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Ban C, Tian X, Lu Q, Lounglawan P, Wen G. Enhancing Rumen Fermentation and Bacteria Community in Sika Deer ( Cervus nippon) through Varying Levels of Dragon Fruit Peel Polyphenolic Extract: An In Vitro Study. Animals (Basel) 2024; 14:1139. [PMID: 38672287 PMCID: PMC11047680 DOI: 10.3390/ani14081139] [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: 03/05/2024] [Revised: 04/06/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
The aim of this study is to investigate the effect of dragon fruit peel polyphenolic extract (DFPE) on gas production, rumen fermentation, and bacterial communities in sika deer using an in vitro technique. Three treatments with different DFPE levels (DFPE0, base diet; DFPE5, base diet + 5 mg/g DFPE; DFPE10, base diet + 10 mg/g DFPE, respectively; n = 6) were implemented. The phenolic composition of DFPE, gas production (GP), ammonia nitrogen (NH3-N), volatile fatty acid (VFA), and bacteria communities was evaluated after 24 h of incubation. The results showed that GP and NH3-N were reduced by DFPE supplementation. Total VFA, isovaleric acid, and valeric acid were increased (p < 0.05) by the addition of DFPE. No changes (p > 0.05) were observed in pH, acetic acid, propionic acid, isobutyric acid, butyric acid, and the ratio of acetic acid to propionic acid. Additionally, the alpha indexes, including Sobs, Shannon, and Ace, were increased by DFPE supplementation. Moreover, at the phylum level, DFPE supplementation increased (p = 0.01) Bacteroidota but reduced (p < 0.01) Firmicutes. At the genus level, compared to DFPE0, the DFPE10 had increased relative abundances of Rikenellaceae_RC9_gut_group (p < 0.01), norank_f_Muribaculaceae (p = 0.01), Lachnospiraceae_NK3A20_group (p < 0.01), Christensenellaceae_R-7_group (p < 0.01), and NK4A214_group (p < 0.01), decreased relative abundances of Streptococcus (p < 0.01), Oribacterium (p = 0.01), and Enterococcus (p < 0.01). Compared to DFPE0, DFPE5 had no change (p > 0.05) in all bacteria at the genus level except for decreased relative abundance of Enterococcus (p < 0.01). These results indicated that DFPE may be able to be used as a feed additive to enhance fermentation parameters and improve ruminal bacteria communities in Sika deer.
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Affiliation(s)
- Chao Ban
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Xingzhou Tian
- College of Animal Science, Guizhou University, Guiyang 550025, China (Q.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Qi Lu
- College of Animal Science, Guizhou University, Guiyang 550025, China (Q.L.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Pipat Lounglawan
- School of Animal Technology and Innovation, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Guilan Wen
- College of Animal Science, Guizhou University, Guiyang 550025, China (Q.L.)
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Takagi T, Murakami R, Takano A, Torii H, Kaneko S, Tamate HB. A historic religious sanctuary may have preserved ancestral genetics of Japanese sika deer ( Cervus nippon). J Mammal 2023; 104:303-315. [PMID: 37032702 PMCID: PMC10075338 DOI: 10.1093/jmammal/gyac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/10/2022] [Indexed: 01/31/2023] Open
Abstract
Abstract
Deer have been a major resource for human populations for thousands of years. Anthropogenic activities, such as hunting, have influenced the genetic structure and distribution of deer populations. In Japan, wild Japanese sika deer (Cervus nippon) have been hunted since ancient times but have also been historically protected as sacred animals in several sanctuaries. Sika deer have been protected for over a thousand years in the religious sanctuary around the Kasuga Taisha Shrine on the Kii Peninsula, located in the center of Japan. Here, we used short sequence repeats (SSR) and mitochondrial DNA (mtDNA) to investigate the genetic diversity, population structure, and demography of Japanese sika deer inhabiting the Kii Peninsula, Japan, and discuss possible anthropogenic influences. Using SSR, three distinct genetic groups were distinguished on the Kii Peninsula: an Eastern genetic group, a Western genetic group, and an isolated genetic group with individuals in the religious sanctuary of Kasuga Taisha Shrine in Nara city. The isolated genetic sanctuary group had only the mtDNA haplotype S4. The SSR genotype data suggested a newer divergence time of the genetic groups of the religious sanctuary than would have occurred as a result of Late Quaternary climate change. This time scale coincided with the establishment of the sanctuary with Kasuga Taisha Shrine. Thus, the religious protection conserved genetic variation over a thousand years.
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Affiliation(s)
- Toshihito Takagi
- Fukushima University, Graduate School of Symbiotic Systems Science and Technology , Fukushima 960-1296 , Japan
| | - Ryoko Murakami
- Yamagata University, Faculty of Medicine , Yamagata 990-9585 , Japan
| | - Ayako Takano
- Nara University of Education, Center for Natural Environment Education , Nara 630-8528 , Japan
| | - Harumi Torii
- Nara University of Education, Center for Natural Environment Education , Nara 630-8528 , Japan
| | - Shingo Kaneko
- Fukushima University, Faculty of Symbiotic Systems Science , Fukushima 960-1296 , Japan
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Ohsaki H, Miyamoto R, Sembongi Y, Tajima M, Sakamoto Y, Okuda K, Yamawo A. Plant–plant interaction by Aster leiophyllus affects herbivory by Sika deer, Cervus nippon. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2022; 109:54. [DOI: 10.1007/s00114-022-01827-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
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Not all is black and white: phylogeography and population genetics of the endemic blackbuck (Antilope cervicapra). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01479-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Yan J, Wu X, Wang X, Shang Y, Zhang H. Uncovering the Fecal Bacterial Communities of Sympatric Sika Deer (Cervus nippon) and Wapiti (Cervus canadensis). Animals (Basel) 2022; 12:ani12182468. [PMID: 36139327 PMCID: PMC9495088 DOI: 10.3390/ani12182468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary There are many microbial communities in the digestive tracts of animals, and the complex gut microbiome constitutes an intricate ecosystem and intestinal microbial community which has co-adapted with its host. The intestinal microecology plays an important role in the host’s maintenance of normal physical activities, such as substance metabolism, energy transmission, signal transduction, and the immune system. This study used high-throughput sequencing technology to sequence the fecal microbiota of sika deer (Cervus nippon) and wapiti (Cervus canadensis) in order to explore the composition of, and the similarity between, the fecal microbiota structures of sika deer and wapiti in the similar living environment. The species composition, relative abundance of fecal microbiota, alpha diversity, and differences in beta diversity were analyzed. The maintenance of the composition of the gut microbiota and a balanced intestinal environment through the diet plays a key role in maintaining the host’s health. The results demonstrate that the fecal microbiota of sika deer and wapiti share a similar fecal microbiota structure, but there was some evidence showing that the gut microbiota of these two animals exhibit a clear divergence at the species level. Abstract Microbial symbiotic associations may be beneficial, neutral, or harmful to the host. Symbionts exploit the host space and nutrition or use hosts as carriers to spread to other environments. In order to investigate the fecal bacterial communities of wild sika deer (Cervus nippon) and wapiti (Cervus canadensis), this study aimed to sequence and explore the composition of, and similarity between, the fecal microbiota of sika deer and wapiti using high-throughput sequencing. The composition and relative abundance of fecal microbiota, alpha diversity, and differences in beta diversity between the two species were analyzed. We found that no pathogenic bacteria were present in large quantities in the hosts. The dominant bacterial phyla found in the two deer species were similar and included Firmicutes, Bacteroidetes, Proteobacteria, and Spirochaetes. Moreover, the deer also shared similar dominant genera, including the Rikenellaceae RC9 gut group, Ruminococcaceae_UCG-010, Ruminococcaceae_UCG-005, and Bacteroides. These results demonstrate that the sika deer and wapiti share a similar fecal microbiotal structure, probably due to their common diet and living environment, but there was some evidence of a difference at the species level. These analyses provide new insights into the health status of deer populations outside protected environments and offer a scientific framework for monitoring the health conditions of sika deer and wapiti.
