Conservation implications of distinct genetic structuring in the endangered freshwater fish Nannoperca oxleyana (Percichthyidae)

2009 ◽  
Vol 60 (1) ◽  
pp. 34 ◽  
Author(s):  
James T. Knight ◽  
Catherine J. Nock ◽  
Martin S. Elphinstone ◽  
Peter R. Baverstock
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Sand Dunes ◽  
Restricted Gene Flow ◽  
Genetic Structuring ◽  
Conservation Implications ◽  
South Wales ◽  
Haplotypic Diversity ◽  
Genetic Diversity And Structure ◽  
Fragmented Distribution

The maintenance of genetic diversity and gene flow in threatened species is a vital consideration for recovery programs. The endangered Oxleyan pygmy perch Nannoperca oxleyana has a fragmented distribution within coastal freshwater drainages of southern Queensland and northern New South Wales, Australia. In the present study, mitochondrial DNA control region variation was used to assess genetic diversity and structure across the geographical range of this species. Haplotypic diversity was highest in a small NSW subcatchment south of Evans Head (h = 0.594) followed by Marcus Creek in Queensland (h = 0.475). Distinct genetic differentiation was evident among the Queensland localities and the NSW subcatchments, implying restricted gene flow between coastal river systems. One of the nine haplotypes detected was distributed over 83.4% of the species’ range, suggesting historical connectivity among the now fragmented populations. These patterns were concordant with eustatic changes associated with the last glacial maximum. High barrier sand dunes may also act as barriers to gene flow and dispersal between adjacent NSW subcatchments. Conservation efforts should focus on the preservation of genetic diversity by maintaining as many genetically differentiated populations as possible. The relatively diverse populations inhabiting the South Evans Head subcatchment and Marcus Creek require special management consideration.

scholarly journals Genetic Structure and Eco-Geographical Differentiation of Lancea tibetica in the Qinghai-Tibetan Plateau

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 97 ◽  
Author(s):  
Xiaofeng Chi ◽  
Faqi Zhang ◽  
Qingbo Gao ◽  
Rui Xing ◽  
Shilong Chen
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Gene Flow ◽  
Tibetan Plateau ◽  
Environmental Changes ◽  
Restricted Gene Flow ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Tanggula Mountains

The uplift of the Qinghai-Tibetan Plateau (QTP) had a profound impact on the plant speciation rate and genetic diversity. High genetic diversity ensures that species can survive and adapt in the face of geographical and environmental changes. The Tanggula Mountains, located in the central of the QTP, have unique geographical significance. The aim of this study was to investigate the effect of the Tanggula Mountains as a geographical barrier on plant genetic diversity and structure by using Lancea tibetica. A total of 456 individuals from 31 populations were analyzed using eight pairs of microsatellite makers. The total number of alleles was 55 and the number per locus ranged from 3 to 11 with an average of 6.875. The polymorphism information content (PIC) values ranged from 0.2693 to 0.7761 with an average of 0.4378 indicating that the eight microsatellite makers were efficient for distinguishing genotypes. Furthermore, the observed heterozygosity (Ho), the expected heterozygosity (He), and the Shannon information index (I) were 0.5277, 0.4949, and 0.9394, respectively, which indicated a high level of genetic diversity. We detected high genetic differentiation among all sampling sites and restricted gene flow among populations. Bayesian-based cluster analysis (STRUCTURE), principal coordinates analysis (PCoA), and Neighbor-Joining (NJ) cluster analysis based on microsatellite markers grouped the populations into two clusters: the southern branch and the northern branch. The analysis also detected genetic barriers and restricted gene flow between the two groups separated by the Tanggula Mountains. This study indicates that the geographical isolation of the Tanggula Mountains restricted the genetic connection and the distinct niches on the two sides of the mountains increased the intraspecific divergence of the plants.

Genetic diversity and structure in the northern populations of European hazelnut (Corylus avellana L.)

Genome ◽  
2019 ◽  
Vol 62 (8) ◽  
pp. 537-548
Author(s):  
Pirjo Tanhuanpää ◽  
Maarit Heinonen ◽  
Lidija Bitz ◽  
Veli-Matti Rokka
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Plant Conservation ◽  
Corylus Avellana ◽  
Ice Age ◽  
Genetic Structuring ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Corylus Avellana L

European hazelnut (Corylus avellana L.) is a strictly cross-pollinated diploid tree species, which has its northernmost populations in Fennoscandia, and it was one of the first species to recolonize northern Europe after the last ice age. Hazelnut produces edible nuts in Finland but nowadays they are underutilized as food, and currently no breeding programmes exist. In the present study, 300 hazelnut specimens were collected from 20 different locations (= populations) in Finland, and they were genetically analyzed using nine simple sequence repeat (SSR) markers. Most of the genetic diversity existed within populations (83%). According to different genetic analyses (STRUCTURE, principal coordinates analysis, and clustering), a general lack of structure was observed, suggesting extensive gene flow among hazelnuts between 17 investigated populations. However, genetic structuring was clearly observed in three populations: Hakavuori, Mustiala, and Pähkinämäki, which might have become isolated due to geographical barriers that kept them separate, diminishing gene flow from other populations. Studying the diversity of European hazelnut is of great interest for understanding population genetics of a species distributed in its marginal areas in the north, and the results are also valuable for further uses in plant conservation, selection, and possible future breeding actions in Finland.

