201
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Steinbach P, Heddergott M, Weigand H, Weigand AM, Wilwert E, Stubbe M, Helm B, Campbell RE, Stubbe A, Frantz AC. Rare migrants suffice to maintain high genetic diversity in an introduced island population of roe deer (Capreolus capreolus): Evidence from molecular data and simulations. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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202
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Šťastný M, Gasper J, Bauer M. Genetic structure of Apis mellifera carnica in Slovakia based on microsatellite DNA polymorphism. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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203
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Dubois Q, Lebigre C, Schtickzelle N, Turlure C. Sex, size and timing: Sampling design for reliable population genetics analyses using microsatellite data. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Quentin Dubois
- Biodiversity Research Centre, Earth and Life InstituteUniversité catholique de Louvain Louvain‐la‐Neuve Belgium
| | - Christophe Lebigre
- Biodiversity Research Centre, Earth and Life InstituteUniversité catholique de Louvain Louvain‐la‐Neuve Belgium
- IFREMER Centre BretagneUnité Sciences et Techniques Halieutiques Plouzané France
| | - Nicolas Schtickzelle
- Biodiversity Research Centre, Earth and Life InstituteUniversité catholique de Louvain Louvain‐la‐Neuve Belgium
| | - Camille Turlure
- Biodiversity Research Centre, Earth and Life InstituteUniversité catholique de Louvain Louvain‐la‐Neuve Belgium
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204
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Jackson TM, Roegner GC, O'Malley KG. Evidence for interannual variation in genetic structure of Dungeness crab (Cancer magister
) along the California Current System. Mol Ecol 2017; 27:352-368. [DOI: 10.1111/mec.14443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 11/08/2017] [Accepted: 11/14/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Tyler M. Jackson
- Westward Region; Division of Commercial Fisheries; Alaska Department of Fish and Game; Kodiak AK USA
- Coastal Oregon Marine Experiment Station; Department of Fisheries and Wildlife; Hatfield Marine Science Center; Oregon State University; Newport OR USA
| | | | - Kathleen G. O'Malley
- Coastal Oregon Marine Experiment Station; Department of Fisheries and Wildlife; Hatfield Marine Science Center; Oregon State University; Newport OR USA
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205
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Looking back to go forward: genetics informs future management of captive and reintroduced populations of the black-footed rock-wallaby Petrogale lateralis. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1030-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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206
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Kopatz A, Eiken HG, Schregel J, Aspi J, Kojola I, Hagen SB. Genetic substructure and admixture as important factors in linkage disequilibrium-based estimation of effective number of breeders in recovering wildlife populations. Ecol Evol 2017; 7:10721-10732. [PMID: 29299252 PMCID: PMC5743533 DOI: 10.1002/ece3.3577] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 01/18/2023] Open
Abstract
The number of effective breeders (Nb ) and effective population size (Ne ) are population parameters reflective of evolutionary potential, susceptibility to stochasticity, and viability. We have estimated these parameters using the linkage disequilibrium-based approach with LDNE through the latest phase of population recovery of the brown bears (Ursus arctos) in Finland (1993-2010; N = 621). This phase of the recovery was recently documented to be associated with major changes in genetic composition. In particular, differentiation between the northern and the southern genetic cluster declined rapidly within 1.5 generations. Based on this, we have studied effects of the changing genetic structure on Nb and Ne , by comparing estimates for whole Finland with the estimates for the two genetic clusters. We expected a potentially strong relationship between estimate sizes and genetic differentiation, which should disappear as the population recovers and clusters merge. Consistent with this, our estimates for whole Finland were lower than the sum of the estimates of the two genetic clusters and both approaches produced similar estimates in the end. Notably, we also found that admixed genotypes strongly increased the estimates. In all analyses, our estimates for Ne were larger than Nb and likely reflective for brown bears of the larger region of Finland and northwestern Russia. Conclusively, we find that neglecting genetic substructure may lead to a massive underestimation of Nb and Ne . Our results also suggest the need for further empirical analysis focusing on individuals with admixed genotypes and their potential high influence on Nb and Ne .
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Affiliation(s)
| | - Hans Geir Eiken
- NIBIO—Norwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Julia Schregel
- NIBIO—Norwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Jouni Aspi
- Department of BiologyUniversity of OuluOuluFinland
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke)RovaniemiFinland
| | - Snorre B. Hagen
- NIBIO—Norwegian Institute of Bioeconomy ResearchSvanvikNorway
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207
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Hapeman P, Latch EK, Rhodes OE, Swanson B, Kilpatrick CW. Genetic population structure of fishers (Pekania pennanti) in the Great Lakes region: remnants and reintroductions. CAN J ZOOL 2017. [DOI: 10.1139/cjz-2016-0325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Reintroduction programs have been pivotal in augmenting populations of fishers (Pekania pennanti (Erxleben, 1777)) and re-establishing them to their former range in North America. The majority of reintroduction efforts in fishers have been considered demographically successful, but reintroductions can alter genetic population structure and success has rarely been evaluated in fishers from a genetic standpoint. We used microsatellite data (n = 169) to examine genetic population structure of fishers in the Great Lakes region and comment on the success of past reintroductions at two different spatial scales. We found significant genetic population structure among source and reintroduced populations within the Great Lakes region and large-scale genetic structure between fisher populations located in two geographically distant regions (Great Lakes and Northeast) in the eastern United States. Reintroductions associated with the Great Lakes produced results that were largely consistent with other studies of fisher reintroductions in the Northeast. However, our data are the first to support a measurable impact on genetic population structure in Pekania pennanti pennanti (Erxleben, 1777) from a reintroduction using geographically distant source and reintroduced populations. When feasible, we strongly recommend that reintroduction programs include an investigation of the underlying genetic structure to better define intended goals and supplement measures of demographic success.
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Affiliation(s)
- Paul Hapeman
- Department of Biology, Central Connecticut State University, New Britain, CT 06050, USA
| | - Emily K. Latch
- Department of Biological Sciences, University of Wisconsin–Milwaukee, 3209 North Maryland Avenue, Milwaukee, WI 53211-3102, USA
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory P.O. Drawer E, Aiken, SC 29802, USA
| | - Brad Swanson
- Department of Biology, Central Michigan University, Mount Pleasant, MI 05405-0086, USA
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208
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Eastwood JR, Ribot RFH, Rollins LA, Buchanan KL, Walder K, Bennett ATD, Berg ML. Host heterozygosity and genotype rarity affect viral dynamics in an avian subspecies complex. Sci Rep 2017; 7:13310. [PMID: 29042596 PMCID: PMC5645371 DOI: 10.1038/s41598-017-13476-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/25/2017] [Indexed: 11/09/2022] Open
Abstract
Genetic diversity at community, population and individual levels is thought to influence the spread of infectious disease. At the individual level, inbreeding and heterozygosity are associated with increased risk of infection and disease severity. Host genotype rarity may also reduce infection risk if pathogens are co-adapted to common or local hosts, but to date, no studies have investigated the relative importance of genotype rarity and heterozygosity for infection in a wild, sexually reproducing vertebrate. With beak and feather disease virus (BFDV) infection in a wild parrot (Platycercus elegans), we show that both heterozygosity and genotype rarity of individual hosts predicted infection, but in contrasting ways. Heterozygosity was negatively associated with probability of infection, but not with infection load. In contrast, increased host genotype rarity was associated with lower viral load in infected individuals, but did not predict infection probability. These effects were largely consistent across subspecies, but were not evident at the population level. Subspecies and age were also strongly associated with infection. Our study provides novel insights into infection dynamics by quantifying rarity and diversity simultaneously. We elucidate roles that host genetic diversity can play in infection dynamics, with implications for understanding population divergence, intraspecific diversity and conservation.
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Affiliation(s)
- Justin R Eastwood
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia. .,School of Biological Sciences, Monash University, Melbourne, Victoria, 3800, Australia.
| | - Raoul F H Ribot
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
| | - Lee Ann Rollins
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
| | - Katherine L Buchanan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
| | - Ken Walder
- Metabolic Research Unit, School of Medicine, Deakin University, Geelong, 3216, Victoria, Australia
| | - Andrew T D Bennett
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
| | - Mathew L Berg
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3216, Victoria, Australia
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209
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Fountain T, Husby A, Nonaka E, DiLeo MF, Korhonen JH, Rastas P, Schulz T, Saastamoinen M, Hanski I. Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly. Evol Appl 2017. [DOI: 10.1111/eva.12552] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Toby Fountain
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Arild Husby
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Etsuko Nonaka
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Department of Biology; Lund University; Lund Sweden
| | | | - Janne H. Korhonen
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Department of Computer Science; Aalto University; Aalto Finland
| | - Pasi Rastas
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Department of Zoology; University of Cambridge; Cambridge UK
| | - Torsti Schulz
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | | | - Ilkka Hanski
- Department of Biosciences; University of Helsinki; Helsinki Finland
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210
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De Luca D, Cennamo P, Del Guacchio E, Di Novella R, Caputo P. Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity. Genetica 2017; 146:29-44. [PMID: 29030763 DOI: 10.1007/s10709-017-9994-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/25/2017] [Indexed: 11/26/2022]
Abstract
Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.