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Takagi T, Tsuda Y, Torii H, Tamate HB, Kaneko S, Nagata J. Development of paternally‐inherited Y chromosome simple sequence repeats of sika deer and their application in genetic structure, artificial introduction, and interspecific hybridization analyses. POPUL ECOL 2022. [DOI: 10.1002/1438-390x.12109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshihito Takagi
- Graduate School of Symbiotic Systems Science and Technology Fukushima University Kanayagawa Fukushima Japan
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center (MSC) University of Tsukuba Ueda Nagano Japan
| | - Harumi Torii
- Center for Natural Environment Education Nara University of Education Takahata‐cho Nara Japan
| | | | - Shingo Kaneko
- Faculty of Symbiotic Systems Science Fukushima University Kanayagawa Fukushima Japan
| | - Junco Nagata
- Forestry and Forest Products Research Institute (FFPRI) Tsukuba Ibaraki Japan
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Chew PC, Christianus A, Zudaidy JM, Ina-Salwany MY, Chong CM, Tan SG. Microsatellite Characterization of Malaysian Mahseer ( Tor spp.) for Improvement of Broodstock Management and Utilization. Animals (Basel) 2021; 11:ani11092633. [PMID: 34573599 PMCID: PMC8471032 DOI: 10.3390/ani11092633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, a mixture of Tor tambra and T. tambroides with unknown genetic background were collected from 11 localities in Malaysia for broodstock development and sperm cryo-banking. This study aims to assess the microsatellite (simple sequence repeat, SSR) variation, genetic diversity, genetic differentiation, level of gene flow, population structure, genetic relatedness and their demographic aspects among these Tor populations, in addition to establishing their SSR profile by employing 22 SSR markers via fragment analysis. Total genomic DNA was extracted from 181 samples (91 cryopreserved milt samples and 90 scale samples of live broodfish). Results showed the Tor spp. collection retained their genetic variation but exhibited excessive homozygosity among individuals within population. Moderate genetic differentiation was shown among the populations, with highly significant (p < 0.001) fixation indices (FST, FIS and FIT). A low gene flow over all loci (Nm 1.548) indicates little genetic variation transfer between populations. The genetic structures of all the populations were successfully resolved into four main clusters by an unweighted pair group method with arithmetic mean (UPGMA) dendrogram generated based on Nei's genetic distances. The population structures based on principal coordinates analysis (PCoA) and the Bayesian model also suggested four distinct clusters following geographical regions and eight closely related populations. This study provided a useful baseline reference for better genetic management and utilization of the Tor spp. stocks in their breeding and conservation programmes.
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Affiliation(s)
- Poh Chiang Chew
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Freshwater Fisheries Research Division, Fisheries Research Institute Glami Lemi, Jelebu 71650, Malaysia;
| | - Annie Christianus
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
- Correspondence: ; Tel.: +60-3-8947-4884
| | - Jaapar M. Zudaidy
- Freshwater Fisheries Research Division, Fisheries Research Institute Glami Lemi, Jelebu 71650, Malaysia;
| | - Md Yasin Ina-Salwany
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Chou Min Chong
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia; (P.C.C.); (M.Y.I.-S.); (C.M.C.)
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Soon Guan Tan
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
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Nagata J, Yasuda M, Yamashiro A. Genetic Analysis of a Newly Established Deer Population Expanding in the Sasebo Area in Nagasaki Prefecture, Japan Reveals No Evidence of Genetic Disturbance by Formosan Sika Deer. MAMMAL STUDY 2021. [DOI: 10.3106/ms2020-0084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Junco Nagata
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Masatoshi Yasuda
- Kyushu Research Center, Forestry and Forest Products Research Institute, 4-11-16 Kurokami, Chuo-ku, Kumamoto, Kumamoto 860-0862, Japan
| | - Asuka Yamashiro
- Graduate School of Technology, Industrial and Social Science, Tokushima University, 2-1 Minami-josanjima, Tokushima 770-8513, Japan
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Terada C, Yahara T, Kuroiwa A, Saitoh T. Spatial Genetic Structure of the Sika Deer (Cervus nippon) Population on Yakushima: Significant Genetic Differentiation on a Small Island. MAMMAL STUDY 2021. [DOI: 10.3106/ms2020-0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Chisato Terada
- Field Science Center, Hokkaido University, Hirai 559, Kozagawa, Wakayama 649-4563, Japan
| | - Tetsukazu Yahara
- Department of Biology, Faculty of Science, West 1-C-915, Kyushu University, Moto-oka 744, Fukuoka 819-0395, Japan
| | - Arika Kuroiwa
- Graduate School of Systems Life Sciences, West 1-C-804, Kyushu University, Moto-oka 744, Fukuoka 819-0395, Japan
| | - Takashi Saitoh
- Field Science Center, Hokkaido University, North 11, West 10, Sapporo 060-0811, Japan
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Phylogeography of sika deer (Cervus nippon) inferred from mitochondrial cytochrome-b gene and microsatellite DNA. Gene 2020; 772:145375. [PMID: 33359125 DOI: 10.1016/j.gene.2020.145375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/15/2020] [Indexed: 11/24/2022]
Abstract
The genetic diversity and phylogenetic relationships of sika deer of different subspecies are uncertain. In order to explore the phylogenetic relationship of different sika deer subspecies, this study used a wider sample collection to analyze mitochondrial sequences and nuclear microsatellites of sika deer. The full lengths of cytochrome-b gene of 134 sika deer were sequenced, and 16 haplotypes were obtained. Based on phylogenetic and haplotype networks analysis, the sika deer was not clustered according to subspecies but was divided into four lineages. Lineage I includes individuals from C.n.kopschi, C.n.sichuanicus, and C.n.hortulorum subspecies; Lineage II includes individuals from C.n.hortulorum subspecies; Lineage III includes individuals from C.n.centralis, C.n.yakushime, C.n.mageshimae, and C.n.keramae subspecies, namely southern Japanese population; Lineage IV includes individuals from C.n.centralis and C.n.yesoensis subspecies, namely northern Japanese population. The microsatellite analysis showed that the sika deer in China and Japan originated independently. The three subspecies of China have significant genetic differentiation, while the three subspecies of Japan have no significant differentiation. This study provides reference for the research of genetic diversity and phylogenetic relationship of sika deer, and also provides scientific data for the evaluation, protection, and utilization of sika deer resources.
