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Capobianco A, Friedman M. Fossils indicate marine dispersal in osteoglossid fishes, a classic example of continental vicariance. Proc Biol Sci 2024; 291:20241293. [PMID: 39137888 PMCID: PMC11321865 DOI: 10.1098/rspb.2024.1293] [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: 02/05/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 08/15/2024] Open
Abstract
The separation of closely related terrestrial or freshwater species by vast marine barriers represents a biogeographical riddle. Such cases can provide evidence for vicariance, a process whereby ancient geological events like continental rifting divided ancestral geographical ranges. With an evolutionary history extending tens of millions of years, freshwater ecology, and distribution encompassing widely separated southern landmasses, osteoglossid bonytongue fishes are a textbook case of vicariance attributed to Mesozoic fragmentation of the Gondwanan supercontinent. Largely overlooked fossils complicate the clean narrative invoked for extant species by recording occurrences on additional continents and in marine settings. Here, we present a new total-evidence phylogenetic hypothesis for bonytongue fishes combined with quantitative models of range evolution and show that the last common ancestor of extant osteoglossids was likely marine, and that the group colonized freshwater settings at least four times when both extant and extinct lineages are considered. The correspondence between extant osteoglossid relationships and patterns of continental fragmentation therefore represents a striking example of biogeographical pseudocongruence. Contrary to arguments against vicariance hypotheses that rely only on temporal or phylogenetic evidence, these results provide direct palaeontological support for enhanced dispersal ability early in the history of a group with widely separated distributions in the modern day.
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Affiliation(s)
- Alessio Capobianco
- GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
| | - Matt Friedman
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI, USA
- Museum of Paleontology, University of Michigan, Ann Arbor, MI, USA
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2
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Wilenzik IV, Barger BB, Pyron RA. Fossil-informed biogeographic analysis suggests Eurasian regionalization in crown Squamata during the early Jurassic. PeerJ 2024; 12:e17277. [PMID: 38708352 PMCID: PMC11067913 DOI: 10.7717/peerj.17277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/01/2024] [Indexed: 05/07/2024] Open
Abstract
Background Squamata (lizards, snakes, and amphisbaenians) is a Triassic lineage with an extensive and complex biogeographic history, yet no large-scale study has reconstructed the ancestral range of early squamate lineages. The fossil record indicates a broadly Pangaean distribution by the end- Cretaceous, though many lineages (e.g., Paramacellodidae, Mosasauria, Polyglyphanodontia) subsequently went extinct. Thus, the origin and occupancy of extant radiations is unclear and may have been localized within Pangaea to specific plates, with potential regionalization to distinct Laurasian and Gondwanan landmasses during the Mesozoic in some groups. Methods We used recent tectonic models to code extant and fossil squamate distributions occurring on nine discrete plates for 9,755 species, with Jurassic and Cretaceous fossil constraints from three extinct lineages. We modeled ancestral ranges for crown Squamata from an extant-only molecular phylogeny using a suite of biogeographic models accommodating different evolutionary processes and fossil-based node constraints from known Jurassic and Cretaceous localities. We hypothesized that the best-fit models would not support a full Pangaean distribution (i.e., including all areas) for the origin of crown Squamata, but would instead show regionalization to specific areas within the fragmenting supercontinent, likely in the Northern Hemisphere where most early squamate fossils have been found. Results Incorporating fossil data reconstructs a localized origin within Pangaea, with early regionalization of extant lineages to Eurasia and Laurasia, while Gondwanan regionalization did not occur until the middle Cretaceous for Alethinophidia, Scolecophidia, and some crown Gekkotan lineages. While the Mesozoic history of extant squamate biogeography can be summarized as a Eurasian origin with dispersal out of Laurasia into Gondwana, their Cenozoic history is complex with multiple events (including secondary and tertiary recolonizations) in several directions. As noted by previous authors, squamates have likely utilized over-land range expansion, land-bridge colonization, and trans-oceanic dispersal. Tropical Gondwana and Eurasia hold more ancient lineages than the Holarctic (Rhineuridae being a major exception), and some asymmetries in colonization (e.g., to North America from Eurasia during the Cenozoic through Beringia) deserve additional study. Future studies that incorporate fossil branches, rather than as node constraints, into the reconstruction can be used to explore this history further.
