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Bishop PJ, Pierce SE. The fossil record of appendicular muscle evolution in Synapsida on the line to mammals: Part II-Hindlimb. Anat Rec (Hoboken) 2024; 307:1826-1896. [PMID: 37727023 DOI: 10.1002/ar.25310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/15/2023] [Accepted: 08/08/2023] [Indexed: 09/21/2023]
Abstract
This paper is the second in a two-part series that charts the evolution of appendicular musculature along the mammalian stem lineage, drawing upon the exceptional fossil record of extinct synapsids. Here, attention is focused on muscles of the hindlimb. Although the hindlimb skeleton did not undergo as marked a transformation on the line to mammals as did the forelimb skeleton, the anatomy of extant tetrapods indicates that major changes to musculature have nonetheless occurred. To better understand these changes, this study surveyed the osteological evidence for muscular attachments in extinct mammalian and nonmammalian synapsids, two extinct amniote outgroups, and a large selection of extant mammals, saurians, and salamanders. Observations were integrated into an explicit phylogenetic framework, comprising 80 character-state complexes covering all muscles crossing the hip, knee, and ankle joints. These were coded for 33 operational taxonomic units spanning >330 Ma of tetrapod evolution, and ancestral state reconstruction was used to evaluate the sequence of muscular evolution along the stem lineage from Amniota to Theria. The evolutionary history of mammalian hindlimb musculature was complex, nonlinear, and protracted, with several instances of convergence and pulses of anatomical transformation that continued well into the crown group. Numerous traits typically regarded as characteristically "mammalian" have much greater antiquity than previously recognized, and for some traits, most synapsids are probably more reflective of the ancestral amniote condition than are extant saurians. More broadly, this study highlights the utility of the fossil record in interpreting the evolutionary appearance of distinctive anatomies.
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Affiliation(s)
- Peter J Bishop
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Geosciences Program, Queensland Museum, Brisbane, Queensland, Australia
| | - Stephanie E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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2
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Kort AE, Jones KE. Function of revolute zygapophyses in the lumbar vertebrae of early placental mammals. Anat Rec (Hoboken) 2024; 307:1918-1929. [PMID: 37712919 DOI: 10.1002/ar.25323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/11/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
The unique morphology of mammalian lumbar vertebrae allows the spine to flex and extend in the sagittal plane during locomotion. This movement increases stride length and allows mammals to efficiently breathe while running with an asymmetric gait. In extant mammals, the amount of flexion that occurs varies across different locomotor styles, with dorsostable runners relying more on movement of long limbs to run and dorsomobile runners incorporating more flexion of the back. Although long limbs and a stabilized lumbar region are commonly associated with each other in extant mammals, many "archaic" placental mammals with short limbs had lumbar vertebrae with revolute zygapophyses. These articulations with an interlocking S-shape are found only in artiodactyls among extant mammals and have been hypothesized to stabilize against flexion of the back. This would suggest that archaic placental mammals may not have incorporated dorsoventral flexion into locomotion to the same extent as extant mammals with similar proportions. We tested the relative mobility of fossil lumbar vertebrae from two early placental mammals, the creodonts Patriofelis and Limnocyon, to see how these vertebrae may have functioned. We compared range of motion (ROM) between the original vertebrae, with revolute morphology and digitally altered vertebrae with a flat morphology. We found that the revolute morphology had relatively little effect on dorsoventral flexion and instead that it likely prevented disarticulation due to shear forces on the spine. These results show that flexion of the spine has been an important part of mammalian locomotion for at least 50 million years.
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Affiliation(s)
- Anne E Kort
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Katrina E Jones
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, UK
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3
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Bishop PJ, Pierce SE. The fossil record of appendicular muscle evolution in Synapsida on the line to mammals: Part I-Forelimb. Anat Rec (Hoboken) 2024; 307:1764-1825. [PMID: 37726984 DOI: 10.1002/ar.25312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/15/2023] [Accepted: 08/08/2023] [Indexed: 09/21/2023]
Abstract
This paper is the first in a two-part series that charts the evolution of appendicular musculature along the mammalian stem lineage, drawing upon the exceptional fossil record of extinct synapsids. Here, attention is focused on muscles of the forelimb. Understanding forelimb muscular anatomy in extinct synapsids, and how this changed on the line to mammals, can provide important perspective for interpreting skeletal and functional evolution in this lineage, and how the diversity of forelimb functions in extant mammals arose. This study surveyed the osteological evidence for muscular attachments in extinct mammalian and nonmammalian synapsids, two extinct amniote outgroups, and a large selection of extant mammals, saurians, and salamanders. Observations were integrated into an explicit phylogenetic framework, comprising 73 character-state complexes covering all muscles crossing the shoulder, elbow, and wrist joints. These were coded for 33 operational taxonomic units spanning >330 Ma of tetrapod evolution, and ancestral state reconstruction was used to evaluate the sequence of muscular evolution along the stem lineage from Amniota to Theria. In addition to producing a comprehensive documentation of osteological evidence for muscle attachments in extinct synapsids, this work has clarified homology hypotheses across disparate taxa and helped resolve competing hypotheses of muscular anatomy in extinct species. The evolutionary history of mammalian forelimb musculature was a complex and nonlinear narrative, punctuated by multiple instances of convergence and concentrated phases of anatomical transformation. More broadly, this study highlights the great insight that a fossil-based perspective can provide for understanding the assembly of novel body plans.
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Affiliation(s)
- Peter J Bishop
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Geosciences Program, Queensland Museum, Brisbane, Queensland, Australia
| | - Stephanie E Pierce
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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4
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Petrullo L, Delaney D, Boutin S, Lane JE, McAdam AG, Dantzer B. A future food boom rescues the negative effects of early-life adversity on adult lifespan in a small mammal. Proc Biol Sci 2024; 291:20232681. [PMID: 38654643 PMCID: PMC11040256 DOI: 10.1098/rspb.2023.2681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Early-life adversity, even when transient, can have lasting effects on individual phenotypes and reduce lifespan across species. If these effects can be mitigated by a high-quality later-life environment, then differences in future resources may explain variable resilience to early-life adversity. Using data from over 1000 wild North American red squirrels, we tested the hypothesis that the costs of early-life adversity for adult lifespan could be offset by later-life food abundance. We identified six adversities that reduced juvenile survival in the first year of life, though only one-birth date-had continued independent effects on adult lifespan. We then built a weighted early-life adversity (wELA) index integrating the sum of adversities and their effect sizes. Greater weighted early-life adversity predicted shorter adult lifespans in males and females, but a naturally occurring food boom in the second year of life ameliorated this effect. Experimental food supplementation did not replicate this pattern, despite increasing lifespan, indicating that the buffering effect of a future food boom may hinge on more than an increase in available calories. Our results suggest a non-deterministic role of early-life conditions for later-life phenotype, highlighting the importance of evaluating the consequences of early-life adversity in the context of an animal's entire life course.
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Affiliation(s)
- Lauren Petrullo
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, 857192, AZ, USA
| | - David Delaney
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, 803023, CO, USA
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, 500114, IA, USA
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, T6G 2R35, Alberta, Canada
| | - Jeffrey E. Lane
- Department of Biology, University of Saskatchewan, Saskatoon, S7N 5A26, Saskatchewan, Canada
| | - Andrew G. McAdam
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, 500114, IA, USA
| | - Ben Dantzer
- Department of Psychology, University of Michigan, Ann Arbor, 481097, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 481097, MI, USA
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5
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Mendes CP, Albert WR, Amir Z, Ancrenaz M, Ash E, Azhar B, Bernard H, Brodie J, Bruce T, Carr E, Clements GR, Davies G, Deere NJ, Dinata Y, Donnelly CA, Duangchantrasiri S, Fredriksson G, Goossens B, Granados A, Hearn A, Hon J, Hughes T, Jansen P, Kawanishi K, Kinnaird M, Koh S, Latinne A, Linkie M, Loi F, Lynam AJ, Meijaard E, Mohd-Azlan J, Moore JH, Nathan SKSS, Ngoprasert D, Novarino W, Nursamsi I, O'Brien T, Ong R, Payne J, Priatna D, Rayan DM, Reynolds G, Rustam R, Selvadurai S, Shia A, Silmi M, Sinovas P, Sribuarod K, Steinmetz R, Struebig MJ, Sukmasuang R, Sunarto S, Tarmizi T, Thapa A, Traeholt C, Wearn OR, Wibisono HB, Wilting A, Wong ST, Wong ST, Word J, Chiok WX, Zainuddin ZZ, Luskin MS. CamTrapAsia: A dataset of tropical forest vertebrate communities from 239 camera trapping studies. Ecology 2024:e4299. [PMID: 38650359 DOI: 10.1002/ecy.4299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 09/26/2023] [Accepted: 01/30/2024] [Indexed: 04/25/2024]
Abstract
Information on tropical Asian vertebrates has traditionally been sparse, particularly when it comes to cryptic species inhabiting the dense forests of the region. Vertebrate populations are declining globally due to land-use change and hunting, the latter frequently referred as "defaunation." This is especially true in tropical Asia where there is extensive land-use change and high human densities. Robust monitoring requires that large volumes of vertebrate population data be made available for use by the scientific and applied communities. Camera traps have emerged as an effective, non-invasive, widespread, and common approach to surveying vertebrates in their natural habitats. However, camera-derived datasets remain scattered across a wide array of sources, including published scientific literature, gray literature, and unpublished works, making it challenging for researchers to harness the full potential of cameras for ecology, conservation, and management. In response, we collated and standardized observations from 239 camera trap studies conducted in tropical Asia. There were 278,260 independent records of 371 distinct species, comprising 232 mammals, 132 birds, and seven reptiles. The total trapping effort accumulated in this data paper consisted of 876,606 trap nights, distributed among Indonesia, Singapore, Malaysia, Bhutan, Thailand, Myanmar, Cambodia, Laos, Vietnam, Nepal, and far eastern India. The relatively standardized deployment methods in the region provide a consistent, reliable, and rich count data set relative to other large-scale pressence-only data sets, such as the Global Biodiversity Information Facility (GBIF) or citizen science repositories (e.g., iNaturalist), and is thus most similar to eBird. To facilitate the use of these data, we also provide mammalian species trait information and 13 environmental covariates calculated at three spatial scales around the camera survey centroids (within 10-, 20-, and 30-km buffers). We will update the dataset to include broader coverage of temperate Asia and add newer surveys and covariates as they become available. This dataset unlocks immense opportunities for single-species ecological or conservation studies as well as applied ecology, community ecology, and macroecology investigations. The data are fully available to the public for utilization and research. Please cite this data paper when utilizing the data.
