scholarly journals Hopping or Jumping on the Cliffs: The Unusual Phylogeographical and Demographic Structure of an Extremely Narrow Endemic Mediterranean Plant

2021 ◽  
Vol 12 ◽  
Author(s):  
Sandro Strumia ◽  
Annalisa Santangelo ◽  
Teresa Rosa Galise ◽  
Salvatore Cozzolino ◽  
Donata Cafasso
Keyword(s):  
Current Distribution ◽  
Demographic History ◽  
Random Mating ◽  
Small Population ◽  
Wind Pollination ◽  
High Genetic Diversity ◽  
Coastal Species ◽  
Population Sizes ◽  
Study Sites ◽  
Mediterranean Plant

Several past and recent climatic and geological events have greatly influenced the current distribution of coastal species around the Mediterranean Basin. As a consequence, the reconstruction of the distributional history of these species is challenging. In this study, we used both chloroplast and nuclear SNPs to assess the levels of genetic differentiation, contemporary/historical levels of gene flow, and demographic history for the three only known (one mainland and two insular) populations of Eokochia saxicola, a rare Mediterranean coastal rocky halophyte. Plastid genome analysis revealed very low intraspecific haplotype variation and partial admixture among Capri and Palinuro populations with at least two independent colonization events for the Strombolicchio islet. Nuclear SNPs variation consistently identified three distinct genetic clusters corresponding to our sampling localities. Furthermore, strong genetic isolation was confirmed by both historical and contemporary levels of migration among the three populations. The DIYABC analysis identified two introductions temporally separated from Palinuro to Capri (ca.25 Mya) and subsequently to Strombolicchio (ca.09 Mya) as the most likely hypothesis for the current distribution of E. saxicola. Regardless of their small population sizes, all study sites supported high-genetic diversity maintained by outcrossing and random mating between individuals owing largely to wind pollination, an exclusive trait among Mediterranean narrow endemics. In conclusion, the patterns observed confirm that some Mediterranean endemics are not necessarily “evolutionary dead-ends” but rather represent species that have extensive demographic stability and a strong evolutionary legacy.

Estimating the exposure of carnivorous plants to rapid climatic change

2018 ◽  
Author(s):  
Matthew C. Fitzpatrick ◽  
Aaron M. Ellison
Keyword(s):  
Climatic Change ◽  
Habitat Suitability ◽  
Species Distributions ◽  
Dispersal Limitation ◽  
Small Population ◽  
Carnivorous Plant ◽  
Carnivorous Plants ◽  
Habitat Specialization ◽  
Population Sizes ◽  
Suitable Habitats

Climatic change likely will exacerbate current threats to carnivorous plants. However, estimating the severity of climatic change is challenged by the unique ecology of carnivorous plants, including habitat specialization, dispersal limitation, small ranges, and small population sizes. We discuss and apply methods for modeling species distributions to overcome these challenges and quantify the vulnerability of carnivorous plants to rapid climatic change. Results suggest that climatic change will reduce habitat suitability for most carnivorous plants. Models also project increases in habitat suitability for many species, but the extent to which these increases may offset habitat losses will depend on whether individuals can disperse to and establish in newly suitable habitats outside of their current distribution. Reducing existing stressors and protecting habitats where numerous carnivorous plant species occur may ameliorate impacts of climatic change on this unique group of plants.

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

scholarly journals Construction of a breeding parent population of Populus tomentosa based on SSR genetic distance analysis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhiqiang Han ◽  
Qiang Han ◽  
Yufei Xia ◽  
Xining Geng ◽  
Kang Du ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Combining Ability ◽  
Growth Traits ◽  
Random Mating ◽  
Specific Combining Ability ◽  
Hybrid Breeding ◽  
High Fertility ◽  
Germplasm Resources ◽  
Parent Population ◽  
High Genetic Diversity

Abstract Parent selection is the core of hybrid breeding. The breeding strategy involving the parental identification of superior open-pollinated progeny of Populous tomentosa germplasm resources can significantly improve the efficiency of parental matching. However, due to some factors such as loose powdering time and pollen competitiveness, the offspring derived from open-pollination families which do not undergo completely random mating. Although hybrid combinations based on the male identification method have a high combining ability, this method cannot easily cover the mating combinations of all male and female specimens in the germplasm bank. In addition, the performance of superior plants in open-pollinated families also affects the selection result. If the trait performance value is higher than the population average, then the special combining ability of the reconstructed hybrid combination may be overestimated. Obtaining a solution to the above problems is of great significance for improving the efficiency and accuracy of selecting hybrid parents of P. tomentosa. In this study, 24 pairs of SSR (Simple Sequence Repeats) molecular markers were used to analyze the genetic differentiation of P. tomentosa germplasm resources. The results showed that the genetic variation of the P. tomentosa population was derived from individuals within the provenance, indicating that high genetic diversity is preserved in provenances. The correlation analysis showed that there was a significant positive correlation between the special combining ability of planting height and diameter at breast height (dbh) of the 34 full-sib progeny population and the genetic distance between the parents. Then, the genetic distance between 18 female plants with high fertility and 68 male plants with large pollen quantity was analyzed using this correlation. Fifteen female parents and 12 male parents were screened out, and 52 hybrid combinations with high specific combining ability for growth traits were predicted. Furthermore, for the male parent identification of superior individual plants, we constructed the breeding parent population including 10 female parents and 5 male parents, generating 14 hybrid combinations with potentially high combining ability. The results of the hybridization test showed that the specific combining ability of plant height and dbh was significantly higher than the controlled pollination. Moreover, genetic distance and paternal identification can be used to rapidly and efficiently construct hybrid parent combinations and breeding parent populations.

