1
|
Riofrío M, Naranjo C, Mendoza A, Draper D, Marques I. Genetic diversity and structure in two epiphytic orchids from the montane forests of southern Ecuador: The role of overcollection on Masdevallia rosea in comparison with the widespread Pleurothallis lilijae. PLoS One 2023; 18:e0290604. [PMID: 37713402 PMCID: PMC10503748 DOI: 10.1371/journal.pone.0290604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 08/11/2023] [Indexed: 09/17/2023] Open
Abstract
Ecuador has a high diversity of orchids, but little is known about levels of genetic diversity for the great majority of species. Understanding how orchids might adapt to changes is crucial as deforestation and fragmentation of forest ecosystems threaten the survival of many epiphytic orchids that depend on other species, such as fungi and their host trees, for germination, growth, and establishment. Overcollection and the illegal trade are also major concerns for the survival of wild populations of orchids. Despite increasing awareness, effective interventions are often limited by a lack of data concerning the impacts that overexploitation might have. To fill this gap, we tested the effects of overcollection in the genetic diversity and structure of Masdevallia rosea, a narrow distributed epiphytic orchid historically collected in Ecuador, in comparison with the widely distributed Pleurothallis lilijae. Genotyping based on AFLPs showed reduced levels of diversity in wild populations but most especially in the overcollected, M. rosea. Overall, genetic admixture was high in P. lilijae segregating populations by altitude levels while fewer genetic groups were found in M. rosea. Genetic differentiation was low in both species. A spatial genetic structure was found in P. lilijae depending on altitude levels, while no spatial genetic structure was found in M. rosea. These results suggest different scenarios for the two species: while gene flow over long distance is possible in P. lilijae, the same seems to be unlikely in M. rosea possibly due to the low levels of individuals in the known populations. In situ and ex situ conservation strategies should be applied to protect the genetic pool in these epiphytic orchid species, and to promote the connectivity between wild populations. Adopting measures to reduce overexploitation and to understand the impacts of harvesting in wild populations are necessary to strengthen the legal trade of orchids.
Collapse
Affiliation(s)
- María Riofrío
- Department of Biology Sciences, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Carlos Naranjo
- Department of Biology Sciences, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - Alberto Mendoza
- Department of Biology Sciences, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - David Draper
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Lisbon, Portugal
| | - Isabel Marques
- Forest Research Centre (CEF) & Associate Laboratory TERRA, Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
2
|
Takayama K, Ohnishi N, Zedrosser A, Anezaki T, Tochigi K, Inagaki A, Naganuma T, Yamazaki K, Koike S. Timing and distance of natal dispersal in Asian black bears. J Mammal 2023; 104:265-278. [PMID: 37032704 PMCID: PMC10075337 DOI: 10.1093/jmammal/gyac118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/13/2022] [Indexed: 02/16/2023] Open
Abstract
Abstract
Dispersal has important implications for population ecology and genetics of a species through redistribution of individuals. In most mammals, males leave their natal area before they reach sexual maturity, whereas females are commonly philopatric. Here, we investigate the patterns of natal dispersal in the Asian black bear (Ursus thibetanus) based on data from 550 bears (378 males, 172 females) captured or removed in Gunma and Tochigi prefectures on central Honshu Island, Japan in 2003–2018. We used genetic data and parentage analysis to investigate sex-biased differences in the distance of natal dispersal. We further investigated the age of dispersal using spatial autocorrelation analysis, that is, the change in the correlation between genetic and geographic distances in each sex and age group. Our results revealed that male dispersal distances (mean ± SE = 17.4 ± 3.5 km) were significantly farther than female distances (4.8 ± 1.7 km), and the results were not affected by years of mast failures, a prominent forage source for this population. Based on an average adult female home range radius of 1.8 km, 96% of the males and 50% of the females dispersed. In the spatial autocorrelation analysis, the changes in the relationship between genetic and geographic distances were more pronounced in males compared to females. Males seem to mostly disperse at age 3 regardless of mast productivity, and they gradually disperse far from their home range, but young and inexperienced males may return to their natal home range in years with poor food conditions. The results suggest that factors driving the dispersal process seem to be population structure-based instead of forage availability-based. In females, a significant genetic relationship was observed among all individuals in the group with a minimum age of 6 years within a distance of 2 km, which resulted in the formation of matrilineal assemblages.
Collapse
Affiliation(s)
- Kaede Takayama
- Faculty of Agriculture, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-Cho, Fuchu, Tokyo 183-8509 , Japan
| | - Naoki Ohnishi
- Tohoku Research Center, Forestry and Forest Products Research Institute , 92-25 Nabeyashiki, Morioka, Iwate 020-0123 , Japan
| | - Andreas Zedrosser
- Department of Natural Sciences and Environmental Health, University of South-Eastern Norway , N-3800 Bø in Telemark , Norway
- Institute for Wildlife Biology and Game Management, University for Natural Resources and Life Sciences , Vienna, Gregor Mendel Str. 33, A-1180 Vienna , Austria
- Institute of Global Innovation, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-Cho, Fuchu, Tokyo 183-8509 , Japan
| | - Tomoko Anezaki
- Gunma Museum of Natural History , 1674-1 Kamikuroiwa, Tomioka, Gunma 370-2345 , Japan
| | - Kahoko Tochigi
- Faculty of Agriculture, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-Cho, Fuchu, Tokyo 183-8509 , Japan
| | - Akino Inagaki
- Faculty of Agriculture, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-Cho, Fuchu, Tokyo 183-8509 , Japan
| | - Tomoko Naganuma
- Institute of Global Innovation, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-Cho, Fuchu, Tokyo 183-8509 , Japan
| | - Koji Yamazaki
- Faculty of Regional Environmental Science, Tokyo University of Agriculture , 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502 , Japan
| | - Shinsuke Koike
- Institute of Global Innovation, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-Cho, Fuchu, Tokyo 183-8509 , Japan
- Institute of Agriculture, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-Cho, Fuchu, Tokyo 183-8509 , Japan
| |
Collapse
|
3
|
Liebgold EB, Dickey MJ, Lamb SM, Howell HJ, Ransom TS. (Not) far from home: No sex bias in dispersal, but limited genetic patch size, in an endangered species, the Spotted Turtle ( Clemmys guttata). Ecol Evol 2023; 13:e9734. [PMID: 36620419 PMCID: PMC9812832 DOI: 10.1002/ece3.9734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
Sex-biased dispersal is common in many animals, with male-biased dispersal often found in studies of mammals and reptiles, including interpretations of spatial genetic structure, ostensibly as a result of male-male competition and a lack of male parental care. Few studies of sex-biased dispersal have been conducted in turtles, but a handful of studies, in saltwater turtles and in terrestrial turtles, have detected male-biased dispersal as expected. We tested for sex-biased dispersal in the endangered freshwater turtle, the spotted turtle (Clemmys guttata) by investigating fine-scale genetic spatial structure of males and females. We found significant spatial genetic structure in both sexes, but the patterns mimicked each other. Both males and females typically had higher than expected relatedness at distances <25 km, and in many distance classes greater than 25 km, less than expected relatedness. Similar patterns were apparent whether we used only loci in Hardy-Weinberg equilibrium (n = 7) or also included loci with potential null alleles (n = 5). We conclude that, contrary to expectations, sex-biased dispersal is not occurring in this species, possibly related to the reverse sexual dimorphism in this species, with females having brighter colors. We did, however, detect significant spatial genetic structure in males and females, separate and combined, showing philopatry within a genetic patch size of <25 km in C. guttata, which is concerning for an endangered species whose populations are often separated by distances greater than the genetic patch size.
Collapse
Affiliation(s)
- Eric B. Liebgold
- Department of Biological SciencesSalisbury UniversitySalisburyMarylandUSA
| | - Myra J. Dickey
- Department of EntomologyTexas A & M UniversityCollege StationTexasUSA
| | - Stephanie M. Lamb
- Department of Biological SciencesSalisbury UniversitySalisburyMarylandUSA
| | | | - Tami S. Ransom
- Department of Environmental StudiesSalisbury UniversitySalisburyMarylandUSA
| |
Collapse
|
4
|
Szép E, Trubenová B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Mol Ecol Resour 2022; 22:2941-2955. [PMID: 35765749 PMCID: PMC9796524 DOI: 10.1111/1755-0998.13676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 06/02/2022] [Accepted: 06/16/2022] [Indexed: 01/01/2023]
Abstract
Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST , a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST . Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size.
Collapse
Affiliation(s)
- Enikő Szép
- IST Austria (Institute of Science and Technology Austria)KlosterneuburgAustria
| | - Barbora Trubenová
- IST Austria (Institute of Science and Technology Austria)KlosterneuburgAustria,Department of Environmental Systems ScienceETH ZurichZurichSwitzerland
| | - Katalin Csilléry
- Biodiversity and Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
| |
Collapse
|
5
|
Trapnell DW, Hamrick JL. Genetic inference of orchid population dynamics on different‐aged lava flows in Costa Rica. Biotropica 2022. [DOI: 10.1111/btp.13163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
6
|
Wang F, Mi X, Chen L, Xu W, Durka W, Swenson NG, Johnson DJ, Worthy SJ, Xue J, Zhu Y, Schmid B, Liang Y, Ma K. Differential impacts of adult trees on offspring and non-offspring recruits in a subtropical forest. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1905-1913. [PMID: 36098896 DOI: 10.1007/s11427-021-2148-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
An important mechanism promoting species coexistence is conspecific negative density dependence (CNDD), which inhibits conspecific neighbors by accumulating host-specific enemies near adult trees. Natural enemies may be genotype-specific and regulate offspring dynamics more strongly than non-offspring, which is often neglected due to the difficulty in ascertaining genetic relatedness. Here, we investigated whether offspring and non-offspring of a dominant species, Castanopsis eyrei, suffered from different strength of CNDD based on parentage assignment in a subtropical forest. We found decreased recruitment efficiency (proxy of survival probability) of offspring compared with non-offspring near adult trees during the seedling-sapling transition, suggesting genotype-dependent interactions drive tree demographic dynamics. Furthermore, the genetic similarity between individuals of same cohort decreased in late life history stages, indicating genetic-relatedness-dependent tree mortality throughout ontogeny. Our results demonstrate that within-species genetic relatedness significantly affects the strength of CNDD, implying genotype-specific natural enemies may contribute to population dynamics in natural forests.
