scholarly journals Loss of Mitochondrial Genetic Diversity in Overexploited Mediterranean Swordfish (Xiphias gladius, 1759) Population

Diversity ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 170 ◽  
Author(s):  
Tommaso Righi ◽  
Andrea Splendiani ◽  
Tatiana Fioravanti ◽  
Elia Casoni ◽  
Giorgia Gioacchini ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Stock Assessment ◽  
Extinction Risk ◽  
Haplotype Diversity ◽  
Effective Population ◽  
Mitochondrial Haplotypes ◽  
Short Period ◽  
The Mediterranean ◽  
Over Exploitation

Intense and prolonged mortality caused by over-exploitation could drive the decay of genetic diversity which may lead to decrease species’ resilience to environmental changes, thus increasing their extinction risk. Swordfish is a high commercial value species, especially in the Mediterranean Sea, where it is affected by high catch levels. Mediterranean swordfish consist of a population genetically and biologically distinct from Atlantic ones and therefore managed as a separate stock. The last Mediterranean swordfish stock assessment reported that in the last forty years Mediterranean swordfish has been overfished and, to date, it is still subject to overfishing. A comparison between an available mitochondrial sequence dataset and a homologous current sample was carried out to investigate temporal genetic variation in the Mediterranean swordfish population over near twenty years. Our study provides the first direct measure of reduced genetic diversity for Mediterranean swordfish during a short period, as measured both in the direct loss of mitochondrial haplotypes and reduction in haplotype diversity. A reduction of the relative females’ effective population size in the recent sample has been also detected. The possible relationship between fishery activities and the loss of genetic diversity in the Mediterranean swordfish population is discussed.

Inbreeding and loss of genetic diversity increase extinction risk

2019 ◽  
pp. 31-48
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Inbreeding Depression ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Raw Material ◽  
Heterozygote Advantage ◽  
Isolated Populations ◽  
Survival And Reproduction ◽  
Loss Of Genetic Diversity ◽  
Harmful Effects

Inbreeding reduces survival and reproduction (i.e. it causes inbreeding depression), and thereby increases extinction risk. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies. Impacts of inbreeding are generally greater in species that naturally outbreed than those that inbreed, in stressful than benign environments, and for fitness than peripheral traits. Harmful effects accumulate across the life cycle, resulting in devastating effects on total fitness in outbreeding species.Species face ubiquitous environmental change and must adapt or they will go extinct. Genetic diversity is the raw material required for evolutionary adaptation. However, loss of genetic diversity is unavoidable in small isolated populations, diminishing their capacity to evolve in response to environmental changes, and thereby increasing extinction risk.

Spatial and temporal genetic diversity of the Texas kangaroo rat, Dipodomys elator (Rodentia: Heteromyidae)

2019 ◽  
Vol 100 (4) ◽  
pp. 1169-1181 ◽  
Author(s):  
Russell S Pfau ◽  
Jim R Goetze ◽  
Robert E Martin ◽  
Kenneth G Matocha ◽  
Allan D Nelson
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
Allelic Diversity ◽  
Effective Population ◽  
Kangaroo Rat ◽  
Time Periods ◽  
Mtdna Diversity ◽  
Using Data

Abstract The Texas kangaroo rat (Dipodomys elator) is listed as a threatened species in Texas because of its scarcity and small geographic range. We assessed patterns of genetic diversity in D. elator that could affect extinction risk or influence management decisions. Specific objectives included: 1) document levels of genetic diversity, 2) document the degree and patterns of genetic divergence among localities, and 3) compare levels of genetic diversity between different time periods at the same locality. Portions of the mitochondrial genome (mtDNA; control region, cytochrome c oxidase subunit I, and cytochrome b) were sequenced and nuclear microsatellites were examined. Low mtDNA diversity was observed, which could be explained by an historical, species-wide genetic bottleneck. In contrast, microsatellites exhibited ample variation, and analyses were conducted using data from 11 loci and four populations (designated Quanah, Iowa Park, Vernon, and Harrold). Allelic diversity and heterozygosity were similar between populations and temporal samples. Estimates of effective population size (Ne) ranged from 5 to 856, depending on method and population, with Iowa Park showing consistently lower values than Quanah. All methods addressing population structure indicated that the Iowa Park population was divergent from the others, with Vernon and Harrold showing a somewhat intermediate relationship but with a closer affiliation with Quanah than Iowa Park, despite their closer proximity to Iowa Park. This pattern did not conform to isolation by distance, thus genetic drift appears to have played a greater role than gene flow in establishing genetic structure. There was much less difference between temporal samples compared to geographic samples, indicating that genetic drift has had only minimal impacts in shifting allelic frequencies over the time periods examined (17–36 years).

