1
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Quintero I, Lartillot N, Morlon H. Imbalanced speciation pulses sustain the radiation of mammals. Science 2024; 384:1007-1012. [PMID: 38815022 DOI: 10.1126/science.adj2793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
The evolutionary histories of major clades, including mammals, often comprise changes in their diversification dynamics, but how these changes occur remains debated. We combined comprehensive phylogenetic and fossil information in a new "birth-death diffusion" model that provides a detailed characterization of variation in diversification rates in mammals. We found an early rising and sustained diversification scenario, wherein speciation rates increased before and during the Cretaceous-Paleogene (K-Pg) boundary. The K-Pg mass extinction event filtered out more slowly speciating lineages and was followed by a subsequent slowing in speciation rates rather than rebounds. These dynamics arose from an imbalanced speciation process, with separate lineages giving rise to many, less speciation-prone descendants. Diversity seems to have been brought about by these isolated, fast-speciating lineages, rather than by a few punctuated innovations.
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Affiliation(s)
- Ignacio Quintero
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Nicolas Lartillot
- Université Claude Bernard Lyon 1, CNRS, VetAgroSup, LBBE, UMR 5558, F-69100 Villeurbanne, France
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
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2
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Chimento NR, Agnolín FL, García-Marsà J, Manabe M, Tsuihiji T, Novas FE. A large therian mammal from the Late Cretaceous of South America. Sci Rep 2024; 14:2854. [PMID: 38310138 PMCID: PMC10838296 DOI: 10.1038/s41598-024-53156-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/29/2024] [Indexed: 02/05/2024] Open
Abstract
Theria represent an extant clade that comprises placental and marsupial mammals. Here we report on the discovery of a new Late Cretaceous mammal from southern Patagonia, Patagomaia chainko gen. et sp. nov., represented by hindlimb and pelvic elements with unambiguous therian features. We estimate Patagomaia chainko attained a body mass of 14 kg, which is considerably greater than the 5 kg maximum body mass of coeval Laurasian therians. This new discovery demonstrates that Gondwanan therian mammals acquired large body size by the Late Cretaceous, preceding their Laurasian relatives, which remained small-bodied until the beginning of the Cenozoic. Patagomaia supports the view that the Southern Hemisphere was a cradle for the evolution of modern mammalian clades, alongside non-therian extinct groups such as meridiolestidans, gondwanatherians and monotremes.
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Affiliation(s)
- Nicolás R Chimento
- Laboratorio de Anatomía Comparada y Evolución de los Vertebrados (LACEV), Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Av. Ángel Gallardo 470, C1405DJR, Ciudad Autónoma de Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Federico L Agnolín
- Laboratorio de Anatomía Comparada y Evolución de los Vertebrados (LACEV), Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Av. Ángel Gallardo 470, C1405DJR, Ciudad Autónoma de Buenos Aires, Argentina
- Fundación de Historia Natural "Félix de Azara", Departamento de Ciencias Naturales y Antropología, CEBBAD - Universidad Maimónides, Hidalgo 767, C1405BDB, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jordi García-Marsà
- Laboratorio de Anatomía Comparada y Evolución de los Vertebrados (LACEV), Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Av. Ángel Gallardo 470, C1405DJR, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Makoto Manabe
- National Museum of Nature and Science, 4‑1‑1 Amakubo, Tsukuba, 305‑0005, Japan
| | - Takanobu Tsuihiji
- Department of Earth and Planetary Science, The University of Tokyo, 7‑3‑1 Hongo, Bunkyo-ku, Tokyo, 305‑0005, Japan
| | - Fernando E Novas
- Laboratorio de Anatomía Comparada y Evolución de los Vertebrados (LACEV), Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (MACN-CONICET), Av. Ángel Gallardo 470, C1405DJR, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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3
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Osozawa S. Geologically calibrated mammalian tree and its correlation with global events, including the emergence of humans. Ecol Evol 2023; 13:e10827. [PMID: 38116126 PMCID: PMC10728886 DOI: 10.1002/ece3.10827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/09/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