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Affiliation(s)
- Ian V. Wilenzik
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - Benjamin B. Barger
- Department of Biology, George Washington University, Washington D.C., United States of America
| | - R. Alexander Pyron
- Department of Biology, George Washington University, Washington D.C., United States of America
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3
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Quintero I, Landis MJ, Jetz W, Morlon H. The build-up of the present-day tropical diversity of tetrapods. Proc Natl Acad Sci U S A 2023; 120:e2220672120. [PMID: 37159475 PMCID: PMC10194011 DOI: 10.1073/pnas.2220672120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/04/2023] [Indexed: 05/11/2023] Open
Abstract
The extraordinary number of species in the tropics when compared to the extra-tropics is probably the most prominent and consistent pattern in biogeography, suggesting that overarching processes regulate this diversity gradient. A major challenge to characterizing which processes are at play relies on quantifying how the frequency and determinants of tropical and extra-tropical speciation, extinction, and dispersal events shaped evolutionary radiations. We address this question by developing and applying spatiotemporal phylogenetic and paleontological models of diversification for tetrapod species incorporating paleoenvironmental variation. Our phylogenetic model results show that area, energy, or species richness did not uniformly affect speciation rates across tetrapods and dispute expectations of a latitudinal gradient in speciation rates. Instead, both neontological and fossil evidence coincide in underscoring the role of extra-tropical extinctions and the outflow of tropical species in shaping biodiversity. These diversification dynamics accurately predict present-day levels of species richness across latitudes and uncover temporal idiosyncrasies but spatial generality across the major tetrapod radiations.
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Affiliation(s)
- Ignacio Quintero
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université Paris Science & Lettres, Paris75005, France
| | - Michael J. Landis
- Landis Lab, Department of Biology, Washington University in St. Louis, St. Louis, MO63130
| | - Walter Jetz
- Jetz Lab, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT06511
- Center for Biodiversity and Global Change, Yale University, New Haven, CT06511
| | - Hélène Morlon
- Institut de Biologie de l’ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université Paris Science & Lettres, Paris75005, France
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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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Testo WL, de Gasper AL, Molino S, Galán JMGY, Salino A, Dittrich VADO, Sessa EB. Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family. AMERICAN JOURNAL OF BOTANY 2022; 109:1579-1595. [PMID: 36063431 DOI: 10.1002/ajb2.16062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The historical biogeography of ferns is typically expected to be dominated by long-distance dispersal due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims were to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres. METHODS We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification. RESULTS Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas. CONCLUSIONS Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.
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Affiliation(s)
- Weston L Testo
- Department of Biology, 876 Newell Drive, University of Florida, Gainesville, FL, 32611, USA
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76102, USA
- Department of Science and Education, Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - André L de Gasper
- Departamento de Ciências Naturais, Universidade Regional de Blumenau, Rua Antônio da Veiga, 140, Victor Konder, CEP 89030-903, Blumenau, SC, Brazil
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Minas Gerais, P.O. Box 486, 31270-901, Belo Horizonte, MG, Brazil
| | - Sonia Molino
- Unit of Botany, Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense, Avda. Jose Antonio Nováis 12, 28040, Madrid, Spain
| | - José María Gabriel Y Galán
- Unit of Botany, Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense, Avda. Jose Antonio Nováis 12, 28040, Madrid, Spain
| | - Alexandre Salino
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Minas Gerais, P.O. Box 486, 31270-901, Belo Horizonte, MG, Brazil
| | | | - Emily B Sessa
- Department of Biology, 876 Newell Drive, University of Florida, Gainesville, FL, 32611, USA
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Velasco JA, Pinto-Ledezma JN. Mapping species diversification metrics in macroecology: Prospects and challenges. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.951271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The intersection of macroecology and macroevolution is one of today’s most active research in biology. In the last decade, we have witnessed a steady increment of macroecological studies that use metrics attempting to capture macroevolutionary processes to explain present-day biodiversity patterns. Evolutionary explanations of current species richness gradients are fundamental for understanding how diversity accumulates in a region. Although multiple hypotheses have been proposed to explain the patterns we observe in nature, it is well-known that the present-day diversity patterns result from speciation, extinction, colonization from nearby areas, or a combination of these macroevolutionary processes. Whether these metrics capture macroevolutionary processes across space is unknown. Some tip-rate metrics calculated directly from a phylogenetic tree (e.g., mean root distance -MRD-; mean diversification rate -mDR-) seem to return very similar geographical patterns regardless of how they are estimated (e.g., using branch lengths explicitly or not). Model-based tip-rate metrics —those estimated using macroevolutionary mixtures, e.g., the BAMM approach— seem to provide better net diversification estimates than only speciation rates. We argue that the lack of appropriate estimates of extinction and dispersal rates in phylogenetic trees may strongly limit our inferences about how species richness gradients have emerged at spatial and temporal scales. Here, we present a literature review about this topic and empirical comparisons between select taxa with several of these metrics. We implemented a simple null model approach to evaluate whether mapping of these metrics deviates from a random sampling process. We show that phylogenetic metrics by themselves are relatively poor at capturing speciation, extinction, and dispersal processes across geographical gradients. Furthermore, we provide evidence of how parametric biogeographic methods can improve our inference of past events and, therefore, our conclusions about the evolutionary processes driving biodiversity patterns. We recommend that further studies include several approaches simultaneously (e.g., spatial diversification modeling, parametric biogeographic methods, simulations) to disentangle the relative role of speciation, extinction, and dispersal in the generation and maintenance of species richness gradients at regional and global scales.
