1
|
De Luca LA, Laurin M, Menani JV. Control of fluid intake in dehydrated rats and evolution of sodium appetite. Physiol Behav 2024; 284:114642. [PMID: 39032667 DOI: 10.1016/j.physbeh.2024.114642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 07/04/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
The objective of the present work is to examine from a new perspective the existence of causal factors not predicted by the classical theory that thirst and sodium appetite are two distinct motivations. For example, we ask why water deprivation induces sodium appetite, thirst is not "water appetite", and intracellular dehydration potentially causes sodium appetite. Contrary to the classical theory, we suggest that thirst first, and sodium appetite second, designate a temporal sequence underlying the same motivation. The single motivation becomes an "intervenient variable" a concept borrowed from the literature, fully explained in the text, between causes of dehydration (extracellular, intracellular, or both together), and respective behavioral responses subserved by hindbrain-dependent inhibition (e.g., lateral parabrachial nucleus) and forebrain facilitation (e.g., angiotensin II). A corollary is homology between rat sodium appetite and marine teleost thirst-like motivation that we name "protodipsia". The homology argument rests on similarities between behavior (salty water intake) and respective neuroanatomical as well as functional mechanisms. Tetrapod origin in a marine environment provides additional support for the homology. The single motivation hypothesis is also consistent with ingestive behaviors in nature given similarities (e.g., thirst producing brackish water intake) between the behavior of the laboratory rat and wild animals, rodents included. The hypotheses of single motivation and homology might explain why hyperosmotic rats, or eventually any other hyperosmotic tetrapod, shows paradoxical signs of sodium appetite. They might also explain how ingestive behaviors determined by dehydration and subserved by hindbrain inhibitory mechanisms contributed to tetrapod transition from sea to land.
Collapse
Affiliation(s)
- Laurival A De Luca
- Department of Physiology & Pathology, School of Dentistry, São Paulo State University (UNESP), 14801-903 Araraquara, São Paulo, Brazil.
| | - Michel Laurin
- CR2P, UMR 7207, CNRS/MNHN/SU, Muséum National d'Histoire Naturelle, Bâtiment de Géologie, CP 48, F-75231 Paris cedex 05, France
| | - José Vanderlei Menani
- Department of Physiology & Pathology, School of Dentistry, São Paulo State University (UNESP), 14801-903 Araraquara, São Paulo, Brazil
| |
Collapse
|
2
|
Bresee CS, Belli HM, Luo Y, Hartmann MJZ. Comparative morphology of the whiskers and faces of mice (Mus musculus) and rats (Rattus norvegicus). J Exp Biol 2023; 226:jeb245597. [PMID: 37577985 PMCID: PMC10617617 DOI: 10.1242/jeb.245597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Abstract
Understanding neural function requires quantification of the sensory signals that an animal's brain evolved to interpret. These signals in turn depend on the morphology and mechanics of the animal's sensory structures. Although the house mouse (Mus musculus) is one of the most common model species used in neuroscience, the spatial arrangement of its facial sensors has not yet been quantified. To address this gap, the present study quantifies the facial morphology of the mouse, with a particular focus on the geometry of its vibrissae (whiskers). The study develops equations that establish relationships between the three-dimensional (3D) locations of whisker basepoints, whisker geometry (arclength, curvature) and the 3D angles at which the whiskers emerge from the face. Additionally, the positions of facial sensory organs are quantified relative to bregma-lambda. Comparisons with the Norway rat (Rattus norvegicus) indicate that when normalized for head size, the whiskers of these two species have similar spacing density. The rostral-caudal distances between facial landmarks of the rat are a factor of ∼2.0 greater than the mouse, while the scale of bilateral distances is larger and more variable. We interpret these data to suggest that the larger size of rats compared with mice is a derived (apomorphic) trait. As rodents are increasingly important models in behavioral neuroscience, the morphological model developed here will help researchers generate naturalistic, multimodal patterns of stimulation for neurophysiological experiments and allow the generation of synthetic datasets and simulations to close the loop between brain, body and environment.
Collapse
Affiliation(s)
- Chris S. Bresee
- Northwestern University Institute for Neuroscience, Northwestern University, Evanston, IL 60208,USA
| | - Hayley M. Belli
- Department of Biomedical Engineering,Northwestern University, Evanston, IL 60208, USA
| | - Yifu Luo
- Department of Mechanical Engineering,Northwestern University, Evanston, IL 60208,USA
| | - Mitra J. Z. Hartmann
- Department of Biomedical Engineering,Northwestern University, Evanston, IL 60208, USA
- Department of Mechanical Engineering,Northwestern University, Evanston, IL 60208,USA
| |
Collapse
|
3
|
Richard Albert J, Kobayashi T, Inoue A, Monteagudo-Sánchez A, Kumamoto S, Takashima T, Miura A, Oikawa M, Miura F, Takada S, Hirabayashi M, Korthauer K, Kurimoto K, Greenberg MVC, Lorincz M, Kobayashi H. Conservation and divergence of canonical and non-canonical imprinting in murids. Genome Biol 2023; 24:48. [PMID: 36918927 PMCID: PMC10012579 DOI: 10.1186/s13059-023-02869-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 02/09/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behavior. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we use low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extraembryonic tissues at allele-specific resolution. RESULTS We identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse reveal that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extraembryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extraembryonic imprinting. Meta-analysis of novel imprinted genes reveals multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the appearance of ZFP57 binding motifs, and the insertion of endogenous retroviral promoters. CONCLUSIONS In summary, we provide an expanded list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.
Collapse
Affiliation(s)
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Azusa Inoue
- YCI Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Soichiro Kumamoto
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Asuka Miura
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Mami Oikawa
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Japan
| | - Keegan Korthauer
- Department of Statistics, University of British Columbia, Vancouver, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan
| | | | - Matthew Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | | |
Collapse
|
4
|
Rowsey DM, Duya MRM, Ibañez JC, Jansa SA, Rickart EA, Heaney LR. A new genus and species of shrew-like mouse (Rodentia: Muridae) from a new center of endemism in eastern Mindanao, Philippines. J Mammal 2022; 103:1259-1277. [PMID: 36660555 PMCID: PMC9841421 DOI: 10.1093/jmammal/gyac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/13/2022] [Indexed: 01/17/2023] Open
Abstract
The Philippine archipelago hosts an exceptional diversity of murid rodents that have diversified following several independent colonization events. Here, we report the discovery of a new species of rodent from Mt. Kampalili on eastern Mindanao Island. Molecular and craniodental analyses reveal this species as a member of a Philippine "New Endemic" clade consisting of Tarsomys, Limnomys, and Rattus everetti (tribe Rattini). This new species of "shrew-mouse" is easily distinguished from its relatives in both craniodental and external characteristics including a long, narrow snout; small eyes and ears; short, dark, dense fur dorsally and ventrally; stout body with a tapering, visibly haired tail shorter than head and body length; stout forepaws; bulbous and nearly smooth braincase; narrow, tapering rostrum; short incisive foramina; slender mandible; and narrow, slightly opisthodont incisors. This new genus and species of murid rodent illustrates that murids of the tribe Rattini have exhibited greater species and morphological diversification within the Philippines than previously known and provides evidence that Mt. Kampalili represents a previously unrecognized center of mammalian endemism on Mindanao Island that is deserving of conservation action.