A robust timetree for Mammalia was constructed using the time calibration function of BEAST v1.10.4 and MEGA 11. The analysis involved the application of times of the most recent common ancestors, including a total of 19 mammalian fossil calibration ages following Benton et al. (Palaeontologia Electronica, 2015, 1-106) for their minimum ages. Additionally, fossil calibration ages for Gorilla, Pan, and a geologic event calibration age for otters were incorporated. Using these calibration ages, I constructed a geologically calibrated tree that estimates the age of the Homo and Pan splitting to be 5.69 Ma. The tree carries several significant implications. First, after the initial rifting at 120 Ma, the Atlantic Ocean expanded by over 500 km around Chron 34 (84 Ma), and vicariant speciation between Afrotheria (Africa) and Xenarthra (South America) appears to have commenced around 70 Ma. Additionally, ordinal level differentiations began immediately following the K-Pg boundary (66.0 Ma), supporting previous hypothesis that mammalian radiation rapidly filled ecological niches left vacant by non-avian dinosaurs. I constructed a diagram depicting the relationship between base substitution rate and age using an additional function in BEAST v1.10.4. The diagram reveals an exponential increase in the base substitution rate approaching recent times. This increased base substitution rate during the Neogene period may have contributed to the expansion of biodiversity, including the extensive adaptive radiation that led to the evolution of Homo sapiens. One significant driving factor behind this radiation could be attributed to the emergence and proliferation of C4 grasses since 20 Ma. These grasses have played a role in increasing carbon fixation, reducing atmospheric CO2 concentration, inducing global cooling, and initiating Quaternary glacial-interglacial cycles, thereby causing significant climatic changes.
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Affiliation(s)
- Soichi Osozawa
- Faculty of Science, Institute of Geology and PaleontologyTohoku UniversitySendaiJapan
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4
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Smyčka J, Toszogyova A, Storch D. The relationship between geographic range size and rates of species diversification. Nat Commun 2023; 14:5559. [PMID: 37689787 PMCID: PMC10492861 DOI: 10.1038/s41467-023-41225-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 08/24/2023] [Indexed: 09/11/2023] Open
Abstract
Range size is a universal characteristic of every biological species, and is often assumed to affect diversification rate. There are strong theoretical arguments that large-ranged species should have higher rates of diversification. On the other hand, the observation that small-ranged species are often phylogenetically clustered might indicate high diversification of small-ranged species. This discrepancy between theory and the data may be caused by the fact that typical methods of data analysis do not account for range size changes during speciation. Here we use a cladogenetic state-dependent diversification model applied to mammals to show that range size changes during speciation are ubiquitous and small-ranged species indeed diversify generally slower, as theoretically expected. However, both range size and diversification are strongly influenced by idiosyncratic and spatially localized events, such as colonization of an archipelago or a mountain system, which often override the general pattern of range size evolution.
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Affiliation(s)
- Jan Smyčka
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, CZ-11000, Prague, Czech Republic.
| | - Anna Toszogyova
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, CZ-11000, Prague, Czech Republic
| | - David Storch
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, CZ-11000, Prague, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, CZ-12844, Prague, Czech Republic
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5
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Liang X, Heath LS. Towards understanding paleoclimate impacts on primate de novo genes. G3 (BETHESDA, MD.) 2023; 13:jkad135. [PMID: 37313728 PMCID: PMC10468307 DOI: 10.1093/g3journal/jkad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/15/2023]
Abstract
De novo genes are genes that emerge as new genes in some species, such as primate de novo genes that emerge in certain primate species. Over the past decade, a great deal of research has been conducted regarding their emergence, origins, functions, and various attributes in different species, some of which have involved estimating the ages of de novo genes. However, limited by the number of species available for whole-genome sequencing, relatively few studies have focused specifically on the emergence time of primate de novo genes. Among those, even fewer investigate the association between primate gene emergence with environmental factors, such as paleoclimate (ancient climate) conditions. This study investigates the relationship between paleoclimate and human gene emergence at primate species divergence. Based on 32 available primate genome sequences, this study has revealed possible associations between temperature changes and the emergence of de novo primate genes. Overall, findings in this study are that de novo genes tended to emerge in the recent 13 MY when the temperature continues cooling, which is consistent with past findings. Furthermore, in the context of an overall trend of cooling temperature, new primate genes were more likely to emerge during local warming periods, where the warm temperature more closely resembled the environmental condition that preceded the cooling trend. Results also indicate that both primate de novo genes and human cancer-associated genes have later origins in comparison to random human genes. Future studies can be in-depth on understanding human de novo gene emergence from an environmental perspective as well as understanding species divergence from a gene emergence perspective.
