1
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Ceballos G, Ehrlich PR. Mutilation of the tree of life via mass extinction of animal genera. Proc Natl Acad Sci U S A 2023; 120:e2306987120. [PMID: 37722053 PMCID: PMC10523489 DOI: 10.1073/pnas.2306987120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/31/2023] [Indexed: 09/20/2023] Open
Abstract
Mass extinctions during the past 500 million y rapidly removed branches from the phylogenetic tree of life and required millions of years for evolution to generate functional replacements for the extinct (EX) organisms. Here we show, by examining 5,400 vertebrate genera (excluding fishes) comprising 34,600 species, that 73 genera became EX since 1500 AD. Beyond any doubt, the human-driven sixth mass extinction is more severe than previously assessed and is rapidly accelerating. The current generic extinction rates are 35 times higher than expected background rates prevailing in the last million years under the absence of human impacts. The genera lost in the last five centuries would have taken some 18,000 y to vanish in the absence of human beings. Current generic extinction rates will likely greatly accelerate in the next few decades due to drivers accompanying the growth and consumption of the human enterprise such as habitat destruction, illegal trade, and climate disruption. If all now-endangered genera were to vanish by 2,100, extinction rates would be 354 (average) or 511 (for mammals) times higher than background rates, meaning that genera lost in three centuries would have taken 106,000 and 153,000 y to become EX in the absence of humans. Such mutilation of the tree of life and the resulting loss of ecosystem services provided by biodiversity to humanity is a serious threat to the stability of civilization. Immediate political, economic, and social efforts of an unprecedented scale are essential if we are to prevent these extinctions and their societal impacts.
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Affiliation(s)
- Gerardo Ceballos
- Departamento de Ecologia de la Biodiversidad, Instituto de Ecologia, Universidad Nacional Autonoma de Mexico, Tercer Circuito Exterior SN, C.U., 04510Ciudad de Mexico, Mexico
| | - Paul R. Ehrlich
- Department of Biology, Center for Conservation Biology, Stanford University, Stanford, CA94305
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2
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Pimiento C, Antonelli A. Integrating deep-time palaeontology in conservation prioritisation. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.959364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Halting biodiversity loss under growing anthropogenic pressure is arguably the greatest environmental challenge we face. Given that not all species are equally threatened and that resources are always limited, establishing robust prioritisation schemes is critical for implementing effective conservation actions. To this end, the International Union for Conservation of Nature (IUCN) Red List of Threatened Species has become a widely used source of information on species’ extinction risk. Various metrics have been proposed that combine IUCN status with different aspects of biodiversity to identify conservation priorities. However, current strategies do not take full advantage of palaeontological data, with conservation palaeobiology often focussing on the near-time fossil record (the last 2 million years). Here, we make a case for the value of the deep-time (over 2 million years ago), as it can offer tangible parallels with today’s biodiversity crisis and inform on the intrinsic traits that make species prone to extinction. As such, palaeontological data holds great predictive power, which could be harnessed to flag species likely to be threatened but that are currently too poorly known to be identified as such. Finally, we identify key IUCN-based prioritisation metrics and outline opportunities for integrating palaeontological data to validate their implementation. Although the human signal of the current extinction crisis makes direct comparisons with the geological past challenging, the deep-time fossil record has more to offer to conservation than is currently recognised.
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3
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Machado FF, Jardim L, Dinnage R, Brito D, Cardillo M. Diet disparity and diversity predict extinction risk in primates. Anim Conserv 2022. [DOI: 10.1111/acv.12823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- F. F. Machado
- Departamento de Ecologia Instituto de Ciências Biológicas, Universidade Federal de Goiás Goiânia Goiás Brazil
| | - L. Jardim
- Departamento de Ecologia, Instituto Nacional de Ciências e Tecnologia em Ecologia, Evolução e Conservação da Biodiversidade, Instituto de Ciências Biológicas Universidade Federal de Goiás Goiânia Goiás Brazil
| | - R. Dinnage
- Macroevolution and Macroecology Group, Research School of Biology Australian National University Canberra ACT Australia
- Department of Biological Sciences, Institute of Environment Florida International University Miami FL USA
| | - D. Brito
- Departamento de Ecologia Instituto de Ciências Biológicas, Universidade Federal de Goiás Goiânia Goiás Brazil
| | - M. Cardillo
- Macroevolution and Macroecology Group, Research School of Biology Australian National University Canberra ACT Australia
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4
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Extinction risk in vascular plants and vertebrates is negatively correlated with family size. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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5
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Nunn CL, Vining AQ, Chakraborty D, Reiskind MH, Young HS. Effects of host extinction and vector preferences on vector-borne disease risk in phylogenetically structured host-hector communities. PLoS One 2021; 16:e0256456. [PMID: 34424937 PMCID: PMC8382198 DOI: 10.1371/journal.pone.0256456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/08/2021] [Indexed: 11/26/2022] Open
Abstract
Anthropogenic disturbance impacts the phylogenetic composition and diversity of ecological communities. While changes in diversity are known to dramatically change species interactions and alter disease dynamics, the effects of phylogenetic changes in host and vector communities on disease have been relatively poorly studied. Using a theoretical model, we investigated how phylogeny and extinction influence network structural characteristics relevant to disease transmission in disturbed environments. We modelled a multi-host, multi-vector community as a bipartite ecological network, where nodes represent host and vector species and edges represent connections among them through vector feeding, and we simulated vector preferences and threat status on host and parasite phylogenies. We then simulated loss of hosts, including phylogenetically clustered losses, to investigate how extinction influences network structure. We compared effects of phylogeny and extinction to those of host specificity, which we predicted to strongly increase network modularity and reduce disease prevalence. The simulations revealed that extinction often increased modularity, with higher modularity as species loss increased, although not as much as increasing host specificity did. These results suggest that extinction itself, all else being equal, may reduce disease prevalence in disturbed communities. However, in real communities, systematic patterns in species loss (e.g. favoring high competence species) or changes in abundance may counteract these effects. Unexpectedly, we found that effects of phylogenetic signal in host and vector traits were relatively weak, and only important when phylogenetic signal of host and vector traits were similar, or when these traits both varied.
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Affiliation(s)
- Charles L. Nunn
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | - Alexander Q. Vining
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- Graduate Program in Animal Behavior, UC Davis, Davis, California, United States of America
| | - Debapriyo Chakraborty
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, United States of America
- INRAE ENVT IHAP, National Veterinary School of Toulouse, Toulouse, France
| | - Michael H. Reiskind
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Hillary S. Young
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, California, United States of America
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6
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Louca S, Pennell MW. Why extinction estimates from extant phylogenies are so often zero. Curr Biol 2021; 31:3168-3173.e4. [PMID: 34019824 DOI: 10.1016/j.cub.2021.04.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/11/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022]
Abstract
Time-calibrated phylogenies of extant species ("extant timetrees") are widely used to estimate historical speciation and extinction rates by fitting stochastic birth-death models.1 These approaches have long been controversial, as many phylogenetic studies report zero extinction in many taxa, contradicting the high extinction rates seen in the fossil record and the fact that the majority of species ever to have existed are now extinct.2-9 To date, the causes of this discrepancy remain unresolved. Here, we provide a novel and simple explanation for these "zero-inflated" extinction estimates, based on the recent discovery that there exist many alternative "congruent" diversification scenarios that cannot be distinguished based solely on extant timetrees.10 Due to such congruencies, estimation methods tend to converge to some scenario congruent to (i.e., statistically indistinguishable from) the true diversification scenario, but not necessarily to the true diversification scenario itself. This congruent scenario may exhibit negative extinction rates, a biologically meaningless but mathematically feasible situation, in which case estimators will tend to stick to the boundary of zero extinction. Based on this explanation, we make multiple testable predictions, which we confirm using analyses of simulated trees and 121 empirical trees. In contrast to other proposed mechanisms for erroneous extinction rate estimates,5,11-14 our proposed mechanism specifically explains the zero inflation of previous extinction rate estimates in the absence of detectable model violations, even for large trees. Not only do our results likely resolve a long-standing mystery in phylogenetics, they demonstrate that model congruencies can have severe consequences in practice.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, 1210 University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, 5289 University of Oregon, Eugene, OR 97403, USA.
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC V6T1Z4, Canada; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T1Z4, Canada.
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7
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Abstract
Quantifying the abundance of species is essential to ecology, evolution, and conservation. The distribution of species abundances is fundamental to numerous longstanding questions in ecology, yet the empirical pattern at the global scale remains unresolved, with a few species' abundance well known but most poorly characterized. In large part because of heterogeneous data, few methods exist that can scale up to all species across the globe. Here, we integrate data from a suite of well-studied species with a global dataset of bird occurrences throughout the world-for 9,700 species (∼92% of all extant species)-and use missing data theory to estimate species-specific abundances with associated uncertainty. We find strong evidence that the distribution of species abundances is log left skewed: there are many rare species and comparatively few common species. By aggregating the species-level estimates, we find that there are ∼50 billion individual birds in the world at present. The global-scale abundance estimates that we provide will allow for a line of inquiry into the structure of abundance across biogeographic realms and feeding guilds as well as the consequences of life history (e.g., body size, range size) on population dynamics. Importantly, our method is repeatable and scalable: as data quantity and quality increase, our accuracy in tracking temporal changes in global biodiversity will increase. Moreover, we provide the methodological blueprint for quantifying species-specific abundance, along with uncertainty, for any organism in the world.
