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Varela L, Tambusso S, Fariña R. Femora nutrient foramina and aerobic capacity in giant extinct xenarthrans. PeerJ 2024; 12:e17815. [PMID: 39131616 PMCID: PMC11316464 DOI: 10.7717/peerj.17815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 07/04/2024] [Indexed: 08/13/2024] Open
Abstract
Nutrient foramina are small openings in the periosteal surface of the mid-shaft region of long bones that traverse the cortical layer and reach the medullary cavity. They are important for the delivery of nutrients and oxygen to bone tissue and are crucial for the repair and remodeling of bones over time. The nutrient foramina in the femur's diaphysis are related to the energetic needs of the femur and have been shown to be related to the maximum metabolic rate (MMR) of taxa. Here, we investigate the relationship between nutrient foramen size and body mass as a proxy to the aerobic capacity of taxa in living and extinct xenarthrans, including living sloths, anteaters, and armadillos, as well as extinct xenarthrans such as glyptodonts, pampatheres, and ground sloths. Seventy femora were sampled, including 20 from extant taxa and 50 from extinct taxa. We obtained the blood flow rate (Q̇) based on foramina area and performed PGLS and phylogenetic ANCOVA in order to explore differences among mammalian groups. Our results show that, among mammals, taxa commonly associated with lower metabolism like living xenarthrans showed relatively smaller foramina, while the foramina of giant extinct xenarthrans like ground sloths and glyptodonts overlapped with non-xenarthran placentals. Consequently, Q̇ estimations indicated aerobic capacities comparable to other placental giant taxa like elephants or some ungulates. Furthermore, the estimation of the MMR for fossil giant taxa showed similar results, with almost all taxa showing high values except for those for which strong semi-arboreal or fossorial habits have been proposed. Moreover, the results are compatible with the diets predicted for extinct taxa, which indicate a strong consumption of grass similar to ungulates and in contrast to the folivorous or insectivorous diets of extant xenarthrans. The ancestral reconstruction of the MMR values indicated a lack of a common pattern for all xenarthrans, strongly supporting the occurrence of low metabolic rates in extant forms due to their particular dietary preferences and arboreal or fossorial habits. Our results highlight the importance of considering different evidence beyond the phylogenetic position of extinct taxa, especially when extinct forms are exceptionally different from their extant relatives. Future studies evaluating the energetic needs of giant extinct xenarthrans should not assume lower metabolic rates for these extinct animals based solely on their phylogenetic position and the observations on their extant relatives.
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Affiliation(s)
- Luciano Varela
- Department of Paleontology, Universidad de la República, Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudio Paleontológicos (SAUCE-P), Universidad de la República, Sauce, Canelones, Uruguay
| | - Sebastián Tambusso
- Department of Paleontology, Universidad de la República, Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudio Paleontológicos (SAUCE-P), Universidad de la República, Sauce, Canelones, Uruguay
| | - Richard Fariña
- Department of Paleontology, Universidad de la República, Montevideo, Uruguay
- Servicio Académico Universitario y Centro de Estudio Paleontológicos (SAUCE-P), Universidad de la República, Sauce, Canelones, Uruguay
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Gupta A, Mirarab S, Turakhia Y. Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.596098. [PMID: 38854139 PMCID: PMC11160643 DOI: 10.1101/2024.05.27.596098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Inference of species trees plays a crucial role in advancing our understanding of evolutionary relationships and has immense significance for diverse biological and medical applications. Extensive genome sequencing efforts are currently in progress across a broad spectrum of life forms, holding the potential to unravel the intricate branching patterns within the tree of life. However, estimating species trees starting from raw genome sequences is quite challenging, and the current cutting-edge methodologies require a series of error-prone steps that are neither entirely automated nor standardized. In this paper, we present ROADIES, a novel pipeline for species tree inference from raw genome assemblies that is fully automated, easy to use, scalable, free from reference bias, and provides flexibility to adjust the tradeoff between accuracy and runtime. The ROADIES pipeline eliminates the need to align whole genomes, choose a single reference species, or pre-select loci such as functional genes found using cumbersome annotation steps. Moreover, it leverages recent advances in phylogenetic inference to allow multi-copy genes, eliminating the need to detect orthology. Using the genomic datasets released from large-scale sequencing consortia across three diverse life forms (placental mammals, pomace flies, and birds), we show that ROADIES infers species trees that are comparable in quality with the state-of-the-art approaches but in a fraction of the time. By incorporating optimal approaches and automating all steps from assembled genomes to species and gene trees, ROADIES is poised to improve the accuracy, scalability, and reproducibility of phylogenomic analyses.
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Affiliation(s)
- Anshu Gupta
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Siavash Mirarab
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego; San Diego, CA 92093, USA
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Liu G, Pan Q, Dai Y, Wang X, Li M, Zhu P, Zhou X. Phylogenomics of Afrotherian mammals and improved resolution of extant Paenungulata. Mol Phylogenet Evol 2024; 195:108047. [PMID: 38460890 DOI: 10.1016/j.ympev.2024.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Molecular investigations have gathered a diverse set of mammals-predominantly African natives like elephants, hyraxes, and aardvarks-into a clade known as Afrotheria. Nevertheless, the precise phylogenetic relationships among these species remain contentious. Here, we sourced orthologous markers and ultraconserved elements to discern the interordinal connections among Afrotherian mammals. Our phylogenetic analyses bolster the common origin of Afroinsectiphilia and Paenungulata, and propose Afrosoricida as the closer relative to Macroscelidea rather than Tubulidentata, while also challenging the notion of Sirenia and Hyracoidea as sister taxa. The approximately unbiased test and the gene concordance factor uniformly recognized the alliance of Proboscidea with Hyracoidea as the dominant topology within Paenungulata. Investigation into sites with extremly high phylogenetic signal unveiled their potential to intensify conflicts in the Paenungulata topology. Subsequent exploration suggested that incomplete lineage sorting was predominantly responsible for the observed contentious relationships, whereas introgression exerted a subsidiary influence. The divergence times estimated in our study hint at the Cretaceous-Paleogene (K-Pg) extinction event as a catalyst for Afrotherian diversification. Overall, our findings deliver a tentative but insightful overview of Afrotheria phylogeny and divergence, elucidating these relationships through the lens of phylogenomics.
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Affiliation(s)
- Gaoming Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingfen Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Liang M, Zhang L, Lai L, Li Z. Unraveling the role of Xist in X chromosome inactivation: insights from rabbit model and deletion analysis of exons and repeat A. Cell Mol Life Sci 2024; 81:156. [PMID: 38551746 PMCID: PMC10980640 DOI: 10.1007/s00018-024-05151-0] [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: 10/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 04/01/2024]
Abstract
X chromosome inactivation (XCI) is a process that equalizes the expression of X-linked genes between males and females. It relies on Xist, continuously expressed in somatic cells during XCI maintenance. However, how Xist impacts XCI maintenance and its functional motifs remain unclear. In this study, we conducted a comprehensive analysis of Xist, using rabbits as an ideal non-primate model. Homozygous knockout of exon 1, exon 6, and repeat A in female rabbits resulted in embryonic lethality. However, X∆ReAX females, with intact X chromosome expressing Xist, showed no abnormalities. Interestingly, there were no significant differences between females with homozygous knockout of exons 2-5 and wild-type rabbits, suggesting that exons 2, 3, 4, and 5 are less important for XCI. These findings provide evolutionary insights into Xist function.
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Affiliation(s)
- Mingming Liang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Lichao Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China
| | - Liangxue Lai
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, 100039, China.
- Research Unit of Generation of Large Animal Disease Models, Chinese Academy of Medical Sciences, Guangzhou, 510530, China.
| | - Zhanjun Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, China.
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Bowman J, Enard D, Lynch VJ. Phylogenomics reveals an almost perfect polytomy among the almost ungulates ( Paenungulata). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570590. [PMID: 38106080 PMCID: PMC10723481 DOI: 10.1101/2023.12.07.570590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., the Paenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates. We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships and that despite strong support for a Proboscidea+Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea, Hyracoidea, and Sirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea, Hyracoidea, and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.
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Affiliation(s)
- Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
| | - David Enard
- Department of Ecology and Evolutionary Biology. University of Arizona, Tucson, AZ, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, USA
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Kunze PE, Cortés-Hinojosa G, Williams CV, Archer LL, Ferrante JA, Wellehan JFX. Identification of 3 novel herpesviruses in prosimians with lymphoproliferative disease. J Vet Diagn Invest 2023; 35:514-520. [PMID: 37381927 PMCID: PMC10467458 DOI: 10.1177/10406387231183431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Although many studies have characterized catarrhine and platyrrhine primate herpesviruses, little is known about herpesviruses in prosimians. We aimed to identify and characterize herpesviruses in prosimians with proliferative lymphocytic disease. DNA was extracted from tissues of 9 gray mouse lemurs (Microcebus murinus) and 3 pygmy slow lorises (Nycticebus pygmaeus) with lymphoproliferative lesions, and we performed nested PCR and sequencing for detection of herpesviruses and polyomaviruses. We identified 3 novel herpesviruses and performed phylogenetic analyses to characterize their relationship with other herpesviruses. A gray mouse lemur herpesvirus clustered with other primate herpesviruses within the subfamily Betaherpesvirinae, just basal to the genus Cytomegalovirus. The other gray mouse lemur herpesvirus and the pygmy slow loris herpesvirus clustered within the subfamily Gammaherpesvirinae, although the relationships within the subfamily were less resolved. Quantitative PCR assays were developed for the 2 new gray mouse lemur viruses, providing specific, faster, less expensive, and quantitative detection tools. Further studies are needed to elucidate the relationship between the presence of these viruses and the severity or presence of lymphoproliferative lesions in prosimians.