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Affiliation(s)
- Xiao Liang
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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6
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Carlisle E, Janis CM, Pisani D, Donoghue PCJ, Silvestro D. A timescale for placental mammal diversification based on Bayesian modeling of the fossil record. Curr Biol 2023; 33:3073-3082.e3. [PMID: 37379845 DOI: 10.1016/j.cub.2023.06.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/21/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023]
Abstract
The timing of the placental mammal radiation has been the focus of debate over the efficacy of competing methods for establishing evolutionary timescales. Molecular clock analyses estimate that placental mammals originated before the Cretaceous-Paleogene (K-Pg) mass extinction, anywhere from the Late Cretaceous to the Jurassic. However, the absence of definitive fossils of placentals before the K-Pg boundary is compatible with a post-Cretaceous origin. Nevertheless, lineage divergence must occur before it can be manifest phenotypically in descendent lineages. This, combined with the non-uniformity of the rock and fossil records, requires the fossil record to be interpreted rather than read literally. To achieve this, we introduce an extended Bayesian Brownian bridge model that estimates the age of origination and, where applicable, extinction through a probabilistic interpretation of the fossil record. The model estimates the origination of placentals in the Late Cretaceous, with ordinal crown groups originating at or after the K-Pg boundary. The results reduce the plausible interval for placental mammal origination to the younger range of molecular clock estimates. Our findings support both the Long Fuse and Soft Explosive models of placental mammal diversification, indicating that the placentals originated shortly prior to the K-Pg mass extinction. The origination of many modern mammal lineages overlapped with and followed the K-Pg mass extinction.
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Affiliation(s)
- Emily Carlisle
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - Christine M Janis
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Davide Pisani
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Bristol Palaeobiology Group, School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland; Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland; Department of Biological and Environmental Sciences, University of Gothenburg, 413 19 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, 413 19 Gothenburg, Sweden.
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7
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Murali G, Meiri S, Roll U. Chemical signaling glands are unlinked to species diversification in lizards. Evolution 2023; 77:1829-1841. [PMID: 37279331 DOI: 10.1093/evolut/qpad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 05/17/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023]
Abstract
Sexual selection has long been thought to increase species diversification. Sexually selected traits, such as sexual signals that contribute to reproductive isolation, were thought to promote diversification. However, studies exploring links between sexually selected traits and species diversification have thus far primarily focused on visual or acoustic signals. Many animals often employ chemical signals (i.e., pheromones) for sexual communications, but large-scale analyses on the role of chemical communications in driving species diversification have been missing. Here, for the first time, we investigate whether traits associated with chemical communications-the presence of follicular epidermal glands-promote diversification across 6,672 lizard species. In most analyses, we found no strong association between the presence of follicular epidermal glands and species diversification rates, either across all lizard species or at lower phylogenetic scales. Previous studies suggest that follicular gland secretions act as species recognition signals that prevent hybridization during speciation in lizards. However, we show that geographic range overlap was no different in sibling species pairs with and without follicular epidermal glands. Together, these results imply that either follicular epidermal glands do not primarily function in sexual communications or sexually selected traits in general (here chemical communication) have a limited effect on species diversification. In our additional analysis accounting for sex-specific differences in glands, we again found no detectable effect of follicular epidermal glands on species diversification rates. Thus, our study challenges the general role of sexually selected traits in broad-scale species diversification patterns.