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Affiliation(s)
- Daniele De Luca
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, via Foria 223, 80139, Naples, Italy.
| | - Paola Cennamo
- Facoltà di Lettere, Università degli Studi Suor Orsola Benincasa di Napoli, Via Santa Caterina da Siena 37, 80135, Naples, Italy
| | - Emanuele Del Guacchio
- Facoltà di Scienze della Formazione, Università degli Studi Suor Orsola Benincasa di Napoli, Via Santa Caterina da Siena 37, 80135, Naples, Italy
| | | | - Paolo Caputo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, via Foria 223, 80139, Naples, Italy
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211
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Field DL, Broadhurst LM, Elliott CP, Young AG. Population assignment in autopolyploids. Heredity (Edinb) 2017; 119:389-401. [PMID: 28976495 DOI: 10.1038/hdy.2017.51] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 07/07/2017] [Accepted: 07/24/2017] [Indexed: 11/09/2022] Open
Abstract
Understanding the patterns of contemporary gene dispersal within and among populations is of critical importance to population genetics and in managing populations for conservation. In contrast to diploids, there are few studies of gene dispersal in autopolyploids, in part due to complex polysomic inheritance and genotype ambiguity. Here we develop a novel approach for population assignment for codominant markers for autotetraploids and autohexaploids. This method accounts for polysomic inheritance, unreduced gametes and unknown allele dosage. It can also utilise information regarding the origin and genotype of one parent for population assignment of maternal or paternal parents. Using simulations, we demonstrate that our approach achieves high levels of accuracy for assignment even when population divergence is low (FST~0.06) and with only 12 microsatellite loci. We also show that substantially higher accuracy is achieved when known maternal information is utilised, regardless of whether allele dosage is known. Although this novel method exhibited near identical levels of accuracy to Structure when population divergence was high, it performed substantially better for most parameters at moderate (FST=0.06) to low levels of divergence (FST=0.03). These methods fill an important gap in the toolset for autopolyploids and pave the way for investigating contemporary gene dispersal in a widespread group of organisms.
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Affiliation(s)
- D L Field
- Department of Botany and Biodiversity Research, University of Vienna, Faculty of Life Sciences, Vienna, Austria
| | | | - C P Elliott
- Biodiversity Conservation Centre, Kings Park, Western Australia, Australia
| | - A G Young
- CSIRO Plant Industry, Canberra, ACT, Australia
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212
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A comparison of genetic diversity and population structure of the endangered scaleshell mussel (Leptodea leptodon), the fragile papershell (Leptodea fragilis) and their host-fish the freshwater drum (Aplodinotus grunniens). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1015-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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213
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Jahnke M, Casagrandi R, Melià P, Schiavina M, Schultz ST, Zane L, Procaccini G. Potential and realized connectivity of the seagrassPosidonia oceanicaand their implication for conservation. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12633] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
| | - Renato Casagrandi
- Dipartimento di Elettronica, Informazione e Bioingegneria; Politecnico di Milano; Milano Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare; Roma Italy
| | - Paco Melià
- Dipartimento di Elettronica, Informazione e Bioingegneria; Politecnico di Milano; Milano Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare; Roma Italy
| | - Marcello Schiavina
- Dipartimento di Elettronica, Informazione e Bioingegneria; Politecnico di Milano; Milano Italy
- Consorzio Nazionale Interuniversitario per le Scienze del Mare; Roma Italy
| | | | - Lorenzo Zane
- Consorzio Nazionale Interuniversitario per le Scienze del Mare; Roma Italy
- Dipartimento di Biologia; Università di Padova; Padova Italy
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214
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Yadav DK, Arora R, Jain A. Classification and conservation priority of five Deccani sheep ecotypes of Maharashtra, India. PLoS One 2017; 12:e0184691. [PMID: 28910329 PMCID: PMC5598990 DOI: 10.1371/journal.pone.0184691] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/29/2017] [Indexed: 11/19/2022] Open
Abstract
Characterization of Indian livestock breeds has mostly been limited to single breed/population focused on either physical description of traditionally recognized breeds/populations or to their genetic description. Usually, morphological and genetic characterization has taken place in isolation. A parallel morphological characterization of genetically identified breeds or genetic characterization of morphologically described breeds is mostly missing, and their conservation priorities have largely been based on solely considering degree of endangerment. This study uses parallel approach based on morphometric and genetic differentiation for classification of five sheep ecotypes of Maharashtra state, and sets their conservation priority using threat parameters, current utilities/merits and contribution to genetic diversity. A total of 1101 animals were described for 7 body measurements for morphometric characterization. From this sample set, 456 animals were genotyped for 25 microsatellite markers for genetic characterization. Conservation priorities were assessed combining genetic and non-genetic factors. All studied traits varied significantly among ecotypes (p<0.05). All morphometric traits exhibited substantial sexual dimorphism except ear length. Males were 42% heavier than females. Madgyal sheep were the largest amongst the five ecotypes. In the stepwise discriminant analysis, all measured traits were significant and were found to have potential discriminatory power. Tail length was the most discriminatory trait. The Mahalanobis distance of the morphological traits between Kolhapuri and Madgyal was maximum (12.07) while the least differentiation was observed between Madgyal and Solapuri (1.50). Discriminant analysis showed that 68.12% sheep were classified into their source population. The Sangamneri sheep showed least assignment error (22%) whilst Solapuri exhibited maximum error level (41%). A total of 407 alleles were observed, with an average of 16.28 alleles per locus. Sufficient levels of genetic diversity were observed in all the ecotypes with observed heterozygosity values exceeding 0.47 and gene diversity values exceeding 0.76. About 6% of the total genetic variation was explained by population differences (FST = 0.059). Pairwise FST values indicated least differentiation between Solapuri and Madgyal (0.025). In terms of genetic distances, Kolhapuri and Lonand were most closely related (Ds = 0.177). The most probable structure clustering of the five studied populations was at K = 5. The study showed a fair congruence between the dendrogram constructed on the basis of Mahalanobis distances and Nei’s as well as Reynolds genetic distances. The findings gave highest conservation priority to Lonand and least to Solapuri ecotype.
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Affiliation(s)
- Dinesh Kumar Yadav
- ICAR-National Bureau of Animal Genetic Resources, Karnal (Haryana), India
- * E-mail:
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal (Haryana), India
| | - Anand Jain
- ICAR-National Bureau of Animal Genetic Resources, Karnal (Haryana), India
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215
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Chen I, Nishida S, Yang WC, Isobe T, Tajima Y, Hoelzel AR. Genetic diversity of bottlenose dolphin ( Tursiops sp.) populations in the western North Pacific and the conservation implications. MARINE BIOLOGY 2017; 164:202. [PMID: 28983128 PMCID: PMC5592193 DOI: 10.1007/s00227-017-3232-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/29/2017] [Indexed: 06/07/2023]
Abstract
The evolutionary processes that shape patterns of diversity in highly mobile marine species are poorly understood, but important towards transferable inference on their effective conservation. In this study, bottlenose dolphins (Tursiops sp.) are studied to address this broader question. They exhibit remarkable geographical variation for morphology, life history, and genetic diversity, and this high level of variation has made the taxonomy of the genus controversial. A significant population structure has been reported for the most widely distributed species, the common bottlenose dolphin (T. truncatus), in almost all ocean basins, though no data have been available for the western North Pacific Ocean (WNP). The genetic diversity of bottlenose dolphins in the WNP was investigated based on 20 microsatellite and one mitochondrial DNA markers for samples collected from Taiwanese, Japanese, and Philippine waters (9°-39°N, 120°-140°E) during 1986-2012. The results indicated that there are at least four genetically differentiated populations of common bottlenose dolphins in the western and central North Pacific Ocean. The pattern of differentiation appears to correspond to habitat types, resembling results seen in other populations of the same species. Our analyses also showed that there was no evident gene flow between the two "sister species", the common bottlenose dolphins, and the Indo-Pacific bottlenose dolphins (T. aduncus) occurring sympatrically in our study region.