Collapse
Affiliation(s)
| | - Mariano Roy M Duya
- Institute of Biology, University of the Philippines–Diliman, Quezon City, Philippines
| | - Jayson C Ibañez
- Philippine Eagle Foundation, Philippine Eagle Center, Malagos, Baguio District Davao City, Philippines
| | - Sharon A Jansa
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Eric A Rickart
- Natural History Museum of Utah, University of Utah, Salt Lake City, Utah, USA
| | | |
Collapse
|
5
|
Fay EJ, Balla KM, Roach SN, Shepherd FK, Putri DS, Wiggen TD, Goldstein SA, Pierson MJ, Ferris MT, Thefaine CE, Tucker A, Salnikov M, Cortez V, Compton SR, Kotenko SV, Hunter RC, Masopust D, Elde NC, Langlois RA. Natural rodent model of viral transmission reveals biological features of virus population dynamics. J Exp Med 2021; 219:212940. [PMID: 34958350 PMCID: PMC8713297 DOI: 10.1084/jem.20211220] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/05/2021] [Accepted: 12/08/2021] [Indexed: 12/21/2022] Open
Abstract
Emerging viruses threaten global health, but few experimental models can characterize the virus and host factors necessary for within- and cross-species transmission. Here, we leverage a model whereby pet store mice or rats-which harbor natural rodent pathogens-are cohoused with laboratory mice. This "dirty" mouse model offers a platform for studying acute transmission of viruses between and within hosts via natural mechanisms. We identified numerous viruses and other microbial species that transmit to cohoused mice, including prospective new members of the Coronaviridae, Astroviridae, Picornaviridae, and Narnaviridae families, and uncovered pathogen interactions that promote or prevent virus transmission. We also evaluated transmission dynamics of murine astroviruses during transmission and spread within a new host. Finally, by cohousing our laboratory mice with the bedding of pet store rats, we identified cross-species transmission of a rat astrovirus. Overall, this model system allows for the analysis of transmission of natural rodent viruses and is a platform to further characterize barriers to zoonosis.
Collapse
Affiliation(s)
- Elizabeth J. Fay
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Keir M. Balla
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Shanley N. Roach
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Frances K. Shepherd
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Dira S. Putri
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN
| | - Talia D. Wiggen
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | | | - Mark J. Pierson
- Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Martin T. Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Claire E. Thefaine
- Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN
| | - Andrew Tucker
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Mark Salnikov
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - Valerie Cortez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA
| | - Susan R. Compton
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT
| | - Sergei V. Kotenko
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ
| | - Ryan C. Hunter
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN
| | - David Masopust
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Center for Immunology, University of Minnesota, Minneapolis, MN
| | - Nels C. Elde
- Department of Human Genetics, University of Utah, Salt Lake City, UT
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN,Center for Immunology, University of Minnesota, Minneapolis, MN,Correspondence to Ryan A. Langlois:
| |
Collapse
|
6
|
Pradhan N, Norris RW, Decher J, Peterhans JK, Gray CR, Bauer G, Carleton MD, Kilpatrick CW. Phylogenetic relationships and biogeography of the Hybomys division (Muridae: Murinae: Arvicanthini), rodents endemic to Africa's rainforests. JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nelish Pradhan
- Department of Biology, University of Vermont, Burlington, USA; e-mail: ,
| | - Ryan W. Norris
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University at Lima, Lima, USA; e-mail: ,
| | - Jan Decher
- Mammal Section, Zoological Research Museum Alexander Koenig, Bonn, Germany; e-mail:
| | | | | | - George Bauer
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University at Lima, Lima, USA; e-mail: ,
| | - Michael D. Carleton
- Department of Vertebrate Zoology, Mammal Division, National Museum of Natural History, Washington, USA; e-mail:
| | | |
Collapse
|
7
|
Camacho-Sanchez M, Leonard JA. Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland. J Hered 2021; 111:392-404. [PMID: 32485737 PMCID: PMC7423070 DOI: 10.1093/jhered/esaa014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/25/2020] [Indexed: 01/16/2023] Open
Abstract
Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.
Collapse
Affiliation(s)
- Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| |
Collapse
|
8
|
Parada A, Hanson J, D'Elía G. Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae). Syst Biol 2021; 70:1090-1100. [PMID: 33787920 DOI: 10.1093/sysbio/syab023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/23/2021] [Accepted: 03/29/2021] [Indexed: 11/14/2022] Open
Abstract
Sigmodontine rodents (Cricetidae, Sigmodontinae) represent the second largest muroid subfamily and the most species-rich group of New World mammals, encompassing above 410 living species and ca. 87 genera. Even with advances on the clarification of sigmodontine phylogenetic relationships that have been made recently, the phylogenetic relationships among the 12 main group of genera (i.e., tribes) remain poorly resolved, in particular among those forming the large clade Oryzomyalia. This pattern has been interpreted as consequence of a rapid radiation upon the group entrance into South America. Here, we attempted to resolve phylogenetic relationships within Sigmodontinae using target capture and high-throughput sequencing of ultraconserved elements (UCEs). We enriched and sequenced UCEs for 56 individuals and collected data from four already available genomes. Analyses of distinct data sets, based on the capture of 4,634 loci, resulted in a highly resolved phylogeny consistent across different methods. Coalescent species-tree based approaches, concatenated matrices, and Bayesian analyses recovered similar topologies that were congruent at the resolution of difficult nodes. We recovered good support for the intertribal relationships within Oryzomyalia; for instance, the tribe Oryzomyini appears as the sister taxa of the remaining oryzomyalid tribes. The estimates of divergence times agree with results of previous studies. We inferred the crown age of the sigmodontine rodents at the end of Middle Miocene, while the main lineages of Oryzomyalia appear to have radiated in a short interval during the Late Miocene. Thus, the collection of a genomic scale data set with a wide taxonomic sampling, provided resolution for the first time of the relationships among the main lineages of Sigmodontinae. We expect the phylogeny presented here will become the backbone for future systematic and evolutionary studies of the group.