scholarly journals Being abundant is not enough: a decrease in effective population size over eight generations in a Norwegian population of the seaweed, Fucus serratus

2008 ◽  
Vol 4 (6) ◽  
pp. 755-757 ◽  
Author(s):  
James A Coyer ◽  
Galice Hoarau ◽  
Kjersti Sjøtun ◽  
Jeanine L Olsen
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allelic Richness ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Rocky Intertidal ◽  
Effective Population ◽  
Norwegian Population ◽  
Fucus Serratus ◽  
Southern Norway

The brown alga Fucus serratus is a key foundation species on rocky intertidal shores of northern Europe. We sampled the same population off the coast of southern Norway in 2000 and 2008, and using 26 microsatellite loci, we estimated the changes in genetic diversity and effective population size ( N e ). The unexpectedly low N e (73–386) and N e / N ratio (10 −3 –10 −4 ), in combination with a significant decrease (14%) in allelic richness over the 8-year period, suggests an increased local extinction risk. If small N e proves to be a common feature of F. serratus , then being abundant may not be enough for the species to weather future environmental changes.

scholarly journals Phenological and molecular studies on the introduced seaweed Dictyota cyanoloma (Dictyotales, Phaeophyceae) along the Mediterranean coast of the Iberian Peninsula

2016 ◽  
Vol 17 (3) ◽  
pp. 766 ◽  
Author(s):  
J. ARAGAY ◽  
D. VITALES ◽  
A. GÓMEZ GARRETA ◽  
M. A. RIBERA SIGUAN ◽  
F. STEEN ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Mediterranean Sea ◽  
Algal Species ◽  
Haplotype Diversity ◽  
Morphological Plasticity ◽  
Mediterranean Coast ◽  
Long Distance ◽  
Multiple Introductions ◽  
Mitochondrial Haplotypes ◽  
The Mediterranean

Dictyota cyanoloma, a distinctive brown algal species characterized by a blue-iridescent margin, was recently reported as an introduced species in the Mediterranean Sea (Steen et al., 2016) but little is known about its distribution dynamics, morphological plasticity and genetic structure. In the present integrative study, we evaluate its past and present occurrence along the Mediterranean Iberian coast, assess the species’ phenology in Palamós (Girona, Spain) and analyze the haplotype diversity by sequencing 49 individuals from nine sampling sites for different chloroplast and mitochondrial DNA regions. Although D. cyanoloma currently occurs along the Mediterranean Iberian coast (in 19 of 36 localities sampled between Algeciras and Llançà, mostly in marinas and harbour environments), we were not able to find any herbarium material of this species (at BCN-Phyc and MA) predating the year 1987. In Palamós, D. cyanoloma is present all through the year, with a maximum development in winter and a minimum in summer. Fertile specimens are absent during summer (July and August). Sporophytes are dominant from January to June and dioecious gametophytes were found only in February, March and June. Information about the antheridia, which has never been described before, is provided. Two chloroplast and three mitochondrial haplotypes were observed, indicating that multiple introductions of D. cyanoloma occurred in the study area. Additionally, the genetic structure suggests that spread did not occur through simple advancing wave fronts but by several long-distance dispersal events. Further studies employing microsatellite markers could potentially offer a better resolution to unravel expansion and colonisation dynamics of D. cyanoloma in the Mediterranean Sea.

scholarly journals Continent-wide effects of urbanization on bird and mammal genetic diversity

2019 ◽  
Author(s):  
C. Schmidt ◽  
M. Domaratzki ◽  
R.P. Kinnunen ◽  
J. Bowman ◽  
C.J. Garroway
Keyword(s):  
Genetic Diversity ◽  
Environmental Changes ◽  
Bird Species ◽  
Population Level ◽  
Natural Environments ◽  
Population Declines ◽  
Effective Population ◽  
Human Footprint ◽  
Rate Of Increase ◽  
Population Sizes

