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Hauffe T, Cantalapiedra JL, Silvestro D. Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks. SCIENCE ADVANCES 2024; 10:eadl2643. [PMID: 39047110 DOI: 10.1126/sciadv.adl2643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Species life-history traits, paleoenvironment, and biotic interactions likely influence speciation and extinction rates, affecting species richness over time. Birth-death models inferring the impact of these factors typically assume monotonic relationships between single predictors and rates, limiting our ability to assess more complex effects and their relative importance and interaction. We introduce a Bayesian birth-death model using unsupervised neural networks to explore multifactorial and nonlinear effects on speciation and extinction rates using fossil data. It infers lineage- and time-specific rates and disentangles predictor effects and importance through explainable artificial intelligence techniques. Analysis of the proboscidean fossil record revealed speciation rates shaped by dietary flexibility and biogeographic events. The emergence of modern humans escalated extinction rates, causing recent diversity decline, while regional climate had a lesser impact. Our model paves the way for an improved understanding of the intricate dynamics shaping clade diversification.
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Affiliation(s)
- Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
| | - Juan L Cantalapiedra
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
- GloCEE Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, Universidad de Alcalá, 28801 Alcalá de Henares, Spain
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, 40530 Gothenburg, Sweden
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2
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Sun X, Hu S, He R, Zeng J, Zhao D. Ecological restoration enhanced the stability of epiphytic microbial food webs of submerged macrophytes: Insights from predation characteristics of epiphytic predators. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174547. [PMID: 38992355 DOI: 10.1016/j.scitotenv.2024.174547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/03/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
The application of various submerged macrophytes for ecological restoration has gained increasing attention in urban lake ecosystems. The multitrophic microbial communities that colonized in various submerged macrophytes constitute microbial food webs through trophic cascade effects, which affect the biogeochemical cycles of the lake ecosystem and directly determine the effects of ecological restoration. Therefore, it is essential to reveal the diversity, composition, assembly processes, and stability of the microbial communities within epiphytic food webs of diverse submerged macrophytes under eutrophication and ecological restoration scenarios. In this study, we explored the epiphytic microbial food webs of Vallisneria natans and Hydrilla verticillata in both eutrophic and ecological restoration regions. The obtained results indicated that the two regions with different nutrient levels remarkably affected the diversity and composition of epiphytic multitrophic microbial communities of submerged macrophytes, among them, the community composition of epiphytic predators were more prone to change. Secondly, environmental filtering effects played a more important role in driving the community assembly of epiphytic predators than that of prey. Furthermore, the generality and intraguild predation of epiphytic predators were significantly improved within ecological restoration regions, which increased the stability of epiphytic microbial food webs. Additionally, compared with Hydrilla verticillata, the epiphytic microbial food webs of Vallisneria natans exhibited higher multitrophic diversity and higher network stability regardless of regions. Overall, this study focused on the role of the epiphytic microbial food webs of submerged macrophytes in ecological restoration and uncovered the potential of epiphytic predators to enhance the stability of microbial food webs, which may provide new insights into the development of ecological restoration strategies.
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Affiliation(s)
- Xiaojian Sun
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Siwen Hu
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Rujia He
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China; Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing 100039, China; Poyang Lake Wetland Research Station, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Jiujiang 332899, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, the National Key Laboratory of Water Disaster Prevention, Hohai University, Nanjing 210098, China; College of Geography and Remote Sensing, Hohai University, Nanjing 210098, China.
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3
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Park T, Burin G, Lazo-Cancino D, Rees JPG, Rule JP, Slater GJ, Cooper N. Charting the course of pinniped evolution: insights from molecular phylogeny and fossil record integration. Evolution 2024; 78:1212-1226. [PMID: 38644688 DOI: 10.1093/evolut/qpae061] [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: 08/23/2023] [Revised: 04/02/2024] [Accepted: 04/19/2024] [Indexed: 04/23/2024]
Abstract
Pinnipeds (seals, sea lions, walruses, and their fossil relatives) are one of the most successful mammalian clades to live in the oceans. Despite a well-resolved molecular phylogeny and a global fossil record, a complete understanding of their macroevolutionary dynamics remains hampered by a lack of formal analyses that combine these 2 rich sources of information. We used a meta-analytic approach to infer the most densely sampled pinniped phylogeny to date (36 recent and 93 fossil taxa) and used phylogenetic paleobiological methods to study their diversification dynamics and biogeographic history. Pinnipeds mostly diversified at constant rates. Walruses, however, experienced rapid turnover in which extinction rates ultimately exceeded speciation rates from 12 to 6 Ma, possibly due to changing sea levels and/or competition with otariids (eared seals). Historical biogeographic analyses, including fossil data, allowed us to confidently identify the North Pacific and the North Atlantic (plus or minus Paratethys) as the ancestral ranges of Otarioidea (eared seals + walrus) and crown phocids (earless seals), respectively. Yet, despite the novel addition of stem pan-pinniped taxa, the region of origin for Pan-Pinnipedia remained ambiguous. These results suggest further avenues of study in pinnipeds and provide a framework for investigating other groups with substantial extinct and extant diversity.
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Affiliation(s)
- Travis Park
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
- Sciences, Museums Victoria, Melbourne, Australia
| | - Gustavo Burin
- Science Group, Natural History Museum London, London, United Kingdom
| | - Daniela Lazo-Cancino
- Laboratorio de Mastozoología, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Joseph P G Rees
- Science Group, Natural History Museum London, London, United Kingdom
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James P Rule
- School of Biological Sciences, Monash University, Melbourne, Australia
- Science Group, Natural History Museum London, London, United Kingdom
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Natalie Cooper
- Science Group, Natural History Museum London, London, United Kingdom
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4
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Monarrez PM, Heim NA, Payne JL. Reduced strength and increased variability of extinction selectivity during mass extinctions. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230795. [PMID: 37771968 PMCID: PMC10523066 DOI: 10.1098/rsos.230795] [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: 06/14/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
Two of the traits most often observed to correlate with extinction risk in marine animals are geographical range and body size. However, the relative effects of these two traits on extinction risk have not been investigated systematically for either background times or during mass extinctions. To close this knowledge gap, we measure and compare extinction selectivity of geographical range and body size of genera within five classes of benthic marine animals across the Phanerozoic using capture-mark-recapture models. During background intervals, narrow geographical range is strongly associated with greater extinction probability, whereas smaller body size is more weakly associated with greater extinction probability. During mass extinctions, the association between geographical range and extinction probability is reduced in every class and fully eliminated in some, whereas the association between body size and extinction probability varies in strength and direction across classes. While geographical range is universally the stronger predictor of survival during background intervals, variation among classes during mass extinction suggests a fundamental shift in extinction processes during these global catastrophes.
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Affiliation(s)
- Pedro M. Monarrez
- Department of Earth and Planetary Sciences, Stanford University, Stanford, CA 94305, USA
| | - Noel A. Heim
- Department of Earth and Climate Sciences, Tufts University, Medford, MA 02155, USA
| | - Jonathan L. Payne
- Department of Earth and Planetary Sciences, Stanford University, Stanford, CA 94305, USA
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5
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Saupe EE. Explanations for latitudinal diversity gradients must invoke rate variation. Proc Natl Acad Sci U S A 2023; 120:e2306220120. [PMID: 37535654 PMCID: PMC10433455 DOI: 10.1073/pnas.2306220120] [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] [Indexed: 08/05/2023] Open
Abstract
The latitudinal diversity gradient (LDG) describes the pattern of increasing numbers of species from the poles to the equator. Although recognized for over 200 years, the mechanisms responsible for the largest-scale and longest-known pattern in macroecology are still actively debated. I argue here that any explanation for the LDG must invoke differential rates of speciation, extinction, extirpation, or dispersal. These processes themselves may be governed by numerous abiotic or biotic factors. Hypotheses that claim not to invoke differential rates, such as 'age and area' or 'time for diversification', eschew focus from rate variation that is assumed by these explanations. There is still significant uncertainty in how rates of speciation, extinction, extirpation, and dispersal have varied regionally over Earth history. However, to better understand the development of LDGs, we need to better constrain this variation. Only then will the drivers of such rate variation - be they abiotic or biotic in nature - become clearer.