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Affiliation(s)
- Corey T Callaghan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia;
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shinichi Nakagawa
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - William K Cornwell
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
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8
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Unveiling African rainforest composition and vulnerability to global change. Nature 2021; 593:90-94. [PMID: 33883743 DOI: 10.1038/s41586-021-03483-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/22/2021] [Indexed: 11/08/2022]
Abstract
Africa is forecasted to experience large and rapid climate change1 and population growth2 during the twenty-first century, which threatens the world's second largest rainforest. Protecting and sustainably managing these African forests requires an increased understanding of their compositional heterogeneity, the environmental drivers of forest composition and their vulnerability to ongoing changes. Here, using a very large dataset of 6 million trees in more than 180,000 field plots, we jointly model the distribution in abundance of the most dominant tree taxa in central Africa, and produce continuous maps of the floristic and functional composition of central African forests. Our results show that the uncertainty in taxon-specific distributions averages out at the community level, and reveal highly deterministic assemblages. We uncover contrasting floristic and functional compositions across climates, soil types and anthropogenic gradients, with functional convergence among types of forest that are floristically dissimilar. Combining these spatial predictions with scenarios of climatic and anthropogenic global change suggests a high vulnerability of the northern and southern forest margins, the Atlantic forests and most forests in the Democratic Republic of the Congo, where both climate and anthropogenic threats are expected to increase sharply by 2085. These results constitute key quantitative benchmarks for scientists and policymakers to shape transnational conservation and management strategies that aim to provide a sustainable future for central African forests.
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9
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Bucking the trend of pollinator decline: the population genetics of a range expanding bumblebee. Evol Ecol 2021. [DOI: 10.1007/s10682-021-10111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Bartish IV, Ozinga WA, Bartish MI, Wamelink GW, Hennekens SM, Yguel B, Prinzing A. Anthropogenic threats to evolutionary heritage of angiosperms in the Netherlands through an increase in high-competition environments. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2020; 34:1536-1548. [PMID: 32463531 PMCID: PMC7754312 DOI: 10.1111/cobi.13556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 06/01/2023]
Abstract
Present biodiversity comprises the evolutionary heritage of Earth's epochs. Lineages from particular epochs are often found in particular habitats, but whether current habitat decline threatens the heritage from particular epochs is unknown. We hypothesized that within a given region, humans threaten specifically habitats that harbor lineages from a particular geological epoch. We expect so because humans threaten environments that dominated and lineages that diversified during these epochs. We devised a new approach to quantify, per habitat type, diversification of lineages from different epochs. For Netherlands, one of the floristically and ecologically best-studied regions, we quantified the decline of habitat types and species in the past century. We defined habitat types based on vegetation classification and used existing ranking of decline of vegetation classes and species. Currently, most declining habitat types and the group of red-listed species are characterized by increased diversification of lineages dating back to Paleogene, specifically to Paleocene-Eocene and Oligocene. Among vulnerable habitat types with large representation of lineages from these epochs were sublittoral and eulittoral zones of temperate seas and 2 types of nutrient-poor, open habitats. These losses of evolutionary heritage would go unnoticed with classical measures of evolutionary diversity. Loss of heritage from Paleocene-Eocene became unrelated to decline once low competition, shade tolerance, and low proportion of non-Apiaceae were accounted for, suggesting that these variables explain the loss of heritage from Paleocene-Eocene. Losses of heritage from Oligocene were partly explained by decline of habitat types occupied by weak competitors and shade-tolerant species. Our results suggest a so-far unappreciated human threat to evolutionary heritage: habitat decline threatens descendants from particular epochs. If the trends persist into the future uncontrolled, there may be no habitats within the region for many descendants of evolutionary ancient epochs, such as Paleogene.
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Affiliation(s)
- Igor V. Bartish
- Department of Genetic Ecology, Institute of BotanyAcademy of Sciences of Czech RepublicZamek 1Průhonice25243Czech Republic
| | - Wim A. Ozinga
- Wageningen Environmental Research (Alterra)P.O. Box 47WageningenNL‐6700 AAThe Netherlands
- Experimental Plant EcologyRadboud University NijmegenP.O. Box 9010Nijmegen6500 GLThe Netherlands
| | | | - G.W. Wieger Wamelink
- Wageningen Environmental Research (Alterra)P.O. Box 47WageningenNL‐6700 AAThe Netherlands
| | - Stephan M. Hennekens
- Wageningen Environmental Research (Alterra)P.O. Box 47WageningenNL‐6700 AAThe Netherlands
| | - Benjamin Yguel
- Centre d'Ecologie et des Sciences de la Conservation (CESCO‐UMR 7204)Sorbonne Universités‐MNHN‐CNRS‐UPMCCP51, 55‐61 rue BuffonParis75005France
| | - Andreas Prinzing
- University Rennes 1Centre National de la Recherche Scientifique, Research Unit "Ecosystèmes, Biodiversité, Evolution"Evolution (UMR 6553), Campus Beaulieu, Bâtiment 14 ARennes35042France
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11
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Molina-Venegas R, Ramos-Gutiérrez I, Moreno-Saiz JC. Phylogenetic Patterns of Extinction Risk in the Endemic Flora of a Mediterranean Hotspot as a Guiding Tool for Preemptive Conservation Actions. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.571587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Dinnage R, Skeels A, Cardillo M. Spatiophylogenetic modelling of extinction risk reveals evolutionary distinctiveness and brief flowering period as threats in a hotspot plant genus. Proc Biol Sci 2020; 287:20192817. [PMID: 32370670 DOI: 10.1098/rspb.2019.2817] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Comparative models used to predict species threat status can help identify the diagnostic features of species at risk. Such models often combine variables measured at the species level with spatial variables, causing multiple statistical challenges, including phylogenetic and spatial non-independence. We present a novel Bayesian approach for modelling threat status that simultaneously deals with both forms of non-independence and estimates their relative contribution, and we apply the approach to modelling threat status in the Australian plant genus Hakea. We find that after phylogenetic and spatial effects are accounted for, species with greater evolutionary distinctiveness and a shorter annual flowering period are more likely to be threatened. The model allows us to combine information on evolutionary history, species biology and spatial data, calculate latent extinction risk (potential for non-threatened species to become threatened), estimate the most important drivers of risk for individual species and map spatial patterns in the effects of different predictors on extinction risk. This could be of value for proactive conservation decision-making based on the early identification of species and regions of potential conservation concern.
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Affiliation(s)
- Russell Dinnage
- Macroevolution and Macroecology Group, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Alexander Skeels
- Macroevolution and Macroecology Group, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Marcel Cardillo
- Macroevolution and Macroecology Group, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia
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13
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Hao M, Jin Q, Meng G, Yang C, Yang S, Shi Z, Tang M, Liu S, Li Y, Zhang D, Su X, Shih C, Sun Y, Zhou X, Zhang AB. Regional assemblages shaped by historical and contemporary factors: Evidence from a species-rich insect group. Mol Ecol 2020; 29:2492-2510. [PMID: 32163643 DOI: 10.1111/mec.15412] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/04/2020] [Accepted: 03/03/2020] [Indexed: 11/30/2022]
Abstract
Understanding diversity patterns requires accounting for the roles of both historical and contemporary factors in the assembly of communities. Here, we compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State Speciation and Extinction model, to track the origins of these patterns. Further, we estimated diversification rates of the two moth assemblages and explored the effects of contemporary ecological factors. From 7,788 specimens we identified 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Moths in Yanshan mountains showed higher species diversity than in Taihang mountains. Ancestral range analysis indicated Yanshan as the origin, with significant historical dispersals from Yanshan to Taihang. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we demonstrate that a multiscale (community, population and species level) analysis incorporating both historical and contemporary factors can be useful in delineating factors contributing to community assembly and patterning in diversity.
