Low genetic variation of foliar traits among Prosopis chilensis (Leguminosae) provenances.

Prosopis chilensis (Molina) Stuntz (Leguminosae) is a valuable native species in Argentina that has been proposed to be used in reforestation, afforestation and restoration programmes. Natural provenances show important differentiation in height, shape, spine size, fruits and foliar traits throughout their distribution in the semiarid Monte ecoregion. The goal of this work was to characterize the genetic basis of the leaf variation in P. chilensis aiming to contribute to the improvement management program. We analyzed morphological variation and estimate narrow sense heritability for ten quantitative traits from a provenance-progeny trial founded from open pollinated families. We assessed the variance components by a generalized linear mixed model. Differences among provenances were quantified through univariate QST statistics and multivariate discriminant analysis of principal components. Finally, univariate and multivariate neutrality test were conducted to unveil the evolutionary forces that shape the variation. Univariate and multivariate analysis showed low genetic variation in foliar traits among provenances grown in the common garden. Consistently, the QST estimates for each trait were low. Both, the univariate (QST-FST comparison) and the multivariate neutrality test suggest that the leaf variation among provenances may be shaped by genetic drift rather than selective forces. Heritability estimates were significant only for leaflet apex and leaflet apex/leaflet area. Since genetic variation for most foliar traits among provenances estimated under controlled environmental conditions were very low or absent, the variation described in the wild would be explained merely by plastic response to varying environments. These results are discussed in terms of adaptive strategies and the use of different provenances as seed sources within the framework of the improvement program. It is expected that P. chilensis seeds or seedlings from trees selected under economical criteria will be able to develop in different areas thanks to the phenotypic plasticity of leaf traits.

Genetic diversity and differentiation among Prosopis alba (Leguminosae) populations from dry valleys of Bolivia with different levels of human disturbance and altitude.

The fast expansion of human population around La Paz, Bolivia (3,200-4,100 m.a.s.l.) triggered new suburban settlements in nearby areas in valleys and mountain feet. The white mesquite, Prosopis alba Griseb. (Leguminosae), is a resource (originally used by native communities) that is strongly affected by changes in land use. A gradient in the level of disturbance is found moving away from the La Paz city toward less altitude areas. The main objective of this study was to characterize genetically three P. alba populations with different levels of human disturbance located at different altitudes in Bolivia, in order to provide some guidelines for management and conservation of these species. Based on 10 SSR loci, the populations showed high level of genetic diversity in comparison with other forest species. The population less disturbed and situated at the lowest altitude was the most variable (H e  = 0.51-0.42), whereas the less variable was the most disturbed and situated at the highest altitude. Heterozygote excess was observed in all populations. Most of genetic diversity (99%) is contained within populations. Genetic differentiation among populations is low (1%), suggesting low gene flow among populations. No evidence of recent bottlenecks events was detected. The estimates of the effective population size were low in all populations. The results are in agreement with the hypothesis that genetic diversity is reduced by the impact of anthropic disturbance in the population located at higher altitude in comparison with the lightly disturbed situated at lower altitude and farther from urban settlements.

Spatial genetic structure within populations and management implications of the South American species Acacia aroma (Fabaceae).

The identification of factors that structure intraspecific diversity is of particular interest for biological conservation and restoration ecology. All rangelands in Argentina are currently experiencing some form of deterioration or desertification. Acacia aroma is a multipurpose species widely distributed throughout this country. In this study, we used the AFLP technique to study genetic diversity, population genetic structure, and fine-scale spatial genetic structure in 170 individuals belonging to 6 natural Argentinean populations. With 401 loci, the mean heterozygosity (HE = 0.2) and the mean percentage of polymorphic loci (PPL = 62.1%) coefficients indicated that the genetic variation is relatively high in A. aroma. The analysis with STRUCTURE showed that the number of clusters (K) was 3. With Geneland analysis, the number of clusters was K = 4, sharing the same grouping as STRUCTURE but dividing one population into two groups. When studying SGS, significant structure was detected in 3 of 6 populations. The neighbourhood size in these populations ranged from 15.2 to 64.3 individuals. The estimated gene dispersal distance depended on the effective population density and disturbance level and ranged from 45 to 864 m. The combined results suggest that a sampling strategy, which aims to maintain a considerable part of the variability contained in natural populations sampled here, would include at least 3 units defined by the clusters analyses that exhibit particular genetic properties. Moreover, the current SGS analysis suggests that within the wider management units/provinces, seed collection from A. aroma should target trees separated by a minimum distance of 50 m but preferably 150 m to reduce genetic relatedness among seeds from different trees.

