1111/ele.13321] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 04/10/2019] [Accepted: 05/11/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Rubén Bernardo‐Madrid
- Department of Conservation Biology Estación Biológica de Doñana (EBD‐CSIC) Sevilla Spain
| | - Joaquín Calatayud
- Department of Life Science Universidad de Alcalá Alcalá de Henares Spain
- Department of Biogeography and Global Change Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
- Integrated Science Lab, Department of Physics Umeå University 901 87Umeå Sweden
| | - Manuela González‐Suárez
- Ecology and Evolutionary Biology, School of Biological Sciences University of Reading Reading UK
| | - Martin Rosvall
- Integrated Science Lab, Department of Physics Umeå University 901 87Umeå Sweden
| | - Pablo M. Lucas
- Department of Conservation Biology Estación Biológica de Doñana (EBD‐CSIC) Sevilla Spain
- Department of Wildlife Conservation Institute of Nature Conservation (IOP‐PAS) Kraków Poland
| | - Marta Rueda
- Department of Conservation Biology Estación Biológica de Doñana (EBD‐CSIC) Sevilla Spain
| | - Alexandre Antonelli
- Gothenburg Global Biodiversity Centre Box 461 SE‐405 30 Göteborg Sweden
- Department of Biological and Environmental Sciences University of Gothenburg Box 461405 30Göteborg Sweden
- Royal Botanic Gardens Kew, RichmondTW9 3ABUK
| | - Eloy Revilla
- Department of Conservation Biology Estación Biológica de Doñana (EBD‐CSIC) Sevilla Spain
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