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Affiliation(s)
- Mengdi Hao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Qian Jin
- College of Life Sciences, Capital Normal University, Beijing, China.,Suqian Institute of Agricultural Sciences, Jiangsu Academy of Agricultural Sciences, Suqian, China
| | - Guanliang Meng
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Caiqing Yang
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shenzhou Yang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Zhiyong Shi
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Min Tang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shanlin Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yinan Li
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Dan Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xu Su
- Guizhou Provincial Center for Disease Control and Prevention, Guizhou, China
| | - Chungkun Shih
- College of Life Sciences, Capital Normal University, Beijing, China.,Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Yiran Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xin Zhou
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ai-Bing Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
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14
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Culshaw V, Stadler T, Sanmartín I. Exploring the power of Bayesian birth-death skyline models to detect mass extinction events from phylogenies with only extant taxa. Evolution 2019; 73:1133-1150. [PMID: 31017656 PMCID: PMC6767073 DOI: 10.1111/evo.13753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 03/30/2019] [Accepted: 04/14/2019] [Indexed: 01/03/2023]
Abstract
Mass extinction events (MEEs), defined as significant losses of species diversity in significantly short time periods, have attracted the attention of biologists because of their link to major environmental change. MEEs have traditionally been studied through the fossil record, but the development of birth-death models has made it possible to detect their signature based on extant-taxa phylogenies. Most birth-death models consider MEEs as instantaneous events where a high proportion of species are simultaneously removed from the tree ("single pulse" approach), in contrast to the paleontological record, where MEEs have a time duration. Here, we explore the power of a Bayesian Birth-Death Skyline (BDSKY) model to detect the signature of MEEs through changes in extinction rates under a "time-slice" approach. In this approach, MEEs are time intervals where the extinction rate is greater than the speciation rate. Results showed BDSKY can detect and locate MEEs but that precision and accuracy depend on the phylogeny's size and MEE intensity. Comparisons of BDSKY with the single-pulse Bayesian model, CoMET, showed a similar frequency of Type II error and neither model exhibited Type I error. However, while CoMET performed better in detecting and locating MEEs for smaller phylogenies, BDSKY showed higher accuracy in estimating extinction and speciation rates.
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Affiliation(s)
- Victoria Culshaw
- Real Jardín Botánico (RJB)CSICPlaza de Murillo 228014MadridSpain
| | - Tanja Stadler
- Department of Biosystems Science and EngineeringEidgenössische Technische Hochschule Zürich4058BaselSwitzerland
| | - Isabel Sanmartín
- Real Jardín Botánico (RJB)CSICPlaza de Murillo 228014MadridSpain
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15
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Carta A, Gargano D, Rossi G, Bacchetta G, Fenu G, Montagnani C, Abeli T, Peruzzi L, Orsenigo S. Phylogenetically informed spatial planning as a tool to prioritise areas for threatened plant conservation within a Mediterranean biodiversity hotspot. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 665:1046-1052. [PMID: 30893736 DOI: 10.1016/j.scitotenv.2019.02.127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
Global plant diversity is at risk due to anthropogenic changes to ecosystems, but given severely limited conservation resources, a reliable prioritisation strategy for species and sites is needed. Our objective was to identify key areas for conserving the phylogenetic diversity (PD) of threatened vascular plants in Italy, one of the most species-rich regions in the Mediterranean Basin. We used spatial data and the conservation status of 995 threatened vascular plants and applied a phylogenetically informed spatial planning to minimize conservation costs. We then determined the degree of overlap with existing protected areas and evaluated whether this PD-based prioritisation of areas provides adequate protection for threatened phylogenetically distinctive species (EDGE). The cost-effective procedure identified as priority for conservation 12% of the study territory, while achieving over 90% of conservation targets (total PD). We showed that priority areas and protected areas are moderately spatially mismatched. We also showed that not all top-EDGE species were met by the procedure applied, hence we conclude that the PD-based model indicated key areas for protection, but nevertheless additional attention is needed to protect top-EDGE species. This study represents one of the most comprehensive analyses, to date, for the conservation of the native flora in the Mediterranean, incorporating both spatial distribution and evolutionary relationships. Our work on the prioritisation of threatened plant species across Italy can serve as a guide for future conservation applications.
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Affiliation(s)
| | - Domenico Gargano
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Arcavacata di Rende, Cosenza, Italy
| | - Graziano Rossi
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Gianluigi Bacchetta
- Centre for the Conservation of Biodiversity (CCB), Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Giuseppe Fenu
- Centre for the Conservation of Biodiversity (CCB), Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Chiara Montagnani
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milano, Italy
| | - Thomas Abeli
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | | | - Simone Orsenigo
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Milan, Italy
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16
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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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17
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Unmack PJ, Adams M, Bylemans J, Hardy CM, Hammer MP, Georges A. Perspectives on the clonal persistence of presumed 'ghost' genomes in unisexual or allopolyploid taxa arising via hybridization. Sci Rep 2019; 9:4730. [PMID: 30894575 PMCID: PMC6426837 DOI: 10.1038/s41598-019-40865-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/20/2019] [Indexed: 01/19/2023] Open
Abstract
Although hybridization between non-sibling species rarely results in viable or fertile offspring, it occasionally produces self-perpetuating or sexually-parasitic lineages in which ancestral genomes are inherited clonally and thus may persist as ‘ghost species’ after ancestor extinction. Ghost species have been detected in animals and plants, for polyploid and diploid organisms, and across clonal, semi-clonal, and even sexual reproductive modes. Here we use a detailed investigation of the evolutionary and taxonomic status of a newly-discovered, putative ghost lineage (HX) in the fish genus Hypseleotris to provide perspectives on several important issues not previously explored by other studies on ghost species, but relevant to ongoing discussions about their detection, conservation, and artificial re-creation. Our comprehensive genetic (allozymes, mtDNA) and genomic (SNPs) datasets successfully identified a threatened sexual population of HX in one tiny portion of the extensive distribution displayed by two hemi-clonal HX-containing lineages. We also discuss what confidence should be placed on any assertion that an ancestral species is actually extinct, and how to assess whether any putative sexual ancestor represents a pure remnant, as shown here, or a naturally-occurring resurrection via the crossing of compatible clones or hemi-clones.
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Affiliation(s)
- P J Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.
| | - M Adams
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia.,Department of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - J Bylemans
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - C M Hardy
- CSIRO Land and Water, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - M P Hammer
- Museum & Art Gallery of the Northern Territory, Darwin, Northern Territory, 0810, Australia
| | - A Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
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18
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Mitchell JS, Etienne RS, Rabosky DL. Inferring Diversification Rate Variation From Phylogenies With Fossils. Syst Biol 2018; 68:1-18. [PMID: 29788398 DOI: 10.1093/sysbio/syy035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification-extinction rates in particular-can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of extant and extinct species. The model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree. We implemented the model in BAMM, a computational framework that uses reversible jump Markov chain Monte Carlo to simulate a posterior distribution of macroevolutionary rate regimes conditional on the branching times and topology of a phylogeny. The implementation, we describe can be applied to paleontological phylogenies, neontological phylogenies, and to phylogenies that include both extant and extinct taxa. We evaluate performance of the model on data sets simulated under a range of diversification scenarios. We find that speciation rates are reliably inferred in the absence of paleontological data. However, the inclusion of fossil observations substantially increases the accuracy of extinction rate estimates. We demonstrate that inferences are relatively robust to at least some violations of model assumptions, including heterogeneity in preservation rates and misspecification of the number of occurrences in paleontological data sets.
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Affiliation(s)
- Jonathan S Mitchell
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
- Department of Biology, West Virginia University Institute of Technology, 410 Neville Street, Beckley, WV 25801, USA
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
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19
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Trotta LB, Baiser B, Possley J, Li D, Lange J, Martin S, Sessa EB. Community phylogeny of the globally critically imperiled pine rockland ecosystem. AMERICAN JOURNAL OF BOTANY 2018; 105:1735-1747. [PMID: 30300935 DOI: 10.1002/ajb2.1168] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Community phylogenetic methods incorporate information on evolutionary relationships into studies of organismal assemblages. We used a community phylogenetic framework to investigate relationships and biogeographic affinities and to calculate phylogenetic signal of endemism and invasiveness for the flora of the pine rocklands-a globally critically imperiled ecosystem with a significant portion of its distribution in South Florida, United States. METHODS We reconstructed phylogenetic relationships of 538 vascular plant taxa, which represent 92.28% of the vascular flora of the pine rocklands. We estimated phylogenetic signal for endemism and invasiveness using phylogenetic generalized linear mixed models. We determined the native range for each species in the data set and calculated the total number of species sourced from each region and all possible combinations of these regions. KEY RESULTS The pine rockland flora includes representatives of all major vascular plant lineages, and most species have native ranges in the New World. There was strong phylogenetic signal for endemism, but not for invasiveness. CONCLUSIONS Community phylogenetics has high potential value for conservation planning, particularly for fragmented and endangered ecosystems like the pine rockland. Strong phylogenetic signal for endemic species in our data set, which also tend to be threatened or endangered, can help to identify species at risk, as well as fragments where those species occur, highlighting conservation priorities. Our results indicate, at least in the pine rockland ecosystem, no phylogenetic signal for invasive species, and thus other information must be used to predict the potential for invasiveness.
