Nicaraguan population data on LDLR,GYPA, D7S8, HBGG,GC and HLA-DQA1 loci

Nicaraguans have become the most numerous and fastest increasing minority in Costa Rica: at present they represent around 6% of the total population of the country. We have analyzed the allele and genotype frequencies of six PCR-based genetic markers (LDLR, GYPA, HBGG, D7S8, GC, and HLA-DQA1) in 100 unrelated Nicaraguans living in Costa Rica. All loci studied were in Hardy-Weinberg equilibrium. Some statistical parameters of forensic interest were also calculated (h, PD and CE). Allele frequencies of the markers HLA-DQA1 and GYPA were found to be significantly different between the populations of Nicaragua and Costa Rica. Nevertheless, genetic distances showed that Nicaragua is close to other Hispanic-admixed populations like those from Argentina, Chile, Colombia, Costa Rica, and USA Hispanics. The loci set was assessed to be useful for paternity testing and individual identification in the Nicaraguan population residing in Costa Rica.     

Weak genetic structuring indicates ongoing gene flow across White-ruffed Manakin (<Emphasis Type="Italic">Corapipo altera</Emphasis>) populations in a highly fragmented Costa Rica landscape

We explored the effects of recent forest fragmentation on fine-scale patterns of population structuring and genetic diversity in populations of White-ruffed Manakins (Corapipo altera) inhabiting premontane forest fragments of varying size in southwestern Costa Rica. Habitat fragmentation is a major conservation concern for avian populations worldwide, but studies of the genetic effects of fragmentation on Neotropical birds are limited. We sampled 159 manakins from nine forest fragments of varying size within an 18 km radius, and genotyped these birds at 13 microsatellite loci. Bayesian clustering methods revealed that birds from all fragments comprised a single genetic population, and an MCMC approach showed that the fragments were likely to be at migration-drift equilibrium. F-statistics showed only modest levels of differentiation between forest fragments. We calculated allelic diversity indices for each fragment but found no correlation between genetic diversity and fragment size. These results suggest that manakins may retain substantial connectivity via inter-fragment dispersal despite habitat fragmentation.     

Structure and genetic variability of golden mussel (Limnoperna fortunei) populations from Brazilian reservoirs

The golden mussel, Limnoperna fortunei a highly invasive species in Brazil, has generated productive, economical, and biological impacts. To evaluate genetic structure and variability of L. fortunei populations present in fish farms in the reservoirs of Canoas I (CANFF), Rosana (ROSFF), and Capivara (CAPFF) (Paranapanema River, Paraná, Brazil), eight microsatellite loci were amplified. Five of those eight loci resulted in 38 alleles. The observed heterozygosity (Ho) was lower than the expected heterozygosity (He) in all populations, with a deviation from the Hardy–Weinberg equilibrium (HWE). The average value for the inbreeding coefficient (Fis) was positive and significative for all populations. There was higher genetic variability within populations than among them. The fixation index (Fst) showed a small genetic variability among these populations. The occurrence of gene flow was identified in all populations, along with the lack of a recent bottleneck effect. The clustering analysis yielded K = 2, with genetic similarity between the three populations. The results demonstrate low genetic structure and suggest a founding population with greater genetic variability (ROSFF). Our data point to the possible dispersal of L. fortunei aided by anthropic factors in the upstream direction. It was concluded that the three populations presented a unique genetic pool for Paranapanema River, with occurrence of gene flow.     

Geographic Variation in Male Sexual Signals in Strawberry Poison Frogs (Dendrobates pumilio)

In this paper, we compare the advertisement calls of 207 neotropical strawberry poison frogs (Dendrobates pumilio) collected in 21 localities along a transect from northern Costa Rica to western Panama. Populations varied most in call duration and call rate, while pulse rate and duty cycle were less variable. Multivariate analyses showed that call variation followed a cline with higher call rates, shorter calls, lower duty cycles and higher pulse rates in the southeast. Body size decreased towards the southeast and explained most variation in dominant frequency, as well as some residual variation in call rate. We conclude that a combination of geography and morphology is largely responsible for call variation within this species. Two inferred bio‐acoustic groups were roughly in accordance with two genetic groups, geographically separated in central Costa Rica. However, genetic distances among populations did not co‐vary with call dissimilarity after correction for geographic distances. Thus, differences in calls between genetic groups are probably mainly a result of clinal variation. These findings agree with the general observation that bio‐acoustic variation is often not (highly) associated with genetic divergence. Moreover, colour polymorphism observed among Panamanian populations was not reflected in a higher variability in call parameters relative to the monomorphic Costa Rican populations.     