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Affiliation(s)
- Calebe P Mendes
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
- School of the Environment, University of Queensland, Brisbane, Queensland, Australia
| | | | - Zachary Amir
- School of the Environment, University of Queensland, Brisbane, Queensland, Australia
| | | | - Eric Ash
- WildCRU, Department of Zoology, University of Oxford, Oxford, UK
| | - Badrul Azhar
- Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang, Malaysia
| | - Henry Bernard
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Jedediah Brodie
- Wildlife Biology, University of Montana, Missoula, Montana, USA
| | - Tom Bruce
- School of the Environment, University of Queensland, Brisbane, Queensland, Australia
| | - Elliot Carr
- School of the Environment, University of Queensland, Brisbane, Queensland, Australia
| | | | - Glyn Davies
- Sabah Landscape Programme, World Wildlife Fund, Kota Kinabalu, Malaysia
| | - Nicolas J Deere
- Durrell Institute of Conservation and Ecology (DICE), University of Kent, Canterbury, UK
| | - Yoan Dinata
- Indonesia Program, Zoological Society of London, London, UK
| | | | - Somphot Duangchantrasiri
- Wildlife Research Division, "Department of National Parks, Plant, and Wildlife Conservation", Bangkok, Thailand
| | | | | | - Alys Granados
- Felidae Conservation Fund, Mill Valley, California, USA
| | - Andrew Hearn
- WildCRU, Department of Zoology, University of Oxford, Oxford, UK
| | - Jason Hon
- Malaysia Program, World Wildlife Fund, Kuching, Malaysia
| | - Tom Hughes
- Conservation Medicine, Sungai Buloh, Malaysia
| | - Patrick Jansen
- Wildlife Ecology and Conservation, Wageningen University, Wageningen, Netherlands
| | - Kae Kawanishi
- Malaysian Conservation Alliance for Tigers (MYCAT), Kuala Lumpur, Malaysia
| | | | - Sharon Koh
- Malaysia Program, World Wildlife Fund, Kuching, Malaysia
| | - Alice Latinne
- Viet Nam Country Program, Wildlife Conservation Society, New York, New York, USA
| | - Matthew Linkie
- Indonesia Program, Wildlife Conservation Society, Bogor, Indonesia
| | - Federica Loi
- Regional Veterinary Epidemiological Observatory, Istituto Zooprofilattico Sperimentale della Sardegna, Cagliari, Italy
| | - Anthony J Lynam
- Thailand Program, Wildlife Conservation Society, Nonthaburi, Thailand
| | | | | | | | | | - Dusit Ngoprasert
- Conservation Ecology, King Mongkut's University of Technology Thonburi, Thon Buri, Thailand
| | - Wilson Novarino
- Department of Biology, Andalas University, Padang, Indonesia
| | - Ilyas Nursamsi
- School of the Environment, University of Queensland, Brisbane, Queensland, Australia
| | | | - Robert Ong
- Borneo Rhino Alliance, Kota Kinabalu, Malaysia
| | - John Payne
- Borneo Rhino Alliance, Kota Kinabalu, Malaysia
| | - Dolly Priatna
- Graduate School of Environmental Management, Pakuan University, Bogor, Indonesia
| | - D Mark Rayan
- Malaysia Program, Wildlife Conservation Society, New York, New York, USA
| | - Glen Reynolds
- Conservation Programme, South East Asia Rainforest Research Partnership (SEARRP), Kota Kinabalu, Malaysia
| | - Rustam Rustam
- Faculty of Forestry, Mulawarman University, Kota Samarinda, Indonesia
| | - Sasidhran Selvadurai
- Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang, Malaysia
| | | | - Muhammad Silmi
- Biodiversity Division, United Plantations Berhad-PT Surya Sawit Sejati, Central Kalimantan, Indonesia
| | - Pablo Sinovas
- Cambodia Programme, Fauna & Flora International, Phnom Penh, Cambodia
| | - Kriangsak Sribuarod
- Klongsang Wildlife Research Station, Department of National Park Wildlife and Plant, Khlong Saeng Wildlife Research Station, Bangkok, Thailand
| | | | - Matthew J Struebig
- Durrell Institute of Conservation and Ecology (DICE), University of Kent, Canterbury, UK
| | | | | | | | - Arjun Thapa
- School of the Environment, University of Queensland, Brisbane, Queensland, Australia
| | - Carl Traeholt
- Research and Conservation Division, Copenhagen Zoo, Copenhagen, Denmark
| | - Oliver R Wearn
- Vietnam Programme, Fauna & Flora International, Hanoi, Vietnam
| | | | - Andreas Wilting
- Department of Ecological Dynamics, Leibniz Institute of Zoo and Wildlife Research, Berlin, Germany
| | - Seth Timothy Wong
- Department of Ecological Dynamics, Leibniz Institute of Zoo and Wildlife Research, Berlin, Germany
| | - Siew Te Wong
- Bornean Sun Bear Conservation Centre, Sandakan, Malaysia
| | | | - Wen Xuan Chiok
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | | | - Matthew Scott Luskin
- School of the Environment, University of Queensland, Brisbane, Queensland, Australia
- Centre for Biodiversity and Conservation Science, University of Queensland, Brisbane, Queensland, Australia
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Guzmán-Cornejo C, Herrera-Mares A, García-Prieto L, Oceguera-Figueroa A, López-Pérez AM, Dzul-Rosado K. Potential zoonotic role of the tick Amblyomma cf. oblongoguttatum (Ixodida: Ixodidae) in the bacterial transmission of Ehrlichia chaffeensis (Rickettsiales: Anaplasmataceae) in a deciduous tropical forest in Mexico. J Med Entomol 2024:tjae047. [PMID: 38616043 DOI: 10.1093/jme/tjae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/20/2024] [Accepted: 03/29/2024] [Indexed: 04/16/2024]
Abstract
Ehrlichia chaffeensis is a bacterium belonging to the Anaplasmataceae family. In Mexico, only 2 species have been recorded in association with tick species and humans. The objective of the present study was to detect the presence of bacteria of the genus Ehrlichia in ticks collected from the Chamela-Cuixmala Biosphere Reserve, Jalisco, Mexico. The collected ticks were identified and analyzed individually by polymerase chain reaction to amplify a fragment of the Anaplasmataceae 16S rRNA gene and the Ehrlichia-specific dsb gene. A total of 204 ticks, corresponding to 5 species of Ixodidae and 1 of Argasidae, were collected from 147 mammals of 6 species and 4 orders; 57 ticks collected from vegetation were also included. Among the total ticks collected, 1.47% (3/204) was positive for Ehrlichia sp. DNA was obtained using the primers EHR 16SD and EHR 16SR for 16S rRNA and DSB-330 and DSB-728 for dsb. The positive samples corresponded to a larva (Amblyomma sp.) associated with Didelphis virginiana and 2 nymphs (Amblyomma cf. oblongoguttatum) infesting Nasua narica. None of the ticks collected from the vegetation tested positive for Ehrlichia sp. DNA on the basis of the 16S rRNA and dsb genes. The sequences from the larvae of Amblyomma sp. and the nymphs of A. cf. oblongoguttatum were similar to those of E. chaffeensis. The phylogenetic analysis inferred with maximum likelihood corroborated the identity as E. chaffeensis. Although the role of these tick species as vectors of E. chaffeensis is still undetermined, the presence of infected ticks in the area indicates a potential zoonotic risk.
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Affiliation(s)
- Carmen Guzmán-Cornejo
- Laboratorio de Acarología, Departamento de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Angel Herrera-Mares
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis García-Prieto
- Laboratorio de Helmintología, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Alejandro Oceguera-Figueroa
- Laboratorio de Helmintología, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Andrés M López-Pérez
- Red de Biología y Conservación de Vertebrados, Instituto de Ecología (INECOL A.C.), Veracruz, México
| | - Karla Dzul-Rosado
- Centro de Investigaciones Regionales "Dr. Hideyo Noguchi," Universidad Autónoma de Yucatán, Mérida, Yucatán, México
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Seeber PA, Batke L, Dvornikov Y, Schmidt A, Wang Y, Stoof-Leichsenring K, Moon K, Vohr SH, Shapiro B, Epp LS. Mitochondrial genomes of Pleistocene megafauna retrieved from recent sediment layers of two Siberian lakes. eLife 2024; 12:RP89992. [PMID: 38488477 PMCID: PMC10942779 DOI: 10.7554/elife.89992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Abstract
Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals-both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g. >400 K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.
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Affiliation(s)
| | - Laura Batke
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Yury Dvornikov
- Agroengineering Department/Department of Landscape Design and Sustainable Ecosystems, Agrarian and Technological Institute, RUDN University, Moscow, Russian Federation
- Laboratory of Carbon Monitoring in Terrestrial Ecosystems, Institute of Physicochemical and Biological Problems of Soil Science of the Russian Academy of Sciences, Pushchino, Russian Federation
| | | | - Yi Wang
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kathleen Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, Potsdam, Germany
| | - Katie Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, United States
| | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, United States
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, United States
| | - Laura S Epp
- Department of Biology, University of Konstanz, Konstanz, Germany
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8
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Pasciullo Boychuck S, Brenner LJ, Gagorik CN, Schamel JT, Baker S, Tran E, vonHoldt BM, Koepfli K, Maldonado JE, DeCandia AL. The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations. Ecol Evol 2024; 14:e11017. [PMID: 38362164 PMCID: PMC10867392 DOI: 10.1002/ece3.11017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024] Open
Abstract
California's Channel Islands are home to two endemic mammalian carnivores: island foxes (Urocyon littoralis) and island spotted skunks (Spilogale gracilis amphiala). Although it is rare for two insular terrestrial carnivores to coexist, these known competitors persist on both Santa Cruz Island and Santa Rosa Island. We hypothesized that examination of their gut microbial communities would provide insight into the factors that enable this coexistence, as microbial symbionts often reflect host evolutionary history and contemporary ecology. Using rectal swabs collected from island foxes and island spotted skunks sampled across both islands, we generated 16S rRNA amplicon sequencing data to characterize their gut microbiomes. While island foxes and island spotted skunks both harbored the core mammalian microbiome, host species explained the largest proportion of variation in the dataset. We further identified intraspecific variation between island populations, with greater differentiation observed between more specialist island spotted skunk populations compared to more generalist island fox populations. This pattern may reflect differences in resource utilization following fine-scale niche differentiation. It may further reflect evolutionary differences regarding the timing of intraspecific separation. Considered together, this study contributes to the growing catalog of wildlife microbiome studies, with important implications for understanding how eco-evolutionary processes enable the coexistence of terrestrial carnivores-and their microbiomes-in island environments.
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Affiliation(s)
| | | | | | | | | | - Elton Tran
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | | | - Klaus‐Peter Koepfli
- Center for Species SurvivalSmithsonian's National Zoo & Conservation Biology InstituteFront RoyalVirginiaUSA
- Smithsonian‐Mason School of ConservationGeorge Mason UniversityFront RoyalVirginiaUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian's National Zoo & Conservation Biology InstituteWashingtonDCUSA
| | - Alexandra L. DeCandia
- Biology, Georgetown UniversityWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian's National Zoo & Conservation Biology InstituteWashingtonDCUSA
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9
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Crandall KE, Millien V, Kerr JT. High-resolution environmental and host-related factors impacting questing Ixodes scapularis at their northern range edge. Ecol Evol 2024; 14:e10855. [PMID: 38384829 PMCID: PMC10879908 DOI: 10.1002/ece3.10855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 02/23/2024] Open
Abstract
The geographic range of tick populations has expanded in Canada due to climate warming and the associated poleward range shifts of their vertebrate hosts. Abiotic factors, such as temperature, precipitation, and snow, are known to directly affect tick abundance. Yet, biotic factors, such as the abundance and diversity of mammal hosts, may also alter tick abundance and consequent tick-borne disease risk. Here, we incorporated host surveillance data with high-resolution environmental data to evaluate the combined impact of abiotic and biotic factors on questing Ixodes scapularis abundance in Ontario and Quebec, Canada. High-resolution abiotic factors were derived from remote sensing satellites and meteorological towers, while biotic factors related to mammal hosts were derived from active surveillance data that we collected in the field. Generalized additive models were used to determine the relative importance of abiotic and biotic factors on questing I. scapularis abundance. Combinations of abiotic and biotic factors were identified as important drivers of abundances of questing I. scapularis. Positive and negative linear relationships were found for questing I. scapularis abundance with monthly mean precipitation and accumulated snow, but no effect was found for the relative abundance of white-footed mice. Positive relationships were also identified between questing I. scapularis abundance with monthly mean precipitation and mammal species richness. Therefore, future studies that assess I. scapularis should incorporate host surveillance data with high-resolution environmental factors to determine the key drivers impacting the abundance and geographic spread of tick populations and tick-borne pathogens.
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Affiliation(s)
- Kirsten E. Crandall
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
- Department of BiologyMcGill UniversityMontréalQuébecCanada
- Redpath MuseumMcGill UniversityMontréalQuébecCanada
| | - Virginie Millien
- Department of BiologyMcGill UniversityMontréalQuébecCanada
- Redpath MuseumMcGill UniversityMontréalQuébecCanada
| | - Jeremy T. Kerr
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
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10
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Laundon D, Gostling NJ, Sengers BG, Chavatte-Palmer P, Lewis RM. Placental evolution from a three-dimensional and multiscale structural perspective. Evolution 2024; 78:13-25. [PMID: 37974468 DOI: 10.1093/evolut/qpad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
The placenta mediates physiological exchange between the mother and the fetus. In placental mammals, all placentas are descended from a single common ancestor and functions are conserved across species; however, the placenta exhibits radical structural diversity. The selective pressures behind this structural diversity are poorly understood. Traditionally, placental structures have largely been investigated by grouping them into qualitative categories. Assessing the placenta on this basis could be problematic when inferring the relative "efficiency" of a placental configuration to transfer nutrients from mother to fetus. We argue that only by considering placentas as three-dimensional (3D) biological structures, integrated across scales, can the evolutionary questions behind their enormous structural diversity be quantitatively determined. We review the current state of placental evolution from a structural perspective, detail where 3D imaging and computational modeling have been used to gain insight into placental function, and outline an experimental roadmap to answer evolutionary questions from a multiscale 3D structural perspective. Our approach aims to shed light on placental evolution, and can be transferred to evolutionary investigations in any organ system.