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Affiliation(s)
- Erin E. Saupe
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, United Kingdom
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6
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Chen Y, Sun Y, Hua M, Shi K, Dudgeon D. Using genetic tools to inform conservation of fragmented populations of Asian elephants (Elephas maximus) across their range in China. Integr Zool 2023; 18:453-468. [PMID: 36052971 DOI: 10.1111/1749-4877.12680] [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] [Indexed: 12/01/2022]
Abstract
A herd of 15 Chinese elephants attracted international attention during their 2021 northward trek, motivating the government to propose establishment of an Asian elephant national park. However, planning is hampered by a lack of genetic information on the remaining populations in China. We collected DNA from 497 dung samples from all 5 populations encompassing the entire range of elephants in China and used mitochondrial and microsatellite markers to investigate their genetic and demographic structure. We identified 237 unique genotypes (153 females, 84 males), representing 81% of the known population. However, the effective population size was small (28, range 25-32). Historic demographic contraction appeared to account for low haplotype diversity (Hd = 0.235), but moderate nucleotide and nuclear diversity (π = 0.6%, He = 0.55) was attributable to post-bottleneck recovery involving recent population expansion plus historical gene exchange with elephants in Myanmar, Lao PDR, and Vietnam. The 5 populations fell into 3 clusters, with Nangunhe elephants differing consistently from the other 4 populations (FST = 0.23); elephants from Mengyang, Simao, and Jiangcheng belonged to a single population (henceforth, MSJ), and differed from the Shangyong population (FST = 0.11). Interpopulation genetic variation reflected isolation by distance and female-biased dispersal. Chinese elephants should be managed as 2 distinct units: Nangunhe and another combining Shangyong and MSJ; their long-term viability will require restoring gene flow between Shangyong and MSJ, and between elephants in China and neighboring countries. Our results have the potential to inform conservation planning for an iconic megafaunal species.
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Affiliation(s)
- Ying Chen
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Yakuan Sun
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Mei Hua
- Institute of Agro-food Technology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Kun Shi
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Eco-Bridge Continental, Beijing, China
| | - David Dudgeon
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
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7
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Hay EM, McGee MD, Chown SL. Geographic range size and speciation in honeyeaters. BMC Ecol Evol 2022; 22:86. [PMID: 35768772 PMCID: PMC9245323 DOI: 10.1186/s12862-022-02041-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Darwin and others proposed that a species’ geographic range size positively influences speciation likelihood, with the relationship potentially dependent on the mode of speciation and other contributing factors, including geographic setting and species traits. Several alternative proposals for the influence of range size on speciation rate have also been made (e.g. negative or a unimodal relationship with speciation). To examine Darwin’s proposal, we use a range of phylogenetic comparative methods, focusing on a large Australasian bird clade, the honeyeaters (Aves: Meliphagidae).
Results
We consider the influence of range size, shape, and position (latitudinal and longitudinal midpoints, island or continental species), and consider two traits known to influence range size: dispersal ability and body size. Applying several analytical approaches, including phylogenetic Bayesian path analysis, spatiophylogenetic models, and state-dependent speciation and extinction models, we find support for both the positive relationship between range size and speciation rate and the influence of mode of speciation.
Conclusions
Honeyeater speciation rate differs considerably between islands and the continental setting across the clade’s distribution, with range size contributing positively in the continental setting, while dispersal ability influences speciation regardless of setting. These outcomes support Darwin’s original proposal for a positive relationship between range size and speciation likelihood, while extending the evidence for the contribution of dispersal ability to speciation.
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8
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Diversity of the MHC class II DRB gene in the wolverine (Carnivora: Mustelidae: Gulo gulo) in Finland. PLoS One 2022; 17:e0267609. [PMID: 35536786 PMCID: PMC9089919 DOI: 10.1371/journal.pone.0267609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 11/19/2022] Open
Abstract
The wolverine (Gulo gulo) in Finland has undergone significant population declines in the past. Since major histocompatibility complex (MHC) genes encode proteins involved in pathogen recognition, the diversity of these genes provides insights into the immunological fitness of regional populations. We sequenced 862 amplicons (242 bp) of MHC class II DRB exon 2 from 32 Finnish wolverines and identified 11 functional alleles and three pseudogenes. A molecular phylogenetic analysis indicated trans-species polymorphism, and PAML and MEME analyses indicated positive selection, suggesting that the Finnish wolverine DRB genes have evolved under balancing and positive selection. In contrast to DRB gene analyses in other species, allele frequencies in the Finnish wolverines clearly indicated the existence of two regional subpopulations, congruent with previous studies based on neutral genetic markers. In the Finnish wolverine, rapid population declines in the past have promoted genetic drift, resulting in a lower genetic diversity of DRB loci, including fewer alleles and positively selected sites, than other mustelid species analyzed previously. Our data suggest that the MHC region in the Finnish wolverine population was likely affected by a recent bottleneck.
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Hauffe T, Pires MM, Quental TB, Wilke T, Silvestro D. A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Torsten Hauffe
- Department of Biology University of Fribourg and Swiss Institute of Bioinformatics Fribourg Switzerland
| | - Mathias M. Pires
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas Campinas Brazil
| | - Tiago B. Quental
- Departamento de Ecologia, Universidade de São Paulo São Paulo Brazil
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Germany
| | - Daniele Silvestro
- Department of Biology University of Fribourg and Swiss Institute of Bioinformatics Fribourg Switzerland
- Department of Biological and Environmental Sciences University of Gothenburg and Gothenburg Global Biodiversity Centre Gothenburg Sweden
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10
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The multicausal twilight of South American native mammalian predators (Metatheria, Sparassodonta). Sci Rep 2022; 12:1224. [PMID: 35075186 PMCID: PMC8786871 DOI: 10.1038/s41598-022-05266-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/23/2021] [Indexed: 11/08/2022] Open
Abstract
Sparassodonts were the apex mammalian predators of South America throughout most of the Cenozoic, diversifying into a wide array of niches including fox-like and even saber-toothed forms. Their extinction is still controversial, with different authors suggesting competition with other predators (placental carnivorans, terror birds, and carnivorous opossums), extinction of prey, and climate change as causal explanations. Here, we analyse these hypotheses using a novel approach implicating Bayesian analyses. We find that speciation and extinction rates of sparassodonts can be correlated with (i) intrinsic biotic factors such as changes in body mass and diversity of sparassodonts, (ii) extrinsic biotic factors such as potential prey diversity, and iii) extrinsic abiotic factors like the atmospheric CO2, sea level, temperature, and uplift of the Andes. Thus, sparassodonts are a good example of a multilevel mixed model of evolution, where various factors drove the evolutionary history of this clade in a pluralistic way. There is no evidence for competition between Sparassodonta and others predators, and the effect of competition in the face of extinctions of fossil species should be tested and not assumed. Furthermore, we propose a novel approach for evaluating the fossil record when performing macroevolutionary analyses.
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11
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Lidgard S, Di Martino E, Zágoršek K, Liow LH. When fossil clades 'compete': local dominance, global diversification dynamics and causation. Proc Biol Sci 2021; 288:20211632. [PMID: 34547910 PMCID: PMC8456135 DOI: 10.1098/rspb.2021.1632] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/26/2021] [Indexed: 01/14/2023] Open
Abstract
Examining the supposition that local-scale competition drives macroevolutionary patterns has become a familiar goal in fossil biodiversity studies. However, it is an elusive goal, hampered by inadequate confirmation of ecological equivalence and interactive processes between clades, patchy sampling, few comparative analyses of local species assemblages over long geological intervals, and a dearth of appropriate statistical tools. We address these concerns by reevaluating one of the classic examples of clade displacement in the fossil record, in which cheilostome bryozoans surpass the once dominant cyclostomes. Here, we analyse a newly expanded and vetted compilation of 40 190 fossil species occurrences to estimate cheilostome and cyclostome patterns of species proportions within assemblages, global genus richness and genus origination and extinction rates while accounting for sampling. Comparison of time-series models using linear stochastic differential equations suggests that inter-clade genus origination and extinction rates are causally linked to each other in a complex feedback relationship rather than by simple correlations or unidirectional relationships, and that these rates are not causally linked to changing within-assemblage proportions of cheilostome versus cyclostome species.
