scholarly journals Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

2017 ◽  
Vol 114 (45) ◽  
pp. E9589-E9597 ◽  
Author(s):  
Andrea Benazzo ◽  
Emiliano Trucchi ◽  
James A. Cahill ◽  
Pierpaolo Maisano Delser ◽  
Stefano Mona ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Extinction Risk ◽  
Skeletal Development ◽  
Population Decline ◽  
Central Italy ◽  
Nuclear Genome ◽  
Brown Bear ◽  
Small Population ◽  
Energy Deficit ◽  
Random Drift

About 100 km east of Rome, in the central Apennine Mountains, a critically endangered population of ∼50 brown bears live in complete isolation. Mating outside this population is prevented by several 100 km of bear-free territories. We exploited this natural experiment to better understand the gene and genomic consequences of surviving at extremely small population size. We found that brown bear populations in Europe lost connectivity since Neolithic times, when farming communities expanded and forest burning was used for land clearance. In central Italy, this resulted in a 40-fold population decline. The overall genomic impact of this decline included the complete loss of variation in the mitochondrial genome and along long stretches of the nuclear genome. Several private and deleterious amino acid changes were fixed by random drift; predicted effects include energy deficit, muscle weakness, anomalies in cranial and skeletal development, and reduced aggressiveness. Despite this extreme loss of diversity, Apennine bear genomes show nonrandom peaks of high variation, possibly maintained by balancing selection, at genomic regions significantly enriched for genes associated with immune and olfactory systems. Challenging the paradigm of increased extinction risk in small populations, we suggest that random fixation of deleterious alleles (i) can be an important driver of divergence in isolation, (ii) can be tolerated when balancing selection prevents random loss of variation at important genes, and (iii) is followed by or results directly in favorable behavioral changes.

Supergene degeneration opposes polymorphism: The curious case of balanced lethals

2021 ◽  
Author(s):  
Emma Berdan ◽  
Alexandre Blanckaert ◽  
Roger K Butlin ◽  
Thomas Flatt ◽  
Tanja Slotte ◽  
...  
Keyword(s):  
Equilibrium State ◽  
Balancing Selection ◽  
Mutation Accumulation ◽  
Small Population ◽  
Quasi Equilibrium ◽  
Deleterious Mutations ◽  
Critical Factors ◽  
Critical Aspect ◽  
Allopatric Divergence

Supergenes offer some of the most spectacular examples of long-term balancing selection in nature but their origin and maintenance remain a mystery. A critical aspect of supergenes is reduced recombination between arrangements. Reduced recombination protects adaptive multi-trait phenotypes, but can also lead to degeneration through mutation accumulation. Mutation accumulation can stabilize the system through the emergence of associative overdominance (AOD), destabilize the system, or lead to new evolutionary outcomes. One such outcome is the formation of balanced lethal systems, a maladaptive system where both supergene arrangements have accumulated deleterious mutations to the extent that both homozygotes are inviable, leaving only heterozygotes to reproduce. Here, we perform a simulation study to understand the conditions under which these different outcomes occur, assuming a scenario of introgression after allopatric divergence. We found that AOD aids the invasion of a new supergene arrangement and the establishment of a polymorphism. However, this polymorphism is easily destabilized by further mutation accumulation. While degradation may strengthen AOD, thereby stabilizing the supergene polymorphism, it is often asymmetric, which is the key disrupter of the quasi-equilibrium state of the polymorphism. Furthermore, mechanisms that accelerate degeneration also tend to amplify asymmetric mutation accumulation between the supergene arrangements and vice versa. As the evolution of a balanced lethal system requires symmetric degradation of both arrangements, this leaves highly restricted conditions under which such a system could evolve. We show that small population size and low dominance coefficients are critical factors, as these reduce the efficacy of selection. The dichotomy between the persistence of a polymorphism and degradation of supergene arrangements likely underlies the rarity of balanced lethal systems in nature.

Conservation biology of marine fishes: perceptions and caveats regarding assignment of extinction risk

2001 ◽  
Vol 58 (1) ◽  
pp. 108-121 ◽  
Author(s):  
Jeffrey A Hutchings
Keyword(s):  
Population Size ◽  
Extinction Risk ◽  
Population Decline ◽  
Empirical Support ◽  
Marine Fishes ◽  
Marine Biodiversity ◽  
Population Declines ◽  
High Fecundity ◽  
Reproductive Rates ◽  
Biological Extinction

Quantitative criteria used to assign species to categories of extinction risk may seriously overestimate these risks for marine fishes. Contemporary perception is that marine fishes may be less vulnerable to extinction than other taxa, because of great natural variability in abundance, high fecundity, rapid population growth, and an intrinsically high capability of recovering from low population size. Contrary to perception, however, there appears to be generally little theoretical or empirical support for the hypotheses that marine fish are more likely to experience large reductions in population size, to produce unusually high levels of recruitment, to have higher reproductive rates, or to recover more rapidly from prolonged population declines than nonmarine fishes. Although existing population-decline criteria may not accurately reflect probabilities of biological extinction, they do appear to reflect the converse-population recovery. Insufficient support for contemporary perceptions of their susceptibility to extinction, coupled with caveats associated with the assignment of extinction risk, suggest that significant increases in the population-decline thresholds used to assign marine fishes to at-risk categories would be inconsistent with a precautionary approach to fisheries management and the conservation of marine biodiversity.