AbstractUrbanization and associated environmental changes are causing global declines in vertebrate populations. In general, population declines of the magnitudes now detected should lead to reduced effective population sizes for animals living in proximity to humans and disturbed lands. This is cause for concern because effective population sizes set the rate of genetic diversity loss due to genetic drift, the rate of increase in inbreeding, and the efficiency with which selection can act on beneficial alleles. We predicted that the effects of urbanization should decrease effective population size and genetic diversity, and increase population-level genetic differentiation. To test for such patterns, we repurposed and reanalyzed publicly archived genetic data sets for North American birds and mammals. After filtering, we had usable raw genotype data from 85 studies and 41,023 individuals, sampled from 1,008 locations spanning 41 mammal and 25 bird species. We used census-based urban-rural designations, human population density, and the Human Footprint Index as measures of urbanization and habitat disturbance. As predicted, mammals sampled in more disturbed environments had lower effective population sizes and genetic diversity, and were more genetically differentiated from those in more natural environments. There were no consistent relationships detectable for birds. This suggests that, in general, mammal populations living near humans may have less capacity to respond adaptively to further environmental changes, and be more likely to suffer from effects of inbreeding.

scholarly journals Range-wide neutral and adaptive genetic structure of an endemic herb from Amazonian Savannas

AoB Plants ◽  
2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Amanda R Silva ◽  
Luciana C Resende-Moreira ◽  
Carolina S Carvalho ◽  
Eder C M Lanes ◽  
Mabel P Ortiz-Vera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Extinction Risk ◽  
Clustering Methods ◽  
Effective Population ◽  
Evolutionary Potential ◽  
Management Actions ◽  
Temperature And Precipitation ◽  
Population Sizes ◽  
Genetic Clustering

Abstract Conserving genetic diversity in rare and narrowly distributed endemic species is essential to maintain their evolutionary potential and minimize extinction risk under future environmental change. In this study we assess neutral and adaptive genetic structure and genetic diversity in Brasilianthus carajensis (Melastomataceae), an endemic herb from Amazonian Savannas. Using RAD sequencing we identified a total of 9365 SNPs in 150 individuals collected across the species’ entire distribution range. Relying on assumption-free genetic clustering methods and environmental association tests we then compared neutral with adaptive genetic structure. We found three neutral and six adaptive genetic clusters, which could be considered management units (MU) and adaptive units (AU), respectively. Pairwise genetic differentiation (FST) ranged between 0.024 and 0.048, and even though effective population sizes were below 100, no significant inbreeding was found in any inferred cluster. Nearly 10 % of all analysed sequences contained loci associated with temperature and precipitation, from which only 25 sequences contained annotated proteins, with some of them being very relevant for physiological processes in plants. Our findings provide a detailed insight into genetic diversity, neutral and adaptive genetic structure in a rare endemic herb, which can help guide conservation and management actions to avoid the loss of unique genetic variation.

scholarly journals Spatio-temporal population structuring and genetic diversity retention in depleted Atlantic Bluefin tuna of the Mediterranean Sea

2010 ◽  
Vol 107 (5) ◽  
pp. 2102-2107 ◽  
Author(s):  
Giulia Riccioni ◽  
Monica Landi ◽  
Giorgia Ferrara ◽  
Ilaria Milano ◽  
Alessia Cariani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mediterranean Sea ◽  
Population Size ◽  
Effective Population Size ◽  
Large Population ◽  
Bluefin Tuna ◽  
Effective Population ◽  
Microsatellite Variation ◽  
Atlantic Bluefin Tuna ◽  
The Mediterranean

Fishery genetics have greatly changed our understanding of population dynamics and structuring in marine fish. In this study, we show that the Atlantic Bluefin tuna (ABFT, Thunnus thynnus), an oceanic predatory species exhibiting highly migratory behavior, large population size, and high potential for dispersal during early life stages, displays significant genetic differences over space and time, both at the fine and large scales of variation. We compared microsatellite variation of contemporary (n = 256) and historical (n = 99) biological samples of ABFTs of the central-western Mediterranean Sea, the latter dating back to the early 20th century. Measures of genetic differentiation and a general heterozygote deficit suggest that differences exist among population samples, both now and 96–80 years ago. Thus, ABFTs do not represent a single panmictic population in the Mediterranean Sea. Statistics designed to infer changes in population size, both from current and past genetic variation, suggest that some Mediterranean ABFT populations, although still not severely reduced in their genetic potential, might have suffered from demographic declines. The short-term estimates of effective population size are straddled on the minimum threshold (effective population size = 500) indicated to maintain genetic diversity and evolutionary potential across several generations in natural populations.

scholarly journals Evidence for an extreme founding effect in a highly successful invasive species