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Affiliation(s)
- Scott Lidgard
- Negaunee Integrative Research Center, Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605 USA
| | | | - Kamil Zágoršek
- Department of Geography, Technical University of Liberec, Studentská 2, CZ-461 Liberec, Czech Republic
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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13
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Aymen J, Freedman M, Delnatte P, McAdie M, Beaufrère H. Retrospective analysis of hibernation parameters and breeding success in captive Vancouver Island marmots (Marmota vancouverensis): 1997-2018. Zoo Biol 2021; 40:273-279. [PMID: 33848361 DOI: 10.1002/zoo.21607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/05/2021] [Accepted: 03/24/2021] [Indexed: 11/07/2022]
Abstract
Vancouver Island marmots (Marmota vancouverensis) have been managed in a captive-breeding program since 1997, as in situ conservation efforts were insufficient in raising the numbers of this critically endangered species. The success of captive-breeding programs centers on sustainable reproduction and survival of individuals once released into the wild. Captive-born Vancouver Island marmots released to the wild have lower survival rates than their wild-born counterparts; this difference may arise from compromised hibernation patterns or behaviors. Hibernation duration, body weight over the hibernation season, and reproductive success of captive Vancouver Island marmots were reviewed to assess the effect of these variables on each other. Data from a total of 1782 hibernations and 456 breeding attempts were compiled from 1997 to 2018. The number of winters spent in captivity, the origin of the marmot (captive-born or wild-born), the facility at which hibernation occurred, and the body weight all had a significant effect on hibernation length (all p < .001). Increased weight was associated with increased hibernation length by 0.4 ± 0.1 day/kg on average (p = .0015). Captive, wild-born marmots hibernated for significantly longer than their captive-born counterparts by about 21 ± 2 days (p < .001). The odds of successful breeding were significantly increased with increasing hibernation length by approximatively 20% for every 10 additional days of hibernation. This study provides information on the intrinsic relationship between body weight, reproduction, and hibernation in captive Vancouver Island marmots.
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Affiliation(s)
- Jessica Aymen
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Toronto Zoo, Toronto, Ontario, Canada
| | - Megan Freedman
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | | | - Malcolm McAdie
- Marmot Recovery Foundation, Nanaimo, British Columbia, Canada
| | - Hugues Beaufrère
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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14
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Bradshaw CJ, Johnson CN, Llewelyn J, Weisbecker V, Strona G, Saltré F. Relative demographic susceptibility does not explain the extinction chronology of Sahul's megafauna. eLife 2021; 10:63870. [PMID: 33783356 PMCID: PMC8043753 DOI: 10.7554/elife.63870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/29/2021] [Indexed: 11/17/2022] Open
Abstract
The causes of Sahul’s megafauna extinctions remain uncertain, although several interacting factors were likely responsible. To examine the relative support for hypotheses regarding plausible ecological mechanisms underlying these extinctions, we constructed the first stochastic, age-structured models for 13 extinct megafauna species from five functional/taxonomic groups, as well as 8 extant species within these groups for comparison. Perturbing specific demographic rates individually, we tested which species were more demographically susceptible to extinction, and then compared these relative sensitivities to the fossil-derived extinction chronology. Our models show that the macropodiformes were the least demographically susceptible to extinction, followed by carnivores, monotremes, vombatiform herbivores, and large birds. Five of the eight extant species were as or more susceptible than the extinct species. There was no clear relationship between extinction susceptibility and the extinction chronology for any perturbation scenario, while body mass and generation length explained much of the variation in relative risk. Our results reveal that the actual mechanisms leading to the observed extinction chronology were unlikely related to variation in demographic susceptibility per se, but were possibly driven instead by finer-scale variation in climate change and/or human prey choice and relative hunting success.
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Affiliation(s)
- Corey Ja Bradshaw
- Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Tarndanya (Adelaide), Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
| | - Christopher N Johnson
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia.,Dynamics of Eco-Evolutionary Pattern, University of Tasmania, Hobart, Australia
| | - John Llewelyn
- Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Tarndanya (Adelaide), Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
| | - Vera Weisbecker
- ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia.,College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Giovanni Strona
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Frédérik Saltré
- Global Ecology Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Tarndanya (Adelaide), Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, Australia
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15
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Cally JG, Stuart-Fox D, Holman L, Dale J, Medina I. Male-biased sexual selection, but not sexual dichromatism, predicts speciation in birds. Evolution 2021; 75:931-944. [PMID: 33559135 DOI: 10.1111/evo.14183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/13/2021] [Indexed: 01/04/2023]
Abstract
Sexual selection is thought to shape phylogenetic diversity by affecting speciation or extinction rates. However, the net effect of sexual selection on diversification is hard to predict because many of the hypothesized effects on speciation or extinction have opposing signs and uncertain magnitudes. Theoretical work also suggests that the net effect of sexual selection on diversification should depend strongly on ecological factors, though this prediction has seldom been tested. Here, we test whether variation in sexual selection can predict speciation and extinction rates across passerine birds (up to 5812 species, covering most genera) and whether this relationship is mediated by environmental factors. Male-biased sexual selection, and specifically sexual size dimorphism, predicted two of the three measures of speciation rates that we examined. The link we observed between sexual selection and speciation was independent of environmental variability, though species with smaller ranges had higher speciation rates. There was no association between any proxies of sexual selection and extinction rate. Our findings support the view that male-biased sexual selection, as measured by frequent predictors of male-male competition, has shaped diversification in the largest radiation of birds.
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Affiliation(s)
- Justin G Cally
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Devi Stuart-Fox
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Luke Holman
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - James Dale
- School of Natural and Computational Sciences, Massey University (Albany Campus), Auckland, 0632, New Zealand
| | - Iliana Medina
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
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16
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Fuller A, Mitchell D, Maloney SK, Hetem RS, Fonsêca VFC, Meyer LCR, van de Ven TMFN, Snelling EP. How dryland mammals will respond to climate change: the effects of body size, heat load and a lack of food and water. J Exp Biol 2021; 224:224/Suppl_1/jeb238113. [PMID: 33627465 DOI: 10.1242/jeb.238113] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Mammals in drylands are facing not only increasing heat loads but also reduced water and food availability as a result of climate change. Insufficient water results in suppression of evaporative cooling and therefore increases in body core temperature on hot days, while lack of food reduces the capacity to maintain body core temperature on cold nights. Both food and water shortage will narrow the prescriptive zone, the ambient temperature range over which body core temperature is held relatively constant, which will lead to increased risk of physiological malfunction and death. Behavioural modifications, such as shifting activity between night and day or seeking thermally buffered microclimates, may allow individuals to remain within the prescriptive zone, but can incur costs, such as reduced foraging or increased competition or predation, with consequences for fitness. Body size will play a major role in predicting response patterns, but identifying all the factors that will contribute to how well dryland mammals facing water and food shortage will cope with increasing heat loads requires a better understanding of the sensitivities and responses of mammals exposed to the direct and indirect effects of climate change.
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Affiliation(s)
- Andrea Fuller
- Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa .,Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa.,Centre for Veterinary Wildlife Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Duncan Mitchell
- Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa.,School of Human Sciences, Faculty of Science, University of Western Australia, Crawley 6009, WA, Australia
| | - Shane K Maloney
- Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa.,School of Human Sciences, Faculty of Science, University of Western Australia, Crawley 6009, WA, Australia
| | - Robyn S Hetem
- Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa.,School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Vinicius F C Fonsêca
- Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa.,Innovation Group of Biometeorology and Animal Welfare (INOBIO-MANERA), Universidade Federal da Paraíba, Areia, 58397000, Brazil
| | - Leith C R Meyer
- Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa.,Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa.,Centre for Veterinary Wildlife Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Tanja M F N van de Ven
- Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa
| | - Edward P Snelling
- Brain Function Research Group, School of Physiology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa.,Centre for Veterinary Wildlife Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa.,Department of Anatomy and Physiology, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
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17
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Lambdon P, Cronk Q. Extinction Dynamics Under Extreme Conservation Threat: The Flora of St Helena. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Steffens TS, Mercado Malabet F, Lehman SM. Occurrence of lemurs in landscapes and their species-specific scale responses to habitat loss. Am J Primatol 2020; 82:e23110. [PMID: 32083335 DOI: 10.1002/ajp.23110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 01/31/2020] [Accepted: 02/09/2020] [Indexed: 11/08/2022]
Abstract
Studies on the impact of habitat loss on species occurrence consistently find that the amount of habitat (measured as patch area) is a major determinant of species occurrence at a patch-level. However, patch-level research may fail to detect important patterns and processes only observable at a landscape-level. A landscape-level approach that incorporates species-specific scale responses is needed to better understand what drives species occurrence. Our aim was to determine the landscape-level scale of effect of habitat amount on the occurrence of three species of nocturnal lemurs (Cheirogaleus medius, Microcebus murinus, and M. ravelobensis). We surveyed line transects to determine the occurrence of three lemur species within a fragmented landscape of deciduous dry forest and anthropogenic grassland in northwestern Madagascar. To determine the scale of effect of habitat loss on lemur occurrence, we compared logistic regression models of occurrence against habitat amount among eight different landscape scales using Akaike's Information Criterion values. We found differing scale responses among the lemurs in our study. Occurrence of C. medius responded to habitat amount at scales between 0.5-4 ha, M. murinus at scales between 1 and 4 ha and M. ravelobensis at scales between 0.125 and 4 ha. We suggest that the scale of effect for C. medius is mediated by their ability to hibernate. A relatively lower scale-response for Microcebus spp. likely reflect their omnivorous diet, small habitat requirements, and limited dispersal ability. Differences in scale responses between M. murinus and M. ravelobensis are likely a result of differing dispersal ability and responses to edge effects between these species. Our study is among the first on lemurs to show the value of a landscape-level approach when assessing the effects of habitat loss on species occurrence.
