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Ning R, Li C, Xia M, Zhang Y, Gan Y, Huang Y, Zhang T, Song H, Zhang S, Guo W. Pseudomonas-associated bacteria play a key role in obtaining nutrition from bamboo for the giant panda ( Ailuropoda melanoleuca). Microbiol Spectr 2024; 12:e0381923. [PMID: 38305171 PMCID: PMC10913395 DOI: 10.1128/spectrum.03819-23] [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: 11/02/2023] [Accepted: 12/28/2023] [Indexed: 02/03/2024] Open
Abstract
Gut microbiota plays a vital role in obtaining nutrition from bamboo for giant pandas. However, low cellulase activity has been observed in the panda's gut. Besides, no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. Therefore, the mechanism by which they obtain nutrients is still controversial. It is necessary to elucidate the precise pathways employed by gut microbiota of pandas to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. Lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. The gut microbiome of wild bamboo-eating specialists was enriched with genes from pathways implicated in degrading ferulate and p-coumarate into acetyl-CoA and succinyl-CoA, which can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in lignin or lignin derivative degradation. Herein, three Pseudomonas-associated strains isolated from the feces of wild pandas showed the laccase, lignin peroxidase, and manganese peroxidase activity and extracellular lignin degradation ability in vitro. A potential mechanism for pandas to obtain nutrition from bamboo was proposed based on the results. This study provides novel insights into the adaptive evolution of pandas from the perspective of lignin metabolism. IMPORTANCE Although giant pandas only feed on bamboo, the mechanism of lignin digestion in pandas is unclear. Here, the metabolic pathways for lignin degradation in wild pandas were explored by comparing gut metagenomic from species with different feeding habits. Results showed that lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. Genes from pathways involved in degrading ferulate and p-coumarate via beta-ketoadipate pathway were also enriched in bamboo-eating pandas. The final products of the above process, such as acetyl-CoA, can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, mainly provides genes involved in lignin degradation. Herein, Pseudomonas-associated strains isolated from the feces of pandas could degrade extracellular lignin. These findings suggest that gut microbiome of pandas is crucial in obtaining nutrition from lignin via Pseudomonas, as the main lignin-degrading bacteria.
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Affiliation(s)
- Ruihong Ning
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Maohua Xia
- Beijing Key Laboratory of Captive Wildlife Technology, Beijing Zoo, Beijing, P.R. China
| | - Yu Zhang
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yunong Gan
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Tianyou Zhang
- Chimelong Safari Park in Guangdong Province, Guangzhou, China
| | - Haitao Song
- Key Laboratory of State Forestry and Grassland Administration (SFGA) on Conservation Biology of Rare Animals in the Giant Panda National Park, The China Conservation and Research Center for the Giant Panda (CCRCGP), Chengdu, China
| | - Siyuan Zhang
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Wei Guo
- Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, China
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2
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Cueva DF, Zug R, Pozo MJ, Molina S, Cisneros R, Bustamante MR, Torres MDL. Evidence of population genetic structure in Ecuadorian Andean bears. Sci Rep 2024; 14:2834. [PMID: 38310153 PMCID: PMC10838292 DOI: 10.1038/s41598-024-53003-5] [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: 03/31/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024] Open
Abstract
Wildlife conservation in Andean countries is a global priority because of the high levels of biodiversity and endemism. Historically, these countries have had limited resources to monitor wildlife (e.g., through genetic tools) and establish conservation programs. Focusing on the study and emblematic use of a few charismatic species has been a strategic approach to direct efforts for conservation and development planning. Consequently, the Andean bear is a flagship and umbrella species for highly biodiverse Andean countries like Ecuador. The few studies exploring the population genetics of this species have concluded that it has low genetic diversity and few units for conservation as populations appear to be well connected. However, these results might be attributed to ascertainment bias as studies have been performed with heterologous molecular markers. Here, using both mtDNA sequences and species-specific microsatellite markers, we show that Andean bears in Ecuador have population structure. Additionally, we found through the study of three Ecuadorian populations that the species might have a higher genetic diversity than we previously thought. These results could support the revision of research priorities, conservation, and planning strategies to improve connectivity for this species which occurs in crucial biodiversity hotspots.
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Affiliation(s)
- Dario F Cueva
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador
| | - Rebecca Zug
- Laboratorio de Carnívoros, Universidad San Francisco de Quito USFQ, Diego de Robles y Vía Interoceanica s/n, Quito, 170157, Ecuador
| | - María José Pozo
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador
| | - Santiago Molina
- Laboratorio de Carnívoros, Universidad San Francisco de Quito USFQ, Diego de Robles y Vía Interoceanica s/n, Quito, 170157, Ecuador
- Fundación Zoológica del Ecuador, Pircapamaba s/n y Rumichupa, Guayllabamba, Quito, Ecuador
| | - Rodrigo Cisneros
- Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, San Cayetano Alto, C/París s/n., 1101608, Loja, Ecuador
| | - Martín R Bustamante
- Fundación Zoológica del Ecuador, Pircapamaba s/n y Rumichupa, Guayllabamba, Quito, Ecuador
| | - María de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito USFQ, Diego de Robles y Via Interoceanica s/n, Quito, 170157, Ecuador.
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3
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Gimranov DO. Morphotypic Characteristics of the First Molar (M1) of the Brown Bear (Ursus arctos) and the Polar Bear (Ursus maritimus) (Carnivora, Ursidae). BIOL BULL+ 2022. [DOI: 10.1134/s1062359022070056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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4
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Willey C, Korstanje R. Sequencing and assembling bear genomes: the bare necessities. Front Zool 2022; 19:30. [PMID: 36451195 PMCID: PMC9710173 DOI: 10.1186/s12983-022-00475-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Unique genetic adaptations are present in bears of every species across the world. From (nearly) shutting down important organs during hibernation to preventing harm from lifestyles that could easily cause metabolic diseases in humans, bears may hold the answer to various human ailments. However, only a few of these unique traits are currently being investigated at the molecular level, partly because of the lack of necessary tools. One of these tools is well-annotated genome assemblies from the different, extant bear species. These reference genomes are needed to allow us to identify differences in genetic variants, isoforms, gene expression, and genomic features such as transposons and identify those that are associated with biomedical-relevant traits. In this review we assess the current state of the genome assemblies of the eight different bear species, discuss current gaps, and the future benefits these reference genomes may have in informing human biomedical applications, while at the same time improving bear conservation efforts.
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Affiliation(s)
- Courtney Willey
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory, Bar Harbor, ME 04609 USA
| | - Ron Korstanje
- grid.249880.f0000 0004 0374 0039The Jackson Laboratory, Bar Harbor, ME 04609 USA
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5
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Multi-locus phylogeny and species delimitations of the striped-back shrew group (Eulipotyphla: Soricidae): Implications for cryptic diversity, taxonomy and multiple speciation patterns. Mol Phylogenet Evol 2022; 177:107619. [PMID: 36007821 DOI: 10.1016/j.ympev.2022.107619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 08/01/2022] [Accepted: 08/17/2022] [Indexed: 11/23/2022]
Abstract
The striped-back shrew group demonstrates remarkable variation in skull and body size, tail length, and brightness of the dorsal stripe; and karyotypic and DNA variation has been reported in recent years. In this study, we investigated the phylogenetic structure of the group, as well as speciation patterns and demographic history in Mountains of Southwestern China and adjacent mountains, including the southern Himalayas, Mts. Bashan, Wushan, and Qinling. We sequenced a total of 462 specimens from 126 localities in the known range of the group, which were sequenced and analyzed based on 6.2 kb of sequence data from two mitochondrial, six nuclear, and two Y chromosome markers. Phylogenetic analyses of the concatenated mtDNA data revealed 14 sympatric and independently evolving lineages within the striped-back shrew group, including Sorex bedfordiae, S. cylindricauda, S. excelsus, S. sinalis and several cryptic species. All concatenated data (ten genes) showed a consistent genetic structure compared to the mtDNA lineages for the group, whereas the nuclear and the Y chromosome data showed a discordant genetic structure compared to the mtDNA lineages for the striped-back shrew group. Species delimitation analyses and deep genetic distance clearly support the species status of the 14 evolving lineages. The divergence time estimation suggested that the striped-back shrew group began to diversify from the middle Pleistocene (2.34 Ma), then flourished at approximately 2.14 Ma, followed by a series of rapid diversifications through the Pleistocene. Our results also revealed multiple mechanisms of speciation in the Mountains of Southwestern China and Adjacent Mountains with complex landscapes and climate. The uplifting of the Qinghai-Tibetan Plateau, Quaternary climate oscillations, riverine barriers, ecological elevation gradients, topographical diversity, and their own low dispersal capacity may have driven the speciation, genetic structure, and phylogeographic patterns of the striped-back shrew group.