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Wisniewski AL, Lloyd GT, Slater GJ. Extant species fail to estimate ancestral geographical ranges at older nodes in primate phylogeny. Proc Biol Sci 2022; 289:20212535. [PMID: 35582793 DOI: 10.1098/rspb.2021.2535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A clade's evolutionary history is shaped, in part, by geographical range expansion, sweepstakes dispersal and local extinction. A rigorous understanding of historical biogeography may therefore yield insights into macroevolutionary dynamics such as adaptive radiation. Modern historical biogeographic analyses typically fit statistical models to molecular phylogenies, but it remains unclear whether extant species provide sufficient signal or if well-sampled phylogenies of extinct and extant taxa are necessary to produce meaningful estimates of past ranges. We investigated the historical biogeography of Primates and their euarchontan relatives using a novel meta-analytical phylogeny of over 900 extant (n= 419) and extinct (n = 483) species spanning their entire evolutionary history. Ancestral range estimates for young nodes were largely congruent with those derived from molecular phylogeny. However, node age exerts a significant effect on ancestral range estimate congruence, and the probability of congruent inference dropped below 0.5 for nodes older than the late Eocene, corresponding to the origins of higher-level clades. Discordance was not observed in analyses of extinct taxa alone. Fossils are essential for robust ancestral range inference and biogeographic analyses of extant clades originating in the deep past should be viewed with scepticism without them.
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Affiliation(s)
- Anna L Wisniewski
- Department of the Geophysical Sciences, University of Chicago, Chicago IL, USA
| | - Graeme T Lloyd
- School of Earth and Environment, University of Leeds, Leeds, UK
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago IL, USA
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Hauffe T, Pires MM, Quental TB, Wilke T, Silvestro D. A quantitative framework to infer the effect of traits, diversity and environment on dispersal and extinction rates from fossils. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Torsten Hauffe
- Department of Biology University of Fribourg and Swiss Institute of Bioinformatics Fribourg Switzerland
| | - Mathias M. Pires
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas Campinas Brazil
| | - Tiago B. Quental
- Departamento de Ecologia, Universidade de São Paulo São Paulo Brazil
| | - Thomas Wilke
- Department of Animal Ecology and Systematics, Justus Liebig University Germany
| | - Daniele Silvestro
- Department of Biology University of Fribourg and Swiss Institute of Bioinformatics Fribourg Switzerland
- Department of Biological and Environmental Sciences University of Gothenburg and Gothenburg Global Biodiversity Centre Gothenburg Sweden
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Hackel J, Sanmartín I. Modelling the tempo and mode of lineage dispersal. Trends Ecol Evol 2021; 36:1102-1112. [PMID: 34462154 DOI: 10.1016/j.tree.2021.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
Abstract
Lineage dispersal is a basic macroevolutionary process shaping the distribution of biodiversity. Probabilistic approaches in biogeography, epidemiology, and macroecology often model dispersal as a background process to explain extant or infer past distributions. We propose framing questions around the mode, timing, rate, and direction of lineage dispersal itself, from a lineage- or geography-centric perspective. We review available methods for modelling lineage dispersal. Likelihood- and simulation-based approaches to modelling dispersal have made progress in accounting for the variation of lineage dispersal over space, time, and branches of a phylogeny and its interaction with diversification. Methodological improvements, guided by a focus on model adequacy, will lead to more realistic models that can answer fundamental questions about the tempo and mode of lineage dispersal.
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Affiliation(s)
- Jan Hackel
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, UK.
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Raja NB, Kiessling W. Out of the extratropics: the evolution of the latitudinal diversity gradient of Cenozoic marine plankton. Proc Biol Sci 2021; 288:20210545. [PMID: 33975476 DOI: 10.1098/rspb.2021.0545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many ecological and evolutionary hypotheses have been proposed to explain the latitudinal diversity gradient, i.e. the increase in species richness from the poles to the tropics. Among the evolutionary hypotheses, the 'out of the tropics' (OTT) hypothesis has received considerable attention. The OTT posits that the tropics are both a cradle and source of biodiversity for extratropical regions. To test the generality of the OTT hypothesis, we explored the spatial biodiversity dynamics of unicellular marine plankton over the Cenozoic era (the last 66 Myr). We find large-scale climatic changes during the Cenozoic shaped the diversification and dispersal of marine plankton. Origination was generally more likely in the extratropics and net dispersal was towards the tropics rather than in the opposite direction, especially during the warmer climates of the early Cenozoic. Although migration proportions varied among major plankton groups and climate phases, we provide evidence that the extratropics were a source of tropical microplankton biodiversity over the last 66 Myr.