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Fuller J, Ferchaud A, Laporte M, Le Luyer J, Davis TB, Côté SD, Bernatchez L. Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white‐tailed deer (
Odocoileus virginianus
). Mol Ecol 2019; 29:86-104. [DOI: 10.1111/mec.15317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Jérémie Fuller
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Jérémy Le Luyer
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | | | - Steeve D. Côté
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
| | - Louis Bernatchez
- Département de Biologie Université Laval Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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Kalb DM, Delaney DA, DeYoung RW, Bowman JL. Genetic diversity and demographic history of introduced sika deer on the Delmarva Peninsula. Ecol Evol 2019; 9:11504-11517. [PMID: 31641489 PMCID: PMC6802040 DOI: 10.1002/ece3.5655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/01/2019] [Accepted: 08/26/2019] [Indexed: 01/13/2023] Open
Abstract
The introduction of non-native species can have long-term effects on native plant and animal communities. Introduced populations are occasionally not well understood and offer opportunities to evaluate changes in genetic structure through time and major population changes such as bottleneck and or founder events. Invasive species can often evolve rapidly in new and novel environments, which could be essential to their long-term success. Sika deer are native to East Asia, and their introduction and establishment to the Delmarva Peninsula, USA, is poorly documented, but probably involved ≥1 founder and/or bottleneck events. We quantified neutral genetic diversity in the introduced population and compared genetic differentiation and diversity to the presumed source population from Yakushima Island, Japan, and a captive population of sika deer in Harrington, Delaware, USA. Based on the data from 10 microsatellite DNA loci, we observed reduced genetic variation attributable to founder events, support for historic hybridization events, and evidence that the population did originate from Yakushima Island stocks. Estimates of population structure through Bayesian clustering and demographic history derived from approximate Bayesian computation (ABC), were consistent with the hypothesized founder history of the introduced population in both timing and effective population size (approximately five effective breeding individuals, an estimated 36 generations ago). Our ABC results further supported a single introduction into the wild happening before sika deer spread throughout the Delmarva. We conclude that free-ranging sika deer on Delmarva are descended from ca. five individuals introduced about 100 years ago from captive stocks of deer maintained in the United Kingdom. Free-ranging sika deer on Delmarva have lost neutral diversity due to founder and bottleneck events, yet populations have expanded in recent decades and show no evidence of abnormalities associated with inbreeding. We suggest management practices including increasing harvest areas and specifically managing sika deer outside of Maryland.
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Affiliation(s)
- David M. Kalb
- Virginia Department of Game and Inland FisheriesMarionVAUSA
| | - Deborah A. Delaney
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research InstituteTexas A&M University‐KingsvilleKingsvilleTXUSA
| | - Jacob L. Bowman
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDEUSA
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Iwahori A, Kitamura JI, Kawamura K. Genetic Characteristics of the Japanese Serow Capricornis crispus in the Kii Mountain Range, Central Japan. Zoolog Sci 2019; 36:306-315. [PMID: 34664901 DOI: 10.2108/zs180187] [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: 11/25/2018] [Accepted: 02/28/2019] [Indexed: 11/17/2022]
Abstract
The Japanese serow, Capricornis crispus, is an indigenous bovid species exclusively inhabiting mountain regions in the main Japanese islands, excepting Hokkaido. It had decreased in abundance to its lowest level due to overhunting and deforestation, with its distribution severely fragmented from the middle of the 20th century, many populations of C. crispus currently facing the risk of extinction. The Kii Mountain Range (KM) on Honshu is one such location that has seen a drastic population decline of C. crispus. In this study, we examined genetic characteristics of C. crispus in KM and neighboring regions of the Chubu district, using mtDNA and microsatellite markers, in order to devise strategies for its conservation. Results for mtDNA were characterized by low nucleotide diversity with five endemic and two dominant haplotypes shared by individuals in neighboring regions. A Bayesian skyline plot indicated a gradual increase after the last glacial maximum. For microsatellites, the genetic diversity of C. crispus in KM was comparable to Shizuoka and higher than Shikoku. Recent genetic bottlenecks were strongly suggested in C. crispus in KM. Bayesian clustering showed a genetic cline between KM and neighboring regions, where multivariate analysis suggested three local populations. A Mantel test indicated male-biased dispersal. These results indicate that C. crispus in KM and neighboring regions constitute multiple local populations, connected through restricted gene flow. For the conservation of C. crispus, it is important to define small-scale conservation units, among which genetic connectivity should be facilitated to prevent further loss of genetic diversity.
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Affiliation(s)
- Arisa Iwahori
- Faculty of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | | | - Kouichi Kawamura
- Faculty of Bioresources, Mie University, Tsu, Mie 514-8507, Japan,
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Eva SN, Yamazaki Y. Population Structure, Admixture, and Migration Patterns of Japanese Sika Deer ( Cervus nippon) Inhabiting Toyama Prefecture in Japan. Zoolog Sci 2019; 36:128-135. [PMID: 31120647 DOI: 10.2108/zs180114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/25/2018] [Indexed: 11/17/2022]
Abstract
Rapid expansion of sika deer, in both number and distribution, in the Japanese Archipelago has resulted in serious ecological disturbance. In the present study, the population structure and migration patterns of sika deer (Cervus nippon) among Toyama and adjacent Prefectures were investigated using 11 polymorphic microsatellite loci. Deviation from Hardy-Weinberg equilibrium was detected in both total and individual regional sika deer samples from Toyama Prefecture. Results of pairwise FST results, factorial correspondence analysis, and STRUCTURE analysis indicated that sika deer in Toyama are not genetically distinct from those in adjacent Prefectures. Bayesian STRUCTURE results suggested the existence of two distinct clusters. However, multiple lines of genetic structure and high admixture were detected across the populations located in the central region of Toyama Prefecture. Both contemporary and historical migration analyses showed that dispersal into Toyama Prefecture from neighboring prefectures was high, especially migration from the prefecture on the east into Toyama Prefecture, and bidirectional dispersion between Toyama Prefecture and the prefecture to the south. Knowledge of such genetic structures and population dynamics is required for appropriate management and conservation of sika deer populations in the Japanese Archipelago.