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Affiliation(s)
- Travis S Steffens
- Department of Anthropology, University of Toronto, Ontario, Canada.,Planet Madagascar, Ontario, Guelph, Canada.,Department of Sociology and Anthropology, University of Guelph, Ontario, Canada
| | | | - Shawn M Lehman
- Department of Anthropology, University of Toronto, Ontario, Canada
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19
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Verboom GA, Boucher FC, Ackerly DD, Wootton LM, Freyman WA. Species Selection Regime and Phylogenetic Tree Shape. Syst Biol 2020; 69:774-794. [DOI: 10.1093/sysbio/syz076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 11/12/2022] Open
Abstract
Abstract
Species selection, the effect of heritable traits in generating between-lineage diversification rate differences, provides a valuable conceptual framework for understanding the relationship between traits, diversification, and phylogenetic tree shape. An important challenge, however, is that the nature of real diversification landscapes—curves or surfaces which describe the propensity of species-level lineages to diversify as a function of one or more traits—remains poorly understood. Here, we present a novel, time-stratified extension of the QuaSSE model in which speciation/extinction rate is specified as a static or temporally shifting Gaussian or skewed-Gaussian function of the diversification trait. We then use simulations to show that the generally imbalanced nature of real phylogenetic trees, as well as their generally greater than expected frequency of deep branching events, are typical outcomes when diversification is treated as a dynamic, trait-dependent process. Focusing on four basic models (Gaussian-speciation with and without background extinction; skewed-speciation; Gaussian-extinction), we also show that particular features of the species selection regime produce distinct tree shape signatures and that, consequently, a combination of tree shape metrics has the potential to reveal the species selection regime under which a particular lineage diversified. We evaluate this idea empirically by comparing the phylogenetic trees of plant lineages diversifying within climatically and geologically stable environments of the Greater Cape Floristic Region, with those of lineages diversifying in environments that have experienced major change through the Late Miocene-Pliocene. Consistent with our expectations, the trees of lineages diversifying in a dynamic context are less balanced, show a greater concentration of branching events close to the present, and display stronger diversification rate-trait correlations. We suggest that species selection plays an important role in shaping phylogenetic trees but recognize the need for an explicit probabilistic framework within which to assess the likelihoods of alternative diversification scenarios as explanations of a particular tree shape. [Cape flora; diversification landscape; environmental change; gamma statistic; species selection; time-stratified QuaSSE model; trait-dependent diversification; tree imbalance.]
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Affiliation(s)
- G Anthony Verboom
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7700, South Africa
| | - Florian C Boucher
- Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
- Université Grenoble Alpes, CNRS, Laboratoire d’Ecologie Alpine (LECA), 2233 Rue de la Piscine, FR-38000 Grenoble, France
| | - David D Ackerly
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Department of Environmental Sciences, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Lara M Wootton
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch 7700, South Africa
| | - William A Freyman
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
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20
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Abstract
Reconstructing prehistoric animal communities is important for understanding the emergence of modern ecosystems and the environmental context of human evolution. A new study of African fossils spanning seven million years shows that ancient large-herbivore assemblages were functionally distinct from those that exist today.
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Affiliation(s)
- Robert M Pringle
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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21
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Bennett DJ, Sutton MD, Turvey ST. How the past impacts the future: modelling the performance of evolutionarily distinct mammals through time. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190210. [PMID: 31679492 PMCID: PMC6863496 DOI: 10.1098/rstb.2019.0210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2019] [Indexed: 11/12/2022] Open
Abstract
How does past evolutionary performance impact future evolutionary performance? This is an important question not just for macroevolutionary biologists who wish to chart the phenomena that describe deep-time changes in biodiversity but also for conservation biologists, as evolutionarily distinct species-which may be deemed 'low-performing' in our current era-are increasingly the focus of conservation efforts. Contrasting hypotheses exist to account for the history and future of evolutionarily distinct species: on the one hand, they may be relicts of large radiations, potentially 'doomed' to extinction; or they may be slow-evolving, 'living fossils', likely neither to speciate nor go extinct; or they may be seeds of future radiations. Here, we attempt to test these hypotheses in Mammalia by combining a molecular phylogenetic supertree with fossil record occurrences and measuring change in evolutionary distinctness (ED) at different time slices. With these time slices, we modelled future ED as a function of past ED. We find that past evolutionary performance does indeed have an impact on future evolutionary performance: the most evolutionarily isolated clades tend to become more evolutionarily distinct with time, indicating that low-performing clades tend to remain low-performing throughout their evolutionary history. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'
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Affiliation(s)
- D. J. Bennett
- Gothenburg Global Biodiversity Centre, PO Box 461, 405 30 Gothenburg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, 405 30 Gothenburg, Sweden
| | - M. D. Sutton
- Department of Earth Sciences and Engineering, Imperial College London, London SW7 2BP, UK
| | - S. T. Turvey
- Institute of Zoology, Zoological Society of London, London NW1 4RY, UK
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22
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Schachat SR, Labandeira CC, Clapham ME, Payne JL. A Cretaceous peak in family-level insect diversity estimated with mark-recapture methodology. Proc Biol Sci 2019; 286:20192054. [PMID: 31847775 PMCID: PMC6939917 DOI: 10.1098/rspb.2019.2054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022] Open
Abstract
The history of insects' taxonomic diversity is poorly understood. The two most common methods for estimating taxonomic diversity in deep time yield conflicting results: the 'range through' method suggests a steady, nearly monotonic increase in family-level diversity, whereas 'shareholder quorum subsampling' suggests a highly volatile taxonomic history with family-level mass extinctions occurring repeatedly, even at the midpoints of geological periods. The only feature shared by these two diversity curves is a steep increase in standing diversity during the Early Cretaceous. This apparent diversification event occurs primarily during the Aptian, the pre-Cenozoic interval with the most described insect occurrences, raising the possibility that this feature of the diversity curves reflects preservation and sampling biases rather than insect evolution and extinction. Here, the capture-mark-recapture (CMR) approach is used to estimate insects' family-level diversity. This method accounts for the incompleteness of the insect fossil record as well as uneven sampling among time intervals. The CMR diversity curve shows extinctions at the Permian/Triassic and Cretaceous/Palaeogene boundaries but does not contain any mass extinctions within geological periods. This curve also includes a steep increase in diversity during the Aptian, which appears not to be an artefact of sampling or preservation bias because this increase still appears when time bins are standardized by the number of occurrences they contain rather than by the amount of time that they span. The Early Cretaceous increase in family-level diversity predates the rise of angiosperms by many millions of years and can be better attributed to the diversification of parasitic and especially parasitoid insect lineages.
