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Silva FLD, de Medeiros BAS, Farrell BD. Once upon a fly: The biogeographical odyssey of Labrundinia (Chironomidae, Tanypodinae), an aquatic non-biting midge towards diversification. Mol Phylogenet Evol 2024; 194:108025. [PMID: 38342160 DOI: 10.1016/j.ympev.2024.108025] [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: 07/23/2023] [Revised: 01/17/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Labrundinia is a highly recognizable lineage in the Pentaneurini tribe (Diptera, Chironomidae). The distinct predatory free-swimming larvae of this genus are typically present in unpolluted aquatic environments, such as small streams, ponds, lakes, and bays. They can be found on the bottom mud, clinging to rocks and wood, and dwelling among aquatic vegetation. Labrundinia has been extensively studied in ecological research and comprises 39 species, all but one of which has been described from regions outside the Palearctic. Earlier phylogenetic studies have suggested that the initial diversification of the genus likely occurred in the Neotropical Region, with its current presence in the Nearctic Region and southern South America being the result of subsequent dispersal events. Through the integration of molecular and morphological data in a calibrated phylogeny, we reveal a complex and nuanced evolutionary history for Labrundinia, providing insights into its biogeographical and diversification patterns. In this comprehensive study, we analyze a dataset containing 46 Labrundinia species, totaling 10,662 characters, consisting of 10,616 nucleotide sites and 46 morphological characters. The molecular data was generated mainly by anchored enrichment hybrid methods. Using this comprehensive dataset, we inferred the phylogeny of the group based on a total evidence matrix. Subsequently, we employed the generated tree for time calibration and further analysis of biogeography and diversification patterns. Our findings reveal multiple dispersal events out of the Neotropics, where the group originated in the late Cretaceous approximately 72 million years ago (69-78 Ma). We further reveal that the genus experienced an early burst of diversification rates during the Paleocene, which gradually decelerated towards the present-day. We also find that the Neotropics have played a pivotal role in the evolution of Labrundinia by serving as both a cradle and a museum. By "cradle," we mean that the region has been a hotspot for the origin and diversification of new Labrundinia lineages, while "museum" refers to the region's ability to preserve ancestral lineages over extended periods. In summary, our findings indicate that the Neotropics have been a key source of genetic diversity for Labrundinia, resulting in the development of distinctive adaptations and characteristics within the genus. This evidence highlights the crucial role that these regions have played in shaping the evolutionary trajectory of Labrundinia.
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Affiliation(s)
- Fabio Laurindo da Silva
- Laboratory of Aquatic Insect Biodiversity and Ecology, Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA.
| | - Bruno A S de Medeiros
- Field Museum of Natural History, Negaunee Integrative Research Center, Chicago, USA; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
| | - Brian D Farrell
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA
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2
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Thomas VJ, Shaw J, Tay N, Warburton NM. Comparative three-dimensional jaw muscle anatomy of marsupial carnivores (Dasyurus spp.) and the termite-eating numbat (Myrmecobius fasciatus). J Morphol 2024; 285:e21684. [PMID: 38439588 DOI: 10.1002/jmor.21684] [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: 12/14/2023] [Revised: 12/14/2023] [Accepted: 02/21/2024] [Indexed: 03/06/2024]
Abstract
Among marsupials, the endangered numbat (Myrmecobius fasciatus) is the only obligate myrmecophage with a diet comprised strictly of termites. Like many other specialised myrmecophagous mammals, numbats have a gracile and highly specialised skull morphology with an elongated rostrum and small braincase. Myrmecobiidae is one of four taxonomic families within the Australasian marsupial order Dasyuromorphia, and to date, the muscular anatomy of any member of this group is relatively poorly known. We utilised microdissection and contrast-enhanced microcomputed tomography scanning to provide the first comprehensive qualitative and quantitative descriptions of jaw muscle anatomy in numbats and quolls (Dasuyrus species). The arrangement of the jaw muscles across these species was conservative, both in gross anatomy and muscle proportions, corresponding to a 'generalised' mammalian pattern. In contrast to Dasyurus, the jaw muscles of the numbat were greatly reduced. Many aspects of the muscle anatomy of the numbat were similar to patterns reported in other myrmecophagous species, particularly a greatly reduced temporalis muscle. Unusually, the digastric muscle in the numbat was comprised of a single, large anterior belly while the posterior belly was absent. We propose that the enlarged anterior belly of the digastric may be linked to jaw stabilisation and coordination of tongue movements during feeding. The lateral insertion and fascial connection of the digastric to the tongue in numbats may also aid in distributing stress evenly across the jaw and minimise muscle fatigue. The muscle descriptions and three-dimensional models provided in this study will facilitate further analysis of musculoskeletal adaptation and evolution within the Dasyuromorphia.
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Affiliation(s)
- Vanessa J Thomas
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia
| | - Jeremy Shaw
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, Australia
| | - Natasha Tay
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Research Institute, Murdoch University, Murdoch, Australia
| | - Natalie M Warburton
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia
- Centre for Terrestrial Ecosystem Science and Sustainability, Harry Butler Research Institute, Murdoch University, Murdoch, Australia
- Western Australian Museum, Welshpool, Australia
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3
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Uvizl M, Puechmaille SJ, Power S, Pippel M, Carthy S, Haerty W, Myers EW, Teeling EC, Huang Z. Comparative Genome Microsynteny Illuminates the Fast Evolution of Nuclear Mitochondrial Segments (NUMTs) in Mammals. Mol Biol Evol 2024; 41:msad278. [PMID: 38124445 PMCID: PMC10764098 DOI: 10.1093/molbev/msad278] [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: 07/18/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.