Collapse
Affiliation(s)
- Fang Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lei Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wubing Xu
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Walter Durka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Department Community Ecology, Centre for Environmental Research-UFZ, Theodor-Lieser-Str. 4, Halle, 06120, Germany
| | - Nathan G Swenson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, 46556, USA
- University of Notre Dame Environmental Research Center, Land O'Lakes, Wisconsin, 54540, USA
| | - Daniel J Johnson
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, 32611, USA
| | - Samantha J Worthy
- Department of Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Jianhua Xue
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yan Zhu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Bernhard Schmid
- Department of Geography, Remote Sensing Laboratories, University of Zürich, Zürich, CH-8006, Switzerland
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100085, China
| | - Yu Liang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
7
|
Scientometric Analysis for Spatial Autocorrelation-Related Research from 1991 to 2021. ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION 2022. [DOI: 10.3390/ijgi11050309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Spatial autocorrelation describes the interdependent relationship between the realizations or observations of a variable that is distributed across a geographical landscape, which may be divided into different units/areas according to natural or political boundaries. Researchers of Geographical Information Science (GIS) always consider spatial autocorrelation. However, spatial autocorrelation research covers a wide range of disciplines, not only GIS, but spatial econometrics, ecology, biology, etc. Since spatial autocorrelation relates to multiple disciplines, it is difficult gain a wide breadth of knowledge on all its applications, which is very important for beginners to start their research as well as for experienced scholars to consider new perspectives in their works. Scientometric analyses are conducted in this paper to achieve this end. Specifically, we employ scientometrc indicators and scientometric network mapping techniques to discover influential journals, countries, institutions, and research communities; key topics and papers; and research development and trends. The conclusions are: (1) journals categorized into ecological and biological domains constitute the majority of TOP journals;(2) northern American countries, European countries, Australia, Brazil, and China contribute the most to spatial autocorrelation-related research; (3) eleven research communities consisting of three geographical communities and eight communities of other domains were detected; (4) hot topics include spatial autocorrelation analysis for molecular data, biodiversity, spatial heterogeneity, and variability, and problems that have emerged in the rapid development of China; and (5) spatial statistics-based approaches and more intensive problem-oriented applications are, and still will be, the trend of spatial autocorrelation-related research. We also refine the results from a geographer’s perspective at the end of this paper.
Collapse
|
8
|
Honka J, Baini S, Searle JB, Kvist L, Aspi J. Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population. Ecol Evol 2022; 12:e8547. [PMID: 35127046 PMCID: PMC8796947 DOI: 10.1002/ece3.8547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸ ST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise F ST-values = 0.002-0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average H E = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (F IS = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (Anser brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.
Collapse
Affiliation(s)
- Johanna Honka
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Serena Baini
- Department of BiologyUniversity of Rome “Tor Vergata”RomeItaly
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| |
Collapse
|
9
|
OUP accepted manuscript. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac031] [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]
|
10
|
Population genetics informs the management of a controversial Australian waterbird. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01393-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
11
|
Onley IR, Austin JJ, Mitchell KJ, Moseby KE. Understanding dispersal patterns can inform future translocation strategies: A case study of the threatened greater stick‐nest rat (
Leporillus conditor
). AUSTRAL ECOL 2021. [DOI: 10.1111/aec.13100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Isabelle R. Onley
- School of Biological Sciences Australian Centre for Ancient DNA (ACAD) University of Adelaide Adelaide South Australia 5005Australia
| | - Jeremy J. Austin
- School of Biological Sciences Australian Centre for Ancient DNA (ACAD) University of Adelaide Adelaide South Australia 5005Australia
| | - Kieren J. Mitchell
- School of Biological Sciences Australian Centre for Ancient DNA (ACAD) University of Adelaide Adelaide South Australia 5005Australia
- School of Biological Sciences ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH) University of Adelaide Adelaide South AustraliaAustralia
| | - Katherine E. Moseby
- Centre for Ecosystem Sciences, Earth and Environmental Sciences University of New South Wales Sydney New South Wales Australia
| |
Collapse
|
12
|
Major EI, Höhn M, Avanzi C, Fady B, Heer K, Opgenoorth L, Piotti A, Popescu F, Postolache D, Vendramin GG, Csilléry K. Fine-scale spatial genetic structure across the species range reflects recent colonization of high elevation habitats in silver fir (Abies alba Mill.). Mol Ecol 2021; 30:5247-5265. [PMID: 34365696 PMCID: PMC9291806 DOI: 10.1111/mec.16107] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 07/07/2021] [Accepted: 07/16/2021] [Indexed: 12/03/2022]
Abstract
Variation in genetic diversity across species ranges has long been recognized as highly informative for assessing populations’ resilience and adaptive potential. The spatial distribution of genetic diversity within populations, referred to as fine‐scale spatial genetic structure (FSGS), also carries information about recent demographic changes, yet it has rarely been connected to range scale processes. We studied eight silver fir (Abies alba Mill.) population pairs (sites), growing at high and low elevations, representative of the main genetic lineages of the species. A total of 1,368 adult trees and 540 seedlings were genotyped using 137 and 116 single nucleotide polymorphisms (SNPs), respectively. Sites revealed a clear east‐west isolation‐by‐distance pattern consistent with the post‐glacial colonization history of the species. Genetic differentiation among sites (FCT = 0.148) was an order of magnitude greater than between elevations within sites (FSC = 0.031), nevertheless high elevation populations consistently exhibited a stronger FSGS. Structural equation modelling revealed that elevation and, to a lesser extent, post‐glacial colonization history, but not climatic and habitat variables, were the best predictors of FSGS across populations. These results suggest that high elevation habitats have been colonized more recently across the species range. Additionally, paternity analysis revealed a high reproductive skew among adults and a stronger FSGS in seedlings than in adults, suggesting that FSGS may conserve the signature of demographic changes for several generations. Our results emphasize that spatial patterns of genetic diversity within populations provide information about demographic history complementary to non‐spatial statistics, and could be used for genetic diversity monitoring, especially in forest trees.
Collapse
Affiliation(s)
- Enikő I Major
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Mária Höhn
- Department of Botany, Hungarian University of Agronomy and Life Sciences, Budapest, Hungary
| | - Camilla Avanzi
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Bruno Fady
- Ecology of Mediterranean Forests (URFM), INRAE, UR629, Avignon, France
| | - Katrin Heer
- Conservation Biology, Philipps Universität Marburg, Marburg, Germany
| | - Lars Opgenoorth
- Plant Ecology and Geobotany, Philipps Universität Marburg, Marburg, Germany.,Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Andrea Piotti
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Flaviu Popescu
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Dragos Postolache
- National Institute for Research and Development in Forestry "Marin Drăcea", Ilfov County, Romania
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Sesto Fiorentino (Firenze), Italy
| | - Katalin Csilléry
- Land Change Science, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| |
Collapse
|
13
|
Garrett LJH, Myatt JP, Sadler JP, Dawson DA, Hipperson H, Colbourne JK, Dickey RC, Weber SB, Reynolds SJ. Spatio-temporal processes drive fine-scale genetic structure in an otherwise panmictic seabird population. Sci Rep 2020; 10:20725. [PMID: 33244100 PMCID: PMC7691516 DOI: 10.1038/s41598-020-77517-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/09/2020] [Indexed: 11/09/2022] Open
Abstract
When and where animals breed can shape the genetic structure and diversity of animal populations. The importance of drivers of genetic diversity is amplified in island populations that tend to have more delineated gene pools compared to continental populations. Studies of relatedness as a function of the spatial distribution of individuals have demonstrated the importance of spatial organisation for individual fitness with outcomes that are conditional on the overall genetic diversity of the population. However, few studies have investigated the impact of breeding timing on genetic structure. We characterise the fine-scale genetic structure of a geographically-isolated population of seabirds. Microsatellite markers provide evidence for largely transient within-breeding season temporal processes and limited spatial processes, affecting genetic structure in an otherwise panmictic population of sooty terns Onychoprion fuscatus. Earliest breeders had significantly different genetic structure from the latest breeders. Limited evidence was found for localised spatial structure, with a small number of individuals being more related to their nearest neighbours than the rest of the population. Therefore, population genetic structure is shaped by heterogeneities in collective movement in time and to a lesser extent space, that result in low levels of spatio-temporal genetic structure and the maintenance of genetic diversity.