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Affiliation(s)
- Ing Chen
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE UK
- Department of Life Sciences, National Cheng Kung University, 1 Da-Xue Road, East District, Tainan, 70101 Taiwan
| | - Shin Nishida
- Science Education, Faculty of Education and Culture, University of Miyazaki, 1-1 Gakuen-Kibanadai-Nishi, Miyazaki, 889-2192 Japan
| | - Wei-Cheng Yang
- Department of Veterinary Medicine, National Chiayi University, 580 Xinmin Road, Chiayi, 60054 Taiwan
| | - Tomohiko Isobe
- National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, 305-8506 Japan
| | - Yuko Tajima
- Division of Vertebrates, Department of Zoology, National Museum of Nature and Science, 4–1–1 Amakubo, Tsukuba-shi, Ibaraki, 305-0005 Japan
| | - A. Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE UK
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216
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Desvars-Larrive A, Pascal M, Gasqui P, Cosson JF, Benoît E, Lattard V, Crespin L, Lorvelec O, Pisanu B, Teynié A, Vayssier-Taussat M, Bonnet S, Marianneau P, Lacôte S, Bourhy P, Berny P, Pavio N, Le Poder S, Gilot-Fromont E, Jourdain E, Hammed A, Fourel I, Chikh F, Vourc’h G. Population genetics, community of parasites, and resistance to rodenticides in an urban brown rat (Rattus norvegicus) population. PLoS One 2017; 12:e0184015. [PMID: 28886097 PMCID: PMC5590879 DOI: 10.1371/journal.pone.0184015] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 08/16/2017] [Indexed: 11/18/2022] Open
Abstract
Brown rats are one of the most widespread urban species worldwide. Despite the nuisances they induce and their potential role as a zoonotic reservoir, knowledge on urban rat populations remains scarce. The main purpose of this study was to characterize an urban brown rat population from Chanteraines park (Hauts-de-Seine, France), with regards to haematology, population genetics, immunogenic diversity, resistance to anticoagulant rodenticides, and community of parasites. Haematological parameters were measured. Population genetics was investigated using 13 unlinked microsatellite loci. Immunogenic diversity was assessed for Mhc-Drb. Frequency of the Y139F mutation (conferring resistance to rodenticides) and two linked microsatellites were studied, concurrently with the presence of anticoagulant residues in the liver. Combination of microscopy and molecular methods were used to investigate the occurrence of 25 parasites. Statistical approaches were used to explore multiple parasite relationships and model parasite occurrence. Eighty-six rats were caught. The first haematological data for a wild urban R. norvegicus population was reported. Genetic results suggested high genetic diversity and connectivity between Chanteraines rats and surrounding population(s). We found a high prevalence (55.8%) of the mutation Y139F and presence of rodenticide residues in 47.7% of the sampled individuals. The parasite species richness was high (16). Seven potential zoonotic pathogens were identified, together with a surprisingly high diversity of Leptospira species (4). Chanteraines rat population is not closed, allowing gene flow and making eradication programs challenging, particularly because rodenticide resistance is highly prevalent. Parasitological results showed that co-infection is more a rule than an exception. Furthermore, the presence of several potential zoonotic pathogens, of which four Leptospira species, in this urban rat population raised its role in the maintenance and spread of these pathogens. Our findings should stimulate future discussions about the development of a long-term rat-control management program in Chanteraines urban park.
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Affiliation(s)
- Amélie Desvars-Larrive
- Conservation Medicine, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | - Michel Pascal
- Joint Research Unit (JRU) Écologie et Santé des Écosystèmes (ESE), Institut National de la Recherche Agronomique, INRA, Agrocampus Ouest, Rennes, France
| | - Patrick Gasqui
- Joint Research Unit (JRU) Epidémiologie des Maladies Animales et Zoonotiques (EPIA), Institut National de la Recherche Agronomique, INRA, VetAgro Sup, Saint-Genès Champanelle, France
| | - Jean-François Cosson
- Joint Research Unit (JRU) Biologie Moléculaire et Immunologie Parasitaire (BIPAR), Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES), Institut National de la Recherche Agronomique, INRA, Ecole Nationale Vétérinaire d'Alfort (ENVA), Maisons-Alfort, France
- Joint Research Unit (JRU) Centre de Biologie pour la Gestion des Populations (CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Institut National de la Recherche Agronomique, INRA, Institut de Recherche pour le Développement (IRD), SupAgro Montpellier, France
| | - Etienne Benoît
- Contract-based Research Unit (CBRU) Rongeurs Sauvages–Risques Sanitaires et Gestion des Populations (RS2GP), VetAgro Sup, Institut National de la Recherche Agronomique, INRA, Lyon University, Marcy-L’Etoile, France
| | - Virginie Lattard
- Contract-based Research Unit (CBRU) Rongeurs Sauvages–Risques Sanitaires et Gestion des Populations (RS2GP), VetAgro Sup, Institut National de la Recherche Agronomique, INRA, Lyon University, Marcy-L’Etoile, France
| | - Laurent Crespin
- Joint Research Unit (JRU) Epidémiologie des Maladies Animales et Zoonotiques (EPIA), Institut National de la Recherche Agronomique, INRA, VetAgro Sup, Saint-Genès Champanelle, France
| | - Olivier Lorvelec
- Joint Research Unit (JRU) Écologie et Santé des Écosystèmes (ESE), Institut National de la Recherche Agronomique, INRA, Agrocampus Ouest, Rennes, France
| | - Benoît Pisanu
- Unité Mixte de Services (UMS) 2006 Patrimoine Naturel, Agence Française pour la Biodiversité (AFB), Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Alexandre Teynié
- Joint Research Unit (JRU) Epidémiologie des Maladies Animales et Zoonotiques (EPIA), Institut National de la Recherche Agronomique, INRA, VetAgro Sup, Saint-Genès Champanelle, France
| | - Muriel Vayssier-Taussat
- Joint Research Unit (JRU) Biologie Moléculaire et Immunologie Parasitaire (BIPAR), Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES), Institut National de la Recherche Agronomique, INRA, Ecole Nationale Vétérinaire d'Alfort (ENVA), Maisons-Alfort, France
| | - Sarah Bonnet
- Joint Research Unit (JRU) Biologie Moléculaire et Immunologie Parasitaire (BIPAR), Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES), Institut National de la Recherche Agronomique, INRA, Ecole Nationale Vétérinaire d'Alfort (ENVA), Maisons-Alfort, France
| | - Philippe Marianneau
- Virology Unit, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES), Lyon, France
| | - Sandra Lacôte
- Virology Unit, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES), Lyon, France
| | - Pascale Bourhy
- Institut Pasteur, Biology of Spirochetes Unit, National Reference Center and WHO Collaborating Center for Leptospirosis, Paris, France
| | - Philippe Berny
- Contract-based Research Unit (CBRU) Rongeurs Sauvages–Risques Sanitaires et Gestion des Populations (RS2GP), VetAgro Sup, Institut National de la Recherche Agronomique, INRA, Lyon University, Marcy-L’Etoile, France
| | - Nicole Pavio
- Joint Research Unit (JRU) Virology, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES), Institut National de la Recherche Agronomique, INRA, Ecole Nationale Vétérinaire d'Alfort (ENVA), Maisons-Alfort, France
| | - Sophie Le Poder
- Joint Research Unit (JRU) Virology, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail (ANSES), Institut National de la Recherche Agronomique, INRA, Ecole Nationale Vétérinaire d'Alfort (ENVA), Maisons-Alfort, France
| | - Emmanuelle Gilot-Fromont
- Joint Research Unit (JRU) Laboratoire de Biométrie et Biologie Évolutive (LBBE), Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1, VetAgro Sup, Marcy-L’Etoile, France
| | - Elsa Jourdain
- Joint Research Unit (JRU) Epidémiologie des Maladies Animales et Zoonotiques (EPIA), Institut National de la Recherche Agronomique, INRA, VetAgro Sup, Saint-Genès Champanelle, France
| | - Abdessalem Hammed
- Contract-based Research Unit (CBRU) Rongeurs Sauvages–Risques Sanitaires et Gestion des Populations (RS2GP), VetAgro Sup, Institut National de la Recherche Agronomique, INRA, Lyon University, Marcy-L’Etoile, France
| | - Isabelle Fourel
- Contract-based Research Unit (CBRU) Rongeurs Sauvages–Risques Sanitaires et Gestion des Populations (RS2GP), VetAgro Sup, Institut National de la Recherche Agronomique, INRA, Lyon University, Marcy-L’Etoile, France
| | - Farid Chikh
- Conseil Départemental Hauts-de-Seine, Parc de Chanteraines, Villeneuve-la-Garenne, Paris, France
| | - Gwenaël Vourc’h
- Joint Research Unit (JRU) Epidémiologie des Maladies Animales et Zoonotiques (EPIA), Institut National de la Recherche Agronomique, INRA, VetAgro Sup, Saint-Genès Champanelle, France
- * E-mail:
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Honnen AC, Monaghan MT. City-Dwellers and Country Folks: Lack of Population Differentiation Along an Urban-Rural Gradient in the Mosquito Culex pipiens (Diptera: Culicidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2017; 17:4560636. [PMID: 29117382 PMCID: PMC5717708 DOI: 10.1093/jisesa/iex086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Indexed: 06/07/2023]
Abstract
Mosquitoes (Diptera, Culicidae) occur in natural, urban, and peri-urban areas throughout the globe. Although the characteristics of urban and peri-urban habitats differ from those of natural habitats in many ways (e.g., fragmentation, pollution, noise, and light), few studies have examined the population connectivity of mosquitoes in urban areas. To obtain an overview of the species composition, we sampled mosquitoes from 23 sites in and around the city of Berlin, Germany. Of 23 species, five occurred in urban, 10 in peri-urban, and 20 in rural areas. Culex pipiens Linnaeus (Diptera: Culicidae) was the most common species collected (75% of all individuals) and occurred in all habitats. Hence this species was selected to be analysed at 10 microsatellite markers. There was no significant differentiation (FST = 0.016, P = 0.9) or isolation by distance (P = 0.06) among Cx. pipiens populations along an urban-rural gradient. The only significant differences detected were between Cx. pipiens and a laboratory population of Cx. pipiens f. molestus (pairwise FST = 0.114-0.148, P ≤ 0.001 in all comparisons), suggesting that the markers chosen were suitable for the identification of population differentiation. Our results indicate that Cx. pipiens gene flow is widespread within and among urban, peri-urban, and rural areas and that urban habitat does not necessarily impede or enhance gene flow among these populations.