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Affiliation(s)
- Marek Uvizl
- Department of Zoology, National Museum, 19300 Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, 12844 Prague, Czech Republic
| | - Sebastien J Puechmaille
- Institut des Sciences de l’Evolution de Montpellier (ISEM), University of Montpellier, 34095 Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Sarahjane Power
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Samuel Carthy
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Colney Ln, NR4 7UZ Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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4
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Hand SJ, Maugoust J, Beck RMD, Orliac MJ. A 50-million-year-old, three-dimensionally preserved bat skull supports an early origin for modern echolocation. Curr Biol 2023; 33:4624-4640.e21. [PMID: 37858341 DOI: 10.1016/j.cub.2023.09.043] [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: 09/19/2022] [Revised: 07/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023]
Abstract
Bats are among the most recognizable, numerous, and widespread of all mammals. But much of their fossil record is missing, and bat origins remain poorly understood, as do the relationships of early to modern bats. Here, we describe a new early Eocene bat that helps bridge the gap between archaic stem bats and the hyperdiverse modern bat radiation of more than 1,460 living species. Recovered from ∼50 million-year-old cave sediments in the Quercy Phosphorites of southwestern France, Vielasia sigei's remains include a near-complete, three-dimensionally preserved skull-the oldest uncrushed bat cranium yet found. Phylogenetic analyses of a 2,665 craniodental character matrix, with and without 36.8 kb of DNA sequence data, place Vielasia outside modern bats, with total evidence tip-dating placing it sister to the crown clade. Vielasia retains the archaic dentition and skeletal features typical of early Eocene bats, but its inner ear shows specializations found in modern echolocating bats. These features, which include a petrosal only loosely attached to the basicranium, an expanded cochlea representing ∼25% basicranial width, and a long basilar membrane, collectively suggest that the kind of laryngeal echolocation used by most modern bats predates the crown radiation. At least 23 individuals of V. sigei are preserved together in a limestone cave deposit, indicating that cave roosting behavior had evolved in bats by the end of the early Eocene; this period saw the beginning of significant global climate cooling that may have been an evolutionary driver for bats to first congregate in caves.
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Affiliation(s)
- Suzanne J Hand
- ESSRC, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jacob Maugoust
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Robin M D Beck
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK.
| | - Maeva J Orliac
- Institut des Sciences de l'Evolution, UMR 5554 CNRS, IRD, EPHE, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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5
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Harvey E, Mifsud JCO, Holmes EC, Mahar JE. Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids). Virus Evol 2023; 9:vead061. [PMID: 37941997 PMCID: PMC10630069 DOI: 10.1093/ve/vead061] [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: 06/27/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023] Open
Abstract
Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host-a chu-like virus in Tasmanian devils-thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.
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Affiliation(s)
- Erin Harvey
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jonathon C O Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jackie E Mahar
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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6
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Luo A, Zhang C, Zhou QS, Ho SYW, Zhu CD. Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process. Syst Biol 2023; 72:781-801. [PMID: 36919368 PMCID: PMC10405359 DOI: 10.1093/sysbio/syad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/18/2023] [Accepted: 03/14/2023] [Indexed: 03/16/2023] Open
Abstract
Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].
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Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qing-Song Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- International College, University of Chinese Academy of Sciences, Beijing, 100049, China
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7
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Prideaux GJ, Warburton NM. A review of the late Cenozoic genus Bohra (Diprotodontia: Macropodidae) and the evolution of tree-kangaroos. Zootaxa 2023; 5299:1-95. [PMID: 37518576 DOI: 10.11646/zootaxa.5299.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 08/01/2023]
Abstract
Tree-kangaroos of the genus Dendrolagus occupy forest habitats of New Guinea and extreme northeastern Australia, but their evolutionary history is poorly known. Descriptions in the 2000s of near-complete Pleistocene skeletons belonging to larger-bodied species in the now-extinct genus Bohra broadened our understanding of morphological variation in the group and have since helped us to identify unassigned fossils in museum collections, as well as to reassign species previously placed in other genera. Here we describe these fossils and analyse tree-kangaroo systematics via comparative osteology. Including B. planei sp. nov., B. bandharr comb. nov. and B. bila comb. nov., we recognise the existence of at least seven late Cenozoic species of Bohra, with a maximum of three in any one assemblage. All tree-kangaroos (Dendrolagina subtribe nov.) exhibit skeletal adaptations reflective of greater joint flexibility and manoeuvrability, particularly in the hindlimb, compared with other macropodids. The Pliocene species of Bohra retained the stepped calcaneocuboid articulation characteristic of ground-dwelling macropodids, but this became smoothed to allow greater hindfoot rotation in the later species of Bohra and in Dendrolagus. Tree-kangaroo diversification may have been tied to the expansion of forest habitats in the early Pliocene. Following the onset of late Pliocene aridity, some tree-kangaroo species took advantage of the consequent spread of more open habitats, becoming among the largest late Cenozoic tree-dwellers on the continent. Arboreal Old World primates and late Quaternary lemurs may be the closest ecological analogues to the species of Bohra.
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Affiliation(s)
- Gavin J Prideaux
- College of Science & Engineering; Flinders University; Bedford Park; South Australia 5042; Australia.