Collapse
Affiliation(s)
- Andrés Parada
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - John Hanson
- RTLGenomics, Lubbock, TX, USA. Department of Biology, Columbus State University, Columbus, GA, USA
| | - Guillermo D'Elía
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| |
Collapse
|
9
|
Kimura Y, Flynn LJ, Jacobs LL. Tempo and Mode: Evidence on a Protracted Split From a Dense Fossil Record. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.642814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Fossil records generally inform paleobiologists about extinct taxa and rates of evolution measured at the scale of millions of years. Good records that are densely sampled through time can reveal species level details such as longevity in local sections. Yet fossil data normally do not address details of lineage microevolution because the density through time of lineage sampling is insufficient to perceive patterns at a precision finer than 106 years in most cases. This study concerns details of a splitting event in the evolution of murine rodents, an event for which multiple fossil samples dated to a precision of 105 years fortuitously document the tempo and mode of origin of sister species, the stems of two extant tribes of mice. Evolution of early Murinae in the northern part of the biogeographically restricted Indian subcontinent between 11.6 and 10.5 Ma involved cladogenesis of two crown taxa, the extant tribes Murini and Arvicanthini. Large samples of fossil rodent teeth document their divergence from a common morphological pool. Definitive basal Murini and Arvicanthini at 10.5 Ma are similar in size and differ by subtle features of the dentition. Those features occur sporadically in the common pool of older fossil teeth at 11.2, 11.4, and 11.6 Ma as inconsistent polymorphisms. Interpreted as a single lineage in the 11.6–11.2 Ma interval, variability of this abundant murine incorporated the roots of the two crown tribes. The pattern through time suggests morphological stasis for several hundred thousand years prior to splitting. This special case informs us on one example of evolution and shows that the tempo of splitting evolution in some cases may be measured in hundreds of thousands of years, followed by stasis once daughter species have differentiated morphologically.
Collapse
|
10
|
Balakirev AE, Abramov AV, Rozhnov VV. Distribution pattern and phylogeography of tree rats Chiromyscus (Rodentia, Muridae) in eastern Indochina. ZOOSYST EVOL 2021. [DOI: 10.3897/zse.97.57490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The study combines available data on species distribution in eastern Indochina to investigate the phylogeographical genetic and morphological diversity of tree rats (Chiromyscus, Rodentia, Muridae) and to specify their natural ranges. We examined the diversity and distribution of tree rats over its range, based on recent molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, RAG1 and GHR) genes. The study presents the most complete and up-to-date data on the distribution and phylogeography of the genus in eastern Indochina. As revealed by mitochondrial genes, C. langbianis splits into at least four coherent geographically-distributed clades, whereas C. thomasi and C. chiropus form two distinctive mitochondrial clades each. Chiromyscus langbianis and C. chiropus show significant inconsistency in nuclear genes, whereas C. thomasi shows the same segregation pattern as can be traced by mitochondrial markers. The Northern and Southern phylogroups of C. thomasi appear to be distributed sympatrically with northern phylogroups of C. langbianis in most parts of eastern Indochina. The mitochondrial clades discovered are geographically subdivided and divergent enough to suspect independent subspecies within C. langbianis and C. thomasi. However, due to the insufficiency of obvious morphological traits, a formal description is not carried out here. The processes of recent fauna formation, species distribution patterns, dispersion routes and possible natural history in Indochina are discussed.
Collapse
|
11
|
Mikula O, Nicolas V, Šumbera R, Konečný A, Denys C, Verheyen E, Bryjová A, Lemmon AR, Moriarty Lemmon E, Bryja J. Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Mol Phylogenet Evol 2021; 157:107069. [PMID: 33421615 DOI: 10.1016/j.ympev.2021.107069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 12/17/2020] [Accepted: 01/04/2021] [Indexed: 01/09/2023]
Abstract
The tribe Arvicanthini (Muridae: Murinae) is a highly diversified group of rodents (ca. 100 species) and with 18 African genera (plus one Asiatic) represents probably the most successful adaptive radiation of extant mammals in Africa. They colonized a broad spectrum of habitats (from rainforests to semi-deserts) in whole sub-Saharan Africa and their members often belong to most abundant parts of mammal communities. Despite intensive efforts, the phylogenetic relationships among major lineages (i.e. genera) remained obscured, which was likely caused by the intensive radiation of the group, dated to the Late Miocene. Here we used genomic scale data (377 nuclear loci; 581,030 bp) and produced the first fully resolved species tree containing all currently delimited genera of the tribe. Mitogenomes were also extracted, and while the results were largely congruent, there was less resolution at basal nodes of the mitochondrial phylogeny. Results of a fossil-based divergence dating analysis suggest that the African radiation started early after the colonization of Africa by a single arvicanthine ancestor from Asia during the Messinian stage (ca. 7 Ma), and was likely linked with a fragmentation of the pan-African Miocene forest. Some lineages remained in the rain forest, while many others successfully colonized broad spectrum of new open habitats (e.g. savannas, wetlands or montane moorlands) that appeared at the beginning of Pliocene. One lineage even evolved partially arboricolous life style in savanna woodlands, which allowed them to re-colonize equatorial forests. We also discuss delimitation of genera in Arvicanthini and propose corresponding taxonomic changes.
Collapse
Affiliation(s)
- Ondřej Mikula
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, 602 00 Brno, Czech Republic
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Radim Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Adam Konečný
- Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium; Evolutionary Ecology Group, Biology Department, University of Antwerp, 2020 Antwerp, Belgium
| | - Anna Bryjová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4295, United States
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, PO Box 3064295, Tallahassee, FL 32306-4295, United States
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic.
| |
Collapse
|
12
|
Abstract
Background and aims Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question. Methods We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined. Results The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders. Conclusions Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.