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Affiliation(s)
- Sandra R. Schachat
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Conrad C. Labandeira
- Department of Paleobiology, Smithsonian Institution, Washington, DC 20013, USA
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
- College of Life Sciences, Capital Normal University, Beijing 100048, People’s Republic of China
| | - Matthew E. Clapham
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, CA 95064, USA
| | - Jonathan L. Payne
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
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23
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Tucker CM, Aze T, Cadotte MW, Cantalapiedra JL, Chisholm C, Díaz S, Grenyer R, Huang D, Mazel F, Pearse WD, Pennell MW, Winter M, Mooers AO. Assessing the utility of conserving evolutionary history. Biol Rev Camb Philos Soc 2019; 94:1740-1760. [PMID: 31149769 PMCID: PMC6852562 DOI: 10.1111/brv.12526] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 01/05/2023]
Abstract
It is often claimed that conserving evolutionary history is more efficient than species-based approaches for capturing the attributes of biodiversity that benefit people. This claim underpins academic analyses and recommendations about the distribution and prioritization of species and areas for conservation, but evolutionary history is rarely considered in practical conservation activities. One impediment to implementation is that arguments related to the human-centric benefits of evolutionary history are often vague and the underlying mechanisms poorly explored. Herein we identify the arguments linking the prioritization of evolutionary history with benefits to people, and for each we explicate the purported mechanism, and evaluate its theoretical and empirical support. We find that, even after 25 years of academic research, the strength of evidence linking evolutionary history to human benefits is still fragile. Most - but not all - arguments rely on the assumption that evolutionary history is a useful surrogate for phenotypic diversity. This surrogacy relationship in turn underlies additional arguments, particularly that, by capturing more phenotypic diversity, evolutionary history will preserve greater ecosystem functioning, capture more of the natural variety that humans prefer, and allow the maintenance of future benefits to humans. A surrogate relationship between evolutionary history and phenotypic diversity appears reasonable given theoretical and empirical results, but the strength of this relationship varies greatly. To the extent that evolutionary history captures unmeasured phenotypic diversity, maximizing the representation of evolutionary history should capture variation in species characteristics that are otherwise unknown, supporting some of the existing arguments. However, there is great variation in the strength and availability of evidence for benefits associated with protecting phenotypic diversity. There are many studies finding positive biodiversity-ecosystem functioning relationships, but little work exists on the maintenance of future benefits or the degree to which humans prefer sets of species with high phenotypic diversity or evolutionary history. Although several arguments link the protection of evolutionary history directly with the reduction of extinction rates, and with the production of relatively greater future biodiversity via increased adaptation or diversification, there are few direct tests. Several of these putative benefits have mismatches between the relevant spatial scales for conservation actions and the spatial scales at which benefits to humans are realized. It will be important for future work to fill in some of these gaps through direct tests of the arguments we define here.
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Affiliation(s)
- Caroline M. Tucker
- Department of BiologyUniversity of North Carolina at Chapel Hill, Coker Hall, CB #3280 120 South RoadChapel Hill, NC 27599‐3280U.S.A.
- Centre d'Écologie Fonctionnelle et Évolutive (UMR 5175), CNRS34090 MontpellierFrance
| | - Tracy Aze
- School of Earth and Environment, Maths/Earth and Environment BuildingUniversity of LeedsLeedsLS2 9JTU.K.
| | - Marc W. Cadotte
- Department of Biological SciencesUniversity of Toronto Scarborough, 1265 Military TrailTorontoONM1C 1A4Canada
- Department of Ecology and Evolutionary BiologyUniversity of Toronto, 25 Willcocks StreetTorontoONM5S 3B2Canada
| | - Juan L. Cantalapiedra
- Museum für Naturkunde, Leibniz‐Institut für Evolutions und Biodiversitätsforschung, Invalidenstraße 4310115BerlinGermany
- Departamento de Ciencias de la VidaUniversidad de Alcalá28805Alcalá de HenaresMadridSpain
| | - Chelsea Chisholm
- Department of Ecology and EvolutionQuartier UNIL‐Sorge Batiment Biophore CH‐1015 LausanneSwitzerland
| | - Sandra Díaz
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas and Facultad de Ciencias Exactas, Físicas y NaturalesUniversidad Nacional de Córdoba, Casilla de Correo 4955000CórdobaArgentina
| | - Richard Grenyer
- School of Geography and the EnvironmentSouth Parks Road, University of OxfordOxfordOX1 3QYU.K.
| | - Danwei Huang
- Department of Biological Sciences and Tropical Marine Science InstituteNational University of Singapore, 16 Science Drive 4, 117558Singapore
| | - Florent Mazel
- Department of Biological Sciences8888 University Drive, Simon Fraser UniversityBurnabyBCV5A 1S6, Canada
- Department of Botany2329 West Mall, University of British ColumbiaVancouverBCV6T 1Z4Canada
- Biodiversity Research Centre2212 Main Mall, University of British ColumbiaVancouverBCV6T 1Z4Canada
| | - William D. Pearse
- Department of Biology & Ecology Center5205 Old Main Hill, Utah State UniversityLoganUT84322, U.S.A.
| | - Matthew W. Pennell
- Biodiversity Research Centre2212 Main Mall, University of British ColumbiaVancouverBCV6T 1Z4Canada
- Department of ZoologySouth Parks Road, University of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv)Deutscher Platz 5E, 04103 LeipzigGermany
| | - Arne O. Mooers
- Department of Biological Sciences8888 University Drive, Simon Fraser UniversityBurnabyBCV5A 1S6, Canada
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24
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Lyons SK, Smith FA, Ernest SKM. Macroecological patterns of mammals across taxonomic, spatial, and temporal scales. J Mammal 2019. [DOI: 10.1093/jmammal/gyy171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- S Kathleen Lyons
- University of Nebraska–Lincoln, School of Biological Sciences, St. Lincoln, NE
| | - Felisa A Smith
- University of New Mexico, Department of Biology, Albuquerque, NM
| | - S K Morgan Ernest
- University of Florida, Department of Wildlife Ecology and Conservation, Gainesville, FL
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25
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Zettlemoyer MA, McKenna DD, Lau JA. Species characteristics affect local extinctions. AMERICAN JOURNAL OF BOTANY 2019; 106:547-559. [PMID: 30958894 DOI: 10.1002/ajb2.1266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/04/2019] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Human activities threaten thousands of species with extinction. However, it remains difficult to predict extinction risk for many vulnerable species. Species traits, species characteristics such as rarity or habitat use, and phylogenetic patterns are associated with responses to anthropogenic environmental change and may help predict likelihood of extinction. METHODS We used historical botanical data from Kalamazoo County, Michigan, USA, to examine whether species traits (growth form, life history, nitrogen-fixation, photosynthetic pathway), species characteristics (community association, species origin, range edge, habitat specialization, rarity), or phylogenetic relatedness explain local species loss at the county level. KEY RESULTS Across Kalamazoo County, prairie species, species at the edge of their native range, regionally rare species, and habitat specialists were most likely to become locally extinct. Prairie species experienced the highest local extinction rates of any habitat type, and among prairie species, regionally rare and specialist species were most vulnerable to loss. We found no evidence for a phylogenetic pattern in plant extinctions. CONCLUSIONS Our study illustrates the value of historical datasets for understanding and potentially predicting biodiversity loss. Not surprisingly, rare, specialist species occupying threatened habitats are most at risk of local extinction. As a result, identifying mechanisms to conserve or restore rare or declining species and preventing further habitat destruction may be the most effective strategies for reducing future extinction.
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Affiliation(s)
- Meredith A Zettlemoyer
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824-6406, USA
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, 49060-9505, USA
| | - Duane D McKenna
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee, 38152-3560, USA
| | - Jennifer A Lau
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824-6406, USA
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, 49060-9505, USA
- Department of Biology, Indiana University-Bloomington, Bloomington, Indiana, 47405-7005, USA
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26
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Alhajeri BH, Steppan SJ. Ecological and Ecomorphological Specialization Are Not Associated with Diversification Rates in Muroid Rodents (Rodentia: Muroidea). Evol Biol 2018. [DOI: 10.1007/s11692-018-9449-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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27
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Yeakel JD, Kempes CP, Redner S. Dynamics of starvation and recovery predict extinction risk and both Damuth's law and Cope's rule. Nat Commun 2018; 9:657. [PMID: 29440734 PMCID: PMC5811595 DOI: 10.1038/s41467-018-02822-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 01/02/2018] [Indexed: 11/09/2022] Open
Abstract
The eco-evolutionary dynamics of species are fundamentally linked to the energetic constraints of their constituent individuals. Of particular importance is the interplay between reproduction and the dynamics of starvation and recovery. To elucidate this interplay, here we introduce a nutritional state-structured model that incorporates two classes of consumers: nutritionally replete, reproducing consumers, and undernourished, nonreproducing consumers. We obtain strong constraints on starvation and recovery rates by deriving allometric scaling relationships and find that population dynamics are typically driven to a steady state. Moreover, these rates fall within a "refuge" in parameter space, where the probability of population extinction is minimized. We also show that our model provides a natural framework to predict steady state population abundances known as Damuth's law, and maximum mammalian body size. By determining the relative stability of an otherwise homogeneous population to a competing population with altered percent body fat, this framework provides a principled mechanism for a selective driver of Cope's rule.