Collapse
Affiliation(s)
- Lucy J H Garrett
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK. .,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK. .,Department of Animal and Agriculture, Hartpury University, Gloucester, UK.
| | - Julia P Myatt
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Jon P Sadler
- School of Geography, Earth and Environmental Sciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Deborah A Dawson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - John K Colbourne
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Roger C Dickey
- The Army Ornithological Society (AOS), c/o Prince Consort Library, Knollys Road, Aldershot, Hampshire, UK
| | - Sam B Weber
- Ascension Island Government Conservation and Fisheries Department (AIGCFD), Ascension Island, UK.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - S James Reynolds
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK.,The Army Ornithological Society (AOS), c/o Prince Consort Library, Knollys Road, Aldershot, Hampshire, UK
| |
Collapse
|
14
|
SHARMA HIMANI, SHARMA REKHA, AHLAWAT SONIKA, N RAJAK, JAIN ASIT, TANTIA MS. Genetic diversity status of only registered cattle breed of Chhattisgarh-Kosali. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i6.104993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Assessment of diversity is essential for germplasm characterization and management. Kosali is the first and only registered breed of Chhattisgarh state which immensely contributes to the local economy of 70% farmers. Genomic microsatellite markers being valuable tool for estimating genetic diversity were selected for exploring existing genetic variability in Kosali cattle population. The standard metrics of genomic diversity detected high variability in this breed. All the loci were polymorphic resulting in 297 alleles. Mean values of observed and expected number of alleles were 11.423±0.877 and 4.989±0.372, respectively. Similarly, higher mean values of observed heterozygosity (0.693±0.031) also corroborated with the allelic diversity. Mean expected heterozygosity (0.765±0.02) under Hardy-Weinberg equilibrium (HWE) was higher than the observed values indicating some deviations from assumptions of the model. It can be attributed to the forces such as inbreeding. In fact a positive FIS value of 0.088±0.038 indicated some heterozygote deficiency in the population. Bottleneck analysis indicated that Kosali cattle have not suffered any population bottleneck event during evolutionary trajectory. This study is first to report the genetic diversity status of Kosali cattle based on microsatellite markers.The results imply the necessity of management programs in order to conserve the existing genetic variation and to avoid any escalation of inbreeding.
Collapse
|
15
|
Latorre-Cardenas MC, Gutiérrez-Rodríguez C, Rico Y. Estimating genetic and demographic parameters relevant for the conservation of the Neotropical otter, Lontra longicaudis, in Mexico. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
16
|
Pacioni C, Atkinson A, Wayne AF, Maxwell MA, Ward CG, Spencer PBS. Spatially sensitive harvest design can minimize genetic relatedness and enhance genetic outcomes in translocation programmes. J Zool (1987) 2020. [DOI: 10.1111/jzo.12791] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. Pacioni
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
- Department of Environment, Land, Water and Planning Arthur Rylah Institute Heidelberg Vic Australia
| | - A. Atkinson
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
| | - A. F. Wayne
- Department of Biodiversity, Conservation and Attractions Biodiveristy and Conservation Science Manjimup WA Australia
| | - M. A. Maxwell
- Department of Biodiversity, Conservation and Attractions Biodiveristy and Conservation Science Manjimup WA Australia
| | - C. G. Ward
- Department of Biodiversity, Conservation and Attractions Biodiveristy and Conservation Science Manjimup WA Australia
| | - P. B. S. Spencer
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
| |
Collapse
|
17
|
Cuypers LN, Baird SJE, Hánová A, Locus T, Katakweba AS, Gryseels S, Bryja J, Leirs H, Goüy de Bellocq J. Three arenaviruses in three subspecific natal multimammate mouse taxa in Tanzania: same host specificity, but different spatial genetic structure? Virus Evol 2020; 6:veaa039. [PMID: 33033629 PMCID: PMC7532547 DOI: 10.1093/ve/veaa039] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mastomys natalensis is widespread in sub-Saharan Africa and hosts several arenavirus species, including the pathogenic zoonotic Lassa virus in West Africa. Mitochondrial lineages sub-divide the range of M. natalensis and have been associated with cryptic structure within the species. To test specificity of arenaviruses to hosts carrying these lineages, we screened 1772 M. natalensis in a large area of Tanzania where three mitochondrial lineages meet. We detected fifty-two individuals that were positive for one of three arenaviruses: Gairo, Morogoro, and Luna virus. This is the first record of Luna virus in Tanzania. We confirmed the specificity of each arenavirus to a distinct host mitochondrial lineage except for three cases in one locality at the centre of a host hybrid zone. No arenaviruses were detected in a large part of the study area. Morogoro and Gairo virus showed differences in prevalence (Morogoro virus lower than Gairo virus) and in genetic structure (Morogoro virus more structured than Gairo virus). However, both viruses have genetic neighbourhood size estimates of the same order of magnitude as Lassa virus. While differences in arenavirus and/or host evolutionary and ecological dynamics may exist, Tanzanian arenaviruses could be suited to model Lassa virus dynamics in M. natalensis.
Collapse
Affiliation(s)
- Laura N Cuypers
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Stuart J E Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
| | - Alexandra Hánová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Tatjana Locus
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Abdul S Katakweba
- Pest Management Centre, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sophie Gryseels
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic.,Department of Botany and Zoology, Masaryk University, Brno, Czech Republic
| | - Herwig Leirs
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | | |
Collapse
|
18
|
Scherm B, Balmas V, Infantino A, Aragona M, Valente MT, Desiderio F, Marcello A, Phanthavong S, Burgess LW, Rau D. Clonality, spatial structure, and pathogenic variation in Fusarium fujikuroi from rain-fed rice in southern Laos. PLoS One 2019; 14:e0226556. [PMID: 31869352 PMCID: PMC6927642 DOI: 10.1371/journal.pone.0226556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 11/29/2019] [Indexed: 11/18/2022] Open
Abstract
Bakanae disease, caused by the fungal phytopathogen Fusarium fujikuroi, can be detected in most rice (Oryza sativa L.) growing areas worldwide. In this study, we investigated the population structure of this fungus in southern Lao PDR, a country located near the geographic origin of rice domestication. Microsatellites (SSRs) and mating type (MAT) analyses, pathogenicity and fungicide sensitivity tests were integrated in the study. The first key finding is that the population genetic structure of F. fujikuroi in Lao PDR is consistent with high clonal reproduction. Indeed, (i) “true” clones were identified; (ii) within populations, MAT types were frequently skewed from 1:1 ratio, (iii) linkage disequilibrium (among SSRs as also among SSRs and MAT) was present, and (iv) gene-flow between opposite MAT types within the same population is restricted. The presence of genetic divergence among areas and populations and the occurrence of positive spatial autocorrelation of genetic variation, indicate that migration is restricted, and that genetic drift plays an important role in the evolution of this fungus. Two main well-defined groups of isolates were detected (FST = 0.213) that display a non-random spatial distribution. They differ in the ability to induce seedlings death but not seedlings elongation (the typical Bakanae symptom) suggesting that the pathogen’s ability to induce the two symptoms is under different genetic control. Finally, we compared two agroecosystems with contrasting characteristics: low-input and traditional (Lao PDR) vs high-input and modern (Italy). We found differences in the level of population structuring and of spatial autocorrelation. This suggests that the evolutionary potential of the fungus not only depends on its intrinsic characteristics, but is strongly influenced by other external factors, most likely by the dynamics of infested seed exchange. Thus, quarantine and chemical treatments are a way to reduce population connectivity and hence the evolutionary potential of this pathogen.
Collapse
Affiliation(s)
- Barbara Scherm
- Dipartimento di Agraria, Sezione di Patologia ed Entomologia, Università degli Studi di Sassari, Sassari, Italy
| | - Virgilio Balmas
- Dipartimento di Agraria, Sezione di Patologia ed Entomologia, Università degli Studi di Sassari, Sassari, Italy
| | - Alessandro Infantino
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Maria Aragona
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Maria Teresa Valente
- Council for Agricultural Research and Economics (CREA), Research Centre for Plant Protection and Certification, Rome, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda (PC), Italy
| | - Angela Marcello
- Dipartimento di Agraria, Sezione di Patologia ed Entomologia, Università degli Studi di Sassari, Sassari, Italy
| | - Sengphet Phanthavong
- Provincial Agriculture and Forestry, Thaluang Village, Pakse, Champasak, Lao PDR
| | - Lester W. Burgess
- Sydney Insitute of Agriculture, Faculty of Science, University of Sydney, New South Wales, Australia
| | - Domenico Rau
- Dipartimento di Agraria, Sezione di Patologia ed Entomologia, Università degli Studi di Sassari, Sassari, Italy
- * E-mail:
| |
Collapse
|
19
|
Binns LA, Loughry WJ, McDonough CM, Anderson CD. Spatial genetic structure within a population of nine-banded armadillos in western Mississippi. J Mammal 2019. [DOI: 10.1093/jmammal/gyz174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractThe nine-banded armadillo (Dasypus novemcinctus) is unique among mammals because females produce litters of genetically identical quadruplets via monozygotic polyembryony. This unusual form of reproduction could have profound impacts on the spatial genetic structure of populations of armadillos, but at present it is unclear whether littermates remain together as adults, or if sex-biased dispersal occurs. The goal of our study was to determine whether fine-scale spatial genetic structure (FSGS) within a population of armadillos diminishes with age (i.e., from juvenile to adult due to the dispersal of littermates away from one another), and if the degree of FSGS for a given age class differs between the sexes. We obtained genotype data at seven microsatellite DNA loci for 421 individuals in a wild population of armadillos inhabiting the Yazoo National Wildlife Refuge in western Mississippi. Correlogram analyses based on measures of spatial genetic autocorrelation showed weak but significant FSGS that was driven by positive spatial genetic autocorrelation among both male and female juveniles and adult males, but not adult females. Positive spatial genetic autocorrelation among adult males could be due to either female-biased dispersal or high variance in male reproductive success. Further work is required to discriminate between these two possibilities.