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Affiliation(s)
- Davis Laundon
- Faculty of Medicine, School of Human Development and Health, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Neil J Gostling
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Faculty of Environmental and Life Sciences, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Bram G Sengers
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- Faculty of Engineering and Physical Sciences, School of Engineering, University of Southampton, Southampton, United Kingdom
| | - Pascale Chavatte-Palmer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | - Rohan M Lewis
- Faculty of Medicine, School of Human Development and Health, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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11
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Rabaiotti D, Coulson T, Woodroffe R. Climate change is predicted to cause population collapse in a cooperative breeder. Glob Chang Biol 2023; 29:6002-6017. [PMID: 37605853 DOI: 10.1111/gcb.16890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 05/29/2023] [Accepted: 06/05/2023] [Indexed: 08/23/2023]
Abstract
It has been suggested that animals may have evolved cooperative breeding strategies in response to extreme climatic conditions. Climate change, however, may push species beyond their ability to cope with extreme climates, and reduce the group sizes in cooperatively breeding species to a point where populations are no longer viable. Predicting the impact of future climates on these species is challenging as modelling the impact of climate change on their population dynamics requires information on both group- and individual-level responses to climatic conditions. Using a single-sex individual-based model incorporating demographic responses to ambient temperature in an endangered species, the African wild dog Lycaon pictus, we show that there is a threshold temperature above which populations of the species are predicted to collapse. For simulated populations with carrying capacities equivalent to the median size of real-world populations (nine packs), extinction risk increases once temperatures exceed those predicted in the best-case climate warming scenario (Representative Concentration Pathway [RCP] 2.6). The threshold is higher (between RCP 4.5 and RCP 6.0) for larger simulated populations (30 packs), but 84% of real-world populations number <30 packs. Simulated populations collapsed because, at high ambient temperatures, juvenile survival was so low that packs were no longer recruiting enough individuals to persist, leading them to die out. This work highlights the importance of social dynamics in determining impacts of climatic variables on social species, and the critical role that recruitment can play in driving population-level impacts of climate change. Population models parameterised on long-term data are essential for predicting future population viability under climate change.
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Affiliation(s)
- Daniella Rabaiotti
- Institute of Zoology, Zoological Society of London, London, UK
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, Division of Biosciences, University College London, London, UK
| | - Tim Coulson
- Department of Biology, University of Oxford, Oxford, UK
| | - Rosie Woodroffe
- Institute of Zoology, Zoological Society of London, London, UK
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, Division of Biosciences, University College London, London, UK
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13
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Seeber PA, Palmer Z, Schmidt A, Chagas A, Kitagawa K, Marinova-Wolff E, Tafelmaier Y, Epp LS. The first European woolly rhinoceros mitogenomes, retrieved from cave hyena coprolites, suggest long-term phylogeographic differentiation. Biol Lett 2023; 19:20230343. [PMID: 37909055 PMCID: PMC10618854 DOI: 10.1098/rsbl.2023.0343] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
The woolly rhinoceros (Coelodonta antiquitatis) is an iconic species of the Eurasian Pleistocene megafauna, which was abundant in Eurasia in the Pleistocene until its demise beginning approximately 10 000 years ago. Despite the early recovery of several specimens from well-known European archaeological sites, including its type specimen (Blumenbach 1799), no genomes of European populations were available so far, and all available genomic data originated exclusively from Siberian populations. Using coprolites of cave hyenas (Crocuta crocuta spelea) recovered from Middle Palaeolithic layers of two caves in Germany (Bockstein-Loch and Hohlenstein-Stadel), we isolated and enriched predator and prey DNA to assemble the first European woolly rhinoceros mitogenomes, in addition to cave hyena mitogenomes. Both coprolite samples produced copious sequences assigned to C. crocuta (27% and 59% mitogenome coverage, respectively) and woolly rhinoceros (Coelodonta antiquitatis; 27% and 81% coverage, respectively). The sequences suggested considerable DNA degradation, which may limit the conclusions to be drawn; however, the mitogenomes of European woolly rhinoceros are genetically distinct from the Siberian woolly rhinoceros, and analyses of the more complete mitogenome suggest a split of the populations potentially coinciding with the earliest fossil records of woolly rhinoceros in Europe.
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Affiliation(s)
- P. A. Seeber
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - Z. Palmer
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - A. Schmidt
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - A. Chagas
- Limnological Institute, University of Konstanz, Konstanz, Germany
| | - K. Kitagawa
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tubingen, Germany
- Institute of Archaeological Sciences, Department of Geosciences, University of Tübingen, Tubingen, Germany
| | - E. Marinova-Wolff
- Laboratory for Archaeobotany Baden-Württemberg, State Office for Cultural Heritage, Gaienhofen-Hemmenhofen, Germany
| | - Y. Tafelmaier
- State Office for Cultural Heritage Baden-Württemberg, Palaeolithic & Mesolithic Research Unit, Gaienhofen-Hemmenhofen, Germany
| | - L. S. Epp
- Limnological Institute, University of Konstanz, Konstanz, Germany
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14
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Lavery TH, Holland A, Jino N, Judge A, Judge H, Onga P, Sese K. Vangunu giant rat ( Uromys vika) survives in the Zaira Community Resource Management Area, Solomon Islands. Ecol Evol 2023; 13:e10703. [PMID: 38020687 PMCID: PMC10659236 DOI: 10.1002/ece3.10703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Described in 2017 and known only from the holotype, Uromys vika is surely among the world's least studied rodents. This critically endangered species is facing a rapidly increasing scale for threat from logging of its primary lowland forest habitat, on the only island on which it occurs-Vangunu, Solomon Islands. However, a deep traditional ecological knowledge of U. vika is held by Vangunu's people. Using camera traps and guided by this knowledge, we aimed to make additional records of U. vika in the last major block of Vangunu's primary forest. We successfully captured 95 images of what we postulate is four different individuals. The forests at Zaira represent the last suitable habitat remaining for this species, and recent development consent for logging at Zaira will lead to its extinction if permitted to proceed.
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Affiliation(s)
- Tyrone H. Lavery
- School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
| | - Adrian Holland
- Zaira RangersZaira VillageWestern ProvinceSolomon Islands
| | - Nixon Jino
- Zaira RangersZaira VillageWestern ProvinceSolomon Islands
| | - Atuna Judge
- Zaira RangersZaira VillageWestern ProvinceSolomon Islands
| | - Hikuna Judge
- Zaira RangersZaira VillageWestern ProvinceSolomon Islands
| | - Pandakai Onga
- Zaira RangersZaira VillageWestern ProvinceSolomon Islands
| | - Kevin Sese
- School of Natural Resources and Applied SciencesSolomon Islands National UniversityHoniaraSolomon Islands
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15
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Nakagawa S, Yamaguchi Y. Spontaneous recurrence of a summer-like diel rhythm in the body temperature of the Syrian hamster after hibernation. Proc Biol Sci 2023; 290:20230922. [PMID: 37848068 PMCID: PMC10581774 DOI: 10.1098/rspb.2023.0922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Mammalian hibernation is a survival strategy characterized by metabolic suppression and drastically lowering body temperature (Tb), used during harsh seasons with food shortages and cold. The Syrian hamster commences hibernation in response to a short photoperiod and cold but spontaneously concludes hibernation after several months without environmental cues. Little is known about the changes in diel rhythms during hibernation. Using long-term and high-resolution Tb data, we analysed the diel Tb rhythm time-course changes in Syrian hamsters raised under summer-like conditions (long photoperiod (LP) and warm; LP-warm) and transferred to winter-like conditions (short photoperiod (SP) and cold; SP-cold). The diel Tb rhythm was undetectable during the hibernation period (HIBP), reappearing after the HIBP. The phase of this returning rhythm reverted to the LP entrainment phase characteristics despite the ambient SP and then re-entrained to the ambient SP as if the hamsters were transferred from the LP-warm to SP-cold conditions. The diel Tb rhythm reverted from the SP- to LP-type in a hibernation-dependent manner. Under constant dark and cold conditions, the circadian Tb rhythm recovered without photic stimuli following the HIBP. These findings suggest that hibernation involves a program that anticipates the ambient photoperiod when animals emerge from hibernation.
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Affiliation(s)
- Satoshi Nakagawa
- Graduate School of Environmental Sciences, Hokkaido University, Sapporo 060-0819, Japan
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Yoshifumi Yamaguchi
- Graduate School of Environmental Sciences, Hokkaido University, Sapporo 060-0819, Japan
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
- Inamori Research Institute for Science, Kyoto 600-8411, Japan
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16
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Beichman AC, Robinson J, Lin M, Moreno-Estrada A, Nigenda-Morales S, Harris K. Evolution of the Mutation Spectrum Across a Mammalian Phylogeny. Mol Biol Evol 2023; 40:msad213. [PMID: 37770035 PMCID: PMC10566577 DOI: 10.1093/molbev/msad213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/21/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023] Open
Abstract
Although evolutionary biologists have long theorized that variation in DNA repair efficacy might explain some of the diversity of lifespan and cancer incidence across species, we have little data on the variability of normal germline mutagenesis outside of humans. Here, we shed light on the spectrum and etiology of mutagenesis across mammals by quantifying mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k-mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clock-like mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these signatures to fit each species' 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the 1-mer spectrum's phylogenetic signal in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.
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Affiliation(s)
- Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Meixi Lin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity, Advanced Genomics Unit (UGA-LANGEBIO), CINVESTAV, Irapuato, Mexico
| | - Sergio Nigenda-Morales
- Department of Biological Sciences, California State University, San Marcos, San Marcos, CA, USA
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA
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17
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Travouillon KJ, Cooper C, Bouzin JT, Umbrello LS, Lewis SW. All-a-glow: spectral characteristics confirm widespread fluorescence for mammals. R Soc Open Sci 2023; 10:230325. [PMID: 37800154 PMCID: PMC10548093 DOI: 10.1098/rsos.230325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Mammalian fluorescence has been reported from numerous species of monotreme, marsupial and placental mammal. However, it is unknown how widespread this phenomenon is among mammals, it is unclear for many species if these observations of 'glowing' are true fluorescence and the biological function of fluorescence remains undetermined. We examined a wide range of mammal species held in a museum collection for the presence of apparent fluorescence using UV light, and then analysed a subset of preserved and non-preserved specimens by fluorescent spectroscopy at three different excitation wavelengths to assess whether the observations were fluorescence or optical scatter, and the impact of specimen preservation. We also evaluated if fluorescence was related to biological traits. We found that fluorescence is widespread in mammalian taxa; we identified examples of the phenomena among 125 species representing all 27 living mammalian orders and 79 families. For a number of model species, there was no evidence of a corresponding shift in the emission spectra when the wavelength of excitation was shifted, suggesting that observations of 'glowing' mammals were indeed fluorescence. Preservation method impacted the intensity of fluorescence. Fluorescence was most common and most intense among nocturnal species and those with terrestrial, arboreal and fossorial habits, with more of their body being more fluorescent. It remains unclear if fluorescence has any specific biological role for mammals. It appears to be a ubiquitous property of unpigmented fur and skin but may function to make these areas appear brighter and therefore enhance visual signalling, especially for nocturnal species.