The Coalescent in a Continuous, Finite, Linear Population

Genetics ◽  
2002 ◽  
Vol 161 (2) ◽  
pp. 873-888
Author(s):  
Jon F Wilkins ◽  
John Wakeley
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Simulated Data ◽  
Restricted Gene Flow ◽  
Demographic Parameters ◽  
Common Ancestry ◽  
Linear Habitat ◽  
Mean Time ◽  
Finite Linear

Abstract In this article we present a model for analyzing patterns of genetic diversity in a continuous, finite, linear habitat with restricted gene flow. The distribution of coalescent times and locations is derived for a pair of sequences sampled from arbitrary locations along the habitat. The results for mean time to coalescence are compared to simulated data. As expected, mean time to common ancestry increases with the distance separating the two sequences. Additionally, this mean time is greater near the center of the habitat than near the ends. In the distant past, lineages that have not undergone coalescence are more likely to have been at opposite ends of the population range, whereas coalescent events in the distant past are biased toward the center. All of these effects are more pronounced when gene flow is more limited. The pattern of pairwise nucleotide differences predicted by the model is compared to data collected from sardine populations. The sardine data are used to illustrate how demographic parameters can be estimated using the model.

Weak genetic structuring suggests historically high genetic connectivity among recently fragmented urban populations of the scincid lizard, Ctenotus fallens

2015 ◽  
Vol 63 (4) ◽  
pp. 279 ◽  
Author(s):  
Josef Krawiec ◽  
Siegfried L. Krauss ◽  
Robert A. Davis ◽  
Peter B. S. Spencer
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Large Population ◽  
Geographic Distance ◽  
Genetic Erosion ◽  
Genetic Connectivity ◽  
Genetic Structuring ◽  
Low Genetic Diversity ◽  
Population Sizes

Populations in fragmented urban remnants may be at risk of genetic erosion as a result of reduced gene flow and elevated levels of inbreeding. This may have serious genetic implications for the long-term viability of remnant populations, in addition to the more immediate pressures caused by urbanisation. The population genetic structure of the generalist skink Ctenotus fallens was examined using nine microsatellite markers within and among natural vegetation remnants within a highly fragmented urban matrix in the Perth metropolitan area in Western Australia. These data were compared with samples from a large unfragmented site on the edge of the urban area. Overall, estimates of genetic diversity and inbreeding within all populations were similar and low. Weak genetic differentiation, and a significant association between geographic and genetic distance, suggests historically strong genetic connectivity that decreases with geographic distance. Due to recent fragmentation, and genetic inertia associated with low genetic diversity and large population sizes, it is not possible from these data to infer current genetic connectivity levels. However, the historically high levels of gene flow that our data suggest indicate that a reduction in contemporary connectivity due to fragmentation in C. fallens is likely to result in negative genetic consequences in the longer term.

scholarly journals Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhe Zhang ◽  
Stephan W. Gale ◽  
Ji-Hong Li ◽  
Gunter A. Fischer ◽  
Ming-Xun Ren ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Polynomial Regression ◽  
Genetic Erosion ◽  
Population Level ◽  
Hainan Island ◽  
Paternity Analysis ◽  
Genetic Structuring ◽  
Long Distance ◽  
High Genetic Diversity

Abstract Background Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchid Phalaenopsis pulcherrima on Hainan Island, China. Results Phalaenopsis pulcherrima is self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules of P. pulcherrima to each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next. Conclusions Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity in P. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.

Genetic Variation in Invasive Populations of Yellow Toadflax (Linaria vulgaris) in the Western United States

Weed Science ◽  
2008 ◽  
Vol 56 (3) ◽  
pp. 394-399 ◽  
Author(s):  
Sarah M. Ward ◽  
Scott D. Reid ◽  
Judy Harrington ◽  
Jason Sutton ◽  
K George Beck
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Recombination ◽  
Diversity Index ◽  
Gene Diversity ◽  
Group Method ◽  
Restricted Gene Flow ◽  
Genetic Structuring ◽  
Invasive Weed ◽  
Yellow Toadflax