Collapse
Affiliation(s)
- Loren A Binns
- Department of Biology, Valdosta State University, Valdosta, GA, USA
| | - W J Loughry
- Department of Biology, Valdosta State University, Valdosta, GA, USA
| | | | | |
Collapse
|
20
|
Li J, Lv L, Wang P, Wang Y, Hatchwell BJ, Zhang Z. Sex-biased dispersal patterns of a social passerine: complementary approaches and evidence for a role of spatial scale. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractAnimal dispersal patterns have important implications for many biological processes, but the measurement of dispersal is challenging and often requires the use of complementary approaches. In this study, we investigated the local-scale sex-biased dispersal pattern in a social bird, the black-throated tit (Aegithalos concinnus), in central China. Spatial genetic autocorrelation analyses suggested that significant fine-scale genetic structure existed in males but not in females. Mark–recapture analyses of ringed individuals also showed that female offspring were more dispersive than male offspring, supporting genetic evidence of local female-biased dispersal. These results were contrary to a previous finding of male-biased long-distance dispersal in this species that was based on analyses of gene flow across the species range in China. This implies that the species might potentially have a scale-dependent dispersal strategy, with females frequently dispersing further than males at the local level, but with a proportion of males occasionally dispersing over long distances and contributing more to gene flow at a larger geographical scale. Long-distance dispersal by male black-throated tits might be induced by competition for resources or by unfavourable environmental conditions, warranting further investigation, but our findings increase the evidence that geographical scale is an important factor to be considered when investigating animal dispersal patterns.
Collapse
Affiliation(s)
- Jianqiang Li
- School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Lei Lv
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Pengcheng Wang
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yong Wang
- Department of Biological and Environmental Sciences, School of Agricultural, Life and Natural Sciences, Alabama A&M University, Normal, AL, USA
| | - Ben J Hatchwell
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Zhengwang Zhang
- Ministry of Education Key Laboratory for Biodiversity Sciences and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
21
|
Santos TL, Fernandes C, Henley MD, Dawson DA, Mumby HS. Conservation Genetic Assessment of Savannah Elephants ( Loxodonta africana) in the Greater Kruger Biosphere, South Africa. Genes (Basel) 2019; 10:E779. [PMID: 31590388 PMCID: PMC6826889 DOI: 10.3390/genes10100779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/12/2019] [Accepted: 09/29/2019] [Indexed: 11/24/2022] Open
Abstract
Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500-700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.
Collapse
Affiliation(s)
- Teresa L Santos
- Bull Elephant Network Project, Conservation Science Group, David Attenborough Building, Pembroke St, Cambridge CB2 3QY, UK.
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire S10 2TN, UK.
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal.
| | - Carlos Fernandes
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal.
| | - Michelle D Henley
- Applied Behavioural Ecology and Ecosystem Research Unit, University of South Africa, Florida Campus, Private Bag X6, Florida 1710, Johannesburg, South Africa.
- Elephants Alive, P.O. Box 960. Hoedspruit 1380, South Africa.
| | - Deborah A Dawson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire S10 2TN, UK.
| | - Hannah S Mumby
- Bull Elephant Network Project, Conservation Science Group, David Attenborough Building, Pembroke St, Cambridge CB2 3QY, UK.
- Centre for African Ecology, School of Animal, Plant and Environmental Sciences, University of Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg 2000, South Africa.
- Wissenschaftskolleg zu Berlin, Wallotstraße 19, Berlin 14193, Germany.
- School of Biological Sciences and Department of Politics and Public Administration, University of Hong Kong, Hong Kong, China.
| |
Collapse
|
22
|
Schlesselmann AV, Dussex N, Cooper J, Monks JM, O'Donnell CFJ, Robertson BC. Contrasting patterns of population structure at large and fine geographical scales in a migratory avian disturbance specialist of braided river ecosystems. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Ann‐Kathrin V. Schlesselmann
- Manaaki Whenua Landcare Research Dunedin New Zealand
- Department of Zoology University of Otago Dunedin New Zealand
| | - Nicolas Dussex
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Jamie Cooper
- Department of Zoology University of Otago Dunedin New Zealand
| | - Joanne M. Monks
- Department of Conservation Biodiversity Group Dunedin New Zealand
| | | | | |
Collapse
|
23
|
Morales‐González S, Giles EC, Quesada‐Calderón S, Saenz‐Agudelo P. Fine-scale hierarchical genetic structure and kinship analysis of the ascidian Pyura chilensis in the southeastern Pacific. Ecol Evol 2019; 9:9855-9868. [PMID: 31534699 PMCID: PMC6745665 DOI: 10.1002/ece3.5526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Studying population structure and genetic diversity at fine spatial scales is key for a better understanding of demographic processes that influence population connectivity. This is particularly important in marine benthic organisms that rely on larval dispersal to maintain connectivity among populations. Here, we report the results of a genetic survey of the ascidian Pyura chilensis from three localities along the southeastern Pacific. This study follows up on a previous report that described a genetic break in this region among localities only 20 km apart. By implementing a hierarchical sampling design at four spatial levels and using ten polymorphic microsatellite markers, we test whether differences in fine-scale population structure explain the previously reported genetic break. We compared genetic spatial autocorrelations, as well as kinship and relatedness distributions within and among localities adjacent to the genetic break. We found no evidence of significant autocorrelation at the scale up to 50 m despite the low dispersal potential of P. chilensis that has been reported in the literature. We also found that the proportion of related individuals in close proximity (<1 km) was higher than the proportion of related individuals further apart. These results were consistent in the three localities. Our results suggest that the spatial distribution of related individuals can be nonrandom at small spatial scales and suggests that dispersal might be occasionally limited in this species or that larval cohorts can disperse in the plankton as clustered groups. Overall, this study sheds light on new aspects of the life of this ascidian as well as confirms the presence of a genetic break at 39°S latitude. Also, our data indicate there is not enough evidence to confirm that this genetic break can be explained by differences in fine-scale genetic patterns among localities.
Collapse
Affiliation(s)
- Sarai Morales‐González
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
- Magister en Ciencias Mención GenéticaEscuela de GraduadosFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Emily C. Giles
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
- Doctorado en Ciencias Mención Ecología y EvoluciónEscuela de GraduadosFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Suany Quesada‐Calderón
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
- Doctorado en Ciencias Mención Ecología y EvoluciónEscuela de GraduadosFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Pablo Saenz‐Agudelo
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de ChileValdiviaChile
| |
Collapse
|
24
|
Bonzi VR, Carneiro CM, Wisely SM, Monadjem A, McCleery RA, Gumbi B, Austin JD. Comparative spatial genetic structure of two rodent species in an agro-ecological landscape in southern Africa. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
25
|
Genetic consequences of social dynamics in the Andean condor: the role of sex and age. Behav Ecol Sociobiol 2019. [DOI: 10.1007/s00265-019-2714-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
26
|
Xu NN, Jiang K, Biswas SR, Tong X, Wang R, Chen XY. Clone Configuration and Spatial Genetic Structure of Two Halophila ovalis Populations With Contrasting Internode Lengths. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
27
|
Yu S, Wu Y, Serrao EA, Zhang J, Jiang Z, Huang C, Cui L, Thorhaug A, Huang X. Fine-scale genetic structure and flowering output of the seagrass Enhalus acoroides undergoing disturbance. Ecol Evol 2019; 9:5186-5195. [PMID: 31110671 PMCID: PMC6509391 DOI: 10.1002/ece3.5106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/04/2022] Open
Abstract
Seagrass are under great stress in the tropical coast of Asia, where Enhalus acoroides is frequently the dominant species with a large food web. Here, we investigate the question of the fine-scale genetic structure of this ecologically important foundation species, subject to severe anthropogenic disturbance in China. The genetic structure will illuminate potential mechanisms for population dynamics and sustainability, which are critical for preservation of biodiversity and for decision-making in management and restoration. We evaluated the fine-scale spatial genetic structure (SGS) and flowering output of E. acoroides, and indirectly estimated the relative importance of sexual versus asexual reproduction for population persistence using spatial autocorrelation analysis. Results reveal high clonal diversity for this species, as predicted from its high sexual reproduction output. The stronger Sp statistic at the ramet-level compared with genet-level indicates that clonality increases the SGS pattern for E. acoroides. Significant SGS at the genet-level may be explained by the aggregated dispersal of seed/pollen cohorts. The estimated gene dispersal variance suggests that dispersal mediated by sexual reproduction is more important than clonal growth in this study area. The ongoing anthropogenic disturbance will negatively affect the mating pattern and the SGS patterns in the future due to massive death of shoots, and less frequency of sexual reproduction.