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Affiliation(s)
- Kenny J. Travouillon
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia 6102, Australia
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
| | - Christine Cooper
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia 6102, Australia
| | - Jemmy T. Bouzin
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia 6102, Australia
| | - Linette S. Umbrello
- Collections and Research, Western Australian Museum, Welshpool, Western Australia 6106, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Gardens Point Campus, 2 George Street, Brisbane, Queensland 4001, Australia
| | - Simon W. Lewis
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia 6102, Australia
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18
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Sall IM, Flaviu TA. Plant and mammalian-derived extracellular vesicles: a new therapeutic approach for the future. Front Bioeng Biotechnol 2023; 11:1215650. [PMID: 37781539 PMCID: PMC10534050 DOI: 10.3389/fbioe.2023.1215650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 10/03/2023] Open
Abstract
Background: In recent years, extracellular vesicles have been recognized as important mediators of intercellular communication through the transfer of active biomolecules (proteins, lipids, and nucleic acids) across the plant and animal kingdoms and have considerable roles in several physiological and pathological mechanisms, showing great promise as new therapeutic strategies for a variety of pathologies. Methods: In this study, we carefully reviewed the numerous articles published over the last few decades on the general knowledge of extracellular vesicles, their application in the therapy of various pathologies, and their prospects as an approach for the future. Results: The recent discovery and characterization of extracellular vesicles (EVs) of diverse origins and biogenesis have altered the current paradigm of intercellular communication, opening up new diagnostic and therapeutic perspectives. Research into these EVs released by plant and mammalian cells has revealed their involvement in a number of physiological and pathological mechanisms, such as embryonic development, immune response, tissue regeneration, and cancer. They are also being studied as potential biomarkers for disease diagnosis and vectors for drug delivery. Conclusion: Nanovesicles represent powerful tools for intercellular communication and the transfer of bioactive molecules. Their molecular composition and functions can vary according to their origin (plant and mammalian), so their formation, composition, and biological roles open the way to therapeutic applications in a variety of pathologies, which is arousing growing interest in the scientific community. Clinical Trial Registration: ClinicalTrials.gov identifier: NCT03608631.
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Affiliation(s)
| | - Tabaran Alexandru Flaviu
- Department of Anatomic Pathology, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
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19
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Flies AS, Flies EJ, Fountain-Jones NM, Musgrove RE, Hamede RK, Philips A, Perrott MRF, Dunowska M. Wildlife nidoviruses: biology, epidemiology, and disease associations of selected nidoviruses of mammals and reptiles. mBio 2023; 14:e0071523. [PMID: 37439571 PMCID: PMC10470586 DOI: 10.1128/mbio.00715-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023] Open
Abstract
Wildlife is the source of many emerging infectious diseases. Several viruses from the order Nidovirales have recently emerged in wildlife, sometimes with severe consequences for endangered species. The order Nidovirales is currently classified into eight suborders, three of which contain viruses of vertebrates. Vertebrate coronaviruses (suborder Cornidovirineae) have been extensively studied, yet the other major suborders have received less attention. The aim of this minireview was to summarize the key findings from the published literature on nidoviruses of vertebrate wildlife from two suborders: Arnidovirineae and Tornidovirineae. These viruses were identified either during investigations of disease outbreaks or through molecular surveys of wildlife viromes, and include pathogens of reptiles and mammals. The available data on key biological features, disease associations, and pathology are presented, in addition to data on the frequency of infections among various host populations, and putative routes of transmission. While nidoviruses discussed here appear to have a restricted in vivo host range, little is known about their natural life cycle. Observational field-based studies outside of the mortality events are needed to facilitate an understanding of the virus-host-environment interactions that lead to the outbreaks. Laboratory-based studies are needed to understand the pathogenesis of diseases caused by novel nidoviruses and their evolutionary histories. Barriers preventing research progress include limited funding and the unavailability of virus- and host-specific reagents. To reduce mortalities in wildlife and further population declines, proactive development of expertise, technologies, and networks should be developed. These steps would enable effective management of future outbreaks and support wildlife conservation.
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Affiliation(s)
- Andrew S. Flies
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Emily J. Flies
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- Healthy Landscapes Research Group, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Ruth E. Musgrove
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo K. Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Annie Philips
- Natural Resources and Environment Tasmania, Hobart, Tasmania, Australia
| | | | - Magdalena Dunowska
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
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Deeming DC. Nest construction in mammals: a review of the patterns of construction and functional roles. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220138. [PMID: 37427481 DOI: 10.1098/rstb.2022.0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023] Open
Abstract
Nesting behaviour in mammals has been investigated in a wide variety of species but to date there has not been any scholarly review of the incidence and roles of these nests. Not all mammals build nests but, while some large species regularly build nests, nest-building behaviour is more commonly associated with small mammals weighing less than a kilogram. Quantitative data for the amounts of different materials used in a nest are rarely reported but mammal nests are typically constructed from fresh (rather than dead) plant materials. Animal-derived materials seem to be rare in nests, but anthropogenic materials are reported. Few studies have examined the roles these different materials play but more physically robust materials provide support for the structure. Many mammal nests have maternity roles, but a variety of other roles were recognized. A wide range of mammalian orders use nests for resting and environmental protection. Less common roles were as sites for torpor or hibernation, or as a refuge from predation, or the materials may have anti-parasite properties. These different roles were often not mutually exclusive. It is hoped that this review will stimulate interest in the functional properties of mammalian nests. It also suggests various themes that would be interesting areas for future research. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.
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Affiliation(s)
- D Charles Deeming
- School of Life and Environmental Sciences, University of Lincoln, Joseph Banks Laboratories, Lincoln LN6 7DL, UK
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21
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Hope AG, Headlee KM, Olson ZH, Wiens BJ. Systematics, biogeography and phylogenomics of northern bog lemmings (Cricetidae), cold-temperate rodents of conservation concern under global change. SYST BIODIVERS 2023; 21:2237050. [PMID: 38523662 PMCID: PMC10959253 DOI: 10.1080/14772000.2023.2237050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Northern bog lemmings, Mictomys (Synaptomys) borealis, are currently being assessed for protections under the U.S. Endangered Species Act. A major impediment to comprehensive evaluation is a deficiency of data towards understanding the biology of these rodents. Inherent rarity and scarce specimen sampling, despite a continent-wide distribution, has precluded our ability to implement modern methods for resolving taxonomy, evolutionary history, and investigating multiple other species traits. Here we use a maternally inherited locus (mitochondrial cytochrome b) and between 5,939 and 11,513 nuclear loci from reduced representation sequencing (ddRADseq) to investigate the evolutionary history of northern bog lemmings. We 1) qualify evidence based on morphological and early molecular studies for the genus assignment of Mictomys, 2) test the validity of multiple sub-species designations, 3) provide spatial and temporal historical biogeographic perspectives, and 4) discuss how incomplete sampling might influence conservation efforts. Both mitochondrial and nuclear datasets exhibit deep divergence and paraphyly between two recognized species, the northern (Mictomys borealis) and southern (Synaptomys cooperi) bog lemmings. Based on mtDNA, the geographically isolated subspecies (M. b. sphagnicola) was found to be divergent from all other specimens. The remainder of the species exhibited shallow intra-specific differentiation in mtDNA, however nuclear data supports genetic distinction consistent with four geographic subspecies. Recent coalescence of all northern bog lemmings (except for M. b. sphagnicola) reflects divergence in multiple refugia through the last glacial cycle, including a well-known coastal center of endemism and multiple regions south of continental ice-sheets. Regional lineages across North America suggest strong latitudinal displacement with global climate change, coupled with isolation-reconnection dynamics. This taxon suffers from a lack of modern samples through most of its distribution, severely limiting interpretation of ongoing evolutionary processes, particularly in southern portions of the species' range. Limited voucher specimen sampling of vulnerable populations could aid in rigorous conservation decision-making.
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Affiliation(s)
- Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Kaitlyn M Headlee
- Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
| | - Zachary H Olson
- School of Social and Behavioral Science, University of New England, Biddeford, Maine 04005, USA
| | - Ben J Wiens
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA
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Silberstein Y, Felmy F, Scheumann M. Encoding of Arousal and Physical Characteristics in Audible and Ultrasonic Vocalizations of Mongolian Gerbil Pups Testing Common Rules for Mammals. Animals (Basel) 2023; 13:2553. [PMID: 37627344 PMCID: PMC10451175 DOI: 10.3390/ani13162553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
In mammals, common rules for the encoding of arousal and physical characteristics of the sender are suggested based on a similar vocal production apparatus. In this study, we want to investigate to what extent vocalizations of developing Mongolian gerbil pups fulfill these rules. We recorded vocalizations of 28 Mongolian gerbil pups in four developmental stages using a separation paradigm, suggested to induce different arousal levels. For low arousal, a pup was placed in an arena isolated from its siblings and parents; for high arousal, the pup was additionally stressed through the simulation of a predator. An unsupervised cluster analysis revealed three call types: ultrasonic (USV), audible vocalizations (ADV), and transitions between both (USV-ADV). The USV and USV-ADV rate showed an age-dependent decrease, contrasting an age-dependent increase for ADVs. Vocal correlates for the encoding of arousal were found for USVs and of physical characteristics for USVs and ADVs. However, the pattern of encoding these cues differed between call types and only partly confirmed the common rules suggested for mammals. Our results show that divergent encoding patterns do not only differ between species but also between call types within a species, indicating that coding rules can be shaped by socio-ecological factors or call type specific production mechanisms.
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Affiliation(s)
- Yara Silberstein
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, 30559 Hannover, Germany
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23
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Graaf A, Piesche R, Sehl-Ewert J, Grund C, Pohlmann A, Beer M, Harder T. Low Susceptibility of Pigs against Experimental Infection with HPAI Virus H5N1 Clade 2.3.4.4b. Emerg Infect Dis 2023; 29:1492-1495. [PMID: 37347930 PMCID: PMC10310384 DOI: 10.3201/eid2907.230296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
We found that nasal and alimentary experimental exposure of pigs to highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b was associated with marginal viral replication, without inducing any clinical manifestation or pathological changes. Only 1 of 8 pigs seroconverted, pointing to high resistance of pigs to clade 2.3.4.4b infection.
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Liu P, Li D, Zhang J, He M, Gao D, Wang Y, Lin Y, Pan D, Li P, Wang T, Li J, Kong F, Zeng B, Lu L, Ma J, Long K, Li G, Tang Q, Jin L, Li M. Comparative three-dimensional genome architectures of adipose tissues provide insight into human-specific regulation of metabolic homeostasis. J Biol Chem 2023; 299:104757. [PMID: 37116707 PMCID: PMC10245122 DOI: 10.1016/j.jbc.2023.104757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/22/2023] [Accepted: 04/19/2023] [Indexed: 04/30/2023] Open
Abstract
Elucidating the regulatory mechanisms of human adipose tissues (ATs) evolution is essential for understanding human-specific metabolic regulation, but the functional importance and evolutionary dynamics of three-dimensional (3D) genome organizations of ATs are not well defined. Here, we compared the 3D genome architectures of anatomically distinct ATs from humans and six representative mammalian models. We recognized evolutionarily conserved and human-specific chromatin conformation in ATs at multiple scales, including compartmentalization, topologically associating domain (TAD), and promoter-enhancer interactions (PEI), which have not been described previously. We found PEI are much more evolutionarily dynamic with respect to compartmentalization and topologically associating domain. Compared to conserved PEIs, human-specific PEIs are enriched for human-specific sequence, and the binding motifs of their potential mediators (transcription factors) are less conserved. Our data also demonstrated that genes involved in the evolutionary dynamics of chromatin organization have weaker transcriptional conservation than those associated with conserved chromatin organization. Furthermore, the genes involved in energy metabolism and the maintenance of metabolic homeostasis are enriched in human-specific chromatin organization, while housekeeping genes, health-related genes, and genetic variations are enriched in evolutionarily conserved compared to human-specific chromatin organization. Finally, we showed extensively divergent human-specific 3D genome organizations among one subcutaneous and three visceral ATs. Together, these findings provide a global overview of 3D genome architecture dynamics between ATs from human and mammalian models and new insights into understanding the regulatory evolution of human ATs.