Rediscovery of Oocephalus foliosus (Hyptidinae—Lamiaceae): notes on taxonomy and conservation of a species endemic to the campo rupestre of Central Brazil

Phytotaxa ◽  
2021 ◽  
Vol 525 (2) ◽  
pp. 156-162
Author(s):  
ARTHUR DE SOUZA SOARES ◽  
RAQUEL NEGRÃO ◽  
RAYMOND MERVYN HARLEY ◽  
JOSÉ FLORIANO BARÊA PASTORE ◽  
JOMAR GOMES JARDIM
Keyword(s):  
19Th Century ◽  
Extinction Risk ◽  
Conservation Status ◽  
Small Population ◽  
Species Description ◽  
Second Step ◽  
Campo Rupestre ◽  
Central Brazil ◽  
Surrounding Areas ◽  
Narrow Area

Oocephalus foliosus was described in the first half of 19th century, based on a collection from central Goiás state, Brazil, being collected again only three times in surrounding areas. Although this species seems to be rare and endemic to a narrow area, it has never been listed on any threatened list or had its conservation status assessed. Recently, we recorded a small population of O. foliosus in the Pireneus peak, an area of campo rupestre located in the municipality of Pirenópolis, Goiás, allowing us to improve the species description, assess its extinction risk and comment on its taxonomy. Also, a second step lectotypification was needed to the species and is here proposed.

scholarly journals The dynamics underlying avian extinction trajectories forecast a wave of extinctions

2019 ◽  
Vol 15 (12) ◽  
pp. 20190633 ◽  
Author(s):  
Melanie J. Monroe ◽  
Stuart H. M. Butchart ◽  
Arne O. Mooers ◽  
Folmer Bokma
Keyword(s):  
Extinction Risk ◽  
Population Decline ◽  
Bird Species ◽  
Iucn Red List ◽  
Red List ◽  
Extinction Rate ◽  
Critically Endangered Species ◽  
Extinction Rates ◽  
Historical Times ◽  
Risk Categories

Population decline is a process, yet estimates of current extinction rates often consider just the final step of that process by counting numbers of species lost in historical times. This neglects the increased extinction risk that affects a large proportion of species, and consequently underestimates the effective extinction rate. Here, we model observed trajectories through IUCN Red List extinction risk categories for all bird species globally over 28 years, and estimate an overall effective extinction rate of 2.17 × 10 −4 /species/year. This is six times higher than the rate of outright extinction since 1500, as a consequence of the large number of species whose status is deteriorating. We very conservatively estimate that global conservation efforts have reduced the effective extinction rate by 40%, but mostly through preventing critically endangered species from going extinct rather than by preventing species at low risk from moving into higher-risk categories. Our findings suggest that extinction risk in birds is accumulating much more than previously appreciated, but would be even greater without conservation efforts.

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 Predicting how populations decline to extinction

2011 ◽  
Vol 366 (1577) ◽  
pp. 2577-2586 ◽  
Author(s):  
Ben Collen ◽  
Louise McRae ◽  
Stefanie Deinet ◽  
Adriana De Palma ◽  
Tharsila Carranza ◽  
...  
Keyword(s):  
At Risk ◽  
Extinction Risk ◽  
Mammalian Species ◽  
Local Population ◽  
Population Decline ◽  
Scale Up ◽  
Population Level ◽  
Biological Traits ◽  
Population Declines ◽  
Trend Data

Global species extinction typically represents the endpoint in a long sequence of population declines and local extinctions. In comparative studies of extinction risk of contemporary mammalian species, there appear to be some universal traits that may predispose taxa to an elevated risk of extinction. In local population-level studies, there are limited insights into the process of population decline and extinction. Moreover, there is still little appreciation of how local processes scale up to global patterns. Advancing the understanding of factors which predispose populations to rapid declines will benefit proactive conservation and may allow us to target at-risk populations as well as at-risk species. Here, we take mammalian population trend data from the largest repository of population abundance trends, and combine it with the PanTHERIA database on mammal traits to answer the question: what factors can be used to predict decline in mammalian abundance? We find in general that environmental variables are better determinants of cross-species population-level decline than intrinsic biological traits. For effective conservation, we must not only describe which species are at risk and why, but also prescribe ways to counteract this.

scholarly journals Wildlife conservation in a fragmented landscape: the Eurasian red squirrel on the Isle of Wight