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Affiliation(s)
- Gopal Murali
- Jacob Blaustein Center for Scientific Cooperation, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Mitrani Department of Desert Ecology, The Swiss Institute for Dryland Environments and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States
| | - Shai Meiri
- School of Zoology and The Steinhardt Museum of Natural History, Tel Aviv University, Tel Aviv, Beersheva, Sede-Boqer Campus, 8499000, Israel
| | - Uri Roll
- Mitrani Department of Desert Ecology, The Swiss Institute for Dryland Environments and Energy Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
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8
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Verzi DH, De Santi NA, Olivares AI, Morgan CC, Basso NG, Brook F. A new species of the highly polytypic South American rodent Ctenomys increases the diversity of the magellanicus clade. VERTEBRATE ZOOLOGY 2023. [DOI: 10.3897/vz.73.e96656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
The subterranean rodent Ctenomys is the most polytypic South American mammal genus and one of the most speciose and rapidly diversifying mammal genera in the world. Its systematics is unstable due to the underlying accelerated diversification processes that give rise to evolutionary lineages at different stages of differentiation and to remarkable morphological homogeneity even among long-differentiated species. As a result, species boundaries are often difficult to define. Diversity of this genus in the coastal area of central Argentina has been extensively studied, with two independent lineages currently recognized while a distinct third population had not been previously detected. Through a phylogenetic analysis based on combined morphological and molecular evidence, Bayesian estimates of divergence times, and morphometric and morphological assessments, we recognize this third population as an independently evolving lineage. The new species, Ctenomys pulcersp. nov., is here described for both the living fauna and the fossil record of the Pampean region of central Argentina. According to phylogenetic results, Ctenomys pulcersp. nov. belongs to the essentially Patagonian magellanicus clade, and would have diverged from its sister species, Ctenomys bidaui, during the middle Pleistocene (ca. 0.4 Ma). Its current distribution in the fixed and semifixed dunes of the coastal Pampean region is assumed to represent a relict of a wider and continuous distribution of potentially suitable environments during the late Pleistocene. Ctenomys pulcersp. nov. occurs in a particularly fragile natural system subjected to profound disturbances caused by diverse anthropic actions and therefore measures for the conservation of its habitat will be indispensable.
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9
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Liow LH, Uyeda J, Hunt G. Cross-disciplinary information for understanding macroevolution. Trends Ecol Evol 2023; 38:250-260. [PMID: 36456381 DOI: 10.1016/j.tree.2022.10.013] [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: 07/04/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/30/2022]
Abstract
Many different macroevolutionary models can produce the same observations. Despite efforts in building more complex and realistic models, it may still be difficult to distinguish the processes that have generated the biodiversity we observe. In this opinion we argue that we can make new progress by reaching out across disciplines, relying on independent data and theory to constrain macroevolutionary inference. Using mainly paleontological insights and data, we illustrate how we can eliminate less plausible or implausible models, and/or parts of parameter space, while applying comparative phylogenetic approaches. We emphasize that such cross-disciplinary insights and data can be drawn between many other disciplines relevant to macroevolution. We urge cross-disciplinary training, and collaboration using common-use databases as a platform for increasing our understanding.
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Affiliation(s)
- Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo 0562, Norway.
