1
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Scott JE. The macroevolutionary dynamics of activity pattern in mammals: Primates in context. J Hum Evol 2023; 184:103436. [PMID: 37741141 DOI: 10.1016/j.jhevol.2023.103436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/25/2023]
Abstract
Activity pattern has played a prominent role in discussions of primate evolutionary history. Most primates are either diurnal or nocturnal, but a small number are active both diurnally and nocturnally. This pattern-cathemerality-also occurs at low frequency across mammals. Using a large sample of mammalian species, this study evaluates two macroevolutionary hypotheses proposed to explain why cathemerality is less common than diurnality and nocturnality: 1) that cathemeral lineages have higher extinction probabilities (differential diversification) and 2) that transitions out of cathemerality are more frequent, making it a less persistent state (differential state persistence). Rates of speciation, extinction, and transition between character states were estimated using hidden-rates models applied to a phylogenetic tree containing 3013 mammals classified by activity pattern. The models failed to detect consistent differences in diversification dynamics among activity patterns, but there is strong support for differential state persistence. Transition rates out of cathemerality tend to be much higher than transition rates out of nocturnality. Transition rates out of diurnality are similar to those for cathemerality in most clades, with two important exceptions: diurnality is unusually persistent in anthropoid primates and sciurid rodents. These two groups combine very low rates of transition out of diurnality with high speciation rates. This combination has no parallels among cathemeral lineages, explaining why diurnality has become more common than cathemerality in mammals. Similarly, the combination of rates found in anthropoids is sufficient to explain the low relative frequency of cathemerality in primates, making it unnecessary to appeal to high extinction probabilities in cathemeral lineages in this clade. These findings support the hypothesis that the distribution of activity patterns across mammals has been influenced primarily by differential state persistence, whereas the effect of differential diversification appears to have been more idiosyncratic.
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Affiliation(s)
- Jeremiah E Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA.
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2
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Thompson JB, Davis KE, Dodd HO, Wills MA, Priest NK. Speciation across the Earth driven by global cooling in terrestrial orchids. Proc Natl Acad Sci U S A 2023; 120:e2102408120. [PMID: 37428929 PMCID: PMC10629580 DOI: 10.1073/pnas.2102408120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/03/2023] [Indexed: 07/12/2023] Open
Abstract
Although climate change has been implicated as a major catalyst of diversification, its effects are thought to be inconsistent and much less pervasive than localized climate or the accumulation of species with time. Focused analyses of highly speciose clades are needed in order to disentangle the consequences of climate change, geography, and time. Here, we show that global cooling shapes the biodiversity of terrestrial orchids. Using a phylogeny of 1,475 species of Orchidoideae, the largest terrestrial orchid subfamily, we find that speciation rate is dependent on historic global cooling, not time, tropical distributions, elevation, variation in chromosome number, or other types of historic climate change. Relative to the gradual accumulation of species with time, models specifying speciation driven by historic global cooling are over 700 times more likely. Evidence ratios estimated for 212 other plant and animal groups reveal that terrestrial orchids represent one of the best-supported cases of temperature-spurred speciation yet reported. Employing >2.5 million georeferenced records, we find that global cooling drove contemporaneous diversification in each of the seven major orchid bioregions of the Earth. With current emphasis on understanding and predicting the immediate impacts of global warming, our study provides a clear case study of the long-term impacts of global climate change on biodiversity.
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Affiliation(s)
- Jamie B. Thompson
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
| | - Katie E. Davis
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | - Harry O. Dodd
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
| | - Matthew A. Wills
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
| | - Nicholas K. Priest
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, BathBA2 7AY, United Kingdom
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3
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Blaimer BB, Santos BF, Cruaud A, Gates MW, Kula RR, Mikó I, Rasplus JY, Smith DR, Talamas EJ, Brady SG, Buffington ML. Key innovations and the diversification of Hymenoptera. Nat Commun 2023; 14:1212. [PMID: 36869077 PMCID: PMC9984522 DOI: 10.1038/s41467-023-36868-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most diverse animal lineages, but whether specific key innovations have contributed to its diversification is still unknown. We assembled the largest time-calibrated phylogeny of Hymenoptera to date and investigated the origin and possible correlation of particular morphological and behavioral innovations with diversification in the order: the wasp waist of Apocrita; the stinger of Aculeata; parasitoidism, a specialized form of carnivory; and secondary phytophagy, a reversal to plant-feeding. Here, we show that parasitoidism has been the dominant strategy since the Late Triassic in Hymenoptera, but was not an immediate driver of diversification. Instead, transitions to secondary phytophagy (from parasitoidism) had a major influence on diversification rate in Hymenoptera. Support for the stinger and the wasp waist as key innovations remains equivocal, but these traits may have laid the anatomical and behavioral foundations for adaptations more directly associated with diversification.
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Affiliation(s)
- Bonnie B Blaimer
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany.
- National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA.
| | - Bernardo F Santos
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Center for Integrative Biodiversity Discovery, Invalidenstraße 43, Berlin, 10115, Germany
- National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Astrid Cruaud
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - Michael W Gates
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Robert R Kula
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - István Mikó
- Department of Biological Sciences, University of New Hampshire, Durham, NH, USA
| | - Jean-Yves Rasplus
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | - David R Smith
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Elijah J Talamas
- Florida State Collection of Arthropods, Division of Plant Industry, Florida Department of Agriculture and Consumer Services, 1911 SW 34th St, Gainesville, FL, 32608, USA
| | - Seán G Brady
- National Museum of Natural History, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
| | - Matthew L Buffington
- Systematic Entomology Laboratory, USDA-ARS, c/o NMNH, Smithsonian Institution, 10th & Constitution Ave. NW, Washington, DC, USA
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4
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Scott JE. Variation in macroevolutionary dynamics among extant primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022; 179:405-416. [PMCID: PMC9826261 DOI: 10.1002/ajpa.24622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/05/2022] [Accepted: 09/03/2022] [Indexed: 09/25/2023]
Abstract
Objectives This study examines how speciation and extinction rates vary across primates, with a focus on the recent macroevolutionary dynamics that have shaped extant primate biodiversity. Materials and methods Lineage‐specific macroevolutionary rates were estimated for each tip in a tree containing 307 species using a hidden‐state likelihood model. Differences in tip rates among major clades were evaluated using phylogenetic ANOVA. Differences among diurnal, nocturnal, and cathemeral lineages were also evaluated, based on previous work indicating that activity pattern influences primate diversification. Results Rate variation in extant primates is low within clades and high between clades. As in previous studies, cercopithecoids stand out in having high net diversification rates, driven by high speciation rates and very low extinction rates. Platyrrhines combine high speciation and high extinction rates, giving them high rates of lineage turnover. Strepsirrhines and tarsiids have low rates of speciation, extinction, turnover, and net diversification. Hominoids are intermediate between platyrrhines and the strepsirrhine‐tarsiid group, and there is evidence for differentiation between hominids and hylobatids. Diurnal lineages have significantly higher speciation rates than nocturnal lineages. Conclusions Recent anthropoid macroevolution has been characterized by marked variation in diversification dynamics among clades. Strepsirrhines and tarsiids are more uniform, despite divergent evolutionary and biogeographic histories. Higher speciation rates in diurnal lineages may be driven by greater ecological opportunity or reliance on visual signals for mate recognition. However, the differences among anthropoids indicate that factors other than activity pattern (e.g., clade competition, historical contingency) have had a more influential role in shaping recent primate diversification.
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Affiliation(s)
- Jeremiah E. Scott
- Department of Medical Anatomical Sciences, College of Osteopathic Medicine of the PacificWestern University of Health SciencesPomonaCaliforniaUSA
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5
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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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Vasconcelos T, O'Meara BC, Beaulieu JM. A flexible method for estimating tip diversification rates across a range of speciation and extinction scenarios. Evolution 2022; 76:1420-1433. [PMID: 35661352 DOI: 10.1111/evo.14517] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/08/2022] [Indexed: 01/21/2023]
Abstract
Estimates of diversification rates at the tips of a phylogeny provide a flexible approach for correlation analyses with multiple traits and to map diversification rates in space while also avoiding the uncertainty of deep time rate reconstructions. Available methods for tip rate estimation make different assumptions, and thus their accuracy usually depends on the characteristics of the underlying model generating the tree. Here, we introduce MiSSE, a trait-free, state-dependent speciation and extinction approach that can be used to estimate varying speciation, extinction, net diversification, turnover, and extinction fractions at the tips of the tree. We compare the accuracy of tip rates inferred by MiSSE against similar methods and demonstrate that, due to certain characteristics of the model, the error is generally low across a broad range of speciation and extinction scenarios. MiSSE can be used alongside regular phylogenetic comparative methods in trait-related diversification hypotheses, and we also describe a simple correction to avoid pseudoreplication from sister tips in analyses of independent contrasts. Finally, we demonstrate the capabilities of MiSSE, with a renewed focus on classic comparative methods, to examine the correlation between plant height and turnover rates in eucalypts, a species-rich lineage of flowering plants.
