Daniel Piñero

Treefall age determination and gap dynamics in a tropical forest

(1) Most individuals of Astrocaryum mexicanum, a monopodial neotropical understorey palm, endure treefalls that form gaps in the forest, by bending under falling trees and limbs. After one year, a bent palm recovers vertical growth at its terminal meristem and forms a permanent kink in its stem. Previous detailed demographic studies have allowed us to determine with accuracy the passage of time, based on the age-constant rate of stem elongation of the palm. (2) Using this morphological feature of the palm, together with its high density (3001230 mature individuals ha-1) in a 5-ha tract of rainforest at Los Tuxtlas, Veracruz, Mx more than 50% of the quadrats suffered disturbance in the last thirty years and 28% suffered more than one disturbance in the last seventy years. These results provide evidence that canopy disturbances capable of promoting the release of suppressed seedlings and saplings of forest trees may occur at the small scale of some tens of square metres. (4) The long-term treefall patterns analysed (up to seventy years) show that canopy disturbances are a permanent ecological factor in the rainforest environment. Annual rainfall explains more than 50% of the annual variation of the proportion of forest opened to gaps per year. (5) The yearly disturbance does not indicate the gap availability for species regeneration: for example, a year of high disturbance (e.g. 6 1 % of the forest opened to gaps) may have a similar number of sizeable gaps suitable for pioneer regeneration as a year of low disturbance (e.g. 1 5% of the forest opened to gaps). (6) The results obtained in this study show that the gap-formation process operating at Los Tuxtlas forest promotes a strong temporally and spatially random variation in the physical environment of plants. This heterogeneity may be one of the factors involved in determining the high biological diversity found in most tropical rainforests.

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference

Restriction site‐associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single‐nucleotide polymorphisms. As an empirical example, we use a double‐digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high‐altitude mountains in Mexico.

Genetic structure, outcrossing rate and heterosis in Astrocaryum mexicanum (tropical palm): implications for evolution and conservation

The population genetics of the understory tropical rain forest palm Astrocaryum mexicanum were studied in Los Tuxtlas, Veracruz, Mexico, using enzyme electrophoresis. The percentage of polymorphic loci was 31.8 and the mean expected heterozygosity was 0.153. Segregation patterns for five polymorphic loci met Mendelian expectations. Outcrossing rates were estimated using single and multilocus methods, and in most cases were not statistically different from 1.0. An excess of heterozygotes, both for seeds and adults, was found, as shown by the fixation indices estimated in 1987 (mean F for adults = −0.41, mean F for seeds = −0.19). Low but significant levels of genetic differentiation were found, especially for adults (mean Fst for adults = 0.040, mean Fst for seeds = 0.009). There was a positive relationship for adults between trunk growth and an individuals heterozygosity. No significant correlation was found between heterozygosity and fecundity. The genetic structure of A. mexicanum appears to be the result of a balance between cross-pollination and long distance movement of pollen by pollinators (beetles) that reduce genetic differentiation among plots, and natural selection that could operate during the long life cycle of this palm, and may increase the genetic differentiation among sites and the proportion of heterozygotes. The relatively high level of genetic variation, low genetic spatial differentiation, excess of heterozygotes, high outcrossing rate and heterosis found in A. mexicanum seem to be common in tropical trees. These population genetics characteristics appear not to satisfy the conditions necessary for non-adaptive evolution, a hypothesis commonly invoked to explain high tropical tree diversity. Management and conservation strategies aimed at preserving tropical trees high intrapopulation genetic variation will probably require the maintenance of large tree populations.

Effects of experimental defoliation on growth, reproduction and survival of Astrocaryum mexicanum

(1) The effects of three levels of defoliation at four stages of development on leaf production, reproduction probability, fruit production and survival of an understorey palm, Astrocaryum mexicanum, were studied from 1978 to 1981. (2) Three portions of the crown were factorized with the partial defoliation treatments. (3) Completely defoliated juvenile and immature palms produced significantly fewer leaves than control plants. In mature palms, the removal of the oldest portions of the crown increased leaf production by 30%. (4) Complete defoliation and the removal of two-thirds of the oldest leaves had the effect of reducing leaf abscission in all stages, except for seedlings. (5) Defoliation had a significant effect on reproduction during all years, except 1978. Completely defoliated palms had a lower probability of reproduction and produced no fruits for three years. The removal of a small proportion of the oldest tissue significantly increased fruit production. Defoliations greater than 33% of the total number of leaves reduced the reproductive capacity of palms, except when the oldest tissue was removed. (6) The survival of totally defoliated juvenile and immature individuals was 50% less than that of undefoliated plants. The survival of mature individuals was not significanly affected by the defoliation.