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6
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Uncovering the enigmatic evolution of bears in greater depth: The hybrid origin of the Asiatic black bear. Proc Natl Acad Sci U S A 2022; 119:e2120307119. [PMID: 35858381 PMCID: PMC9351369 DOI: 10.1073/pnas.2120307119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Bears are fascinating mammals because of their complex pattern of speciation and rapid evolution of distinct phenotypes. Interspecific hybridization has been common and has shaped the complex evolutionary history of bears. In this study, based on the largest population-level genomic dataset to date involving all Ursinae species and recently developed methods for detecting hybrid speciation, we provide explicit evidence for the hybrid origin of Asiatic black bears, which arose through historical hybridization between the ancestor of polar bear/brown bear/American black bears and the ancestor of sun bear/sloth bears. This was inferred to have occurred soon after the divergence of the two parental lineages in Eurasia due to climate-driven population expansion and dispersal. In addition, we found that the intermediate body size of this hybrid species arose from its combination of relevant genes derived from two parental lineages of contrasting sizes. This and alternate fixation of numerous other loci that had diverged between parental lineages may have initiated the reproductive isolation of the Asiatic black bear from its two parents. Our study sheds further light on the evolutionary history of bears and documents the importance of hybridization in new species formation and phenotypic evolution in mammals.
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7
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İbiş O, Yesari Selçuk A, Teber S, Baran M, Kaya A, Özcan S, Kefelioğlu H, Tez C. Complete mitogenomes of Turkish tree squirrels, Sciurus anomalus and S. vulgaris, (Sciuridae: Rodentia: Mammalia) and their phylogenetic status within the tribe Sciurini. Gene 2022; 841:146773. [PMID: 35905846 DOI: 10.1016/j.gene.2022.146773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/03/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
The genus Sciurus, a member of the family Sciuridae, is widely distributed in the Holarctic region. To better understand mitogenomic characteristics and to reveal internal phylogenetic relationships of the genus, 20 complete mitogenomes of Turkish tree squirrels were successfully sequenced for the first time, including 19 for S. anomalus (from 16,505 bp to 16,510 bp) and one for S. vulgaris (16,511 bp). The mitogenomes of two species were AT-biased. All tRNAs for two species displayed a typical clover-leaf structure, except for tRNASer(AGY). The tRNA Serine1 (S1)-GCT structure lacked the dihydrouridine (DHU) loop and stem. Based on mitogenomic dataset for phylogeny of Sciurinae, phylogenetic analyses (Bayesian Inference and Maximum Likelihood) did not support monophyly of Sciurus and proposed that S. anomalus, the most basal taxa in the Sciurini tribe, had at least five mitogenome lineages, which were also supported by network analysis. The dissimilarities among the five linegaes of S. anomalus ranged from 0.0042 (0.42%) to 0.0062 (0.62%) using K2P sequence pairwise distances. In addition to this mitogenomic analysis result, phylogenetic analyses using the CYTB + D-loop dataset proposed the existence of at least nine lineages for S. anomalus, which was different than those of the previous studies. The current study proposed that the use of mitogenomic data for reconstructing the phylogeny of Turkey' Sciurus holds an important value for revealing evolutionary relationships.
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Affiliation(s)
- Osman İbiş
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Vectors and Vector-Born Diseases Research and Implementation Center, Erciyes University, Kayseri, Turkey.
| | - Ahmet Yesari Selçuk
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey; Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Saffet Teber
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Mehmet Baran
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey.
| | - Alaettin Kaya
- Department of Basic Sciences, Faculty of Veterinary Medicine, Dicle University, Diyarbakır, Turkey.
| | - Servet Özcan
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey.
| | - Haluk Kefelioğlu
- Department of Biology, Faculty of Science and Letters, Ondokuz Mayıs University, Samsun, Turkey.
| | - Coşkun Tez
- Genome and Stem Cell Center, GENKOK, Erciyes University, Kayseri, Turkey; Department of Biology, Faculty of Sciences, Erciyes University, Kayseri, Turkey.
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8
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ŞEKER PS, SELÇUK AY, SELVİ E, BARAN M, TEBER S, KELEŞ GA, KEFELİOĞLU H, TEZ C, İBİŞ O. Complete mitochondrial genomes of Chionomys roberti and Chionomys nivalis (Mammalia: Rodentia) from Turkey: Insight into their phylogenetic position within Arvicolinae. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00559-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Ning S, Lu X, Zhao M, Wang X, Yang S, Shen Q, Wang H, Zhang W. Virome in Fecal Samples From Wild Giant Pandas ( Ailuropoda Melanoleuca). Front Vet Sci 2021; 8:767494. [PMID: 34869737 PMCID: PMC8636094 DOI: 10.3389/fvets.2021.767494] [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: 08/30/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
The giant panda (Ailuropoda melanoleuca) is one of the most endangered mammals in the world; anthropogenic habitat loss and poaching still threaten the survival of wild pandas. Viral infection has become one of the potential threats to the health of these animals, but the available information related to these infections is still limited. In order to detect possible vertebrate viruses, the virome in the fecal samples of seven wild giant pandas from Qinling Mountains was investigated by using the method of viral metagenomics. From the fecal virome of wild giant pandas, we determined six nearly complete genomes belonging to the order Picornavirales, two of which may be qualified as a novel virus family or genus. In addition, four complete genomes belonging to the Genomoviridae family were also fully characterized. This virological investigation has increased our understanding of the gut viral community in giant pandas. Whether these viruses detected in fecal samples can really infect giant panda needs further research.
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Affiliation(s)
- Songyi Ning
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Min Zhao
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Quan Shen
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, China
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10
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Puckett EE, Davis IS. Spatial patterns of genetic diversity in eight bear (Ursidae) species. URSUS 2021. [DOI: 10.2192/ursus-d-20-00029.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Emily E. Puckett
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Isis S. Davis
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
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11
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Lai WL, Ratnayeke S, Austin C, Rahman S, Ayub Q, Mohd Kulaimi NA, Kuppusamy S, Chew J. Complete mitochondrial genome of a sun bear from Malaysia and its position in the phylogeny of Ursidae. URSUS 2021. [DOI: 10.2192/ursus-d-20-00032.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Wai Ling Lai
- Department of Biological Sciences, School of Science and Technology, Sunway University, No. 5, Jalan Universiti, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Shyamala Ratnayeke
- Department of Biological Sciences, School of Science and Technology, Sunway University, No. 5, Jalan Universiti, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Christopher Austin
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisplinary Platform, Jalan Lagoon Selatan, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Sadequr Rahman
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisplinary Platform, Jalan Lagoon Selatan, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Qasim Ayub
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisplinary Platform, Jalan Lagoon Selatan, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Noor Azleen Mohd Kulaimi
- National Wildlife Forensic Laboratory (NWFL), Ex-situ Conservation Division, Department of Wildlife and National Parks (DWNP), KM 10 Jalan Cheras, 56100 Kuala Lumpur, Malaysia
| | - Sagathevan Kuppusamy
- Science and Engineering Resources, Sunway University, No. 5, Jalan Universiti, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
| | - Jactty Chew
- Department of Biological Sciences, School of Science and Technology, Sunway University, No. 5, Jalan Universiti, Bandar Sunway, 47500 Selangor Darul Ehsan, Malaysia
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12
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Saremi NF, Oppenheimer J, Vollmers C, O'Connell B, Milne SA, Byrne A, Yu L, Ryder OA, Green RE, Shapiro B. An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus. J Hered 2021; 112:377-384. [PMID: 33882130 PMCID: PMC8280923 DOI: 10.1093/jhered/esab021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.
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Affiliation(s)
- Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Christopher Vollmers
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Brendan O'Connell
- Department of Medical and Molecular Genetics, Oregon Health & Science University, Portland, OR
| | - Shard A Milne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Ashley Byrne
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | | | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
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13
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Pedersen MW, De Sanctis B, Saremi NF, Sikora M, Puckett EE, Gu Z, Moon KL, Kapp JD, Vinner L, Vardanyan Z, Ardelean CF, Arroyo-Cabrales J, Cahill JA, Heintzman PD, Zazula G, MacPhee RDE, Shapiro B, Durbin R, Willerslev E. Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Curr Biol 2021; 31:2728-2736.e8. [PMID: 33878301 DOI: 10.1016/j.cub.2021.04.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Analysis of ancient environmental DNA (eDNA) has revolutionized our ability to describe biological communities in space and time,1-3 by allowing for parallel sequencing of DNA from all trophic levels.4-8 However, because environmental samples contain sparse and fragmented data from multiple individuals, and often contain closely related species,9 the field of ancient eDNA has so far been limited to organellar genomes in its contribution to population and phylogenetic studies.5,6,10,11 This is in contrast to data from fossils12,13 where full-genome studies are routine, despite these being rare and their destruction for sequencing undesirable.14-16 Here, we report the retrieval of three low-coverage (0.03×) environmental genomes from American black bear (Ursus americanus) and a 0.04× environmental genome of the extinct giant short-faced bear (Arctodus simus) from cave sediment samples from northern Mexico dated to 16-14 thousand calibrated years before present (cal kyr BP), which we contextualize with a new high-coverage (26×) and two lower-coverage giant short-faced bear genomes obtained from fossils recovered from Yukon Territory, Canada, which date to ∼22-50 cal kyr BP. We show that the Late Pleistocene black bear population in Mexico is ancestrally related to the present-day Eastern American black bear population, and that the extinct giant short-faced bears present in Mexico were deeply divergent from the earlier Beringian population. Our findings demonstrate the ability to separately analyze genomic-scale DNA sequences of closely related species co-preserved in environmental samples, which brings the use of ancient eDNA into the era of population genomics and phylogenetics.