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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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Pozzi L, Penna A. Rocks and clocks revised: New promises and challenges in dating the primate tree of life. Evol Anthropol 2022; 31:138-153. [PMID: 35102633 DOI: 10.1002/evan.21940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/04/2021] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
Abstract
In recent years, multiple technological and methodological advances have increased our ability to estimate phylogenies, leading to more accurate dating of the primate tree of life. Here we provide an overview of the limitations and potentials of some of these advancements and discuss how dated phylogenies provide the crucial temporal scale required to understand primate evolution. First, we review new methods, such as the total-evidence dating approach, that promise a better integration between the fossil record and molecular data. We then explore how the ever-increasing availability of genomic-level data for more primate species can impact our ability to accurately estimate timetrees. Finally, we discuss more recent applications of mutation rates to date divergence times. We highlight example studies that have applied these approaches to estimate divergence dates within primates. Our goal is to provide a critical overview of these new developments and explore the promises and challenges of their application in evolutionary anthropology.
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Affiliation(s)
- Luca Pozzi
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
| | - Anna Penna
- Department of Anthropology, The University of Texas at San Antonio, San Antonio, Texas, USA
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10
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Mitogenome of the extinct Desert 'rat-kangaroo' times the adaptation to aridity in macropodoids. Sci Rep 2022; 12:5829. [PMID: 35388060 PMCID: PMC8987032 DOI: 10.1038/s41598-022-09568-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/25/2022] [Indexed: 01/31/2023] Open
Abstract
The evolution of Australia's distinctive marsupial fauna has long been linked to the onset of continent-wide aridity. However, how this profound climate change event affected the diversification of extant lineages is still hotly debated. Here, we assemble a DNA sequence dataset of Macropodoidea-the clade comprising kangaroos and their relatives-that incorporates a complete mitogenome for the Desert 'rat-kangaroo', Caloprymnus campestris. This enigmatic species went extinct nearly 90 years ago and is known from a handful of museum specimens. Caloprymnus is significant because it was the only macropodoid restricted to extreme desert environments, and therefore calibrates the group's specialisation for increasingly arid conditions. Our robustly supported phylogenies nest Caloprymnus amongst the bettongs Aepyprymnus and Bettongia. Dated ancestral range estimations further reveal that the Caloprymnus-Bettongia lineage originated in nascent xeric settings during the middle to late Miocene, ~ 12 million years ago (Ma), but subsequently radiated into fragmenting mesic habitats after the Pliocene to mid-Pleistocene. This timeframe parallels the ancestral divergences of kangaroos in woodlands and forests, but predates their adaptive dispersal into proliferating dry shrublands and grasslands from the late Miocene to mid-Pleistocene, after ~ 7 Ma. We thus demonstrate that protracted changes in both climate and vegetation likely staged the emergence of modern arid zone macropodoids.
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11
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Hazkani-Covo E. A Burst of Numt Insertion in the Dasyuridae Family During Marsupial Evolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.844443] [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
Nuclear pseudogenes of mitochondrial origin (numts) are common in all eukaryotes. Our previous scan of numts in sequenced nuclear genomes suggested that the highest numt content currently known in animals is that in the gray short-tailed opossum. The present work sought to determine numt content in marsupials and to compare it to those in placental and monothematic mammals as well as in non-mammalian vertebrates. To achieve this, 70 vertebrate species with available nuclear and mitochondrial genomes were scanned for numt content. An extreme numt content was found in the Dasyuridae, with 3,450 in Sarcophilus harrisii (1,955 kb) and 2,813 in Antechinus flavipes (847 kb). The evolutionarily closest species analyzed, the extinct Thylacinus cynocephalus belonging to the Thylacindae family, had only 435 numts (238 kb). These two Dasyuridae genomes featured the highest numt content identified in animals to date. A phylogenetic analysis of numts longer than 300 bp, using a Diprotodonita mitochondrial tree, indicated a burst of numt insertion that began before the divergence of the Dasyurini and Phascogalini, reaching a peak in the early evolution of the two tribes. No comparable increase was found in the early divergent species T. cynocephalus. Divergence of the Dasyuridae tribes has been previously dated to shortly after the Miocene climate transition, characterized by a rapid temperature decline. Interestingly, deviation from optimal growth temperature is one of the environmental factors reported to increase numt insertions in a laboratory setting.
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12
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McCurry MR, Cantrill DJ, Smith PM, Beattie R, Dettmann M, Baranov V, Magee C, Nguyen JMT, Forster MA, Hinde J, Pogson R, Wang H, Marjo CE, Vasconcelos P, Frese M. A Lagerstätte from Australia provides insight into the nature of Miocene mesic ecosystems. SCIENCE ADVANCES 2022; 8:eabm1406. [PMID: 34995110 PMCID: PMC8741189 DOI: 10.1126/sciadv.abm1406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Reduced precipitation in the Miocene triggered the geographic contraction of rainforest ecosystems around the world. In Australia, this change was particularly pronounced; mesic rainforest ecosystems that once dominated the landscape transformed into the shrublands, grasslands, and deserts of today. A lack of well-preserved fossils has made it difficult to understand the nature of Australian ecosystems before the aridification. Here, we report on an exceptionally well-preserved rainforest biota from New South Wales, Australia. This Konservat-Lagerstätte hosts a rich diversity of microfossils, plants, insects, spiders, and vertebrate remains preserved in goethite. We document evidence for several species interactions including predation, parasitism, and pollination. The fossils are indicative of an oxbow lake in a mesic rainforest and suggest that rainforest distributions have shifted since the Miocene. The variety of fossils preserved, together with high fidelity of preservation, allows for unprecedented insights into the mesic ecosystems that dominated Australia during the Miocene.
