Mutant allele frequencies in domestic cat populations on the Spanish Mediterranean coast,and their genetic distances from other European and North African cat populations

New genetic profiles of domestic cat populations were studied in different parts of the Spanish Mediterranean coast. The t ^b frequency is the most outstanding differentiated factor between the populations analyzed. The low t ^b frequencies found in Barcelona and other Catalan localities are the most important characteristic of these populations and, probably, find an explanation in the extraordinarily high historical and commercial relationships between Barcelona and the Eastern Mediterranean (Greece, especially) during the 14th and 15th centuries. In other Spanish Mediterranean littoral cities the t ^b frequencies reach higher values and are more similar to those found in other Western European cat populations. Significant differences found in certain allelic frequencies (Orange and Blotched) caused by the urban-rural effect are discovered between Barcelona and two nearby rural cat populations.     

Genetic relationships among some new cat populations sampled in Europe: A spatial autocorrelation analysis

The allelic frequencies of nine Mendelizing genetic characteristics that control coat colour, tabby and length and some skeletal abnormalities have been studied in four feral domestic cat populations, two in the north of Catalonia (Girona and Roses & L’Estartit, northeastern Spain) and two Adriatic Italian populations (Rimini and Venice). Using different genetic and multivariate analyses (Nei’s and Cavalli-Sforza and Edwards’s genetic distances, phenograms and cladograms using different algorithms, strict consensus trees, canonical population, principal coordinates and nonmetric multidimensional scaling analyses), I show the genetic relationships between these populations and other Western European cat populations previously studied. In the Western European area comprising Catalonia, Italy, France and Great Britain, I found significant spatial structure for thet ^b, l andW alleles and for the average correlogram for the seven alleles studied as a whole using a spatial autocorrelation analysis. The genetic distance matrices between these European cat populations also showed a significant correlation with the geographical distance between these populations using Mantel’s test. These analyses showed that in each of these countries, local cat populations have characteristic genetic profiles which were different to neighbouring populations in nearby countries. At least in this area of Western Europe, the geographical distances between cat populations (although the gene flow can be relatively high) is an important factor which can explain differences in allele frequencies between these populations.     

Genetic structure of populations of the domestic cat in Catalonia (Spain) and upper midwestern USA: A microgeographic and macrogeographic study

The genetic structure of natural populations of the domestic cat was examined at the microgeographic level (in the Spanish city of Barcelona) and the macrogeographic level (in Catalonia in Spain, and in upper midwestern USA) using frequency data for seven monogenic morphological traits. At the microgeographic level in the city of Barcelona there was no evidence for nonrandom mating within colonies, and estimates of between-colony gene flow were quite high. At the macrogeographic level, the populations from Catalonia and upper midwestern USA differed in two major respects: (i) The Catalan populations were in reasonably good agreement with expectations of Hardy-Weinberg equilibrium while the North American populations showed some evidence of the Wahlund effect (overall heterozygote deficiency indicating population substructuring). (ii) In the Catalan populations, approximately fifty per cent of the genetic differentiation between populations could be explained by geographical separation while in North America only four per cent of the total differentiation was attributable to geographical distance.     

Fur color gene profiles and length of hair of several cat populations in Cuba, Costa Rica, Colombia, Paraguay, Chile and Argentina, and possible genetic origins of these cat populations

Until the present moment, only a scarce number of Latin American domestic cat populations have been studied from a population genetic standpoint. For this reason, the cat populations of La Havana (Cuba), San José (Costa Rica), Bogota and Ibagué (Colombia), Asuncion (Paraguay), Santiago (Chile) and Buenos Aires (Argentina) were sampled for several coat genes. The results obtained were as follows: (1) there was a strong genetic resemblance between several Hispanic American cat populations (especially, those of Buenos Aires, San José and the two Colombian populations studied) and those from South Western United States (California, Texas and Colorado), which adds support to the suspicion that these populations probably have a common origin; (2) The cat population of Santiago (Chile), contrarily to the other Hispanic American populations studied, showed a strong genetic resemblance with some Anglo North American populations; and (3) The l (long hair) and d (dilution) alleles showed systematic higher frequencies in the Hispanic American populations than those observed in Spain. Although the Hispanic American populations were not identical to the current Spanish populations (with the exception of Asuncion), this historic genetic experiment was very different to that found for the British populations and their overseas colonies.     

