scholarly journals Lingering Impacts of Hurricane Hugo on Rhizophora mangle (Red Mangrove) Population Genetics on St. John, USVI

Diversity ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 65 ◽  
Author(s):  
Bologna ◽  
Campanella ◽  
Restaino ◽  
Fetske ◽  
Lourenco ◽  
...  
Keyword(s):  
Population Size ◽  
Population Analysis ◽  
Biosphere Reserve ◽  
Rhizophora Mangle ◽  
Effective Population ◽  
Island Populations ◽  
Inbreeding Coefficients ◽  
Red Mangrove ◽  
Stochastic Events ◽  
Hurricane Hugo

Stochastic events can have catastrophic effects on island populations through a series of genetic stressors from reduced population size. We investigated five populations of red mangrove (Rhizophora mangle) from St. John, USVI, an UNESCO Biosphere Reserve, which were impacted by Hurricane Hugo in 1989. Our goal was to determine diversity and to ascertain potential population bottlenecks two decades after the event. With the lowest observed heterozygosity, highest inbreeding coefficient, and evidence of a major bottleneck, our results demonstrated that the Great Lameshur mangroves, devastated by Hurricane Hugo, were the least diverse stand of trees. The other four populations from St. John manifested diversity reflecting the vegetation patterns of “fringing” mangrove or “developed forest” characteristics. The two fringing mangrove populations (Hurricane Hole and New Found Bay) evinced low observed heterozygosity and high inbreeding coefficients, while the fully forested sites showed higher heterozygosity and lower inbreeding frequencies. As such, fringing mangroves may be at greater risk to disturbance events and especially susceptible to sea level rise since they do not have room landward to expand. Our pair-wise population analysis indicated genetic similarity between the hurricane-damaged Great Lameshur and Coral Bay population, whose propagules were used in previous restoration attempts and is the geographically closest population. While the effective population size for Great Lameshur Bay places it in risk of genetic dysfunction, future rehabilitation of the site may be possible by the introduction of propagules from other regions of the island. However, recovery will ultimately be contingent upon hydrological connectivity and environmental improvements.

scholarly journals Population structure of Czech cold-blooded breeds of horses

2011 ◽  
Vol 54 (1) ◽  
pp. 1-9
Author(s):  
L. Vostrý ◽  
Z. Čapková ◽  
J. Přibyl ◽  
B. Hofmanová ◽  
H. Vostrá Vydrová ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
The Czech Republic ◽  
Generation Interval ◽  
Average Value ◽  
Inbreeding Coefficients

Abstract. In order to estimate effective population size, generation interval and the development of inbreeding coefficients (Fx) in three original breeds of cold-blooded horses kept in the Czech Republic: Silesian Noriker (SN), Noriker (N) and Czech-Moravian Belgian horse (CMB) all animals of the particular breeds born from 1990 to 2007 were analysed. The average values of generation interval between parents and their offspring were: 8.53 in SN, 8.88 in N and 8.56 in CMB. Average values of effective population size were estimated to be: 86.3 in SN, 162.3 in N and 104.4 in CMB. The average values of inbreeding coefficient were 3.13 % in SN stallions and 3.39 % in SN mares, in the N breed 1.76 % and 1.26 % and in the CMB breed 3.84 % and 3.26 % respectively. Overall averages of Fx were: 3.23 %, 1.51 % and 3.55 % for the breeds SN, N and CMB. The average value of inbreeding coefficient Fx increased by 1.22 % in SN, by 0.35 % in N and by 1.01 % in CMB, respectively. This may lead to a reduction in genetic variability. Reduction in genetic variability could be either controlled in cooperation with corresponding populations of cold-blooded breeds in other European countries or controlled by number of sires used in population

Population structure of the Sahiwal breed in Pakistan

1995 ◽  
Vol 60 (2) ◽  
pp. 163-168 ◽  
Author(s):  
A. Dahlin ◽  
U. N. Khan ◽  
A. H. Zafar ◽  
M. Saleem ◽  
M. A. Chaudhry ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Breeding Population ◽  
Effective Population ◽  
Data Set ◽  
Inbreeding Coefficients ◽  
Sahiwal Cows ◽  
The Mean ◽  
Average Population Size