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Affiliation(s)
- Saifun Nahaer Eva
- Graduate School of Science and Engineering for Research, University of Toyama, Toyama 930-8555, Japan
| | - Yuji Yamazaki
- Graduate School of Science and Engineering for Research, University of Toyama, Toyama 930-8555, Japan,
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16
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Yamazaki Y. Genetic Population Structure of Sika Deer, Cervus nippon, Derived from Multiple Origins, Around Toyama Prefecture of Japan. Zoolog Sci 2018; 35:215-221. [PMID: 29882493 DOI: 10.2108/zs170187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recently, expansion of the number and distribution of sika deer, Cervus nippon, in the Japanese Archipelago has resulted in the disturbance of indigenous gene pools and ecosystems. There are also concerns that the artificial introduction of sika deer to certain areas may aggravate this situation. In order to contribute to the conservation of ecosystems, I examined the current state of genetic disturbance and dispersal routes in the sika deer populations around Toyama Prefecture, one of the main areas of expanding sika deer distribution. Of 12 haplotypes detected by mitochondrial DNA D-loop sequence analysis, 10 were found to belong to a previously detected sika deer group in northern Japan, although the remaining two haplotypes corresponded to the southern Japanese sika deer group. The latter two haplotypes were detected at especially high frequencies in the southern area of Toyama Prefecture, suggesting that these haplotypes may derive from artificially introduced individuals. Occurrence patterns of indigenous haplotypes around Toyama Prefecture revealed immigration into Toyama Prefecture through different routes, mainly in the east and south-west. The genetic results presented here may have application in predicting future dispersal routes, as well as aid in the establishment of effective measures for management of sika deer.
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Affiliation(s)
- Yuji Yamazaki
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
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Smith SL, Senn HV, Pérez‐Espona S, Wyman MT, Heap E, Pemberton JM. Introgression of exotic Cervus ( nippon and canadensis) into red deer ( Cervus elaphus) populations in Scotland and the English Lake District. Ecol Evol 2018; 8:2122-2134. [PMID: 29468030 PMCID: PMC5817139 DOI: 10.1002/ece3.3767] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 11/04/2017] [Accepted: 11/14/2017] [Indexed: 11/10/2022] Open
Abstract
Since the mid-19th century, multiple introductions of Japanese sika deer (Cervus nippon nippon) and North American wapiti (C. canadensis) have taken place in the British Isles. While wapiti have generally been unsuccessful, sika have been very successful, especially in Scotland where they now overlap at least 40% of the range of native red deer (C. elaphus). Hybridization between these two species and red deer has been demonstrated in captivity and in the wild. Using a panel of 22 microsatellite loci that are highly diagnostic between red deer and sika, and moderately diagnostic between red deer and wapiti, we investigated the extent of introgression between these species in 2,943 deer sampled from around Scotland and from the English Lake District using the Bayesian clustering software STRUCTURE. We also used a diagnostic mitochondrial marker for red deer and sika. Our survey extends previous studies indicating little introgression of wapiti nuclear alleles into red deer, in particular in Northern Scotland, Kintyre, and the Lake District. We found a new area of extensive sika introgression in South Kintyre. In the North Highlands, we show for the first time geographically scattered evidence of past hybridization followed by extensive backcrossing, including one red-like individual with sika introgression, two sika-like individuals with red deer introgression, and six individuals that were apparently pure sika at the nuclear markers assessed but which carried red deer mitochondria. However, there has not been a collapse of assortative mating in this region. Similarly, in the English Lake District red deer, we found only traces of past sika introgression. No sika alleles were detected in the Central Highlands or the Hebridean red deer refugia. We make suggestions for management to prevent further spread of sika alleles into red deer and vice versa.
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Affiliation(s)
- Stephanie L. Smith
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Helen V. Senn
- WildGenes LaboratoryRoyal Zoological Society of ScotlandEdinburghUK
| | | | - Megan T. Wyman
- Mammal Vocal Communication and Cognition ResearchSchool of PsychologyUniversity of SussexFalmerUK
| | - Elizabeth Heap
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
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Galarza JA, Sánchez-Fernández B, Fandos P, Soriguer R. Intensive Management and Natural Genetic Variation in Red Deer (Cervus elaphus). J Hered 2017; 108:496-504. [PMID: 28863451 DOI: 10.1093/jhered/esx052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/31/2017] [Indexed: 11/13/2022] Open
Abstract
The current magnitude of big-game hunting has outpaced the natural growth of populations, making artificial breeding necessary to rapidly boost hunted populations. In this study, we evaluated if the rapid increase of red deer (Cervus elaphus) abundance, caused by the growing popularity of big-game hunting, has impacted the natural genetic diversity of the species. We compared several genetic diversity metrics between 37 fenced populations subject to intensive management and 21 wild free-ranging populations. We also included a historically protected population from a national park as a baseline for comparisons. Contrary to expectations, our results showed no significant differences in genetic diversity between wild and fenced populations. Relatively lower genetic diversity was observed in the protected population, although differences were not significant in most cases. Bottlenecks were detected in both wild and fenced populations, as well as in the protected population. Assignment tests identified individuals that did not belong to their population of origin, indicating anthropogenic movement. We discuss the most likely processes, which could have led to the observed high levels of genetic variability and lack of differentiation between wild and fenced populations and suggest cautionary points for future conservation. We illustrate our comparative approach in red deer. However, our results and interpretations can be largely applicable to most ungulates subject to big-game hunting as most of them share a common exploitation-recovery history as well as many ecological traits.