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Affiliation(s)
- Justin D Yeakel
- School of Natural Sciences, University of California, Merced, CA, 95340, USA. .,The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
| | | | - Sidney Redner
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
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28
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Heim NA, Payne JL, Finnegan S, Knope ML, Kowalewski M, Lyons SK, McShea DW, Novack-Gottshall PM, Smith FA, Wang SC. Hierarchical complexity and the size limits of life. Proc Biol Sci 2018. [PMID: 28637850 DOI: 10.1098/rspb.2017.1039] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Over the past 3.8 billion years, the maximum size of life has increased by approximately 18 orders of magnitude. Much of this increase is associated with two major evolutionary innovations: the evolution of eukaryotes from prokaryotic cells approximately 1.9 billion years ago (Ga), and multicellular life diversifying from unicellular ancestors approximately 0.6 Ga. However, the quantitative relationship between organismal size and structural complexity remains poorly documented. We assessed this relationship using a comprehensive dataset that includes organismal size and level of biological complexity for 11 172 extant genera. We find that the distributions of sizes within complexity levels are unimodal, whereas the aggregate distribution is multimodal. Moreover, both the mean size and the range of size occupied increases with each additional level of complexity. Increases in size range are non-symmetric: the maximum organismal size increases more than the minimum. The majority of the observed increase in organismal size over the history of life on the Earth is accounted for by two discrete jumps in complexity rather than evolutionary trends within levels of complexity. Our results provide quantitative support for an evolutionary expansion away from a minimal size constraint and suggest a fundamental rescaling of the constraints on minimal and maximal size as biological complexity increases.
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Affiliation(s)
- Noel A Heim
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Jonathan L Payne
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Seth Finnegan
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Matthew L Knope
- Department of Biology, University of Hawaii, Hilo, HI 96720, USA
| | - Michał Kowalewski
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - S Kathleen Lyons
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Daniel W McShea
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Felisa A Smith
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Steve C Wang
- Department of Mathematics and Statistics, Swarthmore College, Swarthmore, PA 19081, USA
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29
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Huang S, Eronen JT, Janis CM, Saarinen JJ, Silvestro D, Fritz SA. Mammal body size evolution in North America and Europe over 20 Myr: similar trends generated by different processes. Proc Biol Sci 2018; 284:rspb.2016.2361. [PMID: 28202809 DOI: 10.1098/rspb.2016.2361] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/25/2017] [Indexed: 11/12/2022] Open
Abstract
Because body size interacts with many fundamental biological properties of a species, body size evolution can be an essential component of the generation and maintenance of biodiversity. Here we investigate how body size evolution can be linked to the clade-specific diversification dynamics in different geographical regions. We analyse an extensive body size dataset of Neogene large herbivores (covering approx. 50% of the 970 species in the orders Artiodactyla and Perissodactyla) in Europe and North America in a Bayesian framework. We reconstruct the temporal patterns of body size in each order on each continent independently, and find significant increases of minimum size in three of the continental assemblages (except European perissodactyls), suggesting an active selection for larger bodies. Assessment of trait-correlated birth-death models indicates that the common trend of body size increase is generated by different processes in different clades and regions. Larger-bodied artiodactyl species on both continents tend to have higher origination rates, and both clades in North America show strong links between large bodies and low extinction rate. Collectively, our results suggest a strong role of species selection and perhaps of higher-taxon sorting in driving body size evolution, and highlight the value of investigating evolutionary processes in a biogeographic context.
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Affiliation(s)
- Shan Huang
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany
| | - Jussi T Eronen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.,BIOS Research Unit, Helsinki, Finland
| | - Christine M Janis
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Juha J Saarinen
- Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland.,Natural History Museum, London, UK
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Susanne A Fritz
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Frankfurt am Main, Germany.,Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
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Estimating Rates and Probabilities of Origination and Extinction Using Taxonomic Occurrence Data: Capture-Mark-Recapture (CMR) Approaches. ACTA ACUST UNITED AC 2017. [DOI: 10.1017/s1089332600001820] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We rely on observations of occurrences of fossils to infer the rates and timings of origination and extinction of taxa. These estimates can then be used to shed light on questions such as whether extinction and origination rates have been higher or lower at different times in earth history or in different geographical regions, etc. and to investigate the possible underlying causes of varying rates. An inherent problem in inference using occurrence data is one of incompleteness of sampling. Even if a taxon is present at a given time and place, we are guaranteed to detect or sample it less than 100% of the time we search in a random outcrop or sediment sample that should contain it, either because it was not preserved, it was preserved but then eroded, or because we simply did not find it. Capture-mark-recapture (CMR) methods rely on replicate sampling to allow for the simultaneous estimation of sampling probability and the parameters of interest (e.g. extinction, origination, occupancy, diversity). Here, we introduce the philosophy of CMR approaches especially as applicable to paleontological data and questions. The use of CMR is in its infancy in paleobiological applications, but the handful of studies that have used it demonstrate its utility and generality. We discuss why the use of CMR has not matched its development in other fields, such as in population ecology, as well as the importance of modelling the sampling process and estimating sampling probabilities. In addition, we suggest some potential avenues for the development of CMR applications in paleobiology.
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Greenberg DA, Mooers AØ. Linking speciation to extinction: Diversification raises contemporary extinction risk in amphibians. Evol Lett 2017; 1:40-48. [PMID: 30283637 PMCID: PMC6121784 DOI: 10.1002/evl3.4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/14/2017] [Accepted: 03/21/2017] [Indexed: 11/08/2022] Open
Abstract
Many of the traits associated with elevated rates of speciation, including niche specialization and having small and isolated populations, are similarly linked with an elevated risk of extinction. This suggests that rapidly speciating lineages may also be more extinction prone. Empirical tests of a speciation-extinction correlation are rare because assessing paleontological extinction rates is difficult. However, the modern biodiversity crisis allows us to observe patterns of extinction in real time, and if this hypothesis is true then we would expect young clades that have recently diversified to have high contemporary extinction risk. Here, we examine evolutionary patterns of modern extinction risk across over 300 genera within one of the most threatened vertebrate classes, the Amphibia. Consistent with predictions, rapidly diversifying amphibian clades also had a greater share of threatened species. Curiously, this pattern is not reflected in other tetrapod classes and may reflect a greater propensity to speciate through peripheral isolation in amphibians, which is partly supported by a negative correlation between diversification rate and mean geographic range size. This clustered threat in rapidly diversifying amphibian genera means that protecting a small number of species can achieve large gains in preserving amphibian phylogenetic diversity. Nonindependence between speciation and extinction rates has many consequences for patterns of biodiversity and how we may choose to conserve it.
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Affiliation(s)
- Dan A Greenberg
- Department of Biological Sciences Simon Fraser University Burnaby British Columbia V5A 1S6 Canada.,Earth-to-Ocean Research Group Simon Fraser University Burnaby British Columbia V5A 1S6 Canada.,Crawford Lab for Evolutionary Studies Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
| | - Arne Ø Mooers
- Department of Biological Sciences Simon Fraser University Burnaby British Columbia V5A 1S6 Canada.,Crawford Lab for Evolutionary Studies Simon Fraser University Burnaby British Columbia V5A 1S6 Canada
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33
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Towards a mechanistic understanding of the responses of large terrestrial mammals to heat and aridity associated with climate change. ACTA ACUST UNITED AC 2016. [DOI: 10.1186/s40665-016-0024-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Hunt G, Slater G. Integrating Paleontological and Phylogenetic Approaches to Macroevolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-112414-054207] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With proliferation of molecular phylogenies and advances in statistical modeling, phylogeneticists can now address macroevolutionary questions that had traditionally been the purview of paleontology. Interest has focused on three areas at the intersection of phylogenetic and paleontological research: time-scaling phylogenies, understanding trait evolution, and modeling species diversification. Fossil calibrations have long been crucial for scaling phylogenies to absolute time, but recent advances allow more equal integration of extinct taxa. Simulation and empirical studies have shown that fossil data can markedly improve inferences about trait evolution, especially for models with heterogeneous temporal dynamics and in clades for which the living forms are unrepresentative remnants of their larger clade. Recent years have also seen a productive cross-disciplinary conversation about the nature and uncertainties of inferring diversification dynamics. Challenges remain, but the present time represents a flowering of interest in integrating these two views on the history of life.