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Affiliation(s)
- Nussaïbah B Raja
- GeoZentrum Nordbayern, Department of Geography and Geosciences, Friedrich-Alexander University Erlangen-Nürnberg, Loewenichstr. 28, 91054 Erlangen, Germany
| | - Wolfgang Kiessling
- GeoZentrum Nordbayern, Department of Geography and Geosciences, Friedrich-Alexander University Erlangen-Nürnberg, Loewenichstr. 28, 91054 Erlangen, Germany
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Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange. Proc Natl Acad Sci U S A 2020; 117:26281-26287. [PMID: 33020313 PMCID: PMC7585031 DOI: 10.1073/pnas.2009397117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The biological interchange between North and South America associated with the formation of the Isthmus of Panama is key to defining current gradients of species diversity. A major gap in our understanding of the interchange is its asymmetry, where mammals of North American origin attained higher diversity in South America than vice versa. The prevailing view is that this asymmetry resulted from higher origination of immigrant mammals in South America. In contrast, we find that asymmetry results from high extinction of native mammals in South America, which reduced the diversity of native mammals available to disperse northwards. These results shed light on the legacy of the biotic interchange to understand the current patterns of species diversity across the Americas. The interchange between the previously disconnected faunas of North and South America was a massive experiment in biological invasion. A major gap in our understanding of this invasion is why there was a drastic increase in the proportion of mammals of North American origin found in South America. Four nonmutually exclusive mechanisms may explain this asymmetry: 1) Higher dispersal rate of North American mammals toward the south, 2) higher origination of North American immigrants in South America, 3) higher extinction of mammals with South American origin, and 4) similar dispersal rate but a larger pool of native taxa in North versus South America. We test among these mechanisms by analyzing ∼20,000 fossil occurrences with Bayesian methods to infer dispersal and diversification rates and taxonomic selectivity of immigrants. We find no differences in the dispersal and origination rates of immigrants. In contrast, native South American mammals show higher extinction. We also find that two clades with North American origin (Carnivora and Artiodactyla) had significantly more immigrants in South America than other clades. Altogether, the asymmetry of the interchange was not due to higher origination of immigrants in South America as previously suggested, but resulted from higher extinction of native taxa in southern South America. These results from one of the greatest biological invasions highlight how biogeographic processes and biotic interactions can shape continental diversity.
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Wilke T, Hauffe T, Jovanovska E, Cvetkoska A, Donders T, Ekschmitt K, Francke A, Lacey JH, Levkov Z, Marshall CR, Neubauer TA, Silvestro D, Stelbrink B, Vogel H, Albrecht C, Holtvoeth J, Krastel S, Leicher N, Leng MJ, Lindhorst K, Masi A, Ognjanova-Rumenova N, Panagiotopoulos K, Reed JM, Sadori L, Tofilovska S, Van Bocxlaer B, Wagner-Cremer F, Wesselingh FP, Wolters V, Zanchetta G, Zhang X, Wagner B. Deep drilling reveals massive shifts in evolutionary dynamics after formation of ancient ecosystem. SCIENCE ADVANCES 2020; 6:eabb2943. [PMID: 32998898 PMCID: PMC7527215 DOI: 10.1126/sciadv.abb2943] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 08/17/2020] [Indexed: 05/27/2023]
Abstract
The scarcity of high-resolution empirical data directly tracking diversity over time limits our understanding of speciation and extinction dynamics and the drivers of rate changes. Here, we analyze a continuous species-level fossil record of endemic diatoms from ancient Lake Ohrid, along with environmental and climate indicator time series since lake formation 1.36 million years (Ma) ago. We show that speciation and extinction rates nearly simultaneously decreased in the environmentally dynamic phase after ecosystem formation and stabilized after deep-water conditions established in Lake Ohrid. As the lake deepens, we also see a switch in the macroevolutionary trade-off, resulting in a transition from a volatile assemblage of short-lived endemic species to a stable community of long-lived species. Our results emphasize the importance of the interplay between environmental/climate change, ecosystem stability, and environmental limits to diversity for diversification processes. The study also provides a new understanding of evolutionary dynamics in long-lived ecosystems.