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Affiliation(s)
- Lauren B Trotta
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - Benjamin Baiser
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | | | - Daijiang Li
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - James Lange
- Fairchild Tropical Botanic Garden, Coral Gables, FL
| | - Sarah Martin
- The Nature Conservancy, Maitland, FL
- Institute for Regional Conservation, Delray Beach, FL
| | - Emily B Sessa
- Department of Biology, University of Florida, Gainesville, FL
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20
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Ashman LG, Bragg JG, Doughty P, Hutchinson MN, Bank S, Matzke NJ, Oliver P, Moritz C. Diversification across biomes in a continental lizard radiation. Evolution 2018; 72:1553-1569. [PMID: 29972238 DOI: 10.1111/evo.13541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 12/23/2022]
Abstract
Ecological opportunity is a powerful driver of evolutionary diversification, and predicts rapid lineage and phenotypic diversification following colonization of competitor-free habitats. Alternatively, topographic or environmental heterogeneity could be key to generating and sustaining diversity. We explore these hypotheses in a widespread lineage of Australian lizards: the Gehyra variegata group. This clade occurs across two biomes: the Australian monsoonal tropics (AMT), where it overlaps a separate, larger bodied clade of Gehyra and is largely restricted to rocks; and in the larger Australian arid zone (AAZ) where it has no congeners and occupies trees and rocks. New phylogenomic data and coalescent analyses of AAZ taxa resolve lineages and their relationships and reveal high diversity in the western AAZ (Pilbara region). The AMT and AAZ radiations represent separate radiations with no difference in speciation rates. Most taxa occur on rocks, with small geographic ranges relative to widespread generalist taxa across the vast central AAZ. Rock-dwelling and generalist taxa differ morphologically, but only the lineage-poor central AAZ taxa have accelerated evolution. This accords with increasing evidence that lineage and morphological diversity are poorly correlated, and suggests environmental heterogeneity and refugial dynamics have been more important than ecological release in elevating lineage diversity.
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Affiliation(s)
- L G Ashman
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
| | - J G Bragg
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Royal Botanic Garden, Sydney, NSW 2000, Australia
| | - P Doughty
- Department of Terrestrial Zoology, Western Australian Museum, Perth, WA 6016, Australia
| | - M N Hutchinson
- South Australian Museum, Adelaide, SA 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- School of Biological Sciences, Flinders University, Adelaide, SA 5042, Australia
| | - S Bank
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Göttingen, Göttingen 37073, Germany
| | - N J Matzke
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - P Oliver
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
- Environmental Futures Research Institute, Griffith University, Nathan, QLD 4111, Australia
- Biodiversity and Geosciences Program, Queensland Museum, Brisbane, QLD 4101, Australia
| | - C Moritz
- Research School of Biology, Australian National University, Canberra, ACT 0200, Australia
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21
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Burin G, Alencar LRV, Chang J, Alfaro ME, Quental TB. How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline? Syst Biol 2018; 68:47-62. [DOI: 10.1093/sysbio/syy037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/09/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- Gustavo Burin
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Laura R V Alencar
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Tiago B Quental
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
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22
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Maliet O, Gascuel F, Lambert A. Ranked Tree Shapes, Nonrandom Extinctions, and the Loss of Phylogenetic Diversity. Syst Biol 2018; 67:1025-1040. [DOI: 10.1093/sysbio/syy030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 04/08/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Odile Maliet
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- ED 227, Sorbonne Universités, Paris, France
| | - Fanny Gascuel
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- ED 227, Sorbonne Universités, Paris, France
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
- Laboratoire Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS, Paris, France
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23
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Arbetman MP, Gleiser G, Morales CL, Williams P, Aizen MA. Global decline of bumblebees is phylogenetically structured and inversely related to species range size and pathogen incidence. Proc Biol Sci 2018; 284:rspb.2017.0204. [PMID: 28724728 DOI: 10.1098/rspb.2017.0204] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/20/2017] [Indexed: 11/12/2022] Open
Abstract
Conservation biology can profit greatly from incorporating a phylogenetic perspective into analyses of patterns and drivers of species extinction risk. We applied such an approach to analyse patterns of bumblebee (Bombus) decline. We assembled a database representing approximately 43% of the circa 260 globally known species, which included species extinction risk assessments following the International Union fo Conservation of Nature Red List categories and criteria, and information on species traits presumably associated with bumblebee decline. We quantified the strength of phylogenetic signal in decline, range size, tongue length and parasite presence. Overall, about one-third of the assessed bumblebees are declining and declining species are not randomly distributed across the Bombus phylogeny. Susceptible species were over-represented in the subgenus Thoracobombus (approx. 64%) and under-represented in the subgenus Pyrobombus (approx. 6%). Phylogenetic logistic regressions revealed that species with small geographical ranges and those in which none of three internal parasites were reported (i.e. Crithidia bombi, Nosema spp. or Locustacarus buchneri) were particularly vulnerable. Bumblebee evolutionary history will be deeply eroded if most species from threatened clades, particularly those stemming from basal nodes, become finally extinct. The habitat of species with restricted distribution should be protected and the importance of pathogen tolerance/resistance as mechanisms to deal with pathogens needs urgent research.
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Affiliation(s)
- Marina P Arbetman
- IRNAD, Sede Andina, Universidad Nacional de Río Negro, 8400 Bariloche, Argentina .,Laboratorio Ecotono, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina
| | - Gabriela Gleiser
- Laboratorio Ecotono, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina
| | - Carolina L Morales
- Laboratorio Ecotono, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina
| | - Paul Williams
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Marcelo A Aizen
- Laboratorio Ecotono, INIBIOMA, Universidad Nacional del Comahue-CONICET, 8400 Bariloche, Argentina
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24
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Nowakowski AJ, Watling JI, Thompson ME, Brusch GA, Catenazzi A, Whitfield SM, Kurz DJ, Suárez-Mayorga Á, Aponte-Gutiérrez A, Donnelly MA, Todd BD. Thermal biology mediates responses of amphibians and reptiles to habitat modification. Ecol Lett 2018; 21:345-355. [PMID: 29314479 DOI: 10.1111/ele.12901] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/07/2017] [Accepted: 11/22/2017] [Indexed: 01/07/2023]
Abstract
Human activities often replace native forests with warmer, modified habitats that represent novel thermal environments for biodiversity. Reducing biodiversity loss hinges upon identifying which species are most sensitive to the environmental conditions that result from habitat modification. Drawing on case studies and a meta-analysis, we examined whether observed and modelled thermal traits, including heat tolerances, variation in body temperatures, and evaporative water loss, explained variation in sensitivity of ectotherms to habitat modification. Low heat tolerances of lizards and amphibians and high evaporative water loss of amphibians were associated with increased sensitivity to habitat modification, often explaining more variation than non-thermal traits. Heat tolerances alone explained 24-66% (mean = 38%) of the variation in species responses, and these trends were largely consistent across geographic locations and spatial scales. As habitat modification alters local microclimates, the thermal biology of species will likely play a key role in the reassembly of terrestrial communities.
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Affiliation(s)
- A Justin Nowakowski
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA, 95616, USA
| | - James I Watling
- Department of Biology, John Carroll University, University Heights, OH, 44118, USA
| | - Michelle E Thompson
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - George A Brusch
- School of Life Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | | | | | - David J Kurz
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Ángela Suárez-Mayorga
- Genetic Conservation and Biodiversity Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Andrés Aponte-Gutiérrez
- Genetic Conservation and Biodiversity Group, Institute of Genetics, National University of Colombia, Bogotá, Colombia
| | - Maureen A Donnelly
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Brian D Todd
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA, 95616, USA
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25
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Agha M, Ennen JR, Nowakowski AJ, Lovich JE, Sweat SC, Todd BD. Macroecological patterns of sexual size dimorphism in turtles of the world. J Evol Biol 2018; 31:336-345. [DOI: 10.1111/jeb.13223] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022]
Affiliation(s)
- M. Agha
- Department of Wildlife, Fish, and Conservation Biology; University of California, Davis; Davis CA USA
| | - J. R. Ennen
- Tennessee Aquarium Conservation Institute; Chattanooga TN USA
| | - A. J. Nowakowski
- Department of Wildlife, Fish, and Conservation Biology; University of California, Davis; Davis CA USA
| | - J. E. Lovich
- Southwest Biological Science Center; U.S. Geological Survey; Flagstaff AZ USA
| | - S. C. Sweat
- Tennessee Aquarium Conservation Institute; Chattanooga TN USA
| | - B. D. Todd
- Department of Wildlife, Fish, and Conservation Biology; University of California, Davis; Davis CA USA
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26
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Purvis A, Newbold T, De Palma A, Contu S, Hill SL, Sanchez-Ortiz K, Phillips HR, Hudson LN, Lysenko I, Börger L, Scharlemann JP. Modelling and Projecting the Response of Local Terrestrial Biodiversity Worldwide to Land Use and Related Pressures: The PREDICTS Project. ADV ECOL RES 2018. [DOI: 10.1016/bs.aecr.2017.12.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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27
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Cyriac VP, Kodandaramaiah U. Paleoclimate determines diversification patterns in the fossorial snake family Uropeltidae Cuvier, 1829. Mol Phylogenet Evol 2017; 116:97-107. [PMID: 28867076 DOI: 10.1016/j.ympev.2017.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/17/2017] [Accepted: 08/24/2017] [Indexed: 11/15/2022]
Abstract
Understanding how and why diversification rates vary across evolutionary time is central to understanding how biodiversity is generated and maintained. Recent mathematical models that allow estimation of diversification rates across time from reconstructed phylogenies have enabled us to make inferences on how biodiversity copes with environmental change. Here, we explore patterns of temporal diversification in Uropeltidae, a diverse fossorial snake family. We generate a time-calibrated phylogenetic hypothesis for Uropeltidae and show a significant correlation between diversification rate and paleotemperature during the Cenozoic. We show that the temporal diversification pattern of this group is punctuated by one rate shift event with a decrease in diversification and turnover rate between ca. 11Ma to present, but there is no strong support for mass extinction events. The analysis indicates higher turnover during periods of drastic climatic fluctuations and reduced diversification rates associated with contraction and fragmentation of forest habitats during the late Miocene. Our study highlights the influence of environmental fluctuations on diversification rates in fossorial taxa such as uropeltids, and raises conservation concerns related to present rate of climate change.
