Isolation and characterization of microsatellite loci for the collared pika (Ochotona collaris) and their cross-amplification in five other Ochotona species

We developed primers for eight polymorphic microsatellite loci isolated from the collared pika, Ochotona collaris, and also tested nine loci previously developed for the American pika, O. princeps, for use in O. collaris. Forty-six individuals from an O. collaris population in the southern Yukon were genotyped using all 17 loci. The average number of alleles per locus was six and the average observed heterozygosity was 0.59. All loci were tested for use in four Asian pika species and all but two loci amplified reliably in these species.     

Effects of Acomastylis rossii tannins on a mammalian herbivore,the North American pika,Ochotona princeps

 I investigated the effects of tannin consumption, using plant tannins naturally occurring in the diet, on a herbivorous mammal, the North American pika, Ochotona princeps. The objectives were to determine if a high-tannin diet influenced protein and dry matter apparent digestibility, fiber digestibility and production of detoxification by-products. Additionally, I examined the possibility that pikas produce salivary tannin-binding proteins, a potential mechanism for avoiding detrimental effects of tannins. My results demonstrate that although pikas constitutively produce salivary tannin-binding proteins, animals consuming a high-tannin diet of Acomastylis rossii exhibited lower dry matter, protein and fiber digestion and excreted higher concentrations of detoxification by-products. Thus, A. rossii tannins are potential toxins as well as digestibility reducers. I propose a hypothesis coupling detoxification to reduced fiber digestion that is applicable to pikas as well as other mammalian herbivores consuming phenolic-rich diets. Received: 31 July 1995 / Accepted: 9 July 1996     

Determining natal dispersal patterns in a population of North American pikas (Ochotona princeps) using direct mark-resight and indirect genetic methods

A combination of direct (mark-resight) and indirect geneticmethods were used to investigate natal dispersal patterns andgenetic population structure in a population of North Americanpikas, Ochotona princeps. Pikas are small lagomorphs found intalus habitat of alpine areas throughout western North America.Adult pikas are individually territorial and rarely disperse.I used multilocus DNA fingerprinting to identify the parentsof juvenile animals. The settlement pattern of marked juvenilesand the pattern of relatedness of pikas across the study sitewas then examined within the study area. Although juvenilesborn at the study site exhibited a philopatric settlement pattern,an isolation-by-distance analysis did not reveal clusters ofhighly related individuals within the population. The F_ST estimatesuggests little genetic differentiation between populations2 km apart, and average DNA fingerprinting band-sharing amongadults was similar to values reported for outbred species. Anaverage of 34% of the adult population was replaced each winterby immigrants. DNA fingerprinting band-sharing analysis suggeststhat these immigrants had dispersed short, intermediate, andlong distances. These findings differ from earlier studies whichused observations of marked animals only to characterize dispersalpatterns. Direct observations of marked juveniles had documenteda philopatric settlement pattern, little or no dispersal outof natal populations, and no direct evidence of long distancemovement. Of the three major hypotheses proposed to explainthe evolution of dispersal in birds and mammals, competitionfor resources, competition for mates, and inbreeding avoidance,the results of this study support a competition for resourceshypothesis, where the key resource is territory     

Isolation and characterization of highly polymorphic microsatellite markers in Hypochaeris radicata (Asteraceae)

We developed five highly polymorphic dinucleotide microsatellite loci for the grassland species Hypochaeris radicata (Asteraceae). Polymorphism of these markers was examined in six populations in the Netherlands. All loci were polymorphic in all populations. The number of alleles per locus varied between 18 and 43. Expected heterozygosity was between 0.86 and 0.91. Cross‐species amplification was tested in six Hypochaeris species and was successful for three different loci in four species. These microsatellites are a useful tool in population genetic, dispersal and metapopulation studies or in testing levels of inbreeding.     