scholarly journals Nestling Sex Ratio in the Southwestern Willow Flycatcher

The Condor ◽  
2002 ◽  
Vol 104 (4) ◽  
pp. 877-881
Author(s):  
Eben H. Paxton ◽  
Mark K. Sogge ◽  
Tracy D. McCarthey ◽  
Paul Keim
Keyword(s):  
Sex Ratio ◽  
Molecular Genetic ◽  
Small Population ◽  
Geographic Isolation ◽  
Breeding Populations ◽  
Population Sizes ◽  
Genetic Techniques ◽  
Willow Flycatcher ◽  
Empidonax Traillii ◽  
Negative Impacts

AbstractUsing molecular-genetic techniques, we determined the gender of 202 Southwestern Willow Flycatcher (Empidonax traillii extimus) nestlings from 95 nests sampled over a five-year period. Overall nestling sex ratio did not vary significantly from 50:50 among years, by clutch order, or by mating strategy (monogamous vs. polygamous pairings). However, we did observe significant differences among the four sites sampled, with sex ratios biased either toward males or females at the different sites. Given the small population sizes and geographic isolation of many of the endangered subspecies' breeding populations, sex-ratio differences may have localized negative impacts.Cociente de Sexos en Polluelos de Empidonax traillii extimusResumen. Utilizando técnicas moleculares determinamos el sexo de 202 polluelos de Empidonax traillii extimus pertenecientes a 95 nidos que fueron muestreados durante un período de cinco años. En general, el cociente de sexos no varió significativamente de 50:50 entre años, ya sea por orden de la nidada o por estrategia de apareamiento (monogamia vs. poligamia). Sin embargo, observamos diferencias significativas entre los cuatro sitios muestreados, en los cuales la razón de sexos estuvo sesgada hacia los machos o las hembras dependiendo del sitio. Dados los pequeños tamaños poblacionales y el aislamiento geográfico de muchas de las poblaciones reproductivas de esta subespecie en peligro, las diferencias en el cociente de sexos pueden tener un impacto negativo a nivel local.

scholarly journals Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192613 ◽  
Author(s):  
Elisa G. Dierickx ◽  
Simon Yung Wa Sin ◽  
H. Pieter J. van Veelen ◽  
M. de L. Brooke ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Sex Chromosomes ◽  
Demographic History ◽  
Large Population ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Approaches To Study ◽  
Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

scholarly journals Inferring the Demographic History of Inbred Species from Genome-Wide SNP Frequency Data

2020 ◽  
Vol 37 (7) ◽  
pp. 2124-2136
Author(s):  
Paul D Blischak ◽  
Michael S Barker ◽  
Ryan N Gutenkunst
Keyword(s):  
Puma Concolor ◽  
Demographic History ◽  
Random Mating ◽  
Simulated Data ◽  
Conservation Agriculture ◽  
Model Fit ◽  
Parameter Estimates ◽  
History Of ◽  
Demographic Inference ◽  
Inbred Populations

Abstract Demographic inference using the site frequency spectrum (SFS) is a common way to understand historical events affecting genetic variation. However, most methods for estimating demography from the SFS assume random mating within populations, precluding these types of analyses in inbred populations. To address this issue, we developed a model for the expected SFS that includes inbreeding by parameterizing individual genotypes using beta-binomial distributions. We then take the convolution of these genotype probabilities to calculate the expected frequency of biallelic variants in the population. Using simulations, we evaluated the model’s ability to coestimate demography and inbreeding using one- and two-population models across a range of inbreeding levels. We also applied our method to two empirical examples, American pumas (Puma concolor) and domesticated cabbage (Brassica oleracea var. capitata), inferring models both with and without inbreeding to compare parameter estimates and model fit. Our simulations showed that we are able to accurately coestimate demographic parameters and inbreeding even for highly inbred populations (F = 0.9). In contrast, failing to include inbreeding generally resulted in inaccurate parameter estimates in simulated data and led to poor model fit in our empirical analyses. These results show that inbreeding can have a strong effect on demographic inference, a pattern that was especially noticeable for parameters involving changes in population size. Given the importance of these estimates for informing practices in conservation, agriculture, and elsewhere, our method provides an important advancement for accurately estimating the demographic histories of these species.

scholarly journals High genetic diversity and demographic history of captive Siamese and Saltwater crocodiles suggest the first step toward the establishment of a breeding and reintroduction program in Thailand

PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184526 ◽  
Author(s):  
Sorravis Lapbenjakul ◽  
Watcharaporn Thapana ◽  
Panupon Twilprawat ◽  
Narongrit Muangmai ◽  
Thiti Kanchanaketu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Demographic History ◽  
High Genetic Diversity ◽  
History Of

Population viability analysis on a native Danish cattle breed

2016 ◽  
Vol 59 ◽  
pp. 105-112 ◽  
Author(s):  
Morten Hertz ◽  
Iben Ravnborg Jensen ◽  
Laura Østergaard Jensen ◽  
Iben Vejrum Nielsen ◽  
Jacob Winde ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Extinction Risk ◽  
Population Viability Analysis ◽  
Cattle Breed ◽  
Population Viability ◽  
Small Population ◽  
Viability Analysis ◽  
Probability Of Survival ◽  
Population Sizes ◽  
Breeding Pool

SummaryMany domestic breeds face challenges concerning genetic variability, because of their small population sizes along with a high risk of inbreeding. Therefore, it is important to obtain knowledge on their extinction risk, along with the possible benefits of certain breeding strategies. Since many domestic breeds face the same problems, results from such studies can be applied across breeds and species. Here a Population Viability Analysis (PVA) was implemented to simulate the future probability of extinction for a population of the endangered Danish Jutland cattle (Bos taurus), based on the software Vortex. A PVA evaluates the extinction risk of a population by including threats and demographic values. According to the results from the PVA the population will go extinct after 122 years with the current management. Four scenarios were created to investigate which changes in the breeding scheme would have the largest effect on the survival probabilities, including Scenario 1: More females in the breeding pool, scenario 2: More males in the breeding pool, scenario 3: Increased carrying capacity, and scenario 4: Supplementing males to the population through artificial insemination using semen from bulls used in the populations in past generations. All scenarios showed a positive effect on the population's probability of survival, and with a combination of the different scenarios, the population size seems to be stabilized.

scholarly journals Population Genetic Structure and Genetic Diversity in Twisted-Jaw Fish, Belodontichthys truncatus Kottelat & Ng, 1999 (Siluriformes: Siluridae), from Mekong Basin

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Surapon Yodsiri ◽  
Komgrit Wongpakam ◽  
Adisak Ardharn ◽  
Chadaporn Senakun ◽  
Sutthira Khumkratok
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Demographic History ◽  
Hydropower Plant ◽  
Mekong River ◽  
Demographic Expansion ◽  
High Genetic Diversity ◽  
History Analysis ◽  
History Of ◽  
Important Food Source

The Mekong River and its tributaries possess the second highest diversity in fish species in the world. However, the fish biodiversity in this river is threatened by several human activities, such as hydropower plant construction. Understanding the genetic diversity and genetic structure of the species is important for natural resource management. Belodontichthys truncatus Kottelat & Ng is endemic to the Mekong River basin and is an important food source for people in this area. In this study, the genetic diversity, genetic structure, and demographic history of the twisted-jaw fish, B. truncatus, were investigated using mitochondrial cytochrome b gene sequences. A total of 124 fish specimens were collected from 10 locations in the Mekong and its tributaries. Relatively high genetic diversity was found in populations of B. truncatus compared to other catfish species in the Mekong River. The genetic structure analysis revealed that a population from the Chi River in Thailand was genetically significantly different from other populations, which is possibly due to the effect of genetic drift. Demographic history analysis indicated that B. truncatus has undergone recent demographic expansion dating back to the end of the Pleistocene glaciation.

Biology and conservation of Coptis teeta Wall. – an endemic and endangered medicinal herb of Eastern Himalaya

1998 ◽  
Vol 25 (3) ◽  
pp. 262-272 ◽  
Author(s):  
M. K. PANDIT ◽  
C. R. BABU
Keyword(s):  
Scientific Information ◽  
Small Population ◽  
Vital Role ◽  
Eastern Himalaya ◽  
Evolutionary Divergence ◽  
External Threats ◽  
Population Sizes ◽  
Over Exploitation ◽  
Endangered Medicinal Herb ◽  
The Tropics

Medicinal plants are a valuable resource for regional economic development in the tropics, and the Eastern Himalaya in particular harbours many such species. Extensive deforestation and over-exploitation in this region have brought several species to the brink of extinction, and Coptis teeta is such an endangered species; yet scientific information for its conservation is lacking. Investigations on the distribution range, demography, ecology, cytology, reproductive biology and population genetic structure of C. teeta were carried out; it was found to be endemic to a small area, to occupy a very narrow habitat and to be highly dispersed with very small population sizes. Edaphic factors were found to have played a vital role in ecological preference, natural distribution and evolutionary divergence of the species. The species exhibits a ‘K’ strategy, high male sterility, low reproductive success and efficiency, inadequate seed dispersal, and little genetic variability. A combination of these genetic hurdles and external threats in the form of habitat disturbance and over-exploitation for commercial purposes could result in its extinction. The species was found to have highly specific microsite requirements that cannot be met in other habitats. It is argued that in situ conservation measures would be the best strategy for the continued survival of this species. For effective management of the species it is recommended that its habitat be declared a protected area with the active cooperation of local inhabitants including the sharing of benefits of conservation.

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