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Affiliation(s)
- Pengliang Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, Sichuan, China.
| | - Jiaman Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Wildlife Conservation Research Department, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan, China
| | - Dengfeng Gao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yujie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu Lin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dengke Pan
- Institute of Organ Transplantation, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine & Genetics, Chengdu Xi'nan Gynecology Hospital, Chengdu, Sichuan, China
| | - Tao Wang
- School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Jing Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fanli Kong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lu Lu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guisen Li
- Renal Department & Nephrology Institute, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Qianzi Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Long Jin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
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Minghui F, Ran S, Yuxue J, Minjia S. Toxic effects of titanium dioxide nanoparticles on reproduction in mammals. Front Bioeng Biotechnol 2023; 11:1183592. [PMID: 37251560 PMCID: PMC10213439 DOI: 10.3389/fbioe.2023.1183592] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Titanium dioxide nanoparticles (nano-TiO2) are widely used in food, textiles, coatings and personal care products; however, they cause environmental and health concerns. Nano-TiO2 can accumulate in the reproductive organs of mammals in different ways, affect the development of the ovum and sperm, damage reproductive organs and harm the growth and development of offspring. The oxidative stress response in germ cells, irregular cell apoptosis, inflammation, genotoxicity and hormone synthesis disorder are the main mechanisms of nano-TiO2 toxicity. Possible measures to reduce the harmful effects of nano-TiO2 on humans and nontarget organisms have emerged as an underexplored topic requiring further investigation.
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Abstract
MicroRNAs (miRNAs) are believed to play important roles in mammalian spermatogenesis mainly because spermatogenesis is more or less disrupted when genes encoding key enzymes for miRNA biogenesis are mutated. However, it is challenging to study the functions of individual miRNAs due to their family-wise high sequence similarities and the clustered genomic distributions of their genes, both of which expose difficulties in using genetic methods. Accumulating evidence shows that a number of miRNAs indeed play important roles in mammalian spermatogenesis and the underlying mechanisms start to be understood. In this mini review, we focus on highlighting the roles of miRNAs in mammalian spermatogenesis elucidated mainly by using in vivo genetic methods and on discussing the underlying mechanisms. We propose that studies on the roles of miRNAs in spermatogenesis should and can be conducted in a more fruitful way given the progress in traditional methods and the birth of new technologies.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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27
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T.Sinnott J, Somboonwit C, F.Alrabaa S, Shapshak P. Dangerous Risk Group-4 (RG-4) emergent viruses. Bioinformation 2023; 19:345-347. [PMID: 37822829 PMCID: PMC10563550 DOI: 10.6026/97320630019345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 10/13/2023] Open
Abstract
World Health Organization (WHO) Risk Group-4 (RG-4) pathogens are among the most dangerous of the emergent and re-emergent viruses. International health agencies, working in concert, bridge the gaps in health care for populations at risk for RG-4 viral pathogen exposure. RG-4 virus research incorporates Biodefense Program and Biosafety Laboratory (BSL)-4 technologies. RG-4 viruses include Arena-viridae, Filo-viridae, Flavi-viridae, Herpes-viridae, Nairo-viridae, Paramyxo-viridae, and Pox-viridae.
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Affiliation(s)
- John T.Sinnott
- 1Department of Internal Medicine, Morsani College of Medicine, Tampa, Florida 33606, USA
| | - Charurut Somboonwit
- 1Department of Internal Medicine, Morsani College of Medicine, Tampa, Florida 33606, USA
| | - Sally F.Alrabaa
- 1Department of Internal Medicine, Morsani College of Medicine, Tampa, Florida 33606, USA
| | - Paul Shapshak
- 1Department of Internal Medicine, Morsani College of Medicine, Tampa, Florida 33606, USA
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28
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White HE, Tucker AS, Fernandez V, Portela Miguez R, Hautier L, Herrel A, Urban DJ, Sears KE, Goswami A. Pedomorphosis in the ancestry of marsupial mammals. Curr Biol 2023:S0960-9822(23)00457-8. [PMID: 37119816 DOI: 10.1016/j.cub.2023.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 02/27/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
Within mammals, different reproductive strategies (e.g., egg laying, live birth of extremely underdeveloped young, and live birth of well-developed young) have been linked to divergent evolutionary histories. How and when developmental variation across mammals arose is unclear. While egg laying is unquestionably considered the ancestral state for all mammals, many long-standing biases treat the extreme underdeveloped state of marsupial young as the ancestral state for therian mammals (clade including both marsupials and placentals), with the well-developed young of placentals often considered the derived mode of development. Here, we quantify mammalian cranial morphological development and estimate ancestral patterns of cranial shape development using geometric morphometric analysis of the largest comparative ontogenetic dataset of mammals to date (165 specimens, 22 species). We identify a conserved region of cranial morphospace for fetal specimens, after which cranial morphology diversified through ontogeny in a cone-shaped pattern. This cone-shaped pattern of development distinctively reflected the upper half of the developmental hourglass model. Moreover, cranial morphological variation was found to be significantly associated with the level of development (position on the altricial-precocial spectrum) exhibited at birth. Estimation of ancestral state allometry (size-related shape change) reconstructs marsupials as pedomorphic relative to the ancestral therian mammal. In contrast, the estimated allometries for the ancestral placental and ancestral therian were indistinguishable. Thus, from our results, we hypothesize that placental mammal cranial development most closely reflects that of the ancestral therian mammal, while marsupial cranial development represents a more derived mode of mammalian development, in stark contrast to many interpretations of mammalian evolution.
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Affiliation(s)
- Heather E White
- Science Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK; Centre for Craniofacial and Regenerative Biology, King's College London, Great Maze Pond, London SE1 9RT, UK; Division of Biosciences, University College London, Gower Street, London WC1E 6DE, UK.
| | - Abigail S Tucker
- Centre for Craniofacial and Regenerative Biology, King's College London, Great Maze Pond, London SE1 9RT, UK
| | - Vincent Fernandez
- European Synchrotron Radiation Facility, 71 rue des Martyrs, 38000 Grenoble, France
| | | | - Lionel Hautier
- Science Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK; Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Anthony Herrel
- UMR 7179, Centre National de la Recherche Scientifique/Muséum National d'Histoire Naturelle, Département Adaptations du Vivant, 55 rue Buffon, 75005 Paris, France
| | - Daniel J Urban
- Institute of Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Anjali Goswami
- Science Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK; Division of Biosciences, University College London, Gower Street, London WC1E 6DE, UK
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29
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Zuleger AM, Perino A, Wolf F, Wheeler HC, Pereira HM. Long-term monitoring of mammal communities in the Peneda-Gerês National Park using camera-trap data. Biodivers Data J 2023; 11:e99588. [PMID: 38327315 PMCID: PMC10848441 DOI: 10.3897/bdj.11.e99588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/03/2023] [Indexed: 02/09/2024] Open
Abstract
Background In the past decades, agricultural land abandonment and declining land-use intensity became common, especially in the Mediterranean countries of southern Europe. In some areas, this development opened up possibilities for rewilding and the recolonisation or expansion of large mammal populations. Yet, in some instances, co-occurrence of wild mammals and free-ranging domestic herbivores might lead to potential conflicts. It is, therefore, necessary to study the ecological interactions between wild and domestic mammal species to understand the effects of land abandonment and rewilding on biodiversity and ecosystem services. Camera traps are an effective tool for studying species interactions and occupancy dynamics as they allow for long-term monitoring with minimal interference. We conducted a long-term monitoring programme with camera traps in the Peneda-Gerês National Park in northern Portugal. The area has undergone substantial land-use changes following the abandonment of agricultural areas in the past 60 years. While agro-pastoral activities, especially the breeding of free-ranging horses and cattle, are still common in the area, the intensity of these activities has decreased significantly, promoting natural succession and an increase or return of several large mammal species in recent years. Overall, our project aims at: (1) assessing the population trends of the medium and large sized mammals in the area over time; (2) analysing the effects of passive rewilding on occurrence, abundance and behaviour; and (3) understanding potential interactions or conflicts between wild and domestic herbivores. In this publication, we present results of a primary occupancy analysis between 2015 and 2020, as well as a comparison between occupancy and density estimates for 2019. New information Our publication provides a dataset from long-term camera-trap monitoring in the Peneda-Gerês National Park between 2015 and 2021. We established a 16 km² grid of 64 cameras deployed yearly during the summer months. Together with this publication, we publish the data and images collected between 2015 and 2021, using both the Camtrap DP standard and the GBIF Darwin Event Core. We obtained a total of 934,810 pictures on 41,234 trap nights. The pictures were automatically grouped into sequences with each sequence representing a distinct occurrence event, resulting in 80,191 occurrences. Out of those, 14,442 contained observations of a species, while the remaining were either blank or the species was not identifiable. We only obtained the information whether a species was present or absent on a picture, disregarding the number of individuals. Most observations were of domestic cattle (Bostaurus) and horses (Equuscaballus), followed by European roe deer (Capreoluscapreolus) and wild boar (Susscrofa). Further observations include red fox (Vulpesvulpes), gray wolf (Canislupus), Eurasian badger (Melesmeles), stone marten (Martesfoina), common genet (Genettagenetta), Iberian ibex (Caprapyrenaica) and red deer (Cervuselaphus). We estimated occupancy and densities for the most common species. The project is on-going and additional data will be included in the future. The dataset is freely available for ecological analysis, but also for training machine-learning systems in automated image classification as all pictures have been manually classified.
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Affiliation(s)
- Annika M Zuleger
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany Institute of Biology, Martin Luther University Halle-Wittenberg Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig Leipzig Germany
| | - Andrea Perino
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig Leipzig Germany
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany Institute of Biology, Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Florian Wolf
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany Institute of Biology, Martin Luther University Halle-Wittenberg Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig Leipzig Germany
| | - Helen C Wheeler
- School of Life Sciences, Anglia Ruskin University, Cambridge, United Kingdom School of Life Sciences, Anglia Ruskin University Cambridge United Kingdom
| | - Henrique M Pereira
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany Institute of Biology, Martin Luther University Halle-Wittenberg Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena- Leipzig Leipzig Germany
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO Vairão Portugal
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Weiss KCB, Green AM, Herrera DJ, Hubbard TM, Rega-Brodsky CC, Allen ML. Effect of species-level trait variation on urban exploitation in mammals. Ecology 2023:e4055. [PMID: 37074821 DOI: 10.1002/ecy.4055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023]
Abstract
Identifying drivers of urban association in wildlife is a central challenge in conservation biology. Traits facilitating access to novel resources and avoiding humans often correspond with urban exploitation in mammal species, but these relationships differ by taxa and trophic guild. Variation among or within traits may be a yet untested explanation for the non-generality of species-trait relationships in cities. Using camera trap data from 1,492 sites throughout the contiguous USA in 2019, we investigated if mammal species with greater intraspecific trait variation have higher degrees of urban occupancy. We hypothesized that intraspecific trait variation would correspond with urban occupancy, but that the strength of these relationships would vary by taxonomic order due to expected phylogenetic constraints. Mean trait values (average home range size, body mass, group size, weaning age, litter size, and diet composition) varied widely across orders. The only traits that affected urban association across all species corresponded with demography (litter size), while responses across orders were more variable and informative. Mean trait values associated with home range and body size had informative relationships with urbanization for Cetartiodactyla, Rodentia, and Carnivora, while intraspecific variation in traits corresponding with diet (Carnivora), demography (Cetartiodactyla, Carnivora, Rodentia), and temporal responses to humans (Carnivora) had informative relationships to urbanization. This is the first study investigating mammalian species-level trait variation and its relationship to urban exploitation across many traits and taxa. Since natural selection requires trait variation, the variation of demographic traits, like litter size, can have significant implications for wildlife management and conservation. Our results also provide further evidence for omnivory as a form of dietary plasticity supporting urban accessibility in higher trophic guilds (e.g., Carnivora). Using this information, we can better manage and understand which species occupy and adapt to cities, thereby promoting human-wildlife coexistence.
