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Steiner M, Huettmann F, Bryans N, Barker B. With super SDMs (machine learning, open access big data, and the cloud) towards more holistic global squirrel hotspots and coldspots. Sci Rep 2024; 14:5204. [PMID: 38433273 PMCID: PMC10909860 DOI: 10.1038/s41598-024-55173-8] [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: 05/01/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Species-habitat associations are correlative, can be quantified, and used for powerful inference. Nowadays, Species Distribution Models (SDMs) play a big role, e.g. using Machine Learning and AI algorithms, but their best-available technical opportunities remain still not used for their potential e.g. in the policy sector. Here we present Super SDMs that invoke ML, OA Big Data, and the Cloud with a workflow for the best-possible inference for the 300 + global squirrel species. Such global Big Data models are especially important for the many marginalized squirrel species and the high number of endangered and data-deficient species in the world, specifically in tropical regions. While our work shows common issues with SDMs and the maxent algorithm ('Shallow Learning'), here we present a multi-species Big Data SDM template for subsequent ensemble models and generic progress to tackle global species hotspot and coldspot assessments for a more inclusive and holistic inference.
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Affiliation(s)
- Moriz Steiner
- IUCN Small Mammal Specialist Group (SMSG), IUCN, Rue Mauverney 28, 1196, Gland, Switzerland.
- IUCN Species Survival Commission (SSC), IUCN, Rue Mauverney 28, 1196, Gland, Switzerland.
- EWHALE Lab-Biology and Wildlife Department, Institute of Arctic Biology, University of Alaska Fairbanks (UAF), Fairbanks, AK, USA.
| | - F Huettmann
- EWHALE Lab-Biology and Wildlife Department, Institute of Arctic Biology, University of Alaska Fairbanks (UAF), Fairbanks, AK, USA
| | - N Bryans
- Oracle for Research, 2300 Oracle Wy, Austin, TX, 78741, USA
| | - B Barker
- Oracle for Research, 2300 Oracle Wy, Austin, TX, 78741, USA
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Kim AS, Kreiner JM, Hernández F, Bock DG, Hodgins KA, Rieseberg LH. Temporal collections to study invasion biology. Mol Ecol 2023; 32:6729-6742. [PMID: 37873879 DOI: 10.1111/mec.17176] [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: 08/22/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.
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Affiliation(s)
- Amy S Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fernando Hernández
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Mora JM, Ruedas LA. Updated list of the mammals of Costa Rica, with notes on recent taxonomic changes. Zootaxa 2023; 5357:451-501. [PMID: 38220635 DOI: 10.11646/zootaxa.5357.4.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Indexed: 01/16/2024]
Abstract
Although Costa Rica occupies a mere 0.03% of the Earths land area, it nevertheless has recorded within its borders approximately 5% of the global diversity of mammals, thus making it one of the worlds megadiverse countries. Over the past ten years, 22 species have been added to the countrys inventory, bringing the total number known as here documented to 271; Chiroptera account for ten of these, having grown to 124 from 114; rodents have increased by eight species, from 47 to 55, with the caveat that we include three invasive species of Muridae that have gone feral. In contrast, the number of orders has decreased by one, by Artiodactyla incorporating the former Cetacea. Notes are provided for all taxonomic novelties since the last update. Since the first taxonomic compendium of the mammals of Costa Rica in 1869, the number of known species has grown by approximately 1.22 species year-1 (R2 = 0.96). Since 1983 however, this growth rate has been 1.64 species year-1 (R2 = 0.98). Despite this strong growth, an asymptote in the number of known species has not been reached. Conservation remains a primary need: over 60% of the countrys mammal species show population trends that are decreasing (13%), unknown (37%), or not assessed (11%), based on IUCN criteria. These analyses suggest that much remains to be known regarding the number of mammal species living in Costa Rica, but also that much more remains to be done to safeguard Costa Ricas exceptional biodiversity heritage.
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Affiliation(s)
- Jos Manuel Mora
- Department of Biology and Museum of Vertebrate Biology; Portland State University; Portland; Oregon 97207-0751; USA; Carrera de Gestin Ecoturstica; Sede Central; Universidad Tcnica Nacional; Alajuela; Costa Rica.
| | - Luis A Ruedas
- Department of Biology and Museum of Vertebrate Biology; Portland State University; Portland; Oregon 97207-0751; USA.