EcoGenetics: An R package for the management and exploratory analysis of spatial data in landscape genetics.

The integration of ecology and genetics has become established in recent decades, in hand with the development of new technologies, whose implementation is allowing an improvement of the tools used for data analysis. In a landscape genetics context, integrative management of population information from different sources can make spatial studies involving phenotypic, genotypic and environmental data simpler, more accessible and faster. Tools for exploratory analysis of autocorrelation can help to uncover the spatial genetic structure of populations and generate appropriate hypotheses in searching for possible causes and consequences of their spatial processes. This study presents EcoGenetics, an R package with tools for multisource management and exploratory analysis in landscape genetics.

Isolation by distance and stochastic migration in a fragmented population of Prosopis alba.

PREMISE OF THE STUDY: Gene flow through dispersal of seeds and pollen is a fundamental determinant of spatial genetic structure (SGS) in natural populations of trees at different spatial scales. Within continuous populations, restrictions to gene flow should be manifested in a process of local genetic differentiation, known as isolation by distance. The present work examines the SGS of a Prosopis alba population in a patchy region where urban, forest, and agricultural areas coexist. The analysis discussed here expands our knowledge about the processes affecting the distribution of the genetic variability in populations of disturbed landscapes. METHODS: Three sites with different landscape and demographic characteristics were analyzed. Seven highly variable microsatellite markers were used to survey the relevance of both isolation by distance and stochastic migration in the SGS of the population. KEY RESULTS: The analyses showed that (1) the genetic similarity declined with increasing geographic distance, (2) the population may be conceived as a single genetically continuous unit showing spatial differentiation as consequence of isolation by distance, rather than a structured population following the island model, and (3) there is evidence supporting a past immigration event into one of the study sites, which promoted a local pattern of genetic structure. CONCLUSIONS: These results indicate that in spite of the population fragmentation produced by land-use changes, P. alba maintains the genetic cohesion and a continuous genetic structure in the analyzed area.

Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods.

Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other.

New microsatellite loci for Prosopis alba and P. chilensis (Fabaceae).

PREMISE OF THE STUDY: As only six useful microsatellite loci that exhibit broad cross-amplification are so far available for Prosopis species, it is necessary to develop a larger number of codominant markers for population genetic studies. Simple sequence repeat (SSR) markers obtained for Prosopis species from a 454 pyrosequencing run were optimized and characterized for studies in P. alba and P. chilensis. • METHODS AND RESULTS: Twelve markers that were successfully amplified showed polymorphism in P. alba and P. chilensis. The number of alleles per locus ranged between two and seven and heterozygosity estimates ranged from 0.2 to 0.8. Most of these loci cross-amplify in P. ruscifolia, P. flexuosa, P. kuntzei, P. glandulosa, and P. pallida. • CONCLUSIONS: These loci will enable genetic diversity studies of P. alba and P. chilensis and contribute to fine-scale population structure, indirect estimation of relatedness among individuals, and marker-assisted selection.

Durability of five native Argentine wood species of the genera Prosopis and Acacia decayed by rot fungi and its relationship with extractive content.

The natural durability of four Argentinean species of Prosopis and one of Acacia was evaluated in laboratory tests, according to European standards, using three brown rot and one white rot fungi. These tests were complemented by assessing the wood chemical composition. All the species were from moderately slightly durable to very durable (classes 4-1), and in all cases the heartwood was the most resistant to fungal attack. Chemical extractives content (organic, aqueous, tannic and phenolic) was higher in the heartwood. However, species durability was not related to extractive contents nor with wood density. Instead, it is possible that extractives could contribute to natural durability in different ways, including the effects related to the antioxidant properties of some of them.