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Affiliation(s)
- Juan A Galarza
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, 40500 Jyväskylä, Finland; Estación Biológica Doñana (CSIC), Seville, Spain; and Agencia de Medio Ambiente y Agua, Seville, Spain
| | - Beatriz Sánchez-Fernández
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, 40500 Jyväskylä, Finland; Estación Biológica Doñana (CSIC), Seville, Spain; and Agencia de Medio Ambiente y Agua, Seville, Spain
| | - Paulino Fandos
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, 40500 Jyväskylä, Finland; Estación Biológica Doñana (CSIC), Seville, Spain; and Agencia de Medio Ambiente y Agua, Seville, Spain
| | - Ramón Soriguer
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9, 40500 Jyväskylä, Finland; Estación Biológica Doñana (CSIC), Seville, Spain; and Agencia de Medio Ambiente y Agua, Seville, Spain
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Guan Y, Yang H, Han S, Feng L, Wang T, Ge J. Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing. AMB Express 2017; 7:212. [PMID: 29170893 PMCID: PMC5700909 DOI: 10.1186/s13568-017-0517-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
The gut microbiota is characterized as a complex ecosystem that has effects on health and diseases of host with the interactions of many other factors together. Sika deer is the national level for the protection of wild animals in China. The available sequencing data of gut microbiota from feces of wild sika deer, especially for Cervus nippon hortulorum in Northeast China, are limited. Here, we characterized the gastrointestinal bacterial communities of wild (7 samples) and captive (12 samples) sika deer from feces, and compared their gut microbiota by analyzing the V4 region of 16S rRNA gene using high-throughput sequencing technology on the Illumina Hiseq platform [corrected]. Firmicutes (77.624%), Bacteroidetes (18.288%) and Tenericutes (1.342%) were the most predominant phyla in wild sika deer. While in captive sika deer, Firmicutes (50.710%) was the dominant phylum, followed by Bacteroidetes (31.996%) and Proteobacteria (4.806%). A total of 9 major phyla, 22 families and 30 genera among gastrointestinal bacterial communities showed significant differences between wild and captive sika deer. The specific function and mechanism of Tenericutes in wild sika deer need further study. Our results indicated that captive sika deer in farm had higher fecal bacterial diversity than the wild. Abundance and quantity of diet source for sika deer played crucial role in shaping the composition and structure of gut microbiota.
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Li J, Li YK, Liu WH. Autumn bed site selection by sika deer (Cervus nippon) in the Taohongling National Nature Reserve, China. RUSS J ECOL+ 2017. [DOI: 10.1134/s1067413617040105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Krojerová-Prokešová J, Barančeková M, Kawata Y, Oshida T, Igota H, Koubek P. Genetic differentiation between introduced Central European sika and source populations in Japan: effects of isolation and demographic events. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1424-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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A complete history of the establishment of Japanese sika deer on the Delmarva Peninsula: 100 years post-introduction. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1387-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Suzuki Y, Tomozawa M, Koizumi Y, Tsuchiya K, Suzuki H. Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary ice age events with inferred population expansions and dispersals in Japanese Apodemus. BMC Evol Biol 2015; 15:187. [PMID: 26373638 PMCID: PMC4571126 DOI: 10.1186/s12862-015-0463-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 08/21/2015] [Indexed: 11/22/2022] Open
Abstract
Background Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16 % and 22–32 %, respectively, for A. argenteus, and 12–17 % and 17–24 %, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1 %/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17 %/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1 %/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
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Affiliation(s)
- Yutaro Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | | | - Yuki Koizumi
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Kimiyuki Tsuchiya
- Laboratory of Bioresources, Ooyo Seibutsu Co. Ltd., Tokyo, 107-0062, Japan.
| | - Hitoshi Suzuki
- Laboratory of Ecology and Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan.
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Freeman MS, Beatty GE, Dick JTA, Reid N, Provan J. The paradox of invasion:
R
eeves' muntjac deer invade the
B
ritish
I
sles from a limited number of founding females. J Zool (1987) 2015. [DOI: 10.1111/jzo.12283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- M. S. Freeman
- School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
- Quercus, School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
| | - G. E. Beatty
- School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
- Quercus, School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
- Institute for Global Food Security Queen's University Belfast Belfast UK
| | - J. T. A. Dick
- School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
- Quercus, School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
- Institute for Global Food Security Queen's University Belfast Belfast UK
| | - N. Reid
- School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
- Quercus, School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
- Institute for Global Food Security Queen's University Belfast Belfast UK
| | - J. Provan
- School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
- Quercus, School of Biological Sciences Queen's University Belfast Belfast BT9 7BL UK
- Institute for Global Food Security Queen's University Belfast Belfast UK
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Liu YH, Liu XX, Zhang MH. The complete mitochondrial genome of Sika deer Cervus nippon hortulorum (Artiodactyla: Cervidae) and phylogenetic studies. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2967-8. [PMID: 26258510 DOI: 10.3109/19401736.2015.1060463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Sika deer (Cervus nippon Temminck 1836) are classified in the order Artiodactyla, family Cervidae, subfamily Cervinae. At present, the phylogenetic studies of C. nippon are problematic. In this study, we first determined and described the complete mitochondrial sequence of the wild C. nippon hortulorum. The complete mitogenome sequence is 16 566 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR) and a light-strand replication origin (OL). The overall base composition was 33.4% A, 28.6% T, 24.5% C, 13.5% G, with a 62.0% AT bias. The 13 protein-coding genes encode 3782 amino acids in total. To further validate the new determined sequences and phylogeny of Sika deer, phylogenetic trees involving 15 most closely related species available in GenBank database were constructed. These results are expected to provide useful molecular data for deer species identification and further phylogenetic studies of Artiodactyla.
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Affiliation(s)
- Yan-Hua Liu
- a College of Wildlife Resource, Northeast Forestry University , Harbin , China
| | - Xin-Xin Liu
- a College of Wildlife Resource, Northeast Forestry University , Harbin , China
| | - Ming-Hai Zhang
- a College of Wildlife Resource, Northeast Forestry University , Harbin , China
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Min JJ, Ye RH, Zhang GF, Zheng RQ. Microsatellite analysis of genetic diversity and population structure of freshwater mussel (Lamprotula leai). DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2015; 36:34-40. [PMID: 25730459 DOI: 10.13918/j.issn.2095-8137.2015.1.36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Lamprotula leai is one of the most commercially important freshwater pearl mussels in China, but there is limited data on its genetic diversity and population structure. In the present study, 119 individuals from four major geographical populations were investigated using 15 microsatellite loci identified via cross-species amplification. A total of 114 alleles were detected, with an average of 7.6 alleles per locus (range: 2 to 21). Among the four stocks, those from Hung-tse Lake and Poyang Lake had the lowest (0.412) and highest (0.455) observed heterozygosity respectively. The polymorphism information content (PIC) ranged from 0.374 to 0.927 (mean: 0.907). AMOVA showed that 12.56% and 44.68% genetic variances were among populations and within individuals, respectively. Pairwise Fst ranged from 0.073 to 0.146, indicating medium genetic differentiation among the populations. In aggregate, our results suggest that inbreeding is a crucial factor accounting for deviations from Hardy-Weinberg equilibrium at 12 loci. Moreover, the genetic distance among four stocks ranged from 0.192 to 0.890. Poyang Lake and Hung-tse Lake were clustered together, joined with Dongting Lake and Anqing Lake. Given that specimens from Hung-tse Lake showed the highest average allele richness, expected heterozygosity and PIC, this location may be the source of the highest quality germplasm resources and the stock from this area may be the best for future breeding efforts.
