Simple method for calculating confidence limits around inbreeding rate and effective population size estimates from pedigrees

An important concept in population genetics is effective population size (N_e), which describes the expected rate of loss of genetic variability from a population. One way to estimate N_e is using a pedigree. However, there are no methods for comparing the N_e estimated from a pedigree with that expected from life-history models. In the paper we show how N_e can be estimated from the change in inbreeding rate (f) estimated from a pedigree. The mean individual inbreeding rate in a population at a given time must be calculated from averaged values for males and females, where each age class is weighted by its reproductive value. We show an exact method for placing confidence intervals around f and N_e using a binomial distribution, and present a method for approximating this interval for large N_es using a Poisson distribution. These confidence intervals can be used to compare f and N_e from a pedigree to expected values from demographic models, and to compare N_es of two populations.     

The type locality of <Emphasis Type="Italic">Pan troglodytes vellerosus</Emphasis> (Gray, 1862), and implications for the nomenclature of West African chimpanzees

We show that, in 1862, Richard Burton collected the type specimen of Pan troglodytes vellerosus not on Mount Cameroon, as has been generally assumed, but in Gabon. Therefore, P. t. vellerosus is not the correct name for the chimpanzee population of western Cameroon and southern Nigeria, if that population is taxonomically distinct. As First Reviser, we choose the name Pan troglodytes ellioti for this population of chimpanzees, based on Anthropopithecus ellioti named by Matschie [Matschie P (1914) Neue Affen aus Mittelafrika. Sitzungsber Ges Naturforsch Freunde Berlin 1914:323–342] from a specimen in the Humboldt Museum, Berlin, collected in Bascho (=Basho), Cameroon, and given to the museum in 1905.     

Isolation and characterization of polymorphic microsatellite DNA makers for Euphrasia nankotaizanensis (Orobanchaceae) and cross amplification in another Euphrasia L.

Euphrasia nankotaizanensis is an endangered flowering plant distributed restrictedly on rocky slope of high mountain peaks in central and northern Taiwan. In order to undertake a conservation program, especially given impacts of the global warming, it is essential to evaluate its genetic diversity and population structure. We described nine novel microsatellite primer pairs in E. nankotaizanensis and also examined its relative E. transmorrisonensis. The number of alleles per locus ranged from 7 to 29. Expected (H _E) and observed (H _O) heterozygosities ranged from 0.83 to 0.98 and 0.00 to 0.95, respectively. Eight of the nine microsatellite loci displayed significant departures from Hardy–Weinberg expectations, likely due to the loss of habitats and the small population size. Significant linkage disequilibrium (LD) was detected in most loci. Cross-species amplification of microsatellites took place at five loci. These primers may provide a tool for understanding the demography and population structure of Euphrasia species in Taiwan. Kuo-Hsiung Wang, Ming-Jou Wu, and Tzen-Yuh Chiang contributed equally to this work.     

On the study of two interacting populations one of which acts independently of the other

Many ecological and biological systems can be studied in terms of a bivariate stochastic branching process, {X ₁ (t), X ₂ (t)}, each of whose components (or populations) varies in magnitude according to the laws of a generalized birth-death process. Of particular interest is such a model in which the birth and death rates of the first population,X ₁, are constant while those of the second population,X ₂, exhibit a functional dependence upon the magnitude of the first. It is shown, first, that the existence of the stochastic mean of a birth death process implies the existence of all higher moments. The values of all the factorial moments of such a process are then determined. The moments of the dependent population of the bivariate process are given in terms of its expectation and the joint probability density function of the process is determined. It is possible, therefore, to use Bayesian techniques to infer conclusions about the independent population, given information about the variation of the dependent one.     

Estimation of Population Mean Under Successive Sampling Scheme when Various Weights and Regression Coefficients are Unknown

In this paper properties of an estimator of the population mean on current occasion under successive sampling scheme, when various weights (φh'S) and regression coefficients (βh,h-1) are estimated for h ≥ 2, have been studied. Some empirical results on the estimation of the variance of an unbiased estimator of population mean for h = 2 are also given.     