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Affiliation(s)
- Patricia E. Kunze
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Galaxia Cortés-Hinojosa
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Linda L. Archer
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Jason A. Ferrante
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - James F. X. Wellehan
- Department of Comparative Diagnostic and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
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7
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Foley NM, Mason VC, Harris AJ, Bredemeyer KR, Damas J, Lewin HA, Eizirik E, Gatesy J, Karlsson EK, Lindblad-Toh K, Springer MS, Murphy WJ, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. A genomic timescale for placental mammal evolution. Science 2023; 380:eabl8189. [PMID: 37104581 DOI: 10.1126/science.abl8189] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The precise pattern and timing of speciation events that gave rise to all living placental mammals remain controversial. We provide a comprehensive phylogenetic analysis of genetic variation across an alignment of 241 placental mammal genome assemblies, addressing prior concerns regarding limited genomic sampling across species. We compared neutral genome-wide phylogenomic signals using concatenation and coalescent-based approaches, interrogated phylogenetic variation across chromosomes, and analyzed extensive catalogs of structural variants. Interordinal relationships exhibit relatively low rates of phylogenomic conflict across diverse datasets and analytical methods. Conversely, X-chromosome versus autosome conflicts characterize multiple independent clades that radiated during the Cenozoic. Genomic time trees reveal an accumulation of cladogenic events before and immediately after the Cretaceous-Paleogene (K-Pg) boundary, implying important roles for Cretaceous continental vicariance and the K-Pg extinction in the placental radiation.
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Affiliation(s)
- Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Victor C Mason
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Joana Damas
- The Genome Center, University of California, Davis, CA, USA
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA, USA
- Department of Evolution and Ecology, University of California, Davis, CA, USA
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Elinor K Karlsson
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Program in Molecular Medicine, University of Massachussetts Chan Medical School, Worcester, MA 01605, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 32 Uppsala, Sweden
| | - Mark S Springer
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
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Astudillo-Clavijo V, Stiassny MLJ, Ilves KL, Musilova Z, Salzburger W, López-Fernández H. Exon-based phylogenomics and the relationships of African cichlid fishes: tackling the challenges of reconstructing phylogenies with repeated rapid radiations. Syst Biol 2022; 72:134-149. [PMID: 35880863 DOI: 10.1093/sysbio/syac051] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system.
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Affiliation(s)
- Viviana Astudillo-Clavijo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, 10024-5102, USA
| | - Katriina L Ilves
- Research & Collections, Zoology, Canadian Museum of Nature, Ottawa, K1P 6P4, Canada
| | - Zuzana Musilova
- Department of Zoology, Charles University in Prague, Vinicna 7, Prague, CZ-128 44, Czech Republic
| | - Walter Salzburger
- Zoological Institute, University of Basel, Vesalgasse 1, CH-4051, Basel, Switzerland
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, 48109, USA
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Guo W, Liang X, Wu Y, Yu W. The complete mitochondrial genome of Tylonycteris fulvida (Chiroptera: Vespertilionidae) in South China. Mitochondrial DNA B Resour 2021; 6:3274-3275. [PMID: 34712809 PMCID: PMC8547857 DOI: 10.1080/23802359.2021.1993103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The complete mitochondrial genome of Tylonycteris fulvida (Peters, 1872) was obtained using high-throughput sequencing technology. The genome is a circular molecule of 16,621 bp length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region. A phylogenetic tree of 13 protein-coding genes was constructed using IQ-TREE. Our result suggests that T. fulvida cluster within Chiroptera and Fereuungulata. The complete mitochondrial genome sequence of T. fulvida will be helpful for future taxonomic and phylogenetic studies on Chiroptera.
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Affiliation(s)
- Weijian Guo
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoling Liang
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Yi Wu
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Wenhua Yu
- Key Laboratory of Conservation and Application in Biodiversity of South China, School of Life Sciences, Guangzhou University, Guangzhou, China
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Janssenswillen S, Roelants K, Carpentier S, de Rooster H, Metzemaekers M, Vanschoenwinkel B, Proost P, Bossuyt F. Odorant-binding proteins in canine anal sac glands indicate an evolutionarily conserved role in mammalian chemical communication. BMC Ecol Evol 2021; 21:182. [PMID: 34565329 PMCID: PMC8474896 DOI: 10.1186/s12862-021-01910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 09/10/2021] [Indexed: 11/29/2022] Open
Abstract
Background Chemical communication is an important aspect of the behavioural ecology of a wide range of mammals. In dogs and other carnivores, anal sac glands are thought to convey information to conspecifics by secreting a pallet of small volatile molecules produced by symbiotic bacteria. Because these glands are unique to carnivores, it is unclear how their secretions relate to those of other placental mammals that make use of different tissues and secretions for chemical communication. Here we analyse the anal sac glands of domestic dogs to verify the secretion of proteins and infer their evolutionary relationship to those involved in the chemical communication of non-carnivoran mammals. Results Proteomic analysis of anal sac gland secretions of 17 dogs revealed the consistently abundant presence of three related proteins. Homology searches against online databases indicate that these proteins are evolutionary related to ‘odorant binding proteins’ (OBPs) found in a wide range of mammalian secretions and known to contribute to chemical communication. Screening of the dog’s genome sequence show that the newly discovered OBPs are encoded by a single cluster of three genes in the pseudoautosomal region of the X-chromosome. Comparative genomic screening indicates that the same locus is shared by a wide range of placental mammals and that it originated at least before the radiation of extant placental orders. Phylogenetic analyses suggest a dynamic evolution of gene duplication and loss, resulting in large gene clusters in some placental taxa and recurrent loss of this locus in others. The homology of OBPs in canid anal sac glands and those found in other mammalian secretions implies that these proteins maintained a function in chemical communication throughout mammalian evolutionary history by multiple shifts in expression between secretory tissues involved in signal release and nasal mucosa involved in signal reception. Conclusions Our study elucidates a poorly understood part of the biology of a species that lives in close association with humans. In addition, it shows that the protein repertoire underlying chemical communication in mammals is more evolutionarily stable than the variation of involved glands and tissues would suggest. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01910-w.
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Affiliation(s)
- Sunita Janssenswillen
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Kim Roelants
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Sebastien Carpentier
- Proteomics Core - SyBioMa, Katholieke Universiteit Leuven, Herestraat 49 - 03.313, 3000, Leuven, Belgium
| | - Hilde de Rooster
- Small Animal Department, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Mieke Metzemaekers
- Rega Institute, Molecular Immunology, Katholieke Universiteit Leuven, Herestraat 49 - Bus1042, 3000, Leuven, Belgium
| | - Bram Vanschoenwinkel
- Community Ecology Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Center for Environmental Management, University of the Free State, Bloemfontein, 9030, South Africa
| | - Paul Proost
- Rega Institute, Molecular Immunology, Katholieke Universiteit Leuven, Herestraat 49 - Bus1042, 3000, Leuven, Belgium
| | - Franky Bossuyt
- Amphibian Evolution Lab, Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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11
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De novo Assembly, Annotation, and Analysis of Transcriptome Data of the Ladakh Ground Skink Provide Genetic Information on High-Altitude Adaptation. Genes (Basel) 2021; 12:genes12091423. [PMID: 34573405 PMCID: PMC8466045 DOI: 10.3390/genes12091423] [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: 08/10/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
The Himalayan Arc is recognized as a global biodiversity hotspot. Among its numerous cryptic and undiscovered organisms, this composite high-mountain ecosystem harbors many taxa with adaptations to life in high elevations. However, evolutionary patterns and genomic features have been relatively rarely studied in Himalayan vertebrates. Here, we provide the first well-annotated transcriptome of a Greater Himalayan reptile species, the Ladakh Ground skink Asymblepharus ladacensis (Squamata: Scincidae). Based on tissues from the brain, an embryonic disc, and pooled organ material, using pair-end Illumina NextSeq 500 RNAseq, we assembled ~77,000 transcripts, which were annotated using seven functional databases. We tested ~1600 genes, known to be under positive selection in anurans and reptiles adapted to high elevations, and potentially detected positive selection for 114 of these genes in Asymblepharus. Even though the strength of these results is limited due to the single-animal approach, our transcriptome resource may be valuable data for further studies on squamate reptile evolution in the Himalayas as a hotspot of biodiversity.
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12
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Prothero DR, Domning D, Fordyce RE, Foss S, Janis C, Lucas S, Marriott KL, Metais G, Naish D, Padian K, Rössner G, Solounias N, Spaulding M, Stucky RM, Theodor J, Uhen M. On the Unnecessary and Misleading Taxon “Cetartiodactyla”. J MAMM EVOL 2021. [DOI: 10.1007/s10914-021-09572-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Valente R, Alves F, Sousa-Pinto I, Ruivo R, Castro LFC. Functional or Vestigial? The Genomics of the Pineal Gland in Xenarthra. J Mol Evol 2021; 89:565-575. [PMID: 34342686 DOI: 10.1007/s00239-021-10025-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022]
Abstract
Vestigial organs are historical echoes of past phenotypes. Determining whether a specific organ constitutes a functional or vestigial structure can be a challenging task, given that distinct levels of atrophy may arise between and within lineages. The mammalian pineal gland, an endocrine organ involved in melatonin biorhythmicity, represents a classic example, often yielding contradicting anatomical observations. In Xenarthra (sloths, anteaters, and armadillos), a peculiar mammalian order, the presence of a distinct pineal organ was clearly observed in some species (i.e., Linnaeus's two-toed sloth), but undetected in other closely related species (i.e., brown-throated sloth). In the nine-banded armadillo, contradicting evidence supports either functional or vestigial scenarios. Thus, to untangle the physiological status of the pineal gland in Xenarthra, we used a genomic approach to investigate the evolution of the gene hub responsible for melatonin synthesis and signaling. We show that both synthesis and signaling compartments are eroded and were probably lost independently among Xenarthra orders. Additionally, by expanding our analysis to 157 mammal genomes, we offer a comprehensive view showing that species with very distinctive habitats and lifestyles have convergently evolved a similar phenotype: Cetacea, Pholidota, Dermoptera, Sirenia, and Xenarthra. Our findings suggest that the recurrent inactivation of melatonin genes correlates with pineal atrophy and endorses the use of genomic analyses to ascertain the physiological status of suspected vestigial structures.
