Spatial analysis of microgeographic genetic structure in Richardson's ground squirrels

1996 ◽  
Vol 74 (7) ◽  
pp. 1187-1195 ◽  
Author(s):  
Moira J. van Staaden ◽  
Gail R. Michener ◽  
Ronald K. Chesser
Keyword(s):  
Genetic Structure ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Ground Squirrels ◽  
Breeding Systems ◽  
Population Subdivision ◽  
Genetic Structuring ◽  
Candidate Species ◽  
Empirical Demonstration

Local genetic structure has a sound theoretical basis, yet empirical demonstration in animal species has proved elusive, even in apparently ideal candidate species. Techniques based on the distribution of individual genotypes may offer a more complete picture of population structure than traditional measures focusing on isolation by distance and dispersal behavior. We used spatial autocorrelation and contiguous clustering to identify structure in a population of Richardson's ground squirrel (Spermophilus richardsonii) for which deviation from Hardy–Weinberg expectations indicated population subdivision. Nonrandom aggregates of genotypes were detected at five of six enzyme loci examined and selection at one locus. Genetic structuring was highly sex-dependent, being prominent only among females. Isolation by distance cannot account for the patterns of gene diversity observed, but Mantel matrix procedures of inter-individual distance based on demographic–behavioral characteristics and geographic distance were significantly associated. Social and breeding systems of S. richardsonii lead to significant local substructure. While philopatry alone may not account for fine-scale genetic structure in small mammals with sex-biased dispersal, nonrandom aggregates will be detected if appropriate social models and rigorous sampling criteria are adopted. Identification of such localized structure remains fundamental to understanding evolutionary models of population genetic structure and sociality.

scholarly journals Looking through glassfish: marine genetic structure in an estuarine species

2008 ◽  
Vol 59 (7) ◽  
pp. 627 ◽  
Author(s):  
Courtenay E. Mills ◽  
Wade L. Hadwen ◽  
Jane M. Hughes
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
New South ◽  
Geographic Distance ◽  
Genetic Structuring ◽  
The North ◽  
South Wales ◽  
High Dispersal ◽  
Eastern Australia ◽  
Atp8 Gene

Through the use of mitochondrial DNA (ATP8 gene), the prediction of intermediate genetic structuring was investigated in two species of estuarine glassfish (Ambassis marianus and Ambassis jacksoniensis) (Perciformes : Ambassidae) to determine the possibility of a generalised ‘estuarine’ genetic structure. Individuals were collected from estuaries in eastern Australia between Tin Can Bay (Queensland) in the north and Kempsey (New South Wales) in the south. Analysis of the haplotype frequencies found in this region suggested panmictic populations with star-like phylogenies with extremely high levels of genetic diversity, but with no correlation between geographic distance and genetic distance. Non-significant FST and ΦST suggested extensive dispersal among estuaries. However, Tajima’s D and Fu’s FS values suggest ‘mutation–genetic drift equilibrium’ has not been reached, and that population expansions occurring 262 000 (A. marianus) and 300 000 (A. jacksoniensis) years ago may obscure any phylogeographic structuring or isolation by distance. The finding of panmixia was contrary to the prediction of genetic structuring intermediate between that of marine fish (shallowly structured) and freshwater fish (highly structured), suggesting high dispersal capabilities in these species.

scholarly journals Genetic population structure of the monogenean parasite Gyrodactylus thymalli and its host European grayling (Thymallus thymallus) in a large Norwegian lake

Hydrobiologia ◽  
2020 ◽  
Author(s):  
Ruben Alexander Pettersen ◽  
Claudia Junge ◽  
Kjartan Østbye ◽  
Tor Atle Mo ◽  
Leif Asbjørn Vøllestad
Keyword(s):  
Genetic Structure ◽  
Evolutionary Biology ◽  
Isolation By Distance ◽  
Genetic Structuring ◽  
Thymallus Thymallus ◽  
Homing Behavior ◽  
Genetic Population ◽  
Monogenean Parasite ◽  
European Grayling ◽  
Genetic Clusters

