Genetic structure of an isolated population of mantled howler monkeys (Alouatta palliata) on Barro Colorado Island, Panama

Habitat fragmentation may influence genetic variability through reductions in population size and the physical isolation of conspecifics. We explored the effects of these factors on genetic diversity in a population of mantled howler monkeys (Alouatta palliata) on Barro Colorado Island (BCI), Panama. The study population was established in 1914 when an unknown number of resident individuals were isolated from the surrounding mainland by damming of the Río Chagres to create the Panama Canal. Analyses of 10 microsatellite loci indicated that, despite this isolation, the howler monkeys on BCI exhibit levels of genetic diversity (H _S = 0.584 ± 0.063) among the highest reported for any species of Alouatta. These data also revealed that although relatedness among adults in a social group was significantly greater than zero, the BCI population is not highly genetically structured. Tests for genetic bottlenecks based on departures from equilibrium expectations failed to reveal evidence of a recent reduction in population size. In contrast, coalescent modeling indicated that this population has likely experienced a marked decline within the last few 100 years. These findings generate new insights into the genetic structure of A. palliata and suggest that while the formation of BCI may not have substantially reduced genetic variation in these animals, genetic diversity has been influenced by historical changes in population size.     

Root architecture and allocation patterns of eight native tropical species with different successional status used in open-grown mixed plantations in Panama

We investigated biomass allocation and root architecture of eight tropical species with different successional status, as classified from the literature, along a size gradient up to 5 m. We focused on belowground development, which has received less attention than aboveground traits. A discriminant analysis based upon a combination of allocational and architectural traits clearly distinguished functional types and classified species according to successional status at a 100% success rate. For a given plant diameter, the pioneer species presented similar root biomass compared to the non-pioneer ones but higher cumulative root length and a higher number of root apices. A detailed study on the root system of a sub-sample of three species showed that the most late-successional species (Tabebuia rosea) had longer root internodes and a higher proportion of root biomass allocated to the taproot compared to the other two species (Hura crepitans and Luehea seemannii). Most pioneer species showed a higher leaf area ratio due to a higher specific leaf area (SLA). We conclude that the functional differences between pioneer and non-pioneer tree species found in natural forests were maintained in open-grown plantation conditions.     

The Relative Contribution of Specialists and Generalists to Mistletoe Dispersal: Insights from a Neotropical Rain Forest

Mistletoes rely on birds for seed dispersal, but the presumed importance of mistletoe‐specialist frugivores has not been critically examined nor compared with generalist frugivores and opportunistic foragers. The contribution of these three groups was compared directly by quantifying bird visitation to fruiting mistletoe plants ( Oryctanthus occidentalis: Loranthaceae) at Barro Colorado Island, Panama, and by comparing these results with proportions calculated from other empirical studies of mistletoe visitation conducted elsewhere. After more than 100 h of timed watches, 23 bird species were recorded visiting eight heavily infected host trees ( Luehea seemannii: Tiliaceae). Eight of these species visited mistletoe, of which five (all tyrannids) consumed mistletoe fruit. Although two mistletoe specialist frugivores ( Tyrannulus elatus and Zimmerius vilissimus) removed most fruit (73%), more than a quarter was consumed by one generalist frugivore ( Mionectes oleagineus) and two opportunists ( Myiozetetes cayanensis and Myiozetetes similis). Post consumption behaviour varied: the specialists flew from mistletoe to mistletoe, the generalist rested in the subcanopy and understory, and the opportunists spent most time hawking insects and resting high in the canopy. Integrating these data with previous work, the dietary specialization, short gut passage rate and strict habitat preferences of mistletoe specialists suggests that their services relate primarily to intensification and contagious dispersal, while species with broader diets are more likely to visit uninfected trees and establish new infections. The presumed importance of mistletoe‐specialist frugivores was not supported and mistletoes are considered to be comparable to many other bird‐dispersed plants, relying on both specialist and generalist frugivores, while opportunists may be disproportionately important in long‐distance dispersal.     

Polymorphic microsatellite markers for the Caribbean seagrass Thalassia testudinum Banks ex König

We isolated 14 polymorphic microsatellite loci for the western Atlantic tropical seagrass, Thalassia testudinum, using two different enrichment procedures. Polymorphism was screened among samples from Mexico and Panama. Allelic diversity varied between three and 17 alleles per locus, and expected heterozygosity ranged from 0.271 to 0.859.     

Regeneration niche partitioning in neotropical pioneers: effects of gap size,seasonal drought and herbivory on growth and survival

Adaptive trade-offs underlie the specialisation that permits habitat partitioning in species rich plant communities. We investigated the influence of the trade-offs that determine differences in growth and survival among six species of neotropical pioneer trees in gaps in semideciduous forest in Panama. Seedlings of Miconia argentea, Cecropia insignis, Luehea seemannii, Trema micrantha, Ochroma pyramidale and Croton bilbergianus were planted into artificial small (25 m²), medium (64 m²) and large (225 m²) gaps in secondary forest in the Barro Colorado Nature Monument. Trema and Ochroma suffered 50% mortality across all gap sizes, while Cecropia had high mortality only during the dry season and in the small gaps, and Miconia and Croton suffered low to zero mortality across all environments. The highest growth rates in large gaps were attained by Cecropia seedlings and in the smaller gaps by Miconia seedlings, although there were indications that Trema and Ochroma required gaps that were larger than any used in this study. Variation in growth and mortality could not be attributed to differences in foliar herbivore damage. Instead, there was strong evidence of a trade-off between maximum growth in the wet season and the ability to survive seasonal drought, particularly in small gaps. We conclude that variation in allocation in response to multiple limiting resources may be as important as allocation to growth and defence in determining the habitat preferences of neotropical pioneers.     