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Affiliation(s)
- Ann-Christin Honnen
- Swiss Tropical and Public Health Institute (Swiss TPH), Switzerland
- University of Basel, Switzerland
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Germany
| | - Michael T Monaghan
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Germany
- Berlin Center for Genomics in Biodiversity Research, Germany
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218
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Population Genetics Between an Insular and Coastal Population of Gopher Tortoises (Gopherus polyphemus) in Southwest Florida. SOUTHEAST NAT 2017. [DOI: 10.1656/058.016.0305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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219
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Frantz AC, Zachos FE, Bertouille S, Eloy MC, Colyn M, Flamand MC. Using genetic tools to estimate the prevalence of non-native red deer ( Cervus elaphus) in a Western European population. Ecol Evol 2017; 7:7650-7660. [PMID: 29043022 PMCID: PMC5632609 DOI: 10.1002/ece3.3282] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/30/2017] [Accepted: 06/28/2017] [Indexed: 01/17/2023] Open
Abstract
Game species like the red deer have been subjected to anthropogenic impacts for centuries. Translocations are often carried out—sometimes illegally—not only for sporting purposes, but also to increase trophy quality, reduce inbreeding, or mitigate bottlenecks after excessive persecution. Apart from the blurring of large‐scale genetic structure, translocations without adequate quarantine measure risk introducing pathogens into potentially immunologically naïve populations. It is therefore important to understand the frequency of clandestine translocations. Identification of non‐autochthonous animals and their potential origin is often difficult and, in red deer, has been hampered by the lack of large‐scale genotypic datasets for comparison. In the present study, we make use of a recently published European‐wide microsatellite dataset to detect and quantify the presence of non‐autochthonous red deer in a large population sample (n = 1,780) from Central Europe (Belgium). Using factorial correspondence analysis, assignment tests and Bayesian clustering algorithms we arrive at an estimate of 3.7% non‐autochthonous animals (or their descendants). Some of these animals were assigned to a nearby French population and may have immigrated into Belgium naturally, but the large majority must have been introduced by humans. Our analysis pointed to the British Isles and Germany/Poland as the potential origin of many introduced deer, regions known to have been source populations for translocations in Europe and beyond. We found evidence for recreational hunters using carcasses from farmed deer to fulfill mandatory hunting quotas. Our study is the first to quantify the extent of human‐mediated introductions in a European game species at such a large scale with large and representative sample sizes.
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Affiliation(s)
- Alain C Frantz
- Musée National d'Histoire Naturelle Luxembourg Luxembourg.,Fondation faune-flore Luxembourg Luxembourg
| | | | - Sabine Bertouille
- Département de l'Etude du Milieu naturel et agricole Service Public de Wallonie Gembloux Belgium
| | - Marie-Christine Eloy
- Institut des Sciences de la Vie Université catholique de Louvain Louvain-la-Neuve Belgium
| | - Marc Colyn
- CNRS-UMR 6553 Université de Rennes 1 Paimpont France
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220
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Soanes K, Taylor AC, Sunnucks P, Vesk PA, Cesarini S, Ree R. Evaluating the success of wildlife crossing structures using genetic approaches and an experimental design: Lessons from a gliding mammal. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.12966] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kylie Soanes
- School of Ecosystem and Forest Sciences The University of Melbourne Parkville Vic. Australia
| | - Andrea C. Taylor
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Paul Sunnucks
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Peter A. Vesk
- School of BioSciences The University of Melbourne Parkville Vic. Australia
| | - Silvana Cesarini
- School of Biological Sciences Monash University Clayton Vic. Australia
| | - Rodney Ree
- School of BioSciences The University of Melbourne Parkville Vic. Australia
- Ecology and Infrastructure International Wantirna Vic. Australia
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221
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Temporal stability and mixed-stock analyses of humpback whales (Megaptera novaeangliae) in the nearshore waters of the Western Antarctic Peninsula. Polar Biol 2017. [DOI: 10.1007/s00300-017-2193-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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222
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Simonsen MK, Siwertsson A, Adams CE, Amundsen PA, Præbel K, Knudsen R. Allometric trajectories of body and head morphology in three sympatric Arctic charr ( Salvelinus alpinus (L.)) morphs. Ecol Evol 2017; 7:7277-7289. [PMID: 28944016 PMCID: PMC5606865 DOI: 10.1002/ece3.3224] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 01/01/2023] Open
Abstract
A study of body and head development in three sympatric reproductively isolated Arctic charr (Salvelinus alpinus (L.)) morphs from a subarctic lake (Skogsfjordvatn, northern Norway) revealed allometric trajectories that resulted in morphological differences. The three morphs were ecologically assigned to a littoral omnivore, a profundal benthivore and a profundal piscivore, and this was confirmed by genetic analyses (microsatellites). Principal component analysis was used to identify the variables responsible for most of the morphological variation of the body and head shape. The littoral omnivore and the profundal piscivore morph had convergent allometric trajectories for the most important head shape variables, developing bigger mouths and relatively smaller eyes with increasing head size. The two profundal morphs shared common trajectories for the variables explaining most of the body and head shape variation, namely head size relative to body size, placement of the dorsal and pelvic fins, eye size and mouth size. In contrast, the littoral omnivore and the profundal benthivore morphs were not on common allometric trajectories for any of the examined variables. The findings suggest that different selective pressures could have been working on traits related to their trophic niche such as habitat and diet utilization of the three morphs, with the two profundal morphs experiencing almost identical environmental conditions.
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Affiliation(s)
- Marianne Knutsdotter Simonsen
- Department of Arctic and Marine Biology Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Anna Siwertsson
- Department of Arctic and Marine Biology Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Colin Ean Adams
- Scottish Centre for Ecology and the Natural Environment IBAHCM, University of Glasgow Glasgow UK
| | - Per-Arne Amundsen
- Department of Arctic and Marine Biology Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
| | - Kim Præbel
- Faculty of Biosciences, Fisheries and Economics The Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Rune Knudsen
- Department of Arctic and Marine Biology Faculty of Biosciences, Fisheries and Economics UiT The Arctic University of Norway Tromsø Norway
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223
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Tolesa Z, Bekele E, Tesfaye K, Ben Slimen H, Valqui J, Getahun A, Hartl GB, Suchentrunk F. Mitochondrial and nuclear DNA reveals reticulate evolution in hares (Lepus spp., Lagomorpha, Mammalia) from Ethiopia. PLoS One 2017; 12:e0180137. [PMID: 28767659 PMCID: PMC5540492 DOI: 10.1371/journal.pone.0180137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/10/2017] [Indexed: 11/28/2022] Open
Abstract
For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals. For the hares from Ethiopia, genotype composition at twelve microsatellite loci (n = 107) was used to explore both interspecific gene pool separation and levels of current hybridization, as has been observed in some other Lepus species. For phylogenetic analyses ATP6 and TF sequences of Lepus species from South and North Africa (L. capensis, L. saxatilis), the Anatolian peninsula and Europe (L. europaeus, L. timidus) were also produced and additional TF sequences of 18 Lepus species retrieved from GenBank were included as well. Median joining networks, neighbour joining, maximum likelihood analyses, as well as Bayesian inference resulted in similar models of evolution of the three species from Ethiopia for the ATP6 and TF sequences, respectively. The Ethiopian species are, however, not monophyletic, with signatures of contemporary uni- and bidirectional mitochondrial introgression and/ or shared ancestral polymorphism. Lepus habessinicus carries mtDNA distinct from South African L. capensis and North African L. capensis sensu lato; that finding is not in line with earlier suggestions of its conspecificity with L. capensis. Lepus starcki has mtDNA distinct from L. capensis and L. europaeus, which is not in line with earlier suggestions to include it either in L. capensis or L. europaeus. Lepus fagani shares mitochondrial haplotypes with the other two species from Ethiopia, despite its distinct phenotypic and microsatellite differences; moreover, it is not represented by a species-specific mitochondrial haplogroup, suggesting considerable mitochondrial capture by the other species from Ethiopia or species from other parts of Africa. Both mitochondrial and nuclear sequences indicate close phylogenetic relationships among all three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. TF sequences suggest close evolutionary relationships between the three Ethiopian species and Cape hares from South and North Africa; they further suggest that hares from Ethiopia hold a position ancestral to many Eurasian and North American species.