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Affiliation(s)
- Vivek Philip Cyriac
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Thiruvananthapuram, Kerala 695551, India.
| | - Ullasa Kodandaramaiah
- IISER-TVM Centre for Research and Education in Ecology and Evolution (ICREEE) and School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Maruthamala P.O., Vithura, Thiruvananthapuram, Kerala 695551, India
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28
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Mankga LT, Yessoufou K. Factors driving the global decline of cycad diversity. AOB PLANTS 2017; 9:plx022. [PMID: 28721186 PMCID: PMC5506724 DOI: 10.1093/aobpla/plx022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 05/21/2017] [Accepted: 05/26/2017] [Indexed: 06/01/2023]
Abstract
Mounting evidence indicates that we are witnessing the sixth mass extinction period. Given the important goods and services biodiversity delivers to humans, there is a need for a continued commitment to investigate what pre-disposes some taxa to greater risk of extinction. Here, we investigate this question using a phylogenetic comparative method and fitting a cumulative link mixed effect model on biological, ecological and evolutionary data of cycads, the most threatened lineage in the plant kingdom. We identified nine groups of threats to cycads, with habitat loss, over-collection, fire and reproduction failure being the most prominent, but only four of these threats (habitat loss, over-collection, medicinal uses and reproduction failure) clustered on the cycad tree of life. This clustering suggests that closely related species may be exposed to similar threats, perhaps because of geographic regionalization of cycad genera. Nonetheless, the diversity of threats and several variables linked to the biology and ecology of cycads correlate with extinction risk (e.g. altitude, height, diameter, geographic range), and different variables seem to be linked to different IUCN status of cycads. Although their predictive power is generally < 50 %, geographic range and maximum diameter stood out as the best predictors particularly for the Vulnerable (VU) category, with a predictive power of 87 % and 69 %, respectively. Using our best model for VU, we predicted all five Data Deficient (DD) species of cycads to be in the VU category. Collectively, our results elucidate the pattern of extinction risk in cycads and, since most threats that we identified as drivers of extinction risk of cycads are anthropogenically mediated, we recommend stronger legislation to regulate human-cycad interactions and the commitment of all governments globally to implement this regulation.
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Affiliation(s)
- Ledile T. Mankga
- Department of Life and Consumer Sciences, University of South Africa, Florida campus, Florida 1710, South Africa
| | - Kowiyou Yessoufou
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, APK Campus, Auckland Park 2006, Johannesburg, South Africa
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29
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Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa. Mol Phylogenet Evol 2017; 111:132-148. [DOI: 10.1016/j.ympev.2017.03.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 03/26/2017] [Accepted: 03/26/2017] [Indexed: 11/18/2022]
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30
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Verheye ML, Backeljau T, d'Udekem d'Acoz C. Locked in the icehouse: Evolution of an endemic Epimeria (Amphipoda, Crustacea) species flock on the Antarctic shelf. Mol Phylogenet Evol 2017; 114:14-33. [PMID: 28528744 DOI: 10.1016/j.ympev.2017.05.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/12/2017] [Accepted: 05/14/2017] [Indexed: 11/24/2022]
Abstract
The Antarctic shelf's marine biodiversity has been greatly influenced by the climatic and glacial history of the region. Extreme temperature changes led to the extinction of some lineages, while others adapted and flourished. The amphipod genus Epimeria is an example of the latter, being particularly diverse in the Antarctic region. By reconstructing a time-calibrated phylogeny based on mitochondrial (COI) and nuclear (28S and H3) markers and including Epimeria species from all oceans, this study provides a temporal and geographical framework for the evolution of Antarctic Epimeria. The monophyly of this genus is not supported by Bayesian Inference, as Antarctic and non-Antarctic Epimeria form two distinct well-supported clades, with Antarctic Epimeria being a sister clade to two stilipedid species. The monophyly of Antarctic Epimeria suggests that this clade evolved in isolation since its origin. While the precise timing of this origin remains unclear, it is inferred that the Antarctic lineage arose from a late Gondwanan ancestor and hence did not colonize the Antarctic region after the continent broke apart from the other fragments of Gondwanaland. The initial diversification of the clade occurred 38.04Ma (95% HPD [48.46Ma; 28.36Ma]) in a cooling environment. Adaptation to cold waters, along with the extinction of cold-intolerant taxa and resulting ecological opportunities, likely led to the successful diversification of Epimeria on the Antarctic shelf. However, there was neither evidence of a rapid lineage diversification early in the clade's history, nor of any shifts in diversification rates induced by glacial cycles. This suggests that a high turnover rate on the repeatedly scoured Antarctic shelf could have masked potential signals of diversification bursts.
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Affiliation(s)
- Marie L Verheye
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, rue Vautier 29, 1000 Brussels, Belgium; Catholic University of Louvain-la-Neuve, Department of Biology, Marine Biology Laboratory, Croix du Sud 3 bte L7.06.04, 1348 Louvain-la-Neuve, Belgium.
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, rue Vautier 29, 1000 Brussels, Belgium; University of Antwerp, Evolutionary Ecology Group, Universiteitsplein 1, 2160 Antwerp, Belgium
| | - Cédric d'Udekem d'Acoz
- Royal Belgian Institute of Natural Sciences, OD Taxonomy and Phylogeny, rue Vautier 29, 1000 Brussels, Belgium
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31
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Tucker CM, Cadotte MW, Carvalho SB, Davies TJ, Ferrier S, Fritz SA, Grenyer R, Helmus MR, Jin LS, Mooers AO, Pavoine S, Purschke O, Redding DW, Rosauer DF, Winter M, Mazel F. A guide to phylogenetic metrics for conservation, community ecology and macroecology. Biol Rev Camb Philos Soc 2017; 92:698-715. [PMID: 26785932 PMCID: PMC5096690 DOI: 10.1111/brv.12252] [Citation(s) in RCA: 279] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 12/01/2015] [Accepted: 12/14/2015] [Indexed: 01/02/2023]
Abstract
The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriate metric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for α-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices.
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Affiliation(s)
- Caroline M. Tucker
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBox 334BoulderCO80309‐0334U.S.A.
| | - Marc W. Cadotte
- Biological SciencesUniversity of Toronto‐ScarboroughScarboroughM1C 1A4Canada
- Stake Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong, Higher Education Institutes, College of Ecology and EvolutionSun Yat‐sen UniversityGuangzhouPR China
| | - Silvia B. Carvalho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto4485‐661VairãoPortugal
| | - T. Jonathan Davies
- Department of BiologyMcGill UniversityMontréalH3A 1B1Canada
- African Centre for DNA BarcodingUniversity of JohannesburgPO Box 524Johannesburg2006South Africa
| | - Simon Ferrier
- CSIRO Ecosystem Sciences, Climate Adaptation FlagshipGPO BOX 1600Canberra2601Australia
| | - Susanne A. Fritz
- Biodiversity & Climate Research Centre (BiK‐F) and Senckenberg Gesellschaft für Naturforschung60325Frankfurt am MainGermany
- Institute of Ecology, Evolution and DiversityGoethe University60438FrankfurtGermany
| | - Rich Grenyer
- School of Geography and the EnvironmentUniversity of OxfordOxfordOX1 3QYU.K.
| | - Matthew R. Helmus
- Department of Ecological Sciences ‐ Animal EcologyVrije UniversiteitAmsterdamNetherlands
- Center for Biodiversity, Department of BiologyTemple UniversitySuite 502PhiladelphiaPA19122U.S.A.
| | - Lanna S. Jin
- Ecology & Evolutionary BiologyUniversity of TorontoRoom 3055TorontoM5S 3B2Canada
| | - Arne O. Mooers
- Department of BiologySimon Fraser UniversityBurnabyV5A 1S6Canada
| | - Sandrine Pavoine
- Centre of Ecology and Conservation Sciences (UMR 7204 CESCO)Museum National d'Histoire NaturelleParisFrance
- Department of ZoologyUniversity of OxfordOxfordOX1 3QYUK
| | - Oliver Purschke
- German Centre of Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigDeutscher Platz 5eDE‐04103LeipzigGermany
- Geobotany and Botanical Garden, Institute of BiologyMartin Luther University, Halle‐WittenbergDE‐06108Halle (Saale)Germany
- Department of Computer ScienceMartin‐Luther‐University, Halle‐WittenbergDE‐06120Halle (Saale)Germany
| | - David W. Redding
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonWC1E 6BTU.K.