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Affiliation(s)
- Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701
| | - Brian C O'Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Jeremy M Beaulieu
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, 72701
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7
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Louca S, Henao-Diaz LF, Pennell M. The scaling of diversification rates with age is likely explained by sampling bias. Evolution 2022; 76:1625-1637. [PMID: 35567800 DOI: 10.1111/evo.14515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/07/2022] [Indexed: 01/22/2023]
Abstract
Numerous phylogenetic studies reported the existence of a pervasive scaling relationship between the ages of extant eukaryotic clades and their estimated diversification rates. The causes of this age-rate-scaling (ARS), whether biological and/or artifactual, remain unresolved. Here we fit diversification models to thousands of eukaryotic time-calibrated phylogenies to explore multiple potential causes of the ARS including parameter non-identifiability, model inadequacy, biases in taxonomic practice, and an important and ubiquitous form of sampling bias-preferentially analyzing larger extant clades. We distinguish between two mechanism by which such sampling biases can cause an ARS: First, by favoring clades that happen to be unusually large merely by chance (i.e., due to the stochastic nature of the cladogenic process), thus leading to rate overestimation, and second, by favoring clades that have truly higher diversification rates. We find that, of the proposed explanations, only sampling biases are likely to contribute to the observed ARS. We develop methods for fully correcting for sampling bias mechanism 1, and find that despite these corrections a substantial ARS remains. We then confirm using simulations that preferring trees with truly higher rates (mechanism 2) likely explains this residual ARS. Since we do not have a completely unbiased sample of clades, including extinct ones, for phylogenetic analyses, it is difficult to demonstrate unambiguously that sampling biases are the sole cause of the ARS. Sampling biases are, however, a parsimonious and plausible explanation for this widely observed macroevolutionary pattern, and this has implications for how we interpret the distribution of diversification rate estimates in extant clades.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - L Francisco Henao-Diaz
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
| | - Matt Pennell
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada.,Department of Zoology, University of British Columbia, Vancouver, Canada
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8
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Beck RM, Voss RS, Jansa SA. Craniodental Morphology and Phylogeny of Marsupials. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2022. [DOI: 10.1206/0003-0090.457.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Robin M.D. Beck
- School of Science, Engineering and Environment University of Salford, U.K. School of Biological, Earth & Environmental Sciences University of New South Wales, Australia Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Robert S. Voss
- Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History
| | - Sharon A. Jansa
- Bell Museum and Department of Ecology, Evolution, and Behavior University of Minnesota
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9
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Perez‐Lamarque B, Öpik M, Maliet O, Afonso Silva AC, Selosse M, Martos F, Morlon H. Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont. Mol Ecol 2022; 31:3496-3512. [PMID: 35451535 PMCID: PMC9321572 DOI: 10.1111/mec.16478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/15/2022] [Accepted: 04/17/2022] [Indexed: 11/30/2022]
Abstract
Analysing diversification dynamics is key to understanding the past evolutionary history of clades that led to present-day biodiversity patterns. While such analyses are widespread in well-characterized groups of species, they are much more challenging in groups for which diversity is mostly known through molecular techniques. Here, we use the largest global database on the small subunit (SSU) rRNA gene of Glomeromycotina, a subphylum of microscopic arbuscular mycorrhizal fungi that provide mineral nutrients to most land plants by forming one of the oldest terrestrial symbioses, to analyse the diversification dynamics of this clade in the past 500 million years. We perform a range of sensitivity analyses and simulations to control for potential biases linked to the nature of the data. We find that Glomeromycotina tend to have low speciation rates compared to other eukaryotes. After a peak of speciations between 200 and 100 million years ago, they experienced an important decline in speciation rates toward the present. Such a decline could be at least partially related to a shrinking of their mycorrhizal niches and to their limited ability to colonize new niches. Our analyses identify patterns of diversification in a group of obligate symbionts of major ecological and evolutionary importance and illustrate that short molecular markers combined with intensive sensitivity analyses can be useful for studying diversification dynamics in microbial groups.
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Affiliation(s)
- Benoît Perez‐Lamarque
- Institut de biologie de l’École normale supérieure (IBENS)École Normale SupérieureCNRSINSERMUniversité PSLParisFrance
- Institut de Systématique, Évolution, Biodiversité (ISYEB)Muséum National d’histoire NaturelleCNRSSorbonne UniversitéEPHE, UA, CP39ParisFrance
| | | | - Odile Maliet
- Institut de biologie de l’École normale supérieure (IBENS)École Normale SupérieureCNRSINSERMUniversité PSLParisFrance
| | - Ana C. Afonso Silva
- Institut de biologie de l’École normale supérieure (IBENS)École Normale SupérieureCNRSINSERMUniversité PSLParisFrance
- University of LilleCNRS, UMR 8198 ‐ Evo‐Eco‐PaleoLilleFrance
| | - Marc‐André Selosse
- Institut de Systématique, Évolution, Biodiversité (ISYEB)Muséum National d’histoire NaturelleCNRSSorbonne UniversitéEPHE, UA, CP39ParisFrance
- Department of Plant Taxonomy and Nature ConservationUniversity of GdanskGdanskPoland
| | - Florent Martos
- Institut de Systématique, Évolution, Biodiversité (ISYEB)Muséum National d’histoire NaturelleCNRSSorbonne UniversitéEPHE, UA, CP39ParisFrance
| | - Hélène Morlon
- Institut de biologie de l’École normale supérieure (IBENS)École Normale SupérieureCNRSINSERMUniversité PSLParisFrance
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10
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Moen DS. Improving inference and avoiding overinterpretation of hidden-state diversification models: Specialized plant breeding has no effect on diversification in frogs. Evolution 2021; 76:373-384. [PMID: 34854483 DOI: 10.1111/evo.14406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 11/30/2022]
Abstract
The hidden-state speciation and extinction (HiSSE) model helps avoid spurious results when testing whether a character affects diversification rates. However, care must be taken to optimally analyze models and interpret results. Recently, Tonini et al. (TEA hereafter) studied anuran (frog and toad) diversification with HiSSE methods. They concluded that their focal state, breeding in phytotelmata, increases net diversification rates. Yet this conclusion is counterintuitive, because the state that purportedly increases net diversification rates is 14 times rarer among species than the alternative. Herein, I revisit TEA's analyses and demonstrate problems with inferring model likelihoods, conducting post hoc tests, and interpreting results. I also reevaluate their top models and find that diverse strategies are necessary to reach the parameter values that maximize each model's likelihood. In contrast to TEA, I find no support for an effect of phytotelm breeding on net diversification rates in Neotropical anurans. In particular, even though the most highly supported models include the focal character, averaging parameter estimates over hidden states shows that the focal character does not influence diversification rates. Finally, I suggest ways to better analyze and interpret complex diversification models-both state-dependent and beyond-for future studies in other organisms.
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Affiliation(s)
- Daniel S Moen
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, 74078
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11
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Melo BF, Albert JS, Dagosta FCP, Tagliacollo VA. Biogeography of curimatid fishes reveals multiple lowland-upland river transitions and differential diversification in the Neotropics (Teleostei, Curimatidae). Ecol Evol 2021; 11:15815-15832. [PMID: 34824792 PMCID: PMC8601890 DOI: 10.1002/ece3.8251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 09/13/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
The Neotropics harbors a megadiverse ichthyofauna comprising over 6300 species with approximately 80% in just three taxonomic orders within the clade Characiphysi. This highly diverse group has evolved in tropical South America over tens to hundreds of millions of years influenced mostly by re-arrangements of river drainages in lowland and upland systems. In this study, we investigate patterns of spatial diversification in Neotropical freshwater fishes in the family Curimatidae, a species-rich clade of the order Characiformes. Specifically, we examined ancestral areas, dispersal events, and shifts in species richness using spatially explicit biogeographic and macroevolutionary models to determine whether lowlands-uplands serve as museums or cradles of diversification for curimatids. We used fossil information to estimate divergence times in BEAST, multiple time-stratified models of geographic range evolution in BioGeoBEARS, and alternative models of geographic state-dependent speciation and extinction in GeoHiSSE. Our results suggest that the most recent common ancestor of curimatids originated in the Late Cretaceous likely in lowland paleodrainages of northwestern South America. Dispersals from lowland to upland river basins of the Brazilian and Guiana shields occurred repeatedly across independently evolving lineages in the Cenozoic. Colonization of upland drainages was often coupled with increased rates of net diversification in species-rich genera such as Cyphocharax and Steindachnerina. Our findings demonstrate that colonization of novel aquatic environments at higher elevations is associated with an increased rate of diversification, although this pattern is clade-dependent and driven mostly by allopatric speciation. Curimatids reinforce an emerging perspective that Amazonian lowlands act as a museum by accumulating species along time, whereas the transitions to uplands stimulate higher net diversification rates and lineage diversification.
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Affiliation(s)
- Bruno F. Melo
- Department of IchthyologyAmerican Museum of Natural HistoryNew YorkNew YorkUSA
| | - James S. Albert
- Department of BiologyUniversity of Louisiana at LafayetteLafayetteLouisianaUSA
| | - Fernando C. P. Dagosta
- Faculdade de Ciências Biológicas e AmbientaisUniversidade Federal da Grande DouradosDouradosBrazil
| | - Victor A. Tagliacollo
- Museu de ZoologiaUniversidade de São PauloSão PauloBrazil
- Instituto de BiologiaUniversidade Federal de UberlândiaUberlândiaBrazil
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12
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Benson RBJ, Butler R, Close RA, Saupe E, Rabosky DL. Biodiversity across space and time in the fossil record. Curr Biol 2021; 31:R1225-R1236. [PMID: 34637736 DOI: 10.1016/j.cub.2021.07.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fossil record is the primary source of information on how biodiversity has varied in deep time, providing unique insight on the long-term dynamics of diversification and their drivers. However, interpretations of fossil record diversity patterns have been much debated, with a traditional focus on global diversity through time. Problems arise because the fossil record is spatially and temporally patchy, so 'global' diversity estimates actually represent the summed diversity across a set of geographically and environmentally distinct regions that vary substantially in number and identity through time. Furthermore, a focus on global diversity lumps the signal of ecological drivers at local and regional scales with the signal of global-scale processes, including variation in the distribution of environments and in provincialism (the extent of subdivision into distinct biogeographic regions). These signals cannot be untangled by studying global diversity measures alone. These conceptual and empirical concerns necessitate a shift away from the study of 'biodiversity through time' and towards the study of 'biodiversity across time and space'. Spatially explicit investigations, including analyses of local- and regional-scale datasets, are central to achieving this and allow analysis of geographic scale, location and the environmental parameters directly experienced by organisms. So far, research in this area has revealed the stability of species richness variation among environments through time, and the potential climatic and Earth-system drivers of changing biodiversity. Ultimately, this research program promises to address key questions regarding the assembly of biodiversity, and the contributions of local-, regional- and global-scale processes to the diversification of life on Earth.