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Affiliation(s)
- Gene Hunt
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560
| | - Graham Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois 60637
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DeMiguel D. Disentangling adaptive evolutionary radiations and the role of diet in promoting diversification on islands. Sci Rep 2016; 6:29803. [PMID: 27405690 PMCID: PMC4942836 DOI: 10.1038/srep29803] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/20/2016] [Indexed: 12/02/2022] Open
Abstract
Although the initial formulation of modern concepts of adaptive radiation arose from consideration of the fossil data, rigorous attempts to identify this phenomenon in the fossil record are largely uncommon. Here I focus on direct evidence of the diet (through tooth-wear patterns) and ecologically-relevant traits of one of the most renowned fossil vertebrates-the Miocene ruminant Hoplitomeryx from the island of Gargano-to deepen our understanding of the most likely causal forces under which adaptive radiations emerge on islands. Results show how accelerated accumulation of species and early-bursts of ecological diversification occur after invading an island, and provide insights on the interplay between diet and demographic (population-density), ecological (competition/food requirements) and abiotic (climate-instability) factors, identified as drivers of adaptive diversification. A pronounced event of overpopulation and a phase of aridity determined most of the rate and magnitude of radiation, and pushed species to expand diets from soft-leafy foods to tougher-harder items. Unexpectedly, results show that herbivorous mammals are restricted to browsing habits on small-islands, even if bursts of ecological diversification and dietary divergence occur. This study deepens our understanding of the mechanisms promoting adaptive radiations, and forces us to reevaluate the role of diet in the origins and evolution of islands mammals.
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Affiliation(s)
- Daniel DeMiguel
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici Z, C/de les Columnes s/n, Campus de la UAB, 08193 Cerdanyola del Vallès, Barcelona, Spain
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Hilbers JP, Schipper AM, Hendriks AJ, Verones F, Pereira HM, Huijbregts MAJ. An allometric approach to quantify the extinction vulnerability of birds and mammals. Ecology 2016; 97:615-26. [PMID: 27197389 DOI: 10.1890/14-2019.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Methods to quantify the vulnerability of species to extinction are typically limited by the availability of species-specific input data pertaining to life-history characteristics and population dynamics. This lack of data hampers global biodiversity assessments and conservation planning. Here, we developed a new framework that systematically quantifies extinction risk based on allometric relationships between various wildlife demographic parameters and body size. These allometric relationships have a solid theoretical and ecological foundation. Extinction risk indicators included are (1) the probability of extinction, (2) the mean time to extinction, and (3) the critical patch size. We applied our framework to assess the global extinction vulnerability of terrestrial carnivorous and non-carnivorous birds and mammals. Irrespective of the indicator used, large-bodied species were found to be more vulnerable to extinction than their smaller counterparts. The patterns with body size were confirmed for all species groups by a comparison with IUCN data on the proportion of extant threatened species: the models correctly predicted a multimodal distribution with body size for carnivorous birds and a monotonic distribution for mammals and non-carnivorous birds. Carnivorous mammals were found to have higher extinction risks than non-carnivores, while birds were more prone to extinction than mammals. These results are explained by the allometric relationships, predicting the vulnerable species groups to have lower intrinsic population growth rates, smaller population sizes, lower carrying capacities, or larger dispersal distances, which, in turn, increase the importance of losses due to environmental stochastic effects and dispersal activities. Our study is the first to integrate population viability analysis and allometry into a novel, process-based framework that is able to quantify extinction risk of a large number of species without requiring data-intensive, species-specific information. The framework facilitates the estimation of extinction vulnerabilities of data-deficient species. It may be applied to forecast extinction vulnerability in response to a changing environment, by incorporating quantitative relationships between wildlife demographic parameters and environmental drivers like habitat alteration, climate change, or hunting.
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Plotnick RE, Smith FA, Lyons SK. The fossil record of the sixth extinction. Ecol Lett 2016; 19:546-53. [PMID: 26932459 DOI: 10.1111/ele.12589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/21/2015] [Accepted: 01/29/2016] [Indexed: 11/28/2022]
Abstract
Comparing the magnitude of the current biodiversity crisis with those in the fossil record is difficult without an understanding of differential preservation. Integrating data from palaeontological databases with information on IUCN status, ecology and life history characteristics of contemporary mammals, we demonstrate that only a small and biased fraction of threatened species (< 9%) have a fossil record, compared with 20% of non-threatened species. We find strong taphonomic biases related to body size and geographic range. Modern species with a fossil record tend to be large and widespread and were described in the 19(th) century. The expected magnitude of the current extinction based only on species with a fossil record is about half of that of one based on all modern species; values for genera are similar. The record of ancient extinctions may be similarly biased, with many species having originated and gone extinct without leaving a tangible record.
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Affiliation(s)
- Roy E Plotnick
- Earth and Environmental Sciences, University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL, 6060, USA
| | - Felisa A Smith
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - S Kathleen Lyons
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, [NHB, MRC 121], P.O. Box 37012, Washington, DC, 20013-7012, USA
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38
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Finarelli JA, Liow LH. Diversification histories for North American and Eurasian carnivorans. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12777] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John A. Finarelli
- School of Biology and Environment Science; University of College Dublin; Belfield Dublin 4 Ireland
- UCD Earth Institute; University of College Dublin; Belfield Dublin 4 Ireland
| | - Lee Hsiang Liow
- Department of Biosciences; Centre for Ecological and Evolutionary Synthesis (CEES); University of Oslo; 0316 Oslo Norway
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Expected time-invariant effects of biological traits on mammal species duration. Proc Natl Acad Sci U S A 2015; 112:13015-20. [PMID: 26438873 DOI: 10.1073/pnas.1510482112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Determining which biological traits influence differences in extinction risk is vital for understanding the differential diversification of life and for making predictions about species' vulnerability to anthropogenic impacts. Here I present a hierarchical Bayesian survival model of North American Cenozoic mammal species durations in relation to species-level ecological factors, time of origination, and phylogenetic relationships. I find support for the survival of the unspecialized as a time-invariant generalization of trait-based extinction risk. Furthermore, I find that phylogenetic and temporal effects are both substantial factors associated with differences in species durations. Finally, I find that the estimated effects of these factors are partially incongruous with how these factors are correlated with extinction risk of the extant species. These findings parallel previous observations that background extinction is a poor predictor of mass extinction events and suggest that attention should be focused on mass extinctions to gain insight into modern species loss.
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Abstract
Species longevity in the fossil record is related to many paleoecological variables and is important to macroevolutionary studies, yet there are very few reliable data on average species durations in Cenozoic fossil mammals. Many of the online databases (such as the Paleobiology Database) use only genera of North American Cenozoic mammals and there are severe problems because key groups (e.g. camels, oreodonts, pronghorns and proboscideans) have no reliable updated taxonomy, with many invalid genera and species and/or many undescribed genera and species. Most of the published datasets yield species duration estimates of approximately 2.3-4.3 Myr for larger mammals, with small mammals tending to have shorter species durations. My own compilation of all the valid species durations in families with updated taxonomy (39 families, containing 431 genera and 998 species, averaging 2.3 species per genus) yields a mean duration of 3.21 Myr for larger mammals. This breaks down to 4.10-4.39 Myr for artiodactyls, 3.14-3.31 Myr for perissodactyls and 2.63-2.95 Myr for carnivorous mammals (carnivorans plus creodonts). These averages are based on a much larger, more robust dataset than most previous estimates, so they should be more reliable for any studies that need species longevity to be accurately estimated.
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Affiliation(s)
- Donald R Prothero
- Department of Vertebrate Paleontology, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
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Raj Pant S, Goswami A, Finarelli JA. Complex body size trends in the evolution of sloths (Xenarthra: Pilosa). BMC Evol Biol 2014; 14:184. [PMID: 25319928 PMCID: PMC4243956 DOI: 10.1186/s12862-014-0184-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Extant sloths present an evolutionary conundrum in that the two living genera are superficially similar (small-bodied, folivorous, arboreal) but diverged from one another approximately 30 million years ago and are phylogenetically separated by a radiation of medium to massive, mainly ground-dwelling, taxa. Indeed, the species in the two living genera are among the smallest, and perhaps most unusual, of the 50+ known sloth species, and must have independently and convergently evolved small size and arboreality. In order to accurately reconstruct sloth evolution, it is critical to incorporate their extinct diversity in analyses. Here, we used a dataset of 57 species of living and fossil sloths to examine changes in body mass mean and variance through their evolution, employing a general time-variable model that allows for analysis of evolutionary trends in continuous characters within clades lacking fully-resolved phylogenies, such as sloths. RESULTS Our analyses supported eight models, all of which partition sloths into multiple subgroups, suggesting distinct modes of body size evolution among the major sloth lineages. Model-averaged parameter values supported trended walks in most clades, with estimated rates of body mass change ranging as high as 126 kg/million years for the giant ground sloth clades Megatheriidae and Nothrotheriidae. Inclusion of living sloth species in the analyses weakened reconstructed rates for their respective groups, with estimated rates for Megalonychidae (large to giant ground sloths and the extant two-toed sloth) were four times higher when the extant genus Choloepus was excluded. CONCLUSIONS Analyses based on extant taxa alone have the potential to oversimplify or misidentify macroevolutionary patterns. This study demonstrates the impact that integration of data from the fossil record can have on reconstructions of character evolution and establishes that body size evolution in sloths was complex, but dominated by trended walks towards the enormous sizes exhibited in some recently extinct forms.