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Affiliation(s)
- Thomas Wilke
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany.
| | - Torsten Hauffe
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Elena Jovanovska
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
- Department of Palaeoanthropology, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Aleksandra Cvetkoska
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Palaeoecology, Department of Physical Geography, Utrecht University, Utrecht, Netherlands
| | - Timme Donders
- Palaeoecology, Department of Physical Geography, Utrecht University, Utrecht, Netherlands
| | - Klemens Ekschmitt
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Alexander Francke
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, NSW, Australia
| | - Jack H Lacey
- National Environmental Isotope Facility, British Geological Survey, Nottingham, UK
| | - Zlatko Levkov
- Institute of Biology, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Charles R Marshall
- Department of Integrative Biology and University of California Museum of Paleontology, University of California, Berkeley, Berkeley, CA, USA
| | - Thomas A Neubauer
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, Netherlands
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg (Ch. de Musee 10), 1700 Fribourg, Switzerland
| | - Björn Stelbrink
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
- Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Hendrik Vogel
- Institute of Geological Sciences & Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Christian Albrecht
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Jens Holtvoeth
- School of Earth Sciences, University of Bristol, Bristol, UK
- Cambridge University, Conservation Research Institute, 19 Silver Street, Cambridge CB3 9EP, UK
| | - Sebastian Krastel
- Institute of Geosciences, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Niklas Leicher
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany
| | - Melanie J Leng
- National Environmental Isotope Facility, British Geological Survey, Nottingham, UK
- Centre for Environmental Geochemistry, School of Biosciences, University of Nottingham, Nottingham, UK
| | - Katja Lindhorst
- Institute of Geosciences, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Alessia Masi
- Dipartimento di Biologia Ambientale, Università di Roma "La Sapienza", Rome, Italy
| | | | | | - Jane M Reed
- Department of Geography, Geology and Environment, University of Hull, Hull, UK
| | - Laura Sadori
- Dipartimento di Biologia Ambientale, Università di Roma "La Sapienza", Rome, Italy
| | - Slavica Tofilovska
- Institute of Biology, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Bert Van Bocxlaer
- CNRS, Université de Lille, UMR 8198 Evo-Eco-Paleo, Lille, France
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | | | - Frank P Wesselingh
- Naturalis Biodiversity Center, Leiden, Netherlands
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Volkmar Wolters
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | | | - Xiaosen Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Bernd Wagner
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany
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13
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He J, Lin S, Li J, Yu J, Jiang H. Evolutionary history of zoogeographical regions surrounding the Tibetan Plateau. Commun Biol 2020; 3:415. [PMID: 32737418 PMCID: PMC7395132 DOI: 10.1038/s42003-020-01154-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/15/2020] [Indexed: 11/18/2022] Open
Abstract
The Tibetan Plateau (TP) and surrounding regions have one of the most complex biotas on Earth. However, the evolutionary history of these regions in deep time is poorly understood. Here, we quantify the temporal changes in beta dissimilarities among zoogeographical regions during the Cenozoic using 4,966 extant terrestrial vertebrates and 1,278 extinct mammal genera. We identify ten present-day zoogeographical regions and find that they underwent a striking change over time. Specifically, the fauna on the TP was close to the Oriental realm in deep time but became more similar to the Palearctic realms more recently. The present-day zoogeographical regions generally emerged during the Miocene/Pliocene boundary (ca. 5 Ma). These results indicate that geological events such as the Indo-Asian Collision, the TP uplift, and the aridification of the Asian interior underpinned the evolutionary history of the zoogeographical regions surrounding the TP over different time periods.
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Affiliation(s)
- Jiekun He
- Spatial Ecology Lab, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Siliang Lin
- Spatial Ecology Lab, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Jiatang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041, Chengdu, China
| | - Jiehua Yu
- Spatial Ecology Lab, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Haisheng Jiang
- Spatial Ecology Lab, School of Life Sciences, South China Normal University, 510631, Guangzhou, China.
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14
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15
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Chomicki G, Weber M, Antonelli A, Bascompte J, Kiers ET. The Impact of Mutualisms on Species Richness. Trends Ecol Evol 2019; 34:698-711. [DOI: 10.1016/j.tree.2019.03.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/11/2019] [Accepted: 03/18/2019] [Indexed: 11/28/2022]
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16
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Silvestro D, Tejedor MF, Serrano-Serrano ML, Loiseau O, Rossier V, Rolland J, Zizka A, Höhna S, Antonelli A, Salamin N. Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors. Syst Biol 2018; 68:78-92. [PMID: 29931325 PMCID: PMC6292484 DOI: 10.1093/sysbio/syy046] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/06/2018] [Indexed: 12/16/2022] Open
Abstract
New World Monkeys (NWM) (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Herein, we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5–10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small—weighing 0.4 kg—and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of NWM and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,These authors contributed equally to this work
| | - Marcelo F Tejedor
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,Instituto Patagónico de Geología y Paleontología (CCT CONICET-CENPAT), Boulevard Almirante Brown 2915, 9120 Puerto Madryn, Chubut, Argentina.,Facultad de Ciencias Naturales, Sede Trelew, Universidad Nacional de la Patagonia 'San Juan Bosco', 9100 Trelew, Chubut, Argentina.,These authors contributed equally to this work