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Affiliation(s)
- Roger B J Benson
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK.
| | - Richard Butler
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roger A Close
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Erin Saupe
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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13
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Louca S, Pennell MW. Why extinction estimates from extant phylogenies are so often zero. Curr Biol 2021; 31:3168-3173.e4. [PMID: 34019824 DOI: 10.1016/j.cub.2021.04.066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/11/2021] [Accepted: 04/26/2021] [Indexed: 12/18/2022]
Abstract
Time-calibrated phylogenies of extant species ("extant timetrees") are widely used to estimate historical speciation and extinction rates by fitting stochastic birth-death models.1 These approaches have long been controversial, as many phylogenetic studies report zero extinction in many taxa, contradicting the high extinction rates seen in the fossil record and the fact that the majority of species ever to have existed are now extinct.2-9 To date, the causes of this discrepancy remain unresolved. Here, we provide a novel and simple explanation for these "zero-inflated" extinction estimates, based on the recent discovery that there exist many alternative "congruent" diversification scenarios that cannot be distinguished based solely on extant timetrees.10 Due to such congruencies, estimation methods tend to converge to some scenario congruent to (i.e., statistically indistinguishable from) the true diversification scenario, but not necessarily to the true diversification scenario itself. This congruent scenario may exhibit negative extinction rates, a biologically meaningless but mathematically feasible situation, in which case estimators will tend to stick to the boundary of zero extinction. Based on this explanation, we make multiple testable predictions, which we confirm using analyses of simulated trees and 121 empirical trees. In contrast to other proposed mechanisms for erroneous extinction rate estimates,5,11-14 our proposed mechanism specifically explains the zero inflation of previous extinction rate estimates in the absence of detectable model violations, even for large trees. Not only do our results likely resolve a long-standing mystery in phylogenetics, they demonstrate that model congruencies can have severe consequences in practice.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, 1210 University of Oregon, Eugene, OR 97403, USA; Institute of Ecology and Evolution, University of Oregon, 5289 University of Oregon, Eugene, OR 97403, USA.
| | - Matthew W Pennell
- Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC V6T1Z4, Canada; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T1Z4, Canada.
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14
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Černý D, Madzia D, Slater GJ. Empirical and Methodological Challenges to the Model-Based Inference of Diversification Rates in Extinct Clades. Syst Biol 2021; 71:153-171. [PMID: 34110409 DOI: 10.1093/sysbio/syab045] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 02/01/2023] Open
Abstract
Changes in speciation and extinction rates are key to the dynamics of clade diversification, but attempts to infer them from phylogenies of extant species face challenges. Methods capable of synthesizing information from extant and fossil species have yielded novel insights into diversification rate variation through time, but little is known about their behavior when analyzing entirely extinct clades. Here, we use empirical and simulated data to assess how two popular methods, PyRate and Fossil BAMM, perform in this setting. We inferred the first tip-dated trees for ornithischian dinosaurs, and combined them with fossil occurrence data to test whether the clade underwent an end-Cretaceous decline. We then simulated phylogenies and fossil records under empirical constraints to determine whether macroevolutionary and preservation rates can be teased apart under paleobiologically realistic conditions. We obtained discordant inferences about ornithischian macroevolution including a long-term speciation rate decline (BAMM), mostly flat rates with a steep diversification drop (PyRate) or without one (BAMM), and episodes of implausibly accelerated speciation and extinction (PyRate). Simulations revealed little to no conflation between speciation and preservation, but yielded spuriously correlated speciation and extinction estimates while time-smearing tree-wide shifts (BAMM) or overestimating their number (PyRate). Our results indicate that the small phylogenetic datasets available to vertebrate paleontologists and the assumptions made by current model-based methods combine to yield potentially unreliable inferences about the diversification of extinct clades. We provide guidelines for interpreting the results of the existing approaches in light of their limitations, and suggest how the latter may be mitigated.
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Affiliation(s)
- David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA
| | - Daniel Madzia
- Institute of Paleobiology, Polish Academy of Sciences, Warsaw 00-818, Poland
| | - Graham J Slater
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA
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15
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Stireman JO, Cerretti P, O’hara JE, Moulton JK. Extraordinary diversification of the “bristle flies” (Diptera: Tachinidae) and its underlying causes. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The family Tachinidae (“bristle flies”) is the most diverse and ecologically important group of insect parasitoids outside the parasitic wasps. It is among the most species rich families of flies (Diptera) and has experienced a recent adaptive radiation across the globe. We make use of a molecular phylogeny of the family to examine its rapid radiation and explore the traits of tachinid lineages that may have contributed to variation in their diversification. We apply a range of diversification analyses to assess the consistency and robustness of effects. We find that the Tachinidae are among the most rapidly diversifying families of animals. Six to eight clades of bristle flies, distributed across the phylogeny, exhibit strong evidence of accelerated diversification. Our results suggest that the use of holometabolous insect larvae, and specifically caterpillars (Lepidoptera), as hosts, is associated with increased diversification rates. However, these effects were inconsistent across analyses. We detected little influence of oviposition strategy (egg type) or host feeding habit, and we recovered evidence that unmeasured “hidden” traits may explain greater variance in diversification. We evaluated the strengths and weaknesses of different Maximum Likelihood and Bayesian approaches for analysing diversification and the potential for extrinsic factors, such as geography, to influence patterns of richness and diversification. In general, we conclude that although certain traits may provide opportunities for diversification, whether this is capitalized on may depend on additional traits and/or historical contingency.
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Affiliation(s)
- John O Stireman
- Department of Biological Sciences, Wright State University, Dayton, OH, USA
| | - Pierfilippo Cerretti
- Dipartimento di Biologia e Biotecnologie ‘Charles Darwin’, ‘Sapienza’ Università di Roma, Piazzale A. Moro 5, Rome, Italy
- Australian National Insect Collection, CSIRO National Facilities and Collections, Black Mountain, Canberra, Australia
| | - James E O’hara
- Canadian National Collection of Insects, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - John K Moulton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
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16
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Cally JG, Stuart-Fox D, Holman L, Dale J, Medina I. Male-biased sexual selection, but not sexual dichromatism, predicts speciation in birds. Evolution 2021; 75:931-944. [PMID: 33559135 DOI: 10.1111/evo.14183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/13/2021] [Indexed: 01/04/2023]
Abstract
Sexual selection is thought to shape phylogenetic diversity by affecting speciation or extinction rates. However, the net effect of sexual selection on diversification is hard to predict because many of the hypothesized effects on speciation or extinction have opposing signs and uncertain magnitudes. Theoretical work also suggests that the net effect of sexual selection on diversification should depend strongly on ecological factors, though this prediction has seldom been tested. Here, we test whether variation in sexual selection can predict speciation and extinction rates across passerine birds (up to 5812 species, covering most genera) and whether this relationship is mediated by environmental factors. Male-biased sexual selection, and specifically sexual size dimorphism, predicted two of the three measures of speciation rates that we examined. The link we observed between sexual selection and speciation was independent of environmental variability, though species with smaller ranges had higher speciation rates. There was no association between any proxies of sexual selection and extinction rate. Our findings support the view that male-biased sexual selection, as measured by frequent predictors of male-male competition, has shaped diversification in the largest radiation of birds.
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Affiliation(s)
- Justin G Cally
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Devi Stuart-Fox
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Luke Holman
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - James Dale
- School of Natural and Computational Sciences, Massey University (Albany Campus), Auckland, 0632, New Zealand
| | - Iliana Medina
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3052, Australia
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17
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Bonaccorso E, Rodríguez-Saltos CA, Freile JF, Peñafiel N, Rosado-Llerena L, Oleas NH. Recent diversification in the high Andes: unveiling the evolutionary history of the Ecuadorian hillstar, Oreotrochilus chimborazo(Apodiformes: Trochilidae). Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AbstractStudying the genetic signatures of evolutionary diversification in young lineages is among the most promising approaches for unveiling the processes behind speciation. Here, we focus on Oreotrochilus chimborazo, a high Andean species of hummingbird that might have experienced rapid diversification in the recent past. To understand the evolution of this species, we generated a dataset of ten microsatellite markers and complementary data on morphometrics, plumage variation and ecological niches. We applied a series of population and coalescent-based analyses to understand the population structure and differentiation within the species, in addition to the signatures of current and historical gene flow, the location of potential contact zones and the relationships among lineages. We found that O. chimborazo comprises three genetic groups: one corresponding to subspecies O. c. chimborazo, from Chimborazo volcano and surroundings, and two corresponding to the northern and southern ranges of subspecies O. c. jamesonii, found from the extreme south of Colombia to southern Ecuador. We inferred modest levels of both contemporary and historical gene flow and proposed the location of a contact zone between lineages. Also, our coalescent-based analyses supported a rapid split among these three lineages during the mid-to-late Holocene. We discuss our results in the light of past and present potential distributions of the species, in addition to evolutionary trends seen in other Andean hummingbirds.