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Affiliation(s)
- Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Emily E Puckett
- Department of Biological Sciences, University of Memphis, 3770 Walker Avenue, Ellington Hall, Memphis, TN 38152, USA
| | - Zhenquan Gu
- State Key Laboratory of Tibetan Plateau Earth System Science (LATPES), Beijing 100101, China
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Zaruhi Vardanyan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ciprian F Ardelean
- Unidad Académica de Antropología, Universidad Autónoma de Zacatecas, Campus II, Col. Progreso, 98066 Zacatecas, Mexico; The Archaeology Centre, Department of Anthropology, University of Toronto, 19 Ursula Franklin Street, Toronto, ON M5S 2S2, Canada
| | - Joaquin Arroyo-Cabrales
- Laboratorio de Arqueozoologia, Subdireccion de Laboratorios y Apoyo Academico, Instituto Nacional de Antropologia e Historia, Moneda 16, Col. Centro, 06060 Mexico, CdMx, Mexico
| | - James A Cahill
- Laboratory of the Neurogenetics of Language, Rockefeller University, New York, NY, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, PO Box 6050, Langnes, N-9037 Tromsø, Norway
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism & Culture, Government of Yukon, Whitehorse, YT Y1A 2C6, Canada
| | - Ross D E MacPhee
- Department of Mammalogy, American Museum of Natural History, New York, NY 12484, USA; American Museum of Natural History, New York, NY, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK; Wellcome Sanger Institute, Cambridge CB10 1SA, UK; MARUM, University of Bremen, Bremen, Germany.
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14
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Barlow A, Paijmans JLA, Alberti F, Gasparyan B, Bar-Oz G, Pinhasi R, Foronova I, Puzachenko AY, Pacher M, Dalén L, Baryshnikov G, Hofreiter M. Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears. Curr Biol 2021; 31:1771-1779.e7. [PMID: 33592193 DOI: 10.1016/j.cub.2021.01.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 10/19/2020] [Accepted: 01/21/2021] [Indexed: 11/18/2022]
Abstract
Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.
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Affiliation(s)
- Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
| | - Johanna L A Paijmans
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Federica Alberti
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, 0025, RA, Yerevan, 15 Charents st., Armenia
| | - Guy Bar-Oz
- The Zinman Institute of Archaeology, University of Haifa, 199 Aba-Hushi Avenue, Haifa, Israel 3498838
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Irina Foronova
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, 3, Ac. Koptyuga ave., Novosibirsk, Russia 630090
| | - Andrey Y Puzachenko
- Institute of Geography, Russian Academy of Sciences, Staromonetnyy Pereulok, 29, Moscow, Russia 119017
| | - Martina Pacher
- Naturmuseum St. Gallen, Rorschacher Strasse 263, CH-9016 St. Gallen, Switzerland
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 54, 114 18 Stockholm, Sweden
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034 St. Petersburg, Russia
| | - Michael Hofreiter
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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15
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Cserhati M. A tail of two pandas- whole genome k-mer signature analysis of the red panda (Ailurus fulgens) and the Giant panda (Ailuropoda melanoleuca). BMC Genomics 2021; 22:228. [PMID: 33794768 PMCID: PMC8015091 DOI: 10.1186/s12864-021-07531-3] [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: 05/18/2020] [Accepted: 03/14/2021] [Indexed: 11/29/2022] Open
Abstract
Background The red panda (Ailurus fulgens) is a riddle of morphology, making it hard to tell whether it is an ursid, a procyonid, a mustelid, or a member of its own family. Previous genetic studies have given quite contradictory results as to its phylogenetic placement. Results A recently developed whole genome-based algorithm, the Whole Genome K-mer Signature algorithm was used to analyze the genomes of 28 species of Carnivora, including A. fulgens and several felid, ursid, mustelid, one mephitid species. This algorithm has the advantage of holistically using all the information in the genomes of these species. Being a genomics-based algorithm, it also reduces stochastic error to a minimum. Besides the whole genome, the mitochondrial DNA from 52 mustelids, mephitids, ursids, procyonids and A. fulgens were aligned to draw further phylogenetic inferences. The results from the whole genome study suggested that A. fulgens is a member of the mustelid clade (p = 9·10− 97). A. fulgens also separates from the mephitid Spilogala gracilis. The giant panda, Ailuropoda melanoleuca also clusters away from A. fulgens, together with other ursids (p = 1.2·10− 62). This could be due to the geographic isolation of A. fulgens from other mustelid species. However, results from the mitochondrial study as well as neighbor-joining methods based on the sequence identity matrix suggests that A. fulgens forms a monophyletic group. A Maximum Likelihood tree suggests that A. fulgens and Ursidae form a monophyletic group, although the bootstrap value is weak. Conclusions The main conclusion that we can draw from this study is that on a whole genome level A. fulgens possibly belongs to the mustelid clade, and not an ursid or a mephitid. This despite the fact that previously some researchers classified A. fulgens and A. melanoleuca as relatives. Since the genotype determines the phenotype, molecular-based classification takes precedence over morphological classifications. This affirms the results of some previous studies, which studied smaller portions of the genome. However, mitochondrial analyses based on neighbor-joining and maximum likelihood methods suggest otherwise. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07531-3.
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Affiliation(s)
- Matyas Cserhati
- Independent Scholar, 2615C Muscatel Avenue, Rosemead, CA, 91770, USA.
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16
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Fowler NL, Spady TJ, Wang G, Leopold BD, Belant JL. Denning, metabolic suppression, and the realisation of ecological opportunities in Ursidae. Mamm Rev 2021. [DOI: 10.1111/mam.12246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Nicholas L. Fowler
- Global Wildlife Conservation Center State University of New York College of Environmental Science and Forestry 1 Forestry Drive Syracuse NY13210USA
| | - Thomas J. Spady
- Department of Biological Sciences California State University San Marcos San Marcos CA92096USA
| | - Guiming Wang
- Department of Wildlife, Fisheries, and Aquaculture Mississippi State UniversityMississippi State Box 9690MS39762USA
| | - Bruce D. Leopold
- Department of Wildlife, Fisheries, and Aquaculture Mississippi State UniversityMississippi State Box 9690MS39762USA
| | - Jerrold L. Belant
- Global Wildlife Conservation Center State University of New York College of Environmental Science and Forestry 1 Forestry Drive Syracuse NY13210USA
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17
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Pérez-Ramos A, Romero A, Rodriguez E, Figueirido B. Three-dimensional dental topography and feeding ecology in the extinct cave bear. Biol Lett 2020; 16:20200792. [PMID: 33353522 DOI: 10.1098/rsbl.2020.0792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The cave bear (Ursus spelaeus s.l.) was an iconic extinct bear that inhabited the Pleistocene of Eurasia. The cause of extinction of this species is unclear and to identify the actual factors, it is crucial to understand its feeding preferences. Here, we quantified the shape descriptor metrics in three-dimensional (3D) models of the upper teeth (P4-M2) of the cave bear to make inferences about its controversial feeding behaviour. We used comparative samples, including representatives of all living bear species with known diets, as a template. Our topographic analyses show that the complexity of upper tooth rows in living bears is more clearly associated with the mechanical properties of the items consumed than with the type of food. Cave bears exhibit intermediate values on topographic metrics compared with the bamboo-feeder giant panda (Ailuropoda melanoleuca) and specialists in hard mast consumption (Ursus arctos and Ursus thibetanus). The crown topography of cave bear upper teeth suggests that they could chew on tough vegetal resources of low quality with high efficiency, a characteristic that no living bear currently displays. Our results align with a climate-driven hypothesis to explain the extinction of cave bear populations during the Late Pleistocene.
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Affiliation(s)
- Alejandro Pérez-Ramos
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Alejandro Romero
- Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03080 Alicante, Spain
| | - Ernesto Rodriguez
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
| | - Borja Figueirido
- Departamento de Ecología y Geología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
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18
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Yuan H, Ma L, Zhang L, Li X, Xia C. Crystal structure of the giant panda MHC class I complex: First insights into the viral peptide presentation profile in the bear family. Protein Sci 2020; 29:2468-2481. [PMID: 33078460 DOI: 10.1002/pro.3980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 01/03/2023]
Abstract
The viral cytotoxic T lymphocyte (CTL) epitope peptides presented by classical MHC-I molecules require the assembly of a peptide-MHC-I-β2m (pMHC-I) trimolecular complex for T cell receptor (TCR) recognition, which is the critical activation link for triggering antiviral T cell immunity. Research on T cell immunology in the Ursidae family, especially structural immunology, is still lacking. In this study, the structure of the key trimolecular complex pMHC-I, which binds a peptide from canine distemper virus, was solved for the first time using giant panda as a representative species of Ursidae. The structural characteristics of the giant panda pMHC-I complex (pAime-128), including the unique pockets in the peptide-binding groove (PBG), were analyzed in detail. Comparing the pAime-128 to others in the bear family and extending the comparison to other mammals revealed distinct features. The interaction between MHC-I and β2m, the features of pAime-128 involved in TCR docking and cluster of differentiation 8 (CD8) binding, the anchor sites in the PBG, and the CTL epitopes of potential viruses that infect pandas were clarified. Unique features of pMHC-I viral antigen presentation in the panda were revealed by solving the three-dimensional (3D) structure of pAime-128. The distinct characteristics of pAime-128 indicate an unusual event that emerged during the evolution of the MHC system in the bear family. These results provide a new platform for research on panda CTL immunity and the design of vaccines for application in the bear family.