Collapse
|
13
|
Abstract
A major challenge in evolutionary developmental biology is to understand how genetic mutations underlie phenotypic changes. In principle, selective pressures on the phenotype screen the gene pool of the population. Teeth are an excellent model for understanding evolutionary changes in the genotype-phenotype relationship since they exist throughout vertebrates. Genetically modified mice (mutants) with abnormalities in teeth have been used to explore tooth development. The relationship between signaling pathways and molar shape, however, remains elusive due to the high intrinsic complexity of tooth crowns. This hampers our understanding of the extent to which developmental factors explored in mutants explain developmental and phenotypic variation in natural species that represent the consequence of natural selection. Here we combine a novel morphometric method with two kinds of data mining techniques to extract data sets from the three-dimensional surface models of lower first molars: i) machine learning to maximize classification accuracy of 22 mutants, and ii) phylogenetic signal for 31 Murinae species. Major shape variation among mutants is explained by the number of cusps and cusp distribution on a tooth crown. The distribution of mutant mice in morphospace suggests a nonlinear relationship between the signaling pathways and molar shape variation. Comparative analysis of mutants and wild murines reveals that mutant variation overlaps naturally occurring diversity, including more ancestral and derived morphologies. However, taxa with transverse lophs are not fully covered by mutant variation, suggesting experimentally unexplored developmental factors in the evolutionary radiation of Murines.
Collapse
|
14
|
Hallikas O, Das Roy R, Christensen MM, Renvoisé E, Sulic AM, Jernvall J. System-level analyses of keystone genes required for mammalian tooth development. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:7-17. [PMID: 33128445 PMCID: PMC7894285 DOI: 10.1002/jez.b.23009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022]
Abstract
When a null mutation of a gene causes a complete developmental arrest, the gene is typically considered essential for life. Yet, in most cases, null mutations have more subtle effects on the phenotype. Here we used the phenotypic severity of mutations as a tool to examine system‐level dynamics of gene expression. We classify genes required for the normal development of the mouse molar into different categories that range from essential to subtle modification of the phenotype. Collectively, we call these the developmental keystone genes. Transcriptome profiling using microarray and RNAseq analyses of patterning stage mouse molars show highly elevated expression levels for genes essential for the progression of tooth development, a result reminiscent of essential genes in single‐cell organisms. Elevated expression levels of progression genes were also detected in developing rat molars, suggesting evolutionary conservation of this system‐level dynamics. Single‐cell RNAseq analyses of developing mouse molars reveal that even though the size of the expression domain, measured in the number of cells, is the main driver of organ‐level expression, progression genes show high cell‐level transcript abundances. Progression genes are also upregulated within their pathways, which themselves are highly expressed. In contrast, a high proportion of the genes required for normal tooth patterning are secreted ligands that are expressed in fewer cells than their receptors and intracellular components. Overall, even though expression patterns of individual genes can be highly different, conserved system‐level principles of gene expression can be detected using phenotypically defined gene categories. The phenotypic severity of mutations on mouse teeth is used to classify genes. Genes essential for the progression of odontogenesis are highly expressed at the organ and cell level. Many of the genes required for normal patterning are locally expressed ligands.
Collapse
Affiliation(s)
- Outi Hallikas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Rishi Das Roy
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Elodie Renvoisé
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Lycée des Métiers Claude Chappe, Arnage, France
| | - Ana-Marija Sulic
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jukka Jernvall
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland
| |
Collapse
|
15
|
Marcy AE, Guillerme T, Sherratt E, Rowe KC, Phillips MJ, Weisbecker V. Australian Rodents Reveal Conserved Cranial Evolutionary Allometry across 10 Million Years of Murid Evolution. Am Nat 2020; 196:755-768. [PMID: 33211559 DOI: 10.1086/711398] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAmong vertebrates, placental mammals are particularly variable in the covariance between cranial shape and body size (allometry), with rodents being a major exception. Australian murid rodents allow an assessment of the cause of this anomaly because they radiated on an ecologically diverse continent notably lacking other terrestrial placentals. Here, we use 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask whether ecological opportunity resulted in greater allometric diversity compared with other rodents or whether conserved allometry suggests intrinsic constraints and/or stabilizing selection. We also assess whether cranial shape variation follows the proposed rule of craniofacial evolutionary allometry (CREA), whereby larger species have relatively longer snouts and smaller braincases. To ensure we could differentiate parallel versus nonparallel species-level allometric slopes, we compared the slopes of rarefied samples across all clades. We found exceedingly conserved allometry and CREA-like patterns across the 10-million-year split between Mus and Australian murids. This could support both intrinsic-constraint and stabilizing-selection hypotheses for conserved allometry. Large-bodied frugivores evolved faster than other species along the allometric trajectory, which could suggest stabilizing selection on the shape of the masticatory apparatus as body size changes.
Collapse
|
16
|
Affiliation(s)
- Spenser J Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University AgCenter, Baton Rouge, Louisiana, United States of America
| |
Collapse
|
17
|
Species and genetic diversity of Bandicota (Murinae, Rodentia) from Myanmar based on mitochondrial and nuclear gene sequences. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
18
|
Swanson MT, Oliveros CH, Esselstyn JA. A phylogenomic rodent tree reveals the repeated evolution of masseter architectures. Proc Biol Sci 2020; 286:20190672. [PMID: 31064307 DOI: 10.1098/rspb.2019.0672] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Understanding the number of times a trait has evolved is a necessary foundation for comprehending its potential relationships with selective regimes, developmental constraints and evolutionary diversification. Rodents make up over 40% of extant mammalian species, and their ecological and evolutionary success has been partially attributed to the increase in biting efficiency that resulted from a forward shift of one or two portions of the masseter muscle from the zygomatic arch onto the rostrum. This forward shift has occurred in three discrete ways, but the number of times it has occurred has never been explicitly quantified. We estimated an ultrametric phylogeny, the first to include all rodent families, using thousands of ultraconserved elements. We examined support for evolutionary relationships among the five rodent suborders and then incorporated relevant fossils, fitted models of character evolution, and used stochastic character mapping to determine that a portion of the masseter muscle has moved forward onto the rostrum at least seven times (with one reversal) during the approximately 70 Myr history of rodents. Combined, the repeated evolution of this key innovation, its increasing prevalence through time, and the species diversity of clades with this character underscores the adaptive value of improved biting efficiency and the relative ease with which some advantageous traits arise.
