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Fonseca EM, Pelletier TA, Decker SK, Parsons DJ, Carstens BC. Pleistocene glaciations caused the latitudinal gradient of within-species genetic diversity. Evol Lett 2023; 7:331-338. [PMID: 37829497 PMCID: PMC10565891 DOI: 10.1093/evlett/qrad030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/26/2023] [Accepted: 07/10/2023] [Indexed: 10/14/2023] Open
Abstract
Intraspecific genetic diversity is a key aspect of biodiversity. Quaternary climatic change and glaciation influenced intraspecific genetic diversity by promoting range shifts and population size change. However, the extent to which glaciation affected genetic diversity on a global scale is not well established. Here we quantify nucleotide diversity, a common metric of intraspecific genetic diversity, in more than 38,000 plant and animal species using georeferenced DNA sequences from millions of samples. Results demonstrate that tropical species contain significantly more intraspecific genetic diversity than nontropical species. To explore potential evolutionary processes that may have contributed to this pattern, we calculated summary statistics that measure population demographic change and detected significant correlations between these statistics and latitude. We find that nontropical species are more likely to deviate from neutral expectations, indicating that they have historically experienced dramatic fluctuations in population size likely associated with Pleistocene glacial cycles. By analyzing the most comprehensive data set to date, our results imply that Quaternary climate perturbations may be more important as a process driving the latitudinal gradient in species richness than previously appreciated.
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Affiliation(s)
- Emanuel M Fonseca
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Tara A Pelletier
- Department of Biology, Radford University, Radford, VA, United States
| | - Sydney K Decker
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Danielle J Parsons
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, United States
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2
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Bharti DK, Pawar PY, Edgecombe GD, Joshi J. Genetic diversity varies with species traits and latitude in predatory soil arthropods (Myriapoda: Chilopoda). GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2023; 32:1508-1521. [PMID: 38708411 PMCID: PMC7615927 DOI: 10.1111/geb.13709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/13/2023] [Indexed: 05/07/2024]
Abstract
Aim To investigate the drivers of intra-specific genetic diversity in centipedes, a group of ancient predatory soil arthropods. Location Asia, Australasia and Europe. Time Period Present. Major Taxa Studied Centipedes (Class: Chilopoda). Methods We assembled a database of 1245 mitochondrial cytochrome c oxidase subunit I sequences representing 128 centipede species from all five orders of Chilopoda. This sequence dataset was used to estimate genetic diversity for centipede species and compare its distribution with estimates from other arthropod groups. We studied the variation in centipede genetic diversity with species traits and biogeography using a beta regression framework, controlling for the effect of shared evolutionary history within a family. Results A wide variation in genetic diversity across centipede species (0-0.1713) falls towards the higher end of values among arthropods. Overall, 27.57% of the variation in mitochondrial COI genetic diversity in centipedes was explained by a combination of predictors related to life history and biogeography. Genetic diversity decreased with body size and latitudinal position of sampled localities, was greater in species showing maternal care and increased with geographic distance among conspecifics. Main Conclusions Centipedes fall towards the higher end of genetic diversity among arthropods, which may be related to their long evolutionary history and low dispersal ability. In centipedes, the negative association of body size with genetic diversity may be mediated by its influence on local abundance or the influence of ecological strategy on long-term population history. Species with maternal care had higher genetic diversity, which goes against expectations and needs further scrutiny. Hemispheric differences in genetic diversity can be due to historic climatic stability and lower seasonality in the southern hemisphere. Overall, we find that despite the differences in mean genetic diversity among animals, similar processes related to life-history strategy and biogeography are associated with the variation within them.
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Affiliation(s)
- D. K. Bharti
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Jahnavi Joshi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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3
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French CM, Bertola LD, Carnaval AC, Economo EP, Kass JM, Lohman DJ, Marske KA, Meier R, Overcast I, Rominger AJ, Staniczenko PPA, Hickerson MJ. Global determinants of insect mitochondrial genetic diversity. Nat Commun 2023; 14:5276. [PMID: 37644003 PMCID: PMC10465557 DOI: 10.1038/s41467-023-40936-0] [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: 01/20/2022] [Accepted: 08/15/2023] [Indexed: 08/31/2023] Open
Abstract
Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.
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Affiliation(s)
- Connor M French
- Biology Department, City College of New York, New York, NY, USA.