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Affiliation(s)
- Hongyu Yuan
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaoying Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, Henan, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
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19
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Biogeographic problem-solving reveals the Late Pleistocene translocation of a short-faced bear to the California Channel Islands. Sci Rep 2020; 10:15172. [PMID: 32938967 PMCID: PMC7494929 DOI: 10.1038/s41598-020-71572-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/14/2020] [Indexed: 11/08/2022] Open
Abstract
An accurate understanding of biodiversity of the past is critical for contextualizing biodiversity patterns and trends in the present. Emerging techniques are refining our ability to decipher otherwise cryptic human-mediated species translocations across the Quaternary, yet these techniques are often used in isolation, rather than part of an interdisciplinary hypothesis-testing toolkit, limiting their scope and application. Here we illustrate the use of such an integrative approach and report the occurrence of North America's largest terrestrial mammalian carnivore, the short-faced bear, Arctodus simus, from Daisy Cave (CA-SMI-261), an important early human occupation site on the California Channel Islands. We identified the specimen by corroborating morphological, protein, and mitogenomic lines of evidence, and evaluated the potential natural and anthropogenic mechanisms of its transport and deposition. While representing just a single specimen, our combination of techniques opened a window into the behavior of an enigmatic species, suggesting that A. simus was a wide-ranging scavenger utilizing terrestrial and marine carcasses. This discovery highlights the utility of bridging archaeological and paleontological datasets to disentangle complex biogeographic scenarios and reveal unexpected biodiversity for island systems worldwide.
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20
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Decker SK, Ammerman LK. Phylogeographic analysis reveals mito-nuclear discordance in Dasypterus intermedius. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Abstract
Northern yellow bats (Dasypterus intermedius) are tree-roosting bats in the family Vespertilionidae comprised of two subspecies: D. intermedius intermedius and D. intermedius floridanus. The two subspecies are thought to be geographically separated. Due to their cryptic morphology, this hypothesis has never been tested and can benefit from being examined within a molecular framework. In this study, mitochondrial sequence data from 38 D. intermedius and nuclear sequence data from 14 D. intermedius from across their range were used to test the hypothesis that genetically defined groups correspond geographically with the two morphologically defined subspecies. Although high levels of divergence of the mitochondrial sequence (11.6%) suggest genetically distinct clusters sympatric in southern Texas, no genetic structure was recovered with the nuclear marker. Moreover, the mitochondrial sequence data recovered a paraphyletic relationship between the two subspecies of D. intermedius with the Cuban yellow bat (D. insularis), whereas no such paraphyly was recovered from analysis of the nuclear marker. Divergence time based on analyses of mitochondrial sequence for the two subspecies was approximately 5.5 Ma. The patterns observed are hypothesized to be the result of past isolation of lineages and secondary contact that is currently contributing to gene flow.
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Affiliation(s)
- Sydney K Decker
- Department of Biology, Angelo State University, San Angelo, TX, USA
| | - Loren K Ammerman
- Department of Biology, Angelo State University, San Angelo, TX, USA
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21
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Transcriptome Profiling across Five Tissues of Giant Panda. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3852586. [PMID: 32851066 PMCID: PMC7436357 DOI: 10.1155/2020/3852586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/03/2020] [Accepted: 06/01/2020] [Indexed: 11/18/2022]
Abstract
Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney's transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.
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22
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İbiş O. Whole mitochondrial genome sequence and phylogenetic relationships of Williams's jerboa ( Scarturus williamsi) from Turkey. PeerJ 2020; 8:e9569. [PMID: 32742814 PMCID: PMC7369027 DOI: 10.7717/peerj.9569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/29/2020] [Indexed: 11/29/2022] Open
Abstract
Williams’s jerboa (Scarturus williamsi), a medium-sized jerboa distributed in Anatolia and its adjacent regions, is a member of the four- and five-toed jerboas found mostly in Asia. Disagreements about the taxonomy of this taxon at the genus/species level continue to exist. Here, we report the first effort to sequence and assemble the mitochondrial genome of Williams’s jerboa from Turkey. The mitochondrial genome of S. williamsi was 16,653 bp in total length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two non-coding regions (the D-loop and OL region) with intergenic spacer. All of the genes, except ND6 and eight tRNAs, were encoded on the heavy chain strand, similar to the features of mitogenomes of other rodents. When compared with all available rodent mitochondrial genomes, Williams’s jerboa showed (1) a serine deletion at the 3′-end of the ATP8 gene, (2) the ND5 gene terminated with a TAG codon and (3) a tandem repeat cluster (273 bp in length) in the control region. Williams’s jerboa and Siberian jerboa grouped as sister taxa despite the high genetic distance (17.6%) between them, belonging to Allactaginae. This result is consistent with the latest pre-revision, which suggests that Williams’s jerboa and the Siberian jerboa may belong to separate genera, as Scarturus and Orientallactaga, respectively. The present study provides a reference mitochondrial genome for Williams’s jerboa for further molecular studies of other species of Dipodoidea and Rodentia.
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Affiliation(s)
- Osman İbiş
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey.,Genome and Stem Cell Center (GENKOK), Erciyes University, Kayseri, Turkey
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23
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Whole mitochondrial genome of long-clawed mole vole (Prometheomys schaposchnikowi) from Turkey, with its phylogenetic relationships. Genomics 2020; 112:3247-3255. [PMID: 32512144 DOI: 10.1016/j.ygeno.2020.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 11/21/2022]
Abstract
The mitogenome of Prometheomys schaposchnikowi was characterized for the first time as a circular DNA molecule (16.284 bp), containing 37 coding and 2 non-coding regions. In the mitogenome, ND6 and 8 tRNA genes were encoded on the light chain, while 12 PCGs, 14 tRNAs, 2 rRNAs, D-loop and OL were encoded on the heavy chain. The most common initiation codon in PCGs was ATG. As in many mammals, incomplete stop codons in P. schaposchnikowi were in the COX3, ND1 and ND4. Phylogenetic relationships were revealed using Bayesian method and the 13 PCGs. Seven genera (Arvicola, Dicrostonyx, Lasiopodomys, Myodes, Ondatra, Proedromys and Prometheomys) formed a monophyletic group, while Eothenomys, Microtus and Neodon were paraphyletic. P. schaposchnikowi constituted the most basal group within Arvicolinae. Divergence time estimation suggested that P. schaposchnikowi diversified during the Miocene (16.28 Mya). Further molecular studies are needed to test the distinctiveness and diversity of the genus Prometheomys.
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24
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Kistler L, Bieker VC, Martin MD, Pedersen MW, Ramos Madrigal J, Wales N. Ancient Plant Genomics in Archaeology, Herbaria, and the Environment. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:605-629. [PMID: 32119793 DOI: 10.1146/annurev-arplant-081519-035837] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway; ,
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Jazmín Ramos Madrigal
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Nathan Wales
- Department of Archaeology, University of York, York YO1 7EP, United Kingdom;
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25
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Heavy reliance on plants for Romanian cave bears evidenced by amino acid nitrogen isotope analysis. Sci Rep 2020; 10:6612. [PMID: 32313007 PMCID: PMC7170912 DOI: 10.1038/s41598-020-62990-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Heavy reliance on plants is rare in Carnivora and mostly limited to relatively small species in subtropical settings. The feeding behaviors of extinct cave bears living during Pleistocene cold periods at middle latitudes have been intensely studied using various approaches including isotopic analyses of fossil collagen. In contrast to cave bears from all other regions in Europe, some individuals from Romania show exceptionally high δ15N values that might be indicative of meat consumption. Herbivory on plants with high δ15N values cannot be ruled out based on this method, however. Here we apply an approach using the δ15N values of individual amino acids from collagen that offsets the baseline δ15N variation among environments. The analysis yielded strong signals of reliance on plants for Romanian cave bears based on the δ15N values of glutamate and phenylalanine. These results could suggest that the high variability in bulk collagen δ15N values observed among cave bears in Romania reflects niche partitioning but in a general trophic context of herbivory.
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26
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Chen S, Qing J, Liu Z, Liu Y, Tang M, Murphy RW, Pu Y, Wang X, Tang K, Guo K, Jiang X, Liu S. Multilocus phylogeny and cryptic diversity of white-toothed shrews (Mammalia, Eulipotyphla, Crocidura) in China. BMC Evol Biol 2020; 20:29. [PMID: 32059644 PMCID: PMC7023792 DOI: 10.1186/s12862-020-1588-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/27/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.
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Affiliation(s)
- Shunde Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jiao Qing
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Zhu Liu
- College of Life Science and Technology, Mudanjiang Normal University, Mudanjiang, 157011, China
| | - Yang Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Mingkun Tang
- Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Robert W Murphy
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, M5S 2C6, Canada
| | - Yingting Pu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Xuming Wang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China.,Sichuan Academy of Forestry, Chengdu, 610081, China
| | - Keyi Tang
- College of Life Sciences, Sichuan Normal University, Chengdu, 610066, China
| | - Keji Guo
- Central South Forest Inventory and Planning Institute of State Forestry Administration, Changsha, 410014, China
| | - Xuelong Jiang
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Shaoying Liu
- Sichuan Academy of Forestry, Chengdu, 610081, China.