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Affiliation(s)
- Elisa Bonaccorso
- Universidad San Francisco de Quito, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biología Evolutiva, and Instituto Biósfera, Diego de Robles y Pampite, Quito, Ecuador
- Instituto Biósfera, Universidad San Francisco de Quito, Diego de Robles y Pampite, Quito, Ecuador
- Universidad Tecnológica Indoamérica, Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Machala y Sabanilla, Quito, Ecuador
| | | | - Juan F Freile
- Comité Ecuatoriano de Registros Ornitológicos, Pasaje El Moro E4-216 y Norberto Salazar, Tumbaco, Ecuador
| | - Nicolás Peñafiel
- Universidad Tecnológica Indoamérica, Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Machala y Sabanilla, Quito, Ecuador
- Biology Department, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada AIB
| | - Laura Rosado-Llerena
- Universidad San Francisco de Quito, Colegio de Ciencias Biológicas y Ambientales, Laboratorio de Biología Evolutiva, and Instituto Biósfera, Diego de Robles y Pampite, Quito, Ecuador
| | - Nora H Oleas
- Universidad Tecnológica Indoamérica, Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb) e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Machala y Sabanilla, Quito, Ecuador
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18
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Jamie GA, Meier JI. The Persistence of Polymorphisms across Species Radiations. Trends Ecol Evol 2020; 35:795-808. [DOI: 10.1016/j.tree.2020.04.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/08/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
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19
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Condamine FL, Nel A, Grandcolas P, Legendre F. Fossil and phylogenetic analyses reveal recurrent periods of diversification and extinction in dictyopteran insects. Cladistics 2020; 36:394-412. [PMID: 34619806 DOI: 10.1111/cla.12412] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2020] [Indexed: 01/22/2023] Open
Abstract
Variations of speciation and extinction rates determine the fate of clades through time. Periods of high diversification and extinction (possibly mass-extinction events) can punctuate the evolutionary history of various clades, but they remain loosely defined for many biological groups, especially nonmarine invertebrates like insects. Here, we examine whether the cockroaches, mantises and termites (altogether included in Dictyoptera) have experienced episodic pulses of speciation or extinction and how these pulses may be associated with environmental fluctuations or mass extinctions. We relied on molecular phylogeny and fossil data to shed light on the times and rates at which dictyopterans diversified. The diversification of Dictyoptera has alternated between (i) periods of high diversification in the late Carboniferous, Early-Middle Triassic, Early Cretaceous and middle Palaeogene, and (ii) periods of high extinction rates particularly at the Permian-Triassic boundary, but not necessarily correlated with the major global biodiversity crises as in the mid-Cretaceous. This study advocates the importance of analyzing, when possible, both molecular phylogeny and fossil data to unveil diversification and extinction periods for a given group. The causes and consequences of extinction must be studied beyond mass-extinction events alone to gain a broader understanding of how clades wax and wane.
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Affiliation(s)
- Fabien L Condamine
- CNRS, UMR 5554 Institut des Sciences de l'Évolution de Montpellier (Université de Montpellier
- CNRS
- IRD
- EPHE), Place Eugène Bataillon, 34095, Montpellier, France
| | - André Nel
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Philippe Grandcolas
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Frédéric Legendre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, SU, EPHE, UA, 57 rue Cuvier, 75231, Paris Cedex 05, France
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20
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Sun M, Folk RA, Gitzendanner MA, Soltis PS, Chen Z, Soltis DE, Guralnick RP. Estimating rates and patterns of diversification with incomplete sampling: a case study in the rosids. AMERICAN JOURNAL OF BOTANY 2020; 107:895-909. [PMID: 32519354 PMCID: PMC7384126 DOI: 10.1002/ajb2.1479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 03/03/2020] [Indexed: 05/03/2023]
Abstract
PREMISE Recent advances in generating large-scale phylogenies enable broad-scale estimation of species diversification. These now common approaches typically are characterized by (1) incomplete species coverage without explicit sampling methodologies and/or (2) sparse backbone representation, and usually rely on presumed phylogenetic placements to account for species without molecular data. We used empirical examples to examine the effects of incomplete sampling on diversification estimation and provide constructive suggestions to ecologists and evolutionary biologists based on those results. METHODS We used a supermatrix for rosids and one well-sampled subclade (Cucurbitaceae) as empirical case studies. We compared results using these large phylogenies with those based on a previously inferred, smaller supermatrix and on a synthetic tree resource with complete taxonomic coverage. Finally, we simulated random and representative taxon sampling and explored the impact of sampling on three commonly used methods, both parametric (RPANDA and BAMM) and semiparametric (DR). RESULTS We found that the impact of sampling on diversification estimates was idiosyncratic and often strong. Compared to full empirical sampling, representative and random sampling schemes either depressed or inflated speciation rates, depending on methods and sampling schemes. No method was entirely robust to poor sampling, but BAMM was least sensitive to moderate levels of missing taxa. CONCLUSIONS We suggest caution against uncritical modeling of missing taxa using taxonomic data for poorly sampled trees and in the use of summary backbone trees and other data sets with high representative bias, and we stress the importance of explicit sampling methodologies in macroevolutionary studies.
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Affiliation(s)
- Miao Sun
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijing100093China
- Department of BioscienceAarhus UniversityAarhus8000Denmark
| | - Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippi39762USA
| | - Matthew A. Gitzendanner
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32608USA
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary BotanyInstitute of BotanyChinese Academy of SciencesBeijing100093China
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Department of BiologyUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFlorida32608USA
| | - Robert P. Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFlorida32611USA
- Biodiversity InstituteUniversity of FloridaGainesvilleFlorida32611USA
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21
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Patton AH, Margres MJ, Epstein B, Eastman J, Harmon LJ, Storfer A. Hybridizing salamanders experience accelerated diversification. Sci Rep 2020; 10:6566. [PMID: 32300150 PMCID: PMC7162952 DOI: 10.1038/s41598-020-63378-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/23/2020] [Indexed: 11/09/2022] Open
Abstract
Whether hybridization generates or erodes species diversity has long been debated, but to date most studies have been conducted at small taxonomic scales. Salamanders (order Caudata) represent a taxonomic order in which hybridization plays a prevalent ecological and evolutionary role. We employed a recently developed model of trait-dependent diversification to test the hypothesis that hybridization impacts the diversification dynamics of species that are currently hybridizing. We find strong evidence supporting this hypothesis, showing that hybridizing salamander lineages have significantly greater net-diversification rates than non-hybridizing lineages. This pattern is driven by concurrently increased speciation rates and decreased extinction rates in hybridizing lineages. Our results support the hypothesis that hybridization can act as a generative force in macroevolutionary diversification.
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Affiliation(s)
- Austin H Patton
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.
| | - Mark J Margres
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.,Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, 02138, USA
| | - Brendan Epstein
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA.,University of Minnesota, College of Biological Sciences, Saint Paul, MN, 55108, USA
| | | | - Luke J Harmon
- University of Idaho, Department of Biological Sciences and IBEST, Moscow, ID, 83844, USA
| | - Andrew Storfer
- Washington State University, School of Biological Sciences, Pullman, WA, 99164, USA
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22
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Igea J, Tanentzap AJ. Angiosperm speciation cools down in the tropics. Ecol Lett 2020; 23:692-700. [PMID: 32043734 PMCID: PMC7078993 DOI: 10.1111/ele.13476] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/05/2020] [Accepted: 01/19/2020] [Indexed: 01/05/2023]
Abstract
Recent evidence has questioned whether the Latitudinal Diversity Gradient (LDG), whereby species richness increases towards the Equator, results in higher rates of speciation in the tropics. Allowing for time heterogeneity in speciation rate estimates for over 60,000 angiosperm species, we found that the LDG does not arise from variation in speciation rates because lineages do not speciate faster in the tropics. These results were consistently retrieved using two other methods to test the association between occupancy of tropical habitats and speciation rates. Our speciation rate estimates were robust to the effects of both undescribed species and missing taxa. Overall, our results show that speciation rates follow an opposite pattern to global variation in species richness. Greater ecological opportunity in the temperate zones, stemming from less saturated communities, higher species turnover or greater environmental change, may ultimately explain these results.