Abstract Understanding how populations are structured in space and time is a central question in evolutionary biology. Parasites and their hosts are assumed to evolve together, however, detailed understanding of mechanisms leading to genetic structuring of parasites and their hosts are lacking. As a parasite depends on its host, studying the genetic structure of both parasite and host can reveal important insights into these mechanisms. Here, genetic structure of the monogenean parasite Gyrodactylus thymalli and its host the European grayling (Thymallus thymallus) was investigated in 10 tributaries draining into the large Lake Mjøsa in Norway. The population genetic structure of spawning grayling was studied using microsatellite genotyping, while G. thymalli was studied by sequencing a mitochondrial DNA gene (dehydrogenase subunit 5). Two main genetic clusters were revealed in grayling, one cluster comprising grayling from the largest spawning population, while the remaining tributaries formed the second cluster. For both taxa, some genetic differentiation was observed among tributaries, but there was no clear isolation-by-distance signature. The structuring was stronger for the host than for the parasite. These results imply that moderate to high levels of gene flow occur among the sub-populations of both taxa. The high parasite exchange among tributaries could result from a lack of strong homing behavior in grayling as well as interactions among individual fish outside of the spawning season, leading to frequent mixing of both host and parasite.

scholarly journals Genetic Structure of Rhynchosporium secalis in Australia

1999 ◽  
Vol 89 (8) ◽  
pp. 639-645 ◽  
Author(s):  
B. A. McDonald ◽  
J. Zhan ◽  
J. J. Burdon
Keyword(s):  
Genetic Structure ◽  
Gene Diversity ◽  
Sampling Site ◽  
Geographic Distance ◽  
South Australia ◽  
Rflp Markers ◽  
Rhynchosporium Secalis ◽  
Fungal Isolates ◽  
Fungal Populations ◽  
Average Gene

Restriction fragment length polymorphism (RFLP) markers were used to determine the genetic structure of Australian field populations of the barley scald pathogen Rhynchosporium secalis. Fungal isolates were collected by hierarchical sampling from five naturally infected barley fields in different geographic locations during a single growing season. Genetic variation was high in Australian R. secalis populations. Among the 265 fungal isolates analyzed, 214 distinct genotypes were identified. Average genotype diversity within a field population was 65% of its theoretical maximum. Nei's average gene diversity across seven RFLP loci was 0.54. The majority (76%) of gene diversity was distributed within sampling site areas measuring ≈1 m2; 19% of gene diversity was distributed among sampling sites within fields; and 5% of gene diversity was distributed among fields. Fungal populations from different locations differed significantly both in allele frequencies and genotype diversities. The degree of genetic differentiation was significantly correlated with geographic distance between populations. Our results suggest that the R. secalis population in Western Australia has a different genetic structure than populations in Victoria and South Australia.

scholarly journals Genetic structure and dispersal patterns of the invasive psocid Liposcelis decolor (Pearman) in Australian grain storage systems

2010 ◽  
Vol 100 (5) ◽  
pp. 521-527 ◽  
Author(s):  
K.M. Mikac ◽  
N.N. FitzSimmons
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Allelic Diversity ◽  
Mantel Test ◽  
Null Alleles ◽  
Dispersal Patterns ◽  
Long Distance ◽  
Population Comparisons ◽  
Low Levels

AbstractMicrosatellite markers were used to investigate the genetic structure among invasive L. decolor populations from Australia and a single international population from Kansas, USA to determine patterns of dispersal. Six variable microsatellites displayed an average of 2.5–4.2 alleles per locus per population. Observed (HO) heterozygosity ranged from 0.12–0.65 per locus within populations; but, in 13 of 36 tests, HO was less than expected. Despite low levels of allelic diversity, genetic structure estimated as θ was significant for all pairwise comparisons between populations (θ=0.05–0.23). Due to suspected null alleles at four loci, ENA (excluding null alleles) corrected FST estimates were calculated overall and for pairwise population comparisons. The ENA-corrected FST values (0.02–0.10) revealed significant overall genetic structure, but none of the pairwise values were significantly different from zero. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2=0.12, P=0.18) and for Australian populations only (r2=0.19, P=0.44), suggesting that IBD does not describe the pattern of gene flow among populations. This study supports a hypothesis of long distance dispersal by L. decolor at moderate to potentially high levels.

