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Rosindell J, Manson K, Gumbs R, Pearse WD, Steel M. Phylogenetic Biodiversity Metrics Should Account for Both Accumulation and Attrition of Evolutionary Heritage. Syst Biol 2024; 73:158-182. [PMID: 38102727 PMCID: PMC11129585 DOI: 10.1093/sysbio/syad072] [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: 12/06/2022] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
Phylogenetic metrics are essential tools used in the study of ecology, evolution and conservation. Phylogenetic diversity (PD) in particular is one of the most prominent measures of biodiversity and is based on the idea that biological features accumulate along the edges of phylogenetic trees that are summed. We argue that PD and many other phylogenetic biodiversity metrics fail to capture an essential process that we term attrition. Attrition is the gradual loss of features through causes other than extinction. Here we introduce "EvoHeritage", a generalization of PD that is founded on the joint processes of accumulation and attrition of features. We argue that while PD measures evolutionary history, EvoHeritage is required to capture a more pertinent subset of evolutionary history including only components that have survived attrition. We show that EvoHeritage is not the same as PD on a tree with scaled edges; instead, accumulation and attrition interact in a more complex non-monophyletic way that cannot be captured by edge lengths alone. This leads us to speculate that the one-dimensional edge lengths of classic trees may be insufficiently flexible to capture the nuances of evolutionary processes. We derive a measure of EvoHeritage and show that it elegantly reproduces species richness and PD at opposite ends of a continuum based on the intensity of attrition. We demonstrate the utility of EvoHeritage in ecology as a predictor of community productivity compared with species richness and PD. We also show how EvoHeritage can quantify living fossils and resolve their associated controversy. We suggest how the existing calculus of PD-based metrics and other phylogenetic biodiversity metrics can and should be recast in terms of EvoHeritage accumulation and attrition.
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Affiliation(s)
- James Rosindell
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Kerry Manson
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Rikki Gumbs
- EDGE of Existence Programme, Zoological Society of London, Regent’s Park, London NW1 4RY, UK
| | - William D Pearse
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
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Kotov AA, Garibian PG, Bekker EI, Taylor DJ, Karabanov DP. A new species group from the Daphnia curvirostris species complex (Cladocera: Anomopoda) from the eastern Palaearctic: taxonomy, phylogeny and phylogeography. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa046] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The eastern Palaearctic is a centre of diversity for freshwater cladocerans (Crustacea), but little is known about the evolution and taxonomy of this diversity. Daphnia curvirostris is a Holarctic species complex that has most of its diversity in the eastern Palaearctic. We examined the phylogeography, rates of evolution and taxonomic status for each clade of the D. curvirostris complex using morphological and genetic evidence from four genes. The cybertaxonomical and morphological evidence supported an eastern Palaearctic clade, with at least four species (described here as the Daphnia korovchinskyi sp. nov. group) having diagnostic morphological characters. We also detected convergent morphological characters in the D. curvirostris complex that provided information about species boundaries. Two of the new species (Daphnia koreana sp. nov. and Daphnia ishidai sp. nov.) are known from single ponds and are threatened by human activity. Divergence time estimates suggested an ancient origin (12–28 Mya) for the D. korovchinskyi group, but these estimates are complicated by the small number of calibration points.