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Affiliation(s)
- Javier Igea
- Department of Plant SciencesUniversity of CambridgeDowning StCambridgeCB2 3EAUK
| | - Andrew J. Tanentzap
- Department of Plant SciencesUniversity of CambridgeDowning StCambridgeCB2 3EAUK
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23
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Corush JB. Evolutionary patterns of diadromy in fishes: more than a transitional state between marine and freshwater. BMC Evol Biol 2019; 19:168. [PMID: 31412761 PMCID: PMC6694556 DOI: 10.1186/s12862-019-1492-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 07/31/2019] [Indexed: 12/20/2022] Open
Abstract
Background Across the tree of life there are numerous evolutionary transitions between different habitats (i.e., aquatic and terrestrial or marine and freshwater). Many of these dramatic evolutionary shifts parallel developmental shifts that require physiological, anatomical and behavioral changes for survival and reproduction. Diadromy (scheduled movement between marine and freshwater) has been characterized as a behavior that acts as an evolutionary intermediate state between marine and freshwater environments, implying that diadromous lineages are evolutionarily transient. This hypothesis comes with assumptions regarding the rates of evolutionary transitions in and out of diadromy as well as rates of speciation and extinction in diadromous fishes. Results Based on a published phylogeny of 7822 species of ray-finned fishes, state speciation and extinction models of evolutionary transition between marine, freshwater, and diadromous species suggest transition rates out of diadromy are 5–100 times higher that transition between marine and freshwater or into diadromy. Additionally, high speciation and low extinction rates separate diadromous fishes from marine and freshwater species. As a result, net diversification (net diversification = speciation – extinction) is about 7–40 times higher in diadromous fishes compared to freshwater and marine respectively. Together the transition, speciation, and extinction rates suggest diadromy is the least stable of the three states. Conclusion Evolutionary transitions to diadromy are rare in fishes. However, once established, diversification rates in diadromous lineages are high compared to both marine and freshwater species. Diadromous lineages tend to be more transient than marine or freshwater lineages and are found to give rise to marine and freshwater specialists in addition to diadromous descendants. Although diadromy is not a necessary evolutionary intermediate between marine and freshwater, these results support the interpretation of diadromy as an important, occasionally intermediate state, that contributes to biodiversity in fishes in all environments. This evolutionary instability of diadromous lineages is counteracted by their relatively high diversification rates. These findings highlight the importance of integrating the dynamics of diversification and major evolutionary transitions for understanding macroevolutionary patterns. Electronic supplementary material The online version of this article (10.1186/s12862-019-1492-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joel B Corush
- Department of Ecology and Evolutionary Biology, University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996, USA.
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24
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Wessinger CA, Rausher MD, Hileman LC. Adaptation to hummingbird pollination is associated with reduced diversification in Penstemon. Evol Lett 2019; 3:521-533. [PMID: 31636944 PMCID: PMC6791294 DOI: 10.1002/evl3.130] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/12/2019] [Accepted: 07/12/2019] [Indexed: 12/24/2022] Open
Abstract
A striking characteristic of the Western North American flora is the repeated evolution of hummingbird pollination from insect-pollinated ancestors. This pattern has received extensive attention as an opportunity to study repeated trait evolution as well as potential constraints on evolutionary reversibility, with little attention focused on the impact of these transitions on species diversification rates. Yet traits conferring adaptation to divergent pollinators potentially impact speciation and extinction rates, because pollinators facilitate plant reproduction and specify mating patterns between flowering plants. Here, we examine macroevolutionary processes affecting floral pollination syndrome diversity in the largest North American genus of flowering plants, Penstemon. Within Penstemon, transitions from ancestral bee-adapted flowers to hummingbird-adapted flowers have frequently occurred, although hummingbird-adapted species are rare overall within the genus. We inferred macroevolutionary transition and state-dependent diversification rates and found that transitions from ancestral bee-adapted flowers to hummingbird-adapted flowers are associated with reduced net diversification rate, a finding based on an estimated 17 origins of hummingbird pollination in our sample. Although this finding is congruent with hypotheses that hummingbird adaptation in North American Flora is associated with reduced species diversification rates, it contrasts with studies of neotropical plant families where hummingbird pollination has been associated with increased species diversification. We further used the estimated macroevolutionary rates to predict the expected pattern of floral diversity within Penstemon over time, assuming stable diversification and transition rates. Under these assumptions, we find that hummingbird-adapted species are expected to remain rare due to their reduced diversification rates. In fact, current floral diversity in the sampled Penstemon lineage, where less than one-fifth of species are hummingbird adapted, is consistent with predicted levels of diversity under stable macroevolutionary rates.
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Affiliation(s)
- Carolyn A Wessinger
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas 66045
| | - Mark D Rausher
- Department of Biology Duke University Durham North Carolina 27708
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology University of Kansas Lawrence Kansas 66045
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25
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A Nearly Complete Juvenile Skull of the Marsupial Sparassocynus derivatus from the Pliocene of Argentina, the Affinities of “Sparassocynids”, and the Diversification of Opossums (Marsupialia; Didelphimorphia; Didelphidae). J MAMM EVOL 2019. [DOI: 10.1007/s10914-019-09471-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Marin J, Hedges SB. Undersampling Genomes has Biased Time and Rate Estimates Throughout the Tree of Life. Mol Biol Evol 2019; 35:2077-2084. [PMID: 29846659 DOI: 10.1093/molbev/msy103] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Genomic data drive evolutionary research on the relationships and timescale of life but the genomes of most species remain poorly sampled. Phylogenetic trees can be reconstructed reliably using small data sets and the same has been assumed for the estimation of divergence time with molecular clocks. However, we show here that undersampling of molecular data results in a bias expressed as disproportionately shorter branch lengths and underestimated divergence times in the youngest nodes and branches, termed the small sample artifact. In turn, this leads to increasing speciation and diversification rates towards the present. Any evolutionary analyses derived from these biased branch lengths and speciation rates will be similarly biased. The widely used timetrees of the major species-rich studies of amphibians, birds, mammals, and squamate reptiles are all data-poor and show upswings in diversification rate, suggesting that their results were biased by undersampling. Our results show that greater sampling of genomes is needed for accurate time and rate estimation, which are basic data used in ecological and evolutionary research.
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Affiliation(s)
- Julie Marin
- Center for Biodiversity, 502 SERC Building, Temple University, Philadelphia, PA
- Institut de Systématique, Evolution, Biodiversité UMR 7205, Département Systématique et Evolution, Muséum national d'Histoire naturelle, Sorbonne-Universités, Paris Cedex 05 75231, France
| | - S Blair Hedges
- Center for Biodiversity, 502 SERC Building, Temple University, Philadelphia, PA
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Czekanski-Moir JE, Rundell RJ. The Ecology of Nonecological Speciation and Nonadaptive Radiations. Trends Ecol Evol 2019; 34:400-415. [DOI: 10.1016/j.tree.2019.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 01/08/2023]
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28
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Varga T, Krizsán K, Földi C, Dima B, Sánchez-García M, Sánchez-Ramírez S, Szöllősi GJ, Szarkándi JG, Papp V, Albert L, Andreopoulos W, Angelini C, Antonín V, Barry KW, Bougher NL, Buchanan P, Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Dämon W, Desjardin D, Finy P, Geml J, Haridas S, Hughes K, Justo A, Karasiński D, Kautmanova I, Kiss B, Kocsubé S, Kotiranta H, LaButti KM, Lechner BE, Liimatainen K, Lipzen A, Lukács Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C, Rácz N, Riley R, Savchenko A, Shiryaev A, Soop K, Spirin V, Szebenyi C, Tomšovský M, Tulloss RE, Uehling J, Grigoriev IV, Vágvölgyi C, Papp T, Martin FM, Miettinen O, Hibbett DS, Nagy LG. Megaphylogeny resolves global patterns of mushroom evolution. Nat Ecol Evol 2019; 3:668-678. [PMID: 30886374 PMCID: PMC6443077 DOI: 10.1038/s41559-019-0834-1] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/30/2019] [Indexed: 01/27/2023]
Abstract
Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most niches and fulfil diverse roles in the ecosystem, including wood decomposers, pathogens or mycorrhizal mutualists. Despite the importance of mushroom-forming fungi, large-scale patterns of their evolutionary history are poorly known, in part due to the lack of a comprehensive and dated molecular phylogeny. Here, using multigene and genome-based data, we assemble a 5,284-species phylogenetic tree and infer ages and broad patterns of speciation/extinction and morphological innovation in mushroom-forming fungi. Agaricomycetes started a rapid class-wide radiation in the Jurassic, coinciding with the spread of (sub)tropical coniferous forests and a warming climate. A possible mass extinction, several clade-specific adaptive radiations and morphological diversification of fruiting bodies followed during the Cretaceous and the Paleogene, convergently giving rise to the classic toadstool morphology, with a cap, stalk and gills (pileate-stipitate morphology). This morphology is associated with increased rates of lineage diversification, suggesting it represents a key innovation in the evolution of mushroom-forming fungi. The increase in mushroom diversity started during the Mesozoic-Cenozoic radiation event, an era of humid climate when terrestrial communities dominated by gymnosperms and reptiles were also expanding.