Monthly population density and structure patterns of an endangered seahorse Hippocampus capensis: a comparison between natural and artificial habitats

This study investigated aspects of the population ecology of the endangered Knysna seahorse Hippocampus capensis within different habitat types. High densities of H. capensis were found within artificial Reno mattress habitat, within the Knysna Estuary, South Africa. Monthly surveys at three sites were conducted from October 2015 to August 2016 to compare population densities of H. capensis in this artificial habitat with natural eel grass Zostera capensis habitat. Hippocampus capensis densities varied significantly across all sites and highest population densities were consistently observed within the Reno mattress habitat. Hippocampus capensis were also found to be significantly larger within the Reno mattress habitat and pooled data showed that males were significantly larger than females. The overall sex ratio for all three sites was female biased, although this varied across seasons at two sites. The findings suggest that artificial Reno mattresses provide novel habitat for this endangered species and consideration should be given to the usefulness of these structures in future conservation actions.     

Segregation of a population in an environment

A mathematical model for spatial patterns and the segregation of a population is presented. Individuals in a population are assumed to move at random under the influence of a given environment potential V(x). The notion of kinetic excitation K(x) and intensity excitation Q(x) of a population is introduced. Then equilibrium states of a population are defined through a macroscopic relation K(x) + Q(x) + V(x) = constant. The problem of finding out equilibrium distributions is reduced to an eigenvalue problem. It is shown that a population is segregated by the nodal surfaces of the eigenfunctions, if it is excited. Some applications of the model to biological and ecological problems are indicated.     

Adaptive change and conservatism in host specificity in two local populations of the thistle-feeding ladybird beetle Epilachna niponica

We investigated geographic differences in the host specificity of Epilachna niponica Lewis (Coleoptera: Coccinellidae). The Yuwaku population feeds mainly on Cirsium matsumurae Nakai (Asteraceae) and secondarily on Cirsrium kagamontanum Nakai. The Asiu population, located 150 km away from the Yuwaku, feeds exclusively on C. ashiuense Yokoyama et T. Shimizu. Under laboratory conditions, we examined the differences between the two populations in adult feeding acceptance, adult feeding preference, and larval performance, using several closely related thistle species and varieties, including their native hosts. In the Asiu population, adult beetles clearly avoided the host of the Yuwaku population, C. kagamontanum, and no larvae were able to complete their development, whereas in the Yuwaku population, adults accepted and even preferred it to some other thistle species, and about 10% of first instar larvae became adults. This indicates that the Yuwaku population evolved its feeding preference and physiological adaptation to C. kagamontanum through a utilization of this low‐ranked host under natural conditions. Apart from C. kagamontanum, the two populations showed a similar host susceptibility pattern, indicating that this ladybird beetle has a conserved hierarchy in feeding preference and growth performance. We also observed adult leaf choice behavior when given different thistle species, and found that difference in biting rate after palpation determined the leaf areas consumed, implying that factors on the leaf surface played an important role in the choice.     

Abundance of larvae and nymphs of the taiga tick <Emphasis Type="Italic">Ixodes persulcatus</Emphasis> Schulze (Acarina,Ixodidae) on small mammals in deforested areas in the middle taiga subzone of Karelia

The data on long-term studies (1998–2004) of the population density of preimaginal stages of the taiga tick Ixodes persulcatus Schulze, 1930 collected from small mammals in deforested areas (foresting during 7, 12, and 25 years after forest cutting) in the middle taiga zone of Karelia are given. The lowest population density of I. persulcatus was observed in the most recently deforested area. The territory where forestation lasted for 25 years after deforestation was the most favorable biotope for the taiga tick development. Deforested areas, in comparison with secondary forests, are characterized by significantly higher population density of preimaginal stages of ixodid ticks; this phenomenon is determined first of all by the high population density of small mammals.     

The effect of electric fishing on the subsequent capture of fish*

Experiments show that the first of a series of replicate electric fishings can cause a decrease in catchability so that the second and subsequent catches are made from what is, effectively, a reduced population. Depletion (DeLury) estimates can be thus seriously low. Species affected are roach Rutilus rutilus (L.), gudgeon Gobio gobio (L.), rudd Scardinius erythophthalmus (L.) and, from other published data, probably rainbow trout Salmo gairdneri Richardson and eels Anguilla anguilla (L.). Being caught does not, apparently, cause fish to become less catchable. The reason why an electric field causes a proportion of a population to become uncatchable is obscure but it may be that refractory behaviour is involved; the effect lasts for between 3 and 24 h. A method is given for adjusting DeLury estimates for decreased catchability.     