Mutant allele frequencies in domestic cat populations of Macedonia (Yugoslavia)

Three domestic cat populations from Yugoslavia (Bitola, Ohrid, Struga) were surveyed at six colour loci (orange, non agouti, tabby, dilute, piebald spotting, dominant white) and one coat length locus (long hair, allele l). Statistically significant differences were obtained in frequencies of alleles: O, a, l and W. Human preferences and cultural contacts with other countries especially Turkey are discussed in the paper. Genetic distance analysis did not show that Macedonian populations are more similar to Turkish or Greek ones than populations from Dalmatia, where Turkish influence was absent, although there are similarities between Macedonian and Turkish populations as far as the O allele is concerned. There was a statistically significant correlation between the duration of Turkish rule in the middle and eastern part of the Mediterranean and O and l alleles frequencies.     

Mutant allele frequencies in domestic cat populations in the Netherlands

Surveys of gene frequencies in domestic cat (Felis catus) populations were carried out in four cities in the Netherlands. The principal variants recorded included seven mutant alleles affecting coat colour and hair length. Significant differences in frequencies were found between cities at some of the loci considered. The results of these surveys help to clarify certain trends in the distribution of mutant alleles in cat populations across Europe. Some insight is offered into the importance of trade routes in determining these patterns of distribution. In addition, comparisons between owned pets and unwanted cats indicate that human preferences have little effect on mutant allele frequencies.     

Low connectivity and declining genetic variability along a depth gradient in Corallium rubrum populations

This study examines the possible effect of depth on the connectivity and genetic variability in red coral (Corallium rubrum; Octocorallia: Alcyonacea) populations. Patterns of genetic structuring along a depth gradient (from 20 to 70 m) were investigated in two locations of the western Mediterranean coast (northern Catalan and eastern Ligurian Seas) using 10 microsatellite loci. Strong patterns of genetic structuring among the samples were found both within and between the two study sites. In both locations, consistent patterns of reduction in genetic variability along the depth gradient were also observed, suggesting that depth has an important role in determining the patterns of genetic structure in Corallium rubrum. Moreover, a threshold in connectivity was observed among the samples collected across 40–50 m depth, supporting the hypothesis that discrete shallow- and deep-water red coral populations occur. This finding has major implications for management strategies and the conservation of commercially exploited deep red coral populations.     

Mutant allele frequencies in domestic cat populations in Arkansas and Tennessee

We conducted surveys of mutant allele frequencies of four cat populations in Arkansas and Tennessee during 2002. Our calculations and analyses support that Southwestern cat populations were relatively more genetically similar to each other than compared to cat populations in other areas of North America. However, the cat population of Fort Smith is slightly different from the other cat populations studied in the Southwestern United States. Although there is a clear significant spatial geographic pattern for many mutant coat allele frequencies in the United States and Canada cat populations (d, l, S, and W), our results revealed that there is not a significant isolation-by-distance model affecting these cat populations. Our data also support the historical migration hypothesis because our calculated allele frequencies were genetically similar to cat populations located in ancestral areas of Europe. Different phenograms, including new European cat genetic profiles, showed that the Southwestern cat populations studied are of a clear British origin. Therefore, migration routes of early Arkansas and Tennessee settlers help explain the similarities of allele frequencies among domestic cat populations.     

Coat Gene Profiles of Several Cat Populations in Cuba,Costa Rica,Colombia, Paraguay,Chile and Argentina,and Possible Genetic Origins of These Cat Populations

Until the present moment, only a scarce number of Latin American domestic cat populations have been studied from a population genetic standpoint. For this reason, the cat populations of La Havana (Cuba), San José (Costa Rica), Bogotá and Ibagué (Colombia), Asunción (Paraguay), Santiago (Chile) and Buenos Aires (Argentina) were sampled for several coat genes. The results obtained were as follows: (1) there was a strong genetic resemblence between several Hispanic American cat populations (especially, those of Buenos Aires, San José and the two Colombian populations studied) and those from South Western United States (California, Texas and Colorado), which adds suport to the suspicion that these populations probably have a common origin; (2) The cat population of Santiago (Chile), contrarily to the other Hispanic American populations studied, showed a strong genetic resemblance with some Anglo North American populations; and (3) The I (long hair) and d(dilution) alleles showed systematic higher frequencies in the Hispanic American populations than those observed in Spain. Although the Hispanic American populations were not identical to the current Spanish populations (with the exception of Asuncion), this historic genetic experiment was very different to that found for the British populations and their overseas colonies.     

