A conceptual framework to describe the ecology of fragmented landscapes and implications for conservation and management.

The study of the ecology of fragmented landscapes has been dominated by two assumptions: the unique unidirectional path from larger to smaller fragments and the negligible role of fragment species on fragment properties. An accurate conceptualization of fragmented landscapes requires consideration of the age and origin of the fragments, i.e., direct fragmentation or reverse fragmentation (generation or increase of vegetated fragments by colonization), and the habitat modifications of fragment species (autogenic processes). Colonization and autogenic processes alter the fragments' composition and function. Fragment metrics affect colonization. Autogenic processes are antagonized by disturbances and modulated by abiotic inputs. Fragment alterations by autogenic processes may explain the continuous species substitution detected in some fragments or the species persistence in others. Reverse fragmentation, a natural process in commonly disturbed landscapes, challenges the avoidance-of-habitat disturbance as the ultimate strategy for biodiversity conservation and stresses the importance of pioneer species that promote succession as resilience elements in fragmented landscapes. Among-fragment diversity, generated by local disturbances, can be essential for the resilience of fragmented landscapes, suggesting that conservation and habitat utilization can be complementary processes. Traditional agroforestry systems that depend on disturbance, fragmentation, colonization, and autogenic processes may provide important insights into fragmentation ecology.

Climate change increases threat to plant diversity in tropical forests of Central America and southern Mexico.

Global biodiversity is negatively affected by anthropogenic climate change. As species distributions shift due to increasing temperatures and precipitation fluctuations, many species face the risk of extinction. In this study, we explore the expected trend for plant species distributions in Central America and southern Mexico under two alternative Representative Concentration Pathways (RCPs) portraying moderate (RCP4.5) and severe (RCP8.5) increases in greenhouse gas emissions, combined with two species dispersal assumptions (limited and unlimited), for the 2061-2080 climate forecast. Using an ensemble approach employing three techniques to generate species distribution models, we classified 1924 plant species from the region's (sub)tropical forests according to IUCN Red List categories. To infer the spatial and taxonomic distribution of species' vulnerability under each scenario, we calculated the proportion of species in a threat category (Vulnerable, Endangered, Critically Endangered) at a pixel resolution of 30 arc seconds and by family. Our results show a high proportion (58-67%) of threatened species among the four experimental scenarios, with the highest proportion under RCP8.5 and limited dispersal. Threatened species were concentrated in montane areas and avoided lowland areas where conditions are likely to be increasingly inhospitable. Annual precipitation and diurnal temperature range were the main drivers of species' relative vulnerability. Our approach identifies strategic montane areas and taxa of conservation concern that merit urgent inclusion in management plans to improve climatic resilience in the Mesoamerican biodiversity hotspot. Such information is necessary to develop policies that prioritize vulnerable elements and mitigate threats to biodiversity under climate change.

Testing the effectiveness of rbcLa DNA-barcoding for species discrimination in tropical montane cloud forest vascular plants (Oaxaca, Mexico) using BLAST, genetic distance, and tree-based methods.

DNA-barcoding is a species identification tool that uses a short section of the genome that provides a genetic signature of the species. The main advantage of this novel technique is that it requires a small sample of tissue from the tested organism. In most animal groups, this technique is very effective. However, in plants, the recommended standard markers, such as rbcLa, may not always work, and their efficacy remains to be tested in many plant groups, particularly from the Neotropical region. We examined the discriminating power of rbcLa in 55 tropical cloud forest vascular plant species from 38 families (Oaxaca, Mexico). We followed the CBOL criteria using BLASTn, genetic distance, and monophyly tree-based analyses (neighbor-joining, NJ, maximum likelihood, ML, and Bayesian inference, BI). rbcLa universal primers amplified 69.0% of the samples and yielded 91.3% bi-directional sequences. Sixty-three new rbcLa sequences were established. BLAST discriminates 80.8% of the genus but only 15.4% of the species. There was nil minimum interspecific genetic distances in Quercus, Oreopanax, and Daphnopsis. Contrastingly, Ericaceae (5.6%), Euphorbiaceae (4.6%), and Asteraceae (3.3%) species displayed the highest within-family genetic distances. According to the most recent angiosperm classification, NJ and ML trees successfully resolved (100%) monophyletic species. ML trees showed the highest mean branch support value (87.3%). Only NJ and ML trees could successfully discriminate Quercus species belonging to different subsections: Quercus martinezii (white oaks) from Q. callophylla and Q. laurina (red oaks). The ML topology could distinguish species in the Solanaceae clade with similar BLAST matches. Also, the BI topology showed a polytomy in this clade, and the NJ tree displayed low-support values. We do not recommend genetic-distance approaches for species discrimination. Severe shortages of rbcLa sequences in public databases of neotropical species hindered effective BLAST comparisons. Instead, ML tree-based analysis displays the highest species discrimination among the tree-based analyses. With the ML topology in selected genera, rbcLa helped distinguish infra-generic taxonomic categories, such as subsections, grouping affine species within the same genus, and discriminating species. Since the ML phylogenetic tree could discriminate 48 species out of our 55 studied species, we recommend this approach to resolve tropical montane cloud forest species using rbcLa, as an initial step and improve DNA amplification methods.

DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico.

DNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these forests, from a little-explored area in Oaxaca, Mexico, applying the CBOL criteria for barcoding. We used BLASTn, genetic distance, and monophyly tree-based analyses employing neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference methods. Universal primers for rbcLa and trnH-psbA were successfully amplified and bi-directionally sequenced, but matK could not be amplified for most species. rbcLa showed the highest species discrimination in BLASTn (66.67%). trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e-16). Using NJ and ML phylogenetic trees, monophyletic species were successfully resolved (100%), differing only in support values and displaying full agreement with the most recent fern classification. ML trees showed the highest mean support value (80.95%). trnH-psbA was the only barcode that could detect the Elaphoglossoideae subfamily. Species discrimination did not increase using rbcLa + trnH-psbA. rbcLa is useful for fern barcoding, trnH-psbA is most helpful for phylogenetic analyses, and matK may not work as a universal barcoding marker.

On the possible role of nonreproductive traits for the evolution of unisexuality: Life-history variation among males, females, and hermaphrodites in Opuntia robusta (Cactaceae).

In angiosperms, dioecy has arisen in 871-5,000 independent events, distributed in approximately 43% of the flowering families. The reproductive superiority of unisexuals has been the favorite explanation for the evolution of separate sexes. However, in several instances, the observed reproductive performance of unisexuals, if any, does not seem to compensate for the loss of one of the sex functions. The involvement of fitness components not directly associated with reproduction is a plausible hypothesis that has received little attention. Life-history traits recently recognized as predictors of plant performance were compared among males, females, and hermaphrodites of a rare trioecious Opuntia robusta population in the field, using the cladode as the study unit. Cladode mortality by domestic herbivores was common and higher in females and hermaphrodites than in males. Males, females, or both displayed lower shrinkage and higher rates of survival, growth, and reproductive frequency than hermaphrodites. Unisexuals simultaneously outperformed hermaphrodites in demographic traits known to compete for common limiting resources, such as the acceleration of reproductive maturation (progenesis) and survival. A meta-analysis combining the outcomes of each of the analyzed life-history traits revealed a tendency of males (d++ = 1.03) and females (d++ = 0.93) to outperform hermaphrodites in presumably costly demographic options. Clonality is induced by human or domestic animal plant sectioning; and males and females highly exceeded hermaphrodites in their clonality potential by a factor of 8.3 and 5.3, respectively. The performances of unisexuals in the analyzed life-history traits may enhance their reproductive potential in the long run and their clonality potential and could explain the observed increase of unisexuality in the population. Life-history traits can be crucial for the evolution of unisexuality, but their impact appears to be habitat specific and may involve broad ontogenetic changes.

Possible combined effects of climate change, deforestation, and harvesting on the epiphyte Catopsis compacta: a multidisciplinary approach.

Climate change, habitat loss, and harvesting are potential drivers of species extinction. These factors are unlikely to act on isolation, but their combined effects are poorly understood. We explored these effects in Catopsis compacta, an epiphytic bromeliad commercially harvested in Oaxaca, Mexico. We analyzed local climate change projections, the dynamics of the vegetation patches, the distribution of Catopsis in the patches, together with population genetics and demographic information. A drying and warming climate trend projected by most climate change models may contribute to explain the poor forest regeneration. Catopsis shows a positive mean stochastic population growth. A PVA reveals that quasi-extinction probabilities are not significantly affected by the current levels of harvesting or by a high drop in the frequency of wet years (2%) but increase sharply when harvesting intensity duplicates. Genetic analyses show a high population genetic diversity, and no evidences of population subdivision or a past bottleneck. Colonization mostly takes place on hosts at the edges of the fragments. Over the last 27 years, the vegetation cover has being lost at a 0.028 years(-1) rate, but fragment perimeter has increased 0.076 years(-1). The increases in fragment perimeter and vegetation openness, likely caused by climate change and logging, appear to increase the habitat of Catopsis, enhance gene flow, and maintain a growing and highly genetically diverse population, in spite of harvesting. Our study evidences conflicting requirements between the epiphytes and their hosts and antagonistic effects of climate change and fragmentation with harvesting on a species that can exploit open spaces in the forest. A full understanding of the consequences of potential threatening factors on species persistence or extinction requires the inspection of the interactions of these factors among each other and their effects on both the focus species and the species on which this species depends.