Isolation and characterization of 11 polymorphic microsatellite loci in collared lizards (Crotaphytus collaris)

We identified 11 polymorphic microsatellite loci in collared lizards (Crotaphytus collaris). Polymorphism assessment in 512 individuals from 52 populations sampled across much of the species distribution revealed a fairly high degree of genetic diversity (six to 20 alleles per locus) and a wide range of average expected heterozygosity values (0.143–0.530). We found no evidence for linkage, very few deviations from HW expectation (two of 572 possible population/locus analyses) and thus no evidence for null alleles. There was a tendency for reduced polymorphism towards the northern periphery.     

Isolation and characterization of nine polymorphic microsatellite loci of the kelp greenling, Hexagrammos decagrammus, a temperate reef fish

Nine polymorphic microsatellite loci were developed and characterized for the temperate reef fish species, Hexagrammos decagrammus (kelp greenling). The number of alleles varied from three to 22 in a sample of 22 individuals from one population. Expected heterozygosities ranged from 0.354 to 0.979. These microsatellites allow us to investigate reproductive success of individuals, alternative mating strategies as well as population structure and metapopulation dynamics of this species.     

Isolation and introgression in the Intermountain West: contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps)

Aim We studied the history of colonization, diversification and introgression among major phylogroups in the American pika, Ochotona princeps (Lagomorpha), using comparative and statistical phylogeographic methods. Our goal was to understand how Pleistocene climatic fluctuations have shaped the distribution of diversity at mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) loci in this alpine specialist. Location North America’s Intermountain West. Methods We accumulated mtDNA sequence data (c. 560–1700 bp) from 232 pikas representing 64 localities, and sequenced two nuclear introns (mast cell growth factor, c. 550 bp, n = 148; protein kinase C iota, c. 660 bp, n = 139) from a subset of individuals. To determine the distribution of major mtDNA lineages, we conducted a phylogenetic analysis on the mtDNA sequence data, and we calculated divergence times among the lineages using a Bayesian Markov chain Monte Carlo approach. Relationships among nuclear alleles were explored with minimum spanning networks. Finally, we conducted coalescent simulations of alternative models of population history to test for congruence between nDNA and mtDNA responses to Pleistocene glacial cycles. Results We found that: (1) all individuals could be assigned to one of five allopatric mtDNA lineages; (2) lineages are associated with separate mountain provinces; (3) lineages originated from at least two rounds of differentiation; (4) nDNA and mtDNA markers exhibited overall phylogeographic congruence; and (5) introgression among phylogroups has occurred at nuclear loci since their initial isolation. Main conclusions Pika populations associated with different mountain systems have followed separate but not completely independent evolutionary trajectories through multiple glacial cycles. Range expansion associated with climate cooling (i.e. glaciations) promoted genetic admixture among populations within mountain ranges. It also permitted periodic contact and introgression between phylogroups associated with different mountain systems, the record of which is retained at nDNA but not mtDNA loci. Evidence for different histories at nuclear and mtDNA loci (i.e. periodic introgression versus deep isolation, respectively) emphasizes the importance of multilocus perspectives for reconstructing complete population histories.     

Development and characterization of microsatellite loci in the American white pelican (Pelecanus erythrorhynchos)

We isolated and characterized nine microsatellite loci from the American white pelican, Pelecanus erythrorhynchos. The loci were screened in 23 individuals from the eastern and western populations of North America and were polymorphic, with the number of alleles per locus ranging from two to eight. Polymorphic information content ranged from 0.185 to 0.820 and observed heterozygosity from 0.217 to 0.957. These new loci will provide tools for studies of population structure in this species, thereby aiding conservation planning.     

The Structure of the Oocyst and the Excystation Process of Isospora marquardti sp. n. from the Colorado pika, Ochotona princeps

SYNOPSIS. Oocysts of Isospora marquardti sp. n. from the Colorado pika, Ochotona princeps , have spheroid oocysts, 30.5 (23–36) μm in diameter, and ovoid sporocysts, measuring 19.3 × 12.0 (17–22 × 10–14) μm. A polar body, 2 × 4 μm, a spheroid sporocyst residuum (8.3 μm in diameter), a Stieda body, and a distinct substiedal body (3 × 3 μm) are present. A micropyle and an oocyst residuum are absent. Excysted sporozoites, averaging 3.0 × 18.5 (2–4 × 15–20) μm, contain 2 refractile globules, 1 on each side of the nucleus with a prominent nucleolus.
The sporozoite excystation process using a trypsin-sodium taurocholate fluid is described.     