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Affiliation(s)
- Jin-Jin Min
- Institute of Ecology, Zhejiang Normal University, Jinhua Zhejiang 321004, China
| | - Rong-Hui Ye
- Jinhua Polytechnic, Jinhua Zhejiang 321004, China.
| | | | - Rong-Quan Zheng
- Institute of Ecology, Zhejiang Normal University, Jinhua Zhejiang 321004, China
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Hoffmann GS, Johannesen J, Griebeler EM. Species cross-amplification, identification and genetic variation of 17 species of deer (Cervidae) with microsatellite and mitochondrial DNA from antlers. Mol Biol Rep 2014; 42:1059-67. [PMID: 25424838 DOI: 10.1007/s11033-014-3845-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 11/22/2014] [Indexed: 11/26/2022]
Abstract
Strong anthropogenic impact has caused 28 of the currently recognized 55 species of deer (Cervidae) to be listed on the IUCN Red List. Particular threats to vulnerable species include habitat deterioration and hybridization with alien, introduced species. The scarcity of many species has severely hampered genetic analyses of their populations, including the detection of loci for cross-species amplification. Because deer antlers are shed and re-grown annually, antlers offer the possibility for non-invasive genetic sampling of large individual numbers, and may provide material for reference genotyping from historical samples stored in zoos, museums and trophy collections of rare and extinct species/populations. In this paper, we report cross-species amplification of 19 nuclear microsatellite loci and the amplification of 16S mtDNA for barcoding from nearly a third of all deer species worldwide based on high quality DNA extracted from antler bone up to 40 years old. Phylogenetic analysis based on mtDNA of seventeen species and five subspecies corroborate previously published phylogenetic data, thus confirming the specific resolution of the DNA extraction methodology.
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Affiliation(s)
- G Sebastian Hoffmann
- Department of Ecology, Institute of Zoology, Johannes Gutenberg-University of Mainz, 55099, Mainz, Germany,
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Reconstructing the colonization history of lost wolf lineages by the analysis of the mitochondrial genome. Mol Phylogenet Evol 2014; 80:105-12. [PMID: 25132126 DOI: 10.1016/j.ympev.2014.08.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 07/29/2014] [Accepted: 08/03/2014] [Indexed: 11/27/2022]
Abstract
The grey wolves (Canis lupus) originally inhabited major parts of the Northern hemisphere, but many local populations became extinct. Two lineages of wolves in Japan, namely, Japanese or Honshu (C. l. hodophilax) and Ezo or Hokkaido (C. l. hattai) wolves, rapidly went extinct between 100 and 120years ago. Here we analyse the complete mitochondrial genome sequences from ancient specimens and reconstruct the colonization history of the two extinct subspecies. We show a unique status of Japanese wolves in wolf phylogeny, suggesting their long time separation from other grey wolf populations. Japanese wolves appeared to have colonized the Japanese archipelago in the Late Pleistocene (ca. 25,000-125,000years ago). By contrast, Ezo wolves, which are clearly separated from Japanese wolves in phylogeny, are likely to have arrived at Japan relatively recently (<14,000years ago). Interestingly, their colonization history to Japan tallies well with the dynamics of wolf populations in Europe and America during the last several millennia. Our analyses suggest that at least several thousands of wolves once inhabited in the Japanese archipelago. Our analyses also show that an enigmatic clade of domestic dogs is likely to have originated from rare admixture events between male dogs and female Japanese wolves.
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Castellanos-Morales G, Gasca-Pineda J, Ceballos G, Ortega J. Genetic variation in a peripheral and declining population of black-tailed prairie dogs (Cynomys ludovicianus) from Mexico. J Mammal 2014. [DOI: 10.1644/12-mamm-a-099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Yamashiro A, Yamashiro T, Mori K, Kamada M. Indirect estimation of Recent Sika Deer (Cervus nippon) Migration in Tsurugi Quasi-National Park, Shikoku, Japan. MAMMAL STUDY 2014. [DOI: 10.3106/041.039.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Kubo MO, Yamada E. The inter-relationship between dietary and environmental properties and tooth wear: comparisons of mesowear, molar wear rate, and hypsodonty index of extant Sika deer populations. PLoS One 2014; 9:e90745. [PMID: 24603896 PMCID: PMC3946258 DOI: 10.1371/journal.pone.0090745] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/04/2014] [Indexed: 11/18/2022] Open
Abstract
In reference to the evolutionary trend of increasing cheek tooth height in herbivorous ungulates, the causes of dental abrasion have long been debated. Interspecific comparisons of extant ungulates have revealed that both phytoliths in grass and external abrasive matter may play important roles. Using analysis of extant sika deer living in various environments and showing continuous latitudinal variation in food habits from northern grazing to southern browsing, we quantitatively evaluated the influence of dietary and environmental properties on three dental variables: mesowear score (MS), molar wear rate, and M3 hypsodonty index. We used 547 skulls and 740 mandibles from 16 populations of sika deer to obtain the dental measurements. We found that only graminoid proportion in diet correlated with MS and the molar wear rate, implying that phytoliths in grass abrade dental tissues. In contrast, annual precipitation in habitat was not correlated with any of the dental variables. We also found a significant correlation between the molar wear rate (selective pressure for high-crowned molars) and the M3 hypsodonty index of extant sika deer, implying an evolutionary increment in molar height corresponding to the molar wear rate. Our intraspecific comparative analyses provide further support for use of mesowear analysis as a paleodiet estimation method; it not only reveals staple food types (graminoids or dicots) but also implies regional or seasonal variation in the diet of the species.
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Affiliation(s)
- Mugino Ozaki Kubo
- The University Museum, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Eisuke Yamada
- Department of Earth and Environmental Science, Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
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Mukesh, Sharma LK, Kumar VP, Charoo SA, Mohan N, Goyal SP, Sathyakumar S. Loss of genetic diversity and inbreeding in Kashmir red deer (Cervus elaphus hanglu) of Dachigam National Park, Jammu & Kashmir, India. BMC Res Notes 2013; 6:326. [PMID: 24060051 PMCID: PMC3751512 DOI: 10.1186/1756-0500-6-326] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 08/13/2013] [Indexed: 11/10/2022] Open
Abstract
Background Hangul (Cervus elaphus hanglu), the eastern most subspecies of red deer, is now confined only to the mountains in the Kashmir region of Jammu & Kashmir State of India. It is of great conservation significance as this is the last and only hope for Asiatic survivor of the red deer species in India. Wild population of free ranging hangul deer inhabiting in and around Dachigam National Park was genetically assessed in order to account for constitutive genetic attributes of hangul population using microsatellite markers. Results In a pool of 36 multi-locus genotypes, 30 unique individuals were identified based on six microsatellite loci. The estimated cumulative probability of identity assuming all individuals were siblings (PID sibs) was 0.009 (9 in 1000). Altogether, 49 different alleles were observed with mean (± s.e.) allelic number of 8.17 ± 1.05, ranging from 5 to 11 per locus. The observed heterozygosity ranged between 0.08 and 0.83, with mean 0.40 ± 0.11 and the inbreeding coefficient ranged between −0.04 and 0.87 with mean 0.38 ± 0.15. Majority of loci (5/6) were found to be informative (PIC value > 0.5). All loci deviated from Hardy-Weinberg equilibrium except Ca-38 (P > 0.05) and none of the pairs of loci showed significant linkage disequilibrium except the single pair of Ca-30 and Ca-43 (P < 0.05). Conclusions The preliminary findings revealed that hangul population is significantly inbred and exhibited a low genetic diversity in comparison to other deer populations of the world. We suggest prioritizing the potential individuals retaining high heterozygosity for ex situ conservation and genetic monitoring of the hangul population should be initiated covering the entire distribution range to ensure the long term survival of hangul. We speculate further ignoring genetics attributes may lead to a detrimental effect which can negatively influence the reproductive fitness and survivorship of the hangul population in the wild.