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Abreu EF, Pavan SE, Tsuchiya MTN, McLean BS, Wilson DE, Percequillo AR, Maldonado JE. Old specimens for old branches: Assessing effects of sample age in resolving a rapid Neotropical radiation of squirrels. Mol Phylogenet Evol 2022; 175:107576. [PMID: 35809853 DOI: 10.1016/j.ympev.2022.107576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/10/2022] [Accepted: 07/01/2022] [Indexed: 11/15/2022]
Abstract
Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear. Furthermore, there is an ongoing debate on how to curate, filter, and properly analyze UCE data when locus recovery is uneven across sample age and quality. In the present study we address these questions with an empirical dataset composed of over 3800 UCE loci from 219 historical and modern samples of Sciuridae, a globally distributed and ecologically important family of rodents. We provide a genome-scale phylogeny of two squirrel subfamilies (Sciurillinae and Sciurinae: Sciurini) and investigate their placement within Sciuridae. For historical specimens, recovery of UCE loci and mean length per locus were inversely related to sample age; deeper sequencing improved the number of UCE loci recovered but not locus length. Most of our phylogenetic inferences-performed on six datasets with alternative data-filtering strategies, and using three distinct optimality criteria-resulted in distinct topologies. Datasets containing more loci (40% and 50% taxa representativeness matrices) yielded more concordant topologies and higher support values than strictly filtered datasets (60% matrices) particularly with IQ-Tree and SVDquartets, while filtering based on information content provided better topological resolution for inferences with the coalescent gene-tree based approach in ASTRAL-III. We resolved deep relationships in Sciuridae (including among the five currently recognized subfamilies) and relationships among the deepest branches of Sciurini, but conflicting relationships remain at both genus- and species-levels for the rapid Neotropical tree squirrel radiation. Our results suggest that phylogenomic consensus can be difficult and heavily influenced by the age of available samples and the filtering steps used to optimize dataset properties.
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Affiliation(s)
- Edson F Abreu
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil; Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA.
| | - Silvia E Pavan
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Mirian T N Tsuchiya
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA; Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC, USA
| | - Bryan S McLean
- Department of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Don E Wilson
- Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Alexandre R Percequillo
- Laboratório de Mamíferos, Departamento de Ciências Biológicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
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Brito J, Koch C, Tinoco N, Pardiñas UFJ. A new species of Mindomys (Rodentia, Cricetidae) with remarks on external traits as indicators of arboreality in sigmodontine rodents. EVOLUTIONARY SYSTEMATICS 2022. [DOI: 10.3897/evolsyst.6.76879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The diversity of the oryzomyine rat Mindomys (Cricetidae, Sigmodontinae, Oryzomyini), is doubled here with the description of a new species from the remote Cordillera de Kutukú (Ecuador). The novel form can be easily differentiated from Mindomys hammondi –type species of the genus– by a large set of anatomical traits including, among others, larger jugals, parietal “wings” extending to zygomatic roots, larger otic capsules, well-exposed petrosals, narrow zygomatic plates almost without upper free borders, foramen magnum caudally oriented, larger molars, and accessory root of first upper molar present. Until now, the records of Mindomys were restricted to western Andean foothills. The material from Kutukú highlights an Amazonian species and reinforces the valuable biological significance of isolated mountain ranges in eastern Ecuador. Since Mindomys shows some external traits classically related to arboreal life, here we present a brief reappraisal of this poorly explored topic. A partially neglected anatomical system in sigmodontine studies, the fore feet, encloses crucial information reflecting arboreality.
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OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blab177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Fegies AC, Carmignotto AP, Perez MF, Guilardi MD, Lessinger AC. Molecular Phylogeny of Cryptonanus (Didelphidae: Thylamyini): Evidence for a recent and complex diversification in South American open biomes. Mol Phylogenet Evol 2021; 162:107213. [PMID: 34029717 DOI: 10.1016/j.ympev.2021.107213] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022]
Abstract
Systematic revisions of South American marsupials have contributed to our knowledge about genus and species diversity in the last decades, including studies of the most recently described genus Cryptonanus (Didelphidae), currently comprising four recognized species. Herein we provide the first phylogeny for these mouse opossums based on comprehensive sampling, including representatives from all nominal taxa, encompassing most of the geographic distribution of the genus while also extending its known range. The taxonomic status of Cryptonanus species was explored by analyses of multiple mitochondrial and nuclear DNA markers to assess phylogenetic relationships and to provide divergence time estimates, species delimitations and biogeographical hypotheses. Cryptonanus monophyly remained highly supported despite the inclusion of abundant new data from more than a hundred specimens, comprising 10 independent evolutionary lineages. Species-complexes within valid nominal taxa reveal higher species richness in the genus. Based on divergence estimates from a dated phylogeny, we suggest that Cryptonanus diversified along the Quaternary, with speciation events occurring well into the Pleistocene. The best supported biogeographical hypothesis endorses speciation by vicariance and subset speciation across open formations in shaping the evolutionary history of this didelphid genus, strongly associated with dry tropical landscapes of South America.
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Affiliation(s)
- Ana Cláudia Fegies
- Departamento de Engenharia Ambiental, Universidade Estadual Paulista (UNESP), Campus Sorocaba, Av. Três de Março 511, Sorocaba, São Paulo CEP 18087-180, Brazil
| | - Ana Paula Carmignotto
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Campus Sorocaba, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo CEP 18052-780, Brazil.
| | - Manolo Fernandez Perez
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luís km 235, São Carlos, São Paulo CEP 13565-905, Brazil
| | - Mariana Dias Guilardi
- Laboratório de Ecologia e Evolução, Instituto Butantan, Avenida Vital Brazil 1500, São Paulo, São Paulo CEP 05503-000, Brazil
| | - Ana Cláudia Lessinger
- Departamento de Biologia, Universidade Federal de São Carlos (UFSCar), Campus Sorocaba, Rodovia João Leme dos Santos km 110, Sorocaba, São Paulo CEP 18052-780, Brazil.
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