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27
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Barlow A, Hartmann S, Gonzalez J, Hofreiter M, Paijmans JLA. Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates. Genes (Basel) 2020; 11:E50. [PMID: 31906474 PMCID: PMC7017230 DOI: 10.3390/genes11010050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/16/2022] Open
Abstract
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
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28
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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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29
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McGrath K, Rowsell K, Gates St-Pierre C, Tedder A, Foody G, Roberts C, Speller C, Collins M. Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points. Sci Rep 2019; 9:11027. [PMID: 31363122 PMCID: PMC6667708 DOI: 10.1038/s41598-019-47299-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/26/2019] [Indexed: 12/01/2022] Open
Abstract
Today, practical, functional and symbolic choices inform the selection of raw materials for worked objects. In cases where we can discern the origin of worked bone, tooth, ivory and antler objects in the past, we assume that similar choices are being made. However, morphological species identification of worked objects is often impossible due to the loss of identifying characteristics during manufacture. Here, we describe a novel non-destructive ZooMS (Zooarchaeology by Mass Spectrometry) method which was applied to bone points from Pre-Contact St. Lawrence Iroquoian village sites in southern Quebec, Canada. The traditional ZooMS technique requires destructive analysis of a sample, which can be problematic when dealing with artefacts. Here we instead extracted proteins from the plastic bags in which the points had been stored. ZooMS analysis revealed hitherto unexpected species, notably black bear (Ursus americanus) and human (Homo sapiens sapiens), used in point manufacture. These surprising results (confirmed through genomic sequencing) highlight the importance of advancing biomolecular research in artefact studies. Furthermore, they unexpectedly and exceptionally allow us to identify and explore the tangible, material traces of the symbolic relationship between bears and humans, central to past and present Iroquoian cosmology and mythology.
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Affiliation(s)
- Krista McGrath
- BioArCh, Department of Archaeology, University of York, York, UK.
| | - Keri Rowsell
- BioArCh, Department of Archaeology, University of York, York, UK.,London School of Economics and Political Science, London, UK
| | | | - Andrew Tedder
- School of Chemistry & Bioscience, University of Bradford, Bradford, UK
| | - George Foody
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK
| | | | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, UK.,Department of Anthropology, University of British Columbia, Vancouver, Canada
| | - Matthew Collins
- BioArCh, Department of Archaeology, University of York, York, UK.,EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
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30
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Sheng GL, Basler N, Ji XP, Paijmans JL, Alberti F, Preick M, Hartmann S, Westbury MV, Yuan JX, Jablonski NG, Xenikoudakis G, Hou XD, Xiao B, Liu JH, Hofreiter M, Lai XL, Barlow A. Paleogenome Reveals Genetic Contribution of Extinct Giant Panda to Extant Populations. Curr Biol 2019; 29:1695-1700.e6. [DOI: 10.1016/j.cub.2019.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/28/2019] [Accepted: 04/09/2019] [Indexed: 11/30/2022]
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31
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Arnaudo ME, Toledo N, Soibelzon L, Bona P. Phylogenetic signal analysis in the basicranium of Ursidae (Carnivora, Mammalia). PeerJ 2019; 7:e6597. [PMID: 30891368 PMCID: PMC6422017 DOI: 10.7717/peerj.6597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 02/09/2019] [Indexed: 11/29/2022] Open
Abstract
Ursidae is a monophyletic group comprised of three subfamilies: Tremarctinae, Ursinae and Ailuropodinae, all of which have a rich geographical distribution. The phylogenetic relationships within the Ursidae group have been underexamined, especially regarding morphological traits such as the basicranium. Importantly, the basicranium is a highly complex region that covers a small portion of the skull, combining both structural and functional aspects that determine its morphology. Phylogenetic hypotheses of the Ursidae (including Tremarctinae) have been made based on morphological characters that considers skull, mandible and teeth features, while specific characters of the auditory region and basicranium have not been taken into account. To do this, we analyse the shape and size macroevolution of the basicranium of Ursidae, testing its morphological disparity in a phylogenetic context, which is quantified by means of the phylogenetic signal. We investigated phylogenetical autocorrelation by shape (depicted by Principal Components Analysis scores from previous published analyses) and basicranium size (depicted by centroid size, CS) using an orthonormal decomposition analysis and Abouheif C mean. The main advantages of these methods are that they rely exclusively on cladogram topology and do not require branch-length estimates. Also, an optimisation of the ancestral nodes was performed using TNT 1.5 software. In relation to the phylogenetic signal, both methods showed similar results: the presence of autocorrelation was detected in PC1 and PC2, while in PC3, PC4 and PC5 and in the size of the basicranium (CS), the absence of autocorrelation occurred. The most significant nodes (where there is autocorrelation) are the basal nodes 'Ursidae' and 'Ursinae-Tremarctinae'. Within this last group, distinctive basicranium morphology is observed, being more conservative in Tremarctinae than in Ursinae. The differences between these subfamilies could be related to historical events involving varying food and environmental preferences. The high phylogenetic signal in the node Tremarctinae probably indicates that the basicranium configuration of these bears was obtained early in their evolutionary history. Finally, our results of the basicranium and skull length ratios indicate that in Tremarctinae, the basicranium size was not determined by phylogeny but instead by other factors, such as adaptive responses to climatic changes and competition with other carnivores.
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Affiliation(s)
- María Eugenia Arnaudo
- División de Paleontología Vertebrados, Facultad de Ciencias Naturales y Museo-UNLP, La Plata, Buenos Aires, Argentina
- CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Néstor Toledo
- CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- División Paleontología Vertebrados, Unidades de Investigación Anexo Museo, Facultad de Ciencias Naturales y Museo-UNLP, La Plata, Buenos Aires, Argentina
| | - Leopoldo Soibelzon
- CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Laboratorio de Morfología Evolutiva y Desarrollo (MORPHOS)-División de Paleontología Vertebrados, Facultad de Ciencias Naturales y Museo-UNLP, La Plata, Buenos Aires, Argentina
| | - Paula Bona
- CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- División Paleontología Vertebrados, Unidades de Investigación Anexo Museo, Facultad de Ciencias Naturales y Museo-UNLP, La Plata, Buenos Aires, Argentina
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32
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Renaud G, Schubert M, Sawyer S, Orlando L. Authentication and Assessment of Contamination in Ancient DNA. Methods Mol Biol 2019; 1963:163-194. [PMID: 30875054 DOI: 10.1007/978-1-4939-9176-1_17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Contamination from both present-day humans and postmortem microbial sources is a common challenge in ancient DNA studies. Here we present a suite of tools to assist in the assessment of contamination in ancient DNA data sets. These tools perform standard tests of authenticity of ancient DNA data including detecting the presence of postmortem damage signatures in sequence alignments and quantifying the amount of present-day human contamination.
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Affiliation(s)
- Gabriel Renaud
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Susanna Sawyer
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, University Paul Sabatier, Toulouse, France.
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Abstract
Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential is high for contamination of ancient samples, ancient DNA extracts, and genomic sequencing libraries prepared from these extracts with non-degraded DNA from the present-day environment. To minimize the risk of contamination in ancient DNA environments, experimental protocols specific to handling ancient specimens, including those that outline the design and layout of laboratory space, have been introduced. Here, we outline challenges associated with working with ancient samples, including providing guidelines for setting up a new ancient DNA laboratory. We also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination of ancient DNA experiments with exogenous sources of DNA.
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Affiliation(s)
- Tara L Fulton
- Environment and Climate Change Canada, Edmonton, AB, Canada
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
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34
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López-Estrada EK, Sanmartín I, García-París M, Zaldívar-Riverón A. High extinction rates and non-adaptive radiation explains patterns of low diversity and extreme morphological disparity in North American blister beetles (Coleoptera, Meloidae). Mol Phylogenet Evol 2019; 130:156-168. [DOI: 10.1016/j.ympev.2018.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/24/2018] [Accepted: 09/22/2018] [Indexed: 10/28/2022]
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35
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Kadariya R, Shimozuru M, Maldonado JE, Moustafa MAM, Sashika M, Tsubota T. High genetic diversity and distinct ancient lineage of Asiatic black bears revealed by non-invasive surveys in the Annapurna Conservation Area, Nepal. PLoS One 2018; 13:e0207662. [PMID: 30517155 PMCID: PMC6281213 DOI: 10.1371/journal.pone.0207662] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/05/2018] [Indexed: 11/19/2022] Open
Abstract
Asiatic black bears (Ursus thibetanus) have a widespread distribution in mountain landscapes, and are considered vulnerable globally, but are low-priority species for conservation in Nepal. Habitat fragmentation, illegal hunting, and human-bear conflict are the major threats to Asiatic black bears across their global range. Having an adequate level of genetic variation in a population helps with adapting to rapidly changing environments, and thus is important for the long-term health of bear populations. Accordingly, we conducted non-invasive surveys of bear populations in the Annapurna Conservation Area (ACA) to elucidate genetic diversity, genetic structure, and the phylogenetic relationship of Asiatic black bears from this region of Nepal to other subspecies. To assess levels of genetic diversity and population genetic structure, we genotyped eight microsatellite loci using 147 samples, identifying 60 individuals in an area of approximately 525 km2. We found that the Asiatic black bear population in the ACA has maintained high levels of genetic diversity (HE = 0.76) as compared to other bear populations from range countries. We did not detect a signature of population substructure among sampling localities and this suggests that animals are moving freely across the landscape within the ACA. We also detected a moderate population size that may increase with the availability of suitable habitat in the ACA, so bear-related conflict should be addressed to ensure the long-term viability of this expanding bear populations. Primers specific to bears were designed to amplify a 675 bp fragment of the mitochondrial control region from the collected samples. Three haplotypes were observed from the entire conservation area. The complete mitochondrial genome (16,771 bp), the first obtained from wild populations of the Himalayan black bear (U. t. laniger), was also sequenced to resolve the phylogenetic relationships of closely related subspecies of Asiatic black bears. The resulting phylogeny indicated that Himalayan black bear populations in Nepal are evolutionary distinct from other known subspecies of Asiatic black bears.