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Affiliation(s)
- Raul Valente
- CIMAR/CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.,FCUP-Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre, Porto, Portugal
| | - Filipe Alves
- MARE-Marine and Environmental Sciences Centre, ARDITI, Madeira, Portugal.,OOM-Oceanic Observatory of Madeira, Funchal, Portugal
| | - Isabel Sousa-Pinto
- CIMAR/CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.,FCUP-Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre, Porto, Portugal
| | - Raquel Ruivo
- CIMAR/CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
| | - L Filipe C Castro
- CIMAR/CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal. .,FCUP-Department of Biology, Faculty of Sciences, University of Porto (U. Porto), Rua Do Campo Alegre, Porto, Portugal.
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14
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Barbosa S, Andrews KR, Goldberg AR, Gour DS, Hohenlohe PA, Conway CJ, Waits LP. The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern. Mol Ecol 2021; 30:4673-4694. [PMID: 34324748 DOI: 10.1111/mec.16096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 07/10/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus - NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both theinter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype-environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographic barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.
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Affiliation(s)
- Soraia Barbosa
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Kimberly R Andrews
- University of Idaho, Institute for Bioinformatics and Evolutionary Studies (IBEST), Moscow, ID, 83844-1136, USA
| | - Amanda R Goldberg
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Digpal S Gour
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Paul A Hohenlohe
- University of Idaho, Institute for Bioinformatics and Evolutionary Studies (IBEST), Moscow, ID, 83844-1136, USA.,Department of Biological Sciences, College of Science, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-3051, USA
| | - Courtney J Conway
- U.S. Geological Survey, Idaho Cooperative Fish & Wildlife Research Unit, Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID, 83844-1141, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
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15
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Carter AM. Unique Aspects of Human Placentation. Int J Mol Sci 2021; 22:8099. [PMID: 34360862 PMCID: PMC8347521 DOI: 10.3390/ijms22158099] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/22/2022] Open
Abstract
Human placentation differs from that of other mammals. A suite of characteristics is shared with haplorrhine primates, including early development of the embryonic membranes and placental hormones such as chorionic gonadotrophin and placental lactogen. A comparable architecture of the intervillous space is found only in Old World monkeys and apes. The routes of trophoblast invasion and the precise role of extravillous trophoblast in uterine artery transformation is similar in chimpanzee and gorilla. Extended parental care is shared with the great apes, and though human babies are rather helpless at birth, they are well developed (precocial) in other respects. Primates and rodents last shared a common ancestor in the Cretaceous period, and their placentation has evolved independently for some 80 million years. This is reflected in many aspects of their placentation. Some apparent resemblances such as interstitial implantation and placental lactogens are the result of convergent evolution. For rodent models such as the mouse, the differences are compounded by short gestations leading to the delivery of poorly developed (altricial) young.
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Affiliation(s)
- Anthony M Carter
- Cardiovascular and Renal Research, Institute of Molecular Medicine, University of Southern Denmark, DK-5230 Odense, Denmark
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16
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Hovlinc is a recently evolved class of ribozyme found in human lncRNA. Nat Chem Biol 2021; 17:601-607. [PMID: 33753927 DOI: 10.1038/s41589-021-00763-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 01/06/2021] [Accepted: 02/02/2021] [Indexed: 01/31/2023]
Abstract
Although naturally occurring catalytic RNA molecules-ribozymes-have attracted a great deal of research interest, very few have been identified in humans. Here, we developed a genome-wide approach to discovering self-cleaving ribozymes and identified a naturally occurring ribozyme in humans. The secondary structure and biochemical properties of this ribozyme indicate that it belongs to an unidentified class of small, self-cleaving ribozymes. The sequence of the ribozyme exhibits a clear evolutionary path, from its appearance between ~130 and ~65 million years ago (Ma), to acquiring self-cleavage activity very recently, ~13-10 Ma, in the common ancestors of humans, chimpanzees and gorillas. The ribozyme appears to be functional in vivo and is embedded within a long noncoding RNA belonging to a class of very long intergenic noncoding RNAs. The presence of a catalytic RNA enzyme in lncRNA creates the possibility that these transcripts could function by carrying catalytic RNA domains.
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17
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Lv X, Hu J, Hu Y, Li Y, Xu D, Ryder OA, Irwin DM, Yu L. Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships. Mol Phylogenet Evol 2020; 157:107065. [PMID: 33387649 DOI: 10.1016/j.ympev.2020.107065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022]
Abstract
Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.
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Affiliation(s)
- Xue Lv
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yiwen Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Yitian Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China; School of Life Sciences, Yunnan University, Kunming, China
| | - Dongming Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Oliver A Ryder
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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18
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Berlioz E, Cornette R, Lenoir N, Santin MD, Lehmann T. Exploring the ontogenetic development of the inner ear in Aardvarks. J Anat 2020; 238:1128-1142. [PMID: 33345316 PMCID: PMC8053585 DOI: 10.1111/joa.13361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 10/02/2020] [Accepted: 10/28/2020] [Indexed: 11/29/2022] Open
Abstract
The aardvark is the last living Tubulidentata, an order of afrotherian mammals. Afrotheria is supported strongly by molecular analyses, yet sparingly by morphological characters. Moreover, the biology of the aardvark remains incompletely known. The inner ear, and its ontogeny in particular, has not been studied in details yet, though it bears key ecomorphological characters and phylogenetical signal. The aim of this study is to decipher and discuss the ontogenetic development of the different areas of the inner ear of Orycteropus afer. We focused in particular on their relative size and morphological rates of development. Specimens were scanned with 3D imaging techniques. 3D and 2D geometric morphometrics coupled with qualitative descriptions of the petrosal ossification allowed us to evidence several stages through development. Based on our sample, the cochlea is the first structure of the inner ear to reach adult size, but it is the last one to acquire its adult morphology close to parturition. In contrast, after a delayed growth spurt, the semicircular canals reach their mature morphology before the cochlea, concomitantly with the increase of petrosal ossification. The ontogeny of the aardvark inner ear shows similarities with that of other species, but the apex of the cochlea presents some autapomorphies. This work constitutes a first step in the study of the ontogeny of this sensorial organ in Afrotheria.
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Affiliation(s)
- Emilie Berlioz
- PALEVOPRIM (Paléontologie, Evolution, Paléoécosystèmes, Paléoprimatologie) - UMR 7262, Geoscience Department, University SFA Poitiers, Poitiers, France.,TRACES (Travaux et Recherches Archéologiques sur les Cultures, les Espaces, et les Sociétés) - UMR 5608, Maison de la Recherche, University Toulouse Jean Jaurès, Toulouse, France
| | - Raphaël Cornette
- Institut de Systématique, Evolution, Biodiversité (ISYEB) - UMR 7205, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Nicolas Lenoir
- Université Grenoble Alpes, CNRS, Grenoble INP, Grenoble, France
| | - Mathieu D Santin
- Paris Brain Institute (Institut du Cerveau - ICM), Center for Neuroimaging Research - CENIR, Paris, France.,Hôpital Pitié-Salpêtrière, ICM, Sorbonne Université, Inserm U 1127, CNRS, UMR 7225, Paris, France
| | - Thomas Lehmann
- Messel Research and Mammalogy Department, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
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19
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Ciancio MR, Vieytes EC, Castro MC, Carlini AA. Dental enamel structure in long-nosed armadillos (Xenarthra: Dasypus) and its evolutionary implications. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Most xenarthrans have a reduced and simplified dentition that lacks enamel. However, the presence of prismatic enamel has been recorded in the Eocene armadillos Utaetus buccatus (Euphractinae) and Astegotherium dichotomus (Astegotheriini). Among extant xenarthrans, the occurrence of enamel has been recognized only in the long-nosed armadillo, Dasypus novemcinctus (Dasypodinae), but its microstructure has never been described. In this contribution, we analyse the enamel microstructure in deciduous and permanent teeth of four Dasypus species. In deciduous molariform teeth of some species, we identify an apical cap of vestigial enamel (without crystalline structure), interpreted as an amorphous ameloblastic secretion. In permanent teeth, a thin layer of true enamel is found in the apical portion of unworn molariforms. The enamel is prismatic in D. novemcinctus, but in Dasypus hybridus, Dasypus sabanicola and Dasypus punctatus it is prismless. Taking into account the Eocene species of armadillos, the ancestral condition of enamel in cingulates could have been more complex (as in other placentals) and undergone progressive reduction, as shown in the Dasypus lineage. In light of previous genetic and developmental studies, we review and briefly discuss the processes that can account for the reduction/loss of enamel in extant and extinct armadillos. The retention of enamel and the fact that this genus is the only living xenarthran with two functional generations of teeth support the early divergence of the Dasypus lineage among living cingulates. This is in agreement with morphological and molecular analyses.
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Affiliation(s)
- Martín R Ciancio
- Laboratorio de Morfología Evolutiva y Desarrollo (MORPHOS) y División Paleontología Vertebrados, Museo de La Plata, CONICET, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
- Cátedra Anatomía Comparada, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
| | - Emma C Vieytes
- Cátedra Anatomía Comparada, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
- División Zoología Vertebrados, Museo de La Plata, CONICET, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
| | - Mariela C Castro
- Departamento de Ciências Biológicas, IBiotec, Universidade Federal de Catalão, Avenida Dr. Lamartine Pinto de Avelar, 1120, 75704-020, Catalão, Brazil
| | - Alfredo A Carlini
- Laboratorio de Morfología Evolutiva y Desarrollo (MORPHOS) y División Paleontología Vertebrados, Museo de La Plata, CONICET, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
- Cátedra Anatomía Comparada, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque s/n, B1900FWA, La Plata, Argentina
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20
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Murphy WJ, Foley NM, Bredemeyer KR, Gatesy J, Springer MS. Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation. Annu Rev Anim Biosci 2020; 9:29-53. [PMID: 33228377 DOI: 10.1146/annurev-animal-061220-023149] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.