| | | | - Oriane Loiseau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Victor Rossier
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Jonathan Rolland
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Department of Zoology, University of British Columbia, 2212 Main Mall, Vancouver, BC Canada
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden
| | - Sebastian Höhna
- Division of Evolutionary Biology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2, 82152 Munich, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Global Biodiversity Center, Carl Skottsbergs gata 22B, Gothenburg 41319, Sweden.,Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, 413 19 Gothenburg, Sweden.,Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.,These authors are severs as a co-last authorship
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland.,These authors are severs as a co-last authorship
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17
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Capobianco A, Friedman M. Vicariance and dispersal in southern hemisphere freshwater fish clades: a palaeontological perspective. Biol Rev Camb Philos Soc 2018; 94:662-699. [DOI: 10.1111/brv.12473] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Alessio Capobianco
- Museum of Paleontology and Department of Earth and Environmental Sciences; University of Michigan; 1105 N. University Ave, Ann Arbor MI 48109-1079 U.S.A
| | - Matt Friedman
- Museum of Paleontology and Department of Earth and Environmental Sciences; University of Michigan; 1105 N. University Ave, Ann Arbor MI 48109-1079 U.S.A
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18
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Antonelli A, Ariza M, Albert J, Andermann T, Azevedo J, Bacon C, Faurby S, Guedes T, Hoorn C, Lohmann LG, Matos-Maraví P, Ritter CD, Sanmartín I, Silvestro D, Tejedor M, ter Steege H, Tuomisto H, Werneck FP, Zizka A, Edwards SV. Conceptual and empirical advances in Neotropical biodiversity research. PeerJ 2018; 6:e5644. [PMID: 30310740 PMCID: PMC6174874 DOI: 10.7717/peerj.5644] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/27/2018] [Indexed: 01/23/2023] Open
Abstract
The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.
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Affiliation(s)
- Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Gothenburg Botanical Garden, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - María Ariza
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Laboratory Ecologie et Biologie des Interactions, Team “Ecologie, Evolution, Symbiose”, Université de Poitiers, Poitiers, France
| | - James Albert
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Josué Azevedo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Christine Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Thais Guedes
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Federal University of São Paulo, Diadema, Brazil
- Museum of Zoology, University of São Paulo, São Paulo, Brazil
| | - Carina Hoorn
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
- Universidad Regional Amazonica IKIAM, Napo, Ecuador
| | - Lúcia G. Lohmann
- Instituto de Biociências, Departamento de Botânica, Universidade de São Paulo, São Paulo, Brazil
- Integrative Biology, University of California, Berkeley, CA, USA
| | - Pável Matos-Maraví
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Camila D. Ritter
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | | | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marcelo Tejedor
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Instituto Patagónico de Geología y Paleontología, Puerto Madryn, Guatemala
| | - Hans ter Steege
- Naturalis Biodiversity Center, Leiden, Netherlands
- Systems Ecology, Free University, Amsterdam, Netherlands
| | - Hanna Tuomisto
- Department of Biology, University of Turku, Turku, Finland
| | | | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
| | - Scott V. Edwards
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Department of Organismic Biology and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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19
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Abstract
Amazonia is not only the world’s most diverse rainforest but is also the region in tropical America that has contributed most to its total biodiversity. We show this by estimating and comparing the evolutionary history of a large number of animal and plant species. We find that there has been extensive interchange of evolutionary lineages among different regions and biomes, over the course of tens of millions of years. Amazonia stands out as the primary source of diversity, which can be mainly explained by the total amount of time Amazonian lineages have occupied the region. The exceedingly rich and heterogeneous diversity of the American tropics could only be achieved by high rates of dispersal events across the continent. The American tropics (the Neotropics) are the most species-rich realm on Earth, and for centuries, scientists have attempted to understand the origins and evolution of their biodiversity. It is now clear that different regions and taxonomic groups have responded differently to geological and climatic changes. However, we still lack a basic understanding of how Neotropical biodiversity was assembled over evolutionary timescales. Here we infer the timing and origin of the living biota in all major Neotropical regions by performing a cross-taxonomic biogeographic analysis based on 4,450 species from six major clades across the tree of life (angiosperms, birds, ferns, frogs, mammals, and squamates), and integrate >1.3 million species occurrences with large-scale phylogenies. We report an unprecedented level of biotic interchange among all Neotropical regions, totaling 4,525 dispersal events. About half of these events involved transitions between major environmental types, with a predominant directionality from forested to open biomes. For all taxonomic groups surveyed here, Amazonia is the primary source of Neotropical diversity, providing >2,800 lineages to other regions. Most of these dispersal events were to Mesoamerica (∼1,500 lineages), followed by dispersals into open regions of northern South America and the Cerrado and Chaco biomes. Biotic interchange has taken place for >60 million years and generally increased toward the present. The total amount of time lineages spend in a region appears to be the strongest predictor of migration events. These results demonstrate the complex origin of tropical ecosystems and the key role of biotic interchange for the assembly of regional biotas.