Prediction of heterosis in crosses between inbred lines of Drosophila melanogaster

Summary The aim of the experiment was to determine if the estimated genetic distance between two populations could be used to predict the amount of heterosis that would occur when they were crossed. Eight lines of known relatedness to each other were produced by eight generations of sib mating and sub-lining. This produced lines that varied in coefficient of coancestry from zero to 0.78. Fourteen reciprocal crosses of these lines were used to measure heterosis for larval viability and adult fecundity. Gene frequencies at six polymorphic enzyme loci were used to estimate the genetic distances between lines, which were then compared with the known degrees of coancestry. The estimated genetic differences were poorly correlated with the known coancestry coefficients (r=0.4), possibly due to the small number of loci typed. Also genetic distances were only about 1/3 of what was expected. Selection acting on blocks of genes linked to the enzyme loci probably prevented the expected increase in homozygosity. Coancestry coefficient was correlated with heterosis (r=0.44–0.71). This level of correlation implied differences in heterosis among parent lines with the same level of coancestry. This variability is expected if a small number of loci explain most of the heterosis. The average level of heterosis was less than expected after eight generations of sib mating. This is most likely due to selection opposing the increase in homozygosity caused by inbreeding. The combination of these two imperfect correlations resulted in no significant correlation between genetic distance estimated from markers and heterosis.     

Reproductive plasticity in <Emphasis Type="Italic">Petrolisthes armatus</Emphasis> (Anomura,Porcellanidae): a comparison between a Pacific and an Atlantic population

The porcellanid crab Petrolisthes armatus, with a known geographic distribution covering a wide range of latitudes, was selected to conduct a comparative study on egg production and reproductive output between two populations from Pacific and Atlantic coasts. Ovigerous females were collected between September and November 2005 in Punta Morales, Pacific coast of Costa Rica (n = 137) and from March 2005 to July 2006 in Araçá region, São Paulo, Brazil (n = 46). The mean size of females was statistically different between both populations with larger females from Brazil than Costa Rica (7.9 ± 1.31 and 6.6 ± 0.95 mm CW, respectively). Likewise, egg production was significantly different in both populations and started in Pacific Costa Rica at a smaller female size than in Brazil. Specimens from Pacific Costa Rica produced roughly three times more eggs than equally sized females from Brazil, while newly extruded embryos were larger in Brazil than in Costa Rica (0.045 and 0.039 mm³, respectively). Egg volume increased during embryogenesis by 112.8 and 164.5% in Costa Rican and Brazilian populations, respectively. The egg water content increased steadily in both populations; however, eggs produced in Brazil contained always more water than those from the same developmental stage in Costa Rica. Average reproductive output (based on dry weight) was substantially lower in Brazil (0.031) than in Costa Rica (0.065). Our results confirm an impressive intraspecific plasticity of reproductive features in an intertidal decapod. The observed phenotypical variability might be related to local environmental conditions as well as to the location of the studied population concerning its geographic range of distribution.     

Development of microsatellite markers for the white mangrove (Laguncularia racemosa C.F. Gaertn., Combretaceae)

We developed nine new microsatellite markers for the white mangrove (Laguncularia racemosa C.F. Gaertn.), a mangrove species widely distributed in the Western Hemisphere. The loci were developed from a sample collected in Baja California Sur, Mexico, and were screened for polymorphism in 108 individuals from the Pacific Coast of Mexico and Costa Rica. The level of polymorphism was relatively low, from two to four alleles. These are the first set of polymorphic markers described for L. racemosa and should be of value in studying regional genetic differentiation among natural populations of this species.     