AbstractThe present study was undertaken to assist conservation and improvement schemes in the Sahiwal breed of cattle in Pakistan. A data set, consisting of records of 244 pure Sahiwal breeding bulls and 5247 cows, the latter representing about 80% of all recorded Sahiwal cows in Pakistan born during a period covering about 20 years, was analysed with regard to inbreeding, additive relationships, effective population size and generation intervals. Average inbreeding coefficients of 1224 cows and 49 bulls, for which at least the grandparents and great-grandsires were known, were 0·043 and 0·046, respectively. About two-thirds of the inbreeding was due to matings between animals with parents or grandparents in common. The mean additive relationship among the cows was 0·062, with within-herd averages ranging from 0·087 to 0·358. The average population size in a subdata set of recorded Sahiwal cattle from 1980 to 1984 was 1612, whereas the most likely estimate of the effective population size was about 30 animals for the same active breeding population. The study indicated the immediate need for an active conservation programme whereby the Sahiwal subpopulations of India and Kenya also should be involved.

scholarly journals On the prediction of simultaneous inbreeding coefficients at multiple loci

2004 ◽  
Vol 83 (2) ◽  
pp. 113-120 ◽  
Author(s):  
JULES HERNÁNDEZ-SÁNCHEZ ◽  
CHRIS S. HALEY ◽  
JOHN A. WOOLLIAMS
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Conditional Probability ◽  
Prior Probability ◽  
Effective Population ◽  
Infinite Population ◽  
Inbreeding Coefficients ◽  
Multiple Loci ◽  
Monoecious Population ◽  
Marker Spacing

A new deterministic method for predicting simultaneous inbreeding coefficients at three and four loci is presented. The method involves calculating the conditional probability of IBD (identical by descent) at one locus given IBD at other loci, and multiplying this probability by the prior probability of the latter loci being simultaneously IBD. The conditional probability is obtained applying a novel regression model, and the prior probability from the theory of digenic measures of Weir and Cockerham. The model was validated for a finite monoecious population mating at random, with a constant effective population size, and with or without selfing, and also for an infinite population with a constant intermediate proportion of selfing. We assumed discrete generations. Deterministic predictions were very accurate when compared with simulation results, and robust to alternative forms of implementation. These simultaneous inbreeding coefficients were more sensitive to changes in effective population size than in marker spacing. Extensions to predict simultaneous inbreeding coefficients at more than four loci are now possible.

scholarly journals Differentiation with drift: a spatio-temporal genetic analysis of Galápagos mockingbird populations ( Mimus spp.)

2010 ◽  
Vol 365 (1543) ◽  
pp. 1127-1138 ◽  
Author(s):  
Paquita E. A. Hoeck ◽  
Jennifer L. Bollmer ◽  
Patricia G. Parker ◽  
Lukas F. Keller
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Size ◽  
Genetic Drift ◽  
Bird Species ◽  
Effective Population ◽  
Island Size ◽  
Island Populations ◽  
Population Sizes ◽  
Spatio Temporal

Small and isolated island populations provide ideal systems to study the effects of limited population size, genetic drift and gene flow on genetic diversity. We assessed genetic diversity within and differentiation among 19 mockingbird populations on 15 Galápagos islands, covering all four endemic species, using 16 microsatellite loci. We tested for signs of drift and gene flow, and used historic specimens to assess genetic change over the last century and to estimate effective population sizes. Within-population genetic diversity and effective population sizes varied substantially among island populations and correlated strongly with island size, suggesting that island size serves as a good predictor for effective population size. Genetic differentiation among populations was pronounced and increased with geographical distance. A century of genetic drift did not change genetic diversity on an archipelago-wide scale, but genetic drift led to loss of genetic diversity in small populations, especially in one of the two remaining populations of the endangered Floreana mockingbird. Unlike in other Galápagos bird species such as the Darwin's finches, gene flow among mockingbird populations was low. The clear pattern of genetically distinct populations reflects the effects of genetic drift and suggests that Galápagos mockingbirds are evolving in relative isolation.

