Detecting the signature of selection on immune genes in highly structured populations of wild sheep (Ovis dalli)

The confounding effects of population structure complicate efforts to identify regions of the genome under the influence of selection in natural populations. Here we test for evidence of selection in three genes involved in vertebrate immune function - the major histocompatibility complex (MHC), interferon gamma (IFNG) and natural resistance associated macrophage polymorphism (NRAMP) - in highly structured populations of wild thinhorn sheep (Ovis dalli). We examined patterns of variation at microsatellite loci linked to these gene regions and at the DNA sequence level. Simple Watterson's tests indicated balancing selection at all three gene regions. However, evidence for selection was confounded by population structure, as the Watterson's test statistics from linked markers were not outside of the range of values from unlinked and presumably neutral microsatellites. The translated coding sequences of thinhorn IFNG and NRAMP are fixed and identical to those of domestic sheep (Ovis aries). In contrast, the thinhorn MHC DRB locus shows significant evidence of overdominance through both an excess of nonsynonymous substitution and trans-species polymorphism. The failure to detect balancing selection at microsatellite loci linked to the MHC is likely the result of recombination between the markers and expressed gene regions.     

Towards robust evolutionary inference with integral projection models

Integral projection models (IPMs) are extremely flexible tools for ecological and evolutionary inference. IPMs track the distribution of phenotype in populations through time, using functions describing phenotype‐dependent development, inheritance, survival and fecundity. For evolutionary inference, two important features of any model are the ability to (i) characterize relationships among traits (including values of the same traits across ages) within individuals, and (ii) characterize similarity between individuals and their descendants. In IPM analyses, the former depends on regressions of observed trait values at each age on values at the previous age (development functions), and the latter on regressions of offspring values at birth on parent values as adults (inheritance functions). We show analytically that development functions, characterized this way, will typically underestimate covariances of trait values across ages, due to compounding of regression to the mean across projection steps. Similarly, we show that inheritance, characterized this way, is inconsistent with a modern understanding of inheritance, and underestimates the degree to which relatives are phenotypically similar. Additionally, we show that the use of a constant biometric inheritance function, particularly with a constant intercept, is incompatible with evolution. Consequently, current implementations of IPMs will predict little or no phenotypic evolution, purely as artefacts of their construction. We present alternative approaches to constructing development and inheritance functions, based on a quantitative genetic approach, and show analytically and through an empirical example on a population of bighorn sheep how they can potentially recover patterns that are critical to evolutionary inference.     

Heritability of body size in the polar bears of Western Hudson Bay

Among polar bears (Ursus maritimus), fitness is dependent on body size through males’ abilities to win mates, females’ abilities to provide for their young and all bears’ abilities to survive increasingly longer fasting periods caused by climate change. In the Western Hudson Bay subpopulation (near Churchill, Manitoba, Canada), polar bears have declined in body size and condition, but nothing is known about the genetic underpinnings of body size variation, which may be subject to natural selection. Here, we combine a 4449‐individual pedigree and an array of 5,433 single nucleotide polymorphisms (SNPs) to provide the first quantitative genetic study of polar bears. We used animal models to estimate heritability (h²) among polar bears handled between 1966 and 2011, obtaining h² estimates of 0.34–0.48 for strictly skeletal traits and 0.18 for axillary girth (which is also dependent on fatness). We genotyped 859 individuals with the SNP array to test for marker–trait association and combined p‐values over genetic pathways using gene‐set analysis. Variation in all traits appeared to be polygenic, but we detected one region of moderately large effect size in body length near a putative noncoding RNA in an unannotated region of the genome. Gene‐set analysis suggested that variation in body length was associated with genes in the regulatory cascade of cyclin expression, which has previously been associated with body size in mice. A greater understanding of the genetic architecture of body size variation will be valuable in understanding the potential for adaptation in polar bear populations challenged by climate change.     

Genome‐wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate

Past glaciation events have played a major role in shaping the genetic diversity and distribution of wild sheep in North America. The advancement of glaciers can isolate populations in ice‐free refugia, where they can survive until the recession of ice sheets. The major Beringian refugium is thought to have held thinhorn sheep (Ovis dalli) populations during times of glacial advance. While isolation in the major refugium can account for much of the genetic and morphological diversity seen in extant thinhorn sheep populations, mounting evidence suggests the persistence of populations in smaller minor refugia. We investigated the refugial origins of thinhorn sheep using ~10 000 SNPs obtained via a cross‐species application of the domestic sheep ovine HD BeadChip to genotype 52 thinhorn sheep and five bighorn sheep (O. canadensis) samples. Phylogenetic inference revealed a distinct lineage of thinhorn sheep inhabiting British Columbia, which is consistent with the survival of a group of thinhorn sheep in a minor refugium separate from the Beringian refugium. Isolation in separate glacial refugia probably mediated the evolution of the two thinhorn sheep subspecies, the white Dall's sheep (O. d. dalli), which persisted in Beringia, and the dark Stone's sheep (O. d. stonei), which utilized the minor refugium. We also found the first genetic evidence for admixture between sheep from different glacial refugia in south‐central Yukon as a consequence of post glacial expansion and recolonization. These results show that glaciation events can have a major role in the evolution of species inhabiting previously glaciated habitats and the need to look beyond established refugia when examining the evolutionary history of such species.     