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Affiliation(s)
- Sara Raj Pant
- />Department of Genetics, Evolution & Environment, University College London, Gower Street, London, WC1E 6BT UK
| | - Anjali Goswami
- />Department of Genetics, Evolution & Environment, University College London, Gower Street, London, WC1E 6BT UK
- />Department of Earth Sciences, University College London, Gower Street, London, WC1E 6BT UK
| | - John A Finarelli
- />School of Biology & Environment Science, University College Dublin, Science Centre – West, Belfield, Dublin 4, Ireland
- />UCD Earth Institute, University of College Dublin, Belfield, Dublin 4, Ireland
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42
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Glazier DS. Is metabolic rate a universal ‘pacemaker’ for biological processes? Biol Rev Camb Philos Soc 2014; 90:377-407. [DOI: 10.1111/brv.12115] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 12/11/2022]
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43
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Bingham E, Mannila H. Towards Computational Techniques for Identifying Candidate Chronofaunas. ANN ZOOL FENN 2014. [DOI: 10.5735/086.051.0205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Flynn LJ, Morgan ME, Pilbeam D, Barry JC. “Endemism” Relative to Space, Time, and Taxonomic Level. ANN ZOOL FENN 2014. [DOI: 10.5735/086.051.0223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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45
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Silvestro D, Schnitzler J, Liow LH, Antonelli A, Salamin N. Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Syst Biol 2014; 63:349-67. [PMID: 24510972 DOI: 10.1093/sysbio/syu006] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
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Affiliation(s)
- Daniele Silvestro
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
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Body size reductions in nonmammalian eutheriodont therapsids (Synapsida) during the end-Permian mass extinction. PLoS One 2014; 9:e87553. [PMID: 24498335 PMCID: PMC3911975 DOI: 10.1371/journal.pone.0087553] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/23/2013] [Indexed: 11/19/2022] Open
Abstract
The extent to which mass extinctions influence body size evolution in major tetrapod clades is inadequately understood. For example, the 'Lilliput effect,' a common feature of mass extinctions, describes a temporary decrease in body sizes of survivor taxa in post-extinction faunas. However, its signature on existing patterns of body size evolution in tetrapods and the persistence of its impacts during post-extinction recoveries are virtually unknown, and rarely compared in both geologic and phylogenetic contexts. Here, I evaluate temporal and phylogenetic distributions of body size in Permo-Triassic therocephalian and cynodont therapsids (eutheriodonts) using a museum collections-based approach and time series model fitting on a regional stratigraphic sequence from the Karoo Basin, South Africa. I further employed rank order correlation tests on global age and clade rank data from an expanded phylogenetic dataset, and performed evolutionary model testing using Brownian (passive diffusion) models. Results support significant size reductions in the immediate aftermath of the end-Permian mass extinction (ca. 252.3 Ma) consistent with some definitions of Lilliput effects. However, this temporal succession reflects a pattern that was underscored largely by Brownian processes and constructive selectivity. Results also support two recent contentions about body size evolution and mass extinctions: 1) active, directional evolution in size traits is rare over macroevolutionary time scales and 2) geologically brief size reductions may be accomplished by the ecological removal of large-bodied species without rapid originations of new small-bodied clades or shifts from long-term evolutionary patterns.
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Evidence for soft bounds in Ubuntu package sizes and mammalian body masses. Proc Natl Acad Sci U S A 2013; 110:21054-8. [PMID: 24324175 DOI: 10.1073/pnas.1311124110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The development of a complex system depends on the self-coordinated action of a large number of agents, often determining unexpected global behavior. The case of software evolution has great practical importance: knowledge of what is to be considered atypical can guide developers in recognizing and reacting to abnormal behavior. Although the initial framework of a theory of software exists, the current theoretical achievements do not fully capture existing quantitative data or predict future trends. Here we show that two elementary laws describe the evolution of package sizes in a Linux-based operating system: first, relative changes in size follow a random walk with non-Gaussian jumps; second, each size change is bounded by a limit that is dependent on the starting size, an intriguing behavior that we call "soft bound." Our approach is based on data analysis and on a simple theoretical model, which is able to reproduce empirical details without relying on any adjustable parameter and generates definite predictions. The same analysis allows us to formulate and support the hypothesis that a similar mechanism is shaping the distribution of mammalian body sizes, via size-dependent constraints during cladogenesis. Whereas generally accepted approaches struggle to reproduce the large-mass shoulder displayed by the distribution of extant mammalian species, this is a natural consequence of the softly bounded nature of the process. Additionally, the hypothesis that this model is valid has the relevant implication that, contrary to a common assumption, mammalian masses are still evolving, albeit very slowly.
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48
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Shoemaker L, Clauset A. Body mass evolution and diversification within horses (family Equidae). Ecol Lett 2013; 17:211-20. [PMID: 24304872 DOI: 10.1111/ele.12221] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/25/2013] [Accepted: 10/18/2013] [Indexed: 11/28/2022]
Abstract
Horses (family Equidae) are a classic example of adaptive radiation, exhibiting a nearly 60-fold increase in maximum body mass and a peak taxonomic diversity of nearly 100 species across four continents. Such patterns are commonly attributed to niche competition, in which increased taxonomic diversity drives increased size disparity. However, neutral processes, such as macroevolutionary 'diffusion', can produce similar increases in disparity without increased diversity. Using a comprehensive database of Equidae species size estimates and a common mathematical framework, we measure the contributions of diversity-driven and diffusion-driven mechanisms for increased disparity during the Equidae radiation. We find that more than 90% of changes in size disparity are attributable to diffusion alone. These results clarify the role of species competition in body size evolution, indicate that morphological disparity and species diversity may be only weakly coupled in general, and demonstrate that large species may evolve from neutral macroevolutionary diffusion processes alone.
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Affiliation(s)
- Lauren Shoemaker
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
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Jansa SA, Barker FK, Voss RS. THE EARLY DIVERSIFICATION HISTORY OF DIDELPHID MARSUPIALS: A WINDOW INTO SOUTH AMERICA'S “SPLENDID ISOLATION”. Evolution 2013; 68:684-95. [DOI: 10.1111/evo.12290] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 10/01/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Sharon A. Jansa
- Bell Museum of Natural History and Department of Ecology; Evolution, and Behavior, University of Minnesota; St. Paul Minnesota
| | - F. Keith Barker
- Bell Museum of Natural History and Department of Ecology; Evolution, and Behavior, University of Minnesota; St. Paul Minnesota
| | - Robert S. Voss
- Division of Vertebrate Zoology; American Museum of Natural History; Central Park West at 79th Street New York New York
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50
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Tomiya S. Body size and extinction risk in terrestrial mammals above the species level. Am Nat 2013; 182:E196-214. [PMID: 24231545 DOI: 10.1086/673489] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mammalian body mass strongly correlates with life history and population properties at the scale of mouse to elephant. Large body size is thus often associated with elevated extinction risk. I examined the North American fossil record (28-1 million years ago) of 276 terrestrial genera to uncover the relationship between body size and extinction probability above the species level. Phylogenetic comparative analysis revealed no correlation between sampling-adjusted durations and body masses ranging 7 orders of magnitude, an observation that was corroborated by survival analysis. Most of the ecological and temporal groups within the data set showed the same lack of relationship. Size-biased generic extinctions do not constitute a general feature of the Holarctic mammalian faunas in the Neogene. Rather, accelerated loss of large mammals occurred during intervals that experienced combinations of regional aridification and increased biomic heterogeneity within continents. The latter phenomenon is consistent with the macroecological prediction that large geographic ranges are critical to the survival of large mammals in evolutionary time. The frequent lack of size selectivity in generic extinctions can be reconciled with size-biased species loss if extinctions of large and small mammals at the species level are often driven by ecological perturbations of different spatial and temporal scales, while those at the genus level are more synchronized in time as a result of fundamental, multiscale environmental shifts.
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Affiliation(s)
- Susumu Tomiya
- Museum of Paleontology, Museum of Vertebrate Zoology, and Department of Integrative Biology, University of California, Berkeley, California 94720
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