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Gene Hunt
- Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
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10
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Phylogenetics and the Cenozoic radiation of lampreys. Curr Biol 2023; 33:397-404.e3. [PMID: 36586410 DOI: 10.1016/j.cub.2022.12.018] [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: 02/01/2022] [Revised: 10/13/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022]
Abstract
The development of a movable jaw is one of the most important transitions in the evolutionary history of animals.1 Jawed vertebrates rapidly diversified after appearing approximately 470 million years ago. Today, only lampreys and hagfishes represent the once dominant jawless grade2,3,4 and comprise less than 1% of living vertebrate species. Their relationship to other vertebrates ranks among the more contentious problems in animal phylogenetics.5,6,7,8,9,10,11,12 Further, the phylogenetic relationships within lampreys and hagfishes remain unclear,13,14,15 and the ages of their living lineages are largely unexplored.16,17 Because of their importance for the genomic and developmental changes that prefigured jawed vertebrate diversity,18,19,20,21 the evolutionary history of lampreys and hagfishes is a major frontier of organismal biology. Of these two clades, lampreys22 are more ecologically diverse, exhibiting freshwater, anadromous, and fully marine forms, as well as parasitic and nonparasitic species.23,24 Here, we present a new phylogeny and historical biogeographic reconstruction of all living lampreys. Whereas the early diversification of this clade tracks Pangaean fragmentation, lampreys also rapidly radiated in the northern hemisphere during the mid-Cretaceous and directly after the Cretaceous-Paleogene extinction. These radiations mirrored concurrent ones in other animals and plants and coincided with changes to lamprey ecology and feeding behavior. Our results suggest that 80% of living lamprey clades appeared in the last 20 million years of Earth history. Rather than gradually accumulating since the oldest stem-group forms appeared in the early Paleozoic, living lamprey biodiversity results from diversifications extending from the Cretaceous to present.
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11
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Santana SE, Grossnickle DM. Bursts in skull evolution weakened with time. Science 2022; 378:355-356. [DOI: 10.1126/science.add8460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The skull shapes of mammals diversified more rapidly early in their history
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Affiliation(s)
- Sharlene E. Santana
- Department of Biology, University of Washington, Seattle, WA, USA
- Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
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12
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Alternating regimes of shallow and deep-sea diversification explain a species-richness paradox in marine fishes. Proc Natl Acad Sci U S A 2022; 119:e2123544119. [PMID: 36252009 PMCID: PMC9618140 DOI: 10.1073/pnas.2123544119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The deep sea contains a surprising diversity of life, including iconic fish groups such as anglerfishes and lanternfishes. Still, >65% of marine teleost fish species are restricted to the photic zone <200 m, which comprises less than 10% of the ocean's total volume. From a macroevolutionary perspective, this paradox may be explained by three hypotheses: 1) shallow water lineages have had more time to diversify than deep-sea lineages, 2) shallow water lineages have faster rates of speciation than deep-sea lineages, or 3) shallow-to-deep sea transition rates limit deep-sea richness. Here we use phylogenetic comparative methods to test among these three non-mutually exclusive hypotheses. While we found support for all hypotheses, the disparity in species richness is better described as the uneven outcome of alternating phases that favored shallow or deep diversification over the past 200 million y. Shallow marine teleosts became incredibly diverse 100 million y ago during a period of warm temperatures and high sea level, suggesting the importance of reefs and epicontinental settings. Conversely, deep-sea colonization and speciation was favored during brief episodes when cooling temperatures increased the efficiency of the ocean's carbon pump. Finally, time-variable ecological filters limited shallow-to-deep colonization for much of teleost history, which helped maintain higher shallow richness. A pelagic lifestyle and large jaws were associated with early deep-sea colonists, while a demersal lifestyle and a tapered body plan were typical of later colonists. Therefore, we also suggest that some hallmark characteristics of deep-sea fishes evolved prior to colonizing the deep sea.
