scholarly journals To what extent do human-altered landscapes retain population connectivity? Historical changes in gene flow of wetland fish Pungitius pungitius

2015 ◽  
Vol 2 (7) ◽  
pp. 150033 ◽  
Author(s):  
N. Ishiyama ◽  
M. Sueyoshi ◽  
F. Nakamura
Keyword(s):  
Gene Flow ◽  
Population Connectivity ◽  
Source Population ◽  
Pungitius Pungitius ◽  
Historical Changes ◽  
Ninespine Stickleback ◽  
Potential Source ◽  
Contemporary Gene Flow ◽  
Directional Change ◽  
Source Populations

Understanding how human-altered landscapes affect population connectivity is valuable for conservation planning. Natural connectivity among wetlands, which is maintained by floods, is disappearing owing to farmland expansion. Using genetic data, we assessed historical changes in the population connectivity of the ninespine stickleback within a human-altered wetland system. We predicted that: (i) the contemporary gene flow maintained by the artificial watercourse network may be restricted to a smaller spatial scale compared with the gene flow preceding alteration, and (ii) the contemporary gene flow is dominated by the downstream direction owing to the construction of low-head barriers. We evaluated the potential source population in both timescales. Seventeen studied populations were grouped into four genetically different clusters, and we estimated the migration rates among these clusters. Contemporary migration was restricted to between neighbouring clusters, although a directional change was not detected. Furthermore, we consistently found the same potential source cluster, from past to present, characterized by large amounts of remnant habitats connected by artificial watercourses. These findings highlight that: (i) artificial connectivity can sustain the short-distance connectivity of the ninespine stickleback, which contributes to maintaining the potential source populations; however, (ii) population connectivity throughout the landscape has been prevented by agricultural developments.

A temporal perspective on population structure and gene flow in Atlantic salmon (Salmo salar) in Newfoundland, Canada

2010 ◽  
Vol 67 (2) ◽  
pp. 225-242 ◽  
Author(s):  
Friso P. Palstra ◽  
Daniel E. Ruzzante
Keyword(s):  
Population Dynamics ◽  
Population Structure ◽  
Gene Flow ◽  
Atlantic Salmon ◽  
Salmo Salar ◽  
Environmental Changes ◽  
Population Connectivity ◽  
Temporal Perspective ◽  
Atlantic Salmon Salmo Salar ◽  
Contemporary Gene Flow

Studying population structure and gene flow patterns on temporal scales facilitates an evaluation of the consequences of demographic, physical, and environmental changes on the stability and persistence of populations. Here, we examine temporal genetic variation within and among Atlantic salmon ( Salmo salar ) rivers in Newfoundland and Labrador, Canada, using samples collected over a period of six decades (1951–2004). Our objective was to evaluate temporal changes in population connectivity associated with the closure of a commercial marine fishery. Despite demographic instability, we find that population structure remained temporally stable over more than 50 years. However, age structure can affect results when not taken into consideration, particularly in populations of large effective size where genetic drift is not strong. Where weak signals of genetic differentiation did not complicate analyses, contemporary migration was often asymmetric, yet low, suggesting patterns of intermittent gene flow. Nevertheless, we find some links between changes in population dynamics and contemporary gene flow. These findings may therefore imply that management decisions impacting the contemporary population dynamics of individual Atlantic salmon rivers can also affect the genetic stability of this species as a whole.

scholarly journals Genetic structure and historical and contemporary gene flow of Astyanaxmexicanus in the Gulf of Mexico slope: a microsatellite-based analysis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10784
Author(s):  
Rodolfo Pérez-Rodríguez ◽  
Sarai Esquivel-Bobadilla ◽  
Adonaji Madeleine Orozco-Ruíz ◽  
José Luis Olivas-Hernández ◽  
Francisco Javier García-De León
Keyword(s):  
Gene Flow ◽  
Gulf Of Mexico ◽  
Microsatellite Loci ◽  
Evolutionary History ◽  
Population Analysis ◽  
Morphological Variability ◽  
High Capacity ◽  
Genetic Population ◽  
Contemporary Gene Flow ◽  
Taxonomic Uncertainty