| | - Dan F. Rosauer
- Research School of BiologyAustralian National UniversityActon2601Australia
| | - Marten Winter
- German Centre of Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigDeutscher Platz 5eDE‐04103LeipzigGermany
| | - Florent Mazel
- Laboratoire d'Ecologie Alpine (LECA), CNRS ‐ Université Grenoble Alpes (UMR 5553)BP 5338041Grenoble Cedex 9France
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Prinzing A, Ozinga WA, Brändle M, Courty PE, Hennion F, Labandeira C, Parisod C, Pihain M, Bartish IV. Benefits from living together? Clades whose species use similar habitats may persist as a result of eco-evolutionary feedbacks. THE NEW PHYTOLOGIST 2017; 213:66-82. [PMID: 27880007 DOI: 10.1111/nph.14341] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/16/2016] [Indexed: 06/06/2023]
Abstract
Contents 66 I. 67 II. 68 III. 69 IV. 70 V. 73 VI. 75 VII. 77 78 References 78 SUMMARY: Recent decades have seen declines of entire plant clades while other clades persist despite changing environments. We suggest that one reason why some clades persist is that species within these clades use similar habitats, because such similarity may increase the degree of co-occurrence of species within clades. Traditionally, co-occurrence among clade members has been suggested to be disadvantageous because of increased competition and enemy pressure. Here, we hypothesize that increased co-occurrence among clade members promotes mutualist exchange, niche expansion or hybridization, thereby helping species avoid population decline from environmental change. We review the literature and analyse published data for hundreds of plant clades (genera) within a well-studied region and find major differences in the degree to which species within clades occupy similar habitats. We tentatively show that, in clades for which species occupy similar habitats, species tend to exhibit increased co-occurrence, mutualism, niche expansion, and hybridization - and rarely decline. Consistently, throughout the geological past, clades whose species occupied similar habitats often persisted through long time-spans. Overall, for many plant species, the occupation of similar habitats among fellow clade members apparently reduced their vulnerability to environmental change. Future research should identify when and how this previously unrecognized eco-evolutionary feedback operates.
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Affiliation(s)
- Andreas Prinzing
- University Rennes 1/Centre National de la Recherche Scientifique, Research Unit 'Ecobio - Ecosystèmes, Biodiversité, Evolution', Campus Beaulieu, Bâtiment 14 A, 35042, Rennes, France
| | - Wim A Ozinga
- Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, the Netherlands
- Alterra, Wageningen University & Research, PO Box 47, NL-6700, AA Wageningen, the Netherlands
| | - Martin Brändle
- Department of Ecology - Animal Ecology, Faculty of Biology, Philipps-Universität Marburg, Karl-von-Frisch Strasse 8, D-35032, Marburg, Germany
| | - Pierre-Emmanuel Courty
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland
| | - Françoise Hennion
- University Rennes 1/Centre National de la Recherche Scientifique, Research Unit 'Ecobio - Ecosystèmes, Biodiversité, Evolution', Campus Beaulieu, Bâtiment 14 A, 35042, Rennes, France
| | - Conrad Labandeira
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
- Department of Entomology and BEES Program, University of Maryland, College Park, MD, 20742, USA
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Christian Parisod
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchatel, Rue Emile-Argand 11, 2000, Neuchatel, Switzerland
| | - Mickael Pihain
- University Rennes 1/Centre National de la Recherche Scientifique, Research Unit 'Ecobio - Ecosystèmes, Biodiversité, Evolution', Campus Beaulieu, Bâtiment 14 A, 35042, Rennes, France
| | - Igor V Bartish
- Institute of Botany, Academy of Sciences of Czech Republic, Zamek 1, Pruhonice, 25243, Czech Republic
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Overview of Phylogenetic Approaches to Mycorrhizal Biogeography, Diversity and Evolution. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Fenton IS, Pearson PN, Dunkley Jones T, Farnsworth A, Lunt DJ, Markwick P, Purvis A. The impact of Cenozoic cooling on assemblage diversity in planktonic foraminifera. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150224. [PMID: 26977064 PMCID: PMC4810817 DOI: 10.1098/rstb.2015.0224] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Cenozoic planktonic foraminifera (PF) (calcareous zooplankton) have arguably the most detailed fossil record of any group. The quality of this record allows models of environmental controls on macroecology, developed for Recent assemblages, to be tested on intervals with profoundly different climatic conditions. These analyses shed light on the role of long-term global cooling in establishing the modern latitudinal diversity gradient (LDG)--one of the most powerful generalizations in biogeography and macroecology. Here, we test the transferability of environment-diversity models developed for modern PF assemblages to the Eocene epoch (approx. 56-34 Ma), a time of pronounced global warmth. Environmental variables from global climate models are combined with Recent environment-diversity models to predict Eocene richness gradients, which are then compared with observed patterns. The results indicate the modern LDG--lower richness towards the poles--developed through the Eocene. Three possible causes are suggested for the mismatch between statistical model predictions and data in the Early Eocene: the environmental estimates are inaccurate, the statistical model misses a relevant variable, or the intercorrelations among facets of diversity--e.g. richness, evenness, functional diversity--have changed over geological time. By the Late Eocene, environment-diversity relationships were much more similar to those found today.
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Affiliation(s)
- Isabel S Fenton
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
| | - Paul N Pearson
- School of Earth and Ocean Sciences, Cardiff University, Cardiff CF10 3AT, UK
| | - Tom Dunkley Jones
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alexander Farnsworth
- School of Geographical Sciences and Cabot Institute, University of Bristol, Bristol BS8 1SS, UK
| | - Daniel J Lunt
- School of Geographical Sciences and Cabot Institute, University of Bristol, Bristol BS8 1SS, UK
| | - Paul Markwick
- Getech Group plc. Elmete Hall, Elmete Lane, Leeds LS8 2LJ, UK
| | - Andy Purvis
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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35
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A 4000-species dataset provides new insight into the evolution of ferns. Mol Phylogenet Evol 2016; 105:200-211. [DOI: 10.1016/j.ympev.2016.09.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/03/2016] [Accepted: 09/07/2016] [Indexed: 01/17/2023]
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36
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Affiliation(s)
- Alexandre Robert
- UMR 7204 MNHN‐CNRS‐UPMC Centre d'Ecologie et des Sciences de la Conservation Muséum National d'Histoire Naturelle 43, Rue Buffon 75005 Paris France
| | - Charles Thévenin
- UMR 7204 MNHN‐CNRS‐UPMC Centre d'Ecologie et des Sciences de la Conservation Muséum National d'Histoire Naturelle 43, Rue Buffon 75005 Paris France
| | - Karine Princé
- UMR 7204 MNHN‐CNRS‐UPMC Centre d'Ecologie et des Sciences de la Conservation Muséum National d'Histoire Naturelle 43, Rue Buffon 75005 Paris France
| | - François Sarrazin
- UPMC Univ Paris 06 Muséum National d'Histoire Naturelle CNRS CESCO UMR 7204 Sorbonne Universités 75005 Paris France
| | - Joanne Clavel
- UMR 7204 MNHN‐CNRS‐UPMC Centre d'Ecologie et des Sciences de la Conservation Muséum National d'Histoire Naturelle 43, Rue Buffon 75005 Paris France
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37
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Campos L, Salvo AE, Flores-Moya A. Natural taxonomic categories of angiosperms obey Benford's law, but artificial ones do not. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1181683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Lucía Campos
- Departamento de Biología Vegetal (Botánica), Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - A. Enrique Salvo
- Departamento de Biología Vegetal (Botánica), Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
| | - Antonio Flores-Moya
- Departamento de Biología Vegetal (Botánica), Facultad de Ciencias, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
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38
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Sanmartín I, Meseguer AS. Extinction in Phylogenetics and Biogeography: From Timetrees to Patterns of Biotic Assemblage. Front Genet 2016; 7:35. [PMID: 27047538 PMCID: PMC4802293 DOI: 10.3389/fgene.2016.00035] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 02/29/2016] [Indexed: 01/03/2023] Open
Abstract
Global climate change and its impact on biodiversity levels have made extinction a relevant topic in biological research. Yet, until recently, extinction has received less attention in macroevolutionary studies than speciation; the reason is the difficulty to infer an event that actually eliminates rather than creates new taxa. For example, in biogeography, extinction has often been seen as noise, introducing homoplasy in biogeographic relationships, rather than a pattern-generating process. The molecular revolution and the possibility to integrate time into phylogenetic reconstructions have allowed studying extinction under different perspectives. Here, we review phylogenetic (temporal) and biogeographic (spatial) approaches to the inference of extinction and the challenges this process poses for reconstructing evolutionary history. Specifically, we focus on the problem of discriminating between alternative high extinction scenarios using time trees with only extant taxa, and on the confounding effect introduced by asymmetric spatial extinction – different rates of extinction across areas – in biogeographic inference. Finally, we identify the most promising avenues of research in both fields, which include the integration of additional sources of evidence such as the fossil record or environmental information in birth–death models and biogeographic reconstructions, the development of new models that tie extinction rates to phenotypic or environmental variation, or the implementation within a Bayesian framework of parametric non-stationary biogeographic models.