Genetic and morphometric variability in Caiman latirostris (broad-snouted caiman), reptilia, Alligatoridae.

Caiman latirostris (broad-snouted caiman) is a crocodilian species from Argentina subject of management plans. The goal of this study was estimating the distribution of genetic variability using RAPD markers and quantitative traits in wild populations of C. latirostris from Santa Fe province, Argentina. We sampled animals from four populations to obtain DNA and morphometric measurements. Eight RAPD primers were used and PCR products were analyzed on 4% polyacrylamide gels stained with silver nitrate. Eleven allometric measurements were obtained in animals within 48 hr after birth. We were able to reveal a relatively high number of variable markers in the studied populations. Our estimates of polymorphism and heterozygosity are higher than recorded values in other crocodilians using isozymes, the studied populations showed low levels of gene flow and some population subdivision. The study of quantitative traits conducted by nested analysis of variance and principal component analysis indicated higher levels of variance among nests within populations than among populations. We found that some head measurements have the highest contribution to morphological differences among populations; this fact could support the role of these traits in reproductive or feeding behavior. Estimated genetic differentiation value (F(ST)) among populations was higher than quantitative trait differentiation value (Q(ST)), suggesting a higher contribution of neutral than adaptive loci to the genetic differentiation among populations. Quantitative traits are probably more related with fitness and the differentiation among populations remained relatively lower. The high heritability estimated for some traits indicates great potential to improve them in management plans.

Argentinean native wood species: Physical and mechanical characterization of some Prosopis species and Acacia aroma (Leguminosae; Mimosoideae).

One of the problems in marketing the wood of Prosopis and Acacia is the lack of standardization of its qualities. The aim of this paper was to obtain a preliminary detection of some properties of the wood of four species of the genus Prosopis and one species from Acacia grown in Argentina. To accomplish this objective, the content of extractives and some physical and mechanical characteristics were analyzed. The density rho(12) of all the species indicates that these woods range from heavy to very heavy (>or=0.69g/cm(3)). The total volumetric shrinkage values are low, less than 10%, for all species. The parallel compression strength and the shear strength for all the species indicate a very resistant wood (>or=46.93MPa and >or=18.35MPa, respectively). Brinell hardness was higher than 5kg/mm(2) in all cases. The species with less content of extractives is P. ruscifolia (approximately 9% of anhydrous mass) whereas A. aroma was the one with the greatest content (approximately 25% of anhydrous mass in the heartwood).

Evolution of small inversions in chloroplast genome: a case study from a recurrent inversion in angiosperms.

Small inversions (SIs) in the chloroplast genome of angiosperms are ubiquitous. These inversions are always flanked by inverted repeats (palindromes or quasipalindromes) between approximately 8 and 50 bp long that form a hairpin structure when the DNA is single-stranded. We evaluated different methodological and empirical issues about SI evolution. As a case study, we analysed an SI recently discovered in the psbC-trnS intergenic region of Prosopis (Fabaceae). First, we analysed how inversions can be optimized in cases where the inverted segment also shows indels and substitutions, proposing a method based on Fixed States Optimization. Second, we evaluated the occurrence of this inversion on a phylogeny that includes the major lineages of angiosperms. Finally, we assessed whether the occurrence of this inversion was related to the thermodynamic stability of the hairpin structure (measured by its corresponding free energy) and/or the length of the palindromes by using a modified version of Maddison's Concentrated Changes Test. Hairpin structure was conserved in most of the 154 sequences analysed, with the inversion taking place at least 10 times in different lineages (monocots, magnoliids, rosids). As was previously proposed for other SIs, our analysis strongly suggests that the occurrence of this inversion is correlated with higher hairpin stability. In contrast, we found no evidence of a correlation with longer palindromes. Our results are in agreement with the hypothesis that hairpin formation is a requisite for SI occurrence. However, alternative explanations cannot be discarded. © The Willi Hennig Society 2008.