Background Astyanax mexicanus from the river basins of the Gulf of Mexico slope are small freshwater fish that usually live in large groups in different freshwater environments. The group is considered successful due to its high capacity for dispersal and adaptation to different habitats, and the species present high morphological variability throughout their distribution in Mexico. This has produced the most extreme morphotype of the group; the hypogeous or troglobite, which has no eyes or coloration, and is probably the cause of taxonomic uncertainty in the recognition of species across the entire range. Most studies of A. mexicanus have mainly focused on cave individuals, as well as their adjacent surface locations, providing an incomplete evolutionary history, particularly in terms of factors related to dispersal and the potential corridors used, barriers to gene flow, and distribution of genetic variability. The aim of the present study is to determine the population structure and the degree and direction of genetic flow in this complex taxonomic group, incorporating geographic locations not previously included in analyses using microsatellite loci. Our aim is to contribute to the knowledge of the intricate evolutionary history of A. mexicanus throughout most of its range. Methods The present study included a set of several cave and surface locations of A. mexicanus, which have been widely sampled along the Gulf of Mexico slope, in a genetic population analysis using 10 microsatellite loci. Results Ten genetic populations or lineages were identified. In these populations, gene flow was recorded at two time periods. Historical gene flow, both inter and intra-basin, was observed among surface populations, from surface to cave populations, and among cave populations, whereas recording of contemporary gene flow was limited to intra-basin exchanges and observed among surface populations, surface to cave populations, and cave populations.

scholarly journals The Behaviour and Ecology of Austrolittorina antipodum and Austrolittorina cincta: Models for Marine Reserve Connectivity Studies

2021 ◽  
Author(s):  
◽  
Jennifer Vander Veur
Keyword(s):  
Gene Flow ◽  
Larval Mortality ◽  
Marine Reserve ◽  
Sex Ratios ◽  
Marine Conservation ◽  
Population Connectivity ◽  
Adult Density ◽  
Population Surveys ◽  
Multiple Peaks ◽  
High Shore

<p>Determining the magnitude of dispersal and connectivity between populations has important implications for marine conservation. Species with limited dispersal capabilities exhibit restricted gene flow leading to isolation and, ultimately, differentiated populations. In this ecological study I investigated the gastropods Austrolittorina antipodum (Philippi, 1847) and Austrolittorina cincta (Quoy and Gaimard, 1833) to determine how ecology and behaviour influence the dispersal and connectivity of these species. The aim of this study was to determine population size and structure, settlement, fecundity, and adult movement rates. Methodologies included: population surveys, deployment of settlement pads and adult density manipulations, dissections, and a tagging study. These elements of a species ecology and behaviour can enhance or restrict population connectivity by: cohort partitioning resulting from habitat requirements, fluctuating settlement due to variable larval mortality or adult densities impacting dispersal, skewed sex ratios and effective populations sizes altering larval production, and adult movement leading to behavioural isolation or facilitating gene flow, along with other possible effects. Population surveys revealed both species had a Vermeij (1972) "type 1 distribution" (shell size increasing from the low to high shore), with the highest density of individuals on the low shore and the majority of mature adults on the high shore. Overall, A. antipodum was 16 times more abundant than A. cincta. Shifts to a smaller mean size of both species, along all shore heights following periods of peak settlement indicates settlers are potentially triggering competitive interactions or ontogenetic migrations in other cohorts.Settlement surveys revealed that peak settlement for Austrolittorina spp. was from February to April, declining at the beginning of March. Multiple peaks in settlement may act as a buffer limiting the potential of stochastic events to hinder dispersal during reproductive seasons. Settlement rates were not affected by adult density in control treatments; however, settlement was higher on pads deployed within adult populations compared to pads deployed adjacent to adult populations, suggesting the presences of adults has some effect on settlement. Fecundity results revealed A. antipodum to have more mature females than A. cincta, with males of both species reaching sexual maturity before females. Sex ratios of both species were skewed towards more females, with effective population sizes that included approximately 88% of each species population. A. antipodum’s larger population may be due to variation between the species' demographics, such as the distribution of mature females and juveniles leading to greater spawning success and juvenile survivorship. Tagging transplant/translocation experiments used to examine movement revealed that both species traveled similar distances. On average A. antipodum traveled 24.1m (±23.5m) and A. cincta traveled 18.7m (±16m) in eight months. There was no evidence of behavioural isolation occurring between low and high shore individuals. The wide ranging movements of adults indicated adults have the potential to maintain population connectivity on small scales. The findings of this study suggest both species facilitate dispersal with multiple peaks in settlement, large effective populations, and high adult mobility. Behavioural variation between the species appears to affect population connectivity, with the distribution of A. antipodum demographics potentially enhancing connectivity.</p>

scholarly journals Fine-scale landscape genetics unveiling contemporary asymmetric movement of red panda (Ailurus fulgens) in Kangchenjunga landscape, India