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Affiliation(s)
- Torda Varga
- Synthetic and Systems Biology Unit, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Krisztina Krizsán
- Synthetic and Systems Biology Unit, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Csenge Földi
- Synthetic and Systems Biology Unit, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Bálint Dima
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | | | | | - Gergely J Szöllősi
- MTA-ELTE 'Lendület' Evolutionary Genomics Research Group, Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - János G Szarkándi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Viktor Papp
- Department of Botany, Faculty of Horticultural Science, Szent István University, Budapest, Hungary
| | | | | | - Claudio Angelini
- Via Cappuccini 78, Pordenone, Italy
- Jardin Botanico Nacional Ma. Moscoso, Santo Domingo, Dominican Republic
| | | | - Kerrie W Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Neale L Bougher
- Science and Conservation, Department of Biodiversity, Western Australian Herbarium, Kensington, WA, Australia
| | | | - Bart Buyck
- Institut de Systématique, Evolution, Biodiversité (ISYEB-UMR 7205), Muséum National d'Histoire Naturelle, Sorbonne Université, CNRS, Paris, France
| | - Viktória Bense
- Synthetic and Systems Biology Unit, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Pam Catcheside
- State Herbarium of South Australia, Adelaide, South Australia, Australia
| | - Mansi Chovatia
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jerry Cooper
- Manaaki Whenua-Landcare Research, Lincoln, New Zealand
| | | | - Dennis Desjardin
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Péter Finy
- Zsombolyai u. 56., Székesfehérvár, Hungary
| | - József Geml
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Karen Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | | | - Dariusz Karasiński
- Department of Mycology, W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Ivona Kautmanova
- Natural History Museum, Slovak National Museum, Bratislava, Slovakia
| | - Brigitta Kiss
- Synthetic and Systems Biology Unit, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Heikki Kotiranta
- Biodiversity Unit, Finnish Environment Institute, Helsinki, Finland
| | - Kurt M LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Bernardo E Lechner
- Instituto de Micología y Botánica, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Sirma Mihaltcheva
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Louis N Morgado
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| | | | | | - Robin A Ohm
- Department of Biology, Microbiology, Utrecht University, Utrecht, the Netherlands
| | - Beatriz Ortiz-Santana
- Center for Forest Mycology Research, Northern Research Station, US Forest Service, Madison, WI, USA
| | - Clark Ovrebo
- Department of Biology, University of Central Oklahoma, Edmond, OK, USA
| | - Nikolett Rácz
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anton Savchenko
- Botanical Museum, University of Helsinki, Helsinki, Finland
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Anton Shiryaev
- Institute of Plant and Animal Ecology, Russian Academy of Sciences, Ekaterinburg, Russia
| | - Karl Soop
- Department of Cryptogamic Botany, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Csilla Szebenyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- MTA-SZTE 'Lendulet' Fungal Pathogenicity Mechanisms Research Group, Szeged, Hungary
| | - Michal Tomšovský
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - Rodham E Tulloss
- Herbarium Rooseveltensis Amanitarum, Roosevelt, NJ, USA
- The New York Botanical Garden, New York, NY, USA
| | - Jessie Uehling
- Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- MTA-SZTE 'Lendulet' Fungal Pathogenicity Mechanisms Research Group, Szeged, Hungary
| | - Francis M Martin
- Institut National de la Recherche Agronomique, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems, Champenoux, France
| | - Otto Miettinen
- Botanical Museum, University of Helsinki, Helsinki, Finland
| | | | - László G Nagy
- Synthetic and Systems Biology Unit, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.
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29
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Davies TJ. The macroecology and macroevolution of plant species at risk. THE NEW PHYTOLOGIST 2019; 222:708-713. [PMID: 30485443 DOI: 10.1111/nph.15612] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/12/2018] [Indexed: 05/19/2023]
Abstract
Contents Summary 708 I. Introduction 708 II. Fossils and phylogenies: learning from our past 708 III. Threatened species and Red Lists 710 IV. The geography of threat 710 V. The taxonomy of threat 710 VI. Predicting species at risk 711 VII. Conclusion 711 Acknowledgements 712 References 712 SUMMARY: Current rates of extinction are unprecedented in human history. The fossil record and newer molecular phylogenies illuminate historical patterns of speciation and extinction. They reveal both spectacular radiations and the characteristic features of mass extinction events in our geological past. The IUCN Red List provides insight into present-day species declines. There is emerging synthesis that species at risk are nonrandomly distributed across space and phylogeny. This pattern may be explained by geographical variation in driver intensity and species differential sensitivities. However, traits that confer resistance to one global change driver may increase susceptibility to a different driver. A complete understanding of extinction risk requires consideration of the interaction between extinction drivers, ecological traits, and species' evolutionary histories.
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Affiliation(s)
- T Jonathan Davies
- Departments of Botany, Forest & Conservation Sciences, Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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30
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Abstract
For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an incredible variety of organismal traits. Here we analyze a large collection of phylogenetic trees and fossil time series and describe a hidden generality among these seemingly idiosyncratic results: speciation and extinction rates follow a scaling law in which both depend on the age of the group in which they are measured, with the fastest rates in the youngest clades. Using a series of simulations and sensitivity analyses, we demonstrate that the time dependency is unlikely to be a result of simple statistical artifacts. As such, this time scaling is likely a genuine feature of the tree of life, hinting that the dynamics of biodiversity over deep time may be driven in part by surprisingly simple and general principles.
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Sarver BA, Pennell MW, Brown JW, Keeble S, Hardwick KM, Sullivan J, Harmon LJ. The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. PeerJ 2019; 7:e6334. [PMID: 30886768 PMCID: PMC6421065 DOI: 10.7717/peerj.6334] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/23/2018] [Indexed: 11/20/2022] Open
Abstract
Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.
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Affiliation(s)
- Brice A.J. Sarver
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - Matthew W. Pennell
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Joseph W. Brown
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Sara Keeble
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Kayla M. Hardwick
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - Jack Sullivan
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - Luke J. Harmon
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
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Watanabe A, Gignac PM, Balanoff AM, Green TL, Kley NJ, Norell MA. Are endocasts good proxies for brain size and shape in archosaurs throughout ontogeny? J Anat 2019; 234:291-305. [PMID: 30506962 PMCID: PMC6365484 DOI: 10.1111/joa.12918] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2018] [Indexed: 12/21/2022] Open
Abstract
Cranial endocasts, or the internal molds of the braincase, are a crucial correlate for investigating the neuroanatomy of extinct vertebrates and tracking brain evolution through deep time. Nevertheless, the validity of such studies pivots on the reliability of endocasts as a proxy for brain morphology. Here, we employ micro-computed tomography imaging, including diffusible iodine-based contrast-enhanced CT, and a three-dimensional geometric morphometric framework to examine both size and shape differences between brains and endocasts of two exemplar archosaur taxa - the American alligator (Alligator mississippiensis) and the domestic chicken (Gallus gallus). With ontogenetic sampling, we quantitatively evaluate how endocasts differ from brains and whether this deviation changes during development. We find strong size and shape correlations between brains and endocasts, divergent ontogenetic trends in the brain-to-endocast correspondence between alligators and chickens, and a comparable magnitude between brain-endocast shape differences and intraspecific neuroanatomical variation. The results have important implications for paleoneurological studies in archosaurs. Notably, we demonstrate that the pattern of endocranial shape variation closely reflects brain shape variation. Therefore, analyses of endocranial morphology are unlikely to generate spurious conclusions about large-scale trends in brain size and shape. To mitigate any artifacts, however, paleoneurological studies should consider the lower brain-endocast correspondence in the hindbrain relative to the forebrain; higher size and shape correspondences in chickens than alligators throughout postnatal ontogeny; artificially 'pedomorphic' shape of endocasts relative to their corresponding brains; and potential biases in both size and shape data due to the lack of control for ontogenetic stages in endocranial sampling.
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Affiliation(s)
- Akinobu Watanabe
- Department of AnatomyNew York Institute of Technology College of Osteopathic MedicineOld WestburyNYUSA
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNYUSA
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of Life Sciences Vertebrates DivisionNatural History MuseumLondonUK
| | - Paul M. Gignac
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNYUSA
- Department of Anatomy and Cell BiologyOklahoma State University Center for Health SciencesTulsaOKUSA
| | - Amy M. Balanoff
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNYUSA
- Center for Functional Anatomy and EvolutionJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Todd L. Green
- Department of Anatomy and Cell BiologyOklahoma State University Center for Health SciencesTulsaOKUSA
| | - Nathan J. Kley
- Department of Anatomical SciencesStony Brook UniversityStony BrookNYUSA
| | - Mark A. Norell
- Division of PaleontologyAmerican Museum of Natural HistoryNew YorkNYUSA
- Richard Gilder Graduate SchoolAmerican Museum of Natural HistoryNew YorkNYUSA
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33
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Title PO, Rabosky DL. Tip rates, phylogenies and diversification: What are we estimating, and how good are the estimates? Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13153] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pascal O. Title
- Department of Ecology and Evolutionary Biology and Museum of ZoologyUniversity of Michigan Ann Arbor Michigan
- Environmental Resilience InstituteIndiana University Bloomington Indiana
| | - Daniel L. Rabosky
- Department of Ecology and Evolutionary Biology and Museum of ZoologyUniversity of Michigan Ann Arbor Michigan
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Igea J, Tanentzap AJ. Multiple macroevolutionary routes to becoming a biodiversity hotspot. SCIENCE ADVANCES 2019; 5:eaau8067. [PMID: 30775437 PMCID: PMC6365113 DOI: 10.1126/sciadv.aau8067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/21/2018] [Indexed: 05/28/2023]
Abstract
Why is species diversity so unevenly distributed across different regions on Earth? Regional differences in biodiversity may stem from differences in rates of speciation and dispersal and colonization times, but these hypotheses have rarely been tested simultaneously at a global scale. Our study reveals the macroevolutionary routes that have generated hotspots of mammal and bird biodiversity by analyzing the tempo and mode of diversification and dispersal within major biogeographic realms. Hotspots in tropical realms had higher rates of speciation, whereas those in temperate realms received more immigrant species from their surrounding regions. We also found that hotspots had higher spatial complexity and energy availability, providing a link between the environment and macroevolutionary history. Our study highlights how assessing differences in macroevolutionary history can help to explain why biodiversity varies so much worldwide.
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Affiliation(s)
- J. Igea
- Corresponding author. (J.I.); (A.J.T.)