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Affiliation(s)
- Rabin Kadariya
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- National Trust for Nature Conservation, Khumaltar, Lalitpur, Nepal
| | - Michito Shimozuru
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Jesús E. Maldonado
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, United States of America
| | - Mohamed Abdallah Mohamed Moustafa
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Department of Animal Medicine, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Mariko Sashika
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Toshio Tsubota
- Laboratory of Wildlife Biology and Medicine, Department of Environmental Veterinary Science, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- * E-mail:
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36
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Peng C, Niu L, Deng J, Yu J, Zhang X, Zhou C, Xing J, Li J. Can-SINE dynamics in the giant panda and three other Caniformia genomes. Mob DNA 2018; 9:32. [PMID: 30455747 PMCID: PMC6230240 DOI: 10.1186/s13100-018-0137-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/01/2018] [Indexed: 11/10/2022] Open
Abstract
Background Although repeat sequences constitute about 37% of carnivore genomes, the characteristics and distribution of repeat sequences among carnivore genomes have not been fully investigated. Based on the updated Repbase library, we re-annotated transposable elements (TEs) in four Caniformia genomes (giant panda, polar bear, domestic dog, and domestic ferret) and performed a systematic, genome-wide comparison focusing on the Carnivora-specific SINE family, Can-SINEs. Results We found the majority of young recently integrated transposable elements are LINEs and SINEs in carnivore genomes. In particular, SINEC1_AMe, SINEC1B_AMe and SINEC_C1 are the top three most abundant Can-SINE subfamilies in the panda and polar bear genomes. Transposition in transposition analysis indicates that SINEC1_AMe and SINEC1B_AMe are the most active subfamilies in the panda and the polar bear genomes. SINEC2A1_CF and SINEC1A_CF subfamilies show a higher retrotransposition activity in the dog genome, and MVB2 subfamily is the most active Can-SINE in the ferret genome. As the giant panda is an endangered icon species, we then focused on the identification of panda specific Can-SINEs. With the panda-associated two-way genome alignments, we identified 250 putative panda-specific (PPS) elements (139 SINEC1_AMes and 111 SINEC1B_AMes) that inserted in the panda genome but were absent at the orthologous regions of the other three genomes. Further investigation of these PPS elements allowed us to identify a new Can-SINE subfamily, the SINEC1_AMe2, which was distinguishable from the current SINEC1_AMe consensus by four non-CpG sites. SINEC1_AMe2 has a high copy number (> 100,000) in the panda and polar bear genomes and the vast majority (> 96%) of the SINEC1_AMe2 elements have divergence rates less than 10% in both genomes. Conclusions Our results suggest that Can-SINEs show lineage-specific retransposition activity in the four genomes and have an important impact on the genomic landscape of different Caniformia lineages. Combining these observations with results from the COSEG, Network, and target site duplication analysis, we suggest that SINEC1_AMe2 is a young mobile element subfamily and currently active in both the panda and polar bear genomes.
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Affiliation(s)
- Changjun Peng
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
| | - Lili Niu
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Jiabo Deng
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Jianqiu Yu
- Sichuan Wild Animal Research Institute, Chengdu Zoo, Chengdu, China
| | - Xueyan Zhang
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
| | - Chuang Zhou
- 3Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610065 Sichuan China
| | - Jinchuan Xing
- 4Department of Genetics, Human Genetic Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ USA
| | - Jing Li
- 1Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life and Sciences, University of Sichuan, Chengdu, China
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37
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Palaeohistology and life history evolution in cave bears, Ursus spelaeus sensu lato. PLoS One 2018; 13:e0206791. [PMID: 30462690 PMCID: PMC6248942 DOI: 10.1371/journal.pone.0206791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 10/19/2018] [Indexed: 01/29/2023] Open
Abstract
The abundance of skeletal remains of cave bears in Pleistocene deposits can offer crucial information on the biology and life history of this megafaunal element. The histological study of 62 femora from 23 different European localities and comparisons with specimens of five extant ursid species revealed novel data on tissue types and growth patterns. Cave bear’s femoral bone microstructure is characterized by a fibrolamellar complex with increasing amounts of parallel-fibered and lamellar bone towards the outer cortex. Remodelling of the primary bone tissue initially occurs close to the perimedullary margin of the bone cortex around the linea aspera. Although similar histological traits can be observed in many extant bear species, the composition of the fibrolamellar complex can vary greatly. Cave bears reached skeletal maturity between the ages of 10 and 14, which is late compared to other bear species. There is a significant correlation between altitude and growth, which reflects the different body sizes of cave bears from different altitudes.
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38
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Barlow A, Cahill JA, Hartmann S, Theunert C, Xenikoudakis G, Fortes GG, Paijmans JLA, Rabeder G, Frischauf C, Grandal-d'Anglade A, García-Vázquez A, Murtskhvaladze M, Saarma U, Anijalg P, Skrbinšek T, Bertorelle G, Gasparian B, Bar-Oz G, Pinhasi R, Slatkin M, Dalén L, Shapiro B, Hofreiter M. Partial genomic survival of cave bears in living brown bears. Nat Ecol Evol 2018; 2:1563-1570. [PMID: 30150744 DOI: 10.1038/s41559-018-0654-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/27/2018] [Indexed: 02/06/2023]
Abstract
Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.
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Affiliation(s)
- Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christoph Theunert
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Gloria G Fortes
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Gernot Rabeder
- Institute of Palaeontology, University of Vienna, Vienna, Austria
| | | | | | - Ana García-Vázquez
- Instituto Universitario de Xeoloxía, Universidade da Coruña, A Coruña, Spain
| | | | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Peeter Anijalg
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tomaž Skrbinšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Boris Gasparian
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Dublin, Ireland.,Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Lan T, Gill S, Bellemain E, Bischof R, Nawaz MA, Lindqvist C. Evolutionary history of enigmatic bears in the Tibetan Plateau-Himalaya region and the identity of the yeti. Proc Biol Sci 2018; 284:rspb.2017.1804. [PMID: 29187630 PMCID: PMC5740279 DOI: 10.1098/rspb.2017.1804] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/01/2017] [Indexed: 11/12/2022] Open
Abstract
Although anecdotally associated with local bears (Ursus arctos and U. thibetanus), the exact identity of ‘hominid’-like creatures important to folklore and mythology in the Tibetan Plateau–Himalaya region is still surrounded by mystery. Recently, two purported yeti samples from the Himalayas showed genetic affinity with an ancient polar bear, suggesting they may be from previously unrecognized, possibly hybrid, bear species, but this preliminary finding has been under question. We conducted a comprehensive genetic survey of field-collected and museum specimens to explore their identity and ultimately infer the evolutionary history of bears in the region. Phylogenetic analyses of mitochondrial DNA sequences determined clade affinities of the purported yeti samples in this study, strongly supporting the biological basis of the yeti legend to be local, extant bears. Complete mitochondrial genomes were assembled for Himalayan brown bear (U. a. isabellinus) and black bear (U. t. laniger) for the first time. Our results demonstrate that the Himalayan brown bear is one of the first-branching clades within the brown bear lineage, while Tibetan brown bears diverged much later. The estimated times of divergence of the Tibetan Plateau and Himalayan bear lineages overlap with Middle to Late Pleistocene glaciation events, suggesting that extant bears in the region are likely descendants of populations that survived in local refugia during the Pleistocene glaciations.