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Affiliation(s)
- Matthew R. McCurry
- Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia
- Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences (BEES), University of New South Wales, Kensington, New South Wales 2052, Australia
- Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - David J. Cantrill
- Royal Botanic Gardens Victoria, Private Bag 2000, South Yarra, Victoria 3141, Australia
| | - Patrick M. Smith
- Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales 2109, Australia
| | - Robert Beattie
- Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia
| | - Mary Dettmann
- Geosciences, Queensland Museum, South Brisbane, Queensland 4101, Australia
| | - Viktor Baranov
- Ludwig-Maximilian University of Munich, Biocenter, Großhaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Charles Magee
- Geoscience Australia, Symonston 2609, Australian Capital Territory, Australia
| | - Jacqueline M. T. Nguyen
- Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia
- Earth and Sustainability Science Research Centre, School of Biological, Earth and Environmental Sciences (BEES), University of New South Wales, Kensington, New South Wales 2052, Australia
- College of Science and Engineering, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Marnie A. Forster
- Research School of Earth Sciences, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Jack Hinde
- Illawarra Environmental Education Centre, Shell Cove, New South Wales 2529, Australia
| | - Ross Pogson
- Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia
| | - Helen Wang
- Mark Wainwright Analytical Centre, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Christopher E. Marjo
- Mark Wainwright Analytical Centre, University of New South Wales, Kensington, New South Wales 2052, Australia
| | - Paulo Vasconcelos
- School of Earth Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Michael Frese
- Australian Museum Research Institute, 1 William Street, Sydney, New South Wales 2010, Australia
- Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Black Mountain, Australian Capital Territory 2601, Australia
- Faculty of Science and Technology, University of Canberra, Bruce, Australian Capital Territory 2601, Australia
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13
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Westerman M, Loke S, Tan MH. Molecular relationships of the red-bellied dasyure (Phascolosorex doriae) – a rare marsupial from western New Guinea. AUSTRALIAN MAMMALOGY 2022. [DOI: 10.1071/am21011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The mitochondrial genome of the rare endemic New Guinean dasyurid Phascolosorex doriae (Thomas 1886) has been used to clarify relationships within ‘phascolosoricinae’. The mitochondrial genome has the typical gene arrangement seen in other marsupials. Molecular analyses using complete mitogenomes of other dasyurids resolve the red-bellied dasyure as sister to the narrow-striped dasyure Phascolosorex dorsalis and show that these two species diverged in the early Pliocene. The invasion of emergent New Guinean rainforest habitats (in the late Miocene) by the common ancestor of Ph. doriae, Ph. dorsalis and Neophascogale lorentzii represents one of three separate such invasions by dasyurid lineages.
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14
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Phillips MJ, Westerman M, Cascini M. The value of updating GenBank accessions for supermatrix phylogeny: The case of the New Guinean marsupial carnivore genus Myoictis. Mol Phylogenet Evol 2021; 166:107328. [PMID: 34666168 DOI: 10.1016/j.ympev.2021.107328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/12/2021] [Indexed: 01/08/2023]
Abstract
Erroneous taxonomic attributions in GenBank accessions can mislead phylogenetic inference and appear to be widespread within genera. We investigate the influence of taxonomic misattributions for reconstructing the phylogeny of three-striped dasyures, which include four recognized Myoictis species (Marsupialia: Dasyuridae) that are distributed across New Guinea and nearby islands. Molecular phylogenetic studies that have focused on dasyurids consistently resolve the interrelationships of these small carnivores, grouping M. leucura with M. wavicus, and placing M. wallacei and M. melas as successively deeper divergences from these. Two recent marsupial and mammalian supermatrix phylogenies instead favour an alternative Myoictis topology that is discordant with each of these relationships. We add new nuclear and mitochondrial sequences and employ randomized accession resampling that shows the supermatrix topologies are an artefact of several outdated taxonomic attributions in GenBank. Updating these accessions brings agreement across Myoictis phylogenies with randomly resampled accessions. We encourage authors to update GenBank taxonomic attributions and we argue that an option is needed for flagging accessions that are not demonstrably incorrect, but that provide anomalous results. This would serve both as a caution for future supermatrix construction and to highlight accessions of potentially significant biological interest for further study.
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Affiliation(s)
- Matthew J Phillips
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia.
| | - Michael Westerman
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne 3086, VIC, Australia
| | - Manuela Cascini
- School of Biology and Environmental Science, Queensland University of Technology, 2 George Street, Brisbane 4000, QLD, Australia
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15
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Pollock TI, Hocking DP, Evans AR. The killer’s toolkit: remarkable adaptations in the canine teeth of mammalian carnivores. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Often the first point of contact between predator and prey, mammalian canine teeth are essential for killing, dismembering and consuming prey. Yet despite their importance, few associations among shape, function and phylogeny are established. We undertook the first comprehensive analysis of canine tooth shape across predatory mammals (Carnivora, Didelphimorphia and Dasyuromorphia), integrating shape analysis with function of this fundamental feature. Shape was quantified using three-dimensional geometric morphometrics and cross-sectional sharpness. Canines vary in three main ways (sharpness, robustness and curvature) which vary with diet, killing behaviour and phylogeny. Slender, sharp canines are associated with carnivores such as felids that target the neck of their prey and primarily consume the ‘softer’ parts of a carcass. Robust, blunt canines are found in mustelids and dasyurids that typically consume ‘harder’ materials, such as bone, or bite into skulls. Differences in the killing behaviours of felids and canids probably result in more curved canines in the latter, which act as hooks to hold prey. We find functional specialization in the upper and lower canines of individuals and across the major mammalian clades. These patterns demonstrate how canine teeth are adapted to suit diverse diets and hunting styles, enabling mammals to become some of nature's most successful predators.