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Kubo MO, Minami M, Higuchi N, Ohnishi N, Okada A, Kaji K, Ohba T, Hosoi E, Koizumi T, Takatsuki S. Female sika deer have evolved larger incisors than males under relaxed selection against rapid tooth wear. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mugino O. Kubo
- The University Museum; The University of Tokyo; 7-3-1 Hongo; Bunkyo-ku; Tokyo; 113-0033; Japan
| | - Masato Minami
- Laboratory of Wildlife Ecology; Azabu University; 1-17-71 Fuchinobe; Sagamihara; Kanagawa; 229-8501; Japan
| | - Naoko Higuchi
- NPO Earthworm for Bio-Diversity; 1549-3-1 Oiwake; Karuizawa; Nagano; 389-0115; Japan
| | - Nobumasa Ohnishi
- Eco-Planning Research Co. Ltd; 2-28-5 Sakae-cho; Higashimarayama; Tokyo; 189-0013; Japan
| | - Ayumi Okada
- Department of Environmental Bioscience; School of Veterinary Medicine; Kitasato University; 23-35-1 Higashi; Towada; Aomori; 034-8628; Japan
| | - Koichi Kaji
- Department of Ecoregion Science; Laboratory of Wildlife Conservation; Tokyo University of Agriculture and Technology; 3-5-8 Saiwaicho; Fuchu; Tokyo; 183-8509; Japan
| | - Takahiro Ohba
- Forestry and Forest Products Research Center; Shizuoka Research Institute of Agriculture and Forestry; 2542-8 Negata, Hamakita-ku; Hamamatsu; Shizuoka; 434-0016; Japan
| | - Eiji Hosoi
- Department of Biological and Environmental Sciences; Faculty of Agriculture; Yamaguchi University; 1677-1 Yoshida; Yamaguchi; 753-8515; Japan
| | - Toru Koizumi
- Wildlife Ecology Laboratory; Forestry and Forest Products Research Institute; 1 Matsunosato; Tsukuba; Ibaraki; 305-8687; Japan
| | - Seiki Takatsuki
- Laboratory of Wildlife Ecology; Azabu University; 1-17-71 Fuchinobe; Sagamihara; Kanagawa; 229-8501; Japan
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Sato S, Kabeya H, Yamazaki M, Takeno S, Suzuki K, Kobayashi S, Souma K, Masuko T, Chomel BB, Maruyama S. Prevalence and genetic diversity of Bartonella species in sika deer (Cervus nippon) in Japan. Comp Immunol Microbiol Infect Dis 2012; 35:575-81. [DOI: 10.1016/j.cimid.2012.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 06/25/2012] [Accepted: 07/03/2012] [Indexed: 10/28/2022]
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Takiguchi H, Tanaka K, Ono K, Hoshi A, Minami M, Yamauchi K, Takatsuki S. Genetic variation and population structure of the Japanese sika deer (Cervus nippon) in the Tohoku District based on mitochondrial D-loop sequences. Zoolog Sci 2012; 29:433-6. [PMID: 22775251 DOI: 10.2108/zsj.29.433] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The sika deer (Cervus nippon) once inhabited the entire Tohoku District, the northeastern part of the main island of Japan. Currently, they are isolated as three discontinuous populations on Mt. Goyo, the Oshika Peninsula, and Kinkazan Island. To assess the genetic diversity and relationships among the sika deer populations in the Tohoku District, we analyzed the mitochondrial DNA D-loop sequences from 177 individuals. We detected a total of five haplotypes. Three haplotypes were present in the population from Mt. Goyo at a haplotype diversity of 0.235 ± 0.061, two haplotypes in the population from the Oshika Peninsula at 0.171 ± 0.064, and only one haplotype was detected in the population from the Kinkazan Island. A significant genetic differentiation was observed among all population pairs. Collectively, our data supports the observed population bottlenecks in the past. Four of the five haplotypes were specific to one of the three populations, whereas only one haplotype was shared between the Mt. Goyo and the Oshika Peninsula populations. This common haplotype may indicate a common ancestral population in the Tohoku District. Conversely, the D-loop haplotypes were completely different among the Kinkazan Island and Oshika Peninsula populations. The lack of a shared haplotype indicates that female gene flow between the two populations is very limited and that the 0.6 km strait acts as a strong barrier.
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36
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Shefferson RP, Roach DA. The triple helix of
Plantago lanceolata
: Genetics and the environment interact to determine population dynamics. Ecology 2012; 93:793-802. [DOI: 10.1890/11-0742.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
| | - Deborah A. Roach
- University of Virginia, Department of Biology, Charlottesville, Virginia 22904 USA
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37
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Kojo N, Higuchi N, Minami M, Ohnishi N, Okada A, Takatsuki S, Tamate HB. Correlation between Genetic Diversity and Neonatal Weight of Sika Deer (Cervus nippon) Fawns. MAMMAL STUDY 2012. [DOI: 10.3106/041.037.0102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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38
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Kubo MO, Kaji K, Ohba T, Hosoi E, Koizumi T, Takatsuki S. Compensatory response of molar eruption for environment-mediated tooth wear in sika deer. J Mammal 2011. [DOI: 10.1644/10-mamm-a-338.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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39
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Chelomina GN, Korablev VP, Pavlenko MV. Genetic diversity and phylogenetic relationships of the Manchurian zokor Myospalax psilurus (Rodentia, Muridae) according to RAPD-PCR analysis. BIOL BULL+ 2011. [DOI: 10.1134/s1062359011030034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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ZACHOS FE, HARTL GB. Phylogeography, population genetics and conservation of the European red deer Cervus elaphus. Mamm Rev 2011. [DOI: 10.1111/j.1365-2907.2010.00177.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Halkett F, Coste D, Platero GGR, Zapater MF, Abadie C, Carlier J. Genetic discontinuities and disequilibria in recently established populations of the plant pathogenic fungus Mycosphaerella fijiensis. Mol Ecol 2010; 19:3909-23. [PMID: 20723067 DOI: 10.1111/j.1365-294x.2010.04774.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dispersal processes of fungal plant pathogens can be inferred from analysis of spatial genetic structures resulting from recent range expansion. The relative importance of long-distance dispersal (LDD) events vs. gradual dispersal in shaping population structures depends on the geographical scale considered. The fungus Mycosphaerella fijiensis, pathogenic on banana, is an example of a recent worldwide epidemic. Founder effects in this species were detected at both global and continental scale, suggesting stochastic spread of the disease through LDD events. In this study, we analysed the structure of M. fijiensis populations in two recently (∼1979-1980) colonized areas in Costa Rica and Cameroon. Isolates collected in 10-15 sites distributed along a ∼250- to 300- km-long transect in each country were analysed using 19 microsatellite markers. We detected low-to-moderate genetic differentiation among populations in both countries and isolation by distance in Cameroon. Combined with historical data, these observations suggest continuous range expansion at the scale of banana-production area through gradual dispersal of spores. However, both countries displayed specific additional signatures of colonization: a sharp discontinuity in gene frequencies was observed along the Cameroon transect, while the Costa Rican populations seemed not yet to have reached genetic equilibrium. These differences in the genetic characteristics of M. fijiensis populations in two recently colonized areas are discussed in the light of historical data on disease spread and ecological data on landscape features.