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Affiliation(s)
- William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA;
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Mark S Springer
- Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California 92521, USA
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21
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Islam MZ, Sawatari Y, Kojima S, Kiyama Y, Nakamura M, Sasaki K, Otsuka M, Obi T, Shiraishi M, Miyamoto A. Vasomotor effects of 5-hydroxytryptamine, histamine, angiotensin II, acetylcholine, noradrenaline, and bradykinin on the cerebral artery of bottlenose dolphin (Tursiops truncatus). J Vet Med Sci 2020; 82:1456-1463. [PMID: 32814751 PMCID: PMC7653325 DOI: 10.1292/jvms.20-0351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
From an evolutionary aspect, dolphins share a very close phylogenetic relationship with
pigs. Previously, we characterized porcine cerebral artery responsiveness to intrinsic
vasoactive substances. Therefore, here, we investigated dolphin (Tursiops
truncatus) cerebral artery responsiveness to 5-hydroxytryptamine (5-HT),
histamine (His), angiotensin (Ang) II, acetylcholine (ACh), noradrenaline (NA), and
bradykinin (BK) to characterize their related receptor subtypes. We also compared dolphin
cerebral artery responsiveness with porcine cerebral artery responsiveness. We found that
5-HT and His induced concentration-dependent contraction of the dolphin cerebral artery.
Ketanserin (a 5-HT2 antagonist) and methiothepin (a 5-HT1 and
5-HT2 antagonist) shifted the concentration-response curve for 5-HT to the
right. Although diphenhydramine (an H1 antagonist) shifted the
concentration-response curve for His to the right, cimetidine (an H2
antagonist) had no such effect. Ang II and ACh did not produce any vasomotor actions. NA
induced concentration-dependent relaxation. Propranolol (a β antagonist) shifted the
concentration-response curve for NA to the right, whereas phentolamine (an α antagonist)
had no significant effect. BK induced relaxation followed by contraction in pre-contracted
arteries with intact endothelium. HOE140 (a B2 antagonist) shifted the
concentration-response curve for BK to the right, whereas
des-Arg9-[Leu8]-BK (a B1 antagonist) had no significant
effect. These results suggest that 5-HT1, 5-HT2, and H1
receptor subtypes are important in arterial contraction and that β and B2
receptor subtypes modify these contractions to relaxations. The responsiveness of the
dolphin cerebral artery is very similar to that of porcine cerebral artery, supporting
their evolutionary linkage.
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Affiliation(s)
- Md Zahorul Islam
- Department of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan.,Department of Pharmacology, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Yuji Sawatari
- Department of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Shusuke Kojima
- Department of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yusuke Kiyama
- Department of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Moe Nakamura
- Department of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kyouko Sasaki
- Kagoshima Prefecture Meet Hygiene Inspection Center, 10-1 Kamoike-Shinmachi, Kagoshima 890-8577, Japan
| | - Mika Otsuka
- Kagoshima City Aquarium, 3-1 Honkou-Shinmachi, Kagoshima 892-0814, Japan
| | - Takeshi Obi
- Department of Veterinary Microbiology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Mitsuya Shiraishi
- Department of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Atsushi Miyamoto
- Department of Veterinary Pharmacology, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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22
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Santagostino M, Piras FM, Cappelletti E, Del Giudice S, Semino O, Nergadze SG, Giulotto E. Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective. Int J Mol Sci 2020; 21:E2838. [PMID: 32325780 PMCID: PMC7215372 DOI: 10.3390/ijms21082838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Interstitial telomeric sequences (ITSs) are short stretches of telomeric-like repeats (TTAGGG)n at nonterminal chromosomal sites. We previously demonstrated that, in the genomes of primates and rodents, ITSs were inserted during the repair of DNA double-strand breaks. These conclusions were derived from sequence comparisons of ITS-containing loci and ITS-less orthologous loci in different species. To our knowledge, insertion polymorphism of ITSs, i.e., the presence of an ITS-containing allele and an ITS-less allele in the same species, has not been described. In this work, we carried out a genome-wide analysis of 2504 human genomic sequences retrieved from the 1000 Genomes Project and a PCR-based analysis of 209 human DNA samples. In spite of the large number of individual genomes analyzed we did not find any evidence of insertion polymorphism in the human population. On the contrary, the analysis of ITS loci in the genome of a single horse individual, the reference genome, allowed us to identify five heterozygous ITS loci, suggesting that insertion polymorphism of ITSs is an important source of genetic variability in this species. Finally, following a comparative sequence analysis of horse ITSs and of their orthologous empty loci in other Perissodactyla, we propose models for the mechanism of ITS insertion during the evolution of this order.
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Affiliation(s)
| | | | | | | | | | | | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy; (M.S.); (F.M.P.); (E.C.); (S.D.G.); (O.S.); (S.G.N.)
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23
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Partha R, Kowalczyk A, Clark NL, Chikina M. Robust Method for Detecting Convergent Shifts in Evolutionary Rates. Mol Biol Evol 2020; 36:1817-1830. [PMID: 31077321 DOI: 10.1093/molbev/msz107] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Identifying genomic elements underlying phenotypic adaptations is an important problem in evolutionary biology. Comparative analyses learning from convergent evolution of traits are gaining momentum in accurately detecting such elements. We previously developed a method for predicting phenotypic associations of genetic elements by contrasting patterns of sequence evolution in species showing a phenotype with those that do not. Using this method, we successfully demonstrated convergent evolutionary rate shifts in genetic elements associated with two phenotypic adaptations, namely the independent subterranean and marine transitions of terrestrial mammalian lineages. Our original method calculates gene-specific rates of evolution on branches of phylogenetic trees using linear regression. These rates represent the extent of sequence divergence on a branch after removing the expected divergence on the branch due to background factors. The rates calculated using this regression analysis exhibit an important statistical limitation, namely heteroscedasticity. We observe that the rates on branches that are longer on average show higher variance, and describe how this problem adversely affects the confidence with which we can make inferences about rate shifts. Using a combination of data transformation and weighted regression, we have developed an updated method that corrects this heteroscedasticity in the rates. We additionally illustrate the improved performance offered by the updated method at robust detection of convergent rate shifts in phylogenetic trees of protein-coding genes across mammals, as well as using simulated tree data sets. Overall, we present an important extension to our evolutionary-rates-based method that performs more robustly and consistently at detecting convergent shifts in evolutionary rates.
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Affiliation(s)
- Raghavendran Partha
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.,Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA
| | - Amanda Kowalczyk
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.,Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA
| | - Nathan L Clark
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.,Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA.,Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA
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24
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Takakura N, Takemi S, Kumaki S, Matsumoto M, Sakai T, Iwatsuki K, Sakata I. Generation and characterization of Suncus murinus intestinal organoid: a useful tool for studying motilin secretion. Cell Biol Int 2020; 44:62-69. [PMID: 31293061 DOI: 10.1002/cbin.11201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/08/2019] [Indexed: 01/24/2023]
Abstract
Motilin, a 22-amino-acid peptide produced in the upper small intestine, induces strong gastric contraction in fasted state. In many rodents, motilin and its cognate receptors exist as pseudogenes, which has delayed motilin research in the past decades. Recently, the house musk shrew (Suncus murinus) was developed as a useful model for studying motilin and gastrointestinal motility. However, due to a lack of motilin-producing cell lines and difficulties in culturing small intestinal cells, the regulatory mechanisms of motilin secretion and its messenger RNA (mRNA) transcription have remained largely unclear. In this study, we generated small intestinal organoids from S. murinus for the first time. Using methods similar to mouse organoid generation, we found crypt-like budding structures 3 days after isolating intestinal tissues. The organoids grew gradually with time. In addition, the generated organoids were able to be passaged and maintained for 6 months or longer. Motilin messenger RNA (mRNA) and immunopositive cells were observed in both S. murinus intestinal organoids and primary tissues. This is the first report of intestinal organoids in S. murinus, and our results suggest that S. murinus intestinal organoids could be useful for analyzing motilin secretion and transcription.
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Affiliation(s)
- Natsumi Takakura
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Shota Takemi
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Shunsuke Kumaki
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Mio Matsumoto
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Takafumi Sakai
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan.,Area of Life-NanoBio, Division of Strategy, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Ken Iwatsuki
- Department of Nutritional Science and Food Safety, Faculty of Applied Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Ichiro Sakata
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
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25
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Casewell NR, Petras D, Card DC, Suranse V, Mychajliw AM, Richards D, Koludarov I, Albulescu LO, Slagboom J, Hempel BF, Ngum NM, Kennerley RJ, Brocca JL, Whiteley G, Harrison RA, Bolton FMS, Debono J, Vonk FJ, Alföldi J, Johnson J, Karlsson EK, Lindblad-Toh K, Mellor IR, Süssmuth RD, Fry BG, Kuruppu S, Hodgson WC, Kool J, Castoe TA, Barnes I, Sunagar K, Undheim EAB, Turvey ST. Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals. Proc Natl Acad Sci U S A 2019; 116:25745-25755. [PMID: 31772017 PMCID: PMC6926037 DOI: 10.1073/pnas.1906117116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Venom systems are key adaptations that have evolved throughout the tree of life and typically facilitate predation or defense. Despite venoms being model systems for studying a variety of evolutionary and physiological processes, many taxonomic groups remain understudied, including venomous mammals. Within the order Eulipotyphla, multiple shrew species and solenodons have oral venom systems. Despite morphological variation of their delivery systems, it remains unclear whether venom represents the ancestral state in this group or is the result of multiple independent origins. We investigated the origin and evolution of venom in eulipotyphlans by characterizing the venom system of the endangered Hispaniolan solenodon (Solenodon paradoxus). We constructed a genome to underpin proteomic identifications of solenodon venom toxins, before undertaking evolutionary analyses of those constituents, and functional assessments of the secreted venom. Our findings show that solenodon venom consists of multiple paralogous kallikrein 1 (KLK1) serine proteases, which cause hypotensive effects in vivo, and seem likely to have evolved to facilitate vertebrate prey capture. Comparative analyses provide convincing evidence that the oral venom systems of solenodons and shrews have evolved convergently, with the 4 independent origins of venom in eulipotyphlans outnumbering all other venom origins in mammals. We find that KLK1s have been independently coopted into the venom of shrews and solenodons following their divergence during the late Cretaceous, suggesting that evolutionary constraints may be acting on these genes. Consequently, our findings represent a striking example of convergent molecular evolution and demonstrate that distinct structural backgrounds can yield equivalent functions.