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Affiliation(s)
- Tahlia I Pollock
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - David P Hocking
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- Zoology, Tasmanian Museum and Art Gallery, Hobart, Tasmania, Australia
| | - Alistair R Evans
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
- Geosciences, Museums Victoria, Melbourne, Victoria, Australia
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16
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Oliveira ÉV, Carneiro LM, Goin FJ. A new derorhynchid (Mammalia, Metatheria) from the early Eocene Itaboraí fauna of Brazil with comments on its affinities. AN ACAD BRAS CIENC 2021; 93:e20201554. [PMID: 34378646 DOI: 10.1590/0001-3765202120201554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/22/2021] [Indexed: 11/22/2022] Open
Abstract
A new early Eocene, small-sized metatherian from the Itaboraí fauna is described. The new taxon is recognized on the basis of an incomplete dentary recovered from fissure fillings in the travertine limestones from the Itaboraí Basin, State of Rio de Janeiro, Brazil. The phylogenetic analysis placed the new genus and species as the sister taxon of Derorhynchus, undescribed Derorhynchidae, and Coona plus Pauladelphys. When compared to Derorhynchus, the new taxon exhibits a shorter dentary, in which the first lower premolar is not separated from the second by a diastema, and shows second and third lower molars with subequal trigonid and talonid width (in Derorhynchus the talonids are wider than the trigonids). This new taxon shows some plesiomorphic traits when compared with the remaining derorhynchids, such as the shallower dentary (less than 1.5 mm), and conical entoconids rather than flattened in shape. The combination of very small size (~13-20g), sharp crests, tall and slender cuspids, broad talonid basins, as well as trigonid taller than the talonid is suggestive of an insectivorous diet for the new taxon.
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Affiliation(s)
- Édison Vicente Oliveira
- PPGEOC, Programa de Pós-Graduação em Geociências, Departamento de Geologia, Centro de Tecnologia e Geociências, Universidade Federal de Pernambuco, Av. Acadêmico Hélio Ramos, s/n, Cidade Universitária, 50740-530, Recife, PE, Brazil.,Paleolab, Laboratório de Paleontologia, Departamento de Geologia, Centro de Tecnologia e Geociências, Universidade Federal de Pernambuco, Av. Acadêmico Hélio Ramos, s/n, Cidade Universitária, 50740-530, Recife, PE, Brazil
| | - Leonardo M Carneiro
- PPGEOC, Programa de Pós-Graduação em Geociências, Departamento de Geologia, Centro de Tecnologia e Geociências, Universidade Federal de Pernambuco, Av. Acadêmico Hélio Ramos, s/n, Cidade Universitária, 50740-530, Recife, PE, Brazil.,Laboratório de Paleontologia e Paleoecologia da Sociedade de História Natural, Travessa Florêncio Augusto Chagas nº 8B, 2560-230 Torres Vedras, Portugal
| | - Francisco J Goin
- División Paleontología Vertebrados, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque, s/n, B1900FWA La Plata, Argentina
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17
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Quintero-Galvis JF, Saenz-Agudelo P, Celis-Diez JL, Amico GC, Vazquez S, Shafer ABA, Nespolo RF. The biogeography of Dromiciops in southern South America: Middle Miocene transgressions, speciation and associations with Nothofagus. Mol Phylogenet Evol 2021; 163:107234. [PMID: 34146676 DOI: 10.1016/j.ympev.2021.107234] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/28/2021] [Accepted: 06/14/2021] [Indexed: 01/16/2023]
Abstract
The current distribution of the flora and fauna of southern South America is the result of drastic geological events that occurred during the last 20 million years, including marine transgressions, glaciations and active vulcanism. All these have been associated with fragmentation, isolation and subsequent expansion of the biota, south of 35°S, such as the temperate rainforest. This forest is mostly dominated by Nothofagus trees and is the habitat of the relict marsupial monito del monte, genus Dromiciops, sole survivor of the order Microbiotheria. Preliminary analyses using mtDNA proposed the existence of three main Dromiciops lineages, distributed latitudinally, whose divergence was initially attributed to recent Pleistocene glaciations. Using fossil-calibrated dating on nuclear and mitochondrial genes, here we reevaluate this hypothesis and report an older (Miocene) biogeographic history for the genus. We performed phylogenetic reconstructions using sequences from two mitochondrial DNA and four nuclear DNA genes in 159 specimens from 31 sites across Chile and Argentina. Our phylogenetic analysis resolved three main clades with discrete geographic distributions. The oldest and most differentiated clade corresponds to that of the northern distribution (35.2°S to 39.3°S), which should be considered a distinct species (D. bozinovici, sensu D'Elía et al. 2016). According to our estimations, this species shared a common ancestor with D. gliroides (southern clades) about ~13 million years ago. Divergence time estimates for the southern clades (39.6°S to 42.0°S) ranged from 9.57 to 6.5 Mya. A strong genetic structure was also detected within and between clades. Demographic analyses suggest population size stability for the northern clade (D. bozinovici), and recent demographic expansions for the central and southern clades. All together, our results suggest that the diversification of Dromiciops were initiated by the Middle Miocene transgression (MMT), the massive marine flooding that covered several lowlands of the western face of Los Andes between 37 and 48°S. The MMT resulted from an increase in global sea levels at the Miocene climatic optimum, which shaped the biogeographic origin of several species, including Nothofagus forests, the habitat of Dromiciops.
