Hierarchical equilibria of branching populations

The objective of this paper is the study of the equilibrium behavior of a population on the hierarchical group (Omega)N consisting of families of individuals undergoing critical branching random walk and in addition these families also develop according to a critical branching process. Strong transience of the random walk guarantees existence of an equilibrium for this two-level branching system. In the limit N -> (infinity symbol) (called the hierarchical mean field limit), the equilibrium aggregated populations in a nested sequence of balls (symbole)(N) of hierarchical radius (symbol) converge to a backward Markov chain on R+. This limiting Markov chain can be explicitly represented in terms of a cascade of subordinators which in turn makes possible a description of the genealogy of the population.Multilevel branching, hierarchical mean-field limit, strong transience,genealogy.

Isolation of Psoroptes scab mite microsatellite markers (Acari: Psoroptidae)

Nine microsatellite markers have been isolated from the scab mite,Psoroptes ovis. These markers have been tested for polymorphism in individual Psoroptes mites originating from two hosts, the European rabbit, Oryctolagus cuniculus, and sheep, Ovis aries. No definitive picture of Psoroptes species’ status or interrelationships exists. This study provides the basis for a new molecular system to elucidate the systematics of groupings within the genus Psoroptes, allowing us to clarify the population dynamics and epidemiology of the mites causing sheep scab world wide

Abundant variation in microsatellites of the parasitic nematode Trichostrongylus tenuis and linkage to a tandem repeat

An understanding of how genes move between and within populations of parasitic nematodes is important in combating the evolution and spread of anthelmintic resistance. Much has been learned by studying mitochondrial DNA markers, but autosomal markers such as microsatellites have been applied to only a few nematode species, despite their many advantages for studying gene flow in eukaryotes. Here, we describe the isolation of 307 microsatellites from Trichostrongylus tenuis, an intestinal nematode of red grouse. High levels of variation were revealed at sixteen microsatellite loci (including three sex-lined loci) in 111 male T. tenuis nematodes collected from four hosts at a single grouse estate in Scotland (average He = 0.708; mean number of alleles = 12.2). A population genetic analysis detected no deviation from panmixia either between (F(ST) = 0.00) or within hosts (F(IS) = 0.015). We discuss the feasibility of developing microsatellites in parasitic nematodes and the problem of null alleles. We also describe a novel 146-bp repeat element, TteREP1, which is linked to two-thirds of the microsatellites sequenced and is associated with marker development failure. The sequence of TteREP1 is related to the TcREP-class of repeats found in several other trichostrongyloid species including Trichostrongylus colubriformis and Haemonchus contortus

A critique of avian CHD-based molecular sexing protocols illustrated by a Z-chromosome polymorphism detected in auklets

The sexes of non-ratite birds can be determined routinely by PCR amplification of the CHD-Z and CHD-W genes. CHD -based molecular sexing of four species of auklets revealed the presence of a polymorphism in the Z chromosome. No deviation from a 1:1 sex ratio was observed among the chicks, though the analyses were of limited power. Polymorphism in the CHD-Z gene has not been reported previously in any bird, but if undetected it could lead to the incorrect assignment of sex. We discuss the potential difficulties caused by a polymorphism such as that identified in auklets and the merits of alternative CHD -based sexing protocols and primers

Isolation of 39 polymorphic microsatellite loci and the development of a fluorescently labelled marker set for the Eurasian badger

We have isolated 78 microsatellite loci from the Eurasian badger (Meles meles). Of the 52 loci characterized, 39 were found to be polymorphic. A fluorescently labelled primer set was developed to enable individual-specific 17-locus genotypes to be obtained efficiently

A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)

Background: Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four zebra finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled zebra finch genome sequence. Results: We showed that marker order was less reliable and linkage map lengths were inflated for microsatellite maps relative to SNP maps, apparently due to differing error rates between the two types of marker. Guidelines on how to minimise the effects of error are provided. In particular, we show that when combining both types of marker the conventional process of building linkage maps, whereby the most informative markers are added to the map first, has to be modified in order to improve map accuracy. Conclusions: When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). This raises questions about the accuracy of marker order and predicted recombination rates in previous microsatellite linkage maps which were created using the conventional building process, however, provided suitable error detection strategies are followed microsatellite-based maps can continue to be regarded as reasonably reliable

Bessel processes, the Brownian snake and super-Brownian motion

We prove that, both for the Brownian snake and for super-Brownian motion in dimension one, the historical path corresponding to the minimal spatial position is a Bessel process of dimension -5. We also discuss a spine decomposition for the Brownian snake conditioned on the minimizing path.Comment: Submitted to the special volume of S\'eminaire de Probabilit\'es in memory of Marc Yo

The genetic structure of Nautilus pompilius populations surrounding Australia and the Philippines.