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Affiliation(s)
- Katherine C B Weiss
- School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, AZ, USA
| | - Austin M Green
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, USA
| | - Daniel J Herrera
- Department of Environmental Science and Policy, George Mason University, 4400 University Dr, Fairfax, VA, USA
| | - Tru M Hubbard
- Wildlife Ecology and Conservation Science Lab, Department of Biology, Northern Michigan University, Marquette, MI, USA
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Christine C Rega-Brodsky
- School of Science and Mathematics, Pittsburg State University, 1701 S. Broadway, Pittsburg, KS, USA
| | - Maximilian L Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, 1816 S. Oak Street, Champaign, IL
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Carbillet J, Palme R, Maublanc ML, Cebe N, Gilot-Fromont E, Verheyden H, Rey B. Instability of fecal glucocorticoid metabolites at 4°C: Time to freeze matters. J Exp Zool A Ecol Integr Physiol 2023. [PMID: 37058280 DOI: 10.1002/jez.2704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/15/2023]
Abstract
The use of fecal corticosteroid metabolites (FCMs) has proven to be well suited to evaluate adrenocortical activity, a major component of the stress response, particularly in wildlife. As with any tools, confounding factors and drawbacks must be carefully considered. Among them, sample preservation and storage are of particular importance, as they can affect stability of FCMs and lead to biased results and interpretations. Arguably, immediate freezing of fecal samples upon collection is the best practice to preserve FCM integrity, however, for logistical reasons, this condition is rarely feasible in the field. It is generally argued that temporary storage of samples at low above-zero temperature is an acceptable way of preserving samples in the field before freezing them for long-term storage. However, to our knowledge, there is no empirical study that demonstrates the stability of fecal metabolites in samples stored at +4°C. In this study, we collected a fresh fecal sample from 20 captive roe deer, each of which was homogenized and split into three subsamples (60 subsamples in total) to investigate the effects on FCMs levels of temporary storage at +4°C for 24 h and 48 h before freezing versus immediate freezing at -20°C after feces collection. Compared to immediate freezing, mean FCMs levels decreased by 25% every 24 h when feces were stored at +4°C before freezing. The variance of FCMs levels followed the same pattern, leading to a clear reduction in the ability to detect biological effects. Minimizing the storage time at +4°C before freezing should therefore be seriously considered when establishing sampling and storage protocols for feces in the field for adequate hormonal profiling.
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Affiliation(s)
- Jeffrey Carbillet
- CEFS, INRAE, Université de Toulouse, Castanet Tolosan, France
- VetAgro Sup, Université de Lyon, Marcy-l'Etoile, France
| | - Rupert Palme
- Department of Biomedical Sciences, Unit of Physiology, Pathophysiology and Experimental Endocrinology, University of Veterinary Medicine, Vienna, Austria
| | | | - Nicolas Cebe
- CEFS, INRAE, Université de Toulouse, Castanet Tolosan, France
| | - Emmanuelle Gilot-Fromont
- VetAgro Sup, Université de Lyon, Marcy-l'Etoile, France
- UMR CNRS 5558, Université de Lyon, Villeurbanne Cedex, France
| | | | - Benjamin Rey
- UMR CNRS 5558, Université de Lyon, Villeurbanne Cedex, France
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Holt S, Arrey G, Regenberg B. Did circular DNA shape the evolution of mammalian genomes? Trends Biochem Sci 2023; 48:317-320. [PMID: 36280496 DOI: 10.1016/j.tibs.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/05/2022]
Abstract
Extrachromosomal circular DNA (eccDNA) can shape the genomes of somatic cells, but how it impacts genomes across generations is largely unexplored. We propose that genomes can rearrange via circular intermediates across generations and show that up to 6% of a mammalian genome can have changed gene order through eccDNA.
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Affiliation(s)
- Sylvester Holt
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Gerard Arrey
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Birgitte Regenberg
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark.
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Malungo IB, Mokale R, Bertelsen MF, Manger PR. Cholinergic, catecholaminergic, serotonergic, and orexinergic neuronal populations in the brain of the lesser hedgehog tenrec (Echinops telfairi). Anat Rec (Hoboken) 2023; 306:844-878. [PMID: 36179372 DOI: 10.1002/ar.25092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022]
Abstract
The current study provides an analysis of the cholinergic, catecholaminergic, serotonergic, and orexinergic neuronal populations, or nuclei, in the brain of the lesser hedgehog tenrec, as revealed with immunohistochemical techniques. For all four of these neuromodulatory systems, the nuclear organization was very similar to that observed in other Afrotherian species and is broadly similar to that observed in other mammals. The cholinergic system shows the most variation, with the lesser hedgehog tenrec exhibiting palely immunopositive cholinergic neurons in the ventral portion of the lateral septal nucleus, and the possible absence of cholinergic neurons in the parabigeminal nucleus and the medullary tegmental field. The nuclear complement of the catecholaminergic, serotonergic and orexinergic systems showed no specific variances in the lesser hedgehog tenrec when compared to other Afrotherians, or broadly with other mammals. A striking feature of the lesser hedgehog tenrec brain is a significant mesencephalic flexure that is observed in most members of the Tenrecoidea, as well as the closely related Chrysochlorinae (golden moles), but is not present in the greater otter shrew, a species of the Potomogalidae lineage currently incorporated into the Tenrecoidea. In addition, the cholinergic neurons of the ventral portion of the lateral septal nucleus are observed in the golden moles, but not in the greater otter shrew. This indicates that either complex parallel evolution of these features occurred in the Tenrecoidea and Chrysochlorinae lineages, or that the placement of the Potomogalidae within the Tenrecoidea needs to be re-examined.
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Affiliation(s)
- Illke B Malungo
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Reabetswe Mokale
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
| | - Mads F Bertelsen
- Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Paul R Manger
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Republic of South Africa
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34
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Watchorn D, Dickman C, Dunlop J, Sanders E, Watchorn M, Burns P. Ghost rodents: Albinism in Australian rodent species. Ecol Evol 2023; 13:e9942. [PMID: 36993146 PMCID: PMC10042460 DOI: 10.1002/ece3.9942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/22/2023] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
While almost half of all mammal species are rodents, records of albinism in free‐ranging rodents are very rare. Australia has a large and diverse assemblage of native rodent species, but there are no records of free‐ranging albino rodents in the published literature. In this study, we aim to improve our understanding of the occurrence of albinism in Australian rodent species by collating contemporary and historic records of this condition and providing an estimate of its frequency. We found 23 records of albinism (i.e., a complete loss of pigmentation), representing eight species, in free‐ranging rodents native to Australia, with the frequency of albinism being generally <0.1%. Our findings bring the total number of rodent species in which albinism has been recorded globally to 76. While native Australian species represent only 7.8% of the world's murid rodent diversity, they now account for 42.1% of murid rodent species known to exhibit albinism. We also identified multiple concurrent albino records from a small island population of rakali (Hydromys chrysogaster) and discuss the factors that may contribute to the relatively high frequency (2%) of the condition on this island. We suggest that the small number of native albino rodents recorded in mainland Australia over the last 100 years means that traits associated with the condition are likely deleterious within populations and are thus selected against.
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Affiliation(s)
- Darcy Watchorn
- Centre for Integrative Ecology, School of Life and Environmental Sciences (Burwood Campus)Deakin UniversityGeelongVictoriaAustralia
- Wildlife Conservation and ScienceZoos VictoriaParkvilleVictoria3052Australia
| | - Chris Dickman
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South Wales2006Australia
| | - Judy Dunlop
- Western Australian Feral Cat Working Group58 Sutton St, MandurahMandurahWestern Australia6210Australia
| | - Emmalie Sanders
- School of Agricultural, Veterinary and Environmental SciencesCharles Sturt UniversityAlburyNew South Wales2640Australia
| | - Molly Watchorn
- Life SciencesZoos VictoriaParkvilleVictoria3052Australia
| | - Phoebe Burns
- Wildlife Conservation and ScienceZoos VictoriaParkvilleVictoria3052Australia
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Huang X, Wang H, Wang C, Cao Z. The Applications and Potentials of Extracellular Vesicles from Different Cell Sources in Periodontal Regeneration. Int J Mol Sci 2023; 24:ijms24065790. [PMID: 36982864 PMCID: PMC10058679 DOI: 10.3390/ijms24065790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Periodontitis is a chronic infectious disease worldwide that can cause damage to periodontal supporting tissues including gingiva, bone, cementum and periodontal ligament (PDL). The principle for the treatment of periodontitis is to control the inflammatory process. Achieving structural and functional regeneration of periodontal tissues is also essential and remains a major challenge. Though many technologies, products, and ingredients were applied in periodontal regeneration, most of the strategies have limited outcomes. Extracellular vesicles (EVs) are membranous particles with a lipid structure secreted by cells, containing a large number of biomolecules for the communication between cells. Numerous studies have demonstrated the beneficial effects of stem cell-derived EVs (SCEVs) and immune cell-derived EVs (ICEVs) on periodontal regeneration, which may be an alternative strategy for cell-based periodontal regeneration. The production of EVs is highly conserved among humans, bacteria and plants. In addition to eukaryocyte-derived EVs (CEVs), a growing body of literature suggests that bacterial/plant-derived EVs (BEVs/PEVs) also play an important role in periodontal homeostasis and regeneration. The purpose of this review is to introduce and summarize the potential therapeutic values of BEVs, CEVs and PEVs in periodontal regeneration, and discuss the current challenges and prospects for EV-based periodontal regeneration.
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Affiliation(s)
- Xin Huang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Huiyi Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Chuan Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
- Department of Periodontology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
| | - Zhengguo Cao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
- Department of Periodontology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, China
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Browett SS, Synnott R, O'Meara DB, Antwis RE, Browett SS, Bown KJ, Wangensteen OS, Dawson DA, Searle JB, Yearsley JM, McDevitt AD. Resource competition drives an invasion-replacement event among shrew species on an island. J Anim Ecol 2023; 92:698-709. [PMID: 36617677 DOI: 10.1111/1365-2656.13855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/17/2022] [Indexed: 01/10/2023]
Abstract
Invasive mammals are responsible for the majority of native species extinctions on islands. While most of these extinction events will be due to novel interactions between species (e.g. exotic predators and naive prey), it is more unusual to find incidences where a newly invasive species causes the decline/extinction of a native species on an island when they normally coexist elsewhere in their overlapping mainland ranges. We investigated if resource competition between two insectivorous small mammals was playing a significant role in the rapid replacement of the native pygmy shrew Sorex minutus in the presence of the recently invading greater white-toothed shrew Crocidura russula on the island of Ireland. We used DNA metabarcoding of gut contents from >300 individuals of both species to determine each species' diet and measured the body size (weight and length) during different stages of the invasion in Ireland (before, during and after the species come into contact with one another) and on a French island where both species have long coexisted (acting as a natural 'control' site). Dietary composition, niche width and overlap and body size were compared in these different stages. The body size of the invasive C. russula and composition of its diet changes between when it first invades an area and after it becomes established. During the initial stages of the invasion, individual shrews are larger and consume larger sized invertebrate prey species. During later stages of the invasion, C. russula switches to consuming smaller prey taxa that are more essential for the native species. As a result, the level of interspecific dietary overlap increases from between 11% and 14% when they first come into contact with each other to between 39% and 46% after the invasion. Here we show that an invasive species can quickly alter its dietary niche in a new environment, ultimately causing the replacement of a native species. In addition, the invasive shrew could also be potentially exhausting local resources of larger invertebrate species. These subsequent changes in terrestrial invertebrate communities could have severe impacts further downstream on ecosystem functioning and services.
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Affiliation(s)
- Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland.,NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Rebecca Synnott
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Denise B O'Meara
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Stephen S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Kevin J Bown
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway
| | - Deborah A Dawson
- NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Jeremy B Searle
- Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, New York, USA
| | - Jon M Yearsley
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Department of Natural Sciences and the Environment, School of Science and Computing, Atlantic Technological University, Galway, Ireland
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Burnet G, Feng CWA, Cheung KMF, Bowles J, Spiller CM. Generation and characterization of a Ddx4-iCre transgenic line for deletion in the germline beginning at genital ridge colonization. Genesis 2023; 61:e23511. [PMID: 36693128 DOI: 10.1002/dvg.23511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/25/2023]
Abstract
Germline-specific Cre lines are useful for analyses of primordial germ cell, spermatogonial and oogonial development, but also for whole-body deletions when transmitted through subsequent generations. Several germ cell specific Cre mouse strains exist, with various degrees of specificity, efficiency, and temporal activation. Here, we describe the CRISPR/Cas9 targeted insertion of an improved Cre (iCre) sequence in-frame at the 3' end of the Ddx4 locus to generate the Ddx4-P2A-iCre allele. Our functional assessment of this new allele, designated Ddx4iCreJoBo , reveals that Cre activity begins in PGCs from at least E10.5, and that it achieves higher efficiency for early gonadal (E10.5-12.5) germline deletion when compared to the inducible Oct4CreERT2 line. We found the Ddx4iCreJoBo allele to be hypomorphic for Ddx4 expression and homozygous males, but not females, were infertile. Using two reporter lines (R26RLacZ and R26RtdTomato ) and a floxed gene of interest (Criptoflox ) we found ectopic activity in multiple organs; global recombination (a common feature of germline Cre alleles) varies from 10 to 100%, depending on the particular floxed allele. There is a strong maternal effect, and therefore it is preferable for Ddx4iCreJoBo to be inherited from the male parent if ubiquitous deletion is not desired. With these limitations considered, we describe the Ddx4iCreJoBo line as useful for germline studies in which early gonadal deletion is required.