Ancestry and divergence of subtropical montane forest isolates: molecular biogeography of the genus Abies (Pinaceae) in southern México and Guatemala

The genus Abies has a complex history in southern México and Guatemala. In this region, four closely related species, Abies flinckii, A. guatemalensis, A. hickelii, and A. religiosa, are distributed in fragmented and isolated montane populations. Range‐wide genetic variation was investigated across species using cytoplasmic DNA markers with contrasted inheritance. Variation at two maternally inherited mitochondrial DNA markers was low. All species shared two of the nine mitotypes detected, while the remaining seven mitochondrial DNA types were restricted to a few isolated stands. Mitochondrial genetic differentiation across taxa was high (GST = 0.933), it was not related to the taxonomic identity (amova; P > 0.05) of the populations, and it was not phylogeographically structured (GST ≈ NST). In contrast, variation at three paternally inherited chloroplast DNA microsatellites was high. Chloroplast genetic differentiation was lower (GST = 0.402; RST = 0.547) than for mitochondrial DNA, but it was significantly related to taxonomy (amova; P < 0.001), and exhibited a significant phylogeographical structure (GST < RST). Different analyses of population structure indicated that A. flinckii was the most divergent taxon, while the remaining three species formed a relatively homogeneous group. However, a small number of the populations of these three taxa, all located at the limits of their respective ranges or in the Transverse Volcanic Belt, diverged from this main cluster. These trends suggest that the Mesoamerican Abies share a recent common ancestor and that their divergence and speciation is mainly driven by genetic drift and isolation during the warm interglacial periods.

REPRODUCTIVE BEHAVIOUR AND ITS INDIVIDUAL VARIABILITY IN A TROPICAL PALM, ASTROCARYUM MEXICANUM

SUMMARY (1) The reproductive characteristics of a tropical understorey palm, Astrocaryum mexicanum, and the causes of individual variability were observed for 414 adults on six plots during 5 yr. (2) The probability of reproduction is the most plastic of the reproductive characteristics analysed, since it varied between plots, age and years. (3) Individuals appear to respond to an environment that is heterogeneous in time and space since reproductive events were not randomly distributed among them. This probably accounts for the unsynchronized supra-annual seeding behaviour. (4) The reproductive output was correlated with both the spatial location and the leaf area of individual palms which suggests that light may play an important role in controlling seed output. (5) Light gaps and seed predation appear to be the most important selective pressures acting on this species.

Direct and indirect estimates of neighborhood and effective population size in a tropical palm, Astrocaryum mexicanum

To estimate the relative importance of genetic drift, the effective population size ∗∗∗(Ne) can be used. Here we present estimates of the effective population size and related measures in Astrocaryum mexicanum, a tropical palm from Los Tuxtlas rain forest, Veracruz, Mexico. Seed and pollen dispersal were measured. Seeds are primarily dispersed by gravity and secondarily dispersed by small mammals. Mean primary and secondary dispersal distances for seeds were found to be small (0.78 m and 2.35 m, respectively). A. mexicanum is beetle pollinated and pollen movements were measured by different methods: a) using fluorescent dyes, b) as the minimum distance between active female and male inflorescences, and c) using rare allozyme alleles as genetic markers. All three estimates of pollen dispersal were similar, with a mean of approximately 20 m. Using the seed and pollen dispersal data, the genetic neighborhood area (A) was estimated to be 2,551 m2. To obtain the effective population size, three different overlapping generation methods were used to estimate an effective density with demographic data from six permanent plots. The effective density ranged from 0.040 to 0.351 individuals per m2. The product of effective density and neighborhood area yields a direct estimate of the neighborhood effective population size (Nb). Nb ranged from 102 to 895 individuals. Indirect estimates of population size and migration rate (Nm) were obtained using Fst for five different allozymic loci for both adults and seeds. We obtained a range of Nm from 1.2 to 19.7 in adults and a range of Nm from 4.0 to 82.6 for seeds. We discuss possible causes of the smaller indirect estimates of Nm relative to the direct and compare our estimates with values from other plant populations. Gene dispersal distances, neighborhood size, and effective population size in A. mexicanum are relatively high, suggesting that natural selection, rather than genetic drift, may play a dominant role in patterning the genetic variation in this tropical palm.