Genetic factors associated with population size may increase extinction risks and decrease colonization potential in a keystone tropical pine.

Pioneer species are essential for forest regeneration and ecosystem resilience. Pinus chiapensis is an endangered pioneer key species for tropical montane cloud forest regeneration in Mesoamerica. Human activities have severely reduced some P. chiapensis populations, which exhibited a small or null colonization potential suggesting the involvement of genetic factors associated with small populations. We explored the relationships between (i) population genetic diversity (allozymes) and population size, including sampling size effects, (ii) fitness estimates associated with colonization potential (seed viability and seedling performance) in a common environment and population size, and (iii) fitness estimates and observed heterozygosity in populations with sizes spanning five orders of magnitude. All the estimates of genetic diversity and fitness increased significantly with population size. Low fitness was detected in progenies of small populations of disturbed and undisturbed habitats. Progenies with the lowest observed heterozygosity displayed the lowest fitness estimates, which, in turn, increased with heterozygosity, but seed viability peaked at intermediate heterozygosity values suggesting inbreeding and outbreeding depression. Inbreeding depression appears to be the most immediate genetic factor in population decline. Conservation efforts should try to maintain large and genetically diverse populations, enhance gene flow by restoring connectivity between adjacent populations, and avoid genetically distant individuals.

Reproductive implications of combined and separate sexes in a trioecious population of Opuntia robusta (Cactaceae).

Opuntia robusta has hermaphroditic, dioecious, and trioecious populations. To enhance our understanding of this breeding system diversity, we compared the reproductive output of males, females, and hermaphrodites in a trioecious population using field evaluations, controlled crosses, and progeny tests. Unisexuals were fully sterile in one sex function. Hermaphrodites were fully fertile for both functions. Consistent with the sex-allocation theory, unisexuality increased the quality and quantity (in males) of the gametes of the functional sex, relative to those of hermaphrodites, probably explained by maternal and paternal effects. The increase was higher in males than in females, suggesting a more expensive female function. Theoretically, this disproportional increase is required for unisexuals to invade a hermaphroditic population with prior selfing, negligible pollen discounting, and undetectable inbreeding depression, features found in O. robusta, therefore helping to explain dioecious populations. However, in the study population, the actual seed output of females was lower and had a higher variance than that of hermaphrodites, which also reproduce through pollen. Unisexuals are unlikely to be maintained by their actual reproductive output in this pollen-limited environment. Hermaphrodites may persist in this population by producing their seeds autonomously and by reducing interspecific fertilization by prior selfing and ovule discounting.

FITNESS CONSEQUENCES OF MATERNAL AND NONMATERNAL COMPONENTS OF INBREEDING IN THE GYNODIOECIOUS PHACELIA DUBIA.

I assessed the relationship between the level of inbreeding, F, and fitness, and the effects of nonmaternal and maternal components of inbreeding on fitness in Phacelia dubia. I conducted two generations of controlled crosses and tested the performance of the F2 progeny in field and artificial conditions covering the whole life cycle. Inbreeding significantly decreased the individual contribution of seeds to the next generation in the field, but this decrease apparently is not enough to explain the maintenance of gynodioecy. The inbred progeny contributes significantly to the population genetic structure of P. dubia. Fitness estimates and fitness components tended to decrease, usually monotonically, with F. However, nonmonotonic relationships were found in male fitness components and, in some families, in fitness estimates, seed production per fruit, and establishment. Most of the inbreeding depression takes place at the level of seed establishment in the field, but, in artificial conditions the effects of inbreeding were similar at fecundity and establishment. I studied maternal and nonmaternal components of inbreeding by testing the effects of the relatedness of maternal grandparents and parents on the performance of the progeny. Both components affected fitness. Inbreeding depression was conditioned by the level of inbreeding of the maternal plant, but this interaction varied at different fitness components. Also, the magnitude and even the direction of the relationship between fitness and F changed as a result of the combined effects of maternal and nonmaternal components of inbreeding. Such interactions can render convex or concave fitness functions, giving in the latter case the appearance of a false purging. Maternal effects of inbreeding can result from several processes: maternal investment perhaps with serial adjustments during seed development, purging of recessive deleterious genes, and nucleocytoplasmic interactions. These results illustrate the importance of maternal effects of inbreeding, and the complex effects of inbreeding on fitness. A full understanding of the fitness consequences of inbreeding and, therefore, their potential implications in the evolution of breeding systems, should take into account male and female components as well as transgenerational effects in the context of the particular environment in which fitness is evaluated.