Genetics of reintroduced populations of the narrowly endemic thistle, Cirsium pitcheri (Asteraceae)

Botany ◽  
2013 ◽  
Vol 91 (5) ◽  
pp. 301-308 ◽  
Author(s):  
Jeremie B. Fant ◽  
Andrea Kramer ◽  
Eileen Sirkin ◽  
Kayri Havens
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Empirical Studies ◽  
Small Population ◽  
Native Plant ◽  
Effective Population ◽  
Term Survival ◽  
Inbreeding Coefficients ◽  
Native Populations ◽  
Population Sizes

The aim of any reintroduction is to provide sufficient genetic variability to buffer against changing selection pressures and ensure long-term survival. To date, few empirical studies have compared levels of genetic diversity in reintroduced and native plant populations. Using microsatellite markers, we measured the genetic diversity within reintroduced and native populations of the threatened Cirsium pitcher (Eaton) Torrey and Gray. We found that the use of local mixed source was successful in establishing populations with significantly higher genetic diversity (P < 0.005) than the native populations (allelic richness is 3.39 in reintroduced and 1.84 in native populations). However, the reintroduced populations had significantly higher inbreeding coefficients (P < 0.002) (FIS is 0.405 and 0.213 in reintroduced and in native populations, respectively), despite having multiple genetic founders, population sizes equivalent to native populations and a positive growth rate. These results may be due to inbreeding or the Wahlund effect, driven by genetic substructuring. This suggests that the small population size of these reintroduced populations may lead to genetic issues in the future, given the low number of flowering individuals each year. This highlights the importance of considering not only the number of source individuals but the effective population size of the reintroduction.

scholarly journals Genetic Variability in Polish Lowland Sheepdogs Assessed by Pedigree and Genomic Data

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1520
Author(s):  
Paula Wiebke Michels ◽  
Ottmar Distl
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Ductus Arteriosus ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Data ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Candidate Loci

Genetic variability of Polish Lowland Sheepdog (PON) population was evaluated using both pedigree and genomic data. The analyzed pedigree encompassed 8628 PONs, including 153 individuals genotyped on the Illumina CanineHD BeadChip. Runs of homozygosity (ROH) were defined for homozygous stretches extending over 60 to 4300 kb. The inbreeding coefficients FPed based on pedigree data and FROH50 based on ROHs were at 0.18 and 0.31. The correlation between both was 0.41 but 0.52 when excluding animals with less than seven complete generations. The realized effective population size (Ne¯) was 22.2 with an increasing trend over years. Five PONs explained 79% of the genetic diversity of the reference population. The effective population size derived from linkage disequilibrium measured by r² was 36. PANTHER analysis of genes in ROHs shared by ≥50% of the PONs revealed four highly over- or underrepresented biological processes. One among those is the 7.35 fold enriched “forelimb morphogenesis”. Candidate loci for hip dysplasia and patent ductus arteriosus were discovered in frequently shared ROHs. In conclusion, the inbreeding measures of the PONs were high and the genetic variability small compared to various dog breeds. Regarding Ne¯, PON population was minimally endangered according to the European Association for Animal Production.

scholarly journals Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 577
Author(s):  
Huiwen Zhan ◽  
Saixian Zhang ◽  
Kaili Zhang ◽  
Xia Peng ◽  
Shengsong Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Average Length ◽  
The Other ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genomic Regions

Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.

The Role of Dispersal in Structuring the Chitwan Tiger Population

Behaviour ◽  
1993 ◽  
Vol 124 (3-4) ◽  
pp. 165-195 ◽  
Author(s):  
JAMES L. DAVID Smith
Keyword(s):  
Social Interactions ◽  
Population Size ◽  
National Park ◽  
Genetic Variance ◽  
Effective Population ◽  
The World ◽  
Chitwan National Park ◽  
Tiger Population ◽  
Stochastic Events