Collapse
Affiliation(s)
- Shuo Yu
- Fourth Institute of OceanographyMinistry of Natural ResourcesBeihaiChina
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Jingping Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
| | - Chi Huang
- Ocean University of ChinaQingdaoChina
| | - Lijun Cui
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Anitra Thorhaug
- School of Forestry an Environmental StudiesYale UniversityNew HavenConnecticut
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology, South China Sea Institute of OceanologyChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| |
Collapse
|
28
|
Torres E, Riofrío ML, Iriondo JM. Complex fine-scale spatial genetic structure in Epidendrum rhopalostele: an epiphytic orchid. Heredity (Edinb) 2019; 122:458-467. [PMID: 30185924 PMCID: PMC6460762 DOI: 10.1038/s41437-018-0139-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/06/2018] [Accepted: 08/05/2018] [Indexed: 11/08/2022] Open
Abstract
Orchid seeds are presumably dispersed by wind due to their very small size and thus can potentially travel long distances. However, the few related studies indicate that seeds fall close to their mother plants. Because seed dispersal and colonization patterns can have relevant consequences for long-term species persistence, we assessed the fine-scale genetic structure of the epiphytic orchid Epidendrum rhopalostele to provide insight into these patterns. All individuals in the studied population were georeferenced and genotyped with AFLP-markers. Genetic structure was evaluated at two levels (forest and tree) using three approaches: principal coordinates analysis, model-based clustering, and spatial autocorrelation analysis. Results showed two genetic groups, composed of individuals from almost every tree with orchids. Spatial autocorrelation analysis at the forest level found no significant genetic structure when all individuals were considered, but a pattern of genetic patches was revealed when the analysis was performed separately for each group. Genetic patches had an estimated diameter of 4 m and were composed of individuals from more than one tree. A weak genetic structure was detected at the tree level at distances less than 1.5 m. These results suggest that many seeds fall close to the mother plant and become established in the same host tree. Additionally, a sequential colonization process seems to be the predominant mode of expansion, whereby progeny from orchids in one tree colonize neighboring trees. Thus, the existence of two distinct genetic groups and the presence of genetic patches should be considered when seed sampling for ex situ conservation.
Collapse
Affiliation(s)
- Elena Torres
- Department of Biotechnology-Plant Biology, Universidad Politécnica de Madrid, Madrid, Spain.
| | - María-Lorena Riofrío
- Department of Biological Sciences, Universidad Técnica Particular de Loja, Loja, Ecuador
| | - José M Iriondo
- Area of Biodiversity and Conservation, Universidad Rey Juan Carlos, Móstoles, Spain
| |
Collapse
|
29
|
Zecchin B, De Nardi M, Nouvellet P, Vernesi C, Babbucci M, Crestanello B, Bagó Z, Bedeković T, Hostnik P, Milani A, Donnelly CA, Bargelloni L, Lorenzetto M, Citterio C, Obber F, De Benedictis P, Cattoli G. Genetic and spatial characterization of the red fox (Vulpes vulpes) population in the area stretching between the Eastern and Dinaric Alps and its relationship with rabies and canine distemper dynamics. PLoS One 2019; 14:e0213515. [PMID: 30861028 PMCID: PMC6413928 DOI: 10.1371/journal.pone.0213515] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/24/2019] [Indexed: 01/02/2023] Open
Abstract
Information on the population dynamics of a reservoir species have been increasingly adopted to understand and eventually predict the dispersal patterns of infectious diseases throughout an area. Although potentially relevant, to date there are no studies which have investigated the genetic structure of the red fox population in relation to infectious disease dynamics. Therefore, we genetically and spatially characterised the red fox population in the area stretching between the Eastern and Dinaric Alps, which has been affected by both distemper and rabies at different time intervals. Red foxes collected from north-eastern Italy, Austria, Slovenia and Croatia between 2006–2012, were studied using a set of 21 microsatellite markers. We confirmed a weak genetic differentiation within the fox population using Bayesian clustering analyses, and we were able to differentiate the fox population into geographically segregated groups. Our finding might be due to the presence of geographical barriers that have likely influenced the distribution of the fox population, limiting in turn gene flow and spread of infectious diseases. Focusing on the Italian red fox population, we observed interesting variations in the prevalence of both diseases among distinct fox clusters, with the previously identified Italy 1 and Italy 2 rabies as well as distemper viruses preferentially affecting different sub-groups identified in the study. Knowledge of the regional-scale population structure can improve understanding of the epidemiology and spread of diseases. Our study paves the way for an integrated approach for disease control coupling pathogen, host and environmental data to inform targeted control programs in the future.
Collapse
Affiliation(s)
- Bianca Zecchin
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
- * E-mail:
| | - Marco De Nardi
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Pierre Nouvellet
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Barbara Crestanello
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Zoltán Bagó
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control, Mödling, Austria
| | | | - Peter Hostnik
- Virology Unit, Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Adelaide Milani
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Christl Ann Donnelly
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling Methodology, Imperial College London, London, United Kingdom
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Monica Lorenzetto
- Department of Veterinary Epidemiology, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Carlo Citterio
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Federica Obber
- SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Belluno, Italy
| | - Paola De Benedictis
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| | - Giovanni Cattoli
- Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Legnaro, Italy
| |
Collapse
|
30
|
Gopaulchan D, Motilal LA, Bekele FL, Clause S, Ariko JO, Ejang HP, Umaharan P. Morphological and genetic diversity of cacao ( Theobroma cacao L.) in Uganda. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:361-375. [PMID: 30956420 PMCID: PMC6419697 DOI: 10.1007/s12298-018-0632-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Cocoa is among the top foreign exchange earners in Uganda's agriculture sector and has benefitted the livelihood of farmers involved in production. Although cacao cultivation was adopted in the early 1900s, little is known about the on-farm diversity of the crop. A total of 125 cacao landraces were surveyed from eight districts in the Central and Western Regions to evaluate the morphological and genetic diversity of cacao in Uganda. Passport data included site, tree, fruit and seed information. Trees were genotyped using 96 single nucleotide polymorphism markers on a Fluidigm platform. Low heterozygosity was detected in the germplasm in both the Central [observed heterozygosity (H o ) = 0.295, expected heterozygosity (H e) = 0.334] and Western Regions (H o = 0.317, H e = 0.322). Genetic variation in both regions was generally comparable but the regions could be differentiated from each other. Inbreeding was noted in the Central Region while a greater sharing of genetic material was observed in the Western Region. The morphological and genetic data indicated that the Ugandan collection was an interspersed group with low to moderate variation with some separation of the Central from Western regions. Ancestry analysis indicated that the majority of the accessions were hybrids of Marañon lineage but also had Amelonado and Iquitos genetic backgrounds. These findings are consistent with the history of the movement of cacao into Uganda. A core collection of 18 individuals to represent the genetic diversity as well as 12 additional trees with possible advantageous traits is proposed.
Collapse
Affiliation(s)
- David Gopaulchan
- Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, 330912 Republic of Trinidad and Tobago
| | - Lambert A. Motilal
- Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, 330912 Republic of Trinidad and Tobago
| | - Frances L. Bekele
- Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, 330912 Republic of Trinidad and Tobago
| | - Séverine Clause
- Sunshine Agro Products Ltd, 24, Avenue de la Toison d’Or, 1050 Brussels, Belgium
| | - James O. Ariko
- Sunshine Agro Products Ltd, 24, Avenue de la Toison d’Or, 1050 Brussels, Belgium
| | - Harriet P. Ejang
- Sunshine Agro Products Ltd, 24, Avenue de la Toison d’Or, 1050 Brussels, Belgium
| | - Pathmanathan Umaharan
- Cocoa Research Centre, The University of the West Indies, Sir Frank Stockdale Bldg., St. Augustine, 330912 Republic of Trinidad and Tobago
| |
Collapse
|
31
|
Differential role of a persistent seed bank for genetic variation in early vs. late successional stages. PLoS One 2018; 13:e0209840. [PMID: 30586422 PMCID: PMC6306206 DOI: 10.1371/journal.pone.0209840] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/12/2018] [Indexed: 12/03/2022] Open
Abstract
Persistent seed banks are predicted to have an important impact on population genetic processes by increasing effective population size and storing past genetic diversity. Accordingly, persistent seed banks may buffer genetic effects of disturbance, fragmentation and/or selection. However, empirical studies surveying the relationship between aboveground and seed bank genetics under changing environments are scarce. Here, we compared genetic variation of aboveground and seed bank cohorts in 15 populations of the partially cleistogamous Viola elatior in two contrasting early and late successional habitats characterized by strong differences in light-availability and declining population size. Using AFLP markers, we found significantly higher aboveground than seed bank genetic diversity in early successional meadow but not in late successional woodland habitats. Moreover, individually, three of eight woodland populations even showed higher seed bank than aboveground diversity. Genetic differentiation among populations was very strong (фST = 0.8), but overall no significant differentiation could be detected between above ground and seed bank cohorts. Small scale spatial genetic structure was generally pronounced but was much stronger in meadow (Sp-statistic: aboveground: 0.60, seed bank: 0.32) than in woodland habitats (aboveground: 0.11; seed bank: 0.03). Our findings indicate that relative seed bank diversity (i.e. compared to aboveground diversity) increases with ongoing succession and despite decreasing population size. As corroborated by markedly lower small-scale genetic structure in late successional habitats, we suggest that the observed changes in relative seed bank diversity are driven by an increase of outcrossing rates. Persistent seed banks in Viola elatior hence will counteract effects of drift and selection, and assure a higher chance for the species’ long term persistence, particularly maintaining genetic variation in declining populations of late successional habitats and thus enhancing success rates of population recovery after disturbance events.