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20
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Hagen O, Andermann T, Quental TB, Antonelli A, Silvestro D. Estimating Age-Dependent Extinction: Contrasting Evidence from Fossils and Phylogenies. Syst Biol 2018; 67:458-474. [PMID: 29069434 PMCID: PMC5920349 DOI: 10.1093/sysbio/syx082] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/03/2017] [Accepted: 10/15/2017] [Indexed: 01/12/2023] Open
Abstract
The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen's seminal work from 1973 proposed the "Law of constant extinction," which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however, do not directly account for the incompleteness of the fossil record, and have rarely been applied at the species level. Here, we present a Bayesian framework to estimate extinction rates from the fossil record accounting for age-dependent extinction (ADE). Our approach, unlike previous implementations, explicitly models unobserved species and accounts for the effects of fossil preservation on the observed longevity of sampled lineages. We assess the performance and robustness of our method through extensive simulations and apply it to a fossil data set of terrestrial Carnivora spanning the past 40 myr. We find strong evidence of ADE, as we detect the extinction rate to be highest in young species and declining with increasing species age. For comparison, we apply a recently developed analogous ADE model to a dated phylogeny of extant Carnivora. Although the phylogeny-based analysis also infers ADE, it indicates that the extinction rate, instead, increases with increasing taxon age. The estimated mean species longevity also differs substantially, with the fossil-based analyses estimating 2.0 myr, in contrast to 9.8 myr derived from the phylogeny-based inference. Scrutinizing these discrepancies, we find that both fossil and phylogeny-based ADE models are prone to high error rates when speciation and extinction rates increase or decrease through time. However, analyses of simulated and empirical data show that fossil-based inferences are more robust. This study shows that an accurate estimation of ADE from incomplete fossil data is possible when the effects of preservation are jointly modeled, thus allowing for a reassessment of Van Valen's model as a general rule in macroevolution.
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Affiliation(s)
- Oskar Hagen
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zurich, 8092 Zurich, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
| | - Tiago B Quental
- Departamento de Ecologia, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, SE-413 19 Göteborg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, SE-405 30 Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Göteborg, Sweden
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
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21
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A jungle tale: Molecular phylogeny and divergence time estimates of the Desmopsis-Stenanona clade (Annonaceae) in Mesoamerica. Mol Phylogenet Evol 2018; 122:80-94. [PMID: 29407482 DOI: 10.1016/j.ympev.2018.01.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 01/27/2018] [Accepted: 01/27/2018] [Indexed: 01/20/2023]
Abstract
The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus-Tridimeris clade and (ii) a Desmopsis-Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis-Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions.
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22
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Töpel M, Zizka A, Calió MF, Scharn R, Silvestro D, Antonelli A. SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution. Syst Biol 2018; 66:145-151. [PMID: 27486181 PMCID: PMC5410971 DOI: 10.1093/sysbio/syw064] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 07/08/2016] [Indexed: 11/23/2022] Open
Abstract
Understanding the patterns and processes underlying the uneven distribution of biodiversity across space constitutes a major scientific challenge in systematic biology and biogeography, which largely relies on effectively mapping and making sense of rapidly increasing species occurrence data. There is thus an urgent need for making the process of coding species into spatial units faster, automated, transparent, and reproducible. Here we present SpeciesGeoCoder, an open-source software package written in Python and R, that allows for easy coding of species into user-defined operational units. These units may be of any size and be purely spatial (i.e., polygons) such as countries and states, conservation areas, biomes, islands, biodiversity hotspots, and areas of endemism, but may also include elevation ranges. This flexibility allows scoring species into complex categories, such as those encountered in topographically and ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be used to facilitate sorting and cleaning of occurrence data obtained from online databases, and for testing the impact of incorrect identification of specimens on the spatial coding of species. The various outputs of SpeciesGeoCoder include quantitative biodiversity statistics, global and local distribution maps, and files that can be used directly in many phylogeny-based applications for ancestral range reconstruction, investigations of biome evolution, and other comparative methods. Our simulations indicate that even datasets containing hundreds of millions of records can be analyzed in relatively short time using a standard computer. We exemplify the use of SpeciesGeoCoder by inferring the historical dispersal of birds across the Isthmus of Panama, showing that lowland species crossed the Isthmus about twice as frequently as montane species with a marked increase in the number of dispersals during the last 10 million years.