Genetic relationships of introduced Colorado potato beetle Leptinotarsa decemlineata populations in Xinjiang,China

The Colorado potato beetle (CPB), Leptinotarsa decemlineata (Say), is an infamous invasive species worldwide that aggressively attacks potato and other Solanaceae crops. CPB was first found in China in 1993 and has since spread across 2.77 × 10⁵ km² in Xinjiang Uygur Autonomous Region. To better understand genetic variation and migration patterns, we used seven polymorphic microsatellite loci to elucidate the genetic relationships and gene flow among 10 CPB populations across Xinjiang. (i) Overall low levels of genetic diversity were detected on the entire population in Xinjiang but most of the diversity was retained among populations during invasion. (ii) The mean pairwise F_ST was low (0.071 ± 0.043) among populations. The genetic differentiation was little (pairwise F_ST 0.038 ± 0.016) between the five interior populations (Wusu, Urumqi, Jimsar, Qitai and Mulei) and Tacheng population. The six populations might come from the same genetic group via Bayesian clustering and were closely related on a neighbor‐joining tree. Combining the history data, the five interior populations may have originated from Tacheng. (iii) Gene flow was frequent, especially among the five interior populations. Individuals from the interior populations could be assigned to Tacheng at higher probabilities (means 0.518 ± 0.127) than vice versa (means 0.328 ± 0.074), suggesting that the beetle population has spread from the border to the interior in Xinjiang.     

Population genetic analysis of cat populations from Mexico, Colombia, Bolivia, and the Dominican Republic: Identification of different gene pools in Latin America

In this paper we identify new genetic profiles of eight Latin American cat populations. In addition, we combine data from the present study and previously published data on 70 other American and European populations to discuss (1) the points of introduction of mutant alleles for cat coat phenotypes from Europe into Latin America, (2) the heterozygosity levels at these loci in the current Latin American cat populations, (3) the level of genetic heterogeneity among Latin American cat populations, and how this compares with levels found in North American and European cat populations, and (4) how many different cat gene pools are currently present in Latin America. We also include in our purview historical records of human migrations from Europe to and within the Americas. Our analyses clearly support the view that the current genetic profiles and structuring of cat populations in Latin America can be largely explained by the historical migration patterns of humans. This work is dedicated to the memory of Dr Roy Robinson. May he rest in peace.     

Coat color mutation frequencies in domestic cat populations of Primorskii krai, Russia

The frequencies of mutant coat color genes have been estimated in the cat populations of five settlements in Primorskii krai, Russia: two cities (Partizansk and Spassk-Dal'nii), a town (Khorol'), and two villages (Dmitrievka and Brovnichi). The genetic profiles of these populations have been found to be relatively homogenous and to correspond of the cat population of the city of Vladivostok studied earlier. No considerable differences in gene frequencies have been found between urban and rural cat populations. The data suggest a common origin of all domestic cat populations of Primorskii krai.     