Genetic variation of introduced Hawaiian and native Costa Rican populations of an invasive tropical shrub, Clidemia hirta (Melastomataceae)

Clidemia hirta is one of the most common woody invasive plants in mesic to wet forests in Hawaii, where it was introduced around 1940. The species is relatively uncommon by comparison in its native range of Central and South America and some Caribbean Islands. We examined genetic variation in allozymes of 20 C. hirta populations on four Hawaiian Islands to determine the introduction history. For comparison, we measured genetic variation in 20 native populations across Costa Rica. Mean levels of genetic variation in Hawaiian and Costa Rican populations were low compared to other woody or introduced plants (11.5-12.5% polymorphic loci, 2.05-2.50 alleles per polymorphic locus, and 0.045-0.063 expected heterozygosity). Most genetic diversity was held within rather than among populations in both areas (G(ST) = 0.120 and 0.271 in Hawaii and Costa Rica, respectively). Hawaiian populations had a high degree of genetic similarity, and no genetic differentiation was found among the four Hawaiian Islands sampled. These patterns of genetic variation in Hawaii suggest that no intraspecific hybridization of genotypes from different parts of the native range has occurred and that introductions to the different islands came from the same or similar source populations. The low levels of genetic diversity in parts of both the native and introduced ranges suggest that genetic variation is unrelated to invasiveness in C. hirta.     

Genetic Variation of Mantled Howler Monkeys (Alouatta palliata) from Costa Rica1

We examined genetic diversity of howler monkeys (Alouatta palliata) from Costa Rica. Blood samples of howler monkeys were collected at various locations in Costa Rica, and electrophoresis of total plasma proteins yielded no variation. We also conducted starch gel electrophoresis of red cell isozymes and did not find variation for any of the 14 loci analyzed (i.e., ACP, ADA, CA2, EST, GPI, IDH, LDH‐1, LDH‐2, MDH, PGD, PGM‐1, PGM‐2, SOD, and TPI). These findings were compared with the levels of genetic variation for A. seniculus and A. belzebul from one Brazilian population. Four of the 14 isozymes (ADA, GPI, PGD, and SOD) showed more than one allele for these species. Both A. seniculus and A. belzebul from Brazil showed similar levels of genetic variation. The potential causes of the low genetic variation in A. palliata from Costa Rica are discussed.     

Genetic inference of orchid population dynamics on different-aged lava flows in Costa Rica

Colonization is a fundamental ecological process that is important for the persistence of species, particularly when a changing environment necessitates range shifts. Vacant habitats available for colonization often arise from landscape disturbance. Colonization and population expansion processes can be inferred by examining the levels and spatial distribution of genetic variation of plant populations with known disturbance histories. Samples (N = 690) of the terrestrial orchid, Epidendrum radicans, were collected from five lava flow sites on the slopes of Volcán Arenal in Costa Rica that last experienced major eruptions in 1968 and 1992. Individuals were also sampled (N = 188) from four regional populations. Samples were characterized using 15 nuclear genetic markers and analyzed using population genetics statistics. Genetic diversity within sites was moderate (H_e = 0.092–0.192). Contrary to expectation, diversity tended to be lower on the older lava flows (0.131 vs. 0.172) which may reflect their more sheltered topography that restricted pollen/seed immigration, and/or greater intra- and interspecific competition. Genetic diversity measures indicate that the lava flows were colonized by numerous individuals that likely originated from multiple sources while spatial genetic structure (SGS) statistics indicate that most recruitment in the study sites subsequent to colonization resulted from in situ reproduction and localized seed deposition. Younger sites had significantly greater SGS over larger distances which reflects fewer reproductive events, and less spatial and temporal overlap of seed shadows relative to the older sites. Clones were also generally smaller on the younger sites (≤3 m vs. ≤8 m).     