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Affiliation(s)
- Nicholas R Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom;
| | - Daniel Petras
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX 76010
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Vivek Suranse
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, 560012 Bangalore, India
| | - Alexis M Mychajliw
- Department of Biology, Stanford University, Stanford, CA 94305
- Department of Rancho La Brea, Natural History Museum of Los Angeles County, Los Angeles, CA 90036
- Institute of Low Temperature Science, Hokkaido University, 060-0819 Sapporo, Japan
| | - David Richards
- School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, United Kingdom
- Biomedical Research Centre, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
| | - Ivan Koludarov
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology, Onna, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Laura-Oana Albulescu
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Julien Slagboom
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
| | | | - Neville M Ngum
- School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, United Kingdom
| | - Rosalind J Kennerley
- Durrell Wildlife Conservation Trust, Les Augrès Manor, Trinity, Jersey JE3 5BP, British Channel Islands, United Kingdom
| | - Jorge L Brocca
- SOH Conservación, Apto. 401 Residencial Las Galerías, Santo Domingo, 10130, Dominican Republic
| | - Gareth Whiteley
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Robert A Harrison
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Fiona M S Bolton
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom
| | - Jordan Debono
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia, QLD 4067, Australia
| | - Freek J Vonk
- Naturalis Biodiversity Center, 2333 CR Leiden, The Netherlands
| | - Jessica Alföldi
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Jeremy Johnson
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Elinor K Karlsson
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Kerstin Lindblad-Toh
- Vertebrate Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | - Ian R Mellor
- School of Life Sciences, University of Nottingham, University Park, NG7 2RD Nottingham, United Kingdom
| | | | - Bryan G Fry
- Venom Evolution Lab, School of Biological Sciences, University of Queensland, St. Lucia, QLD 4067, Australia
| | - Sanjaya Kuruppu
- Monash Venom Group, Department of Pharmacology, Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
- Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
| | - Wayne C Hodgson
- Monash Venom Group, Department of Pharmacology, Biomedicine Discovery Institute, Monash University, VIC 3800, Australia
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX 76010
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, SW7 5BD London, United Kingdom
| | - Kartik Sunagar
- Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, 560012 Bangalore, India
| | - Eivind A B Undheim
- Centre for Advanced Imaging, The University of Queensland, Brisbane QLD 4072, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072, Australia
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY London, United Kingdom
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26
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Springer MS, Foley NM, Brady PL, Gatesy J, Murphy WJ. Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary. Front Genet 2019; 10:1241. [PMID: 31850081 PMCID: PMC6896846 DOI: 10.3389/fgene.2019.01241] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/08/2019] [Indexed: 01/29/2023] Open
Abstract
Deciphering the timing of the placental mammal radiation is a longstanding problem in evolutionary biology, but consensus on the tempo and mode of placental diversification remains elusive. Nevertheless, an accurate timetree is essential for understanding the role of important events in Earth history (e.g., Cretaceous Terrestrial Revolution, KPg mass extinction) in promoting the taxonomic and ecomorphological diversification of Placentalia. Archibald and Deutschman described three competing models for the diversification of placental mammals, which are the Explosive, Long Fuse, and Short Fuse Models. More recently, the Soft Explosive Model and Trans-KPg Model have emerged as additional hypotheses for the placental radiation. Here, we review molecular and paleontological evidence for each of these five models including the identification of general problems that can negatively impact divergence time estimates. The Long Fuse Model has received more support from relaxed clock studies than any of the other models, but this model is not supported by morphological cladistic studies that position Cretaceous eutherians outside of crown Placentalia. At the same time, morphological cladistics has a poor track record of reconstructing higher-level relationships among the orders of placental mammals including the results of new pseudoextinction analyses that we performed on the largest available morphological data set for mammals (4,541 characters). We also examine the strengths and weaknesses of different timetree methods (node dating, tip dating, and fossilized birth-death dating) that may now be applied to estimate the timing of the placental radiation. While new methods such as tip dating are promising, they also have problems that must be addressed if these methods are to effectively discriminate among competing hypotheses for placental diversification. Finally, we discuss the complexities of timetree estimation when the signal of speciation times is impacted by incomplete lineage sorting (ILS) and hybridization. Not accounting for ILS results in dates that are older than speciation events. Hybridization, in turn, can result in dates than are younger or older than speciation dates. Disregarding this potential variation in "gene" history across the genome can distort phylogenetic branch lengths and divergence estimates when multiple unlinked genomic loci are combined together in a timetree analysis.
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Affiliation(s)
- Mark S. Springer
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - Nicole M. Foley
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Peggy L. Brady
- Department of Evolution, Ecology, and Evolutionary Biology, University of California, Riverside, Riverside, CA, United States
| | - John Gatesy
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, United States
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
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27
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Zhang ML, Li ML, Ayoola AO, Murphy RW, Wu DD, Shao Y. Conserved sequences identify the closest living relatives of primates. Zool Res 2019; 40:532-540. [PMID: 31393097 PMCID: PMC6822925 DOI: 10.24272/j.issn.2095-8137.2019.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.
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Affiliation(s)
- Mei-Ling Zhang
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming Yunnan 650022, China
| | - Ming-Li Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Adeola Oluwakemi Ayoola
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto M5S 2C6, Canada
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China, E-mail:
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28
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Takemi S, Nishio R, Taguchi H, Ojima S, Matsumoto M, Sakai T, Sakata I. Molecular cloning and analysis of Suncus murinus group IIA secretary phospholipase A2 expression. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 100:103427. [PMID: 31278953 DOI: 10.1016/j.dci.2019.103427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/30/2019] [Accepted: 06/30/2019] [Indexed: 06/09/2023]
Abstract
The intestinal epithelial monolayer forms a mucosal barrier between the gut microbes and the host tissue. The mucosal barrier is composed of mucins and antimicrobial peptides and proteins (AMPs). Several animal studies have reported that Paneth cells, which occupy the base of intestinal crypts, play an important role in the intestinal innate immunity by producing AMPs, such as lysozyme, Reg3 lectins, α-defensins, and group IIA secretory phospholipase A2 (GIIA sPLA2). The house musk shrew (Suncus murinus) has only a few intestinal commensal bacteria and is reported to lack Paneth cells in the intestine. Although the expression of lysozyme was reported in the suncus intestine, the expression of other AMPs has not yet been reported. Therefore, the current study was focused on GIIA sPLA2 expression in Suncus murinus. GIIA sPLA2 mRNA was found to be most abundant in the spleen and also highly expressed in the intestine. Cells expressing GIIA sPLA2 mRNA were distributed not only in the crypt, but also in the villi. In addition, intragastric injection of lipopolysaccharide increased GIIA sPLA2 expression in the small intestine of suncus. These results suggest that suncus may host unique AMP-secreting cells in the intestine.
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Affiliation(s)
- Shota Takemi
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Ryo Nishio
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Hayato Taguchi
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Shiomi Ojima
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Mio Matsumoto
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Takafumi Sakai
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan; Area of Life-NanoBio, Division of Strategy Research, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Ichiro Sakata
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan.
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29
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Dattilo M, Read AT, Samuels BC, Ethier CR. Detection and characterization of tree shrew retinal venous pulsations: An animal model to study human retinal venous pulsations. Exp Eye Res 2019; 185:107689. [PMID: 31175860 PMCID: PMC6698406 DOI: 10.1016/j.exer.2019.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 05/15/2019] [Accepted: 06/04/2019] [Indexed: 11/26/2022]
Abstract
Spontaneous retinal venous pulsations (SRVPs), pulsations of branches of the central retinal vein, are affected by intraocular pressure (IOP) and intracranial pressure (ICP) and thus convey potentially-useful information about ICP. However, the exact relationship between SRVPs, IOP, and ICP is unknown. It is not easily feasible to study this relationship in humans, necessitating the use of an animal model. We here propose tree shrews as a suitable animal model to study the complex relationship between SRVPs, IOP, and ICP. Tree shrew SRVP incidence was determined in a population of animals. Following validation of a modified IOP control system to accurately and quickly control IOP, IOP and/or ICP were manipulated in two tree shrews with SRVPs and the effects on SRVP properties were quantified. SRVPs were present in 75% of tree shrews at physiologic IOP and ICP. Altering IOP or ICP produced changes in tree shrew SRVP properties; specifically, increasing IOP caused SRVP amplitude to increase, while increasing ICP caused SRVP amplitude to decrease. In addition, a higher IOP was necessary to generate SRVPs at a higher ICP than at a lower ICP. SRVPs occur with a similar incidence in tree shrews as in humans, and tree shrew SRVPs are affected by changes in IOP and ICP in a manner qualitatively similar to that reported in humans. In view of anatomic similarities, tree shrews are a promising animal model system to further study the complex relationship between SRVPs, IOP, and ICP.
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Affiliation(s)
- Michael Dattilo
- Department of Ophthalmology, Emory University School of Medicine, 1365-B Clifton Road, Atlanta, 30322, GA, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, 30332, GA, USA.
| | - A Thomas Read
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, 30332, GA, USA.
| | - Brian C Samuels
- Department of Ophthalmology, University of Alabama at Birmingham School of Medicine, 1670 University Boulevard, Birmingham, 35294, AL, USA.
| | - C Ross Ethier
- Department of Ophthalmology, Emory University School of Medicine, 1365-B Clifton Road, Atlanta, 30322, GA, USA; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive NW, Atlanta, 30332, GA, USA.