Collapse
Affiliation(s)
- Mark T Swanson
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University , Baton Rouge, LA , USA
| | - Carl H Oliveros
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University , Baton Rouge, LA , USA
| | - Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University , Baton Rouge, LA , USA
| |
Collapse
|
19
|
Dianat M, Darvish J, Aliabadian M, Siahsarvie R, Krystufek B, Nicolas V. Systematics and evolution of the libyan jird based on molecular and morphometric data. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Malahat Dianat
- Department of Biology, Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Jamshid Darvish
- Department of Biology, Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Mansour Aliabadian
- Department of Biology, Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
| | - Roohollah Siahsarvie
- Department of Biology, Faculty of Science Ferdowsi University of Mashhad Mashhad Iran
- Rodentology Research Department, Institute of Applied Zoology, Faculty of Sciences Ferdowsi University of Mashhad Mashhad Iran
| | | | - Violaine Nicolas
- Institut de Systematique, Evolution, Biodiversite, ISYEB‐UMR 7205‐CNRS, MNHN, UPMC EPHE, Museum National d’Histoire Naturelle, Sorbonne Universites Paris France
| |
Collapse
|
20
|
Nicolas V, Fabre PH, Bryja J, Denys C, Verheyen E, Missoup AD, Olayemi A, Katuala P, Dudu A, Colyn M, Kerbis Peterhans J, Demos T. The phylogeny of the African wood mice (Muridae, Hylomyscus) based on complete mitochondrial genomes and five nuclear genes reveals their evolutionary history and undescribed diversity. Mol Phylogenet Evol 2019; 144:106703. [PMID: 31816395 DOI: 10.1016/j.ympev.2019.106703] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/22/2019] [Accepted: 12/05/2019] [Indexed: 11/26/2022]
Abstract
Wood mice of the genus Hylomyscus, are small-sized rodents widely distributed in lowland and montane rainforests in tropical Africa, where they can be locally abundant. Recent morphological and molecular studies have increased the number of recognized species from 8 to 18 during the last 15 years. We used complete mitochondrial genomes and five nuclear genes to infer the number of candidate species within this genus and depict its evolutionary history. In terms of gene sampling and geographical and taxonomic coverage, this is the most comprehensive review of the genus Hylomyscus to date. The six species groups (aeta, alleni, anselli, baeri, denniae and parvus) defined on morphological grounds are monophyletic. Species delimitation analyses highlight undescribed diversity within this genus: perhaps up to 10 taxa need description or elevation from synonymy, pending review of type specimens. Our divergence dating and biogeographical analyses show that diversification of the genus occurred after the end of the Miocene and is closely linked to the history of the African forest. The formation of the Rift Valley combined with the declining global temperatures during the Late Miocene caused the fragmentation of the forests and explains the first split between the denniae group and remaining lineages. Subsequently, periods of increased climatic instability during Plio-Pleistocene probably resulted in elevated diversification in both lowland and montane forest taxa.
Collapse
Affiliation(s)
- Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France.
| | - Pierre-Henri Fabre
- Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS-IRD-UM), Université de Montpellier, Place E. Bataillon CC 064 - 34095, Montpellier Cedex 5, France
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - Erik Verheyen
- Royal Belgian Institute for Natural Sciences, Operational Direction Taxonomy and Phylogeny, 1000 Brussels, Belgium
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, Douala, Cameroon
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005 Ile Ife, Nigeria
| | - Pionus Katuala
- Animal Ecology and Resource Management, Laboratory (LEGERA), University of Kisangani, B.P. 2012, Kisangani, Congo
| | - Akaibe Dudu
- Animal Ecology and Resource Management, Laboratory (LEGERA), University of Kisangani, B.P. 2012, Kisangani, Congo
| | - Marc Colyn
- Université de Rennes 1, CNRS, UMR 6553 Ecobio, Station Biologique, 35380 Paimpont, France
| | - Julian Kerbis Peterhans
- Science & Education, Field Museum of Natural History, 60605 Chicago, IL, USA; College of Arts & Sciences, Roosevelt University, 430 S Michigan, Chicago, IL 60605, USA
| | - Terrence Demos
- College of Arts & Sciences, Roosevelt University, 430 S Michigan, Chicago, IL 60605, USA
| |
Collapse
|
21
|
Lindsay SJ, Rahbari R, Kaplanis J, Keane T, Hurles ME. Similarities and differences in patterns of germline mutation between mice and humans. Nat Commun 2019; 10:4053. [PMID: 31492841 PMCID: PMC6731245 DOI: 10.1038/s41467-019-12023-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 08/02/2019] [Indexed: 01/26/2023] Open
Abstract
Whole genome sequencing (WGS) studies have estimated the human germline mutation rate per basepair per generation (~1.2 × 10−8) to be higher than in mice (3.5–5.4 × 10−9). In humans, most germline mutations are paternal in origin and numbers of mutations per offspring increase with paternal and maternal age. Here we estimate germline mutation rates and spectra in six multi-sibling mouse pedigrees and compare to three multi-sibling human pedigrees. In both species we observe a paternal mutation bias, a parental age effect, and a highly mutagenic first cell division contributing to the embryo. We also observe differences between species in mutation spectra, in mutation rates per cell division, and in the parental bias of mutations in early embryogenesis. These differences between species likely result from both species-specific differences in cellular genealogies of the germline, as well as biological differences within the same stage of embryogenesis or gametogenesis. Estimates of mutation rates differ between species. Here, Lindsay et al. perform side-by-side analyses of germline mutation rates using multi-sibling mouse and human pedigrees and find different mutation rates between species, also stratified by sex and temporal stage of mutation acquisition.
Collapse
Affiliation(s)
| | | | | | - Thomas Keane
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | | |
Collapse
|
22
|
Kobayashi CR, Castillo-González C, Survotseva Y, Canal E, Nelson ADL, Shippen DE. Recent emergence and extinction of the protection of telomeres 1c gene in Arabidopsis thaliana. PLANT CELL REPORTS 2019; 38:1081-1097. [PMID: 31134349 PMCID: PMC6708462 DOI: 10.1007/s00299-019-02427-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/27/2019] [Indexed: 05/20/2023]
Abstract
Duplicate POT1 genes must rapidly diverge or be inactivated. Protection of telomeres 1 (POT1) encodes a conserved telomere binding protein implicated in both chromosome end protection and telomere length maintenance. Most organisms harbor a single POT1 gene, but in the few lineages where the POT1 family has expanded, the duplicate genes have diversified. Arabidopsis thaliana bears three POT1-like loci, POT1a, POT1b and POT1c. POT1a retains the ancestral function of telomerase regulation, while POT1b is implicated in chromosome end protection. Here we examine the function and evolution of the third POT1 paralog, POT1c. POT1c is a new gene, unique to A. thaliana, and was derived from a duplication event involving the POT1a locus and a neighboring gene encoding ribosomal protein S17. The duplicate S17 locus (dS17) is highly conserved across A. thaliana accessions, while POT1c is highly divergent, harboring multiple deletions within the gene body and two transposable elements within the promoter. The POT1c locus is transcribed at very low to non-detectable levels under standard growth conditions. In addition, no discernable molecular or developmental defects are associated with plants bearing a CRISPR mutation in the POT1c locus. However, forced expression of POT1c leads to decreased telomerase enzyme activity and shortened telomeres. Evolutionary reconstruction indicates that transposons invaded the POT1c promoter soon after the locus was formed, permanently silencing the gene. Altogether, these findings argue that POT1 dosage is critically important for viability and duplicate gene copies are retained only upon functional divergence.