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Marin J, Rapacciuolo G, Costa GC, Graham CH, Brooks TM, Young BE, Radeloff VC, Behm JE, Helmus MR, Hedges SB. Evolutionary time drives global tetrapod diversity. Proc Biol Sci 2019; 285:rspb.2017.2378. [PMID: 29436494 DOI: 10.1098/rspb.2017.2378] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/17/2018] [Indexed: 11/12/2022] Open
Abstract
Global variation in species richness is widely recognized, but the explanation for what drives it continues to be debated. Previous efforts have focused on a subset of potential drivers, including evolutionary rate, evolutionary time (maximum clade age of species restricted to a region), dispersal (migration from one region to another), ecological factors and climatic stability. However, no study has evaluated these competing hypotheses simultaneously at a broad spatial scale. Here, we examine their relative contribution in determining the richness of the most comprehensive dataset of tetrapods to our knowledge (84% of the described species), distinguishing between the direct influences of evolutionary rate, evolutionary time and dispersal, and the indirect influences of ecological factors and climatic stability through their effect on direct factors. We found that evolutionary time exerted a primary influence on species richness, with evolutionary rate being of secondary importance. By contrast, dispersal did not significantly affect richness patterns. Ecological and climatic stability factors influenced species richness indirectly by modifying evolutionary time (i.e. persistence time) and rate. Overall, our findings suggest that global heterogeneity in tetrapod richness is explained primarily by the length of time species have had to diversify.
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Affiliation(s)
- Julie Marin
- Center for Biodiversity, Temple University, 502 SERC Building, 1925 N. 12th Street, Philadelphia, PA 19122, USA .,Institut de Systématique, Evolution, Biodiversité UMR 7205, Département Systématique et Evolution, Muséum national d'Histoire naturelle, Sorbonne-Universités, 75231 Paris Cedex 05, France
| | - Giovanni Rapacciuolo
- Life and Environmental Sciences, University of California Merced, 5200 N Lake Road, Merced, CA 95340, USA.,NatureServe, 4600 N. Fairfax Drive, 7th Floor, Arlington, VA 22203, USA
| | - Gabriel C Costa
- Department of Biology, Auburn University at Montgomery, Montgomery, AL 36124, USA
| | - Catherine H Graham
- Swiss Federal Institute for Forest Snow and Landscape, Birmensdorf, Switzerland
| | - Thomas M Brooks
- International Union for Conservation of Nature, Gland, Switzerland.,World Agroforestry Center (ICRAF), University of the Philippines Los Baños, Laguna 4031, Philippines.,Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7001, Australia
| | - Bruce E Young
- NatureServe, 4600 N. Fairfax Drive, 7th Floor, Arlington, VA 22203, USA
| | - Volker C Radeloff
- SILVIS Lab, Department of Forestry and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jocelyn E Behm
- Center for Biodiversity, Temple University, 502 SERC Building, 1925 N. 12th Street, Philadelphia, PA 19122, USA.,Department of Animal Ecology, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Matthew R Helmus
- Center for Biodiversity, Temple University, 502 SERC Building, 1925 N. 12th Street, Philadelphia, PA 19122, USA
| | - S Blair Hedges
- Center for Biodiversity, Temple University, 502 SERC Building, 1925 N. 12th Street, Philadelphia, PA 19122, USA
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36
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Kayondo HW, Mwalili S, Mango JM. Inferring Multi-Type Birth-Death Parameters for a Structured Host Population with Application to HIV Epidemic in Africa. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/cmb.2019.94009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mitchell JS, Etienne RS, Rabosky DL. Inferring Diversification Rate Variation From Phylogenies With Fossils. Syst Biol 2018; 68:1-18. [PMID: 29788398 DOI: 10.1093/sysbio/syy035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification-extinction rates in particular-can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of extant and extinct species. The model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree. We implemented the model in BAMM, a computational framework that uses reversible jump Markov chain Monte Carlo to simulate a posterior distribution of macroevolutionary rate regimes conditional on the branching times and topology of a phylogeny. The implementation, we describe can be applied to paleontological phylogenies, neontological phylogenies, and to phylogenies that include both extant and extinct taxa. We evaluate performance of the model on data sets simulated under a range of diversification scenarios. We find that speciation rates are reliably inferred in the absence of paleontological data. However, the inclusion of fossil observations substantially increases the accuracy of extinction rate estimates. We demonstrate that inferences are relatively robust to at least some violations of model assumptions, including heterogeneity in preservation rates and misspecification of the number of occurrences in paleontological data sets.
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Affiliation(s)
- Jonathan S Mitchell
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
- Department of Biology, West Virginia University Institute of Technology, 410 Neville Street, Beckley, WV 25801, USA
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700 CC Groningen, The Netherlands
| | - Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Avenue, Ann Arbor, Michigan 48109 USA
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38
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Beck RMD, Baillie C. Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny. Proc Biol Sci 2018; 285:20181632. [PMID: 30963896 PMCID: PMC6304057 DOI: 10.1098/rspb.2018.1632] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/23/2018] [Indexed: 01/16/2023] Open
Abstract
Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.
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Affiliation(s)
- Robin M. D. Beck
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
| | - Charles Baillie
- School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, UK
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39
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Rabosky DL. Phylogenies and Diversification Rates: Variance Cannot Be Ignored. Syst Biol 2018; 68:538-550. [DOI: 10.1093/sysbio/syy079] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 11/16/2018] [Accepted: 11/17/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, Biological Sciences Building, 1105 North University Avenue, University of Michigan, Ann Arbor, MI 48109, USA
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Murray EA, Bossert S, Danforth BN. Pollinivory and the diversification dynamics of bees. Biol Lett 2018; 14:rsbl.2018.0530. [PMID: 30429246 PMCID: PMC6283915 DOI: 10.1098/rsbl.2018.0530] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 10/19/2018] [Indexed: 11/23/2022] Open
Abstract
Pollinivory—the consumption of pollen rather than arthropod prey—is a defining feature of bees (Anthophila; the flower lovers). In virtually all bee species, larvae consume a diet composed of pollen mixed with nectar or floral oils. Bees arose from within a group of solitary, carnivorous, apoid wasps in the Early to Mid-Cretaceous, coincident with the rapid rise of flowering plants. It is assumed that the switch from carnivory to pollen-feeding was a key innovation that led to the rapid diversification of bees, but this has never been examined empirically. Here, we explore the hypothesis that pollinivory led to the increased diversification of bees. In contrast to common perception, we find that the switch to pollen-feeding per se does not explain their extensive diversification. Rather, our results indicate that pollinivory was a necessary but not sufficient condition for diversification, and that other complementary innovations, such as a broadening of host-plant diet, allowed the diversification of the major bee lineages. Our results have broad implications for understanding tempo and mode of bee diversification dynamics in light of their floral resources.
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Affiliation(s)
| | - Silas Bossert
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
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41
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Lewitus E, Bittner L, Malviya S, Bowler C, Morlon H. Clade-specific diversification dynamics of marine diatoms since the Jurassic. Nat Ecol Evol 2018; 2:1715-1723. [PMID: 30349092 PMCID: PMC6217985 DOI: 10.1038/s41559-018-0691-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023]
Abstract
Diatoms are one of the most abundant and diverse groups of phytoplankton and play a major role in marine ecosystems and the Earth's biogeochemical cycles. Here we combine DNA metabarcoding data from the Tara Oceans expedition with palaeoenvironmental data and phylogenetic models of diversification to analyse the diversity dynamics of marine diatoms. We reveal a primary effect of variation in carbon dioxide partial pressure (pCO2) on early diatom diversification, followed by a major burst of diversification in the late Eocene epoch, after which diversification is chiefly affected by sea level, an influx of silica availability and competition with other planktonic groups. Our results demonstrate a remarkable heterogeneity of diversification dynamics across diatoms and suggest that a changing climate will favour some clades at the expense of others.
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Affiliation(s)
- Eric Lewitus
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, Université PSL, Paris, France.
- US Military HIV Research Program, WRAIR, Silver Spring, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA.
| | - Lucie Bittner
- Sorbonne Université, Université des Antilles, CNRS, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Paris, France
| | - Shruti Malviya
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, Université PSL, Paris, France
- Tata Institute of Fundamental Research, Bangalore, India
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Hélène Morlon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, Université PSL, Paris, France
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42
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Lewitus E, Morlon H. Detecting Environment-Dependent Diversification From Phylogenies: A Simulation Study and Some Empirical Illustrations. Syst Biol 2018; 67:576-593. [PMID: 29272547 DOI: 10.1093/sysbio/syx095] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 12/11/2017] [Indexed: 01/30/2023] Open
Abstract
Understanding the relative influence of various abiotic and biotic variables on diversification dynamics is a major goal of macroevolutionary studies. Recently, phylogenetic approaches have been developed that make it possible to estimate the role of various environmental variables on diversification using time-calibrated species trees, paleoenvironmental data, and maximum-likelihood techniques. These approaches have been effectively employed to estimate how speciation and extinction rates vary with key abiotic variables, such as temperature and sea level, and we can anticipate that they will be increasingly used in the future. Here we compile a series of biotic and abiotic paleodatasets that can be used as explanatory variables in these models and use simulations to assess the statistical properties of the approach when applied to these paleodatasets. We demonstrate that environment-dependent models perform well in recovering environment-dependent speciation and extinction parameters, as well as in correctly identifying the simulated environmental model when speciation is environment-dependent. We explore how the strength of the environment-dependency, tree size, missing taxa, and characteristics of the paleoenvironmental curves influence the performance of the models. Finally, using these models, we infer environment-dependent diversification in two empirical phylogenies: temperature-dependence in Cetacea and $\delta^{13}C$-dependence in Ruminantia. We illustrate how to evaluate the relative importance of abiotic and biotic variables in these two clades and interpret these results in light of macroevolutionary hypotheses. Given the important role paleoenvironments are presumed to have played in species evolution, our statistical assessment of how environment-dependent models behave is crucial for their utility in macroevolutionary analysis.