Consistency between marker- and genealogy-based heritability estimates in an experimental stand of Prosopis alba (Leguminosae).

Prosopis represents a valuable forest resource in arid and semiarid regions. Management of promising species requires information about genetic parameters, mainly the heritability (h(2)) of quantitative profitable traits. This parameter is traditionally estimated from progeny tests or half-sib analysis conducted in experimental stands. Such an approach estimates h(2) from the ratio of between-family/total phenotypic variance. These analyses are difficult to apply to natural populations of species with a long life cycle, overlapping generations, and a mixed mating system, without genealogical information. A promising alternative is the use of molecular marker information to infer relatedness between individuals and to estimate h(2) from the regression of phenotypic similarity on inferred relatedness. In the current study we compared h(2) of 13 quantitative traits estimated by these two methods in an experimental stand of P. alba, where genealogical information was available. We inferred pairwise relatedness by Ritland's method using six microsatellite loci. Relatedness and heritability estimates from molecular information were highly correlated to the values obtained from genealogical data. Although Ritland's method yields lower h(2) estimates and tends to overestimate genetic correlations between traits, this approach is useful to predict the expected relative gain of different quantitative traits under selection without genealogical information.

Consistency of population genetics parameters estimated from isozyme and RAPDs dataset in species of genus Prosopis (Leguminosae, Mimosoideae).

Genetic variability, population structure and differentiation among 17 populations of 5 species and 2 natural interspecific hybrids of section Algarobia of genus Prosopis were analyzed from data of 23 isozyme and 28 RAPD loci. Both markers indicated that the studied populations are highly variable. P. alba populations in average showed lower values of genetic variability estimates from isozyme data, but this trend was not observed for RAPD markers. The hierarchical analyses of the distribution of genetic variability showed that the highest proportion of variation occurred within populations, the differentiation among species was intermediate and the lowest component was observed among populations within species. The consistency between results from both dataset implies that they are not biased and reflect the actual genetic structure of the populations analyzed. The matrices of Euclidean distances obtained from the two sets of markers were highly correlated according to Mantel test. In both cases the corresponding phenogram and MDS plot tended to cluster conspecific populations while hybrid populations were not intermediate between putative parents. Some disagreements between isozyme and RAPD phenograms were observed mainly in the affinities of hybrid populations. Such inconsistencies might result from reticular rather than dichotomic evolutionary relationships. The phenetic associations retrieved gave no support to the division of the section Algarobia into series.

Genetic relationships among American species of Prosopis (Leguminosae) based on enzyme markers

In the present work, isoenzyme electrophoresis was used to analyze the variability and phenetic relationships among seven American species of genus Prosopis belonging to three different sections: P. argentina (Monilicarpa), P. glandulosa, P. velutina, P. flexuosa, P. ruscifolia, P. kuntzei (Algarobia), and P. reptans (Strombocarpa). The genetic variability in P. argentina, P. reptans, and P. kuntzei was significantly lower than in the rest of the species analyzed. The species belonging to different sections are highly differentiated, but the relationships retrieved among species belonging to the section Algarobia suggested that the series of this section are not natural groups. P. kuntzei is as differentiated from the remaining species of Algarobia as from P. reptans or P. argentina, suggesting that this species might be included in a different section. The series within section Algarobia are not supported by the clusters retrieved in the phenogram based on isoenzymatic data. The results suggest that the two North American species (P. velutina and P. glandulosa) would have originated in different founder events.

First report on RAPDs patterns able to differentiate some Argentinean species of section Algarobia (Prosopis, Leguminosae).