scholarly journals Diverging Genetic Structure of Coexisting Populations of the Black Storm-Petrel and the Least Storm-Petrel in the Gulf of California

2020 ◽  
Vol 13 ◽  
pp. 194008292094917
Author(s):  
Misael D. Mancilla-Morales ◽  
Santiago Romero-Fernández ◽  
Araceli Contreras-Rodríguez ◽  
José J. Flores-Martínez ◽  
Víctor Sánchez-Cordero ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Mate Selection ◽  
Gulf Of California ◽  
Population Genetic ◽  
Life Histories ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Storm Petrel

Estimations on the influence of evolutionary and ecological forces as drivers of population gene diversity and genetic structure have been performed on a growing number of colonial seabirds, but many remain poorly studied. In particular, the population genetic structure of storm-petrels (Hydrobatidae) has been evaluated in only a few of the 24 recognized species. We assessed the genetic diversity and population structure of the Black Storm-Petrel ( Hydrobates melania) and the Least Storm-Petrel ( Hydrobates microsoma) in the Gulf of California. The two species were selected because they are pelagic seabirds with comparable ecological traits and breeding grounds. Recent threats such as introduced species of predators and human disturbance have resulted in a decline of many insular vertebrate populations in this region and affected many different aspects of their life histories (ranging from reproductive success to mate selection), with a concomitant loss of genetic diversity. To elucidate to what extent the population genetic structure occurs in H. melania and H. microsoma, we used 719 base pairs from the mitochondrial cytochrome oxidase c subunit I gene. The evaluation of their molecular diversity, genetic structure, and gene flow were performed through diversity indices, analyses of molecular and spatial variance, and isolation by distance (IBD) across sampling sites, respectively. The population genetic structure (via AMOVA and SAMOVA) and isolation by distance (pairwise p-distances and FST/1– FST (using ΦST) were inferred for H. microsoma. However, for H. melania evidence was inconclusive. We discuss explanations leading to divergent population genetic structure signatures in these species, and the consequences for their conservation.

scholarly journals A strategic sampling design revealed the local genetic structure of cold-water fluvial sculpin: a focus on groundwater-dependent water temperature heterogeneity

2021 ◽  
Author(s):  
Souta Nakajima ◽  
Masanao Sueyoshi ◽  
Shun K. Hirota ◽  
Nobuo Ishiyama ◽  
Ayumi Matsuo ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Low Temperature ◽  
Genetic Differentiation ◽  
Water Temperature ◽  
Sampling Design ◽  
Cold Water ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Sampling Strategy ◽  
Genotyping By Sequencing

A key piece of information for ecosystem management is the relationship between the environment and population genetic structure. However, it is difficult to clearly quantify the effects of environmental factors on genetic differentiation because of spatial autocorrelation and analytical problems. In this study, we focused on stream ecosystems and the environmental heterogeneity caused by groundwater and constructed a sampling design in which geographic distance and environmental differences are not correlated. Using multiplexed ISSR genotyping by sequencing (MIG-seq) method, a fine-scale population genetics study was conducted in fluvial sculpin Cottus nozawae, for which summer water temperature is the determinant factor in distribution and survival. There was a clear genetic structure in the watershed. Although a significant isolation-by-distance pattern was detected in the watershed, there was no association between genetic differentiation and water temperature. Instead, asymmetric gene flow from relatively low-temperature streams to high-temperature streams was detected, indicating the importance of low-temperature streams and continuous habitats. The groundwater-focused sampling strategy yielded unexpected results and provided important insights for conservation.