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Affiliation(s)
- F Halkett
- CIRAD, UMR BGPI, Campus international de Baillarguet, Montpellier Cedex, France
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42
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McCraney WT, Goldsmith G, Jacobs DK, Kinziger AP. Rampant drift in artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi). Mol Ecol 2010; 19:3315-27. [PMID: 20666998 DOI: 10.1111/j.1365-294x.2010.04755.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Habitat fragmentation and its genetic consequences are a critically important issue in evaluating the evolutionary penalties of human habitat modification. Here, we examine the genetic structure and diversity in naturally subdivided and artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi), a small fish restricted to discrete coastal lagoons and estuaries in California, USA. We use five naturally fragmented coastal populations from a 300- km spatial scale as a standard to assess migration and drift relative to eight artificially fragmented bay populations from a 30- km spatial scale. Using nine microsatellite loci in 621 individuals, and a 522-base fragment of mitochondrial DNA control region from 103 individuals, we found striking differences in the relative influences of migration and drift on genetic variation at these two scales. Overall, the artificially fragmented populations exhibited a consistent pattern of higher genetic differentiation and significantly lower genetic diversity relative to the naturally fragmented populations. Thus, even in a species characterized by habitat isolation and subdivision, further artificial fragmentation appears to result in substantial population genetic consequences and may not be sustainable.
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Affiliation(s)
- W Tyler McCraney
- Department of Fisheries Biology, Humboldt State University, 1 Harpst Street, Arcata, CA 95521, USA.
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43
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BIEBACH IRIS, KELLER LUKASF. A strong genetic footprint of the re-introduction history of Alpine ibex (Capra ibex ibex). Mol Ecol 2009; 18:5046-58. [DOI: 10.1111/j.1365-294x.2009.04420.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Pérez-Espona S, Pemberton JM, Putman R. Red and sika deer in the British Isles, current management issues and management policy. Mamm Biol 2009. [DOI: 10.1016/j.mambio.2009.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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SENN HELENV, PEMBERTON JOSEPHINEM. Variable extent of hybridization between invasive sika (Cervus nippon) and native red deer (C. elaphus) in a small geographical area. Mol Ecol 2009; 18:862-76. [DOI: 10.1111/j.1365-294x.2008.04051.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Radespiel U, Rakotondravony R, Chikhi L. Natural and anthropogenic determinants of genetic structure in the largest remaining population of the endangered golden-brown mouse lemur,Microcebus ravelobensis. Am J Primatol 2008; 70:860-70. [DOI: 10.1002/ajp.20574] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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47
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JORDAN MA, SNELL HL. Historical fragmentation of islands and genetic drift in populations of Galápagos lava lizards (Microlophus albemarlensis complex). Mol Ecol 2008; 17:1224-37. [DOI: 10.1111/j.1365-294x.2007.03658.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Tomozawa M, Suzuki H. A Trend of Central Versus Peripheral Structuring in Mitochondrial and Nuclear Gene Sequences of the Japanese Wood Mouse, Apodemus speciosus. Zoolog Sci 2008; 25:273-85. [DOI: 10.2108/zsj.25.273] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 12/09/2007] [Indexed: 11/17/2022]
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49
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Dlugosch KM, Parker IM. Founding events in species invasions: genetic variation, adaptive evolution, and the role of multiple introductions. Mol Ecol 2008; 17:431-49. [PMID: 17908213 DOI: 10.1111/j.1365-294x.2007.03538.x] [Citation(s) in RCA: 1014] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Invasive species are predicted to suffer from reductions in genetic diversity during founding events, reducing adaptive potential. Integrating evidence from two literature reviews and two case studies, we address the following questions: How much genetic diversity is lost in invasions? Do multiple introductions ameliorate this loss? Is there evidence for loss of diversity in quantitative traits? Do invaders that have experienced strong bottlenecks show adaptive evolution? How do multiple introductions influence adaptation on a landscape scale? We reviewed studies of 80 species of animals, plants, and fungi that quantified nuclear molecular diversity within introduced and source populations. Overall, there were significant losses of both allelic richness and heterozygosity in introduced populations, and large gains in diversity were rare. Evidence for multiple introductions was associated with increased diversity, and allelic variation appeared to increase over long timescales (~100 years), suggesting a role for gene flow in augmenting diversity over the long-term. We then reviewed the literature on quantitative trait diversity and found that broad-sense variation rarely declines in introductions, but direct comparisons of additive variance were lacking. Our studies of Hypericum canariense invasions illustrate how populations with diminished diversity may still evolve rapidly. Given the prevalence of genetic bottlenecks in successful invading populations and the potential for adaptive evolution in quantitative traits, we suggest that the disadvantages associated with founding events may have been overstated. However, our work on the successful invader Verbascum thapsus illustrates how multiple introductions may take time to commingle, instead persisting as a 'mosaic of maladaptation' where traits are not distributed in a pattern consistent with adaptation. We conclude that management limiting gene flow among introduced populations may reduce adaptive potential but is unlikely to prevent expansion or the evolution of novel invasive behaviour.
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Affiliation(s)
- K M Dlugosch
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA.
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50
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SHIMADA TOMOHIKO, MATSUI MASAFUMI, SUDIN AHMAD, MOHAMED MARYATI. Identity of larval Meristogenys from a single stream in Sabah, Malaysia (Amphibia: Ranidae). Zool J Linn Soc 2007. [DOI: 10.1111/j.1096-3642.2007.00319.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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