Collapse
Affiliation(s)
- Callie R Kobayashi
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | | | - Yulia Survotseva
- Yale Center for Molecular Discovery, Yale University, New Haven, Connecticut, USA
| | - Elijah Canal
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Andrew D L Nelson
- The School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Dorothy E Shippen
- Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.
| |
Collapse
|
23
|
López-Antoñanzas R, Renaud S, Peláez-Campomanes P, Azar D, Kachacha G, Knoll F. First levantine fossil murines shed new light on the earliest intercontinental dispersal of mice. Sci Rep 2019; 9:11874. [PMID: 31467294 PMCID: PMC6715647 DOI: 10.1038/s41598-019-47894-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/22/2019] [Indexed: 11/09/2022] Open
Abstract
Recent extensive field prospecting conducted in the Upper Miocene of Lebanon resulted in the discovery of several new fossiliferous localities. One of these, situated in the Zahleh area (Bekaa Valley, central Lebanon) has yielded a particularly diverse vertebrate fauna. Micromammals constitute an important part of this assemblage because not only do they represent the first Neogene rodents and insectivores from Lebanon, but they are also the only ones from the early Late Miocene of the Arabian Peninsula and circumambient areas. Analyses of the murines from Zahleh reveal that they belong to a small-sized early Progonomys, which cannot be assigned to any of the species of the genus hitherto described. They are, thereby, shown to represent a new species: Progonomys manolo. Morphometric analyses of the outline of the first upper molars of this species suggest a generalist and omnivorous diet. This record sheds new light onto a major phenomenon in the evolutionary history of rodents, which is the earliest dispersal of mice. It suggests that the arrival of murines in Africa got under way through the Levant rather than via southern Europe and was monitored by the ecological requirements of Progonomys.
Collapse
Affiliation(s)
- Raquel López-Antoñanzas
- Laboratoire de Paléontologie, Institut des Sciences de l'Évolution (UMR-CNRS 5554), Université de Montpellier, Montpellier, France. .,Departamento de Paleobiología, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain.
| | - Sabrina Renaud
- Laboratoire de Biométrie et Biologie Evolutive (UMR-CNRS 5558), Université Lyon 1, Villeurbanne, France
| | | | - Dany Azar
- Natural Sciences Department, Faculty of Sciences II, Lebanese University, Fanar, Lebanon
| | - George Kachacha
- Natural Sciences Department, Faculty of Sciences II, Lebanese University, Fanar, Lebanon
| | - Fabien Knoll
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain.,ARAID-Fundación Conjunto Paleontológico de Teruel-Dinopolis, Teruel, Spain.,Department of Earth and Environmental Sciences, School of Natural Science, University of Manchester, Manchester, United Kingdom
| |
Collapse
|
24
|
Li H, Kong L, Wang K, Zhang S, Motokawa M, Wu Y, Wang W, Li Y. Molecular phylogeographic analyses and species delimitations reveal that Leopoldamys edwardsi (Rodentia: Muridae) is a species complex. Integr Zool 2019; 14:494-505. [PMID: 30688015 DOI: 10.1111/1749-4877.12378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation. We used 2 mitochondrial (Cytb, CO1) and 3 nuclear (GHR, IRBP and RAG1) genes to clarify species phylogeography and geographical differentiation. Maximum likelihood (ML) and Bayesian phylogenetic inference (BI) trees consistently indicated that L. edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter (K2P) divergences (i.e. lineages LN , LS and LHN ) found in the northern and southern China and Hainan Island, respectively. The 3 species delimitation methods, automated barcoding gap discovery, Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography, consistently supported the existence of cryptic species. Divergence times among the main lineages were inferred to be during the Pleistocene, with LHN /LS split at 1.33 Ma and LN /(LHN +LS ) at 2.61 Ma; the diversifications of L. edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau, paleoclimate change and complex topography. The divergence between LHN and LS was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait. Lineages LN and (LS +LHN ) likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier. Our results suggested that L. edwardsi complex contains at least 3 distinct species: LHN represents L. hainanensis, endemic to Hainan Island and previously considered as a subspecies L. e. hainanensis; LS represents a cryptic species distributed throughout the southern Chinese continent; and LN represents the nominotypical species L. edwardsi.
Collapse
Affiliation(s)
- Haotian Li
- Marine College, Shandong University, Weihai, China
| | | | - Kaiyun Wang
- Institute of Ecology and Biodiversity, Shandong University, Jinan, China
| | - Shuping Zhang
- Institute of Ecology and Biodiversity, Shandong University, Jinan, China
| | | | - Yi Wu
- College of Life Science, Guangzhou University, Guangzhou, China
| | - Wenquan Wang
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yuchun Li
- Marine College, Shandong University, Weihai, China
| |
Collapse
|
25
|
Smissen PJ, Rowe KC. Repeated biome transitions in the evolution of Australian rodents. Mol Phylogenet Evol 2018; 128:182-191. [DOI: 10.1016/j.ympev.2018.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/26/2018] [Accepted: 07/16/2018] [Indexed: 12/31/2022]
|
26
|
Casola C. From De Novo to "De Nono": The Majority of Novel Protein-Coding Genes Identified with Phylostratigraphy Are Old Genes or Recent Duplicates. Genome Biol Evol 2018; 10:2906-2918. [PMID: 30346517 PMCID: PMC6239577 DOI: 10.1093/gbe/evy231] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2018] [Indexed: 12/11/2022] Open
Abstract
The evolution of novel protein-coding genes from noncoding regions of the genome is one of the most compelling pieces of evidence for genetic innovations in nature. One popular approach to identify de novo genes is phylostratigraphy, which consists of determining the approximate time of origin (age) of a gene based on its distribution along a species phylogeny. Several studies have revealed significant flaws in determining the age of genes, including de novo genes, using phylostratigraphy alone. However, the rate of false positives in de novo gene surveys, based on phylostratigraphy, remains unknown. Here, I reanalyze the findings from three studies, two of which identified tens to hundreds of rodent-specific de novo genes adopting a phylostratigraphy-centered approach. Most putative de novo genes discovered in these investigations are no longer included in recently updated mouse gene sets. Using a combination of synteny information and sequence similarity searches, I show that ∼60% of the remaining 381 putative de novo genes share homology with genes from other vertebrates, originated through gene duplication, and/or share no synteny information with nonrodent mammals. These results led to an estimated rate of ∼12 de novo genes per million years in mouse. Contrary to a previous study (Wilson BA, Foy SG, Neme R, Masel J. 2017. Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth. Nat Ecol Evol. 1:0146), I found no evidence supporting the preadaptation hypothesis of de novo gene formation. Nearly half of the de novo genes confirmed in this study are within older genes, indicating that co-option of preexisting regulatory regions and a higher GC content may facilitate the origin of novel genes.