Isolation and characterization of microsatellite loci in the dark bush cricket,Pholidoptera griseoaptera (Tettigoniidae)

Twelve novel polymorphic microsatellite loci are presented for the dark bush cricket, Pholidoptera griseoaptera. All loci are polymorphic, with up to 37 alleles per locus. These microsatellites will be useful tools for studying the influence of landscape structure and land use intensity in agricultural landscapes on genetic diversity within and among populations of P. griseoaptera.     

Isolation and characterization of microsatellite loci in Santalum insulare,Santalaceae

The forest tree Santalum insulare is endemic to the archipelagos of eastern Polynesia and is threatened by important anthropic pressures. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. One hundred and sixty‐two individuals distributed in 10 islands were analysed. These loci were all polymorphic and displayed three to 15 alleles per locus. Significant Hardy–Weinberg deviation was detected and interpreted as a result of Wahlund effect. These markers constitute an efficient tool in investigating the genetic patterns of S. insulare populations.     

Identification and characterization of 21 polymorphic microsatellite loci from the mycophagous fly Drosophila neotestacea

Drosophila neotestacea is a mushroom‐feeding fly that is common in the temperate and boreal forests of North America. Here I describe the isolation and characterization of 21 polymorphic microsatellite loci from the D. neotestacea genome. In a sample of flies from Rochester, New York, the expected and observed heterozygosities ranged from 0.344 to 1.000 and from 0.384 to 0.923, respectively. Of the 21 markers, six were likely X‐linked, seven showed a departure from Hardy–Weinberg equilibrium, and none were found to be in linkage disequilibrium. These loci will facilitate future ecological and population genetic studies of D. neotestacea.     

Isolation and characterization of microsatellite loci in Santalum austrocaledonicum,Santalaceae

The forest tree Santalum austrocaledonicum is endemic to the archipelagos of New Caledonia and Vanuatu, and is threatened by the reduction of the populations due to exploitation. In order to investigate the genetic diversity and structure of this species, we developed eight pairs of primers for nuclear microsatellites. These loci were polymorphic in all the populations, with a mean of three to 33 alleles per locus.     

Identification and characterization of polymorphic microsatellite loci in the blue shark Prionace glauca, and cross-amplification in other shark species

Two to 14 alleles were found to be segregating per locus (mean 5·2), with observed and expected heterozygosities ranging from 0·08 to 0·78 and 0·08 to 0·94, respectively. Cross-amplification of six of these microsatellite loci indicated that they are also polymorphic in three species of Carcharhiniformes and two species of Lamniformes. The newly developed primers reported here constitute a useful tool for genetic population analyses on Prionace glauca and, potentially, other related species.     

Isolation and characterization of microsatellite loci in the striped mullet,Mugil cephalus

Forty‐three microsatellites were isolated from grey mullet (Mugil cephalus) of Mediterranean origin using the standard enrichment methods followed by enhanced chemiluminescence for the rapid identification of clones containing microsatellites. Eleven microsatellites were characterized to assess genetic diversity of different populations surrounding the island of Sardinia in Italy. The versatility of these markers was also assessed using an Australian population. All 11 microsatellites were highly polymorphic with a mean heterozygosity of 0.834. The number of alleles ranged from 14 to 38 in the Sardinian populations and from 11 to 25 in the Australian samples.     