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30
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Rando HM, Wadlington WH, Johnson JL, Stutchman JT, Trut LN, Farré M, Kukekova AV. The Red Fox Y-Chromosome in Comparative Context. Genes (Basel) 2019; 10:E409. [PMID: 31142040 PMCID: PMC6627929 DOI: 10.3390/genes10060409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Feliscatus), dog (Canislupusfamiliaris), and grey wolf (Canislupuslupus), providing the opportunity to examine the red fox (Vulpesvulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.
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Affiliation(s)
- Halie M Rando
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - William H Wadlington
- Tropical Research and Education Center, Agronomy Department, University of Florida, Homestead, FL 33031, USA.
| | - Jennifer L Johnson
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Jeremy T Stutchman
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Lyudmila N Trut
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Marta Farré
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Anna V Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Heck CT, Varricchio DJ, Gaudin TJ, Woodward HN, Horner JR. Ontogenetic changes in the long bone microstructure in the nine-banded armadillo (Dasypus novemcinctus). PLoS One 2019; 14:e0215655. [PMID: 31022247 PMCID: PMC6483220 DOI: 10.1371/journal.pone.0215655] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/07/2019] [Indexed: 12/22/2022] Open
Abstract
Analysis of ontogenetic changes in long bone microstructure aid in vertebrate life history reconstructions. Specifically, osteohistological examination of common fauna can be used to infer growth strategies of biologically uncommon, threatened, or extinct vertebrates. Although nine-banded armadillo biology has been studied extensively, work on growth history is limited. Here we describe long bone microstructure in tibiae and femora of a limited ontogenetic series of nine- banded armadillos (Dasypus novemcinctus) to elucidate patterns of bone growth. The cortex of the smallest individual is composed of compacted coarse cancellous bone (CCCB) and woven tissue. Extensive cortical drift is driven by periosteal erosion and further compaction of trabeculae resulting in an increase in the amount of CCCB. The cortex of the largest specimens is primarily CCCB with thickened endosteal bone and thin outer cortices of lamellar and parallel-fibered tissue. The outer cortices of the largest individuals are interpreted as an external fundamental system (EFS) indicating a cessation of appositional bone growth corresponding to skeletal maturity (i.e. asymptotic or adult size). The EFS forms in femora prior to tibiae, indicating femoral growth rates begin decreasing earlier than tibial in D. novemcinctus. Growth trends in common fauna like the nine-banded armadillo can be used as a foundation for understanding life histories of related, but uncommon or extinct, species of cingulates.
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Affiliation(s)
- Christian Thomas Heck
- Department of Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, United States of America
| | - David J Varricchio
- Department of Earth Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Timothy J Gaudin
- Department of Biology, Geology, and Environmental Science, University of Tennessee at Chattanooga, Chattanooga, Tennessee, United States of America
| | - Holly N Woodward
- Department of Anatomy and Cell Biology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, United States of America
| | - John R Horner
- Chapman University, Orange, California, United States of America
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Kleinnijenhuis AJ. Visualization of Genetic Drift Processes Using the Conserved Collagen 1α1 GXY Domain. J Mol Evol 2019; 87:106-130. [PMID: 30863881 DOI: 10.1007/s00239-019-09890-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/06/2019] [Indexed: 11/30/2022]
Abstract
Speciation proceeds by the accumulation of DNA differences in time. The genetic code changes as a result of genetic drift and by selective pressure. In variable domains, exposure to high selective pressure obscures the view on background mutations. Therefore, we characterized and visualized background mutations using the highly conserved collagen 1α1 GXY domain. Typical change routes were identified and the data set showed several indications that changes in the collagen 1α1 GXY domain have taken place randomly within a functionally restricted space. The types of nucleotide and codon group differences are similar across the vertebrate subphylum and gradually become less functionally neutral with increasing distance between species, which offers the opportunity for rapid visualization of evolutionary relations using a single domain. It was concluded that the findings and approach of the study could be important for analytical method development in authenticity research, especially when conserved domains are targeted.
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Bravo GA, Antonelli A, Bacon CD, Bartoszek K, Blom MPK, Huynh S, Jones G, Knowles LL, Lamichhaney S, Marcussen T, Morlon H, Nakhleh LK, Oxelman B, Pfeil B, Schliep A, Wahlberg N, Werneck FP, Wiedenhoeft J, Willows-Munro S, Edwards SV. Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics. PeerJ 2019; 7:e6399. [PMID: 30783571 PMCID: PMC6378093 DOI: 10.7717/peerj.6399] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 01/07/2019] [Indexed: 12/23/2022] Open
Abstract
Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Alexandre Antonelli
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Botanical Garden, Göteborg, Sweden
| | - Christine D. Bacon
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Krzysztof Bartoszek
- Department of Computer and Information Science, Linköping University, Linköping, Sweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stella Huynh
- Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Graham Jones
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Thomas Marcussen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Hélène Morlon
- Institut de Biologie, Ecole Normale Supérieure de Paris, Paris, France
| | - Luay K. Nakhleh
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Bengt Oxelman
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Bernard Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Alexander Schliep
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | | | - Fernanda P. Werneck
- Coordenação de Biodiversidade, Programa de Coleções Científicas Biológicas, Instituto Nacional de Pesquisa da Amazônia, Manaus, AM, Brazil
| | - John Wiedenhoeft
- Department of Computer Science and Engineering, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
- Department of Computer Science, Rutgers University, Piscataway, NJ, USA
| | - Sandi Willows-Munro
- School of Life Sciences, University of Kwazulu-Natal, Pietermaritzburg, South Africa
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
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Takemi S, Ojima S, Tanaka T, Sakai T, Sakata I. Identification and characterization of an antimicrobial peptide, lysozyme, from Suncus murinus. Cell Tissue Res 2019; 376:401-412. [PMID: 30680460 DOI: 10.1007/s00441-019-02991-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/06/2019] [Indexed: 01/29/2023]
Abstract
Lysozyme is one of the most prominent antimicrobial peptides and has been identified from many mammalian species. However, this enzyme has not been studied in the order Insectivora, which includes the most primitive placental mammals. Here, we done the lysozyme cDNA from Suncus murinus (referred to as suncus, its laboratory name) and compare the predicted amino acid sequence to those from other mammalian species. Quantitative PCR analysis revealed a relatively higher expression of this gene in the spleen and gastrointestinal tract of suncus. The lysozyme-immunopositive (ip) cells were found mainly in the red pulp of the spleen and in the mucosa of the whole small intestine, including the follicle-associated epithelium and subepithelial dome of Peyer's patches. The lysozyme-ip cells in the small intestine were mostly distributed in the intestinal crypt, although lysozyme-expressing cells were found not only in the crypt but also in the villi. On the other hand, only a few lysozyme-ip cells were found in the villi and some granules showing intense fluorescence were located toward the lumen. As reported for other mammals, Ki67-ip cells were localized in the crypt and did not co-localize with the lysozyme-ip cells. Moreover, fasting induced a decrease in the mRNA levels of lysozyme in the intestine of suncus. In conclusion, we firstly identified the lysozyme mRNA sequence, clarified expression profile of lysozyme transcripts in suncus and found a unique distribution of lysozyme-producing cells in the suncus intestine.
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Affiliation(s)
- Shota Takemi
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Shiomi Ojima
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Toru Tanaka
- Faculty of Pharmaceutical Sciences, Department of Pharmaceutical and Health Sciences, Josai University, 1-1 Keiyaki dai, Sakado, Saitama, 350-0295, Japan
| | - Takafumi Sakai
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
- Area of Life-NanoBio, Division of Strategy Research, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Ichiro Sakata
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan.
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36
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Hirst JJ, Palliser HK, Shaw JC, Crombie G, Walker DW, Zakar T. Birth and Neonatal Transition in the Guinea Pig: Experimental Approaches to Prevent Preterm Birth and Protect the Premature Fetus. Front Physiol 2018; 9:1802. [PMID: 30618814 PMCID: PMC6297273 DOI: 10.3389/fphys.2018.01802] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/29/2018] [Indexed: 11/13/2022] Open
Abstract
The guinea pig (Cavia porcellus) displays many features of gestational physiology that makes it the most translationally relevant rodent species. Progesterone production undergoes a luteal to placental shift as in human pregnancy with levels rising during gestation and with labor and delivery occurring without a precipitous decline in maternal progesterone levels. In contrast to other laboratory rodents, labor in guinea pigs is triggered by a functional progesterone withdrawal, which involves the loss of uterine sensitivity to progesterone like in women. In both species the amnion membrane is a major source of labor-inducing prostaglandins, which promote functional progesterone withdrawal by modifying myometrial progesterone receptor expression. These similar features appear to result from convergent evolution rather than closer evolutionally relationship to primates compared to other rodents. Nevertheless, the similarities in the production, metabolism and actions of progesterone and prostaglandins allow information gained in pregnant guinea pigs to be extended to pregnant women with confidence. This includes exploring the effects of pregnancy complications including growth restriction and the mechanisms by which stressful conditions increase the incidence of preterm labor. The relatively long gestation of the guinea pig and the maturity of the pups at birth particularly in brain development means that a greater proportion of brain development happens in utero. This allows adverse intrauterine conditions to make a sustained impact on the developing brain like in compromised human pregnancies. In addition, the brain is exposed to a protective neurosteroid environment in utero, which has been suggested to promote development in the guinea pig and the human. Moreover, in utero stresses that have been shown to adversely affect long term neurobehavioral outcomes in clinical studies, can be modeled successfully in guinea pigs. Overall, these parallels to the human have led to increasing interest in the guinea pig for translational studies of treatments and therapies that potentially improve outcomes following adverse events in pregnancy and after preterm birth.