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Affiliation(s)
- Zelalem Tolesa
- Department of Biology, Hawassa University, Hawassa, Ethiopia
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Endashaw Bekele
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Department of Microbial, Cellular, and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Centre of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hichem Ben Slimen
- Institut Supérieur de Biotechnologie de Béja, Avenue Habib Bourguiba, Béja, Tunisia
| | - Juan Valqui
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Abebe Getahun
- Department of Zoological Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Günther B. Hartl
- Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
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224
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Population genetics of the Schistosoma snail host Bulinus truncatus in Egypt. Acta Trop 2017; 172:36-43. [PMID: 28408098 DOI: 10.1016/j.actatropica.2017.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 03/29/2017] [Accepted: 04/08/2017] [Indexed: 11/23/2022]
Abstract
The tropical freshwater snail Bulinus truncatus serves as an important intermediate host of several human and cattle Schistosoma species in many African regions. Despite some ecological and malacological studies, there is no information on the genetic diversity of B. truncatus in Egypt. Here, we sampled 70-100 snails in ten localities in Upper Egypt and the Nile Delta. Per locality, we sequenced 10 snails at a partial fragment of the cytochrome c oxidase subunit 1 gene (cox1) and we genotyped 25-30 snails at six microsatellite markers. A total of nine mitochondrial haplotypes were detected, of which five were unique to the Nile Delta and three were unique to Upper Egypt, indicating that snail populations may have evolved independently in both regions. Bayesian clustering and hierarchical F-statistics using microsatellite markers further revealed strong population genetic structure at the level of locality. Observed heterozygosity was much lower compared to what is expected under random mating, which could be explained by high selfing rates, population size reductions and to a lesser extent by the Wahlund effect. Despite these observations, we found signatures of gene flow and cross-fertilization, even between snails from the Nile Delta and Upper Egypt, indicating that B. truncatus can travel across large distances in Egypt. These observations could have serious consequences for disease epidemiology, as it means that infected snails from one region could rapidly and unexpectedly spark a new epidemic in another distant region. This could be one of the factors explaining the rebound of human Schistosoma infections in the Nile Delta, despite decades of sustained schistosomiasis control.
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225
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Effect of landscape features on genetic structure of the goitered gazelle (Gazella subgutturosa) in Central Iran. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1002-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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226
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Antoni L, Saillant E. Spatial connectivity in an adult-sedentary reef fish with extended pelagic larval phase. Mol Ecol 2017; 26:4955-4965. [PMID: 28746775 DOI: 10.1111/mec.14263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 06/07/2017] [Accepted: 07/05/2017] [Indexed: 11/27/2022]
Abstract
Understanding the spatial scale of demographic connectivity in marine reef fishes dispersing pelagic larvae is a challenging task because of the technical difficulties associated with tagging and monitoring the movements of progeny at early life stages. Several studies highlighted a strong importance of local retention with levels of dispersal of ecological significance restricted to short distances. To date little information is available in species where pelagic dispersal lasts for long periods of time. In this work, population structure and connectivity were studied in the grey triggerfish, Balistes capriscus. Grey triggerfish larvae and juveniles remain associated with floating Sargassum sp. beds for an estimated period of 4-7 months before settling on benthic habitats where they remain sedentary as adults. Analysis of genetic variation among populations along the continental shelf of the northern Gulf of Mexico and U.S. east coast, encompassing over 3,100 km of coastline, revealed homogeneous allele frequencies and a weak isolation-by-distance pattern. Moment and maximum-likelihood estimates of dispersal parameters both indicated occurrence of large neighbourhoods with estimates of the dispersal distribution parameter σ of 914 and 780 km, respectively. Simulated distributions of dispersal distances using several distribution functions all featured substantial fractions of long-distance dispersal events with the 90% percentiles of travel distance prior to settlement averaging 1,809 km. These results suggest a high dependency of local recruitment on the output of nonlocal spawning stocks located hundreds of kilometres away and a reduced role of local retention in this species.
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Affiliation(s)
- L Antoni
- Gulf Coast Research Laboratory, School of Ocean Science and Technology, The University of Southern Mississippi, Ocean Springs, MS, USA
| | - E Saillant
- Gulf Coast Research Laboratory, School of Ocean Science and Technology, The University of Southern Mississippi, Ocean Springs, MS, USA
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227
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Kotsakiozi P, Gloria-Soria A, Caccone A, Evans B, Schama R, Martins AJ, Powell JR. Tracking the return of Aedes aegypti to Brazil, the major vector of the dengue, chikungunya and Zika viruses. PLoS Negl Trop Dis 2017; 11:e0005653. [PMID: 28742801 PMCID: PMC5526527 DOI: 10.1371/journal.pntd.0005653] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/19/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Aedes aegypti, commonly known as "the yellow fever mosquito", is of great medical concern today primarily as the major vector of dengue, chikungunya and Zika viruses, although yellow fever remains a serious health concern in some regions. The history of Ae. aegypti in Brazil is of particular interest because the country was subjected to a well-documented eradication program during 1940s-1950s. After cessation of the campaign, the mosquito quickly re-established in the early 1970s with several dengue outbreaks reported during the last 30 years. Brazil can be considered the country suffering the most from the yellow fever mosquito, given the high number of dengue, chikungunya and Zika cases reported in the country, after having once been declared "free of Ae. aegypti". METHODOLOGY/PRINCIPAL FINDINGS We used 12 microsatellite markers to infer the genetic structure of Brazilian Ae. aegypti populations, genetic variability, genetic affinities with neighboring geographic areas, and the timing of their arrival and spread. This enabled us to reconstruct their recent history and evaluate whether the reappearance in Brazil was the result of re-invasion from neighboring non-eradicated areas or re-emergence from local refugia surviving the eradication program. Our results indicate a genetic break separating the northern and southern Brazilian Ae. aegypti populations, with further genetic differentiation within each cluster, especially in southern Brazil. CONCLUSIONS/SIGNIFICANCE Based on our results, re-invasions from non-eradicated regions are the most likely scenario for the reappearance of Ae. aegypti in Brazil. While populations in the northern cluster are likely to have descended from Venezuela populations as early as the 1970s, southern populations seem to have derived more recently from northern Brazilian areas. Possible entry points are also revealed within both southern and northern clusters that could inform strategies to control and monitor this important arbovirus vector.
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Affiliation(s)
- Panayiota Kotsakiozi
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| | - Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Benjamin Evans
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Renata Schama
- Laboratório de Biologia Computacional e Sistemas, IOC–Fiocruz, Rio de Janeiro, Brazil
| | - Ademir Jesus Martins
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, IOC-FIOCRUZ, Rio de Janeiro, Brazil
| | - Jeffrey R. Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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228
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Sattler RL, Willoughby JR, Swanson BJ. Decline of heterozygosity in a large but isolated population: a 45-year examination of moose genetic diversity on Isle Royale. PeerJ 2017; 5:e3584. [PMID: 28729957 PMCID: PMC5516768 DOI: 10.7717/peerj.3584] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/26/2017] [Indexed: 11/20/2022] Open
Abstract
Wildlife conservation and management approaches typically focus on demographic measurements to assess population viability over both short and long periods. However, genetic diversity is an important predictor of long term population vitality. We investigated the pattern of change in genetic diversity in a large and likely isolated moose (Alces alces) population on Isle Royale (Lake Superior) from 1960–2005. We characterized samples, partitioned into five different 5-year periods, using nine microsatellite loci and a portion of the mtDNA control region. We also simulated the moose population to generate a theoretical backdrop of genetic diversity change. In the empirical data, we found that the number of alleles was consistently low and that observed heterozygosity notably declined from 1960 to 2005 (p = 0.08, R2 = 0.70). Furthermore, inbreeding coefficients approximately doubled from 0.08 in 1960–65 to 0.16 in 2000–05. Finally, we found that the empirical rate of observed heterozygosity decline was faster than the rate of observed heterozygosity loss in our simulations. Combined, these data suggest that genetic drift and inbreeding occurred in the Isle Royale moose populations over the study period, leading to significant losses in heterozygosity. Although inbreeding can be mitigated by migration, we found no evidence to support the occurrence of recent migrants into the population using analysis of our mtDNA haplotypes nor microsatellite data. Therefore, the Isle Royale moose population illustrates that even large populations are subjected to inbreeding in the absence of migration.