AbstractDispersal in tigers was studied in Royal Chitwan National Park, Nepal. Thirty six adult and young were studied to monitor movements and social interactions relative to dispersal. Fourteen subadults were followed from before their dispersal until they died or established post-dispersal territories. Subadult tigers became semi-independent of their mother when her next litter was born. They usually remained within her natal area until the subsequent litter began to move with her at about 2 mos of age. Animals dispersed between 19 and 28 mos. Males dispersed farther than females and settled in poorer habitat. Three of 4 females settled adjacent to their mothers; in two cases the mother shifted her territory allowing the daughter to take over a large portion of the mother's former territory. Wounds on young prior to dispersal indicated that aggression prompted dispersal. Fjghts were observed between dispersers and residents. After fights, dispersers always left the resident's area. All 4 dispersing females established breeding territories. Females settled next to their mothers tending to reduce the genetic variance of a male's offspring. Eight of 10 males became localized in temporary, post-dispersal territories; 4 of the 8 survived. Two males died of poisoning and 2 from intrasexual aggression. Surviving males either expanded temporary territories or shifted to new areas to establish breeding territories. The Chitwan tigers are an isolated remnant of a population once continuous across the lowlands of Nepal. Effective population size was estimated to be <30 animals. Tigers did not disperse across cultivated areas but did travel through degraded forest habitat. No animal dispersed outside the Chitwan region and there appear to be effective barriers separating Chitwan from the two nearest populations 150 and 250 kms distant. The Chitwan population is probably one of the largest tiger populations remaining in the world. Isolation and small size threaten these populations with stochastic events that may lead to further reduction in population size.

scholarly journals LINKAGE DISEQUILIBRIUM IN A FINITE POPULATION THAT IS PARTIALLY SELFING

Genetics ◽  
1980 ◽  
Vol 94 (3) ◽  
pp. 777-789 ◽  
Author(s):  
G B Golding ◽  
C Strobeck
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Finite Population ◽  
Random Mating ◽  
Effective Population ◽  
Infinite Allele Model ◽  
Inbreeding Coefficients ◽  
Linkage Disequilibria ◽  
Recombination Value ◽  
Allele Model

ABSTRACT The linkage disequilibrium expected in a finite, partially selfing population is analyzed, assuming the infinite allele model. Formulas for the expected sum of squares of the linkage disequilibria and the squared standard linkage disequilibrium are derived from the equilibrium values of sixteen inbreeding coefficients required to describe the behavior of the system. These formulas are identical to those obtained with random mating if the effective population size Ne = (l—½S)N and the effective recombination value re = (l-S)r/(l-½S), where S is the proportion of selfing, are substituted for the population size and the recombination value, Therefore, the effect of partial selfing at equilibrium is to reduce the population size by a factor 1 — ½S and the recombination value by a factor (l-S)/(l—½S).

scholarly journals NERÉIDIDOS (NEREIDIDAE, POLYCHAETA, ANNELIDA) ASOCIADOS A RAÍCES DE MANGLE ROJO, RHIZOPHORA MANGLE, EN ISLAS SAN ANDRÉS Y PROVIDENCIA, CARIBE COLOMBIANO

2016 ◽  
Vol 44 (1) ◽  
Author(s):  
Catalina Arteaga Flórez ◽  
Mario H. Londoño Mesa
Keyword(s):  
Biosphere Reserve ◽  
Rhizophora Mangle ◽  
Mangrove Forests ◽  
The North ◽  
Red Mangrove ◽  
The Family ◽  
Neanthes Succinea ◽  
Ecological Importance ◽  
Mangrove Roots ◽  
San Andres

The family Nereididae Blainville, 1818, is one of the most representative group of errant polychaete worms, with about 535 described species in 43 genera, with great biological and ecological importance. The aim of this research was to make a taxonomic analysis of the nereidids associated to red mangrove roots, Rhizophora mangle, in the San Andrés, Old Providence and Santa Catalina Archipelago. This archipelago is part of the Seaflwer Biosphere Reserve. San Andrés is the largest island, having 27 km2 of landmass area, while Old Providence Island, located 95 km to the north of San Andrés, has 17 km2; both islands have well developed mangrove forests, composed mainly by R. mangle. The nereidids, deposited in the Coleccion Estuarina y Marina de la Universidad de Antioquia (CEMUA), were identifid with updated keys, by performing dissections and extracting parts with taxonomic value. Four species of polychaetes from the family Nereididae were found: Neanthes acuminata, Neanthes succinea, Neanthes sp., and Platynereis mucronata. Only N. succinea and N. acuminata had been reported from the Colombian Caribbean, being N. succinea the only species previously reported from the archipielago. In addition, systematic, ecological and biogeographical considerations were added for each species.

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