The Costs of Reproduction in a Tropical Palm, Astrocaryum Mexicanum

(1) A combined demographic and energetic approach was used to try to elucidate the possible cost associated with reproduction in the tropical palm, Astrocaryum mexicanum. (2) Survival and reproduction were recorded for about one thousand palms over a 3-yr period. (3) Dry matter allocation calculations were carried out on the annual growth rates of 140 individuals for 3 yr and from harvesting fifty palms of a wide range of ages. (4) There was an increase in reproductive effort with age and an inverse correlation between various measures of reproductive cost and fecundity. (5) The 3-60% variation in reproductive effort for different ages, years and plots seems to be mainly controlled by the probability of reproduction rather than the amount of reproductive structures produced. (6) The physiological reproductive effort appears to be constant over a wide range of environments and ages.

High population differentiation and genetic variation in the endangered Mexican pine Pinus Rzedowskii (Pinaceae)

Pinus rzedowskii is an endangered pine species from Michoacán (central México), which has been previously reported from only three localities. Classified within the subgenus Strobus, it exhibits intermediate morphological characters between subgenera Strobus and Pinus. We analyzed genetic aspects that could shed light on the evolution and conservation of this species. The genetic structure of nine populations was examined using 14 isozyme loci. Pinus rzedowskii has a relatively high level of genetic variation with 46.8% of the loci assayed being polymorphic, a total of 35 alleles, and a mean heterozygosity per population of 0.219. We calculated Wrights F(ST) statistic to estimate gene flow indirectly and to evaluate whether or not there was genetic structuring among populations. We found a marked differentiation among populations (F(ST) = 0.175) and significant inbreeding (F(IS) = 0.247). No pattern of isolation by distance was found. We also constructed a dendrogram based on a genetic distance matrix to obtain an overview of the possible historical relationships among populations. Finally, we found a convex relationship between the genetic distance among populations and the number of ancestral lineages, suggesting that demographically this species has not been at risk recently. Although endangered, with small and fragmented populations, P. rzedowskii shows higher levels of genetic variation than other conifer species with larger populations or similar conservation status.

Population genetic structure of Taenia solium from Madagascar and Mexico: implications for clinical profile diversity and immunological technology.

Taenia solium is a cestode parasitic of humans and pigs that strongly impacts on public health in developing countries. Its larvae (cysticercus) lodge in the brain, causing neurocysticercosis, and in other tissues, like skeletal muscle and subcutaneous space, causing extraneuronal cysticercosis. Prevalences of these two clinical manifestations vary greatly among continents. Also, neurocysticercosis may be clinically heterogeneous, ranging from asymptomatic forms to severely incapacitating and even fatal presentation. Further, vaccine design and diagnosis technology have met with difficulties in sensitivity, specificity and reproducibility. Parasite diversity underlying clinical heterogeneity and technological difficulties is little explored. Here, T. solium genetic population structure and diversity was studied by way of random amplified polymorphic DNA in individual cysticerci collected from pigs in Madagascar and two regions in Mexico. The amplification profiles of T. solium were also compared with those of the murine cysticercus Taenia crassiceps (ORF strain). We show significant genetic differentiation between Madagascar and Mexico and between regions in Mexico, but less so between cysticerci from different localities in Mexico and none between cysticerci from different tissues from the same pig. We also found restricted genetic variability within populations and gene flow was estimated to be low between populations. Thus, genetic differentiation of T. solium suggests that different evolutionary paths have been taken and provides support for its involvement in the differential tissue distribution of cysticerci and varying degrees of severity of the disease. It may also explain difficulties in the development of vaccines and tools for immunodiagnosis.