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Affiliation(s)
- Mats Töpel
- Department of Marine Sciences, University of Gothenburg, PO Box 460, SE-405 30 Göteborg, Sweden.,Bioinformatics Infrastructure for Life Sciences.,Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Göteborg, Sweden
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Göteborg, Sweden
| | - Maria Fernanda Calió
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Göteborg, Sweden.,Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, Rua do Matão, 277, Cidade Universitária, CEP: 05508-090, São Paulo, SP, Brazil.,Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Biologia Vegetal, Rua Monteiro Lobato, 255, Cidade Universitária, CEP: 13083-862, Campinas, SP, Brazil
| | - Ruud Scharn
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Göteborg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Göteborg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, PO Box 461, SE-405 30 Göteborg, Sweden.,Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, SE-41319 Göteborg, Sweden
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23
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Laurent S, Salamin N, Robinson-Rechavi M. No evidence for the radiation time lag model after whole genome duplications in Teleostei. PLoS One 2017; 12:e0176384. [PMID: 28426792 PMCID: PMC5398669 DOI: 10.1371/journal.pone.0176384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022] Open
Abstract
The short and long term effects of polyploidization on the evolutionary fate of lineages is still unclear despite much interest. First recognized in land plants, it has become clear that polyploidization is widespread in eukaryotes, notably at the origin of vertebrates and teleost fishes. Many hypotheses have been proposed to link the species richness of lineages and whole genome duplications. For instance, the radiation time lag model suggests that paleopolyploidy would favour the apparition of new phenotypic traits, although the radiation of the lineage would not occur before a later dispersion event. Some results indicate that this model may be observed during land plant evolution. In this work, we test predictions of the radiation time lag model using both fossil data and molecular phylogenies in ancient and more recent teleost whole genome duplications. We fail to find any evidence of delayed increase of the species number after any of these events and conclude that paleopolyploidization still remains to be unambiguously linked to taxonomic diversity in teleosts.
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Affiliation(s)
- Sacha Laurent
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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24
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Albert JS, Antonelli A. Society for the Study of Systematic Biology symposium: Frontiers in Parametric Biogeography. Syst Biol 2017; 66:125-127. [DOI: 10.1093/sysbio/syx036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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25
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Jordan SMR, Barraclough TG, Rosindell J. Quantifying the effects of the break up of Pangaea on global terrestrial diversification with neutral theory. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150221. [PMID: 26977062 PMCID: PMC4810815 DOI: 10.1098/rstb.2015.0221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The historic richness of most taxonomic groups increases substantially over geological time. Explanations for this fall broadly into two categories: bias in the fossil record and elevated net rates of diversification in recent periods. For example, the break up of Pangaea and isolation between continents might have increased net diversification rates. In this study, we investigate the effect on terrestrial diversification rates of the increased isolation between land masses brought about by continental drift. We use ecological neutral theory as a means to study geologically complex scenarios tractably. Our models show the effects of simulated geological events that affect all species equally, without the added complexity of further ecological processes. We find that continental drift leads to an increase in diversity only where isolation between continents leads to additional speciation through vicariance, and where higher taxa with very low global diversity are considered. We conclude that continental drift by itself is not sufficient to account for the increase in terrestrial species richness observed in the fossil record.
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Affiliation(s)
- Sean M R Jordan
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK
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Price SA, Schmitz L. A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150228. [PMID: 26977068 DOI: 10.1098/rstb.2015.0228] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart.
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Affiliation(s)
- S A Price
- Department of Evolution & Ecology, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - L Schmitz
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, 925 North Mills Avenue, Claremont, CA 91711, USA
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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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Ezard THG, Quental TB, Benton MJ. The challenges to inferring the regulators of biodiversity in deep time. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150216. [PMID: 26977058 PMCID: PMC4810811 DOI: 10.1098/rstb.2015.0216] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2016] [Indexed: 11/12/2022] Open
Abstract
Attempts to infer the ecological drivers of macroevolution in deep time have long drawn inspiration from work on extant systems, but long-term evolutionary and geological changes complicate the simple extrapolation of such theory. Recent efforts to incorporate a more informed ecology into macroevolution have moved beyond the descriptive, seeking to isolate generating mechanisms and produce testable hypotheses of how groups of organisms usurp each other or coexist over vast timespans. This theme issue aims to exemplify this progress, providing a series of case studies of how novel modelling approaches are helping infer the regulators of biodiversity in deep time. In this Introduction, we explore the challenges of these new approaches. First, we discuss how our choices of taxonomic units have implications for the conclusions drawn. Second, we emphasize the need to embrace the interdependence of biotic and abiotic changes, because no living organism ignores its environment. Third, in the light of parts 1 and 2, we discuss the set of dynamic signatures that we might expect to observe in the fossil record. Finally, we ask whether these dynamics represent the most ecologically informative foci for research efforts aimed at inferring the regulators of biodiversity in deep time. The papers in this theme issue contribute in each of these areas.
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Affiliation(s)
- Thomas H G Ezard
- Ocean and Earth Sciences, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, European Way, Southampton SO14 3ZH, UK Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton SO17 1BJ, UK
| | - Tiago B Quental
- Departamento de Ecologia, Universidade de São Paulo, São Paulo, SP 05508-900, Brazil
| | - Michael J Benton
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
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