Collapse
|
32
|
Corrigan S, Lowther AD, Beheregaray LB, Bruce BD, Cliff G, Duffy CA, Foulis A, Francis MP, Goldsworthy SD, Hyde JR, Jabado RW, Kacev D, Marshall L, Mucientes GR, Naylor GJP, Pepperell JG, Queiroz N, White WT, Wintner SP, Rogers PJ. Population Connectivity of the Highly Migratory Shortfin Mako (Isurus oxyrinchus Rafinesque 1810) and Implications for Management in the Southern Hemisphere. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00187] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
33
|
McDowell JR, Brightman HL. High level of genetic connectivity in a deep-water reef fish, Caulolatilus microps. JOURNAL OF FISH BIOLOGY 2018; 93:766-777. [PMID: 30168143 DOI: 10.1111/jfb.13779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
The life-history characteristics of blueline tilefish make them particularly vulnerable to overfishing. Although North Carolina, U.S.A. was previously considered to be the northern extent of the range of C. microps, concentrations have recently been discovered in Virginia and Maryland, with reports as far north as Montauk, New York. Attempts to manage the fishery have been hampered by a lack of information about whether the U.S. East Coast includes multiple stocks. To assess the appropriateness of alternate management options, we used 25 variable microsatellite loci and sequencing of the mitochondrial (mt)DNA control region (CR) to evaluate the genetic structure of 490 C. microps sampled from across the U.S. East Coast range. Pairwise comparisons of genetic differentiation among collection locations based on both nuclear microsatellite and mtCR sequence data were all low and non significant. No significant autocorrelation was observed across multiple distance classes, consistent with widespread dispersal., Although the assumed sedentary nature of adult C. microps suggests population structuring, the genetic data were consistent with the presence of sufficient gene flow to prevent the accumulation of significant genetic differences and supports management of C. microps as a single stock along the U.S. East Coast.
Collapse
Affiliation(s)
- Jan R McDowell
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia
| | - Heid L Brightman
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, Virginia
| |
Collapse
|
34
|
|
35
|
Tang Q, Low GW, Lim JY, Gwee CY, Rheindt FE. Human activities and landscape features interact to closely define the distribution and dispersal of an urban commensal. Evol Appl 2018; 11:1598-1608. [PMID: 30344630 PMCID: PMC6183452 DOI: 10.1111/eva.12650] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 01/03/2023] Open
Abstract
The rock pigeon, Columba livia, is a cosmopolitan human commensal, domesticated thousands of years ago. However, the human-mediated factors governing its distribution and dispersal are not well understood. In this study, we performed (a) hierarchical distance sampling on ~400 island-wide point transects, (b) a population genomic inquiry based on ~7,000 SNPs from almost 150 individuals, and (c) landscape genomic analyses on the basis of extensive ecological and socio-economic databases to characterize the distribution and dispersal patterns of rock pigeons across Singapore. Our distance sampling results indicated that the volume of intentional "mercy feeding" and availability of high-rise buildings are the most reliable predictors of high pigeon densities in Singapore. Genomic analyses demonstrated that rock pigeons in Singapore form a single population possibly derived from rapid expansion from a genetically homogenous group of founder individuals. In specific, rock pigeons in Singapore lack sex-biased dispersal and are clustered with a genetic patch size of ~3 km. Landscape genomic analyses of great precision pointed to the presence of dense trees as agents of resistance to dispersal, whereas a high road density reduces this resistance. By pinpointing a range of ecological and socio-economic variables determining the distribution and dispersal of pigeons, our study provides urban planners with the tools for optimal management of this human commensal, such as a curtailment of the practice of mercy feeding and modifications to the urban landscape to reduce pigeon density and to lower the likelihood of repopulation by dispersal.
Collapse
Affiliation(s)
- Qian Tang
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Gabriel Weijie Low
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Jia Ying Lim
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Chyi Yin Gwee
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingapore
| |
Collapse
|
36
|
SHARMA HIMANI, SHARMA REKHA, AHLAWAT SONIKA, DAS PJ, JAYAKUMAR S, TANTIA MS. Cattle microsatellite markers successfully established diversity status of Arunachali yak (only registered yak breed of India). THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i9.83553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Yak diversity of the country has remained predominantly unexplored for a long time. Among the 169 registered livestock breeds of India, the sole representation from yak genetic resources is the Arunachali yak. This study for the first time investigated genetic diversity status of Arunachali yak using 26 bovine microsatellite markers. All the markers recommended for cattle except one (ILSTS05) amplified with yak genome. Allelic genotype pattern overlapped between yak and cattle across 25 microsatellite loci and a total of 233 alleles were detected in yak. The number of observed alleles across loci ranged from 3–16 with an average of 9.32±0.70. Observed heterozygosity (0.552±0.04) was less than the expected heterozygosity (0.648±0.035) pointing towards heterozygote deficiency in the population. In addition, positive value of FIS index (0.143±0.043) suggested considerable inbreeding. There was no indication of a recent bottleneck event in this population based on heterozygosity excess tests as well as mode-shift analysis. In summary, bovine microsatellite markers proved to be a valuable tool for characterization of Indian yak population. Arunachali yak represents an interesting gene pool with moderate level of diversity. Inbreeding in population calls for sincere efforts to formulate breeding policy so that this precious germplasm is conserved with substantial genetic diversity.
Collapse
|
37
|
Fine-scale genetic structure in a salamander with two reproductive modes: Does reproductive mode affect dispersal? Evol Ecol 2018. [DOI: 10.1007/s10682-018-9957-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
38
|
Fusani L, Barske J, Natali C, Chelazzi G, Ciofi C. Relatedness within and between leks of golden-collared manakin differ between sexes and age classes. Behav Ecol 2018. [DOI: 10.1093/beheco/ary116] [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] Open
Affiliation(s)
- Leonida Fusani
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Savoyenstraße, Vienna, Austria
- Department of Cognitive Biology, University of Vienna, Althanstraße, Vienna, Austria
| | - Julia Barske
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Chiara Natali
- Department of Biology, University of Florence, Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Guido Chelazzi
- Department of Biology, University of Florence, Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| | - Claudio Ciofi
- Department of Biology, University of Florence, Via Madonna del Piano, Sesto Fiorentino (FI), Italy
| |
Collapse
|
39
|
Torres I, Parra A, Moreno JM, Durka W. No genetic adaptation of the Mediterranean keystone shrub Cistus ladanifer in response to experimental fire and extreme drought. PLoS One 2018; 13:e0199119. [PMID: 29924833 PMCID: PMC6010289 DOI: 10.1371/journal.pone.0199119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/03/2018] [Indexed: 11/19/2022] Open
Abstract
In Mediterranean ecosystems, climate change is projected to increase fire danger and summer drought, thus reducing post-fire recruitment of obligate seeder species, and possibly affecting the population genetic structure. We performed a genome-wide genetic marker study, using AFLP markers, on individuals from one Central Spain population of the obligate post-fire seeder Cistus ladanifer L. that established after experimental fire and survived during four subsequent years under simulated drought implemented with a rainout shelter system. We explored the effects of the treatments on marker diversity, spatial genetic structure and presence of outlier loci suggestive of selection. We found no effect of fire or drought on any of the genetic diversity metrics. Analysis of Molecular Variance showed very low genetic differentiation among treatments. Neither fire nor drought altered the small-scale spatial genetic structure of the population. Only one locus was significantly associated with the fire treatment, but inconsistently across outlier detection methods. Neither fire nor drought are likely to affect the genetic makeup of emerging C. ladanifer, despite reduced recruitment caused by drought. The lack of genetic change suggests that reduced recruitment is a random, non-selective process with no genome-wide consequences on this keystone, drought- and fire tolerant Mediterranean species.
Collapse
Affiliation(s)
- Iván Torres
- Universidad de Castilla-La Mancha. Departamento de Ciencias Ambientales, Toledo, Spain
| | - Antonio Parra
- Universidad de Castilla-La Mancha. Departamento de Ciencias Ambientales, Toledo, Spain
| | - José M. Moreno
- Universidad de Castilla-La Mancha. Departamento de Ciencias Ambientales, Toledo, Spain
| | - Walter Durka
- Helmholtz Centre for Environmental Research, UFZ, Department of Community Ecology, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| |
Collapse
|
40
|
Padró J, Lambertucci SA, Perrig PL, Pauli JN. Evidence of genetic structure in a wide-ranging and highly mobile soaring scavenger, the Andean condor. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12786] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Julian Padró
- Grupo de Investigaciones en Biología de la Conservación; Laboratorio Ecotono; INIBIOMA (Universidad Nacional del Comahue-CONICET); Bariloche Argentina
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; USA
| | - Sergio A. Lambertucci
- Grupo de Investigaciones en Biología de la Conservación; Laboratorio Ecotono; INIBIOMA (Universidad Nacional del Comahue-CONICET); Bariloche Argentina
| | - Paula L. Perrig
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; USA
| | - Jonathan N. Pauli
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; USA
| |
Collapse
|
41
|
Ferreira da Silva MJ, Kopp GH, Casanova C, Godinho R, Minhós T, Sá R, Zinner D, Bruford MW. Disrupted dispersal and its genetic consequences: Comparing protected and threatened baboon populations (Papio papio) in West Africa. PLoS One 2018; 13:e0194189. [PMID: 29614097 PMCID: PMC5882123 DOI: 10.1371/journal.pone.0194189] [Citation(s) in RCA: 4] [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: 11/08/2016] [Accepted: 02/27/2018] [Indexed: 12/04/2022] Open
Abstract
Dispersal is a demographic process that can potentially counterbalance the negative impacts of anthropogenic habitat fragmentation. However, mechanisms of dispersal may become modified in populations living in human-dominated habitats. Here, we investigated dispersal in Guinea baboons (Papio papio) in areas with contrasting levels of anthropogenic fragmentation, as a case study. Using molecular data, we compared the direction and extent of sex-biased gene flow in two baboon populations: from Guinea-Bissau (GB, fragmented distribution, human-dominated habitat) and Senegal (SEN, continuous distribution, protected area). Individual-based Bayesian clustering, spatial autocorrelation, assignment tests and migrant identification suggested female-mediated gene flow at a large spatial scale for GB with evidence of contact between genetically differentiated males at one locality, which could be interpreted as male-mediated gene flow in southern GB. Gene flow was also found to be female-biased in SEN for a smaller scale. However, in the southwest coastal part of GB, at the same geographic scale as SEN, no sex-biased dispersal was detected and a modest or recent restriction in GB female dispersal seems to have occurred. This population-specific variation in dispersal is attributed to behavioural responses to human activity in GB. Our study highlights the importance of considering the genetic consequences of disrupted dispersal patterns as an additional impact of anthropogenic habitat fragmentation and is potentially relevant to the conservation of many species inhabiting human-dominated environments.