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Affiliation(s)
- Jonathan J Hirst
- Mothers and Babies Research Centre, Hunter Medical Research Institute, Newcastle, NSW, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia
| | - Hannah K Palliser
- Mothers and Babies Research Centre, Hunter Medical Research Institute, Newcastle, NSW, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia
| | - Julia C Shaw
- Mothers and Babies Research Centre, Hunter Medical Research Institute, Newcastle, NSW, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia
| | - Gabrielle Crombie
- Mothers and Babies Research Centre, Hunter Medical Research Institute, Newcastle, NSW, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia
| | - David W Walker
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Tamas Zakar
- Mothers and Babies Research Centre, Hunter Medical Research Institute, Newcastle, NSW, Australia.,School of Medicine and Public Health, University of Newcastle, Newcastle, NSW, Australia
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37
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Accurate annotation of accessible chromatin in mouse and human primordial germ cells. Cell Res 2018; 28:1077-1089. [PMID: 30305709 DOI: 10.1038/s41422-018-0096-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/24/2018] [Accepted: 09/02/2018] [Indexed: 12/15/2022] Open
Abstract
Extensive and accurate chromatin remodeling is essential during primordial germ cell (PGC) development for the perpetuation of genetic information across generations. Here, we report that distal cis-regulatory elements (CREs) marked by DNase I-hypersensitive sites (DHSs) show temporally restricted activities during mouse and human PGC development. Using DHS maps as proxy, we accurately locate the genome-wide binding sites of pluripotency transcription factors in mouse PGCs. Unexpectedly, we found that mouse female meiotic recombination hotspots can be captured by DHSs, and for the first time, we identified 12,211 recombination hotspots in mouse female PGCs. In contrast to that of meiotic female PGCs, the chromatin of mitotic-arrested male PGCs is permissive through nuclear transcription factor Y (NFY) binding in the distal regulatory regions. Furthermore, we examined the evolutionary pressure on PGC CREs, and comparative genomic analysis revealed that mouse and human PGC CREs are evolutionarily conserved and show strong conservation across the vertebrate tree outside the mammals. Therefore, our results reveal unique, temporally accessible chromatin configurations during mouse and human PGC development.
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38
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Phifer-Rixey M, Bi K, Ferris KG, Sheehan MJ, Lin D, Mack KL, Keeble SM, Suzuki TA, Good JM, Nachman MW. The genomic basis of environmental adaptation in house mice. PLoS Genet 2018; 14:e1007672. [PMID: 30248095 PMCID: PMC6171964 DOI: 10.1371/journal.pgen.1007672] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 10/04/2018] [Accepted: 08/30/2018] [Indexed: 01/18/2023] Open
Abstract
House mice (Mus musculus) arrived in the Americas only recently in association with European colonization (~400-600 generations), but have spread rapidly and show evidence of local adaptation. Here, we take advantage of this genetic model system to investigate the genomic basis of environmental adaptation in house mice. First, we documented clinal patterns of phenotypic variation in 50 wild-caught mice from a latitudinal transect in Eastern North America. Next, we found that progeny of mice from different latitudes, raised in a common laboratory environment, displayed differences in a number of complex traits related to fitness. Consistent with Bergmann's rule, mice from higher latitudes were larger and fatter than mice from lower latitudes. They also built bigger nests and differed in aspects of blood chemistry related to metabolism. Then, combining exomic, genomic, and transcriptomic data, we identified specific candidate genes underlying adaptive variation. In particular, we defined a short list of genes with cis-eQTL that were identified as candidates in exomic and genomic analyses, all of which have known ties to phenotypes that vary among the studied populations. Thus, wild mice and the newly developed strains represent a valuable resource for future study of the links between genetic variation, phenotypic variation, and climate.
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Affiliation(s)
- Megan Phifer-Rixey
- Department of Biology, Monmouth University, West Long Branch, New Jersey, United States of America
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Ke Bi
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, United States of America
| | - Kathleen G. Ferris
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Michael J. Sheehan
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, United States of America
| | - Dana Lin
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Katya L. Mack
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Sara M. Keeble
- Division of Biological Sciences, University of Montana, Missoula, Missoula, Montana, United States of America
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, Los Angeles, California, United States of America
| | - Taichi A. Suzuki
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, Missoula, Montana, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, United States of America
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Grummer JA, Morando MM, Avila LJ, Sites JW, Leaché AD. Phylogenomic evidence for a recent and rapid radiation of lizards in the Patagonian Liolaemus fitzingerii species group. Mol Phylogenet Evol 2018; 125:243-254. [DOI: 10.1016/j.ympev.2018.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/07/2018] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
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40
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Pasquesi GIM, Adams RH, Card DC, Schield DR, Corbin AB, Perry BW, Reyes-Velasco J, Ruggiero RP, Vandewege MW, Shortt JA, Castoe TA. Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nat Commun 2018; 9:2774. [PMID: 30018307 PMCID: PMC6050309 DOI: 10.1038/s41467-018-05279-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 06/25/2018] [Indexed: 12/14/2022] Open
Abstract
Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance in genome size, squamate genomes exhibit surprisingly high variation among species in abundance (ca. 25–73% of the genome) and composition of identifiable repeat elements. We also demonstrate that snake genomes have experienced microsatellite seeding by transposable elements at a scale unparalleled among eukaryotes, leading to some snake genomes containing the highest microsatellite content of any known eukaryote. Our analyses of transposable element evolution across squamates also suggest that lineage-specific variation in mechanisms of transposable element activity and silencing, rather than variation in species-specific demography, may play a dominant role in driving variation in repeat element landscapes across squamate phylogeny. Large-scale patterns of genomic repeat element evolution have been studied mainly in birds and mammals. Here, the authors analyze the genomes of over 60 squamate reptiles and show high variation in repeat elements compared to mammals and birds, and particularly high microsatellite seeding in snakes.
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Affiliation(s)
- Giulia I M Pasquesi
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Andrew B Corbin
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Jacobo Reyes-Velasco
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA.,Department of Biology, New York University Abu Dhabi, Saadiyat Island, United Arab Emirates
| | - Robert P Ruggiero
- Department of Biology, New York University Abu Dhabi, Saadiyat Island, United Arab Emirates
| | - Michael W Vandewege
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA
| | - Jonathan A Shortt
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA.
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41
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Donath A, Stadler PF. Split-inducing indels in phylogenomic analysis. Algorithms Mol Biol 2018; 13:12. [PMID: 30026791 PMCID: PMC6047143 DOI: 10.1186/s13015-018-0130-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 06/16/2018] [Indexed: 11/13/2022] Open
Abstract
Background Most phylogenetic studies using molecular data treat gaps in multiple sequence alignments as missing data or even completely exclude alignment columns that contain gaps. Results Here we show that gap patterns in large-scale, genome-wide alignments are themselves phylogenetically informative and can be used to infer reliable phylogenies provided the gap data are properly filtered to reduce noise introduced by the alignment method. We introduce here the notion of split-inducing indels (splids) that define an approximate bipartition of the taxon set. We show both in simulated data and in case studies on real-life data that splids can be efficiently extracted from phylogenomic data sets. Conclusions Suitably processed gap patterns extracted from genome-wide alignment provide a surprisingly clear phylogenetic signal and an allow the inference of accurate phylogenetic trees. Electronic supplementary material The online version of this article (10.1186/s13015-018-0130-7) contains supplementary material, which is available to authorized users.
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42
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Phillips MJ, Fruciano C. The soft explosive model of placental mammal evolution. BMC Evol Biol 2018; 18:104. [PMID: 29969980 PMCID: PMC6029115 DOI: 10.1186/s12862-018-1218-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 06/19/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Recent molecular dating estimates for placental mammals echo fossil inferences for an explosive interordinal diversification, but typically place this event some 10-20 million years earlier than the Paleocene fossils, among apparently more "primitive" mammal faunas. RESULTS However, current models of molecular evolution do not adequately account for parallel rate changes, and result in dramatic divergence underestimates for large, long-lived mammals such as whales and hominids. Calibrating among these taxa shifts the rate model errors deeper in the tree, inflating interordinal divergence estimates. We employ simulations based on empirical rate variation, which show that this "error-shift inflation" can explain previous molecular dating overestimates relative to fossil inferences. Molecular dating accuracy is substantially improved in the simulations by focusing on calibrations for taxa that retain plesiomorphic life-history characteristics. Applying this strategy to the empirical data favours the soft explosive model of placental evolution, in line with traditional palaeontological interpretations - a few Cretaceous placental lineages give rise to a rapid interordinal diversification following the 66 Ma Cretaceous-Paleogene boundary mass extinction. CONCLUSIONS Our soft explosive model for the diversification of placental mammals brings into agreement previously incongruous molecular, fossil, and ancestral life history estimates, and closely aligns with a growing consensus for a similar model for bird evolution. We show that recent criticism of the soft explosive model relies on ignoring both experimental controls and statistical confidence, as well as misrepresentation, and inconsistent interpretations of morphological phylogeny. More generally, we suggest that the evolutionary properties of adaptive radiations may leave current molecular dating methods susceptible to overestimating the timing of major diversification events.
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Affiliation(s)
- Matthew J. Phillips
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Australia
| | - Carmelo Fruciano
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Australia
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43
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Sharma V, Lehmann T, Stuckas H, Funke L, Hiller M. Loss of RXFP2 and INSL3 genes in Afrotheria shows that testicular descent is the ancestral condition in placental mammals. PLoS Biol 2018; 16:e2005293. [PMID: 29953435 PMCID: PMC6023123 DOI: 10.1371/journal.pbio.2005293] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 05/24/2018] [Indexed: 01/13/2023] Open
Abstract
Descent of testes from a position near the kidneys into the lower abdomen or into the scrotum is an important developmental process that occurs in all placental mammals, with the exception of five afrotherian lineages. Since soft-tissue structures like testes are not preserved in the fossil record and since key parts of the placental mammal phylogeny remain controversial, it has been debated whether testicular descent is the ancestral or derived condition in placental mammals. To resolve this debate, we used genomic data of 71 mammalian species and analyzed the evolution of two key genes (relaxin/insulin-like family peptide receptor 2 [RXFP2] and insulin-like 3 [INSL3]) that induce the development of the gubernaculum, the ligament that is crucial for testicular descent. We show that both RXFP2 and INSL3 are lost or nonfunctional exclusively in four afrotherians (tenrec, cape elephant shrew, cape golden mole, and manatee) that completely lack testicular descent. The presence of remnants of once functional orthologs of both genes in these afrotherian species shows that these gene losses happened after the split from the placental mammal ancestor. These “molecular vestiges” provide strong evidence that testicular descent is the ancestral condition, irrespective of persisting phylogenetic discrepancies. Furthermore, the absence of shared gene-inactivating mutations and our estimates that the loss of RXFP2 happened at different time points strongly suggest that testicular descent was lost independently in Afrotheria. Our results provide a molecular mechanism that explains the loss of testicular descent in afrotherians and, more generally, highlight how molecular vestiges can provide insights into the evolution of soft-tissue characters. While fossils of whales with legs demonstrate that these species evolved from legged ancestors, the ancestral state of nonfossilizing soft-tissue structures can only be indirectly inferred. This difficulty is also confounded by uncertainties in the phylogenetic relationships between the animals concerned. A prime example is the case of testicular descent, a developmental process that determines the final position of testes, which occurs in most placental mammals but is absent from several afrotherian lineages. Here, we discovered that afrotherians possess remnants of genes known to be required for testicular descent. These “molecular vestiges” show that testicular descent was already present in the placental ancestor and was subsequently lost in Afrotheria. Our study highlights the potential of molecular vestiges in resolving contradictory ancestral states of soft-tissue characters.