Non-additive gene effects in populations under different methods of selection

Summary The genetic parameters of two quantitative traits, 13-day larval weight and pupal weight, in Tribolium populations developed by reciprocal recurrent selection (RRS) and by within-line purebred selection (WLS) were compared each with the other and also with the parameters of the unselected base populations using the genetic model of Carbonell, Nyquist and Bell. The variability for two and three-way crosses of inbred lines derived from companion populations (two strains, breeds, or varieties used for a terminal cross or hybrid) was analyzed into genetic effects: autosomal additivity (^* g), autosomal heterosis (^* s), sex-linked additivity (L), sex-linked heterosis (LL), general maternal (m), specific maternal or reciprocal (r), additive by additive epistasis (aa), and deviations from the model due, among other causes, to higher order epistasis (dev). One series of crosses involved companion populations with diverse origins. For contrast, a second series of crosses involved companion populations originating from a common heterogenous base population. For the heterotic trait larval weight, ^* g and ^* s effects were equally important and accounted for over 50% of the total variation. The aa epistasis contributed another 20% and was followed in importance by higher order epistasis and general maternal effects. For the more highly heritable trait, pupal weight, ^* g effects were most important with ^* s, aa, and m effects having smaller but significant influences. Sex-linked and reciprocal effects were statistically significant for many crosses, but they were relatively unimportant overall. In general, the unselected base populations showed higher ^* g variation than either RRS or WLS populations with the reverse true for ^* s effects. In agreement with theoretical expectations, RRS was more effective than WLS in exploiting ^* s effects. The aa epistatic effects for larval weight were of major importance in the unselected populations, but RRS and WLS did not differ significantly for exploiting superior aa gene combinations. Companion populations with diverse origins revealed significantly larger variation due to ^* g and ^* s effects in crosses than did populations initiated from a common heterogeneous base.Journal Paper No. 11559 from Purdue University Agricultural Experimental Station     

Genetic diversity and integrity of German wildcat (Felis silvestris) populations as revealed by microsatellites,allozymes, and mitochondrial DNA sequences

As a consequence of persecution and habitat fragmentation, wildcats (Felis silvestris silvestris) in Western Europe have experienced a severe reduction in population numbers and sizes. The remaining wildcat populations are considered to be endangered by losses of genetic variability and by hybridisation with free-ranging domestic cats. To investigate genetic diversity within and among wild and domestic cat populations in Germany and to estimate the extent of gene flow between both forms, we analysed a total of 266 individuals. PCR-amplification and sequencing of 322 base pairs of a highly variable part of the mitochondrial control region (HV1) of 244 specimens resulted in 41 haplotypes with 31 polymorphic sites. Additionally, eight microsatellite loci were examined for those 244 cats. Moreover, a total of 46 wildcats and 22 domestic cats could be genotyped for 13 polymorphic out of 31 enzyme loci. Genetic variability in both groups was generally high. Variability in domestic cat populations was higher than in wildcat populations. Almost no differentiation between domestic cat populations could be found (F_ST for microsatellites=3%). In contrast, wildcat populations differed significantly from one another (F_ST for microsatellites=9.55%) Within the smaller wildcat populations, a reduction of genetic diversity was detectable with regard to the nuclear DNA. Wildcat and domestic cat mitochondrial haplotypes were separated, suggesting a very low level of maternal gene flow between both forms. In microsatellites and to a somewhat lesser extent in allozymes, wildcats and domestic cats showed distinct differentiation, suggesting an only low extent of past hybridisation in certain populations. The microsatellite data set indicated a significantly reduced effective population size (bottleneck) in the recent past for one German wildcat population.     

Temporal changes in genetic diversity of isolated populations of perch and roach

Genetic drift, together with natural selection and gene flow, affects genetic variation and is the major source of changes in allele frequencies in small and isolated populations. Temporal shifts in allele frequencies at five polymorphic loci were used to estimate the amount of genetic drift in an isolated population of perch (Perca fluviatilis L.) and roach (Rutilus rutilus L.). Here, I used the populations from the Biotest basin at Forsmark, Sweden, to investigate genetic diversity between 1977 and 2000, during which time the population can be considered to be totally isolated from other populations. Microsatellite data reveal stable levels of gene diversity over time for both species. Estimates of genetic differentiation (F _ST) showed a significant divergence between 1977 and 2000 for both perch and roach. A positive correlation between genetic distance and time was found (Mantel test, perch: r = 0.724, P = 0.0112; roach: r = 0.59, P = 0.036). Estimates of effective population size (N _e) differed with a factor six between two different estimators (NeEstimator and TempoFS) applying the temporal method. Ratios of N _e/N ranged between 10⁻² and 10⁻³, values normally found in marine species. Despite low N _e the populations have not lost their evolutionary potential due to drift. But two decades of isolation have lead to isolation by time for populations of perch and roach, respectively.     