Response of lettuce to pre- and post-transplant phosphorus and pre-transplant inoculation with a VA-mycorrhizal fungus

Pre-transplant inoculation of lettuce (Lactuca sativa L.) seedlings with the vesicular-arbuscular mycorrhizal fungusGlomus aggregatum (Smith and Schenck emend. Koske) increased P uptake and dry matter yields after transplanting into soil when the concentration of P in the soil solution was 0.02 mg L^–1 but had little affect in soil with 0.30 mg L^–1 solution P. Tissue P concentrations and dry matter yields after transplanting were increased by supplying adequate P prior to transplanting. Adequate levels of pre-transplant P appeared to be more important than maximum mycorrhizal infection of transplants for promoting post-transplant growth of the fast maturing lettuce crop.Journal Series No. 0000 of the Hawaii Institute of Tropical Agriculture and Human Resources.     

Mapping the early development of projections from the entorhinal cortex in the embryonic mouse using prenatal surgery techniques.

The purpose of this work was to study the development of specific projections from the postero-lateral cortex during the third trimester of gestation in the mouse. To do this, we labeled undifferentiated lateral cortex with the fluorescent carbocyanine dye, Dil, in the embryonic day (E) 16 mouse embryo using exo utero surgical techniques (Muneoka, Wanek, and Bryant, 1986). Embryos were allowed to develop to term (postnatal day 0, P0) at which time the fiber patterns emanating from the marked regions were studied. Dye placement in the undifferentiated postero-ventral cortex produced labeled fibers in the hippocampal formation. A robust projection of the angular bundle into the CA1 region of the hippocampus was heavily labeled. In addition, in some animals, cortical tracts, such as the anterior commissure, corpus callosum, and a corticotectal tract, were labeled. These tracts have been described previously as scaffolding pathways in the fetal cat (McConnell, Ghosh, and Shatz, 1989), and other vertebrates (Wilson, Ross, Parrett, and Easter, 1990). Dye placement in adjacent, more anterior or dorsal areas showed strong labeling in cortical structures but no labeling in the hippocampal formation. These data indicate that, by birth, the temporal cortex is subdivided along the rostro-caudal axis as entorhinal cortex and perirhinal cortex, and along the dorso-ventral axis, as entorhinal cortex and neocortex. Also, these earliest connections are similar to adult connections in their specificity of target area selection. Therefore, these early, yet specific, connections may play a role int he formation of future connections during postnatal development.     

Mapping the early development of projections from the entorhinal cortex in the embryonic mouse using prenatal surgery techniques

The purpose of this work was to study the development of specific projections from the postero-lateral cortex during the third trimester of gestation in the mouse. To do this, we labeled undifferentiated lateral cortex with the fluorescent carbocyanine dye, Dil, in the embryonic day (E) 16 mouse embryo using exo utero surgical techniques (Muneoka, Wanek, and Bryant, 1986). Embryos were allowed to develop to term (postnatal day 0, P0) at which time the fiber patterns emanating from the marked regions were studied. Dye placement in the undifferentiated postero-ventral cortex produced labeled fibers in the hippocampal formation. A robust projection of the angular bundle into the CA1 region of the hippocampus was heavily labeled. In addition, in some animals, cortical tracts, such as the anterior commissure, corpus callosum, and a corticotectal tract, were labeled. These tracts have been described previously as scaffolding pathways in the fetal cat (McConnell, Ghosh, and Shatz, 1989), and other vertebrates (Wilson, Ross, Parrett, and Easter, 1990). Dye placement in adjacent, more anterior or dorsal areas showed strong labeling in cortical structures but no labeling in the hippocampal formation. These data indicate that, by birth, the temporal cortex is subdivided along the rostro-caudal axis as entorhinal cortex and perirhinal cortex, and along the dorso-ventral axis, as entorhinal cortex and neocortex. Also, these earliest connections are similar to adult connections in their specificity of target area selection. Therefore, these early, yet specific, connections may play a role in the formation of future connections during postnatal development.     

Low MHC DRB class II diversity in the mountain goat: past bottlenecks and possible role of pathogens and parasites

Major histocompatibility complex (MHC) genes are the most polymorphic in vertebrates and code for molecules playing a central role in pathogen resistance. We studied levels of MHC DRB class II diversity in a long-term study population of mountain goats (Oreamnos americanus) at Caw Ridge, Alberta, and two other populations from British Columbia, Canada. Only two alleles were found among the three populations sampled. The Caw Ridge population was fixed for one of the two MHC DRB alleles, but this lack of variation did not appear to have affected it negatively because the population doubled over two decades and had no history of any apparent infectious diseases. Past population bottlenecks during Pleistocene glaciations are thought to have been the main factor contributing to the low levels of MHC diversity in mountain goats, a hypothesis supported by our previous work reporting low polymorphism at neutral loci. Additionally, the limited MHC variability in mountain goats may be related to its northern distribution as we found that allelic diversity at MHC DRB class II in wild ungulates decreases with increasing latitude, possibly as a result of low parasite diversity at high latitudes. The low MHC variation in mountain goats and other northern ungulates such as muskoxen (Ovibos moschatus) may expose these species to population outbreaks that could be generated by introduced pathogens or northward shifts in the distribution of pathogens with global climate warming.     

Isolation and characterization of polymorphic microsatellite loci in muskrat, Ondatra zibethicus

We describe the isolation and characterization of 12 highly polymorphic microsatellite loci for the muskrat, Ondatra zibethicus. Microsatellite markers from three other rodent species were cross-amplified in muskrat and one of them was polymorphic. We observed moderate to high levels of genetic variability in these 13 polymorphic loci (five to 22 alleles per locus) with observed heterozygosity ranging from 0.48 to 0.96. These markers will be useful for further studies on population genetic structure in muskrat and potentially in other rodent species.