Prosopis species constitute a very important resource in arid and semiarid regions. Some species of section Algarobia hybridise and introgress naturally in areas of sympatry. According to previous isoenzymatic studies these species have high variability within populations. However, the genetic differentiation among species was very low, and these markers failed to provide diagnostic loci for species recognition. Here we analysed by the RAPD technique natural populations of Prosopis alba, P. ruscifolia, P. nigra, P. flexuosa, and P. vinalillo with the purpose of obtaining markers for species and hybrid identification, by analysing the distribution of genetic diversity within and among species. Genetic variability (H = 0.12-0.26) was similar in all populations. Genetic differentiation among populations (FST = 0.39) was highly significant. Hierarchical analysis of genetic structure performed by Wright (1978) method and analysis of molecular variance (AMOVA) indicated that the diversity among populations within species is low (4-13%) and most genetic diversity (54-61%) occurs within populations. The differentiation among species is intermediate (26-42%) between the previous components but highly significant. Five bands provided a tool for identifying any of the species studied, with the exception of P. vinalillo. The difficulty in diagnosing this species is discussed in reference to the hypothesis of its hybrid origin.

Mating system and population structure of Acacia aroma and A. macracantha (Fabaceae).

Acacia aroma and A. macracantha are closely related species that inhabit northern and central Argentina. The reproductive barriers between them seem to be weak. They exhibit low genetic differentiation, high levels of interspecific gene flow, and extensive areas of sympatry. Isoenzymatic approaches were used to evaluate the population structure and mating system parameters in natural Argentine populations of A. aroma and A. macracantha and to provide new tools for the analysis of relationships between these two species. All studied populations had high levels of genetic variability and no significant departures from Hardy-Weinberg expectations, but the two species did not differ from each other. Most variability occured within populations. Mating system analysis showed high levels of outcrossing, no biparental inbreeding, and a high probability that individuals within progeny arrays are full rather than half sibs. In all A. aroma and A. macracantha populations, polymorphic loci had the same allelic variants, and no geographic or genetic isolation between species was found. The results favor the hypothesis that these two entities represent a single polymorphic species rather than two distinct species.

Polyporus s. str. in southern South America: isoenzyme analysis.

Forty-two dikaryotic and 42 monokaryotic isolates, and 34 pairings were examined by horizontal polyacrylamide gel electrophoresis (PAGE) for six enzymatic activities, viz. EST, 6PGD, IDH, MDH, SHDH and SOD. 44 bands were analysed. Numerical analysis of the isoenzymatic patterns was undertaken and compared with those from morphological characters. The analysis of six enzymatic systems showed the existence of four monomorphic systems (IDH, MDH, SHDH and SOD). The sterease system (EST) appears to be polymorphic in Polyporus ciliatus and in populations of P. tenuiculus from Argentina, being monomorphic in the remaining species studied. The 6PGD system is polymorphic in P. tucumanensis and monomorphic in the other species. Predominance of monomorphic enzymes and a clear distribution of the electromorphs among the species, indicates that isoenzymatic analysis is a good taxonomic tool within Polyporus. The low intraspecific variability allowed the use of interspecific differences to separate species. Numerical analysis showed a good correlation between morphological and molecular characters. In the isoenzymatic phenogram the similarity index is high only among very close species, showing a stressed separation of species.

First comparative phenetic studies of Argentinean species of Acacia (Fabaceae), using morphometric, isozymal, and RAPD approaches.

Morphological and genetic diversity among Acacia aroma, A. macracantha, A. caven, and A. furcatispina were studied with morphometric, isozymal, and RAPD approaches. The analysis of seven isozyme systems revealed 21 loci, and RAPD analysis showed 34 loci. Most of these loci allowed us to differentiate the species, with the exception of A. aroma and A. macracantha, the two most similar species. The levels of genetic variability estimated by isozymes were higher than those obtained from RAPD analyses. Morphometric characters showed highly significant differences among the species, although A. aroma and A. macracantha are differentiated only by thorn length. The phenogram obtained from isozyme data is consistent with morphological data. The RAPD phenogram based on allelic frequencies showed agreement with morphological and isozymal approaches only at the intraspecific levels, while the RAPD phenogram based on Nei and Li's similarity measures agreed with the phenograms constructed from isozyme and morphological data. High similarities and high indirect gene flow were found between A. aroma and A. macracantha, results that call the relationship between them into question.