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Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Germany
| | - Thomas Lehmann
- Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt am Main, Germany
| | | | - Liane Funke
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Center for Systems Biology Dresden, Germany
- * E-mail:
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Bauer KL, Steeil JC, Adkins EA, Childress AL, Wellehan JFX, Kerns KL, Sarro SJ, Holder KA. Management of Ocular Human herpesvirus 1 Infection in a White-faced Saki Monkey ( Pithecia pithecia). Comp Med 2018; 68:319-323. [PMID: 29907165 DOI: 10.30802/aalas-cm-17-000119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A 20-y-old male intact white-faced saki monkey (Pithecia pithecia) presented with an acute ocular disease of the right eye. Clinical signs included periocular swelling, conjunctivitis, and anisocoria with a miotic right pupil. Conjunctival swabs were positive for Human herpesvirus 1 (HHV1) according to PCR amplification with sequencing. Initial clinical signs resolved with supportive treatment, and the animal was managed chronically by using acyclovir (5 mg/kg PO twice daily) during flare-ups. After more than 2 y, the progression of clinical disease led to enucleation of the right eye. At 2 mo after surgery, acute presentation of severe neurologic signs, including ataxia and blindness, resulted in euthanasia. Histopathology, PCR analysis, and sequencing results were consistent with viral encephalitis due to HHV1; coinfection with Pithecia pithecia lymphocryptovirus 1 was identified. This report describes the first case of managed HHV1 infection in a platyrrhine primate and the first case of HHV1 in a white-faced saki monkey that was not rapidly fatal.
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Affiliation(s)
- Kendra L Bauer
- Animal Care Sciences, Smithsonian Institution National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC, USA.
| | - James C Steeil
- Animal Care Sciences, Smithsonian Institution National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | | | - April L Childress
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - James F X Wellehan
- Department of Comparative, Diagnostic, and Population Medicine, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Kenton L Kerns
- Animal Care Sciences, Smithsonian Institution National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Steven J Sarro
- Animal Care Sciences, Smithsonian Institution National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Kali A Holder
- Animal Care Sciences, Smithsonian Institution National Zoological Park, Smithsonian Conservation Biology Institute, Washington, DC, USA
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Coelho LP, Kultima JR, Costea PI, Fournier C, Pan Y, Czarnecki-Maulden G, Hayward MR, Forslund SK, Schmidt TSB, Descombes P, Jackson JR, Li Q, Bork P. Similarity of the dog and human gut microbiomes in gene content and response to diet. MICROBIOME 2018; 6:72. [PMID: 29669589 PMCID: PMC5907387 DOI: 10.1186/s40168-018-0450-3] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 03/19/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Gut microbes influence their hosts in many ways, in particular by modulating the impact of diet. These effects have been studied most extensively in humans and mice. In this work, we used whole genome metagenomics to investigate the relationship between the gut metagenomes of dogs, humans, mice, and pigs. RESULTS We present a dog gut microbiome gene catalog containing 1,247,405 genes (based on 129 metagenomes and a total of 1.9 terabasepairs of sequencing data). Based on this catalog and taxonomic abundance profiling, we show that the dog microbiome is closer to the human microbiome than the microbiome of either pigs or mice. To investigate this similarity in terms of response to dietary changes, we report on a randomized intervention with two diets (high-protein/low-carbohydrate vs. lower protein/higher carbohydrate). We show that diet has a large and reproducible effect on the dog microbiome, independent of breed or sex. Moreover, the responses were in agreement with those observed in previous human studies. CONCLUSIONS We conclude that findings in dogs may be predictive of human microbiome results. In particular, a novel finding is that overweight or obese dogs experience larger compositional shifts than lean dogs in response to a high-protein diet.
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Affiliation(s)
- Luis Pedro Coelho
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paul Igor Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | - Matthew Robert Hayward
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sofia K. Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | | | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
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Prakash Kumar V, Rajpoot A, Srivastav A, Nigam P, Kumar V, A. M, Prakash Goyal S. Phylogenetic relationship and molecular dating of Indian pangolin (Manis crassicaudata) with other extant pangolin species based on complete cytochrome b mitochondrial gene. Mitochondrial DNA A DNA Mapp Seq Anal 2018. [DOI: 10.1080/24701394.2018.1445241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
| | - Ankita Rajpoot
- Molecular Systematics Laboratory, Zoological Survey of India NRC, Dehradun, Uttarakhand, India
| | | | - Parag Nigam
- Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Vinay Kumar
- Wildlife Institute of India, Dehradun, Uttarakhand, India
| | - Madhanraj A.
- Wildlife Institute of India, Dehradun, Uttarakhand, India
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Metivier SL, Kim J, Addison JA. Genotype by sequencing identifies natural selection as a driver of intraspecific divergence in Atlantic populations of the high dispersal marine invertebrate, Macoma petalum. Ecol Evol 2017; 7:8058-8072. [PMID: 29043056 PMCID: PMC5632645 DOI: 10.1002/ece3.3332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 06/14/2017] [Accepted: 07/18/2017] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial DNA analyses indicate that the Bay of Fundy population of the intertidal tellinid bivalve Macoma petalum is genetically divergent from coastal populations in the Gulf of Maine and Nova Scotia. To further examine the evolutionary forces driving this genetic break, we performed double digest genotype by sequencing (GBS) to survey the nuclear genome for evidence of both neutral and selective processes shaping this pattern. The resulting reads were mapped to a partial transcriptome of its sister species, M. balthica, to identify single nucleotide polymorphisms (SNPs) in protein-coding genes. Population assignment tests, principle components analyses, analysis of molecular variance, and outlier tests all support differentiation between the Bay of Fundy genotype and the genotypes of the Gulf of Maine, Gulf of St. Lawrence, and Nova Scotia. Although both neutral and non-neutral patterns of genetic subdivision were significant, genetic structure among the regions was nearly 20 times higher for loci putatively under selection, suggesting a strong role for natural selection as a driver of genetic diversity in this species. Genetic differences were the greatest between the Bay of Fundy and all other population samples, and some outlier proteins were involved in immunity-related processes. Our results suggest that in combination with limited gene flow across the mouth of the Bay of Fundy, local adaptation is an important driver of intraspecific genetic variation in this marine species with high dispersal potential.
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Affiliation(s)
| | - Jin‐Hong Kim
- Department of BiologyUniversity of New BrunswickFrederictonNBCanada
| | - Jason A. Addison
- Department of BiologyUniversity of New BrunswickFrederictonNBCanada
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Ebel ER, Telis N, Venkataram S, Petrov DA, Enard D. High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites. PLoS Genet 2017; 13:e1007023. [PMID: 28957326 PMCID: PMC5634635 DOI: 10.1371/journal.pgen.1007023] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/10/2017] [Accepted: 09/15/2017] [Indexed: 11/18/2022] Open
Abstract
Plasmodium parasites, along with their Piroplasm relatives, have caused malaria-like illnesses in terrestrial mammals for millions of years. Several Plasmodium-protective alleles have recently evolved in human populations, but little is known about host adaptation to blood parasites over deeper evolutionary timescales. In this work, we analyze mammalian adaptation in ~500 Plasmodium- or Piroplasm- interacting proteins (PPIPs) manually curated from the scientific literature. We show that (i) PPIPs are enriched for both immune functions and pleiotropy with other pathogens, and (ii) the rate of adaptation across mammals is significantly elevated in PPIPs, compared to carefully matched control proteins. PPIPs with high pathogen pleiotropy show the strongest signatures of adaptation, but this pattern is fully explained by their immune enrichment. Several pieces of evidence suggest that blood parasites specifically have imposed selection on PPIPs. First, even non-immune PPIPs that lack interactions with other pathogens have adapted at twice the rate of matched controls. Second, PPIP adaptation is linked to high expression in the liver, a critical organ in the parasite life cycle. Finally, our detailed investigation of alpha-spectrin, a major red blood cell membrane protein, shows that domains with particularly high rates of adaptation are those known to interact specifically with P. falciparum. Overall, we show that host proteins that interact with Plasmodium and Piroplasm parasites have experienced elevated rates of adaptation across mammals, and provide evidence that some of this adaptation has likely been driven by blood parasites.
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Affiliation(s)
- Emily R. Ebel
- Department of Biology, Stanford University, Stanford, California, United States of America
- * E-mail: (ERE); (DE)
| | - Natalie Telis
- Program in Biomedical Informatics, Stanford University, Stanford, California, United States of America
| | - Sandeep Venkataram
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Dmitri A. Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - David Enard
- Department of Biology, Stanford University, Stanford, California, United States of America
- * E-mail: (ERE); (DE)
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Hautier L, Oliver JD, Pierce SE. An Overview of Xenarthran Developmental Studies with a Focus on the Development of the Xenarthrous Vertebrae. J MAMM EVOL 2017. [DOI: 10.1007/s10914-017-9412-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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