scholarly journals Genetic structure is stronger across human-impacted habitats than among islands in the coralPorites lobata

2019 ◽  
Author(s):  
Kaho H. Tisthammer ◽  
Zac H. Forsman ◽  
Robert J. Toonen ◽  
Robert H. Richmond
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
High Stress ◽  
Disruptive Selection ◽  
Single Location ◽  
Isolation By Environment ◽  
Genetic Patterns ◽  
Significant Genetic Structure ◽  
Contrasting Habitats

ABSTRACTWe examined genetic structure in the lobe coralPorites lobataamong pairs of highly variable and high-stress nearshore sites and adjacent less variable and less impacted offshore sites on the islands of Oʻahu and Maui, Hawai‘i. Using an analysis of molecular variance framework, we tested whether populations were more structured by geographic distance or environmental extremes. The genetic patterns we observed followed isolation by environment, where nearshore and adjacent offshore populations showed significant genetic structure at both locations (AMOVAFST= 0.04 ∼ 0.19,P< 0.001), but no significant isolation by distance between islands. In contrast, a third site with a less impacted nearshore site showed no significant structure. Strikingly, corals from the two impacted nearshore sites on different islands over 100km apart with similar environmentally stressful conditions were genetically closer (FST∼ 0, P = 0.733) than those within a single location less than 2 km apart (FST= 0.041∼0.079, P < 0.01). Our results suggest that ecological boundaries appear to play a strong role in forming genetic structure in the coastal environment, and that genetic divergence in the absence of geographical barriers to gene flow may be explained by disruptive selection across contrasting habitats.

scholarly journals Genetic variation and cryptic lineage diversity of the Nigerian red-headed rock agama Agama agama associate with eco-geographic zones

2019 ◽  
Vol 65 (6) ◽  
pp. 713-724 ◽  
Author(s):  
Lotanna M Nneji ◽  
Adeniyi C Adeola ◽  
Fang Yan ◽  
Agboola O Okeyoyin ◽  
Ojo C Oladipo ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Geographic Distance ◽  
Climatic Conditions ◽  
Population Divergence ◽  
Geographic Isolation ◽  
Genetic Structuring ◽  
Derived Savanna ◽  
Wide Range ◽  
Conservation Actions ◽  
The Impact

AbstractNigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic endemism. Among its vertebrate fauna, reptiles have broad distributions, thus, they constitute a compelling system for assessing the impact of ecological variation and geographic isolation on species diversification. The red-headed rock agama, Agama agama, lives in a wide range of habitats and, thus, it may show genetic structuring and diversification. Herein, we tested the hypothesis that ecology affects its genetic structure and population divergence. Bayesian inference phylogenetic analysis of a mitochondrial DNA (mtDNA) gene recovered four well-supported matrilines with strong evidence of genetic structuring consistent with eco-geographic regions. Genetic differences among populations based on the mtDNA also correlated with geographic distance. The ecological niche model for the matrilines had a good fit and robust performance. Population divergence along the environmental axes was associated with climatic conditions, and temperature ranked highest among all environmental variables for forest specialists, while precipitation ranked highest for the forest/derived savanna, and savanna specialists. Our results cannot reject the hypothesis that niche conservatism promotes geographic isolation of the western populations of Nigerian A. agama. Thus, ecological gradients and geographic isolation impact the genetic structure and population divergence of the lizards. This species might be facing threats due to recent habitat fragmentation, especially in western Nigeria. Conservation actions appear necessary.