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Affiliation(s)
- Alexey A Kotov
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
| | - Petr G Garibian
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
| | - Eugeniya I Bekker
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, NY, USA
| | - Dmitry P Karabanov
- A. N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect, Moscow, Russia
- I. D. Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Russia
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Koot EM, Morgan-Richards M, Trewick SA. An alpine grasshopper radiation older than the mountains, on Kā Tiritiri o te Moana (Southern Alps) of Aotearoa (New Zealand). Mol Phylogenet Evol 2020; 147:106783. [DOI: 10.1016/j.ympev.2020.106783] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 12/31/2022]
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Veron S, Haevermans T, Govaerts R, Mouchet M, Pellens R. Distribution and relative age of endemism across islands worldwide. Sci Rep 2019; 9:11693. [PMID: 31406123 PMCID: PMC6690940 DOI: 10.1038/s41598-019-47951-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/22/2019] [Indexed: 01/18/2023] Open
Abstract
Islands have remarkable levels of endemism and contribute greatly to global biodiversity. Establishing the age of island endemics is important to gain insights into the processes that have shaped the biodiversity patterns of island biota. We investigated the relative age of monocots across islands worldwide, using different measures of phylogenetic endemism tested against null models. We compiled a species occurrence dataset across 4,306 islands, and identified 142 sites with neo-, paleo-, mixed and super-endemism. These sites were distributed across the world, although they tended to be more common at low latitudes. The most frequent types of endemism were mixed and super-endemism, which suggests that present-day island biodiversity has frequently been shaped by processes that took place at different points in times. We also identified the environmental factors that contributed most to different types of endemism; we found that latitude, habitat availability and climate stability had a significant impact on the persistence of ancient taxa and on recent diversification events. The islands identified here are irreplaceable both for the uniqueness and the evolutionary history of their flora, and because they are a source of "option values" and evolutionary potential. Therefore, our findings will help guide biodiversity conservation on a global scale.
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Affiliation(s)
- Simon Veron
- Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Muséum National d'Histoire Naturelle (MNHN), CNRS, Sorbonne Université, EPHE, CP 51, 47 rue Buffon, 75005, Paris, France.
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR 7204) MNHN, CNRS, Sorbonne Université - CP51, 55-61 rue Buffon, 75005, Paris, France.
| | - Thomas Haevermans
- Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Muséum National d'Histoire Naturelle (MNHN), CNRS, Sorbonne Université, EPHE, CP 51, 47 rue Buffon, 75005, Paris, France
| | | | - Maud Mouchet
- Centre d'Ecologie et des Sciences de la Conservation (CESCO UMR 7204) MNHN, CNRS, Sorbonne Université - CP51, 55-61 rue Buffon, 75005, Paris, France
| | - Roseli Pellens
- Institut de Systématique, Evolution, Biodiversité (ISYEB UMR 7205), Muséum National d'Histoire Naturelle (MNHN), CNRS, Sorbonne Université, EPHE, CP 51, 47 rue Buffon, 75005, Paris, France
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Kondratyeva A, Grandcolas P, Pavoine S. Reconciling the concepts and measures of diversity, rarity and originality in ecology and evolution. Biol Rev Camb Philos Soc 2019; 94:1317-1337. [PMID: 30861626 PMCID: PMC6850657 DOI: 10.1111/brv.12504] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 12/29/2022]
Abstract
The concept of biological diversity, or biodiversity, is at the core of evolutionary and ecological studies. Many indices of biodiversity have been developed in the last four decades, with species being one of the central units of these indices. However, evolutionary and ecological studies need a precise description of species' characteristics to best quantify inter-species diversity, as species are not equivalent and exchangeable. One of the first concepts characterizing species in biodiversity studies was abundance-based rarity. Abundance-based rarity was then complemented by trait- and phylo-based rarity, called species' trait-based and phylogenetic originalities, respectively. Originality, which is a property of an individual species, represents a species' contribution to the overall diversity of a reference set of species. Originality can also be defined as the rarity of a species' characteristics such as the state of a functional trait, which is often assumed to be represented by the position of the species on a phylogenetic tree. We review and compare various approaches for measuring originality, rarity and diversity and demonstrate that (i) even if attempts to bridge these concepts do exist, only a few ecological and evolutionary studies have tried to combine them all in the past two decades; (ii) phylo- and trait-based diversity indices can be written as a function of species rarity and originality measures in several ways; and (iii) there is a need for the joint use of these three types of indices to understand community assembly processes and species' roles in ecosystem functioning in order to protect biodiversity efficiently.