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13
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Abstract
Computational reconstruction of ancestral mammalian karyotypes revealed a comprehensive picture of the chromosome rearrangements that occurred over the evolutionary history of mammals. Ancient gene order, in some cases extending to full chromosomes, was found conserved for more than 300 My, demonstrating strong evolutionary constraint against rearrangements in some regions. Conserved segments of chromosomes are enriched for genes that control developmental processes. Therefore, Darwinian selection likely maintains ancient gene combinations while allowing for genomic innovations within or near chromosomal sites that break and rearrange over evolutionary time. The revealed relationship between the three-dimensional structure of chromosomes and the evolutionary stability of chromosome segments provides additional insights into the mechanisms of chromosome evolution and diseases associated with genome rearrangements. Decrypting the rearrangements that drive mammalian chromosome evolution is critical to understanding the molecular bases of speciation, adaptation, and disease susceptibility. Using 8 scaffolded and 26 chromosome-scale genome assemblies representing 23/26 mammal orders, we computationally reconstructed ancestral karyotypes and syntenic relationships at 16 nodes along the mammalian phylogeny. Three different reference genomes (human, sloth, and cattle) representing phylogenetically distinct mammalian superorders were used to assess reference bias in the reconstructed ancestral karyotypes and to expand the number of clades with reconstructed genomes. The mammalian ancestor likely had 19 pairs of autosomes, with nine of the smallest chromosomes shared with the common ancestor of all amniotes (three still conserved in extant mammals), demonstrating a striking conservation of synteny for ∼320 My of vertebrate evolution. The numbers and types of chromosome rearrangements were classified for transitions between the ancestral mammalian karyotype, descendent ancestors, and extant species. For example, 94 inversions, 16 fissions, and 14 fusions that occurred over 53 My differentiated the therian from the descendent eutherian ancestor. The highest breakpoint rate was observed between the mammalian and therian ancestors (3.9 breakpoints/My). Reconstructed mammalian ancestor chromosomes were found to have distinct evolutionary histories reflected in their rates and types of rearrangements. The distributions of genes, repetitive elements, topologically associating domains, and actively transcribed regions in multispecies homologous synteny blocks and evolutionary breakpoint regions indicate that purifying selection acted over millions of years of vertebrate evolution to maintain syntenic relationships of developmentally important genes and regulatory landscapes of gene-dense chromosomes.
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14
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Černý D, Natale R. Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes). Mol Phylogenet Evol 2022; 177:107620. [PMID: 36038056 DOI: 10.1016/j.ympev.2022.107620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 01/20/2023]
Abstract
Shorebirds (Charadriiformes) are a globally distributed clade of modern birds and, due to their ecological and morphological disparity, a frequent subject of comparative studies. While molecular phylogenies have been key to establishing the suprafamilial backbone of the charadriiform tree, a number of relationships at both deep and shallow taxonomic levels remain poorly resolved. The timescale of shorebird evolution also remains uncertain as a result of extensive disagreements among the published divergence dating studies, stemming largely from different choices of fossil calibrations. Here, we present the most comprehensive non-supertree phylogeny of shorebirds to date, based on a total-evidence dataset comprising 353 ingroup taxa (90% of all extant or recently extinct species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological characters. We further clarify the timeline of charadriiform evolution by time-scaling this phylogeny using a set of 14 up-to-date and thoroughly vetted fossil calibrations. In addition, we assemble a taxonomically restricted 100-locus dataset specifically designed to resolve outstanding problems in higher-level charadriiform phylogeny. In terms of tree topology, our results are largely congruent with previous studies but indicate that some of the conflicts among earlier analyses reflect a genuine signal of pervasive gene tree discordance. Monophyly of the plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and the relationships among the five subfamilies of the gulls (Laridae) could not be resolved even with greatly increased locus and taxon sampling. Moreover, several localized regions of uncertainty persist in shallower parts of the tree, including the interrelationships of the true auks (Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary rate analyses find support for a Paleocene origin of crown-group shorebirds, as well as exceptionally rapid recent radiations of Old World oystercatchers (Haematopodidae) and select genera of gulls. Our study underscores the challenges involved in estimating a comprehensively sampled and carefully calibrated time tree for a diverse avian clade, and highlights areas in need of further research.