Contributions of subpopulations to total gene diversity

 The concept of the partitioning of genetic diversity into a component within and a component among populations (F _ST - or G _ST -statistics) can be easily expanded to compute the contribution of single subpopulations to total gene diversity. A subpopulation contributes to total gene diversity with its single-population gene diversity plus the (weighted) mean of Nei’s minimum genetic distances to all subpopulations. The suggested method allows one to unambiguously rank subpopulations according to the amount they contribute to the total gene diversity. Genetic polymorphisms at four isozyme gene loci of Alnus acuminata in Costa Rica are used to illustrate the procedure and its biological interpretation. Received: 15 August 1998 / Accepted: 8 September 1998     

Microsatellite variation of cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis> Crantz) in home gardens of Chibchan Amerindians from Costa Rica

We used 13 microsatellite marker loci to determine the genetic diversity of cassava (Manihot esculenta Crantz) grown in home gardens in two Chibchan Amerindian reserves in Costa Rica. We compared the levels of genetic diversity in the reserves with that of commercial varieties typically cultivated in Costa Rica. We found high levels of genetic diversity among cassava plants. Overall, 12 of the 13 loci examined were polymorphic in each Amerindian reserve (P = 92.3). Moreover, we found 36 alleles in the Coto Brus Reserve and 33 in the Talamanca Reserve. In the commercial varieties only nine loci were polymorphic (P = 69.2), and we only found 23 alleles. Heterozygosity was high for all groups of cassava (Coto Brus, Talamanca, and commercial varieties), but it was higher among the commercial varieties. The levels of heterozygosity and allele diversity indicate that there is significant genetic diversity in the home gardens that we examined. Another indication of the high diversity found in these gardens is the number of distinct multilocus genotypes, 28 at Coto Brus and 19 at Talamanca. There was also more than one distinct multilocus genotype found within the commercial varieties, as three were found in Valencia and four in Manyi. Our data also revealed low levels of genetic differentiation between the three groups of cassava (F_st = 0.03), and Nei’s genetic distances ranged from 0.0167 to 0.0343. In addition, F estimates (F_is and F_it) indicate excess heterozygotes, both at the subpopulation and the population level. A hierarchical analysis of the genetic variation revealed that variation between sampling locations within each of the three groups of cassava was larger than that between groups (Theta S = 0.0775 and Theta P = 0.0204, respectively). The variety Manyi was the group genetically most distant from all others. We discuss the consequences of these findings for in situ conservation of genetic resources.     

Genetic structure of Mesoamerican populations of Big-leaf mahogany (Swietenia macrophylla) inferred from microsatellite analysis

While microsatellites have been used to examine genetic structure in local populations of Neotropical trees, genetic studies based on such high-resolution markers have not been carried out for Mesoamerica as a whole. Here we assess the genetic structure of the Mesoamerican mahogany Swietenia macrophylla King (big-leaf mahogany), a Neotropical tree species recently listed as endangered in CITES which is commercially extinct through much of its native range. We used seven variable microsatellite loci to assess genetic diversity and population structure in eight naturally established mahogany populations from six Mesoamerican countries. Measures of genetic differentiation (FST and RST) indicated significant differences between most populations. Unrooted dendrograms based on genetic distances between populations provide evidence of strong phylogeographic structure in Mesoamerican mahogany. The two populations on the Pacific coasts of Costa Rica and Panama were genetically distant from all the others, and from one another. The remaining populations formed two clusters, one comprised of the northern populations of Mexico, Belize and Guatemala and the other containing the southern Atlantic populations of Nicaragua and Costa Rica. Significant correlation was found between geographical distance and all pairwise measures of genetic divergence, suggesting the importance of regional biogeography and isolation by distance in Mesoamerican mahogany. The results of this study demonstrate greater phylogeographic structure than has been found across Amazon basin S. macrophylla. Our findings suggest a relatively complex Mesoamerican biogeographic history and lead to the prediction that other Central American trees will show similar patterns of regional differentiation.     

Demographic bottlenecks and low gene flow in remnant populations of the critically endangered <Emphasis Type="Italic">Berchemiella wilsonii</Emphasis> var<Emphasis Type="Italic">. pubipetiolata</Emphasis> (Rhamnaceae) inferred from microsatellite markers