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Affiliation(s)
- Anna Kondratyeva
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Département Homme et Environnement, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, 57 Rue Cuvier, CP 135, 75005ParisFrance
- Institut Systématique Evolution Biodiversité (ISYEB), Département Origines et Evolution, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université EPHE, 57 Rue Cuvier, CP 50, 75005ParisFrance
| | - Philippe Grandcolas
- Institut Systématique Evolution Biodiversité (ISYEB), Département Origines et Evolution, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université EPHE, 57 Rue Cuvier, CP 50, 75005ParisFrance
| | - Sandrine Pavoine
- Centre d'Ecologie et des Sciences de la Conservation (CESCO), Département Homme et Environnement, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, 57 Rue Cuvier, CP 135, 75005ParisFrance
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Kotov AA, Taylor DJ. Contrasting endemism in pond-dwelling cyclic parthenogens: the Daphnia curvirostris species group (Crustacea: Cladocera). Sci Rep 2019; 9:6812. [PMID: 31048750 PMCID: PMC6497905 DOI: 10.1038/s41598-019-43281-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/17/2019] [Indexed: 01/08/2023] Open
Abstract
Pond-dwelling cyclic parthenogens are often proposed to be highly vagile. However, the Holarctic biogeography of parthenogens has been hampered by very limited sampling in the eastern Palearctic. Here we examine the geographic boundaries, diversity, and connectivity across the Palearctic for the Daphnia curvirostris complex (Cladocera: Daphniidae). Nuclear (HSP90) and mitochondrial (ND2) sequence data supported the existence of five main clades (most of which corresponded to presumptive species) with one eastern Palearctic clade being novel to this study (the average mitochondrial genetic divergence from known species was 19.2%). D. curvirostris s.s. was geographically widespread in the Palearctic, with a population genetic signature consistent with postglacial expansion. The Eastern Palearctic had local nine endemic species and/or subclades (other Holarctic regions lacked more than one endemic subclade). Even though several endemic species appeared to have survived Pleistocene glaciation in the eastern Palearctic, much of the Palearctic has been recolonized by D. curvirostris s.str. from a Western Palearctic refugium. A disjunct population in Mexico also shared its haplotypes with D. curvirostris s.str., consistent with a recent introduction. The only apparently endemic North American lineage was detected in a thermally disturbed pond system in northwestern Alaska. Our results for pond-dwelling cyclic parthenogens further support the hypothesis that the Eastern Palearctic is a diversity hotspot for freshwater invertebrates.
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Affiliation(s)
- Alexey A Kotov
- A. N. Severtsov Institute of Ecology and Evolution, Leninsky Prospect 33, Moscow, 119071, Russia.
| | - Derek J Taylor
- Department of Biological Sciences, The State University of New York at Buffalo, Buffalo, NY, 14260, USA
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Gerhold P, Carlucci MB, Procheş Ş, Prinzing A. The Deep Past Controls the Phylogenetic Structure of Present, Local Communities. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062348] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coexisting species may be evolutionarily proximate or distant, resulting in phylogenetically poor or rich communities. This variation is often considered to result from present assembly processes. We argue that, under certain conditions, deep-past processes might control the phylogenetic diversity of communities. First, deep-past effects involve macroevolutionary processes, such as diversification rate, niche conservatism, or dispersal, in the lineages that constitute communities. Second, deep-past processes in the respective region or in the habitat type play a role, for instance, through age, area, stability, or connectivity. Third, the deep past may affect communities via trophic interactions (i.e., communities of enemies or mutualists or communities of hosts). We suggest that deep-past effects can be identified in local communities by measuring phylogenetic diversity in different species pools. We also show how community phylogenetic diversity results in positive or negative eco-evolutionary feedback, and we identify present-day conservation challenges that may profit from a deep-time perspective.