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Affiliation(s)
- Eric Lewitus
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Hélène Morlon
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
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43
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Singhal S, Huang H, Grundler MR, Marchán-Rivadeneira MR, Holmes I, Title PO, Donnellan SC, Rabosky DL. Does Population Structure Predict the Rate of Speciation? A Comparative Test across Australia’s Most Diverse Vertebrate Radiation. Am Nat 2018; 192:432-447. [DOI: 10.1086/699515] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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44
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Budd GE, Mann RP. History is written by the victors: The effect of the push of the past on the fossil record. Evolution 2018; 72:2276-2291. [PMID: 30257040 PMCID: PMC6282550 DOI: 10.1111/evo.13593] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 09/01/2018] [Indexed: 02/05/2023]
Abstract
Survivorship biases can generate remarkable apparent rate heterogeneities through time in otherwise homogeneous birth‐death models of phylogenies. They are a potential explanation for many striking patterns seen in the fossil record and molecular phylogenies. One such bias is the “push of the past”: clades that survived a substantial length of time are likely to have experienced a high rate of early diversification. This creates the illusion of a secular rate slow‐down through time that is, rather, a reversion to the mean. An extra effect increasing early rates of lineage generation is also seen in large clades. These biases are important but relatively neglected influences on many aspects of diversification patterns in the fossil record and elsewhere, such as diversification spikes after mass extinctions and at the origins of clades; they also influence rates of fossilization, changes in rates of phenotypic evolution and even molecular clocks. These inevitable features of surviving and/or large clades should thus not be generalized to the diversification process as a whole without additional study of small and extinct clades, and raise questions about many of the traditional explanations of the patterns seen in the fossil record.
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Affiliation(s)
- Graham E Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, Uppsala, SE 752 36, Sweden
| | - Richard P Mann
- Department of Statistics, School of Mathematics, University of Leeds, Leeds LS2 9JT, United Kingdom
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Eberle J, Dimitrov D, Valdez-Mondragón A, Huber BA. Microhabitat change drives diversification in pholcid spiders. BMC Evol Biol 2018; 18:141. [PMID: 30231864 PMCID: PMC6145181 DOI: 10.1186/s12862-018-1244-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 08/16/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Microhabitat changes are thought to be among the main drivers of diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we investigate the influence of microhabitat on diversification rates in pholcid spiders (Araneae, Pholcidae). Diversification analyses were conducted in the framework of the largest molecular phylogeny of pholcid spiders to date based on three nuclear and three mitochondrial loci from 600 species representing more than 85% of the currently described pholcid genera. RESULTS Assessments of ancestral microhabitat revealed frequent evolutionary change. In particular, within the largest subfamily Pholcinae, numerous changes from near-ground habitats towards leaves and back were found. In general, taxa occupying leaves and large sheltered spaces had higher diversification rates than ground-dwelling taxa. Shifts in speciation rate were found in leaf- and space-dwelling taxa. CONCLUSIONS Our analyses result in one of the most comprehensive phylogenies available for a major spider family and provide a framework for any subsequent studies of pholcid spider biology. Diversification analyses strongly suggest that microhabitat is an important factor influencing diversification patterns in pholcid spiders.
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Affiliation(s)
- Jonas Eberle
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
| | - Dimitar Dimitrov
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway
- Department of Natural History, University Museum of Bergen, University of Bergen, PO Box 7800, NO-5020 Bergen, Norway
| | - Alejandro Valdez-Mondragón
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
- Instituto de Biologia UNAM, sede Tlaxcala. Contiguo FES-Zaragoza Campus III, Ex Fábrica San Manuel de Morcom s/n, San Miguel Contla, Municipio de Santa Cruz Tlaxcala, C.P, 90640 Tlaxcala, Mexico
| | - Bernhard A. Huber
- Alexander Koenig Research Museum of Zoology, Adenauerallee 160, 53113 Bonn, Germany
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Warren BH, Hagen O, Gerber F, Thébaud C, Paradis E, Conti E. Evaluating alternative explanations for an association of extinction risk and evolutionary uniqueness in multiple insular lineages. Evolution 2018; 72:2005-2024. [DOI: 10.1111/evo.13582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/16/2018] [Accepted: 08/07/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Ben H. Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRSSorbonne Université EPHE, CP 51, 57 Rue Cuvier 75005 Paris France
- Department of Systematic and Evolutionary BotanyUniversity of Zurich Zollikerstrasse 107, 8008 Zurich Switzerland
| | - Oskar Hagen
- Swiss Federal Research Institute WSL 8903 Birmensdorf Switzerland
- Landscape EcologyInstitute of Terrestrial Ecosystems ETH Zurich 8092 Zurich Switzerland
| | - Florian Gerber
- Department of MathematicsUniversity of Zurich 8057 Zurich Switzerland
| | - Christophe Thébaud
- Laboratoire Evolution et Diversité BiologiqueUMR 5174 CNRS‐Université Paul Sabatier‐ENFA 31062 Toulouse Cedex 9 France
| | | | - Elena Conti
- Department of Systematic and Evolutionary BotanyUniversity of Zurich Zollikerstrasse 107, 8008 Zurich Switzerland
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47
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Sauquet H, Magallón S. Key questions and challenges in angiosperm macroevolution. THE NEW PHYTOLOGIST 2018; 219:1170-1187. [PMID: 29577323 DOI: 10.1111/nph.15104] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/05/2018] [Indexed: 05/26/2023]
Abstract
Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid diversification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm diversification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day biodiversity. We present six key questions that explore the origin and diversification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include diversification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for sampling bias and heterogeneity of macroevolutionary processes through time and among lineages; (2) the need for large and standardized synthetic databases of morphological variation; and (3) continuous effort on sampling the fossil record, but with a revolution in current paleobotanical practice.
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Affiliation(s)
- Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, 2000, Australia
- Laboratoire Écologie, Systématique, Évolution, Université Paris-Sud, CNRS, UMR 8079, Orsay, 91405, France
| | - Susana Magallón
- Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacán, México City, 04510, México
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48
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Burin G, Alencar LRV, Chang J, Alfaro ME, Quental TB. How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline? Syst Biol 2018; 68:47-62. [DOI: 10.1093/sysbio/syy037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/09/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- Gustavo Burin
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Laura R V Alencar
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Tiago B Quental
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
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49
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Rabosky DL. Phylogenetic tests for evolutionary innovation: the problematic link between key innovations and exceptional diversification. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0417. [PMID: 29061890 DOI: 10.1098/rstb.2016.0417] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2017] [Indexed: 11/12/2022] Open
Abstract
Evolutionary innovation contributes to the spectacular diversity of species and phenotypes across the tree of life. 'Key innovations' are widely operationalized within evolutionary biology as traits that facilitate increased diversification rates, such that lineages bearing the traits ultimately contain more species than closely related lineages lacking the focal trait. In this article, I briefly review the inference, analysis and interpretation of evolutionary innovation on phylogenetic trees. I argue that differential rates of lineage diversification should not be used as the basis for key innovation tests, despite the statistical tractability of such approaches. Under traditional interpretations of the macroevolutionary 'adaptive zone', we should not necessarily expect key innovations to confer faster diversification rates upon lineages that possess them relative to their extant sister clades. I suggest that a key innovation is a trait that allows a lineage to interact with the environment in a fundamentally different way and which, as a result, increases the total diversification-but not necessarily the diversification rate-of the parent clade. Considered alone, branching patterns in phylogenetic trees are poorly suited to the inference of evolutionary innovation due to their inherently low information content with respect to the processes that produce them. However, phylogenies may be important for identifying transformational shifts in ecological and morphological space that are characteristic of innovation at the macroevolutionary scale.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
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Affiliation(s)
- Daniel L Rabosky
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1079, USA
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50
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Landis JB, Soltis DE, Li Z, Marx HE, Barker MS, Tank DC, Soltis PS. Impact of whole-genome duplication events on diversification rates in angiosperms. AMERICAN JOURNAL OF BOTANY 2018; 105:348-363. [PMID: 29719043 DOI: 10.1002/ajb2.1060] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/12/2017] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Polyploidy or whole-genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants. METHODS Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms. We used a stepwise AIC approach (MEDUSA), a Bayesian mixture model approach (BAMM), and state-dependent diversification analyses (MuSSE) to investigate patterns of diversification. Sister-clade comparisons were used to investigate species richness after WGDs. KEY RESULTS Based on the density of 1KP taxon sampling, 106 WGDs were unambiguously placed on the angiosperm phylogeny. We identified 334-530 shifts in diversification rates. We found that 61 WGD events were tightly linked to changes in diversification rates, and state-dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD. Additionally, 70 of 99 WGD events showed an increase in species richness compared to the sister clade. CONCLUSIONS Forty-six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms. Shifts in diversification do not appear more likely than random within a four-node lag phase following a WGD; however, younger WGD events are more likely to be followed by an upshift in diversification than older WGD events.
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Affiliation(s)
- Jacob B Landis
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California, 92521, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Zheng Li
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
| | - Hannah E Marx
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, 83844, USA
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, 83844, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
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