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Affiliation(s)
- Tianying Lan
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA
| | - Stephanie Gill
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA
| | - Eva Bellemain
- SPYGEN, Savoie Technolac - BP 274, Le Bourget-du-Lac Cedex 73375, France
| | - Richard Bischof
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, Norway
| | - Muhammad Ali Nawaz
- Department of Animal Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Snow Leopard Trust, 4649 Sunnyside Ave N, Suite 325, Seattle, WA 98103, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA .,School of Biological Sciences, Nanyang Technological University, Singapore 637551
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40
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Lei R, Frasier CL, Hawkins MTR, Engberg SE, Bailey CA, Johnson SE, McLain AT, Groves CP, Perry GH, Nash SD, Mittermeier RA, Louis EE. Phylogenomic Reconstruction of Sportive Lemurs (genus Lepilemur) Recovered from Mitogenomes with Inferences for Madagascar Biogeography. J Hered 2018; 108:107-119. [PMID: 28173059 DOI: 10.1093/jhered/esw072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/30/2016] [Indexed: 11/12/2022] Open
Abstract
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species’ boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis. Using modern distribution data, an ancestral area reconstruction and an ecological vicariance analysis were performed to trace the history of diversification and to test biogeographic hypotheses. We estimated the initial split between the eastern and western Lepilemur clades to have occurred in the Miocene. Divergence of most species occurred from the Pliocene to the Pleistocene. The biogeographic patterns recovered in this study were better addressed with a combinatorial approach including climate, watersheds, and rivers. Generally, current climate and watershed hypotheses performed better for western and eastern clades, while speciation of northern clades was not adequately supported using the ecological factors incorporated in this study. Thus, multiple mechanisms likely contributed to the speciation and distribution patterns in Lepilemur.
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Affiliation(s)
- Runhua Lei
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Cynthia L Frasier
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Melissa T R Hawkins
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Shannon E Engberg
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Carolyn A Bailey
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
| | - Steig E Johnson
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
| | - Adam T McLain
- Department of Mathematics and Sciences, State University of New York Polytechnic Institute, Utica, NY, USA
| | - Colin P Groves
- School of Archaeology and Anthropology, Australian National University, Canberra, ACT, Australia
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Edward E Louis
- Grewcock Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE, USA
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41
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Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene. Genes (Basel) 2018; 9:genes9040198. [PMID: 29642393 PMCID: PMC5924540 DOI: 10.3390/genes9040198] [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: 02/24/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 02/02/2023] Open
Abstract
The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.
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Guo W, Mishra S, Zhao J, Tang J, Zeng B, Kong F, Ning R, Li M, Zhang H, Zeng Y, Tian Y, Zhong Y, Luo H, Liu Y, Yang J, Yang M, Zhang M, Li Y, Ni Q, Li C, Wang C, Li D, Zhang H, Zuo Z, Li Y. Metagenomic Study Suggests That the Gut Microbiota of the Giant Panda ( Ailuropoda melanoleuca) May Not Be Specialized for Fiber Fermentation. Front Microbiol 2018; 9:229. [PMID: 29503636 PMCID: PMC5820910 DOI: 10.3389/fmicb.2018.00229] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 01/30/2018] [Indexed: 11/13/2022] Open
Abstract
Bamboo-eating giant panda (Ailuropoda melanoleuca) is an enigmatic species, which possesses a carnivore-like short and simple gastrointestinal tract (GIT). Despite the remarkable studies on giant panda, its diet adaptability status continues to be a matter of debate. To resolve this puzzle, we investigated the functional potential of the giant panda gut microbiome using shotgun metagenomic sequencing of fecal samples. We also compared our data with similar data from other animal species representing herbivores, carnivores, and omnivores from current and earlier studies. We found that the giant panda hosts a bear-like gut microbiota distinct from those of herbivores indicated by the metabolic potential of the microbiome in the gut of giant pandas and other mammals. Furthermore, the relative abundance of genes involved in cellulose- and hemicellulose-digestion, and enrichment of enzymes associated with pathways of amino acid degradation and biosynthetic reactions in giant pandas echoed a carnivore-like microbiome. Most significantly, the enzyme assay of the giant panda's feces indicated the lowest cellulase and xylanase activity among major herbivores, shown by an in-vitro experimental assay of enzyme activity for cellulose and hemicellulose-degradation. All of our results consistently indicate that the giant panda is not specialized to digest cellulose and hemicellulose from its bamboo diet, making the giant panda a good mammalian model to study the unusual link between the gut microbiome and diet. The increased food intake of the giant pandas might be a strategy to compensate for the gut microbiome functions, highlighting a strong need of conservation of the native bamboo forest both in high- and low-altitude ranges to meet the great demand of bamboo diet of giant pandas.
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Affiliation(s)
- Wei Guo
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sudhanshu Mishra
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jiangchao Zhao
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, United States
| | - Jingsi Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Fanli Kong
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ruihong Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Miao Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hengzhi Zhang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yutian Zeng
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Yuanliangzi Tian
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Yihang Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Hongdi Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Yunhan Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Jiandong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Caiwu Li
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Chengdong Wang
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Desheng Li
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Hemin Zhang
- China Conservation and Research Center for the Giant Panda, Ya'an, China
| | - Zhili Zuo
- Chengdu Zoo, Chengdu Institute of Wildlife, Chengdu, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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Elbow Joint Geometry in Bears (Ursidae, Carnivora): a Tool to Infer Paleobiology and Functional Adaptations of Quaternary Fossils. J MAMM EVOL 2017. [DOI: 10.1007/s10914-017-9413-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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44
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Gormezano LJ, Ellis-Felege SN, Iles DT, Barnas A, Rockwell RF. Polar Bear Foraging Behavior During the Ice-Free Period in Western Hudson Bay: Observations, Origins, and Potential Significance. AMERICAN MUSEUM NOVITATES 2017. [DOI: 10.1206/3885.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Linda J. Gormezano
- Division of Vertebrate Zoology, American Museum of Natural History, New York
| | | | - David T. Iles
- Department of Biology, Tufts University, Medford, MA
| | - Andrew Barnas
- Department of Biology, University of North Dakota, Grand Forks, ND
| | - Robert F. Rockwell
- Division of Vertebrate Zoology, American Museum of Natural History, New York
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45
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Lammers F, Gallus S, Janke A, Nilsson MA. Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low-Coverage Genomes. Genome Biol Evol 2017; 9:2862-2878. [PMID: 28985298 PMCID: PMC5737362 DOI: 10.1093/gbe/evx170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2017] [Indexed: 12/15/2022] Open
Abstract
Phylogenetic reconstruction from transposable elements (TEs) offers an additional perspective to study evolutionary processes. However, detecting phylogenetically informative TE insertions requires tedious experimental work, limiting the power of phylogenetic inference. Here, we analyzed the genomes of seven bear species using high-throughput sequencing data to detect thousands of TE insertions. The newly developed pipeline for TE detection called TeddyPi (TE detection and discovery for Phylogenetic Inference) identified 150,513 high-quality TE insertions in the genomes of ursine and tremarctine bears. By integrating different TE insertion callers and using a stringent filtering approach, the TeddyPi pipeline produced highly reliable TE insertion calls, which were confirmed by extensive in vitro validation experiments. Analysis of single nucleotide substitutions in the flanking regions of the TEs shows that these substitutions correlate with the phylogenetic signal from the TE insertions. Our phylogenomic analyses show that TEs are a major driver of genomic variation in bears and enabled phylogenetic reconstruction of a well-resolved species tree, despite strong signals for incomplete lineage sorting and introgression. The analyses show that the Asiatic black, sun, and sloth bear form a monophyletic clade, in which phylogenetic incongruence originates from incomplete lineage sorting. TeddyPi is open source and can be adapted to various TE and structural variation callers. The pipeline makes it possible to confidently extract thousands of TE insertions even from low-coverage genomes (∼10×) of nonmodel organisms. This opens new possibilities for biologists to study phylogenies and evolutionary processes as well as rates and patterns of (retro-)transposition and structural variation.
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Affiliation(s)
- Fritjof Lammers
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne Gallus
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
- Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
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Zhang W, Yang S, Shan T, Hou R, Liu Z, Li W, Guo L, Wang Y, Chen P, Wang X, Feng F, Wang H, Chen C, Shen Q, Zhou C, Hua X, Cui L, Deng X, Zhang Z, Qi D, Delwart E. Virome comparisons in wild-diseased and healthy captive giant pandas. MICROBIOME 2017; 5:90. [PMID: 28780905 PMCID: PMC5545856 DOI: 10.1186/s40168-017-0308-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 07/13/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND The giant panda (Ailuropoda melanoleuca) is a vulnerable mammal herbivore living wild in central China. Viral infections have become a potential threat to the health of these endangered animals, but limited information related to these infections is available. METHODS Using a viral metagenomic approach, we surveyed viruses in the feces, nasopharyngeal secretions, blood, and different tissues from a wild giant panda that died from an unknown disease, a healthy wild giant panda, and 46 healthy captive animals. RESULTS The previously uncharacterized complete or near complete genomes of four viruses from three genera in Papillomaviridae family, six viruses in a proposed new Picornaviridae genus (Aimelvirus), two unclassified viruses related to posaviruses in Picornavirales order, 19 anelloviruses in four different clades of Anelloviridae family, four putative circoviruses, and 15 viruses belonging to the recently described Genomoviridae family were sequenced. Reflecting the diet of giant pandas, numerous insect virus sequences related to the families Iflaviridae, Dicistroviridae, Iridoviridae, Baculoviridae, Polydnaviridae, and subfamily Densovirinae and plant viruses sequences related to the families Tombusviridae, Partitiviridae, Secoviridae, Geminiviridae, Luteoviridae, Virgaviridae, and Rhabdoviridae; genus Umbravirus, Alphaflexiviridae, and Phycodnaviridae were also detected in fecal samples. A small number of insect virus sequences were also detected in the nasopharyngeal secretions of healthy giant pandas and lung tissues from the dead wild giant panda. Although the viral families present in the sick giant panda were also detected in the healthy ones, a higher proportion of papillomaviruses, picornaviruses, and anelloviruses reads were detected in the diseased panda. CONCLUSION This viral survey increases our understanding of eukaryotic viruses in giant pandas and provides a baseline for comparison to viruses detected in future infectious disease outbreaks. The similar viral families detected in sick and healthy giant pandas indicate that these viruses result in commensal infections in most immuno-competent animals.