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA.
| | - Laura D Bertola
- Biology Department, City College of New York, New York, NY, USA
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, N 2200, Denmark
| | - Ana C Carnaval
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - 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
| | - David J Lohman
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Entomology Section, National Museum of Natural History, Manila, Philippines
| | | | - Rudolf Meier
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde Berlin, Berlin, Germany
| | - Isaac Overcast
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Institut de Biologie de l'Ecole Normale Superieure, Paris, France
- Department of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Andrew J Rominger
- School of Biology and Ecology, University of Maine, Orono, ME, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME, USA
| | | | - Michael J Hickerson
- Biology Department, City College of New York, New York, NY, USA
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, USA
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
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4
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Silva SV, Andermann T, Zizka A, Kozlowski G, Silvestro D. Global Estimation and Mapping of the Conservation Status of Tree Species Using Artificial Intelligence. FRONTIERS IN PLANT SCIENCE 2022; 13:839792. [PMID: 35574125 PMCID: PMC9100559 DOI: 10.3389/fpls.2022.839792] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/07/2022] [Indexed: 05/03/2023]
Abstract
Trees are fundamental for Earth's biodiversity as primary producers and ecosystem engineers and are responsible for many of nature's contributions to people. Yet, many tree species at present are threatened with extinction by human activities. Accurate identification of threatened tree species is necessary to quantify the current biodiversity crisis and to prioritize conservation efforts. However, the most comprehensive dataset of tree species extinction risk-the Red List of the International Union for the Conservation of Nature (IUCN RL)-lacks assessments for a substantial number of known tree species. The RL is based on a time-consuming expert-based assessment process, which hampers the inclusion of less-known species and the continued updating of extinction risk assessments. In this study, we used a computational pipeline to approximate RL extinction risk assessments for more than 21,000 tree species (leading to an overall assessment of 89% of all known tree species) using a supervised learning approach trained based on available IUCN RL assessments. We harvested the occurrence data for tree species worldwide from online databases, which we used with other publicly available data to design features characterizing the species' geographic range, biome and climatic affinities, and exposure to human footprint. We trained deep neural network models to predict their conservation status, based on these features. We estimated 43% of the assessed tree species to be threatened with extinction and found taxonomic and geographic heterogeneities in the distribution of threatened species. The results are consistent with the recent estimates by the Global Tree Assessment initiative, indicating that our approach provides robust and time-efficient approximations of species' IUCN RL extinction risk assessments.
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Affiliation(s)
- Sandro Valerio Silva
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Tobias Andermann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Global Gothenburg Biodiversity Centre, Department of Biological and Environmental Sciences, Sweden, University of Gothenburg, Gothenburg, Sweden
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Gregor Kozlowski
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Global Gothenburg Biodiversity Centre, Department of Biological and Environmental Sciences, Sweden, University of Gothenburg, Gothenburg, Sweden
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
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5
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Fountain-Jones NM, Smith ML, Austerlitz F. Machine learning in molecular ecology. Mol Ecol Resour 2021; 21:2589-2597. [PMID: 34738721 DOI: 10.1111/1755-0998.13532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/26/2022]
Affiliation(s)
| | - Megan L Smith
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Abstract
The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.
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Edwards SV, Robin V, Ferrand N, Moritz C. The evolution of comparative phylogeography: putting the geography (and more) into comparative population genomics. Genome Biol Evol 2021; 14:6339579. [PMID: 34347070 PMCID: PMC8743039 DOI: 10.1093/gbe/evab176] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
Comparative population genomics is an ascendant field using genomic comparisons between species to draw inferences about forces regulating genetic variation. Comparative phylogeography, by contrast, focuses on the shared lineage histories of species codistributed geographically and is decidedly organismal in perspective. Comparative phylogeography is approximately 35 years old, and, by some metrics, is showing signs of reduced growth. Here, we contrast the goals and methods of comparative population genomics and comparative phylogeography and argue that comparative phylogeography offers an important perspective on evolutionary history that succeeds in integrating genomics with landscape evolution in ways that complement the suprageographic perspective of comparative population genomics. Focusing primarily on terrestrial vertebrates, we review the history of comparative phylogeography, its milestones and ongoing conceptual innovations, its increasingly global focus, and its status as a bridge between landscape genomics and the process of speciation. We also argue that, as a science with a strong “sense of place,” comparative phylogeography offers abundant “place-based” educational opportunities with its focus on geography and natural history, as well as opportunities for collaboration with local communities and indigenous peoples. Although comparative phylogeography does not yet require whole-genome sequencing for many of its goals, we conclude that it nonetheless plays an important role in grounding our interpretation of genetic variation in the fundamentals of geography and Earth history.
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Affiliation(s)
- Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Vv Robin
- Indian Institute of Science Education and Research (IISER) Tirupati, Karakambadi Road, Tirupati, Andhra Pradesh, 517507, India
| | - Nuno Ferrand
- CIBIO/InBIO, Laboratório Associado, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Universidade do Porto, Portugal
| | - Craig Moritz
- Research School of Biology, The Australian National University, Canberra, ACT, 0200, Australia
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