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Affiliation(s)
- Renae L Sattler
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States of America.,Alaska SeaLife Center, Seward, AK, United States of America
| | - Janna R Willoughby
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
| | - Bradley J Swanson
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States of America
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229
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Investigating gene flow between the blind cavefish Garra barreimiae and its conspecific surface populations. Sci Rep 2017; 7:5130. [PMID: 28698621 PMCID: PMC5506003 DOI: 10.1038/s41598-017-05194-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/25/2017] [Indexed: 11/08/2022] Open
Abstract
Cave-dwelling taxa often share the same phenotypic modifications like absence of eyes and pigmentation. These “troglomorphic characters” are expressed in the populations of Garra barreimiae from the Al Hoota Cave and nearby Hoti Pit in Northern Oman. Surface morphotypes of this cyprinid species are common throughout the distribution area. Very rarely individuals with intermediate phenotypes can be found. In the present study, potential gene flow between cave and surface populations was tested and population structure within five sampling sites was assessed. Overall, 213 individuals were genotyped at 18 microsatellite loci. We found that the cave populations have lower genetic diversity and are clearly isolated from the surface populations, which seem to be sporadically in contact with each other. The results indicate a recent genetic bottleneck in the cave populations. Thus, it can be assumed that during climatic changes the connection between cave and surface water bodies was disjoined, leaving a subpopulation trapped inside. Nevertheless, occasional gene flow between the morphotypes is detectable, but hybridisation seems only possible in cave habitat with permanent connection to surface water. Individuals from surface sites bearing intermediate phenotypes but cave genotypes imply that phenotypic plasticity might play a role in the development of the phenotype.
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Kassa A, Konrad H, Geburek T. Landscape genetic structure of Olea europaea subsp. cuspidata in Ethiopian highland forest fragments. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0993-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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231
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Montecinos AE, Guillemin ML, Couceiro L, Peters AF, Stoeckel S, Valero M. Hybridization between two cryptic filamentous brown seaweeds along the shore: analysing pre- and postzygotic barriers in populations of individuals with varying ploidy levels. Mol Ecol 2017; 26:3497-3512. [PMID: 28295812 DOI: 10.1111/mec.14098] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/07/2017] [Accepted: 02/07/2017] [Indexed: 01/17/2023]
Abstract
We aimed to study the importance of hybridization between two cryptic species of the genus Ectocarpus, a group of filamentous algae with haploid-diploid life cycles that include the principal genetic model organism for the brown algae. In haploid-diploid species, the genetic structure of the two phases of the life cycle can be analysed separately in natural populations. Such life cycles provide a unique opportunity to estimate the frequency of hybrid genotypes in diploid sporophytes and meiotic recombinant genotypes in haploid gametophytes allowing the effects of reproductive barriers preventing fertilization or preventing meiosis to be untangle. The level of hybridization between E. siliculosus and E. crouaniorum was quantified along the European coast. Clonal cultures (568 diploid, 336 haploid) isolated from field samples were genotyped using cytoplasmic and nuclear markers to estimate the frequency of hybrid genotypes in diploids and recombinant haploids. We identified admixed individuals using microsatellite loci, classical assignment methods and a newly developed Bayesian method (XPloidAssignment), which allows the analysis of populations that exhibit variations in ploidy level. Over all populations, the level of hybridization was estimated at 8.7%. Hybrids were exclusively observed in sympatric populations. More than 98% of hybrids were diploids (40% of which showed signs of aneuploidy) with a high frequency of rare alleles. The near absence of haploid recombinant hybrids demonstrates that the reproductive barriers are mostly postzygotic and suggests that abnormal chromosome segregation during meiosis following hybridization of species with different genome sizes could be a major cause of interspecific incompatibility in this system.
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Affiliation(s)
- Alejandro E Montecinos
- UMI, EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688, Roscoff cedex, France
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Marie-Laure Guillemin
- UMI, EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688, Roscoff cedex, France
- Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
| | - Lucia Couceiro
- UMI, EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688, Roscoff cedex, France
| | - Akira F Peters
- Bezhin Rosko, 40 rue des pêcheurs, 29250, Santec, France
| | - Solenn Stoeckel
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Rennes, France
| | - Myriam Valero
- UMI, EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, PUC, UACH, Station Biologique de Roscoff, CS 90074, Place Georges Teissier, 29688, Roscoff cedex, France
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Mclean AJ, Joseph L, Toon A, Schmidt DJ, Drew A, Mason IJ, Hughes JM. Reassessment of a possible case of intraspecific gene flow across Australia’s Great Dividing Range in the variegated fairy wren, Malurus lamberti (Aves: Maluridae), and its systematic consequences. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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234
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Mousavi S, Mariotti R, Bagnoli F, Costantini L, Cultrera NGM, Arzani K, Pandolfi S, Vendramin GG, Torkzaban B, Hosseini-Mazinani M, Baldoni L. The eastern part of the Fertile Crescent concealed an unexpected route of olive (Olea europaea L.) differentiation. ANNALS OF BOTANY 2017; 119:1305-1318. [PMID: 28387783 PMCID: PMC5604562 DOI: 10.1093/aob/mcx027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/28/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Olive is considered a native plant of the eastern side of the Mediterranean basin, from where it should have spread westward along the Mediterranean shores, while little is known about its diffusion in the eastern direction. METHODS Genetic diversity levels and population genetic structure of a wide set of olive ecotypes and varieties collected from several provinces of Iran, representing a high percentage of the entire olive resources present in the area, was screened with 49 chloroplast and ten nuclear simple sequence repeat markers, and coupled with archaeo-botanical and historical data on Mediterranean olive varieties. Approximate Bayesian Computation was applied to define the demographic history of olives including Iranian germplasm, and species distribution modelling was performed to understand the impact of the Late Quaternary on olive distribution. KEY RESULTS The results of the present study demonstrated that: (1) the climatic conditions of the last glacial maximum had an important role on the actual olive distribution, (2) all Iranian olive samples had the same maternal inheritance as Mediterranean cultivars, and (3) the nuclear gene flow from the Mediterranean basin to the Iranian plateau was almost absent, as well as the contribution of subspecies cuspidata to the diversity of Iranian olives. CONCLUSIONS Based on this evidence, a new scenario for the origin and distribution of this important fruit crop has been traced. The evaluation of olive trees growing in the eastern part of the Levant highlighted a new perspective on the spread and distribution of olive, suggesting two routes of olive differentiation, one westward, spreading along the Mediterranean basin, and another moving towards the east and reaching the Iranian plateau before its domestication.