Berchemiella wilsonii var. pubipetiolata (Rhamnaceae) is an endangered plant with only four remnant populations in eastern China. Population genetic information is essential for understanding population history and formulating conservation strategies for this species. Thirteen microsatellite loci were used to investigate genetic variation and population structure of the four remnant populations. Moderate levels of expected heterozygosity (H _E = 0.466–0.543) and low allelic diversity (A = 3.1–3.6 and A _R = 2.2–2.4, respectively) were observed within populations. Bottleneck tests found three out of four populations to deviate from mutation-drift equilibrium under the two-phase model (TPM), suggesting a recent population decline, which is congruent with known demographic history. The evolutionary history of the species seems dominated by genetic drift rather than gene flow. Low historical gene flow was inferred from several different approaches and N _m ranged from 0.582 by the private allele method to 0.783 by the coalescent method. Contemporary gene flow was also found to be even lower for only one first generation migrant was detected with individual-based assignment analysis. Restricted pollen and seed dispersal as well as a recent decline in population size associated with habitat fragmentation may have contributed to low levels of historical and contemporary gene flow, and resulted in a high genetic differentiation. Under this scenario, Berchemiella wilsonii var. pubipetiolata populations are expected to display more pronounced population genetic structure in the future as a result of increased inbreeding and genetic drift.     

Isolation and characterization of microsatellite markers for <Emphasis Type="Italic">Cedrela odorata</Emphasis> L. (Meliaceae), a high value neotropical tree

We describe 9 primers for amplification of microsatellite loci for the Neotropical tree Cedrela odorata L. (Meliaceae). Loci were isolated from an enriched library derived from a single DNA sample from a tree in Costa Rica. Levels of polymorphism were determined using samples from a large progeny trial. Across loci, the number of alleles ranged from 14 to 30. Observed heterozygosity levels ranged from 0.61 to 0.88. No linkage disequilibria were detected although some departures from Hardy-Weinberg equilibrium (HWE) were found, probably due to a Wahlund effect.     

Population genetic structure of <Emphasis Type="Italic">Sargassum thunbergii</Emphasis> (Fucales,Phaeophyta) detected by RAPD and ISSR markers

Genetic variation of four populations of Sargassum thunbergii (Mert.) O. Kuntze and one outgroup of S. fusiforme (Harv.) Setchell from Shandong peninsula of China was studied with random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. A total of 28 RAPD primers and 19 ISSR primers were amplified, showing 174 loci and 125 loci, respectively. Calculation of genetic diversity with different indicators (P%, percentage of polymorphic loci; H, the expected heterozygosity; I, Shannon’s information index) revealed low or moderate levels of genetic variations within each S. thunbergii population. High genetic differentiations were determined with pairwise Nei’s unbiased genetic distance (D) and fixation index (F _ST ) between the populations. The Mantel test showed that two types of matrices of D and F _ST were highly correlated, whether from RAPD or ISSR data, r = 0.9310 (P  = 0.008) and 0.9313 (P = 0.009) respectively. Analysis of molecular variance (AMOVA) was used to apportion the variations between and within the S. thunbergii populations. It indicated that the variations among populations were higher than those within populations, being 57.57% versus 42.43% by RAPD and 59.52% versus 40.08% by ISSR, respectively. Furthermore, the Mantel test suggested that the genetic differentiations between the four populations were related to the geographical distances (r > 0.5), i.e., they conformed to the IBD (isolation by distance) model, as expected from UPGMA (unweighted pair group method with arithmetic averages) cluster analysis. As a whole, the high genetic structuring between the four S. thunbergii populations along distant locations was clearly indicated in the RAPD and ISSR analyses (r > 0.8) in our study.     

High gene flow between populations of Macrotermes michaelseni (Isoptera, Termitidae)

Termite alates are thought to be poor active flyers, and this should lead to considerable genetic differentiation on small spatial scales. However, using four microsatellite loci for the termite Macrotermes michaelseni we found low values of genetic differentiation (F_ST) across a spatial scale of even more than 50 km. Genetic differentiation between populations increased with spatial distance up to 50 km. Furthermore, up to this distance, the scatter around the linear regression of genetic differentiation versus spatial distance increased with spatial distance. This suggests that across such spatial distances gene flow and genetic drift are of about equal importance, and near equilibrium. Using a regional F_ST as well as the distance between populations with non-significant F_ST-values (up to 25 km), gene flow is sufficiently high so that populations may be regarded as panmictic on spatial scales of 25 to 50 km. The apparent contradiction between dispersal distances observed in the field and estimates of gene flow from genetic markers may be due to the masses of swarming alates. Assuming a leptokurtic distribution of dispersal distances, atleast some alates are expected to travel considerable distances, most likely by passive drift. Received 25 January 2005; revised 11 April 2005; accepted 26 April 2005.     