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Affiliation(s)
- Julian F Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile; Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias, Universidad Austral de Chile, Chile
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan L Celis-Diez
- Pontificia Universidad Católica de Valparaíso Escuela de Agronomía Quillota, Chile
| | - Guillermo C Amico
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Soledad Vazquez
- INIBIOMA, CONICET-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Aaron B A Shafer
- Department of Forensic Science & Environmental Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Roberto F Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 6513677, Chile; Millenium Institute for Integrative Biology (iBio), Santiago, Chile.
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18
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Sidlauskas BL, Assega FM, Melo BF, Oliveira C, Birindelli JLO. Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The nearly 150 species of Anostomidae comprise one of the most diverse and taxonomically dynamic families of Neotropical freshwater fishes. A recent revision of the enigmatic and poorly diagnosed genus Anostomoides demonstrated that it contains two valid species, each with complicated taxonomic histories; however, that study did not address their phylogenetic placement. Herein, we integrate molecular and morphological data to demonstrate their distant evolutionary relationship, and thus the polyphyly of Anostomoides. While we reconstruct one of the species in a previously hypothesized placement within a clade also containing Laemolyta, Rhytiodus and Schizodon, the other represents a morphologically and genetically distinctive lineage that diverged early in the history of the family. We describe and illustrate the osteology of this remarkable species, discuss the evolutionary implications of its unique suite of features, and use those characteristics to diagnose a new genus that evolved independently of all other known members of the family for approximately 37 Myr.
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Affiliation(s)
- Brian L Sidlauskas
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USA
| | - Fernando M Assega
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Estadual de Londrina, Centro de Ciencias Biologicas, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, Londrina, PR, Brazil
| | - Bruno F Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antonio C. W. Zanin, Rubião Jr, Botucatu, SP, Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista, R. Prof. Dr. Antonio C. W. Zanin, Rubião Jr, Botucatu, SP, Brazil
| | - José L O Birindelli
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Estadual de Londrina, Centro de Ciencias Biologicas, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, Campus Universitário, Londrina, PR, Brazil
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19
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Joseph GS, Seymour CL. Madagascan highlands: originally woodland and forest containing endemic grasses, not grazing-adapted grassland. Proc Biol Sci 2020; 287:20201956. [PMID: 33109006 DOI: 10.1098/rspb.2020.1956] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long considered a consequence of anthropogenic agropastoralism, the origin of Madagascar's central highland grassland is hotly disputed. Arguments that ancient endemic grasses formed grassland maintained by extinct grazers and fire have been persuasive. Consequent calls to repeal fire-suppression legislation, burn protected areas, and accept pastoralism as the 'salvation' of endemic grasses mount, even as the International Union for Conservation of Nature (IUCN) declares 98% of lemurs face extinction through fire-driven deforestation. By analysing grass data from contemporary studies, and assessing endemic vertebrate habitat and feeding guilds, we find that although the grassland potentially dates from the Miocene, it is inhospitable to endemic vertebrates and lacks obligate grazers. Endemic grasses are absent from dominant grassland assemblages, yet not from woodland and forest assemblages. There is compelling evidence that humans entered a highland dominated by woodland and forest, and burned it; by 1000 current era (CE), grass pollens eclipsed tree pollens, reminiscent of prevailing fire-induced transformation of African miombo woodland to grassland. Endemic grasses are survivors from vanished woody habitats where grassy patches were likely small and ephemeral, precluding adaptive radiation by endemic vertebrates to form grazing-guilds. Today forests, relic tapia woodland, and outcompeted endemic grasses progressively retreat in a burning grassland dominated by non-endemic, grazing-adapted grasses and cattle.
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Affiliation(s)
- Grant S Joseph
- Percy FitzPatrick Institute of African Ornithology, DST/NRF Centre of Excellence, Department of Biological Sciences, University of Cape Town, Rondebosch 7701, South Africa
| | - Colleen L Seymour
- Percy FitzPatrick Institute of African Ornithology, DST/NRF Centre of Excellence, Department of Biological Sciences, University of Cape Town, Rondebosch 7701, South Africa.,South African National Biodiversity Institute, Kirstenbosch Research Centre, Private Bag X7, Claremont 7735, South Africa
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20
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Spasojevic T, Broad GR, Sääksjärvi IE, Schwarz M, Ito M, Korenko S, Klopfstein S. Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae). Syst Biol 2020; 70:322-339. [PMID: 33057674 PMCID: PMC7875445 DOI: 10.1093/sysbio/syaa079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 10/02/2020] [Accepted: 10/02/2020] [Indexed: 01/16/2023] Open
Abstract
Taxon sampling is a central aspect of phylogenetic study design, but it has received limited attention in the context of total-evidence dating, a widely used dating approach that directly integrates molecular and morphological information from extant and fossil taxa. We here assess the impact of commonly employed outgroup sampling schemes and missing morphological data in extant taxa on age estimates in a total-evidence dating analysis under the uniform tree prior. Our study group is Pimpliformes, a highly diverse, rapidly radiating group of parasitoid wasps of the family Ichneumonidae. We analyze a data set comprising 201 extant and 79 fossil taxa, including the oldest fossils of the family from the Early Cretaceous and the first unequivocal representatives of extant subfamilies from the mid-Paleogene. Based on newly compiled molecular data from ten nuclear genes and a morphological matrix that includes 222 characters, we show that age estimates become both older and less precise with the inclusion of more distant and more poorly sampled outgroups. These outgroups not only lack morphological and temporal information but also sit on long terminal branches and considerably increase the evolutionary rate heterogeneity. In addition, we discover an artifact that might be detrimental for total-evidence dating: “bare-branch attraction,” namely high attachment probabilities of certain fossils to terminal branches for which morphological data are missing. Using computer simulations, we confirm the generality of this phenomenon and show that a large phylogenetic distance to any of the extant taxa, rather than just older age, increases the risk of a fossil being misplaced due to bare-branch attraction. After restricting outgroup sampling and adding morphological data for the previously attracting, bare branches, we recover a Jurassic origin for Pimpliformes and Ichneumonidae. This first age estimate for the group not only suggests an older origin than previously thought but also that diversification of the crown group happened well before the Cretaceous-Paleogene boundary. Our case study demonstrates that in order to obtain robust age estimates, total-evidence dating studies need to be based on a thorough and balanced sampling of both extant and fossil taxa, with the aim of minimizing evolutionary rate heterogeneity and missing morphological information. [Bare-branch attraction; ichneumonids; fossils; morphological matrix; phylogeny; RoguePlots.]