Genetic variation and habitat conditions in Betula humilis Schrk. populations in Poland,Belarus and Latvia

A rapidly growing human population and the extirpation of numerous species make modern wetlands among the most threatened of ecosystems. One of the endangered wetland plants in central and eastern Europe is Betula humilis. B. humilis forms comparably abundant populations on both well-preserved and drained fens; thus, we aimed in this paper to investigate the relationships between habitat quality parameters (e.g. concentrations of calcium and magnesium, groundwater levels, pH and conductivity) and genetic diversity in 12 populations of B. humilis from Poland, Belarus and Latvia. For the purposes of this study, alcohol dehydrogenase (ADH) gene sequences and nuclear microsatellites were chosen as molecular markers. Analyses revealed that only the Ca²⁺ concentration was significantly negative relative to the observed heterozygosity of microsatellites, which suggests that calcium access is the only factor influencing genetic variation at B. humilis localities. No genetic differentiation was detected between populations occupying wet and dry habitats in different parts of the species range. A minimum spanning tree based on ADH gene haplotypes appears to confirm the B. humilis population history previously inferred from analyses of nuclear microsatellites and chloroplast markers.     

RAPD variation among and within small and large populations of the rare clonal plant Ranunculus reptans (Ranunculaceae)

In the pre-alpine region of Europe numbers and sizes of populations of the clonal lake shore plant Ranunculus reptans have declined because of the regulation of lake water levels. We investigated genetic variation among and within 17 populations of different size (cover 1–10 000 m²) in R. reptans with RAPD (random amplified polymorphic DNA) profiles. We sampled 127 rosettes in 14 populations at Lake Constance and three populations at or near Lake Como. There was significant genetic variation between plants from the two lake regions (5.9%, analysis of molecular variance [AMOVA], P < 0.001), among populations within lake regions (20.4%, P < 0.001), and within populations (73.7%, P < 0.001). Under the assumptions of Wright's island model the variation among populations corresponds to a gene flow of N_em = 0.70. Within the 14 Lake Constance populations we detected significant genetic variation among subpopulations separated by only a few metres (4.0% of the within-population variation; P < 0.05). Molecular variance was 24% smaller in small populations covering <100 m² area than in larger ones (P < 0.03), indicating that samples from large populations were genetically more variable than samples representing comparable areas of smaller populations. We conclude that gene flow among populations is very limited and that genetic drift has caused reduced genetic variability of smaller populations. Conservation of genetic variability in R. reptans requires persistence of large and also of small populations (because of population differentiation), and it could be enhanced by increasing the size of small populations (to counter genetic drift).     

Estimation of genetic variability and heritability for biofuel feedstock yield in several populations of switchgrass

Information on heritability and predicted gains from selection for increased biomass yield for ethanol production in switchgrass is limited and may vary among breeding populations. The purpose of this study was to estimate heritability and predicted gains from selection for higher biomass yield within a lowland ecotype switchgrass population, Southern Lowland 93 (SL‐93), and two upland ecotype switchgrass populations, Southern Upland Northern Upland Early Maturing (SNU‐EM) and Southern Upland Northern Upland Late Maturing (SNU‐LM). Narrow‐sense heritabilities (h_n²) for biomass yield in each of the three populations were estimated via progeny–parent regression analysis. Half‐sib (HS) progeny families from 130 randomly selected plants from the SL‐93 population were evaluated for biomass yield in replicated trials in 2002 and 2003. Clonal parent plants were evaluated for biomass yield in separate environments to provide unbiased h_n² estimates from progeny–parent regression. Yield differences were highly significant among SL‐93 HS progenies within and over years. For the SL‐93 population, h_n² estimates were 0.13 and 0.12 based on individual plant and phenotypic family mean (PFM) selection, respectively. Predicted genetic gains (ΔG) per selection cycle were 0.15 kg dry matter (dm) plant^?1 and 0.10 kg dm plant^?1 for PFM and individual plant selection methods, respectively. For the SNU‐EM and SNU‐LM populations, year and year × HS family effects were highly significant (P < 0.01) and the HS family effect over years was nonsignificant (P < 0.05). However, HS family effects were highly significant within respective years (P < 0.01). Estimates of h_n² for the SNU‐EM and SNU‐LM populations based on PFM and individual plant selection were similar, ranging from 0.44 to 0.47; ΔG per selection cycle ranged from 0.22 to 0.33 kg dm plant^?1. The magnitudes of the estimates of additive genetic variation suggest that selection for higher biomass yield should be possible. The substantial effect of environment on biomass yields in the upland populations and the failure of families to respond similarly over years stress the importance of adequately testing biomass yield over years to assess yield.     