Collapse
Affiliation(s)
- Maria Joana Ferreira da Silva
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- CAPP, School of Social and Political Sciences, University of Lisbon, Rua Almerindo Lessa, Lisboa, Portugal
- * E-mail:
| | - Gisela H. Kopp
- Cognitive Ethology Laboratory, German Primate Center, Göttingen, Germany
| | - Catarina Casanova
- CAPP, School of Social and Political Sciences, University of Lisbon, Rua Almerindo Lessa, Lisboa, Portugal
| | - Raquel Godinho
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, South Africa
| | - Tânia Minhós
- Departamento de Antropologia, Faculdade de Ciências Sociais e Humanas, Universidade Nova de Lisboa, Lisboa, Portugal
- Centre for Research in Anthropology (CRIA), Instituto Universitário de Lisboa, Lisboa, Portugal
- IGC, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Rui Sá
- Departamento de Ciências Ambientais, Universidade Lusófona da Guiné, Rua Vitorino Costa, Bissau, Guiné-Bissau
- Research Centre for Anthropology and Health, Universidade de Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Göttingen, Germany
| | - Michael W. Bruford
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Cardiff, Wales, United Kingdom
| |
Collapse
|
42
|
Smith JR, Ghazoul J, Burslem DFRP, Itoh A, Khoo E, Lee SL, Maycock CR, Nanami S, Ng KKS, Kettle CJ. Are patterns of fine-scale spatial genetic structure consistent between sites within tropical tree species? PLoS One 2018; 13:e0193501. [PMID: 29547644 PMCID: PMC5856272 DOI: 10.1371/journal.pone.0193501] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/12/2018] [Indexed: 11/18/2022] Open
Abstract
Documenting the scale and intensity of fine-scale spatial genetic structure (FSGS), and the processes that shape it, is relevant to the sustainable management of genetic resources in timber tree species, particularly where logging or fragmentation might disrupt gene flow. In this study we assessed patterns of FSGS in three species of Dipterocarpaceae (Parashorea tomentella, Shorea leprosula and Shorea parvifolia) across four different tropical rain forests in Malaysia using nuclear microsatellite markers. Topographic heterogeneity varied across the sites. We hypothesised that forests with high topographic heterogeneity would display increased FSGS among the adult populations driven by habitat associations. This hypothesis was not supported for S. leprosula and S. parvifolia which displayed little variation in the intensity and scale of FSGS between sites despite substantial variation in topographic heterogeneity. Conversely, the intensity of FSGS for P. tomentella was greater at a more topographically heterogeneous than a homogeneous site, and a significant difference in the overall pattern of FSGS was detected between sites for this species. These results suggest that local patterns of FSGS may in some species be shaped by habitat heterogeneity in addition to limited gene flow by pollen and seed dispersal. Site factors can therefore contribute to the development of FSGS. Confirming consistency in species’ FSGS amongst sites is an important step in managing timber tree genetic diversity as it provides confidence that species specific management recommendations based on species reproductive traits can be applied across a species’ range. Forest managers should take into account the interaction between reproductive traits and site characteristics, its consequences for maintaining forest genetic resources and how this might influence natural regeneration across species if management is to be sustainable.
Collapse
Affiliation(s)
- James R. Smith
- Institute for Terrestrial Ecology, ETH Zurich, Zurich, Switzerland
| | - Jaboury Ghazoul
- Institute for Terrestrial Ecology, ETH Zurich, Zurich, Switzerland
| | | | - Akira Itoh
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | - Eyen Khoo
- Forest Research Centre, Sabah Forestry Department, Sabah, Malaysia
| | - Soon Leong Lee
- Forest Research Institute Malaysia, Kepong, Selangor, Malaysia
| | - Colin R. Maycock
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Sabah, Malaysia
| | - Satoshi Nanami
- Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
| | | | - Chris J. Kettle
- Institute for Terrestrial Ecology, ETH Zurich, Zurich, Switzerland
- * E-mail:
| |
Collapse
|
43
|
McLean AL, Cooper SJB, Lancaster ML, Gaikhorst G, Lambert C, Moseby K, Read J, Ward M, Carthew SM. Small marsupial, big dispersal? Broad- and fine-scale genetic structure of an endangered marsupial from the Australian arid zone. AUST J ZOOL 2018. [DOI: 10.1071/zo18054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The irregular nature of rainfall in the Australian arid and semiarid zones results in a heterogeneous distribution of resources in both time and space. The mammal species that reside in these regions are uniquely adapted to these climatic conditions, often occurring in naturally low densities and increasing significantly in numbers following major rainfall events. We investigated how these adaptations may influence genetic diversity and gene flow across the landscape in an endangered semiarid/arid-zone marsupial, the sandhill dunnart (Sminthopsis psammophila), from three known populations in southern Australia. Analyses of mitochondrial control region (CR) sequences and microsatellite loci revealed that S. psammophila had maintained similar levels of genetic diversity to other sympatric Sminthopsis species despite its endangered status. There was no evidence for significant phylogeographic structure within the species, but each population was genetically differentiated, based on the frequency of microsatellite alleles and CR haplotypes, suggesting that they should be considered as distinct Management Units for conservation. At a fine spatial scale, no significant genetic structure or sex-biased dispersal was detected within a study site of 240km2. These findings suggest that both sexes are highly mobile, which allows individuals to locate localised resource patches when they become available. We detected evidence of a genetic bottleneck within the population, possibly caused by a recent drought. Our study highlights the importance of maintaining connectivity across the landscape for semiarid- and arid-zone species to enable them to track resource pulses and maintain genetic diversity.
Collapse
|
44
|
Graham BA, Heath DD, Mennill DJ. Dispersal influences genetic and acoustic spatial structure for both males and females in a tropical songbird. Ecol Evol 2017; 7:10089-10102. [PMID: 29238539 PMCID: PMC5723598 DOI: 10.1002/ece3.3456] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 08/07/2017] [Accepted: 08/11/2017] [Indexed: 11/21/2022] Open
Abstract
Animals exhibit diverse dispersal strategies, including sex‐biased dispersal, a phenomenon common in vertebrates. Dispersal influences the genetic structure of populations as well as geographic variation in phenotypic traits. Patterns of spatial genetic structure and geographic variation may vary between the sexes whenever males and females exhibit different dispersal behaviors. Here, we examine dispersal, spatial genetic structure, and spatial acoustic structure in Rufous‐and‐white Wrens, a year‐round resident tropical bird. Both sexes sing in this species, allowing us to compare acoustic variation between males and females and examine the relationship between dispersal and song sharing for both sexes. Using a long‐term dataset collected over an 11‐year period, we used banding data and molecular genetic analyses to quantify natal and breeding dispersal distance in Rufous‐and‐white Wrens. We quantified song sharing and examined whether sharing varied with dispersal distance, for both males and females. Observational data and molecular genetic analyses indicate that dispersal is female‐biased. Females dispersed farther from natal territories than males, and more often between breeding territories than males. Furthermore, females showed no significant spatial genetic structure, consistent with expectations, whereas males showed significant spatial genetic structure. Overall, natal dispersal appears to have more influence than breeding dispersal on spatial genetic structure and spatial acoustic structure, given that the majority of breeding dispersal events resulted in individuals moving only short distances. Song sharing between pairs of same‐sex animals decreases with the distance between their territories for both males and females, although males exhibited significantly greater song sharing than females. Lastly, we measured the relationship between natal dispersal distance and song sharing. We found that sons shared fewer songs with their fathers the farther they dispersed from their natal territories, but that song sharing between daughters and mothers was not significantly correlated with natal dispersal distance. Our results reveal cultural differences between the sexes, suggesting a relationship between culture and sex‐biased dispersal.
Collapse
Affiliation(s)
- Brendan A Graham
- Department of Biological Sciences University of Windsor Windsor ON Canada
| | - Daniel D Heath
- Department of Biological Sciences University of Windsor Windsor ON Canada.,Great Lakes Institute of Environmental Research University of Windsor Windsor ON Canada
| | - Daniel J Mennill
- Department of Biological Sciences University of Windsor Windsor ON Canada
| |
Collapse
|
45
|
Morgan EJ, Kaiser-Bunbury CN, Edwards PJ, Fleischer-Dogley F, Kettle CJ. Keeping it in the family: strong fine-scale genetic structure and inbreeding in Lodoicea maldivica, the largest-seeded plant in the world. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0982-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
46
|
Shaw RE, Banks SC, Peakall R. The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers. Mol Ecol 2017; 27:66-82. [PMID: 29154412 DOI: 10.1111/mec.14433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 10/18/2022]
Abstract
For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure.