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Affiliation(s)
- Tamara Spasojevic
- Abteilung Wirbellose Tiere Invertebrates, Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland.,Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland.,Department of Entomology, National Museum of Natural History, Washington, DC 20560, USA
| | - Gavin R Broad
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | | | | | - Masato Ito
- Graduate School of Agricultural Science, Department of Agrobioscience, Kobe University, 657-8501 Japan
| | - Stanislav Korenko
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 21 Prague 6, Suchdol, Czech Republic
| | - Seraina Klopfstein
- Abteilung Wirbellose Tiere Invertebrates, Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005 Bern, Switzerland.,Institute of Ecology and Evolution, Department of Biology, University of Bern, 3012 Bern, Switzerland.,Abteilung für Biowissenschaften, Naturhistorisches Museum Basel, 4051 Basel, Switzerland
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21
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Mongiardino Koch N, Thompson JR. A Total-Evidence Dated Phylogeny of Echinoidea Combining Phylogenomic and Paleontological Data. Syst Biol 2020; 70:421-439. [PMID: 32882040 DOI: 10.1093/sysbio/syaa069] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 08/14/2020] [Accepted: 08/23/2020] [Indexed: 12/13/2022] Open
Abstract
Phylogenomic and paleontological data constitute complementary resources for unraveling the phylogenetic relationships and divergence times of lineages, yet few studies have attempted to fully integrate them. Several unique properties of echinoids (sea urchins) make them especially useful for such synthesizing approaches, including a remarkable fossil record that can be incorporated into explicit phylogenetic hypotheses. We revisit the phylogeny of crown group Echinoidea using a total-evidence dating approach that combines the largest phylogenomic data set for the clade, a large-scale morphological matrix with a dense fossil sampling, and a novel compendium of tip and node age constraints. To this end, we develop a novel method for subsampling phylogenomic data sets that selects loci with high phylogenetic signal, low systematic biases, and enhanced clock-like behavior. Our results demonstrate that combining different data sources increases topological accuracy and helps resolve conflicts between molecular and morphological data. Notably, we present a new hypothesis for the origin of sand dollars, and restructure the relationships between stem and crown echinoids in a way that implies a long stretch of undiscovered evolutionary history of the crown group in the late Paleozoic. Our efforts help bridge the gap between phylogenomics and phylogenetic paleontology, providing a model example of the benefits of combining the two. [Echinoidea; fossils; paleontology; phylogenomics; time calibration; total evidence.].
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Affiliation(s)
| | - Jeffrey R Thompson
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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22
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Engelman RK, Flynn JJ, Wyss AR, Croft DA. Eomakhaira molossus, A New Saber-Toothed Sparassodont (Metatheria: Thylacosmilinae) from the Early Oligocene (?Tinguirirican) Cachapoal Locality, Andean Main Range, Chile. AMERICAN MUSEUM NOVITATES 2020. [DOI: 10.1206/3957.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
| | - John J. Flynn
- Division of Paleontology and Richard Gilder Graduate School, American Museum of Natural History
| | - André R. Wyss
- Department of Earth Science, University of California, Santa Barbara
| | - Darin A. Croft
- Department of Anatomy, Case Western Reserve University, Cleveland
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23
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Field DJ, Benito J, Chen A, Jagt JWM, Ksepka DT. Late Cretaceous neornithine from Europe illuminates the origins of crown birds. Nature 2020; 579:397-401. [PMID: 32188952 DOI: 10.1038/s41586-020-2096-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/04/2020] [Indexed: 11/09/2022]
Abstract
Our understanding of the earliest stages of crown bird evolution is hindered by an exceedingly sparse avian fossil record from the Mesozoic era. The most ancient phylogenetic divergences among crown birds are known to have occurred in the Cretaceous period1-3, but stem-lineage representatives of the deepest subclades of crown birds-Palaeognathae (ostriches and kin), Galloanserae (landfowl and waterfowl) and Neoaves (all other extant birds)-are unknown from the Mesozoic era. As a result, key questions related to the ecology4,5, biogeography3,6,7 and divergence times1,8-10 of ancestral crown birds remain unanswered. Here we report a new Mesozoic fossil that occupies a position close to the last common ancestor of Galloanserae and fills a key phylogenetic gap in the early evolutionary history of crown birds10,11. Asteriornis maastrichtensis, gen. et sp. nov., from the Maastrichtian age of Belgium (66.8-66.7 million years ago), is represented by a nearly complete, three-dimensionally preserved skull and associated postcranial elements. The fossil represents one of the only well-supported crown birds from the Mesozoic era12, and is the first Mesozoic crown bird with well-represented cranial remains. Asteriornis maastrichtensis exhibits a previously undocumented combination of galliform (landfowl)-like and anseriform (waterfowl)-like features, and its presence alongside a previously reported Ichthyornis-like taxon from the same locality13 provides direct evidence of the co-occurrence of crown birds and avialan stem birds. Its occurrence in the Northern Hemisphere challenges biogeographical hypotheses of a Gondwanan origin of crown birds3, and its relatively small size and possible littoral ecology may corroborate proposed ecological filters4,5,9 that influenced the persistence of crown birds through the end-Cretaceous mass extinction.