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Affiliation(s)
| | - Andrea S Meseguer
- INRA, UMR 1062, Centre de Biologie pour la Gestion des Populations - INRA- IRD-CIRAD-Montpellier SupAgro Montferrier-sur-Lez, France
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39
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Tracking Animal Dispersal: From Individual Movement to Community Assembly and Global Range Dynamics. Trends Ecol Evol 2016; 31:204-214. [DOI: 10.1016/j.tree.2016.01.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/12/2015] [Accepted: 01/07/2016] [Indexed: 11/17/2022]
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40
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Di Marco M, Santini L. Climatic tolerance or geographic breadth: what are we measuring? GLOBAL CHANGE BIOLOGY 2016; 22:972-973. [PMID: 26010579 DOI: 10.1111/gcb.12984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 05/19/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Moreno Di Marco
- ARC Centre of Excellence for Environmental Decision, Centre for Biodiversity and Conservation Science, The University of Queensland, St Lucia, Brisbane, Qld, 4072, Australia
- School of Geography Planning and Environmental Management, The University of Queensland, St Lucia, Brisbane, Qld, 4072, Australia
| | - Luca Santini
- Global Mammal Assessment program, Department of Biology and Biotechnologies, Sapienza Università di Roma, Viale dell' Università 32, 00185, Rome, Italy
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41
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Schachat SR, Mulcahy DG, Mendelson JR. Conservation threats and the phylogenetic utility of IUCN Red List rankings in Incilius toads. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2016; 30:72-81. [PMID: 26243724 DOI: 10.1111/cobi.12567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 05/13/2015] [Indexed: 06/04/2023]
Abstract
Phylogenetic analysis of extinction threat is an emerging tool in the field of conservation. However, there are problems with the methods and data as commonly used. Phylogenetic sampling usually extends to the level of family or genus, but International Union for Conservation of Nature (IUCN) rankings are available only for individual species, and, although different species within a taxonomic group may have the same IUCN rank, the species may have been ranked as such for different reasons. Therefore, IUCN rank may not reflect evolutionary history and thus may not be appropriate for use in a phylogenetic context. To be used appropriately, threat-risk data should reflect the cause of extinction threat rather than the IUCN threat ranking. In a case study of the toad genus Incilius, with phylogenetic sampling at the species level (so that the resolution of the phylogeny matches character data from the IUCN Red List), we analyzed causes of decline and IUCN threat rankings by calculating metrics of phylogenetic signal (such as Fritz and Purvis' D). We also analyzed the extent to which cause of decline and threat ranking overlap by calculating phylogenetic correlation between these 2 types of character data. Incilius species varied greatly in both threat ranking and cause of decline; this variability would be lost at a coarser taxonomic resolution. We found far more phylogenetic signal, likely correlated with evolutionary history, for causes of decline than for IUCN threat ranking. Individual causes of decline and IUCN threat rankings were largely uncorrelated on the phylogeny. Our results demonstrate the importance of character selection and taxonomic resolution when extinction threat is analyzed in a phylogenetic context.
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Affiliation(s)
- Sandra R Schachat
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Mississippi State, MS, 39762, U.S.A
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 121, Washington, D.C., 20013, U.S.A
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, MRC 183, Washington, D.C., 20013, U.S.A
| | - Joseph R Mendelson
- Zoo Atlanta, 800 Cherokee Ave SE, Atlanta, GA, 30315, U.S.A
- School of Biology, Georgia Institute of Technology, 301 Ferst Drive, Atlanta, GA, 30332, U.S.A
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42
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Reconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life? BIODIVERSITY CONSERVATION AND PHYLOGENETIC SYSTEMATICS 2016. [DOI: 10.1007/978-3-319-22461-9_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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43
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Krug AZ, Patzkowsky ME. Phylogenetic Clustering of Origination and Extinction across the Late Ordovician Mass Extinction. PLoS One 2015; 10:e0144354. [PMID: 26658946 PMCID: PMC4682825 DOI: 10.1371/journal.pone.0144354] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/17/2015] [Indexed: 11/18/2022] Open
Abstract
Mass extinctions can have dramatic effects on the trajectory of life, but in some cases the effects can be relatively small even when extinction rates are high. For example, the Late Ordovician mass extinction is the second most severe in terms of the proportion of genera eliminated, yet is noted for the lack of ecological consequences and shifts in clade dominance. By comparison, the end-Cretaceous mass extinction was less severe but eliminated several major clades while some rare surviving clades diversified in the Paleogene. This disconnect may be better understood by incorporating the phylogenetic relatedness of taxa into studies of mass extinctions, as the factors driving extinction and recovery are thought to be phylogenetically conserved and should therefore promote both origination and extinction of closely related taxa. Here, we test whether there was phylogenetic selectivity in extinction and origination using brachiopod genera from the Middle Ordovician through the Devonian. Using an index of taxonomic clustering (RCL) as a proxy for phylogenetic clustering, we find that A) both extinctions and originations shift from taxonomically random or weakly clustered within families in the Ordovician to strongly clustered in the Silurian and Devonian, beginning with the recovery following the Late Ordovician mass extinction, and B) the Late Ordovician mass extinction was itself only weakly clustered. Both results stand in stark contrast to Cretaceous-Cenozoic bivalves, which showed significant levels of taxonomic clustering of extinctions in the Cretaceous, including strong clustering in the mass extinction, but taxonomically random extinctions in the Cenozoic. The contrasting patterns between the Late Ordovician and end-Cretaceous events suggest a complex relationship between the phylogenetic selectivity of mass extinctions and the long-term phylogenetic signal in origination and extinction patterns.
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Affiliation(s)
- Andrew Z. Krug
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| | - Mark E. Patzkowsky
- Department of Geosciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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44
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Rabosky DL. Challenges in the estimation of extinction from molecular phylogenies: A response to Beaulieu and O'Meara. Evolution 2015; 70:218-28. [PMID: 26593734 DOI: 10.1111/evo.12820] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/13/2015] [Indexed: 12/15/2022]
Abstract
Time-calibrated phylogenies that contain only living species have been widely used to study the dynamics of speciation and extinction. Concerns about the reliability of phylogenetic extinction estimates were raised by Rabosky (2010), where I suggested that unaccommodated heterogeneity in speciation rate could lead to positively biased extinction estimates. In a recent article, Beaulieu and O'Meara (2015a) correctly point out several technical errors in the execution of my 2010 study and concluded that phylogenetic extinction estimates are robust to speciation rate heterogeneity under a range of model parameters. I demonstrate that Beaulieu and O'Meara underestimated the magnitude of speciation rate variation in real phylogenies and consequently did not incorporate biologically meaningful levels of rate heterogeneity into their simulations. Using parameter values drawn from the recent literature, I find that modest levels of heterogeneity in speciation rate result in a consistent, positive bias in extinction estimates that are exacerbated by phylogenetic tree size. This bias, combined with the inherent lack of information about extinction in molecular phylogenies, suggests that extinction rate estimates from phylogenies of extant taxa only should be treated with caution.
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Affiliation(s)
- Daniel L Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48103.
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45
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Sagot M, Chaverri G. Effects of roost specialization on extinction risk in bats. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1666-1673. [PMID: 26081600 DOI: 10.1111/cobi.12546] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 03/21/2015] [Indexed: 06/04/2023]
Abstract
Understanding causes and consequences of ecological specialization is of major concern in conservation. Specialist species are particularly vulnerable to human activities. If their food or habitats are depleted or lost, they may not be able to exploit alternative resources, and population losses may result. We examined International Union for Conservation of Nature (IUCN) Red List bat data and the number of roosts used per species (accounting for phylogenetic independence) to determine whether roost specialization is correlated with extinction risk. We found a significant correlation between the IUCN Red List category and the number of roost types used. Species that use fewer roost types had a higher risk of extinction. We found that caves and similar structures were the most widely used roost types, particularly by species under some level of risk of extinction. Many critically endangered, endangered, or vulnerable species used natural roosts exclusively, whereas less threatened species used natural and human-made roosts. Our results suggest that roost loss, particularly in species that rely on a single roost type, may be linked to extinction risk. Our focus on a single life history trait prevented us from determining how important this variable is for extinction risk relative to other variables, but we have taken a first step toward prioritizing conservation actions. Our results also suggest that roost specialization may exacerbate population declines due to other risk factors, such as hunting pressure or habitat loss, and thus that management actions to preserve species under risk of extinction should prioritize protection of roosting sites.
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Affiliation(s)
- Maria Sagot
- Department of Biological Sciences, State University of New York at Oswego, Oswego, NY, 13126, U.S.A..