Understanding the distribution of genetic diversity in exploited species is fundamental to successful conservation. Genetic structure and the degree of gene flow among populations must be assessed to design appropriate strategies to prevent the loss of distinct populations. The cephalopod Nautilus pompilius is fished unsustainably in the Philippines for the ornamental shell trade and has limited legislative protection, despite the species' recent dramatic decline in the region. Here, we use 14 microsatellite markers to evaluate the population structure of N. pompilius around Australia and the Philippines. Despite their relative geographical proximity, Great Barrier Reef individuals are genetically isolated from Osprey Reef and Shark Reef in the Coral Sea (FST =0.312, 0.229, respectively). Conversely, despite the larger geographical distances between the Philippines and west Australian reefs, samples display a small degree of genetic structure (FST =0.015). Demographic scenarios modelled using approximate Bayesian computation analysis indicate that this limited divergence is not due to contemporary gene flow between the Philippines and west Australia. Instead, present-day genetic similarity can be explained by very limited genetic drift that has occurred due to large average effective population sizes that persisted at both locations following their separation. The lack of connectivity among populations suggests that immigrants from west Australia would not facilitate natural recolonization if Philippine populations were fished to extinction. These data help to rectify the paucity of information on the species' biology currently inhibiting their conservation classification. Understanding population structure can allow us to facilitate sustainable harvesting, thereby preserving the diversity of genetically distinct stocks. This article is protected by copyright. All rights reserved

Parnassius apollo nevadensis: identification of recent population structure and source–sink dynamics

Population persistence depends in many cases on gene flow between local populations. Parnassius apollo nevadensis is an endemic subspecies of Apollo butterfly in the Sierra Nevada (southern Spain), whose populations are distributed in discrete patches at altitudes between 1850 and 2700 m. In this paper, we use 13 microsatellite loci to examine the genetic structure of this P. apollo subspecies. We revealed both a strong pattern of isolation by distance (which was stronger when calculated with realistic travel distances that accounted for topography) and source–sink dynamics. The observed population genetic structure is consistent with strongly asymmetrical gene flow, leading to constant directional migration and differential connectivity among the populations. The apparently contradictory results from the clustering algorithms (Structure and Geneland) are also consistent with a recent (<100 ya) reduction in the distribution range. The results point to global warming as a possible cause of this reduction, as in other populations of this species. We identify some natural and anthropogenic barriers to gene flow that may be the cause of the recent population structure and source–sink dynamics

A multiplex set for microsatellite typing and sexing of the European bee-eater (Merops apiaster)

Microsatellite loci are widely used in ecological and evolutionary studies to assess inbreeding, genetic parentage and population structure. Such loci are often optimised in multiplexes to allow for economical and efficient use. Here, we tested 11 microsatellite loci designed for use in European bee-eaters (Merops apiaster), along with 31 loci isolated in other species, for their utility in European bee-eaters sampled on Susak Island, Croatia. Of these 42 loci, 20 were polymorphic in 38 individuals. These polymorphic loci were further assessed in a sub-set of 23 adults, excluding close relatives, and exhibited between three and 13 alleles each. All loci were autosomal, as indicated by the presence of heterozygotes in both males and females. One of the polymorphic loci exhibited low heterozygosity, three loci deviated from Hardy-Weinberg equilibrium and three pairs of loci displayed linkage disequilibrium. The remaining selected eight cross-species loci and seven loci isolated in European bee-eaters were combined with two sex-typing markers and optimised in five multiplexes. A combination of 15 autosomal loci of varying degrees of polymorphism makes this multiplex set particularly suitable for both parentage and spatial genetic analyses. This multiplex set therefore provides a useful toolkit for studying kin selection and population genetics in the cooperatively breeding European bee-eater and, potentially, in other closely related species