Collapse
Affiliation(s)
- Robyn E Shaw
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.,The Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Sam C Banks
- The Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| |
Collapse
|
47
|
Zhang L, Qu J, Li K, Li W, Yang M, Zhang Y. Genetic diversity and sex-bias dispersal of plateau pika in Tibetan plateau. Ecol Evol 2017; 7:7708-7718. [PMID: 29043027 PMCID: PMC5632614 DOI: 10.1002/ece3.3289] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/27/2017] [Accepted: 06/30/2017] [Indexed: 11/12/2022] Open
Abstract
Dispersal is an important aspect in organism's life history which could influence the rate and outcome of evolution of organism. Plateau pika is the keystone species in community of grasslands in Tibetan Plateau. In this study, we combine genetic and field data to character the population genetic pattern and dispersal dynamics in plateau pika (Ochotona curzoniae). Totally, 1,352 individual samples were collected, and 10 microsatellite loci were analyzed. Results revealed that plateau pika possessed high genetic diversity and inbreeding coefficient in a fine-scale population. Dispersal distance is short and restricted in about 20 m. An effective sex-biased dispersal strategy is employed by plateau pika: males disperse in breeding period for mating while females do it after reproduction for offspring and resource. Inbreeding avoiding was shown as the common driving force of dispersal, together with the other two factors, environment and resource. In addition, natal dispersal is female biased. More detailed genetic analyzes are needed to confirm the role of inbreeding avoidance and resource competition as ultimate cause of dispersal patterns in plateau pika.
Collapse
Affiliation(s)
- Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology, Chinese Academy of SciencesXiningQinghaiChina
- Qinghai Key Laboratory of Animal Ecological GenomicsNorthwest Institute of Plateau Biology, Chinese Academy of SciencesXiningQinghaiChina
| | - Jiapeng Qu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology, Chinese Academy of SciencesXiningQinghaiChina
| | - Kexin Li
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology, Chinese Academy of SciencesXiningQinghaiChina
| | - Wenjing Li
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology, Chinese Academy of SciencesXiningQinghaiChina
| | - Min Yang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology, Chinese Academy of SciencesXiningQinghaiChina
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau Biology, Chinese Academy of SciencesXiningQinghaiChina
- Qinghai Key Laboratory of Animal Ecological GenomicsNorthwest Institute of Plateau Biology, Chinese Academy of SciencesXiningQinghaiChina
| |
Collapse
|
48
|
Botero-Delgadillo E, Quirici V, Poblete Y, Cuevas É, Kuhn S, Girg A, Teltscher K, Poulin E, Kempenaers B, Vásquez RA. Variation in fine-scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird. Ecol Evol 2017; 7:8363-8378. [PMID: 29075455 PMCID: PMC5648682 DOI: 10.1002/ece3.3342] [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: 05/08/2017] [Revised: 07/23/2017] [Accepted: 08/01/2017] [Indexed: 12/24/2022] Open
Abstract
The distribution of suitable habitat influences natal and breeding dispersal at small spatial scales, resulting in strong microgeographic genetic structure. Although environmental variation can promote interpopulation differences in dispersal behavior and local spatial patterns, the effects of distinct ecological conditions on within‐species variation in dispersal strategies and in fine‐scale genetic structure remain poorly understood. We studied local dispersal and fine‐scale genetic structure in the thorn‐tailed rayadito (Aphrastura spinicauda), a South American bird that breeds along a wide latitudinal gradient. We combine capture‐mark‐recapture data from eight breeding seasons and molecular genetics to compare two peripheral populations with contrasting environments in Chile: Navarino Island, a continuous and low density habitat, and Fray Jorge National Park, a fragmented, densely populated and more stressful environment. Natal dispersal showed no sex bias in Navarino but was female‐biased in the more dense population in Fray Jorge. In the latter, male movements were restricted, and some birds seemed to skip breeding in their first year, suggesting habitat saturation. Breeding dispersal was limited in both populations, with males being more philopatric than females. Spatial genetic autocorrelation analyzes using 13 polymorphic microsatellite loci confirmed the observed dispersal patterns: a fine‐scale genetic structure was only detectable for males in Fray Jorge for distances up to 450 m. Furthermore, two‐dimensional autocorrelation analyzes and estimates of genetic relatedness indicated that related males tended to be spatially clustered in this population. Our study shows evidence for context‐dependent variation in natal dispersal and corresponding local genetic structure in peripheral populations of this bird. It seems likely that the costs of dispersal are higher in the fragmented and higher density environment in Fray Jorge, particularly for males. The observed differences in microgeographic genetic structure for rayaditos might reflect the genetic consequences of population‐specific responses to contrasting environmental pressures near the range limits of its distribution.
Collapse
Affiliation(s)
- Esteban Botero-Delgadillo
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile.,SELVA: Research for conservation in the Neotropics Bogotá Colombia
| | - Verónica Quirici
- Departamento de Ecología y Biodiversidad Facultad de Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile.,Centro de Investigación Para la Sustentabilidad Universidad Andrés Bello Santiago Chile
| | - Yanina Poblete
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile.,Instituto de Ciencias Naturales Universidad de las Américas Santiago Chile
| | - Élfego Cuevas
- Doctorado en Medicina de la Conservación Facultad de Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile
| | - Sylvia Kuhn
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Alexander Girg
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Kim Teltscher
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Plank Institute for Ornithology Seewiesen Germany
| | - Rodrigo A Vásquez
- Instituto de Ecología y Biodiversidad Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
| |
Collapse
|
49
|
Ruibal MP, Triponez Y, Smith LM, Peakall R, Linde CC. Population structure of an orchid mycorrhizal fungus with genus-wide specificity. Sci Rep 2017; 7:5613. [PMID: 28717170 PMCID: PMC5514033 DOI: 10.1038/s41598-017-05855-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/02/2017] [Indexed: 12/02/2022] Open
Abstract
Fundamental life history processes of mycorrhizal fungi with inconspicuous fruiting bodies can be difficult to elucidate. In this study we investigated the species identities and life history of the orchid mycorrhizal Tulasnella fungi, which associate with the south eastern Australia orchid genus Chiloglottis. Tulasnella prima was the primary partner and was found to be associated with all 17 Chiloglottis species across a range of >1000 km, and to occur in the two edaphic conditions investigated (soil and sphagnum hammocks). Another Tulasnella species (T. sphagneti) appears to be restricted to moist conditions of alpine sphagnum hammocks. The population genetic structure of the widespread species T. prima, was investigated at 10 simple sequence repeat (SSR) markers and at four cross-amplified SSR loci for T. sphagneti. For both taxa, no sharing of multilocus genotypes was found between sites, but clones were found within sites. Evidence for inbreeding within T. prima was found at 3 of 5 sites. Significant genetic differentiation was found within and between taxa. Significant local positive spatial genetic autocorrelation was detected among non-clonal isolates at the scale of two metres. Overall, the population genetic patterns indicated that in Tulasnella mating occurs by inbreeding and dispersal is typically restricted to short-distances.
Collapse
Affiliation(s)
- M P Ruibal
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Y Triponez
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - L M Smith
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - R Peakall
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - C C Linde
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia.
| |
Collapse
|
50
|
Schregel J, Kopatz A, Eiken HG, Swenson JE, Hagen SB. Sex-specific genetic analysis indicates low correlation between demographic and genetic connectivity in the Scandinavian brown bear (Ursus arctos). PLoS One 2017; 12:e0180701. [PMID: 28672045 PMCID: PMC5495496 DOI: 10.1371/journal.pone.0180701] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/20/2017] [Indexed: 11/30/2022] Open
Abstract
The degree of gene flow within and among populations, i.e. genetic population connectivity, may closely track demographic population connectivity. Alternatively, the rate of gene flow may change relative to the rate of dispersal. In this study, we explored the relationship between genetic and demographic population connectivity using the Scandinavian brown bear as model species, due to its pronounced male dispersal and female philopatry. Thus, we expected that females would shape genetic structure locally, whereas males would act as genetic mediators among regions. To test this, we used eight validated microsatellite markers on 1531 individuals sampled noninvasively during country-wide genetic population monitoring in Sweden and Norway from 2006 to 2013. First, we determined sex-specific genetic structure and substructure across the study area. Second, we compared genetic differentiation, migration/gene flow patterns, and spatial autocorrelation results between the sexes both within and among genetic clusters and geographic regions. Our results indicated that demographic connectivity was not a reliable indicator of genetic connectivity. Among regions, we found no consistent difference in long-term gene flow and estimated current migration rates between males and females. Within regions/genetic clusters, only females consistently displayed significant positive spatial autocorrelation, indicating male-biased small-scale dispersal. In one cluster, however, males showed a dispersal pattern similar to females. The Scandinavian brown bear population has experienced substantial recovery over the last decades; however, our results did not show any changes in its large-scale population structure compared to previous studies, suggesting that an increase in population size and dispersal of individuals does not necessary lead to increased genetic connectivity. Thus, we conclude that both genetic and demographic connectivity should be estimated, so as not to make false assumptions about the reality of wildlife populations.
Collapse
Affiliation(s)
- Julia Schregel
- Norwegian Institute of Bioeconomy Research, NIBIO - Svanhovd, Svanvik, Norway
- Norwegian University of Life Sciences, Faculty of Environmental Sciences and Natural Resource Management, Ǻs, Norway
- * E-mail: (JS); (SBH)
| | - Alexander Kopatz
- Norwegian Institute of Bioeconomy Research, NIBIO - Svanhovd, Svanvik, Norway
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy Research, NIBIO - Svanhovd, Svanvik, Norway
| | - Jon E. Swenson
- Norwegian University of Life Sciences, Faculty of Environmental Sciences and Natural Resource Management, Ǻs, Norway
- Norwegian Institute for Nature Research, Trondheim, Norway
| | - Snorre B. Hagen
- Norwegian Institute of Bioeconomy Research, NIBIO - Svanhovd, Svanvik, Norway
- * E-mail: (JS); (SBH)
| |
Collapse
|