Assessment of allozyme variation among New Zealand populations of Gracilaria chilensis (Gracialiares,Rhodophyta) using starch-gel electrophoresis

New Zealand populations of Gracilaria chilensis are uniform in anatomical reproductive characteristics but vary morphologically and have been found to separate into two distinct groups with respect to agar methylation level, namely low (24–30%) and high (43–47%). To investigate the genetic variation within New Zealand populations of this species, 14 isozyme loci detected by starch-gel electrophoresis were examined in 17 wild populations from a wide range of localities, and in cultures derived from these populations. Five of these loci were polymorphic, but the genetic variation within populations was low: of the 17 populations examined, 15 were fixed at all loci (heterozygosity 0.000) and in the remaining two populations the observed heterozygosity was still low (0.004 and 0.011). The genetic distances between the populations ranged from 0.00 to 0.43. UPGMA cluster analysis separated the populations into two groups, a northern group and a group found throughout the country. Although these two groups do not correlate with the two groups based on agar methylation level at every locality, the correlation is sufficiently striking to merit further investigation.     

Genetic variation in Costa Rican populations of the tropical timber species Cedrela odorata L., assessed using RAPDs

Cedrela odorata L. (Spanish cedar), an economically important timber species native to the American tropics, is the focus of increasing conservation concern due to high rates of deforestation within its native range. To assess the extent of the genetic diversity within and between populations of this species, samples were obtained from 10 widely dispersed populations within Costa Rica and analysed for random amplified polymorphic DNA (RAPD) variation. Fourteen 10-mer primers were used to generate 97 polymorphic RAPD bands. Presence/absence data for all bands were subjected to a pairwise genetic distance analysis, according to Jaccard's coefficient, then neighbour-joining cluster analysis was performed on these distances, as was an analysis of molecular variance ( AMOVA ), to assess levels of differentiation between populations and regions, and Shannon's Diversity Index was used to quantify levels of diversity within and between populations. Results indicated highly significant genetic differentiation ( P < 0.004, AMOVA ) between populations originating from the North Pacific and Atlantic/South Pacific regions of Costa Rica, with 35.3% of the total variation attributable to a difference between these areas. Little differentiation was recorded between populations from within the same region ( P = 0.757, AMOVA ), and 65.1% of the total variance was attributable to variation within populations. Estimated values for within-population diversity, calculated as H _pop/ H _sp by means of Shannon's Diversity Index, were found to vary greatly between primers, but the overall within-population component of genetic diversity was 0.45. Possible reasons for the high degree of intraspecific genetic variation within this species are discussed and the implications of these results for the conservation and use of its genetic resources are described.     

Analysis of various classical genetic markers in the Costa Rica population

A study of several loci blood groups (ABO, Diego, Duffy, Kell, Kidd, Lewis, Lutheran, MNSs, P, Rhesus and Secretor), and Hp serum protein was carried out on a sample of 2,196 unrelated Costa Rican individuals of both sexes. Data was classified and analyzed according to geographic regions. Gene frequencies and the goodness of fit to Hardy-Weinberg equilibrium were estimated by the maximum likelihood method. A geographic structuring was observed in the Costa Rican population. All the regions of Costa Rica show higher heterozigosity values than the ones observed in the indigenous Costa Rican groups, but similar or slightly higher than the ones observed in the Spanish populations. The genetic distance analysis evidenced that the regions of Costa Rica group close to each other in intermediate positions between the Amerindians and the Spanish, fact that is coherent with the statement that attributes a intermediate origin to the general population of Costa Rica. The data contradicts the idea that the Central region has a radically different population than the rest of the country. The outcome of these markers revealed poor values of exclusion probability in forensic and paternity cases, which confirms the importance of their replacement for DNA markers in the outlines of human identification of judicial investigation systems. These results are similar to other studies made in Latin American populations.