Isolation and characterization of microsatellite loci from the barley scald pathogen,Rhynchosporium secalis

Fifteen primer pairs were designed for 14 polymorphic microsatellite loci, which were isolated and characterized from genomic libraries of Rhynchosporium secalis. Conditions for multiplexing and simultaneous genotyping of up to eight loci in a single run are described. The number of alleles per polymorphic locus ranged from two to 13 in populations from Switzerland and Australia. Genotypic diversity ranged from 61.5 to 66.7. Gene diversity ranged from 0.08 to 0.89 for individual polymorphic loci, with averages of 0.54 and 0.62 for the populations from Switzerland and Australia, respectively. Variable levels of polymorphism make these ideal markers for population genetic analyses.     

Population and species boundaries in the South American subterranean rodent Ctenomys in a dynamic environment

Subterranean rodents of the genus Ctenomys are an interesting system to assess the effects of habitat instability on the genetic structure of populations. The perrensi group is a complex of three species (C. roigi, C. perrensi and C. dorbignyi) and several forms of uncertain taxonomic status, distributed in the vicinity of the Iberá wetland in Argentina. Because of limited availability of suitable dry habitat, Ctenomys populations are distributed patchily around a vast mosaic of marshes, swamps and lagoons and become connected or isolated over time, depending particularly on the precipitation regime. Genetic variation at 16 microsatellite loci in 169 individuals collected in the area revealed eight clusters of populations which are thought to be evolutionary units, but which do not fit previous species limits. We interpret this lack of congruence between taxonomy and genetic structure as the result of a dynamic population structure. Where populations become connected, hybridization is possible. Where populations become isolated, rapid genetic divergence may occur. In the perrensi group, it appears that both of these factors disrupt the association between different genetic and morphological characters. The study of multiple characters is crucial to the understanding of the recent evolutionary history for dynamic systems such as this. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 368–383.     

Development and characterization of nine polymorphic microsatellite markers in the sand goby Pomatoschistus minutus (Gobiidae)

A microsatellite‐enriched genomic library was constructed for the sand goby, Pomatoschistus minutus (Pallas 1770), and nine polymorphic DNA microsatellite markers of high quality were successfully optimized. Characterization of 96 individuals from the Vaccarès lagoon (France) showed moderate to high levels of polymorphism (two to 54 alleles). All the markers conformed to Hardy–Weinberg equilibrium and showed no evidence of null alleles, large allele dropout, stuttering and linkage disequilibrium between pairs of loci. These markers successfully amplify in three closely related species and can be employed to investigate population genetic structure and to clarify paternity in Pomatoschistus species.     

Variation in subsurface thermal characteristics of microrefuges used by range core and peripheral populations of the American pika (Ochotona princeps)

Microrefuges provide microclimates decoupled from inhospitable regional climate regimes that enable range‐peripheral populations to persist and are important to cold‐adapted species in an era of accelerated climate change. However, identifying and describing the thermal characteristics of microrefuge habitats is challenging, particularly for mobile organisms in cryptic, patchy habitats. We examined variation in subsurface thermal conditions of microrefuge habitats among different rock substrate types used by the American pika (Ochotona princeps ), a climate‐sensitive, rock‐dwelling Lagomorph. We compared subsurface temperatures in talus and lava substrates in pika survey sites in two US national park units; one park study area on the range periphery and the other in the range core. We deployed paired sensors to examine within‐site temperature variation. We hypothesized that subsurface temperatures within occupied sites and structurally complex substrates would be cooler in summer and warmer in winter than unoccupied and less complex sites. Although within‐site variability was high, with correlations between paired sensors as low as 47%, we found compelling evidence that pikas occupy microrefuge habitats where subsurface conditions provide more thermal stability than in unoccupied microhabitats. The percentage of days in which microhabitat temperatures were between ?2.5 and 25.5°C was significantly higher in occupied sites. Interestingly, thermal conditions were substantially more stable (p  < .05) in the lava substrate type identified to be preferentially used by pikas (pahoehoe vs. a'a) in a previous study. Our study and others suggest that thermal stability appears to be the defining characteristic of subsurface microrefuges used by American pikas and is a likely explanation for enigmatic population persistence at the range periphery. Our study exemplifies an integrated approach for studying complex microhabitat conditions, paired with site use surveys and contextualized with information about gene flow provided by complementary studies.