Collapse
Affiliation(s)
- Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University
| |
Collapse
|
27
|
Ma L, Cissé OH, Kovacs JA. A Molecular Window into the Biology and Epidemiology of Pneumocystis spp. Clin Microbiol Rev 2018; 31:e00009-18. [PMID: 29899010 PMCID: PMC6056843 DOI: 10.1128/cmr.00009-18] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Pneumocystis, a unique atypical fungus with an elusive lifestyle, has had an important medical history. It came to prominence as an opportunistic pathogen that not only can cause life-threatening pneumonia in patients with HIV infection and other immunodeficiencies but also can colonize the lungs of healthy individuals from a very early age. The genus Pneumocystis includes a group of closely related but heterogeneous organisms that have a worldwide distribution, have been detected in multiple mammalian species, are highly host species specific, inhabit the lungs almost exclusively, and have never convincingly been cultured in vitro, making Pneumocystis a fascinating but difficult-to-study organism. Improved molecular biologic methodologies have opened a new window into the biology and epidemiology of Pneumocystis. Advances include an improved taxonomic classification, identification of an extremely reduced genome and concomitant inability to metabolize and grow independent of the host lungs, insights into its transmission mode, recognition of its widespread colonization in both immunocompetent and immunodeficient hosts, and utilization of strain variation to study drug resistance, epidemiology, and outbreaks of infection among transplant patients. This review summarizes these advances and also identifies some major questions and challenges that need to be addressed to better understand Pneumocystis biology and its relevance to clinical care.
Collapse
Affiliation(s)
- Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
| | - Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, Bethesda, Maryland, USA
| |
Collapse
|
28
|
Cissé OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA. Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis. mBio 2018; 9:e00381-18. [PMID: 29739910 PMCID: PMC5941068 DOI: 10.1128/mbio.00381-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/19/2018] [Indexed: 01/14/2023] Open
Abstract
Pneumocystis species are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivable in vitro Human Pneumocystis infections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations of Pneumocystis infecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate that Pneumocystis species diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation of Pneumocystis populations during their spread across mammals.IMPORTANCE Understanding how natural pathogen populations evolve and identifying the determinants of genetic variation are central issues in evolutionary biology. Pneumocystis, a fungal pathogen which infects mammals exclusively, provides opportunities to explore these issues. In humans, Pneumocystis can cause a life-threatening pneumonia in immunosuppressed individuals. In analysis of different Pneumocystis species infecting humans, rats, and mice, we found that there are high infection rates and that natural populations maintain a high level of genetic variation despite low levels of recombination. We found no evidence of population structuring by geography. Our comparisons of the times of divergence of these species to their respective hosts suggest that Pneumocystis may have undergone recent host shifts. The results demonstrate that Pneumocystis strains are widely disseminated geographically and provide a new understanding of the evolution of these pathogens.
Collapse
Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Da Wei Huang
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel P Khil
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - John P Dekker
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa Bishop
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Xilong Deng
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Philippe M Hauser
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marco Pagni
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vanessa Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Richard A Lempicki
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jason E Stajich
- Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
29
|
Levänen R, Thulin CG, Spong G, Pohjoismäki JLO. Widespread introgression of mountain hare genes into Fennoscandian brown hare populations. PLoS One 2018; 13:e0191790. [PMID: 29370301 PMCID: PMC5784980 DOI: 10.1371/journal.pone.0191790] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/11/2018] [Indexed: 11/29/2022] Open
Abstract
In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.
Collapse
Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Carl-Gustaf Thulin
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Spong
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
- * E-mail:
| |
Collapse
|
30
|
Guerrero-Juarez CF, Astrowski AA, Murad R, Dang CT, Shatrova VO, Astrowskaja A, Lim CH, Ramos R, Wang X, Liu Y, Lee HL, Pham KT, Hsi TC, Oh JW, Crocker D, Mortazavi A, Ito M, Plikus MV. Wound Regeneration Deficit in Rats Correlates with Low Morphogenetic Potential and Distinct Transcriptome Profile of Epidermis. J Invest Dermatol 2018; 138:1409-1419. [PMID: 29317265 DOI: 10.1016/j.jid.2017.12.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 12/14/2017] [Accepted: 12/22/2017] [Indexed: 01/10/2023]
Abstract
Large excisional wounds in mice prominently regenerate new hair follicles (HFs) and fat, yet humans are deficient for this regenerative behavior. Currently, wound-induced regeneration remains a clinically desirable, but only partially understood phenomenon. We show that large excisional wounds in rats across seven strains fail to regenerate new HFs. We compared wound transcriptomes between mice and rats at the time of scab detachment, which coincides with the onset of HF regeneration in mice. In both species, wound dermis and epidermis share core dermal and epidermal transcriptional programs, respectively, yet prominent interspecies differences exist. Compared with mice, rat epidermis expresses distinct transcriptional and epigenetic factors, markers of epidermal repair, hyperplasia, and inflammation, and lower levels of WNT signaling effectors and regulators. When recombined on the surface of excisional wounds with vibrissa dermal papillae, partial-thickness skin grafts containing distal pelage HF segments, but not interfollicular epidermis, readily regenerated new vibrissa-like HFs. Together, our findings establish rats as a nonregenerating rodent model for excisional wound healing and suggest that low epidermal competence and associated transcriptional profile may contribute to its regenerative deficiency. Future comparison between rat and mouse may lend further insight into the mechanism of wounding-induced regeneration and causes for its deficit.