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Affiliation(s)
- Soraya Mousavi
- CNR - Institute for Agricultural and Forest Systems in the Mediterranean, via Madonna Alta, 128, 06128 Perugia, Italy
- Tarbiat Modares University, Department of Horticultural Science, Jalal Ale Ahmad Highway, PO Box 14115111, Tehran, Iran
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
- Co-first authors: These authors contributed equally to this work
| | - Roberto Mariotti
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
- Co-first authors: These authors contributed equally to this work
| | - Francesca Bagnoli
- CNR - Institute of Biosciences and Bioresources, Via Madonna del Piano, 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Lorenzo Costantini
- ISMEO - International Association of Mediterranean and Oriental Studies, Corso Vittorio Emanuele II, 244, 00186 Rome, Italy
| | - Nicolò G. M. Cultrera
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
| | - Kazem Arzani
- Tarbiat Modares University, Department of Horticultural Science, Jalal Ale Ahmad Highway, PO Box 14115111, Tehran, Iran
| | - Saverio Pandolfi
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
| | - Giovanni Giuseppe Vendramin
- CNR - Institute of Biosciences and Bioresources, Via Madonna del Piano, 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Bahareh Torkzaban
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
| | - Mehdi Hosseini-Mazinani
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, Km 15, Tehran - Karaj Highway, PO Box 14965161, Tehran, Iran
- For correspondence. E-mail or
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources, via Madonna Alta, 130, 06128 Perugia, Italy
- For correspondence. E-mail or
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Janecka JE, Zhang Y, Li D, Munkhtsog B, Bayaraa M, Galsandorj N, Wangchuk TR, Karmacharya D, Li J, Lu Z, Uulu KZ, Gaur A, Kumar S, Kumar K, Hussain S, Muhammad G, Jevit M, Hacker C, Burger P, Wultsch C, Janecka MJ, Helgen K, Murphy WJ, Jackson R. Range-Wide Snow Leopard Phylogeography Supports Three Subspecies. J Hered 2017; 108:597-607. [DOI: 10.1093/jhered/esx044] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 04/29/2017] [Indexed: 11/13/2022] Open
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Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: Implications for vector control. PLoS Negl Trop Dis 2017; 11:e0005485. [PMID: 28453513 PMCID: PMC5425221 DOI: 10.1371/journal.pntd.0005485] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 05/10/2017] [Accepted: 03/12/2017] [Indexed: 11/19/2022] Open
Abstract
Uganda is the only country where the chronic and acute forms of human African Trypanosomiasis (HAT) or sleeping sickness both occur and are separated by < 100 km in areas north of Lake Kyoga. In Uganda, Glossina fuscipes fuscipes is the main vector of the Trypanosoma parasites responsible for these diseases as well for the animal African Trypanosomiasis (AAT), or Nagana. We used highly polymorphic microsatellite loci and a mitochondrial DNA (mtDNA) marker to provide fine scale spatial resolution of genetic structure of G. f. fuscipes from 42 sampling sites from the northern region of Uganda where a merger of the two disease belts is feared. Based on microsatellite analyses, we found that G. f. fuscipes in northern Uganda are structured into three distinct genetic clusters with varying degrees of interconnectivity among them. Based on genetic assignment and spatial location, we grouped the sampling sites into four genetic units corresponding to northwestern Uganda in the Albert Nile drainage, northeastern Uganda in the Lake Kyoga drainage, western Uganda in the Victoria Nile drainage, and a transition zone between the two northern genetic clusters characterized by high level of genetic admixture. An analysis using HYBRIDLAB supported a hybrid swarm model as most consistent with tsetse genotypes in these admixed samples. Results of mtDNA analyses revealed the presence of 30 haplotypes representing three main haplogroups, whose location broadly overlaps with the microsatellite defined clusters. Migration analyses based on microsatellites point to moderate migration among the northern units located in the Albert Nile, Achwa River, Okole River, and Lake Kyoga drainages, but not between the northern units and the Victoria Nile drainage in the west. Effective population size estimates were variable with low to moderate sizes in most populations and with evidence of recent population bottlenecks, especially in the northeast unit of the Lake Kyoga drainage. Our microsatellite and mtDNA based analyses indicate that G. f. fuscipes movement along the Achwa and Okole rivers may facilitate northwest expansion of the Rhodesiense disease belt in Uganda. We identified tsetse migration corridors and recommend a rolling carpet approach from south of Lake Kyoga northward to minimize disease dispersal and prevent vector re-colonization. Additionally, our findings highlight the need for continuing tsetse monitoring efforts during and after control. Northern Uganda is an epidemiologically important region affected by human African trypanosomiasis (HAT) because it harbors both forms of the HAT disease (T. b. gambiense and T. b. rhodesiense). The geographic location of this region creates the risk that these distinct foci could merge, which would complicate diagnosis and treatment, and may result in recombination between the two parasite strains with as yet unknown consequences. Both strains require a tsetse fly vector for transmission, and in Uganda, G. f. fuscipes is the major vector of HAT. Controlling the vector remains one of the most effective strategies for controlling trypanosome parasites. However, vector control efforts may not be sustainable in terms of long term reduction in G. f. fuscipes populations due to population rebounds. Population genetics data can allow us to determine the likely source of population rebounds and to establish a more robust control strategy. In this study, we build on a previous broad spatial survey of G. f. fuscipes genetic structure in Uganda by adding more than 30 novel sampling sites that are strategically spaced across a region of northern Uganda that, for historical and political reasons, was severely understudied and faces particularly high disease risk. We identify natural population breaks, migration corridors and a hybrid zone with evidence of free interbreeding of G. f. fuscipes across the geographic region that spans the two HAT disease foci. We also find evidence of low effective population sizes and population bottlenecks in some areas that have been subjects of past control but remain regions of high tsetse density, which stresses the risk of population rebounds if monitoring is not explicitly incorporated into the control strategy. We use these results to make suggestions that will enhance the design and implementation of control activities in northern Uganda.
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Wang IJ, Shaffer HB. Population genetic and field-ecological analyses return similar estimates of dispersal over space and time in an endangered amphibian. Evol Appl 2017; 10:630-639. [PMID: 28616069 PMCID: PMC5469172 DOI: 10.1111/eva.12479] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/13/2017] [Indexed: 01/05/2023] Open
Abstract
The explosive growth of empirical population genetics has seen a proliferation of analytical methods leading to a steady increase in our ability to accurately measure key population parameters, including genetic isolation, effective population size, and gene flow, in natural systems. Assuming they yield similar results, population genetic methods offer an attractive complement to, or replacement of, traditional field‐ecological studies. However, empirical assessments of the concordance between direct field‐ecological and indirect population genetic studies of the same populations are uncommon in the literature. In this study, we investigate genetic isolation, rates of dispersal, and population sizes for the endangered California tiger salamander, Ambystoma californiense, across multiple breeding seasons in an intact vernal pool network. We then compare our molecular results to a previously published study based on multiyear, mark–recapture data from the same breeding sites. We found that field and genetic estimates of population size were only weakly correlated, but dispersal rates were remarkably congruent across studies and methods. In fact, dispersal probability functions derived from genetic data and traditional field‐ecological data were a significant match, suggesting that either method can be used effectively to assess population connectivity. These results provide one of the first explicit tests of the correspondence between landscape genetic and field‐ecological approaches to measuring functional population connectivity and suggest that even single‐year genetic samples can return biologically meaningful estimates of natural dispersal and gene flow.
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Affiliation(s)
- Ian J Wang
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCAUSA.,La Kretz Center for California Conservation Science Institute of the Environment and Sustainability University of California Los Angeles CA USA
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Singh SK, Aspi J, Kvist L, Sharma R, Pandey P, Mishra S, Singh R, Agrawal M, Goyal SP. Fine-scale population genetic structure of the Bengal tiger (Panthera tigris tigris) in a human-dominated western Terai Arc Landscape, India. PLoS One 2017; 12:e0174371. [PMID: 28445499 PMCID: PMC5405937 DOI: 10.1371/journal.pone.0174371] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 03/02/2017] [Indexed: 11/23/2022] Open
Abstract
Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial genetic structure and variation of tigers in TAL is needed to develop proper management strategies for achieving long-term conservation goals. We document, for the first time, the genetic characteristics of this tiger population by genotyping 71 tiger samples using 13 microsatellite markers from the western region of TAL (WTAL) of 1800 km2. Specifically, we aimed to estimate the genetic variability, population structure, and gene flow. The microsatellite markers indicated that the levels of allelic diversity (MNA = 6.6) and genetic variation (Ho = 0.50, HE = 0.64) were slightly lower than those reported previously in other Bengal tiger populations. We observed moderate gene flow and significant genetic differentiation (FST= 0.060) and identified the presence of cryptic genetic structure using Bayesian and non-Bayesian approaches. There was low and significantly asymmetric migration between the two main subpopulations of the Rajaji Tiger Reserve and the Corbett Tiger Reserve in WTAL. Sibship relationships indicated that the functionality of the corridor between these subpopulations may be retained if the quality of the habitat does not deteriorate. However, we found that gene flow is not adequate in view of changing land use matrices. We discuss the need to maintain connectivity by implementing the measures that have been suggested previously to minimize the level of human disturbance, including relocation of villages and industries, prevention of encroachment, and banning sand and boulder mining in the corridors.
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Affiliation(s)
- Sujeet Kumar Singh
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Jouni Aspi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Reeta Sharma
- Population and Conservation Genetics, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Puneet Pandey
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | - Randeep Singh
- Department of Wildlife Sciences, Amity University, Noida, India
| | - Manoj Agrawal
- Wildlife Institute of India, Chandrabani, Dehradun, India
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Ciofi C, Levato S, Manfredi T, Natali C, Nazirides T, Tepsich A, Crivelli AJ, Chelazzi G. Patterns of gene flow along linear habitats: population genetics of the European pond turtle (Emys orbicularis) in floodplain ponds. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blw008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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McDougall CA, Welsh AB, Gosselin T, Anderson WG, Nelson PA. Rethinking the influence of hydroelectric development on gene flow in a long-lived fish, the Lake Sturgeon Acipenser fulvescens. PLoS One 2017; 12:e0174269. [PMID: 28329005 PMCID: PMC5362236 DOI: 10.1371/journal.pone.0174269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/06/2017] [Indexed: 12/02/2022] Open
Abstract
Many hydroelectric dams have been in place for 50 - >100 years, which for most fish species means that enough generations have passed for fragmentation induced divergence to have accumulated. However, for long-lived species such as Lake Sturgeon, Acipenser fulvescens, it should be possible to discriminate between historical population structuring and contemporary gene flow and improve the broader understanding of anthropogenic influence. On the Winnipeg River, Manitoba, two hypotheses were tested: 1) Measureable quantities of former reservoir dwelling Lake Sturgeon now reside downstream of the Slave Falls Generating Station, and 2) genetically differentiated populations of Lake Sturgeon occur upstream and downstream, a result of historical structuring. Genetic methods based on ten microsatellite markers were employed, and simulations were conducted to provide context. With regards to contemporary upstream to downstream contributions, the inclusion of length-at-age data proved informative. Both pairwise relatedness and Bayesian clustering analysis substantiated that fast-growing outliers, apparently entrained after residing in the upstream reservoir for several years, accounted for ~15% of the Lake Sturgeon 525–750 mm fork length captured downstream. With regards to historical structuring, upstream and downstream populations were found to be differentiated (FST = 0.011, and 0.013–0.014 when fast-growing outliers were excluded), and heterozygosity metrics were higher for downstream versus upstream juveniles. Historical asymmetric (downstream) gene flow in the vicinity of the generating station was the most logical explanation for the observed genetic structuring. In this section of the Winnipeg River, construction of a major dam does not appear to have fragmented a previously panmictic Lake Sturgeon population, but alterations to habitat may be influencing upstream to downstream contributions in unexpected ways.