2020 ◽  
Author(s):  
Kateryna V. Kratzer ◽  
Annemarie van der Marel ◽  
Colin Garroway ◽  
Marta López-Darias ◽  
Stephen D. Petersen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Invasive Species ◽  
Population Size ◽  
Genetic Bottleneck ◽  
Ground Squirrels ◽  
Invasion Success ◽  
Island Population ◽  
Effective Population ◽  
Founding Population ◽  
Mitochondrial Haplotypes

AbstractThe adaptive potential of invasive species is thought to decrease during founding events due to reduced genetic diversity, limiting the new population’s ability to colonize novel habitats. Barbary ground squirrels (Atlantoxerus getulus) were purportedly introduced as a single breeding pair to the island of Fuerteventura but have expanded to over a million individuals spread across the island in just over 50 years. We estimated the number of founders and measured the level of genetic diversity in this population using the mitochondrial displacement loop and microsatellite markers. Island samples (n = 19) showed no variation in the d-loop, suggesting a single founding female, while Moroccan samples (n = 6) each had unique mitochondrial haplotypes. The microsatellite data of the island population (n = 256 individuals) revealed a small effective population size, low levels of heterozygosity, and high levels of inbreeding, supporting a founding population size of two to three individuals. Our results suggest that A. getulus has undergone an intense genetic bottleneck during their colonization of the island. They are one of the few species where introduction effort does not explain invasion success, although further investigation may explain how they have avoided the worst expected effects following an extreme genetic bottleneck.

scholarly journals Genetic bottlenecks and successful biological invasions: the case of a recent Lessepsian migrant

2007 ◽  
Vol 3 (5) ◽  
pp. 541-545 ◽  
Author(s):  
Daniel Golani ◽  
Ernesto Azzurro ◽  
Maria Corsini-Foka ◽  
Manuela Falautano ◽  
Franco Andaloro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Biological Invasions ◽  
Unified Theory ◽  
Ideal Case ◽  
Genetic Studies ◽  
Mitochondrial Haplotypes ◽  
Rapid Spread ◽  
Genetic Bottlenecks ◽  
The Mediterranean

Our current understanding of the mechanisms that lead to successful biological invasions is limited. Although adaptations play a central role in biological invasions, genetic studies have so far failed to produce a unified theory. The bluespotted cornetfish, a recent Red Sea invader in the Mediterranean Sea via the Suez Canal, provides an ideal case study for research in the mechanisms of invasive genetics. In this study, we show that the invading bluespotted cornetfish underwent a severe population bottleneck that reduced the genetic diversity of this immigrant to only two mitochondrial haplotypes. Although loss of genetic diversity is considered detrimental to the need to adapt to new environments, bluespotted cornetfish experienced an unprecedented success and rapid spread across the Mediterranean.

scholarly journals Population Genetic Diversity and Structure of Threatened Magnolia Species in Western Mexico

2020 ◽  
Author(s):  
Miguel Angel Muñiz-Castro ◽  
Gabriela Lopez-Barrera ◽  
Maried Ochoa-Zavala ◽  
Patricia Castro-Felix ◽  
Jose Antonio Vazquez-Garcia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
New Species ◽  
Biological Diversity ◽  
Environmental Changes ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Negative Consequences ◽  
Genetic Diversity And Structure

Abstract Background: Genetic diversity is needed to preserve the capability of a species to survive to environmental changes. Due to the presence of small isolated populations, relict species such as Magnolia are at an elevated extinction risk. In recent years, many new species of Magnolia have been described in Mexico, each one classified by its category of risk. To achieve conservation, knowledge of their basic level of biological diversity is essential to design adequate conservation plans and avoid the negative consequences of genetic loss. Here, we implemented nuclear microsatellite markers to assess 13 populations of three new species of Magnolia that were all previously considered to be Magnolia pacifica. We aimed to evaluate the genetic agreement with the distinction of these three different morphological species (e.g., their species integrity) and to determine their levels of genetic diversity and their geographic distribution to propose conservation strategies. Results: We found high levels of genetic diversity compared to other Magnolia species with no sign of inbreeding. We found a small effective population size and a prevalence of bottlenecks in some populations. The patterns of genetic subdivision did not support the current morphological distinction of three different species. Instead, we suggest that the genetic structure pattern is the result of historical connectivity and the continuous natural fragmentation of the forest. Thus, an isolation by distance pattern may have had an important role in shaping allele frequencies, producing local genetic differences. Conclusions: We argue that a major threat underlies the actual trends of habitat loss, which can directly impact the loss of genetic diversity in the current adult individuals and consequently, increase the risk of extinction in further generations. For conservation purposes, we suggest combining in situ and ex situ conservation of populations with the maintenance of connectivity among the local populations.

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