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Affiliation(s)
- Guillaume Burnet
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Chun-Wei Allen Feng
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Ka Man Fiona Cheung
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Josephine Bowles
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Cassy M Spiller
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
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38
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Lu J, Hamblen EE, Brenner LJ, King JL, VonHoldt BM, DeCandia AL. Ear mite infection restructures otic microbial networks in conservation-reliant Santa Catalina Island foxes (Urocyon littoralis catalinae). Mol Ecol 2023; 32:892-903. [PMID: 36435981 DOI: 10.1111/mec.16795] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022]
Abstract
Ceruminous gland tumours are highly prevalent in the ear canals of Santa Catalina Island foxes (Urocyon littoralis catalinae). Previous work suggests that tumours may result from a combination of ectoparasites, disruption of the host-associated microbiome, and host immunopathology. More specifically, ear mite infection has been associated with broad-scale microbial dysbiosis marked by secondary bacterial infection with the opportunistic pathogen Staphylococcus pseudintermedius. Together, ear mites and S. pseudintermedius probably sustain chronic inflammation and promote conditions suitable for tumour development. In the present study, we expanded upon this framework by constructing otic microbial community networks for mite-infected and uninfected foxes sampled in 2017-2019. Across sampling years, we observed consistent signatures of microbial dysbiosis in mite-infected ear canals, including reduced microbial diversity and shifted abundance towards S. pseudintermedius. Network analysis further revealed that mite infection disrupts overall community structure. In mite-infected networks, interaction strengths between taxa were generally weaker, and numerous subnetworks disappeared altogether. We also found that two strains of S. pseudintermedius connected to the main network, suggesting that multistrain biofilm formation may be occurring. In contrast, S. pseudintermedius is peripheral in the uninfected network, with its only connections including a second strain of S. pseudintermedius and the possible competitor Acinetobacter rhizosphaerae. Finally, the lineup of potential keystone taxa shifted across disease states. Fusobacteria spp., a carcinogenesis-promoting microbe, assumed a keystone role in the mite-infected community. Considered together, these findings provide insights into how mite infection may destabilize the microbiome and ultimately contribute to tumour development in this island endemic species.
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Affiliation(s)
- Jasmine Lu
- Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | | | - Lara J Brenner
- Catalina Island Conservancy, Avalon, California, USA.,The Nature Conservancy, Ventura, California, USA
| | - Julie L King
- Catalina Island Conservancy, Avalon, California, USA.,Santa Clara Valley Habitat Agency, Morgan Hill, California, USA
| | - Bridgett M VonHoldt
- Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Alexandra L DeCandia
- Biology, Georgetown University, Washington, District of Columbia, USA.,Smithsonian National Zoo and Conservation Biology Institute, Washington, District of Columbia, USA
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39
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Koga A, Hashimoto K, Honda Y, Nishihara H. Marsupial genome analysis suggests that satellite DNA formation from walb endogenous retrovirus is an event specific to the red-necked wallaby. Genes Cells 2023; 28:149-155. [PMID: 36527312 DOI: 10.1111/gtc.12999] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/29/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
We recently identified walbRep, a satellite DNA residing in the genome of the red-necked wallaby Notamacropus rufogriseus. It originates from the walb endogenous retrovirus and is organized in a manner in which the provirus structure is retained. The walbRep repeat units feature an average pairwise nucleotide identity as high as 99.5%, raising the possibility of a recent origin. The tammar wallaby N. eugenii is a species estimated to have diverged from the red-necked wallaby 2-3 million years ago. In PCR analyses of these two and other related species, walbRep-specific fragment amplification was observed only in the red-necked wallaby. Sequence database searches for the tammar wallaby resulted in sequence alignment lists that were sufficiently powerful to exclude the possibility of walbRep existence. These results suggested that the walbRep formation occurred in the red-necked wallaby lineage after its divergence from the tammar wallaby lineage, thus in a time span of maximum 3 million years.
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Affiliation(s)
- Akihiko Koga
- Center for Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan
| | | | - Yusuke Honda
- Noichi Zoological Park of Kochi Prefecture, Konan, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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40
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Gracanin A, Knipler ML, Mikac KM. Informing Wildlife Corridor Creation through Population Genetics of an Arboreal Marsupial in a Fragmented Landscape. Genes (Basel) 2023; 14. [PMID: 36833276 DOI: 10.3390/genes14020349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Habitat loss and fragmentation contribute significantly to the decline of arboreal mammal populations. As populations become fragmented and isolated, a reduction in gene flow can result in a loss of genetic diversity and have an overall impact upon long-term persistence. Creating wildlife corridors can mitigate such effects by increasing the movement and dispersal of animals, thus acting to reduce population isolation. To evaluate the success of a corridor, a before-after experimental research framework can be used. Here, we report the genetic diversity and structure of sugar glider (Petaurus breviceps) sampling locations within a fragmented landscape prior to the implementation of a wildlife corridor. This study used 5999 genome-wide SNPs from 94 sugar gliders caught from 8 locations in a fragmented landscape in south-eastern New South Wales, Australia. Overall genetic structure was limited, and gene flow was detected across the landscape. Our findings indicate that the study area contains one large population. A major highway dissecting the landscape did not act as a significant barrier to dispersal, though this may be because of its relatively new presence in the landscape (completed in 2018). Future studies may yet indicate its long-term impact as a barrier to gene flow. Future work should aim to repeat the methods of this study to examine the medium-to-long-term impacts of the wildlife corridor on sugar gliders, as well as examine the genetic structure of other native, specialist species in the landscape.
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41
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Ma D, Yuan Q, Peng F, Paredes V, Zeng H, Yang Q, Peddi A, Patel A, Liu MS, Sun Z, Gao X. Engineered PROTAC-CID Systems for Mammalian Inducible Gene Regulation. J Am Chem Soc 2023; 145:1593-1606. [PMID: 36626587 PMCID: PMC10162582 DOI: 10.1021/jacs.2c09129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Gene regulation via chemically induced dimerization (CID) is useful for biomedical research. However, the number, type, versatility, and in vivo applications of CID tools remain limited. Here, we demonstrate the development of proteolysis-targeting chimera-based scalable CID (PROTAC-CID) platforms by systematically engineering the available PROTAC systems for inducible gene regulation and gene editing. Further, we show orthogonal PROTAC-CIDs that can fine-tune gene expression at gradient levels or multiplex biological signals with different logic gating operations. Coupling the PROTAC-CID platform with genetic circuits, we achieve digitally inducible expression of DNA recombinases, base- and prime-editors for transient genome manipulation. Finally, we package a compact PROTAC-CID system into adeno-associated viral vectors for inducible and reversible gene activation in vivo. This work provides a versatile molecular toolbox that expands the scope of chemically inducible gene regulation in human cells and mice.
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Affiliation(s)
- Dacheng Ma
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Qichen Yuan
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Fei Peng
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Victor Paredes
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Hongzhi Zeng
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Qiaochu Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Advaith Peddi
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | - Anika Patel
- Department of Computer Sciences, Rice University, Houston, Texas 77005, USA
| | - Megan S. Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| | - Zheng Sun
- Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Department of Chemistry, Rice University, Houston, TX 77005, USA
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42
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Agüero M, Monne I, Sánchez A, Zecchin B, Fusaro A, Ruano MJ, del Valle Arrojo M, Fernández-Antonio R, Souto AM, Tordable P, Cañás J, Bonfante F, Giussani E, Terregino C, Orejas JJ. Highly pathogenic avian influenza A(H5N1) virus infection in farmed minks, Spain, October 2022. Euro Surveill 2023; 28:2300001. [PMID: 36695488 PMCID: PMC9853945 DOI: 10.2807/1560-7917.es.2023.28.3.2300001] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In October 2022, an outbreak in Europe of highly pathogenic avian influenza (HPAI) A(H5N1) in intensively farmed minks occurred in northwest Spain. A single mink farm hosting more than 50,000 minks was involved. The identified viruses belong to clade 2.3.4.4b, which is responsible of the ongoing epizootic in Europe. An uncommon mutation (T271A) in the PB2 gene with potential public health implications was found. Our investigations indicate onward mink transmission of the virus may have occurred in the affected farm.
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Affiliation(s)
- Montserrat Agüero
- Laboratorio Central de Veterinaria (LCV), Ministry of Agriculture, Fisheries and Food, Algete, Madrid, Spain
| | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Azucena Sánchez
- Laboratorio Central de Veterinaria (LCV), Ministry of Agriculture, Fisheries and Food, Algete, Madrid, Spain
| | - Bianca Zecchin
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - María José Ruano
- Laboratorio Central de Veterinaria (LCV), Ministry of Agriculture, Fisheries and Food, Algete, Madrid, Spain
| | | | | | - Antonio Manuel Souto
- Livestock Service, Counselling of Rural Affairs, Xunta de Galicia, A Coruña, Spain
| | - Pedro Tordable
- Livestock Service, Counselling of Rural Affairs, Xunta de Galicia, A Coruña, Spain
| | - Julio Cañás
- Livestock Service, Counselling of Rural Affairs, Xunta de Galicia, A Coruña, Spain
| | - Francesco Bonfante
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Edoardo Giussani
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Calogero Terregino
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Jesús Javier Orejas
- Animal Health Service, Counselling of Rural Affairs, Xunta de Galicia, A Coruña, Spain
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Yuan XC, Tao YX. Editorial: Glucosensing impact on glucose metabolism: From fish to mammals. Front Endocrinol (Lausanne) 2023; 13:1125993. [PMID: 36686489 PMCID: PMC9854112 DOI: 10.3389/fendo.2022.1125993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Affiliation(s)
- Xiao-Chen Yuan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, China
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
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Kuroda S, Adachi N, Kuratani S. A detailed redescription of the mesoderm/neural crest cell boundary in the murine orbitotemporal region integrates the mammalian cranium into a pan-amniote cranial configuration. Evol Dev 2023; 25:32-53. [PMID: 35909296 DOI: 10.1111/ede.12411] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/14/2022] [Accepted: 07/02/2022] [Indexed: 01/13/2023]
Abstract
The morphology of the mammalian chondrocranium appears to differ significantly from those of other amniotes, since the former possesses uniquely developed brain and cranial sensory organs. In particular, a question has long remained unanswered as to the developmental and evolutionary origins of a cartilaginous nodule called the ala hypochiasmatica. In this study, we investigated the embryonic origin of skeletal elements in the murine orbitotemporal region by combining genetic cell lineage analysis with detailed morphological observation. Our results showed that the mesodermal embryonic environment including the ala hypochiasmatica, which appeared as an isolated mesodermal distribution in the neural crest-derived prechordal region, is formed as a part of the mesoderm that continued from the chordal region during early chondrocranial development. The mesoderm/neural crest cell boundary in the head mesenchyme is modified through development, resulting in the secondary mesodermal expansion to invade into the prechordal region. We thus revealed that the ala hypochiasmatica develops as the frontier of the mesodermal sheet stretched along the cephalic flexure. These results suggest that the mammalian ala hypochiasmatica has evolved from a part of the mesodermal primary cranial wall in ancestral amniotes. In addition, the endoskeletal elements in the orbitotemporal region, such as the orbital cartilage, suprapterygoid articulation of the palatoquadrate, and trabecula, some of which were once believed to represent primitive traits of amniotes and to be lost in the mammalian lineage, have been confirmed to exist in the mammalian cranium. Consequently, the mammalian chondrocranium can now be explained in relation to the pan-amniote cranial configuration.