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Affiliation(s)
- Craig A. McDougall
- North/South Consultants Inc., Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
- * E-mail:
| | - Amy B. Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia, United States of America
| | | | - W. Gary Anderson
- Department of Biological Sciences, University of Manitoba, Winnipeg, Canada
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Heffelfinger JR, Nowak RM, Paetkau D. Clarifying historical range to aid recovery of the Mexican wolf. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21252] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
| | | | - David Paetkau
- Wildlife Genetics International; P. O. Box 274 Nelson BC V1L 5P9 Canada
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Coetzer WG, Downs CT, Perrin MR, Willows-Munro S. Testing of microsatellite multiplexes for individual identification of Cape Parrots ( Poicephalus robustus): paternity testing and monitoring trade. PeerJ 2017; 5:e2900. [PMID: 28344897 PMCID: PMC5363265 DOI: 10.7717/peerj.2900] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/12/2016] [Indexed: 12/04/2022] Open
Abstract
Background Illegal trade in rare wildlife species is a major threat to many parrot species around the world. Wildlife forensics plays an important role in the preservation of endangered or threatened wildlife species. Identification of illegally harvested or traded animals through DNA techniques is one of the many methods used during forensic investigations. Natural populations of the South African endemic Cape Parrot (Poicephalus robustus) are negatively affected by the removal of eggs and chicks for the pet trade. Methods In this study, 16 microsatellite markers specifically designed for the South African endemic Cape Parrot (P. robustus) are assessed for their utility in forensic casework. Using these 16 loci, the genetic diversity of a subset of the captive Cape Parrot population was also assessed and compared to three wild Cape Parrot populations. Results It was determined that the full 16 locus panel has sufficient discriminatory power to be used in parentage analyses and can be used to determine if a bird has been bred in captivity and so can be legally traded or if it has been illegally removed from the wild. In cases where birds have been removed from the wild, this study suggests that a reduced 12 locus microsatellite panel has sufficient power to assign confiscated birds to geographic population of origin. Discussion The level of genetic diversity observed within the captive Cape Parrot population was similar to that observed in the wild populations, which suggests that the captive population is not suffering from decreased levels of genetic diversity. The captive Cape Parrots did however have double the number of private alleles compared to that observed in the most genetically diverse wild population. This is probably due to the presence of rare alleles present in the founder population, which has not been lost due to genetic drift, as many of the individuals tested in this study are F1–F3 wild descendants. The results from this study provide a suit of markers that can be used to aid conservation and law enforcement authorities to better control legal and illegal trade of this South African endemic.
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Affiliation(s)
- Willem G Coetzer
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Colleen T Downs
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Mike R Perrin
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
| | - Sandi Willows-Munro
- School of Life Science, University of KwaZulu-Natal , Pietermaritzburg , South Africa
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Naqvi A, Mahmood S, Vahidi S, Abbas S, Utsunomiya Y, Garcia J, Periasamy K. Assessment of genetic diversity and structure of major sheep breeds from Pakistan. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2016.12.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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245
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A nearest neighbour approach by genetic distance to the assignment of individual trees to geographic origin. Forensic Sci Int Genet 2017; 27:132-141. [DOI: 10.1016/j.fsigen.2016.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 12/21/2016] [Accepted: 12/27/2016] [Indexed: 11/20/2022]
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McMillan LF, Fewster RM. Visualizations for genetic assignment analyses using the saddlepoint approximation method. Biometrics 2017; 73:1029-1041. [PMID: 28182851 DOI: 10.1111/biom.12667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 01/01/2017] [Accepted: 01/01/2017] [Indexed: 11/29/2022]
Abstract
We propose a method for visualizing genetic assignment data by characterizing the distribution of genetic profiles for each candidate source population. This method enhances the assignment method of Rannala and Mountain (1997) by calculating appropriate graph positions for individuals for which some genetic data are missing. An individual with missing data is positioned in the distributions of genetic profiles for a population according to its estimated quantile based on its available data. The quantiles of the genetic profile distribution for each population are calculated by approximating the cumulative distribution function (CDF) using the saddlepoint method, and then inverting the CDF to get the quantile function. The saddlepoint method also provides a way to visualize assignment results calculated using the leave-one-out procedure. This new method offers an advance upon assignment software such as geneclass2, which provides no visualization method, and is biologically more interpretable than the bar charts provided by the software structure. We show results from simulated data and apply the methods to microsatellite genotype data from ship rats (Rattus rattus) captured on the Great Barrier Island archipelago, New Zealand. The visualization method makes it straightforward to detect features of population structure and to judge the discriminative power of the genetic data for assigning individuals to source populations.
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Affiliation(s)
- L F McMillan
- Department of Statistics, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - R M Fewster
- Department of Statistics, The University of Auckland, Private Bag 92019, Auckland, New Zealand
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247
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Isselin-Nondedeu F, Trochet A, Joubin T, Picard D, Etienne R, Chevalier HL, Legrand D, Ribéron A. Spatial genetic structure of Lissotriton helveticus L. following the restoration of a forest ponds network. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0932-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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248
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Moura RF, Dawson DA, Nogueira DM. The use of microsatellite markers in Neotropical studies of wild birds: a literature review. AN ACAD BRAS CIENC 2017; 89:145-154. [PMID: 28177053 DOI: 10.1590/0001-3765201620160378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/16/2016] [Indexed: 11/22/2022] Open
Abstract
Despite extensive habitat fragmentation, the Neotropical region possesses 30% of the world´s bird species. Microsatellites have remained one of the most popular genetic markers and have been used in ecological and conservation studies since the 1990's. We conducted a literature review comparing the number of papers published from January 1990 to July 2015 that used microsatellite markers for studies of wild birds in the Neotropical region, USA and some European countries. We assigned the articles to three categories of studies: population genetics, animal behavior/kinship analysis and the development of species-specific bird microsatellite markers. We also compared the studies in the Neotropics that used heterologous versus species-specific markers and provide a list of heterologous markers of utility in multiple birds. Despite the rich bird fauna in the Neotropics, the number of articles published represents only 5.6% of that published by the USA and selected European countries. Within the Neotropical region, Brazil possessed 60.5% of the total papers published, with the remaining 39.5% shared between five countries. We conclude that the lack of specialized laboratories and resources still represents a limit to microsatellite-based genetic studies of birds within the Neotropical region. To overcome these limitations, we suggest the use of heterologous microsatellite markers as a cost-effective and time-effective tool to assist ecological studies of wild birds.
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Affiliation(s)
- Renan F Moura
- Universidade Federal Rural do Rio de Janeiro/UFRRJ, BR 465, Km 07, 23890-000 Seropédica, RJ, Brazil
| | - Deborah A Dawson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire, S10 2TN, UK
| | - Denise M Nogueira
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro/UFRRJ, BR 465 Km 07, 23890-000 Seropédica, RJ, Brazil
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249
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Rosel PE, Wilcox LA, Sinclair C, Speakman TR, Tumlin MC, Litz JA, Zolman ES. Genetic assignment to stock of stranded common bottlenose dolphins in southeastern Louisiana after the Deepwater Horizon oil spill. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00780] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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250
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Fischer ML, Salgado I, Beninde J, Klein R, Frantz AC, Heddergott M, Cullingham CI, Kyle CJ, Hochkirch A. Multiple founder effects are followed by range expansion and admixture during the invasion process of the raccoon (Procyon lotor) in Europe. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
| | - Iván Salgado
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales; Consejo Superior de Investigaciones Científicas; José Gutiérrez Abascal 2 28006 Madrid Spain
| | - Joscha Beninde
- Department of Biogeography; Trier University; 54286 Trier Germany
| | - Roland Klein
- Department of Biogeography; Trier University; 54286 Trier Germany
| | - Alain C. Frantz
- Musée National d'Histoire Naturelle; 2160 Luxembourg Luxembourg
| | - Mike Heddergott
- Musée National d'Histoire Naturelle; 2160 Luxembourg Luxembourg
| | | | | | - Axel Hochkirch
- Department of Biogeography; Trier University; 54286 Trier Germany
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