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Affiliation(s)
- Daniel J Field
- Department of Earth Sciences, University of Cambridge, Cambridge, UK.
| | - Juan Benito
- Department of Earth Sciences, University of Cambridge, Cambridge, UK.,Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, UK
| | - Albert Chen
- Department of Earth Sciences, University of Cambridge, Cambridge, UK.,Department of Biology & Biochemistry, Milner Centre for Evolution, University of Bath, Bath, UK
| | - John W M Jagt
- Natuurhistorisch Museum Maastricht, Maastricht, The Netherlands
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24
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Luo A, Duchêne DA, Zhang C, Zhu CD, Ho SYW. A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process. Syst Biol 2020; 69:325-344. [PMID: 31132125 PMCID: PMC7175741 DOI: 10.1093/sysbio/syz038] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 11/25/2022] Open
Abstract
Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth-death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth-death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth-death model, which will inform further development of the method and its application to key questions in evolutionary biology.
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Affiliation(s)
- Arong Luo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - David A Duchêne
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
- Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
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25
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Rovinsky DS, Evans AR, Adams JW. The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine. PeerJ 2019; 7:e7457. [PMID: 31534836 PMCID: PMC6727838 DOI: 10.7717/peerj.7457] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/10/2019] [Indexed: 11/20/2022] Open
Abstract
The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15-14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores.
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Affiliation(s)
- Douglass S Rovinsky
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Alistair R Evans
- School of Biological Sciences, Monash University, Clayton, VIC, Australia.,Geosciences, Museums Victoria, Melbourne, VIC, Australia
| | - Justin W Adams
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
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26
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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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27
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Eldridge MDB, Beck RMD, Croft DA, Travouillon KJ, Fox BJ. An emerging consensus in the evolution, phylogeny, and systematics of marsupials and their fossil relatives (Metatheria). J Mammal 2019. [DOI: 10.1093/jmammal/gyz018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Robin M D Beck
- School of Environment and Life Sciences, University of Salford, Manchester, United Kingdom
| | - Darin A Croft
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Barry J Fox
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
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28
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Celik M, Cascini M, Haouchar D, Van Der Burg C, Dodt W, Evans AR, Prentis P, Bunce M, Fruciano C, Phillips MJ. A molecular and morphometric assessment of the systematics of the Macropus complex clarifies the tempo and mode of kangaroo evolution. Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mélina Celik
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Manuela Cascini
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dalal Haouchar
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University, Perth, WA, Australia
| | - Chloe Van Der Burg
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - William Dodt
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Alistair R Evans
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Peter Prentis
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, Curtin University, Perth, WA, Australia
| | - Carmelo Fruciano
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, Paris, France
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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29
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Cascini M, Mitchell KJ, Cooper A, Phillips MJ. Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence. Syst Biol 2018; 68:520-537. [DOI: 10.1093/sysbio/syy080] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/20/2018] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Manuela Cascini
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, North Terrace Campus, South Australia 5005, Australia
| | - Matthew J Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, 2, George Street, Brisbane, QLD 4000, Australia
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30
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Jensen B, Wang T, Moorman AFM. Evolution and Development of the Atrial Septum. Anat Rec (Hoboken) 2018; 302:32-48. [PMID: 30338646 PMCID: PMC6588001 DOI: 10.1002/ar.23914] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 12/27/2017] [Accepted: 01/09/2018] [Indexed: 02/05/2023]
Abstract
The complete division of the atrial cavity by a septum, resulting in a left and right atrium, is found in many amphibians and all amniotes (reptiles, birds, and mammals). Surprisingly, it is only in eutherian, or placental, mammals that full atrial septation necessitates addition from a second septum. The high incidence of incomplete closure of the atrial septum in human, so-called probe patency, suggests this manner of closure is inefficient. We review the evolution and development of the atrial septum to understand the peculiar means of forming the atrial septum in eutherian mammals. The most primitive atrial septum is found in lungfishes and comprises a myocardial component with a mesenchymal cap on its leading edge, reminiscent to the primary atrial septum of embryonic mammals before closure of the primary foramen. In reptiles, birds, and mammals, the primary foramen is closed by the mesenchymal tissues of the atrioventricular cushions, the dorsal mesenchymal protrusion, and the mesenchymal cap. These tissues are also found in lungfishes. The closure of the primary foramen is preceded by the development of secondary perforations in the septal myocardium. In all amniotes, with the exception of eutherian mammals, the secondary perforations do not coalesce to a secondary foramen. Instead, the secondary perforations persist and are sealed by myocardial and endocardial growth after birth or hatching. We suggest that the error-prone secondary foramen allows large volumes of oxygen-rich blood to reach the cardiac left side, needed to sustain the growth of the extraordinary large offspring that characterizes eutherian mammals. Anat Rec, 302:32-48, 2019. © 2018 The Authors. The Anatomical Record published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.
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Affiliation(s)
- Bjarke Jensen
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Tobias Wang
- Department of Bioscience, Zoophysiology, Aarhus University, Aarhus, Denmark
| | - Antoon F M Moorman
- Department of Medical Biology, Academic Medical Center, University of Amsterdam, The Netherlands
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