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Affiliation(s)
- Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241 China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Zhijian Liu
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Lianghua Guo
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Yan Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Peng Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Feifei Feng
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Hua Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chao Chen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013 China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People’s Hospital, Taizhou, Jiangsu 225300 China
| | - Xiuguo Hua
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Li Cui
- School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Xutao Deng
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610081 China
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan 610000 China
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118 USA
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Sun Y, Li Y, Wu Y, Xiong L, Li C, Wang C, Li D, Lan J, Zhang Z, Jing B, Gu X, Xie Y, Lai W, Peng X, Yang G. Fatty-binding protein and galectin of Baylisascaris schroederi: Prokaryotic expression and preliminary evaluation of serodiagnostic potential. PLoS One 2017; 12:e0182094. [PMID: 28750056 PMCID: PMC5531546 DOI: 10.1371/journal.pone.0182094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/12/2017] [Indexed: 11/18/2022] Open
Abstract
Baylisascaris schroederi is a common parasite of captive giant pandas. The diagnosis of this ascariasis is normally carried out by a sedimentation-floatation method or PCR to detect eggs in feces, but neither method is suitable for early diagnosis. Fatty acid-binding protein (FABP) and galectin (GAL) exist in various animals and participate in important biology of parasites. Because of their good immunogenicity, they are seen as potential antigens for the diagnosis of parasitic diseases. In this study, we cloned and expressed recombinant FABP and GAL from B. schroederi (rBs-FABP and rBs-GAL) and developed indirect enzyme-linked immunosorbent assays (ELISAs) to evaluate their potential for diagnosing ascariasis in giant pandas. Immunolocalization showed that Bs-FABP and Bs-GAL were widely distributed in adult worms. The ELISA based on rBs-FABP showed sensitivity of 95.8% (23/24) and specificity of 100% (12/12), and that based on rBs-GAL had sensitivity of 91.7% (22/24) and specificity of 100% (12/12).
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Affiliation(s)
- Ying Sun
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yu Li
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yiran Wu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lang Xiong
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Caiwu Li
- China Conservation and Research Center for Giant Panda, Wolong, China
| | - Chengdong Wang
- China Conservation and Research Center for Giant Panda, Wolong, China
| | - Desheng Li
- China Conservation and Research Center for Giant Panda, Wolong, China
| | - Jingchao Lan
- Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Zhihe Zhang
- Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Bo Jing
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaobing Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Weimin Lai
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xuerong Peng
- College of Science, Sichuan Agricultural University, Ya’an, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- * E-mail:
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Meloro C, Guidarelli G, Colangelo P, Ciucci P, Loy A. Mandible size and shape in extant Ursidae (Carnivora, Mammalia): A tool for taxonomy and ecogeography. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12171] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlo Meloro
- Research Centre in Evolutionary Anthropology and Palaeoecology; School of Natural Sciences and Psychology; Liverpool John Moores University; Liverpool UK
| | | | - Paolo Colangelo
- CNR - Institute for Ecosystem Study; Verbania-Pallanza Italy
| | - Paolo Ciucci
- Department of Biology and Biotechnologies ‘Charles Darwin’; University of Rome ‘La Sapienza’; Roma Italy
| | - Anna Loy
- Department S.T.A.T.; University of Molise; Pesche Italy
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49
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Veitschegger K. The effect of body size evolution and ecology on encephalization in cave bears and extant relatives. BMC Evol Biol 2017; 17:124. [PMID: 28583080 PMCID: PMC5460516 DOI: 10.1186/s12862-017-0976-1] [Citation(s) in RCA: 9] [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: 01/04/2017] [Accepted: 05/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolution of larger brain volumes relative to body size in Mammalia is the subject of an extensive amount of research. Early on palaeontologists were interested in the brain of cave bears, Ursus spelaeus, and described its morphology and size. However, until now, it was not possible to compare the absolute or relative brain size in a phylogenetic context due to the lack of an established phylogeny, comparative material, and phylogenetic comparative methods. In recent years, many tools for comparing traits within phylogenies were developed and the phylogenetic position of cave bears was resolved based on nuclear as well as mtDNA. RESULTS Cave bears exhibit significantly lower encephalization compared to their contemporary relatives and intraspecific brain mass variation remained rather small. Encephalization was correlated with the combined dormancy-diet score. Body size evolution was a main driver in the degree of encephalization in cave bears as it increased in a much higher pace than brain size. In Ursus spelaeus, brain and body size increase over time albeit differently paced. This rate pattern is different in the highest encephalized bear species within the dataset, Ursus malayanus. The brain size in this species increased while body size heavily decreased compared to its ancestral stage. CONCLUSIONS Early on in the evolution of cave bears encephalization decreased making it one of the least encephalized bear species compared to extant and extinct members of Ursidae. The results give reason to suspect that as herbivorous animals, cave bears might have exhibited a physiological buffer strategy to survive the strong seasonality of their environment. Thus, brain size was probably affected by the negative trade-off with adipose tissue as well as diet. The decrease of relative brain size in the herbivorous Ursus spelaeus is the result of a considerable increase in body size possibly in combination with environmental conditions forcing them to rest during winters.
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Affiliation(s)
- Kristof Veitschegger
- Palaeontological Institute and Museum, University of Zurich, Karl Schmid-Strasse 4, 8006, Zürich, Switzerland.
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50
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Xie Y, Hoberg EP, Yang Z, Urban JF, Yang G. Ancylostoma ailuropodae n. sp. (Nematoda: Ancylostomatidae), a new hookworm parasite isolated from wild giant pandas in Southwest China. Parasit Vectors 2017; 10:277. [PMID: 28576124 PMCID: PMC5457663 DOI: 10.1186/s13071-017-2209-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 05/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hookworms belonging to the genus Ancylostoma (Dubini, 1843) cause ancylostomiasis, a disease of considerable concern in humans and domestic and wild animals. Molecular and epidemiological data support evidence for the zoonotic potential among species of Ancylostoma where transmission to humans is facilitated by rapid urbanization and increased human-wildlife interactions. It is important to assess and describe these potential zoonotic parasite species in wildlife, especially in hosts that have physiological similarities to humans and share their habitat. Moreover, defining species diversity within parasite groups that can circulate among free-ranging host species and humans also provides a pathway to understanding the distribution of infection and disease. In this study, we describe a previously unrecognized species of hookworm in the genus Ancylostoma in the giant panda, including criteria for morphological and molecular characterization. METHODS The hookworm specimens were obtained from a wild giant panda that died in the Fengtongzai Natural Reserve in Sichuan Province of China in November 2013. They were microscopically examined and then genetically analyzed by sequencing the nuclear internal transcribed spacer (ITS, ITS1-5.8S-ITS2) and mitochondrial cytochrome c oxidase subunit 1 (cox1) genes in two representative specimens (one female and one male, FTZ1 and FTZ2, respectively). RESULTS Ancylostoma ailuropodae n. sp. is proposed for these hookworms. Morphologically the hookworm specimens differ from other congeneric species primarily based on the structure of the buccal capsule in males and females, characterized by 2 pairs of ventrolateral and 2 pairs of dorsolateral teeth; males differ in the structure and shape of the copulatory bursa, where the dorsal ray possesses 2 digitations. Pairwise nuclear and mitochondrial DNA comparisons, genetic distance analysis, and phylogenetic data strongly indicate that A. ailuropodae from giant pandas is a separate species which shared a most recent common ancestor with A. ceylanicum Looss, 1911 in the genus Ancylostoma (family Ancylostomatidae). CONCLUSION Ancylostoma ailuropodae n. sp. is the fourth species of hookworm described from the Ursidae and the fifteenth species assigned to the genus Ancylostoma. A sister-species association with A. ceylanicum and phylogenetic distinctiveness from the monophyletic Uncinaria Frölich, 1789 among ursids and other carnivorans indicate a history of host colonization in the evolutionary radiation among ancylostomatid hookworms. Further, phylogenetic relationships among bears and a history of ecological and geographical isolation for giant pandas may be consistent with two independent events of host colonization in the diversification of Ancylostoma among ursid hosts. A history for host colonization within this assemblage and the relationship for A. ailuropodae n. sp. demonstrate the potential of this species as a zoonotic parasite and as a possible threat to human health. The cumulative morphological, molecular and phylogenetic data presented for A. ailuropodae n. sp. provides a better understanding of the taxonomy, diagnostics and evolutionary biology of the hookworms.
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Affiliation(s)
- Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.,United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, Maryland, 20705, USA
| | - Eric P Hoberg
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Disease Laboratory, Beltsville, Maryland, 20705, USA
| | - Zijiang Yang
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, 20740, USA
| | - Joseph F Urban
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, Maryland, 20705, USA
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, China.
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