Collapse
Affiliation(s)
- Christian F Guerrero-Juarez
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, California, USA
| | - Aliaksandr A Astrowski
- Department of Medical Biology and Genetics, Grodna State Medical University, Grodna, Belarus
| | - Rabi Murad
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, California, USA
| | - Christina T Dang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Vera O Shatrova
- Department of Medical Biology and Genetics, Grodna State Medical University, Grodna, Belarus
| | - Aksana Astrowskaja
- Department of Medical Biology and Genetics, Grodna State Medical University, Grodna, Belarus
| | - Chae Ho Lim
- The Ronald O. Perelman Department of Dermatology, Department of Cell Biology, New York University School of Medicine, New York, New York, USA
| | - Raul Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, California, USA
| | - Xiaojie Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, California, USA
| | - Yuchen Liu
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Hye-Lim Lee
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Kim T Pham
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Tsai-Ching Hsi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA
| | - Ji Won Oh
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA; Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Republic of Korea; Biomedical Research Institute, Kyungpook National University Hospital, Daegu, Republic of Korea; Hair Transplantation Center, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Daniel Crocker
- Department of Biology, Sonoma State University, Rohnert Park, California, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, California, USA
| | - Mayumi Ito
- The Ronald O. Perelman Department of Dermatology, Department of Cell Biology, New York University School of Medicine, New York, New York, USA
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, California, USA.
| |
Collapse
|
31
|
Genetic diversity and evolution of Pneumocystis fungi infecting wild Southeast Asian murid rodents. Parasitology 2017; 145:885-900. [PMID: 29117878 DOI: 10.1017/s0031182017001883] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pneumocystis organisms are airborne-transmitted fungal parasites that infect the lungs of numerous mammalian species with strong host specificity. In this study, we investigated the genetic diversity and host specificity of Pneumocystis organisms infecting Southeast Asian murid rodents through PCR amplification of two mitochondrial genes and tested the co-phylogeny hypothesis among these fungi and their rodent hosts. Pneumocystis DNA was detected in 215 of 445 wild rodents belonging to 18 Southeast Asian murid species. Three of the Pneumocystis lineages retrieved in our phylogenetic trees correspond to known Pneumocystis species, but some of the remaining lineages may correspond to new undescribed species. Most of these Pneumocystis species infect several rodent species or genera and some sequence types are shared among several host species and genera. These results indicated a weaker host specificity of Pneumocystis species infecting rodents than previously thought. Our co-phylogenetic analyses revealed a complex evolutionary history among Pneumocystis and their rodent hosts. Even if a significant global signal of co-speciation has been detected, co-speciation alone is not sufficient to explain the observed co-phylogenetic pattern and several host switches are inferred. These findings conflict with the traditional view of a prolonged process of co-evolution and co-speciation of Pneumocystis and their hosts.
Collapse
|
32
|
Camacho-Sanchez M, Leonard JA, Fitriana Y, Tilak MK, Fabre PH. The generic status of Rattus annandalei (Bonhote, 1903) (Rodentia, Murinae) and its evolutionary implications. J Mammal 2017. [DOI: 10.1093/jmammal/gyx081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
33
|
Arora A, Beilstein MA, Shippen DE. Evolution of Arabidopsis protection of telomeres 1 alters nucleic acid recognition and telomerase regulation. Nucleic Acids Res 2016; 44:9821-9830. [PMID: 27651456 PMCID: PMC5175356 DOI: 10.1093/nar/gkw807] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 09/01/2016] [Accepted: 09/03/2016] [Indexed: 11/14/2022] Open
Abstract
Protection of telomeres (POT1) binds chromosome ends, recognizing single-strand telomeric DNA via two oligonucleotide/oligosaccharide binding folds (OB-folds). The Arabidopsis thaliana POT1a and POT1b paralogs are atypical: they do not exhibit telomeric DNA binding, and they have opposing roles in regulating telomerase activity. AtPOT1a stimulates repeat addition processivity of the canonical telomerase enzyme, while AtPOT1b interacts with a regulatory lncRNA that represses telomerase activity. Here, we show that OB1 of POT1a, but not POT1b, has an intrinsic affinity for telomeric DNA. DNA binding was dependent upon a highly conserved Phe residue (F65) that in human POT1 directly contacts telomeric DNA. F65A mutation of POT1aOB1 abolished DNA binding and diminished telomerase repeat addition processivity. Conversely, AtPOT1b and other POT1b homologs from Brassicaceae and its sister family, Cleomaceae, naturally bear a non-aromatic amino acid at this position. By swapping Val (V63) with Phe, AtPOT1bOB1 gained the capacity to bind telomeric DNA and to stimulate telomerase repeat addition processivity. We conclude that, in the context of DNA binding, variation at a single amino acid position promotes divergence of the AtPOT1b paralog from the ancestral POT1 protein.
Collapse
Affiliation(s)
- Amit Arora
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
| | - Mark A Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA
| |
Collapse
|
34
|
Rowe KC, Achmadi AS, Esselstyn JA. A new genus and species of omnivorous rodent (Muridae: Murinae) from Sulawesi, nested within a clade of endemic carnivores. J Mammal 2016. [DOI: 10.1093/jmammal/gyw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
35
|
Rowe KC, Achmadi AS, Esselstyn JA. Repeated evolution of carnivory among Indo-Australian rodents. Evolution 2016; 70:653-65. [PMID: 26826614 DOI: 10.1111/evo.12871] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 01/08/2016] [Accepted: 01/12/2016] [Indexed: 12/30/2022]
Abstract
Convergent evolution, often observed in island archipelagos, provides compelling evidence for the importance of natural selection as a generator of species and ecological diversity. The Indo-Australian Archipelago (IAA) is the world's largest island system and encompasses distinct biogeographic units, including the Asian (Sunda) and Australian (Sahul) continental shelves, which together bracket the oceanic archipelagos of the Philippines and Wallacea. Each of these biogeographic units houses numerous endemic rodents in the family Muridae. Carnivorous murids, that is those that feed on animals, have evolved independently in Sunda, Sulawesi (part of Wallacea), the Philippines, and Sahul, but the number of origins of carnivory among IAA murids is unknown. We conducted a comprehensive phylogenetic analysis of carnivorous murids of the IAA, combined with estimates of ancestral states for broad diet categories (herbivore, omnivore, and carnivore) and geographic ranges. These analyses demonstrate that carnivory evolved independently four times after overwater colonization, including in situ origins on the Philippines, Sulawesi, and Sahul. In each biogeographic unit the origin of carnivory was followed by evolution of more specialized carnivorous ecomorphs such as vermivores, insectivores, and amphibious rats.
Collapse
Affiliation(s)
- Kevin C Rowe
- Sciences Department, Museum Victoria, Melbourne, Australia.
| | - Anang S Achmadi
- Research Center for Biology, Museum Zoologicum Bogoriense, Cibinong, Jawa Barat, Indonesia
| | - Jacob A Esselstyn
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| |
Collapse
|