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Veron S, Davies TJ, Cadotte MW, Clergeau P, Pavoine S. Predicting loss of evolutionary history: Where are we? Biol Rev Camb Philos Soc 2015; 92:271-291. [PMID: 26467982 DOI: 10.1111/brv.12228] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 01/29/2023]
Abstract
The Earth's evolutionary history is threatened by species loss in the current sixth mass extinction event in Earth's history. Such extinction events not only eliminate species but also their unique evolutionary histories. Here we review the expected loss of Earth's evolutionary history quantified by phylogenetic diversity (PD) and evolutionary distinctiveness (ED) at risk. Due to the general paucity of data, global evolutionary history losses have been predicted for only a few groups, such as mammals, birds, amphibians, plants, corals and fishes. Among these groups, there is now empirical support that extinction threats are clustered on the phylogeny; however this is not always a sufficient condition to cause higher loss of phylogenetic diversity in comparison to a scenario of random extinctions. Extinctions of the most evolutionarily distinct species and the shape of phylogenetic trees are additional factors that can elevate losses of evolutionary history. Consequently, impacts of species extinctions differ among groups and regions, and even if global losses are low within large groups, losses can be high among subgroups or within some regions. Further, we show that PD and ED are poorly protected by current conservation practices. While evolutionary history can be indirectly protected by current conservation schemes, optimizing its preservation requires integrating phylogenetic indices with those that capture rarity and extinction risk. Measures based on PD and ED could bring solutions to conservation issues, however they are still rarely used in practice, probably because the reasons to protect evolutionary history are not clear for practitioners or due to a lack of data. However, important advances have been made in the availability of phylogenetic trees and methods for their construction, as well as assessments of extinction risk. Some challenges remain, and looking forward, research should prioritize the assessment of expected PD and ED loss for more taxonomic groups and test the assumption that preserving ED and PD also protects rare species and ecosystem services. Such research will be useful to inform and guide the conservation of Earth's biodiversity and the services it provides.
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Affiliation(s)
- Simon Veron
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France
| | - T Jonathan Davies
- Department of Biology, McGill University, 1205 ave Docteur Penfield, Montreal, Quebec H3A 1B1, Canada.,African Centre for DNA Barcoding, University of Johannesburg, APK Campus, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Marc W Cadotte
- Department of Biology, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C 1A4, Canada
| | - Philippe Clergeau
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, CP51, 55-61 rue Buffon, 75005 Paris, France.,Mathematical Ecology Research Group, Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, U.K
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Lootvoet AC, Philippon J, Bessa-Gomes C. Behavioral Correlates of Primates Conservation Status: Intrinsic Vulnerability to Anthropogenic Threats. PLoS One 2015; 10:e0135585. [PMID: 26444966 PMCID: PMC4596868 DOI: 10.1371/journal.pone.0135585] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/24/2015] [Indexed: 11/19/2022] Open
Abstract
Behavioral traits are likely to influence species vulnerability to anthropogenic threats and in consequence, their risk of extinction. Several studies have addressed this question and have highlighted a correlation between reproductive strategies and different viability proxies, such as introduction success and local extinction risk. Yet, very few studies have investigated the effective impact of social behaviour, and evidence regarding global extinction risk remains scant. Here we examined the effects of three main behavioral factors: the group size, the social and reproductive system, and the strength of sexual selection on global extinction risk. Using Primates as biological model, we performed comparative analysis on 93 species. The conservation status as described by the IUCN Red List was considered as a proxy for extinction risk. In addition, we added previously identified intrinsic factors of vulnerability to extinction, and a measure of the strength of the human impact for each species, described by the human footprint. Our analysis highlighted a significant effect of two of the three studied behavioral traits, group size and social and reproductive system. Extinction risk is negatively correlated with mean group size, which may be due to an Allee effect resulting from the difficulties for solitary and monogamous species to find a partner at low densities. Our results also indicate that species with a flexible mating system are less vulnerable. Taking into account these behavioral variables is thus of high importance when establishing conservation plans, particularly when assessing species relative vulnerability.
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Affiliation(s)
- Amélie Christelle Lootvoet
- Laboratory “Ecologie, Systématique, Evolution”, UMR 8079, University Paris-Sud, Bâtiment 362, Orsay, France
- Laboratory “Ecologie, Systématique, Evolution”, UMR 8079, CNRS, Bâtiment 362, Orsay, France
- Laboratory “Ecologie, Systématique, Evolution”, UMR 8079, AgroParisTech, Bâtiment 362, Orsay, France
| | - Justine Philippon
- Laboratory “Ecologie, Systématique, Evolution”, UMR 8079, University Paris-Sud, Bâtiment 362, Orsay, France
- Laboratory “Ecologie, Systématique, Evolution”, UMR 8079, CNRS, Bâtiment 362, Orsay, France
- Laboratory “Ecologie, Systématique, Evolution”, UMR 8079, AgroParisTech, Bâtiment 362, Orsay, France
| | - Carmen Bessa-Gomes
- Laboratory “Ecologie, Systématique, Evolution”, UMR 8079, University Paris-Sud, Bâtiment 362, Orsay, France
- Laboratory “Ecologie, Systématique, Evolution”, UMR 8079, CNRS, Bâtiment 362, Orsay, France
- Laboratory “Ecologie, Systématique, Evolution”, UMR 8079, AgroParisTech, Bâtiment 362, Orsay, France
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Davies TJ. Losing history: how extinctions prune features from the tree of life. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140006. [PMID: 25561667 DOI: 10.1098/rstb.2014.0006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biodiversity provides many valuable services to humanity; however, rapid expansion of the human population has placed increasing pressure on natural systems, and it has been suggested that we may be entering a sixth mass extinction. There is an urgent need, therefore, to prioritize conservation efforts if we are to maintain the provisioning of such service in the future. Phylogenetic diversity (PD), the summed branch lengths that connect species on the tree-of-life, might provide a valuable metric for conservation prioritization because it has been argued to capture feature diversity. Frequently, PD is estimated in millions of years, and therefore implicitly assumes an evolutionary model in which features diverge gradually over time. Here, I explore the expected loss of feature diversity when this assumption is violated. If evolution tends to slow down over time, as might be the case following adaptive radiations, losses of feature diversity might be relatively small. However, if evolution occurs in rapid bursts, following a punctuated model, impacts of extinctions might be much greater. PD captures many important properties, but if we use it as a proxy for feature diversity, we first need to ensure that we have the correct evolutionary model.
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Affiliation(s)
- T Jonathan Davies
- Department of Biology, McGill University, Montreal, Quebec, Canada H3A 1B1 African Centre for DNA Barcoding, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg 2006, South Africa
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Donoghue MJ, Sanderson MJ. Confluence, synnovation, and depauperons in plant diversification. THE NEW PHYTOLOGIST 2015; 207:260-274. [PMID: 25778694 DOI: 10.1111/nph.13367] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/14/2015] [Indexed: 05/02/2023]
Abstract
We review the empirical phylogenetic literature on plant diversification, highlighting challenges in separating the effects of speciation and extinction, in specifying diversification mechanisms, and in making convincing arguments. In recent discussions of context dependence, key opportunities and landscapes, and indirect effects and lag times, we see a distinct shift away from single-point/single-cause 'key innovation' hypotheses toward more nuanced explanations involving multiple interacting causal agents assembled step-wise through a tree. To help crystalize this emerging perspective we introduce the term 'synnovation' (a hybrid of 'synergy' and 'innovation') for an interacting combination of traits with a particular consequence ('key synnovation' in the case of increased diversification rate), and the term 'confluence' for the sequential coming together of a set of traits (innovations and synnovations), environmental changes, and geographic movements along the branches of a phylogenetic tree. We illustrate these concepts using the radiation of Bromeliaceae. We also highlight the generality of these ideas by considering how rate heterogeneity associated with a confluence relates to the existence of particularly species-poor lineages, or 'depauperons.' Many challenges are posed by this re-purposed research framework, including difficulties associated with partial taxon sampling, uncertainty in divergence time estimation, and extinction.
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Affiliation(s)
- Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT, 06520, USA
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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Condamine FL, Nagalingum NS, Marshall CR, Morlon H. Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating. BMC Evol Biol 2015; 15:65. [PMID: 25884423 PMCID: PMC4449600 DOI: 10.1186/s12862-015-0347-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/02/2015] [Indexed: 01/21/2023] Open
Abstract
Background Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads. Results Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior. Conclusions These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0347-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 7641 Centre de Mathématiques Appliquées (École Polytechnique), Route de Saclay, 91128, Palaiseau, France. .,Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Göteborg, Sweden.
| | - Nathalie S Nagalingum
- National Herbarium of New South Wales, Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney, NSW, 2000, Australia.
| | - Charles R Marshall
- Department of Integrative Biology and Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, CA, 94720-4780, USA.
| | - Hélène Morlon
- CNRS, UMR 8197 Institut de Biologie de l'École Normale Supérieure, 46 rue d'Ulm, 75005, Paris, France.
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