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Affiliation(s)
- Pille Gerhold
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu 51014, Estonia
| | - Marcos B. Carlucci
- Department of Botany, Federal University of Paraná, Curitiba, PR 81531–980, Brazil
| | - Şerban Procheş
- Discipline of Geography, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Andreas Prinzing
- Research Unit “Ecosystèmes Biodiversité, Evolution,” University of Rennes 1, CNRS UMR 6553 “Ecobio,” Rennes 35042, France
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8
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Grandcolas P. Ten false ideas about New Caledonia biogeography. Cladistics 2017; 33:481-487. [PMID: 34724758 DOI: 10.1111/cla.12176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2016] [Indexed: 01/21/2023] Open
Abstract
The biogeographical paradigm of New Caledonia has recently changed. Although this island is now considered by many as oceanic, its study is still often impeded by some old misconceptions concerning either regional geology or phylogenetic analysis of evolution and biogeography. I discuss ten points that I feel are especially detrimental, to help focus on the real debate and the real questions: (1) its geological history cannot be understood from the basement only; (2) the island submergence was not due simply to sea-level variation; (3) Zealandia/Tasmantis is not a lost continent; (4) short-distance dispersal is not equivalent to permanence on land; (5) long-distance dispersal is not the sole event opposing vicariance, but short-distance dispersal as well; (6) the occurrence of relicts does not prove biota permanence; (7) a major fault system was not observed in New Caledonia; (8) terranes are not rafts; (9) forest climatic refuges do not necessarily equate to centres of endemism or centres of diversity; and (10) New Caledonia is not only a sink but also a source. Study of New Caledonia will need to focus on old and non-relict clades and there is a need to improve the local fossil record.
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Affiliation(s)
- Philippe Grandcolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, CP 50, 45 rue Buffon, 75005, Paris, France
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McLaughlin BC, Ackerly DD, Klos PZ, Natali J, Dawson TE, Thompson SE. Hydrologic refugia, plants, and climate change. GLOBAL CHANGE BIOLOGY 2017; 23:2941-2961. [PMID: 28318131 DOI: 10.1111/gcb.13629] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/26/2016] [Indexed: 05/25/2023]
Abstract
Climate, physical landscapes, and biota interact to generate heterogeneous hydrologic conditions in space and over time, which are reflected in spatial patterns of species distributions. As these species distributions respond to rapid climate change, microrefugia may support local species persistence in the face of deteriorating climatic suitability. Recent focus on temperature as a determinant of microrefugia insufficiently accounts for the importance of hydrologic processes and changing water availability with changing climate. Where water scarcity is a major limitation now or under future climates, hydrologic microrefugia are likely to prove essential for species persistence, particularly for sessile species and plants. Zones of high relative water availability - mesic microenvironments - are generated by a wide array of hydrologic processes, and may be loosely coupled to climatic processes and therefore buffered from climate change. Here, we review the mechanisms that generate mesic microenvironments and their likely robustness in the face of climate change. We argue that mesic microenvironments will act as species-specific refugia only if the nature and space/time variability in water availability are compatible with the ecological requirements of a target species. We illustrate this argument with case studies drawn from California oak woodland ecosystems. We posit that identification of hydrologic refugia could form a cornerstone of climate-cognizant conservation strategies, but that this would require improved understanding of climate change effects on key hydrologic processes, including frequently cryptic processes such as groundwater flow.
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Affiliation(s)
- Blair C McLaughlin
- Department of Natural Resources and Society, University of Idaho, Moscow, ID, USA
| | - David D Ackerly
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - P Zion Klos
- Department of Environmental Science, University of Idaho, Moscow, ID, USA
| | - Jennifer Natali
- Department of Landscape Architecture and Environmental Planning, University of California, Berkeley, Berkeley, CA, USA
| | - Todd E Dawson
- Departments of Integrative Biology and Environmental Science, Policy & Management, University of California, Berkeley, Berkeley, CA, USA
| | - Sally E Thompson
- Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, CA, USA
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