Intraspecific genetic variation may contribute significantly to invasiveness and control problems, but has been characterized to date in relatively few invasive weed species. We examined 56 intersimple sequence repeat (ISSR) loci in 220 individuals from 11 invading populations of yellow toadflax sampled across five western states. All populations showed high levels of genetic diversity. Estimated values for Shannon's diversity measure ranged from 0.217 to 0.388, and for expected heterozygosity from 0.178 to 0.260. Nei's total gene diversity index (HT), on the basis of all individuals across all populations, was 0.267. Partitioning of genetic variance using analysis of molecular variance revealed 1.7% of genetic variation among regional population groups, 29.1% among populations within groups, and 69.2% within populations, consistent with expectations for an outcrossing species but suggesting little geographic differentiation. Pairs of adjacent individuals identical at all ISSR loci that appeared to be ramets of a single clone were detected in only one population. This indicates that patch expansion in yellow toadflax is driven more by sexual reproduction via seed than by rhizomatous clonal spread, at least at the spatial scale of sampling for this study. Eight populations had significant values for Mantel's R at P = 0.05, suggesting some fine-scale positive genetic structuring, possibly from restricted gene flow. Population clustering on the basis of Nei's genetic distance between populations and unweighted pair group method with arithmetic mean did not reflect geographic location. It is likely that multiple introductions of this species have occurred across the Intermountain West, followed by extensive genetic recombination. High levels of genetic diversity within yellow toadflax populations pose management challenges, as already seen in reports of variable response to herbicide application and limited impacts of biocontrol agent releases.

Crop to wild gene flow and genetic diversity in a vulnerable Macadamia (Proteaceae) species in New South Wales, Australia

2015 ◽  
Vol 191 ◽  
pp. 504-511 ◽  
Author(s):  
Katie O'Connor ◽  
Michael Powell ◽  
Catherine Nock ◽  
Alison Shapcott
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
New South ◽  
New South Wales ◽  
South Wales

Consequences of long- and short-term fragmentation on the genetic diversity and differentiation of a late successional rainforest conifer

2011 ◽  
Vol 59 (4) ◽  
pp. 351 ◽  
Author(s):  
Rohan Mellick ◽  
Andrew Lowe ◽  
Maurizio Rossetto
Keyword(s):  
Genetic Diversity ◽  
New South ◽  
Demographic Stochasticity ◽  
Niche Modelling ◽  
Lag Effects ◽  
South Wales ◽  
Unique System ◽  
Genetic Diversity And Structure ◽  
Modelling Techniques ◽  
Diversity Estimates

The east Australian rainforests provide a unique system with which to study historic climate-driven habitat fragmentation. The long life span of rainforest conifers and consequent lag effects on genetic variation, offer insights into demographic stochasticity in small populations and persistence in increasingly fragmented systems. Microsatellite markers were used to investigate the genetic diversity and structure of Podocarpus elatus (Podocarpaceae), a long-lived rainforest conifer endemic to Australia. Twenty-seven populations throughout the east Australian rainforests were screened and two divergent regions separated by the dry Clarence River valley (New South Wales) were discovered. This biogeographic barrier may be referred to as the Clarence River Corridor. Niche modelling techniques were employed to verify the incidence of habitat divergence between the two regions. Significantly high inbreeding was detected throughout the species range with no evidence of recent bottlenecks. Most of the diversity in the species resides between individuals within populations, which suggest the species would be sensitive to the adverse effects of inbreeding, yet evidence suggests that these populations have been small for several generations. Slightly higher diversity estimates were found in the southern region, but it is likely that the species survived historic population contraction in dispersed refugia within each of these genetically differentiated regions.

scholarly journals Genetic diversity and extent of gene flow in the endangered Japanese population of Hodgson's hawk-eagle, Spizaetus nipalensis

2006 ◽  
Vol 16 (2) ◽  
pp. 113-129 ◽  
Author(s):  
SHIGEKI ASAI ◽  
YOSHIHIRO YAMAMOTO ◽  
SATOSHI YAMAGISHI
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Japanese Population ◽  
Isolation By Distance ◽  
Cladistic Analysis ◽  
Variable Region ◽  
Complete Sequence ◽  
Restricted Gene Flow ◽  
Critical Situation ◽  
Mtdna Sequence

The Japanese subspecies of Hodgson's Hawk-eagle, Spizaetus nipalensis orientalis, is considered threatened and has been designated as Endangered by the Japanese government. We determined the complete mitochondrial DNA (mtDNA) sequence of this species and designed a primer set to amplify a highly variable region of mtDNA, part of the control region (CR), based on this complete sequence. Using the primers, we amplified the CR and then determined the haplotypes of 178 samples collected at different sites in Japan. A nested cladistic analysis indicated that gene flow within some clades was restricted. The inference key implied that isolation by distance had caused the restriction of gene flow. Moreover, the ranges of the clades in which restricted gene flow was detected overlapped with the ranges of other clades. These results suggest that there is no fragmental population of Hodgson's Hawk-eagle in Japan and that this species has dispersed within short distances, at least in some lineages. Genetic diversity was high in comparison with other species. Therefore, at least in terms of genetic diversity, the Japanese population of Hodgson's Hawk-eagle is probably not in a critical situation.

scholarly journals Genetic studies of human diversity in East Asia

2007 ◽  
Vol 362 (1482) ◽  
pp. 987-996 ◽  
Author(s):  
Feng Zhang ◽  
Bing Su ◽  
Ya-ping Zhang ◽  
Li Jin
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
East Asia ◽  
Pacific Islands ◽  
East Asian ◽  
Human Populations ◽  
Genetic Studies ◽  
The North ◽  
Asian Populations ◽  
Genetic Diversity And Structure

East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north–south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.

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