2021 ◽  
Author(s):  
Emilie A. Hardouin ◽  
Helen Butler ◽  
Marin Cvitanović ◽  
Rainer G. Ulrich ◽  
Vanessa Schulze ◽  
...  
Keyword(s):  
Wildlife Conservation ◽  
Extinction Risk ◽  
Landscape Management ◽  
Biodiversity Loss ◽  
Small Population ◽  
Fragmented Landscape ◽  
Red Squirrel ◽  
The South ◽  
Isle Of Wight ◽  
Island Populations

AbstractIsland populations may have a higher extinction risk due to reduced genetic diversity and need to be managed effectively in order to reduce the risk of biodiversity loss. The Eurasian red squirrels (Sciurus vulgaris) in the south of England only survive on three islands (the Isle of Wight, Brownsea and Furzey islands), with the Isle of Wight harbouring the largest population in the region. Fourteen microsatellites were used to determine the genetic structure of red squirrel populations on the Isle of Wight, as well as their relatedness to other populations of the species. Our results demonstrated that squirrels on these islands were less genetically diverse than those in Continental mainland populations, as would be expected. It also confirmed previous results from mitochondrial DNA which indicated that the squirrels on the Isle of Wight were relatively closely related to Brownsea island squirrels in the south of England. Importantly, our findings showed that genetic mixing between squirrels in the east and west of the Isle of Wight was very limited. Given the potential deleterious effects of small population size on genetic health, landscape management to encourage dispersal of squirrels between these populations should be a priority.

scholarly journals Effects of dominance and size of population on response to mass selection

1961 ◽  
Vol 2 (2) ◽  
pp. 177-188 ◽  
Author(s):  
Ken-Ichi Kojima
Keyword(s):  
Gene Frequency ◽  
Finite Size ◽  
Prediction Equation ◽  
Small Population ◽  
Mass Selection ◽  
Gene Frequencies ◽  
Random Drift ◽  
Expected Gain ◽  
The Mean ◽  
Frequency Changes

A theory of mass selection in a small population was developed, and the mean change in gene frequencies, the variance of gene frequency changes and the expected gain in the mean phenotypic value of an offspring population were formulated in terms of a generalized selection differential and the additive and dominance effects of genes.The magnitude of the variance of changes in gene frequency was compared with the magnitude of the variance expected from the genetic random drift in a population with the same gene frequency and of the same size in absence of selection. The former was found to be usually smaller than the latter when the gene frequency ranged from intermediate to high and when selection was directed for a high performance.The usual prediction equation for gain from selection in an infinite population was compared with the expected gain formula derived for a small population. The size of the population did not cause a serious difference between the two expected gains when there was no dominance effect of genes. Dominance alone could cause the usual prediction to be slightly more biased. The joint effects of the finite size of population and dominance gene action could amount to a considerable bias in the usual prediction equation. Such a bias can be, in the main, accounted for by the inbreeding depression.

Human-provoked amphibian decline in central Italy and the efficacy of protected areas

2010 ◽  
Vol 37 (7) ◽  
pp. 547 ◽  
Author(s):  
Manuela D'Amen ◽  
Biancamaria Pietrangeli ◽  
Marco A. Bologna
Keyword(s):  
Protected Areas ◽  
Multiple Stressors ◽  
Population Decline ◽  
Central Italy ◽  
Negative Relationship ◽  
Climatic Conditions ◽  
Amphibian Declines ◽  
Additive Models ◽  
Management Approach ◽  
Amphibian Species

Context Today, more than 32% of amphibian species are threatened and more than 43% face a steep decline in numbers. Most species are being affected simultaneously by multiple stressors and habitat protection is often inadequate to prevent declines. Aims The main goal of the present research was to understand the consequences of alternative human land use in producing landscape disturbance for amphibians. At the same time, we also evaluated the effect of changing climatic conditions as additional potential drivers of population decline. Another goal was to determine whether and to what extent the existing nature reserves have been effective in protecting species in recent decades. Methods We used generalised additive models (GAMs) to investigate the association between the state (stable/decline) of amphibian populations in 5 × 5 km cells in central Italy and proxies of different typology of anthropogenic stressors, climatic variables and protection measures. Key results We found a significant association between anthropogenic landscape modifications and species decline. This negative relationship was revealed with agricultural predictors for the majority of the species, whereas urban fabrics had a slightly smaller impact. We found significant associations between amphibian declines and climatic variation, particularly the increasing number of dry days. Protected areas protected declines of two species only. Conclusions Our results showed that the status of amphibians in this region warrants greater attention than has been given previously. The detrimental effect of agricultural practices, combined with increasing aridity, makes amphibian populations particularly susceptible to extinction, and the conservation measures applied till now are inadequate for species protection in this region. Implications Our results should stimulate the implementation of environmental policies that focus not only on the protection of single habitats, but also on ensuring the environmental quality of the surrounding landscapes. Moreover, an adaptive management approach should be applied to take into account future modification of hydrology and climate.

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