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Overwater M, Pelletier D, Steel M. The expected loss of feature diversity (versus phylogenetic diversity) following rapid extinction at the present. J Math Biol 2023; 87:53. [PMID: 37658909 PMCID: PMC10475005 DOI: 10.1007/s00285-023-01988-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023]
Abstract
The current rapid extinction of species leads not only to their loss but also the disappearance of the unique features they harbour, which have evolved along the branches of the underlying evolutionary tree. One proxy for estimating the feature diversity (FD) of a set S of species at the tips of a tree is 'phylogenetic diversity' (PD): the sum of the branch lengths of the subtree connecting the species in S. For a phylogenetic tree that evolves under a standard birth-death process, and which is then subject to a sudden extinction event at the present (the simple 'field of bullets' model with a survival probability of s per species) the proportion of the original PD that is retained after extinction at the present is known to converge quickly to a particular concave function [Formula: see text] as t grows. To investigate how the loss of FD mirrors the loss of PD for a birth-death tree, we model FD by assuming that distinct discrete features arise randomly and independently along the branches of the tree at rate r and are lost at a constant rate [Formula: see text]. We derive an exact mathematical expression for the ratio [Formula: see text] of the two expected feature diversities (prior to and following an extinction event at the present) as t becomes large. We find that although [Formula: see text] has a similar behaviour to [Formula: see text] (and coincides with it for [Formula: see text]), when [Formula: see text], [Formula: see text] is described by a function that is different from [Formula: see text]. We also derive an exact expression for the expected number of features that are present in precisely one extant species. Our paper begins by establishing some generic properties of FD in a more general (non-phylogenetic) setting and applies this to fixed trees, before considering the setting of random (birth-death) trees.
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Affiliation(s)
- Marcus Overwater
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Daniel Pelletier
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand.
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Species delimitation polyphasic approach reveals Meyerella similis sp. nov.: a new species of “small green balls” within the Chlorella-clade (Trebouxiophyceae, Chlorophyta). ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00590-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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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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: A unifying framework for modelling evolutionary trees. Theor Popul Biol 2020; 133:38-39. [DOI: 10.1016/j.tpb.2019.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/18/2019] [Accepted: 07/01/2019] [Indexed: 11/20/2022]
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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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Steel M, Pourfaraj V, Chaudhary A, Mooers A. Evolutionary isolation and phylogenetic diversity loss under random extinction events. J Theor Biol 2017; 438:151-155. [PMID: 29146280 DOI: 10.1016/j.jtbi.2017.11.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 11/27/2022]
Abstract
The extinction of species at the present leads to the loss of 'phylogenetic diversity' (PD) from the evolutionary tree in which these species lie. Prior to extinction, the total PD present can be divided up among the species in various ways using measures of evolutionary isolation (such as 'fair proportion' and 'equal splits'). However, the loss of PD when certain combinations of species become extinct can be either larger or smaller than the cumulative loss of the isolation values associated with the extinct species. In this paper, we show that for trees generated under neutral evolutionary models, the loss of PD under a null model of random extinction at the present can be predicted from the loss of the cumulative isolation values, by applying a non-linear transformation that is independent of the tree. Moreover, the error in the prediction provably converges to zero as the size of the tree grows, with simulations showing good agreement even for moderate sized trees (n=64).
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Affiliation(s)
- Mike Steel
- Biomathematics Resarch Centre, University of Canterbury, Christchurch, New Zealand.
| | - Vahab Pourfaraj
- Department of Biological Sciences and IRMACS, Simon Fraser University, Burnaby, British Columbia, V5A1S6, Canada.
| | - Abhishek Chaudhary
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 9, Zurich 8092, Switzerland
| | - Arne Mooers
- Department of Biological Sciences and IRMACS, Simon Fraser University, Burnaby, British Columbia, V5A1S6, Canada
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Laurent S, Robinson-Rechavi M, Salamin N. Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions. BMC Evol Biol 2015; 15:157. [PMID: 26260305 PMCID: PMC4530483 DOI: 10.1186/s12862-015-0432-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 07/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent methodological advances allow better examination of speciation and extinction processes and patterns. A major open question is the origin of large discrepancies in species number between groups of the same age. Existing frameworks to model this diversity either focus on changes between lineages, neglecting global effects such as mass extinctions, or focus on changes over time which would affect all lineages. Yet it seems probable that both lineages differences and mass extinctions affect the same groups. RESULTS Here we used simulations to test the performance of two widely used methods under complex scenarios of diversification. We report good performances, although with a tendency to over-predict events with increasing complexity of the scenario. CONCLUSION Overall, we find that lineage shifts are better detected than mass extinctions. This work has significance to assess the methods currently used to estimate changes in diversification using phylogenetic trees. Our results also point toward the need to develop new models of diversification to expand our capabilities to analyse realistic and complex evolutionary scenarios.
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Affiliation(s)
- Sacha Laurent
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, 1015, Switzerland.
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, 1015, Switzerland.
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, 1015, Switzerland.
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Manceau M, Lambert A, Morlon H. Phylogenies support out-of-equilibrium models of biodiversity. Ecol Lett 2015; 18:347-56. [DOI: 10.1111/ele.12415] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/22/2014] [Accepted: 01/06/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Marc Manceau
- École Normale Supérieure; Institut de Biologie; CNRS UMR 8197; 46 rue d'Ulm 75005 Paris France
- Collège de France; Center for Interdisciplinary Research in Biology; CNRS UMR 7241; 11 place Marcelin-Berthelot 75005 Paris France
| | - Amaury Lambert
- Collège de France; Center for Interdisciplinary Research in Biology; CNRS UMR 7241; 11 place Marcelin-Berthelot 75005 Paris France
- UPMC Univ Paris 06; Laboratoire de Probabilités et Modèles Aléatoires; CNRS UMR 7599; 4 place Jussieu 75005 Paris France
| | - Hélène Morlon
- École Normale Supérieure; Institut de Biologie; CNRS UMR 8197; 46 rue d'Ulm 75005 Paris France
- Collège de France; Center for Interdisciplinary Research in Biology; CNRS UMR 7241; 11 place Marcelin-Berthelot 75005 Paris France
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Abstract
The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.
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Affiliation(s)
- Frederick A Matsen
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 91802, USA
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Birth–death models and coalescent point processes: The shape and probability of reconstructed phylogenies. Theor Popul Biol 2013; 90:113-28. [DOI: 10.1016/j.tpb.2013.10.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 11/20/2022]
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