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Affiliation(s)
- David Černý
- Department of the Geophysical Sciences, University of Chicago, Chicago 60637, USA.
| | - Rossy Natale
- Department of Organismal Biology & Anatomy, University of Chicago, Chicago 60637, USA
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15
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Bocharov S, Harris S, Kominek E, Mooers AØ, Steel M. Predicting long pendant edges in model phylogenies, with applications to biodiversity and tree inference. Syst Biol 2022:6671239. [PMID: 35980265 DOI: 10.1093/sysbio/syac059] [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: 09/11/2021] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/12/2022] Open
Abstract
In the simplest phylogenetic diversification model (the pure-birth Yule process), lineages split independently at a constant rate λ for time t. The length of a randomly chosen edge (either interior or pendant) in the resulting tree has an expected value that rapidly converges to 12λ as t grows, and thus is essentially independent of t. However, the behaviour of the length L of the longest pendant edge reveals remarkably different behaviour: L converges to t/2 as the expected number of leaves grows. Extending this model to allow an extinction rate μ (where μ < λ), we also establish a similar result for birth-death trees, except that t/2 is replaced by t/2 ⋅ (1 - μ/λ). This 'complete' tree may contain subtrees that have died out before time t; for the 'reduced tree' that just involves the leaves present at time t and their direct ancestors, the longest pendant edge length L again converges to t/2. Thus, there is likely to be at least one extant species whose associated pendant branch attaches to the tree approximately half-way back in time to the origin of the entire clade. We also briefly consider the length of the shortest edges. Our results are relevant to phylogenetic diversity indices in biodiversity conservation, and to quantifying the length of aligned sequences required to correctly infer a tree. We compare our theoretical results with simulations, and with the branch lengths from a recent phylogenetic tree of all mammals.
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Affiliation(s)
- Sergey Bocharov
- Department of Foundational Mathematics, Xian Jiaotong-Liverpool University, Suzhou, China
| | - Simon Harris
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Emma Kominek
- Biological Sciences, Simon Fraser University, 8888 Univ. Drive, Burnaby BC Canada V5A 1S6
| | - Arne Ø Mooers
- Biological Sciences, Simon Fraser University, 8888 Univ. Drive, Burnaby BC Canada V5A 1S6
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
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16
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Vernygora OV, Campbell EO, Grishin NV, Sperling FA, Dupuis JR. Gauging ages of tiger swallowtail butterflies using alternate SNP analyses. Mol Phylogenet Evol 2022; 171:107465. [DOI: 10.1016/j.ympev.2022.107465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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17
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Lafuma F, Corfe IJ, Clavel J, Di-Poï N. Multiple evolutionary origins and losses of tooth complexity in squamates. Nat Commun 2021; 12:6001. [PMID: 34650041 PMCID: PMC8516937 DOI: 10.1038/s41467-021-26285-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/27/2021] [Indexed: 11/21/2022] Open
Abstract
Teeth act as tools for acquiring and processing food, thus holding a prominent role in vertebrate evolution. In mammals, dental-dietary adaptations rely on tooth complexity variations controlled by cusp number and pattern. Complexity increase through cusp addition has dominated the diversification of mammals. However, studies of Mammalia alone cannot reveal patterns of tooth complexity conserved throughout vertebrate evolution. Here, we use morphometric and phylogenetic comparative methods across fossil and extant squamates to show they also repeatedly evolved increasingly complex teeth, but with more flexibility than mammals. Since the Late Jurassic, multiple-cusped teeth evolved over 20 times independently from a single-cusped common ancestor. Squamates frequently lost cusps and evolved varied multiple-cusped morphologies at heterogeneous rates. Tooth complexity evolved in correlation with changes in plant consumption, resulting in several major increases in speciation. Complex teeth played a critical role in vertebrate evolution outside Mammalia, with squamates exemplifying a more labile system of dental-dietary evolution.
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Affiliation(s)
- Fabien Lafuma
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Ian J Corfe
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland.
- Geological Survey of Finland, FI-02150, Espoo, Finland.
| | - Julien Clavel
- Department of Life Sciences, The Natural History Museum, London, SW7 5BD, UK
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622, Villeurbanne, France
| | - Nicolas Di-Poï
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, FI-00014, Helsinki, Finland.
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