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Affiliation(s)
- Shunya Kuroda
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo, Japan.,Department of Biology, Graduate School of Science, Kobe University, Kobe, Hyogo, Japan
| | - Noritaka Adachi
- Aix-Marseille Université, CNRS UMR 7288, IBDM, Marseille, France.,Laboratory for Evolutionary Morphology, RIKEN Cluster for Pioneering Research (CPR), Kobe, Hyogo, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo, Japan
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45
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Higashiyama H, Koyabu D, Kurihara H. Evolution of the therian face through complete loss of the premaxilla. Evol Dev 2023; 25:103-118. [PMID: 36017615 DOI: 10.1111/ede.12417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 08/01/2022] [Accepted: 08/15/2022] [Indexed: 01/13/2023]
Abstract
The anatomical framework of the jawbones is highly conserved among most of the Osteichthyes, including the tetrapods. However, our recent study suggested that the premaxilla, the rostralmost upper jaw bone, was rearranged during the evolution of therian mammals, being replaced by the septomaxilla at least in the lateral part. In the present study, to understand more about the process of evolution from the ancestral upper jaw to the therian face, we re-examined the development of the therian premaxilla (incisive bone). By comparing mouse, bat, goat, and cattle fetuses, we confirmed that the therian premaxilla has dual developmental origins, the lateral body and the palatine process. This dual development is widely conserved among the therian mammals. Cell-lineage-tracing experiments using Dlx1-CreERT2 mice revealed that the palatine process arises in the ventral part of the premandibular domain, where the nasopalatine nerve distributes, whereas the lateral body develops from the maxillary prominence in the domain of the maxillary nerve. Through comparative analysis using various tetrapods, we concluded that the palatine process should not be considered part of the ancestral premaxilla. It rather corresponds to the anterior region of the vomerine bone of nonmammalian tetrapods. Thus, the present findings indicate that the true premaxilla was completely lost during the evolution of the therian mammals, resulting in the establishment of the unique therian face as an evolutionary novelty. Reconsideration of the homological framework of the cranial skeleton based on the topographical relationships of the ossification center during embryonic development is warranted.
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Affiliation(s)
- Hiroki Higashiyama
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Koyabu
- Research and Development Center for Precision Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hiroki Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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46
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Toussaint SLD, Ponstein J, Thoury M, Métivier R, Kalthoff DC, Habermeyer B, Guilard R, Bock S, Mortensen P, Sandberg S, Gueriau P, Amson E. Fur glowing under ultraviolet: in situ analysis of porphyrin accumulation in the skin appendages of mammals. Integr Zool 2023; 18:15-26. [PMID: 35500584 DOI: 10.1111/1749-4877.12655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Examples of photoluminescence (PL) are being reported with increasing frequency in a wide range of organisms from diverse ecosystems. However, the chemical basis of this PL remains poorly defined, and our understanding of its potential ecological function is still superficial. Among mammals, recent analyses have identified free-base porphyrins as the compounds responsible for the reddish ultraviolet-induced photoluminescence (UV-PL) observed in the pelage of springhares and hedgehogs. However, the localization of the pigments within the hair largely remains to be determined. Here, we use photoluminescence multispectral imaging emission and excitation spectroscopy to detect, map, and characterize porphyrinic compounds in skin appendages in situ. We also document new cases of mammalian UV-PL caused by free-base porphyrins in distantly related species. Spatial distribution of the UV-PL is strongly suggestive of an endogenous origin of the porphyrinic compounds. We argue that reddish UV-PL is predominantly observed in crepuscular and nocturnal mammals because porphyrins are photodegradable. Consequently, this phenomenon may not have a specific function in intra- or interspecific communication but rather represents a byproduct of potentially widespread physiological processes.
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Affiliation(s)
- Séverine L D Toussaint
- AG Vergleichende Zoologie, Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Jasper Ponstein
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,AG Paläobiologie und Evolution, Institut für Biologie, Humboldt Universität zu Berlin, Berlin, Germany
| | - Mathieu Thoury
- IPANEMA, CNRS, ministère de la Culture, UVSQ, MNHN, USR3461, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Rémi Métivier
- Université Paris-Saclay, ENS Paris-Saclay, CNRS, PPSM, Gif-sur-Yvette, France
| | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | | | - Roger Guilard
- ICMUB, UMR CNRS 6302, Université de Bourgogne Franche-Comté, France
| | - Steffen Bock
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Peter Mortensen
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Sverre Sandberg
- Norwegian Porphyria Centre (NAPOS), Haukeland University Hospital, Norwegian Organization for Quality Improvement of Laboratory Examinations (Noklus), and Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Norway
| | - Pierre Gueriau
- IPANEMA, CNRS, ministère de la Culture, UVSQ, MNHN, USR3461, Université Paris-Saclay, Gif-sur-Yvette, France.,Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland
| | - Eli Amson
- Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
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Aso H, Ito J, Ozaki H, Kashima Y, Suzuki Y, Koyanagi Y, Sato K. Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections. Gigascience 2022; 12:giad086. [PMID: 37848618 PMCID: PMC10580374 DOI: 10.1093/gigascience/giad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/12/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Bats harbor various viruses without severe symptoms and act as their natural reservoirs. The tolerance of bats against viral infections is assumed to originate from the uniqueness of their immune system. However, how immune responses vary between primates and bats remains unclear. Here, we characterized differences in the immune responses by peripheral blood mononuclear cells to various pathogenic stimuli between primates (humans, chimpanzees, and macaques) and bats (Egyptian fruit bats) using single-cell RNA sequencing. RESULTS We show that the induction patterns of key cytosolic DNA/RNA sensors and antiviral genes differed between primates and bats. A novel subset of monocytes induced by pathogenic stimuli specifically in bats was identified. Furthermore, bats robustly respond to DNA virus infection even though major DNA sensors are dampened in bats. CONCLUSIONS Overall, our data suggest that immune responses are substantially different between primates and bats, presumably underlying the difference in viral pathogenicity among the mammalian species tested.
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Affiliation(s)
- Hirofumi Aso
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
- Department of AI Systems Medicine, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo 1138510, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba 3050821, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, Tsukuba 3058577, Japan
| | - Yukie Kashima
- Laboratory of Systems Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan
| | - Yoshio Koyanagi
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 1130033, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
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48
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Zeng Z, Zhou S, Xu G, Liu W, Han T, Liu J, Wang J, Deng Y, Xiao F. Prevalence and phylogenetic analysis of Babesia parasites in reservoir host species in Fujian province, Southeast China. Zoonoses Public Health 2022; 69:915-924. [PMID: 35819239 DOI: 10.1111/zph.12988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 01/25/2023]
Abstract
Babesiosis is a tick-borne disease that mainly affects small mammals and has been reported in at least five provinces in China. However, the host range and geographical distribution of the parasite in Fujian province are unclear. Therefore, we investigated the prevalence and genetic characteristics of Babesia in Fujian province, Southeast China, between 2015 and 2020. Rodent blood samples were collected from 26 different surveillance sites across Fujian province. Genomic DNA was extracted to screen for Babesia infection using polymerase chain reaction based on 18S rRNA. DNA samples from 316 domestic goats, 85 water buffalo, 56 domestic dogs and 18 domestic pigs were examined. The prevalence of Babesia was statistically analysed using the Chi-square test or Fisher's exact test. Babesia infections were detected in 3.96% (43/1,087; 95%CI: 2.80%, 5.12%) of rodents and 1.26% (6/475; 95%CI: 0.26%, 2.26%) of other mammals. Multivariate logistic regression analysis revealed that irrigated cropland, shrubs and forests were risk factors for Babesia microti infections. The infection rates among domestic pigs, dogs and goats were 5.56%, 1.79% and 1.27%, respectively, with no infection found in water buffalo. The 18S rRNA gene sequencing revealed that rodents were infected with Babesia (sensu lato), whereas other mammals were infected with Babesia (sensu stricto). The geographical distribution and phylogenetic relationship of Babesia was determined in Southeast China. Mammals, particularly wild rodents, maybe the main natural hosts of Babesia in Fujian. Our findings provide a foundation for public health officials to develop prevention and control measures for Babesia.
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Affiliation(s)
- Zhiwei Zeng
- Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
| | - Shuheng Zhou
- Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
| | - Guoying Xu
- Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
| | - Weijun Liu
- Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
| | - Tengwei Han
- Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
| | - Jing Liu
- Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
| | - Jiaxiong Wang
- Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
| | - Yanqin Deng
- Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
| | - Fangzhen Xiao
- Fujian Center for Disease Control and Prevention, Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
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49
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Mika K, Lynch VJ. Transposable Elements Continuously Remodel the Regulatory Landscape, Transcriptome, and Function of Decidual Stromal Cells. Genome Biol Evol 2022; 14:6845702. [PMID: 36423206 PMCID: PMC9732941 DOI: 10.1093/gbe/evac164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/27/2022] Open
Abstract
Gene expression evolution underlies the origin, divergence, and conservation of biological characters including cell-types, tissues, and organ systems. Previously we showed that large-scale gene expression changes in decidual stromal cells (DSCs) contributed to the origins of pregnancy in eutherians and the divergence of pregnancy traits in primates and that transposable elements likely contributed to these gene expression changes. Here we show that two large waves of TEs remodeled the transcriptome and regulatory landscape of DSCs, including a major wave in primates. Genes nearby TE-derived regulatory elements are among the most progesterone responsive in the genome and play essential roles in orchestrating progesterone responsiveness and the core function of decidual cells by donating progesterone receptor binding sites to the genome. We tested the regulatory abilities of 89 TE consensus sequences and found that nearly all of them acted as repressors in mammalian cells, but treatment with a histone deacetylase inhibitor unmasked latent enhancer functions. These data indicate that TEs have played an important role in the development, evolution, and function of primate DSCs and suggest a two-step model in which latent enhancer functions of TEs are unmasked after they lose primary repressor functions.
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Affiliation(s)
- Katelyn Mika
- Present address: Department of Organismal Biology and Anatomy, University of Chicago, 1025 E 57th Street, Chicago, Illinois 60637, USA
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50
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Lei B, Zheng Z, Cui J, Zhao J, Newman C, Zhou Y. Ecotourist trail-use affects the taxonomic, functional and phylogenetic diversity of mammals in a Protected Area: Lessons for conservation management. Integr Zool 2022. [PMID: 36239540 DOI: 10.1111/1749-4877.12688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ecotourism, by definition, aims to engage peoples' interest in wildlife and the environment. The use of tourist roads and trails to access sites within protected areas can detrimentally affect the behavior and distribution of species. The way mammals respond to anthropogenic pressures may differ across taxonomic, functional and phylogenetic groups; nevertheless, how ecotourist trail-use affects these different diversity remains under-investigated. Here we assessed six metrics of taxonomic, phylogenetic and functional diversity for a mammal community in a Protected Area (PA) in central China, recording how Trail use (using Trail type as a proxy) and habitat variables affected sightings and signs of mammals across 60 replicate 0.5 km transects. We then examined how Trail use affected the taxonomic, functional and phylogenetic diversity indices of species (> 1 kg). Using generalized liner mixed modelling (GLMMs) we identified that more used trail types had a greater adverse effect on all diversity richness indices than did less used trail types. Consequently, tourist pressure was associated with a general tendency to homogenize the site's mammal community. In contrast, the effects of Trail Types on all diversity evenness indices were non-significant. Furthermore, more developed and more heavily used trail types had a greater, significant negative effect on taxonomic, functional and phylogenetic richness, whereas these richness indices were unaffected by minor trail types, used less intensively. As a general principle, lower biodiversity indices reduce ecosystem resilience, and so it is vital to better understand these responses to balance public access against biodiversity management in Protected Areas. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Boyu Lei
- Engineering Research Center of Eco-environment in Three Gorges Reservoir Region, Ministry of Education, China Three Gorges University, Yichang, China
| | - Zhenfei Zheng
- Engineering Research Center of Eco-environment in Three Gorges Reservoir Region, Ministry of Education, China Three Gorges University, Yichang, China
| | - Jifa Cui
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jin Zhao
- Engineering Research Center of Eco-environment in Three Gorges Reservoir Region, Ministry of Education, China Three Gorges University, Yichang, China
| | - Chris Newman
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, The Recanati-Kaplan Centre, Tubney, UK
| | - Youbing Zhou
- Engineering Research Center of Eco-environment in Three Gorges Reservoir Region, Ministry of Education, China Three Gorges University, Yichang, China
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