Sexual reproduction, clonal diversity and genetic differentiation in patchily distributed populations of the temperate forest herb Paris quadrifolia (Trilliaceae)

Clonal plant species have been shown to adopt different strategies to persist in heterogeneous environments by changing relative investments in sexual reproduction and clonal propagation. As a result, clonal diversity and genetic variation may be different along environmental gradients. We examined the regional and local population structure of the clonal rhizomatous forest herb Paris quadrifolia in a complex of forest fragments in Voeren (Belgium). Relationships between population size (the number of shoots), shoot density (the number of shoots per m²) and local growth conditions were investigated for 47 populations. Clonal diversity and genetic variation within and among 19 populations were investigated using amplified fragment length polymorphism markers. To assess the importance of sexual reproduction, seed set, seed weight and germination success were determined in 18 populations. As predicted, local growth conditions largely affected population distribution, size and density of P. quadrifolia. Populations occurring in moist and relatively productive sites contained significantly more shoots. Here, shoots were also much more sparsely distributed compared to populations occurring in dry and relatively unproductive sites, where shoots showed a strongly aggregated distribution pattern. Clonal diversity was relatively high, compared with other clonal species (G/N ratio = 0.43 and Simpson’s D=0.81). Clonal diversity significantly (P<0.01) decreased with increasing shoot density while molecular genetic variation was significantly (P<0.01) affected by population size and local environmental conditions. Lack of recruitment and out-competition of less-adapted genotypes may explain the decreased genetic variation in dry sites. Analysis of molecular variance revealed significant genetic variation among populations (Φ _ST=0.42, P<0.001), whereas pairwise genetic distances were not correlated to geographic distances, suggesting that gene flow among populations is limited. Finally, the number of generative shoots, the number of seeds per fruit and seed weight were significantly and positively related to population size and local growth conditions. We conclude that under stressful conditions populations of clonal forest plant species can slowly evolve into remnant populations characterized by low levels of genetic variation and limited sexual reproduction. Conservation of suitable habitat conditions is therefore a prerequisite for effective long-term conservation of clonal forest plant species.     

Ecology driving genetic variation: a comparative phylogeography of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis) in India

Background

Comparative phylogeography links historical population processes to current/ecological processes through congruent/incongruent patterns of genetic variation among species/lineages. Despite high biodiversity, India lacks a phylogeographic paradigm due to limited comparative studies. We compared the phylogenetic patterns of Indian populations of jungle cat (Felis chaus) and leopard cat (Prionailurus bengalensis). Given similarities in their distribution within India, evolutionary histories, body size and habits, congruent patterns of genetic variation were expected.

Methodology/Principal Findings

We collected scats from various biogeographic zones in India and analyzed mtDNA from 55 jungle cats (460 bp NADH5, 141 bp cytochrome b) and 40 leopard cats (362 bp NADH5, 202 bp cytochrome b). Jungle cats revealed high genetic variation, relatively low population structure and demographic expansion around the mid-Pleistocene. In contrast, leopard cats revealed lower genetic variation and high population structure with a F _ST of 0.86 between North and South Indian populations. Niche-model analyses using two approaches (BIOCLIM and MaxEnt) support absence of leopard cats from Central India, indicating a climate associated barrier. We hypothesize that high summer temperatures limit leopard cat distribution and that a rise in temperature in the peninsular region of India during the LGM caused the split in leopard cat population in India.

Conclusions/Significance

Our results indicate that ecological variables describing a species range can predict genetic patterns. Our study has also resolved the confusion over the distribution of the leopard cat in India. The reciprocally monophyletic island population in the South mandates conservation attention.