Genetic diversity and gene flow patterns in two riverine plant species with contrasting life-history traits and distributions across a large inland floodplain

2020 ◽  
Vol 68 (5) ◽  
pp. 384
Author(s):  
William Higgisson ◽  
Dianne Gleeson ◽  
Linda Broadhurst ◽  
Fiona Dyer
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Water Resource ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Geographic Distance ◽  
Resource Development ◽  
Water Resource Development ◽  
Floodplain River

Gene flow is a key evolutionary driver of spatial genetic structure, reflecting demographic processes and dispersal mechanisms. Understanding how genetic structure is maintained across a landscape can assist in setting conservation objectives. In Australia, floodplains naturally experience highly variable flooding regimes that structure the vegetation communities. Flooding plays an important role, connecting communities on floodplains and enabling dispersal via hydrochory. Water resource development has changed the lateral-connectivity of floodplain-river systems. One possible consequence of these changes is reduced physical and subsequent genetic connections. This study aimed to identify and compare the population structure and dispersal patterns of tangled lignum (Duma florulenta) and river cooba (Acacia stenophylla) across a large inland floodplain using a landscape genetics approach. Both species are widespread throughout flood prone areas of arid and semiarid Australia. Tangled lignum occurs on floodplains while river cooba occurs along rivers. Leaves were collected from 144 tangled lignum plants across 10 sites and 84 river cooba plants across 6 sites, on the floodplain of the lower and mid Lachlan River, and the Murrumbidgee River, NSW. DNA was extracted and genotyped using DArTseq platforms (double digest RADseq). Genetic diversity was compared with floodplain-river connection frequency, and genetic distance (FST) was compared with river distance, geographic distance and floodplain-river connection frequency between sites. Genetic similarity increased with increasing floodplain-river connection frequency in tangled lignum but not in river cooba. In tangled lignum, sites that experience more frequent flooding had greater genetic diversity and were more genetically homogenous. There was also an isolation by distance effect where increasing geographic distance correlated with increasing genetic differentiation in tangled lignum, but not in river cooba. The distribution of river cooba along rivers facilitates regular dispersal of seeds via hydrochory regardless of river level, while the dispersal of seeds of tangled lignum between patches is dependent on flooding events. The genetic impact of water resource development may be greater for species which occur on floodplains compared with species along river channels.

scholarly journals Stochasticity in space, persistence in time: genetic heterogeneity in harbour populations of the introduced ascidianStyela plicata

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2158 ◽  
Author(s):  
Mari-Carmen Pineda ◽  
Beatriz Lorente ◽  
Susanna López-Legentil ◽  
Creu Palacín ◽  
Xavier Turon
Keyword(s):  
Genetic Structure ◽  
Gene Diversity ◽  
Mitochondrial Gene ◽  
Geographic Distance ◽  
Marine Species ◽  
Mediterranean Coast ◽  
Medium Size ◽  
Indigenous Species ◽  
Spatial And Temporal Scales ◽  
Nw Mediterranean

Spatio-temporal changes in genetic structure among populations provide crucial information on the dynamics of secondary spread for introduced marine species. However, temporal components have rarely been taken into consideration when studying the population genetics of non-indigenous species. This study analysed the genetic structure ofStyela plicata,a solitary ascidian introduced in harbours and marinas of tropical and temperate waters, across spatial and temporal scales. A fragment of the mitochondrial gene Cytochrome Oxidase subunit I (COI) was sequenced from 395 individuals collected at 9 harbours along the NW Mediterranean coast and adjacent Atlantic waters (> 1,200 km range) at two time points 5 years apart (2009 and 2014). The levels of gene diversity were relatively low for all 9 locations in both years. Analyses of genetic differentiation and distribution of molecular variance revealed strong genetic structure, with significant differences among many populations, but no significant differences among years. A weak and marginally significant correlation between geographic distance and gene differentiation was found. Our results revealed spatial structure and temporal genetic homogeneity inS. plicata, suggesting a limited role of recurrent, vessel-mediated transport of organisms among small to medium-size harbours. Our study area is representative of many highly urbanized coasts with dense harbours. In these environments, the episodic chance arrival of colonisers appears to determine the genetic structure of harbour populations and the genetic composition of these early colonising individuals persists in the respective harbours, at least over moderate time frames (five years) that encompass ca. 20 generations ofS. plicata.

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