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Supriyo Dalui ◽  
Hiren Khatri ◽  
Sujeet Kumar Singh ◽  
Shambadeb Basu ◽  
Avijit Ghosh ◽  
...  
Keyword(s):  
Gene Flow ◽  
Landscape Connectivity ◽  
Anthropogenic Activities ◽  
Clustering Algorithms ◽  
Area Network ◽  
Fine Scale ◽  
Contemporary Gene Flow ◽  
Red Panda ◽  
Population Structuring ◽  
Ailurus Fulgens

Abstract Wildlife management in rapid changing landscapes requires critical planning through cross cutting networks, and understanding of landscape features, often affected by the anthropogenic activities. The present study demonstrates fine-scale spatial patterns of genetic variation and contemporary gene flow of red panda (Ailurus fulgens) populations with respect to landscape connectivity in Kangchenjunga Landscape (KL), India. The study found about 1,309.54 km2 area suitable for red panda in KL—India, of which 62.21% area fell under the Protected Area network. We identified 24 unique individuals from 234 feces collected at nine microsatellite loci. The spatially explicit and non-explicit Bayesian clustering algorithms evident to exhibit population structuring and supported red panda populations to exist in meta-population frame work. In concurrence to the habitat suitability and landscape connectivity models, gene flow results supported a contemporary asymmetric movement of red panda by connecting KL—India in a crescent arc. We demonstrate the structural-operational connectivity of corridors in KL—India that facilitated red panda movement in the past. We also seek for cooperation in Nepal, Bhutan and China to aid in preparing for a comprehensive monitoring plan for the long-term conservation and management of red panda in trans-boundary landscapes.

scholarly journals Simulation-Based Evaluation of Three Methods for Local Ancestry Deconvolution of Non-model Crop Species Genomes

2019 ◽  
Vol 10 (2) ◽  
pp. 569-579
Author(s):  
Aurélien Cottin ◽  
Benjamin Penaud ◽  
Jean-Christophe Glaszmann ◽  
Nabila Yahiaoui ◽  
Mathieu Gautier
Keyword(s):  
R Package ◽  
Source Population ◽  
Crop Species ◽  
Data Set ◽  
Reproduction Mode ◽  
Local Ancestry ◽  
Ancestry Inference ◽  
Source Populations ◽  
Inference Methods ◽  
Local Ancestry Inference

Hybridizations between species and subspecies represented major steps in the history of many crop species. Such events generally lead to genomes with mosaic patterns of chromosomal segments of various origins that may be assessed by local ancestry inference methods. However, these methods have mainly been developed in the context of human population genetics with implicit assumptions that may not always fit plant models. The purpose of this study was to evaluate the suitability of three state-of-the-art inference methods (SABER, ELAI and WINPOP) for local ancestry inference under scenarios that can be encountered in plant species. For this, we developed an R package to simulate genotyping data under such scenarios. The tested inference methods performed similarly well as far as representatives of source populations were available. As expected, the higher the level of differentiation between ancestral source populations and the lower the number of generations since admixture, the more accurate were the results. Interestingly, the accuracy of the methods was only marginally affected by i) the number of ancestries (up to six tested); ii) the sample design (i.e., unbalanced representation of source populations); and iii) the reproduction mode (e.g., selfing, vegetative propagation). If a source population was not represented in the data set, no bias was observed in inference accuracy for regions originating from represented sources and regions from the missing source were assigned differently depending on the methods. Overall, the selected ancestry inference methods may be used for crop plant analysis if all ancestral sources are known.

Genetic structure of Gahnia radula (Cyperaceae), a key sedge for revegetation

2017 ◽  
Vol 65 (2) ◽  
pp. 128
Author(s):  
Alex Arnold ◽  
Andrea Kodym ◽  
Nancy M. Endersby-Harshman ◽  
John Delpratt ◽  
Ary A. Hoffmann
Keyword(s):  
Genetic Variation ◽  
Adaptive Potential ◽  
Genetic Studies ◽  
Potential Source ◽  
Landscape Processes ◽  
Disturbed Areas ◽  
Eastern Australia ◽  
Genetic Patterns ◽  
Source Populations ◽  
High Level

Genetic studies can help guide effective ecological restoration by identifying potential source populations that contain the genetic variation necessary for adaptive potential, based on past landscape processes. Here we investigate genetic patterns in Gahnia radula (R.Br.) Benth., a sedge from south-eastern Australia that has potential for revegetation of disturbed areas. We developed microsatellite markers for this species and used them to show that it propagates mostly in a clonal manner. Levels of genetic variability differed between populations and the spatial scale of this variability within these populations is identified. A population used in recent restoration efforts and which sets seed has a particularly high level of variability. Recommendations are developed for sourcing material when using this sedge for revegetation.

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