THE PHOTOPERIODIC RESPONSE OF AMERICAN PROSOPIS AND ACACIA FROM A BROAD LATITUDINAL DISTRIBUTION

Prosopis and Acacia from North and South America were studied in the laboratory under constant and increasing night length under two temperature regimes. The Prosopis juliflora (Sw.) DC. complex showed strong populational differentiation; Acacia farnesiana (L.) Willd. showed minimal populational differentiation. In Prosopis a population from Oklahoma (36° N) showed the greatest inhibition of stem height under increasing night length. A population from Peru (6° S) showed least control of stem height by night length. In Acacia the response of the latitudinal series was relatively uniform within each of the 6 sets of light period-temperature conditions. In general the height increase for Acacia was two to three times greater under the warmer regime than under the cooler regime at a given night length. Since Acacia farnesiana occurs sympatrically with the Prosopis juliflora complex over a broad range of latitudes, it is of interest to find that the distributional mechanisms of these two leguminous trees are basically different.     

Reproductive parameters in Guizhou snub‐nosed monkeys (Rhinopithecus brelichi)

In this study, we present data on reproductive parameters and birth seasonality of Guizhou snub‐nosed monkeys (Rhinopithecus brelichi). Our analyses are based on data from a small captive population collected over 15 years and on 5 years of observations of free‐ranging snub‐nosed monkeys. Captive females (n=4) mature at an age of 70.8±6.7 months and reproduce for the first time at 103.4±7.5 months. The mean interbirth interval was 38.2±4.4 months if the infant survived more than 6 months, which is longer than that in R. roxellana and R. bieti. In the wild and in captivity, births are very seasonal and occur only in a period from the end of March to the end of April. Our data suggest that population growth in Guizhou snub‐nosed monkeys is slow compared with the other two Chinese snub‐nosed monkey species. The risk of extinction is therefore particularly high in this species, given the small overall population size and slow population recovery potential. Am. J. Primatol. 71:266–270, 2009. © 2008 Wiley‐Liss, Inc.     

Population structure of the predatory mite <Emphasis Type="Italic">Neoseiulus womersleyi</Emphasis> in a tea field based on an analysis of microsatellite DNA markers

The predatory mite Neoseiulus womersleyi (Schicha) (Acari: Phytoseiidae) is an important natural enemy of the Kanzawa spider mite, Tetranychus kanzawaki Kishida (Acari: Tetranychidae), in tea fields. Attraction and preservation of natural enemies by habitat management to reduce the need for acaricide sprays is thought to enhance the activity of N. womersleyi. To better conserve N. womersleyi in the field, however, it is essential to elucidate the population genetic structure of this species. To this end, we developed ten microsatellite DNA markers for N. womersleyi. We then evaluated population structure of N. womersleyi collected from a tea field, where Mexican sunflower, Tithonia rotundifolia (Mill.), was planted to preserve N. womersleyi. Seventy-seven adult females were collected from four sites within 200 m. The fixation indexes F _ST among subpopulations were not significantly different. The kinship coefficients between individuals did not differ significantly within a site as a function of the sampling dates, but the coefficients gradually decreased with increasing distance. Bayesian clustering analysis revealed that the population consisted of three genetic clusters, and that subpopulations within 100 m, including those collected on T. rotundifolia, were genetically similar to each other. Given the previously observed population dynamics of N. womersleyi, it appears that the area inhabited by a given cluster of the mite did not exceed 100 m. The estimation of population structure using microsatellite markers will provide valuable information in conservation biological control.     

Hieracia balcanica VIII. <Emphasis Type="Italic">Hieracium nigrescens</Emphasis> subsp. <Emphasis Type="Italic">brachytrichellum</Emphasis> (Asteraceae), a new taxon in the Balkan flora

Hieracium nigrescens subsp. brachytrichellum Zahn, known to date only from the Southern Carpathians, was discovered in the Vranica Mountains in Bosnia. This is the first station of H. nigrescens s.l., an arctic-alpine species of H. sect. Alpina (Griseb.) Gremli, on the Balkan Peninsula. A map of general distribution of H. nigrescens s.l. and illustration of the specimens collected in Bosnia are given. The likely origin of the Balkan population is briefly discussed.     

Equilibrium conditions in polysomic inheritance for a panmictic population

A general model of a large 2m-ploid breeding population, withr loci ands _h alleles at the _h ^th locus is considered. It is assumed that the population is bisexual, non-overlapping and breeds by random mating. The genotypic structure of the population is presented as a bilinear form in the gametic output vectors where the genotype distribution is in the matrix form. Using the concept of the segregation distribution, the genotype proportions in the (n+1)^st generation are given. An equilibrium condition for random chromosome segregation is obtained in terms of gene frequencies.     

Fixation probability with multiple alleles and projected average allelic effect on selection

The first-order effect of selection on the probability of fixation of an allele, with respect to an intensity of selection s>0 in a diploid population of fixed finite size N, undergoing discrete, non-overlapping generations, is shown to be given by the sum of the average effects of that allele on the coefficient of selection in the current generation and all future generations, given the population state in the current generation. This projected average allelic effect is a weighted sum of average allelic effects in allozygous and autozygous offspring in the initial generation, with weights given in terms of expected coalescence times, under neutrality, for the lineages of two or three gametes chosen at random in the same generation. This is shown in the framework of multiple alleles at one locus, with genotypic values determining either viability or fertility differences, and with either multinomial or exchangeable reproduction schemes. In the limit of weak selection in a large population such that Ns tends to zero, the initial average allelic effects in allozygous offspring and autozygous offspring have the same weight on the fixation probability only in the domain of application of the Kingman coalescent. With frequency-dependent selection in a linear-game-theoretic context with two phenotypes determined by additive gene action, the first-order effect on the fixation probability is a combination of two effects of frequency-independent selection, one in a haploid population, the other in a diploid population. In the domain of application of the Kingman coalescent as the population size goes to infinity and Ns to zero, the first effect is three times more important than the second effect. This explains the one-third law of evolutionary dynamics in this domain, and shows how this law can be extended beyond this domain.     

Population structure of Squatina guggenheim (Squatiniformes,Squatinidae) from the south‐western Atlantic Ocean

Population genetic analyses based on both mitochondrial cytochrome b and the internal transcribed spacer 2 of recombinant (r)DNA genes were implemented to examine hypotheses of population differentiation in the angular angel shark Squatina guggenheim, one of the four most‐widespread endemic species inhabiting coastal ecosystems in the south‐western Atlantic Ocean. A total of 82 individuals of S. guggenheim from 10 sampling sites throughout the Río de la Plata mouth, its maritime front, the outer shelf at the subtropical confluence and the coastal areas of the south‐west Atlantic Ocean, were included. The analysis of molecular variance (AMOVA) based on the second internal transcribed spacer (its‐2) region supports that the samples from the outer shelf represent an isolated group from other sites. Historical gene flow in a coalescent‐based approach revealed significant immigration and emigration asymmetry between sampling sites. Based on the low level of genetic diversity, the existence of a long‐term population decline or a past recent population expansion following a population bottleneck could be proposed in S. guggenheim. This demographic differentiation suggests a degree of vulnerability to overexploitation in this endemic and endangered south‐west Atlantic Ocean shark, given its longevity and low reproductive potential.     

Population genetics of four heavily exploited shark species around the Arabian Peninsula

The northwestern Indian Ocean harbors a number of larger marine vertebrate taxa that warrant the investigation of genetic population structure given remarkable spatial heterogeneity in biological characteristics such as distribution, behavior, and morphology. Here, we investigate the genetic population structure of four commercially exploited shark species with different biological characteristics (Carcharhinus limbatus, Carcharhinus sorrah, Rhizoprionodon acutus, and Sphyrna lewini) between the Red Sea and all other water bodies surrounding the Arabian Peninsula. To assess intraspecific patterns of connectivity, we constructed statistical parsimony networks among haplotypes and estimated (1) population structure; and (2) time of most recent population expansion, based on mitochondrial control region DNA and a total of 20 microsatellites. Our analysis indicates that, even in smaller, less vagile shark species, there are no contemporary barriers to gene flow across the study region, while historical events, for example, Pleistocene glacial cycles, may have affected connectivity in C. sorrah and R. acutus. A parsimony network analysis provided evidence that Arabian S. lewini may represent a population segment that is distinct from other known stocks in the Indian Ocean, raising a new layer of conservation concern. Our results call for urgent regional cooperation to ensure the sustainable exploitation of sharks in the Arabian region.     

Some Results on Error Rates for Quadratic Discrimination with Known Population Parameters

Let population Π_i, i = 1,2, be characterized by a multivariate normal density function, N(μ_i,∑_i), i = 1, 2, respectively. This paper provides conditions under which simple conditional error rates may be computed for the quadratic discriminant function with known population parameters. Also, a simple bound on the overall error rate is derived. Examples are given which demonstrate the proposed methods.