Symbiotic Relationships of Legumes and Nodule Bacteria on Barro Colorado Island,Panama: A Review

New data on 129 bacterial isolates were analyzed together with prior samples to characterize community-level patterns of legume–rhizobial symbiosis on Barro Colorado Island (BCI), Panama. Nodules have been sampled from 24 BCI legume species in 18 genera, representing about one quarter of the legume species and one half of the genera on the island. Most BCI legumes associated exclusively with nodule symbionts in the genus Bradyrhizobium, which comprised 86.3% of all isolates (315 of 365). Most of the remaining isolates (44 of 365) belonged to the β-proteobacterial genus Burkholderia; these were restricted to two genera in the legume subfamily Mimosoideae. Multilocus sequence analysis indicated that BCI Bradyrhizobium strains were differentiated into at least eight lineages with deoxyribonucleic acid divergence of the same magnitude as found among currently recognized species in this bacterial genus. Two of these lineages were widely distributed across BCI legumes. One lineage was utilized by 15 host species of diverse life form (herbs, lianas, and trees) in 12 genera spanning two legume subfamilies. A second common lineage closely related to the taxon B. elkanii was associated with at least five legume genera in four separate tribes. Thus, BCI legume species from diverse clades within the family frequently share interaction with a few common lineages of nodule symbionts. However, certain host species were associated with unique symbiont lineages that have not been found on other coexisting BCI legumes. More comprehensive sampling of host taxa will be needed to characterize the overall diversity of nodule bacteria and the patterns of symbiont sharing among legumes in this community.     

Stem water storage and diurnal patterns of water use in tropical forest canopy trees

Stem water storage capacity and diurnal patterns of water use were studied in five canopy trees of a seasonal tropical forest in Panama. Sap flow was measured simultaneously at the top and at the base of each tree using constant energy input thermal probes inserted in the sapwood. The daily stem storage capacity was calculated by comparing the diurnal patterns of basal and crown sap flow. The amount of water withdrawn from storage and subsequently replaced daily ranged from 4 kg d^–1 in a 0·20-m-diameter individual of Cecropia longipes to 54 kg d^–1 in a 1·02-m-diameter individual of Anacardium excelsum, representing 9–15% of the total daily water loss, respectively. Ficus insipida, Luehea seemannii and Spondias mombin had intermediate diurnal water storage capacities. Trees with greater storage capacity maintained maximum rates of transpiration for a substantially longer fraction of the day than trees with smaller water storage capacity. All five trees conformed to a common linear relationship between diurnal storage capacity and basal sapwood area, suggesting that this relationship was species-independent and size-specific for trees at the study site. According to this relationship there was an increment of 10 kg of diurnal water storage capacity for every 0·1 m² increase in basal sapwood area. The diurnal withdrawal of water from, and refill of, internal stores was a dynamic process, tightly coupled to fluctuations in environmental conditions. The variations in basal and crown sap flow were more synchronized after 1100 h when internal reserves were mostly depleted. Stem water storage may partially compensate for increases in axial hydraulic resistance with tree size and thus play an important role in regulating the water status of leaves exposed to the large diurnal variations in evaporative demand that occur in the upper canopy of seasonal lowland tropical forests.     

Phylogeography and connectivity of molluscan parasites: Perkinsus spp. in Panama and beyond

Panama is a major hub for commercial shipping between two oceans, making it an ideal location to examine parasite biogeography, potential invasions, and the spread of infectious agents. Our goals were to (i) characterise the diversity and genetic connectivity of Perkinsus spp. haplotypes across the Panamanian Isthmus and (ii) combine these data with sequences from around the world to evaluate the current phylogeography and genetic connectivity of these widespread molluscan parasites. We collected 752 bivalves from 12 locations along the coast of Panama including locations around the Bocas del Toro archipelago and the Caribbean and Pacific entrances to the Panama Canal, from December 2012 to February 2013. We used molecular genetic methods to screen for Perkinsus spp. and obtained internal transcribed spacer region (ITS) ribosomal DNA (rDNA) sequences for all positive samples. Our sequence data were used to evaluate regional haplotype diversity and distribution across both coasts of Panama, and were then combined with publicly available sequences to create global haplotype networks. We found 26 ITS haplotypes from four Perkinsus spp. (1–12 haplotypes per species) in Panama. Perkinsus beihaiensis haplotypes had the highest genetic diversity, were the most regionally widespread, and were associated with the greatest number of hosts. On a global scale, network analyses demonstrated that some haplotypes found in Panama were cosmopolitan (Perkinsus chesapeaki, Perkinsus marinus), while others were more geographically restricted (Perkinsus olseni, P. beihaiensis), indicating different levels of genetic connectivity and dispersal. We found some Perkinsus haplotypes were shared across the Isthmus of Panama and several regions around the world, including across ocean basins. We also found that haplotype diversity is currently underestimated and directly related to the number of sequences. Nevertheless, our results demonstrate long-range dispersal and global connectivity for many haplotypes, suggesting that dispersal through shipping probably contributes to these biogeographical patterns.     

Population Genetic Structure of Pacific White Shrimp (<Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>) from Mexico to Panama: Microsatellite DNA Variation

Genetic variation and population structure of wild white shrimp (Litopenaeus vannamei) from 4 geographic locations from Mexico to Panama were investigated using 5 microsatellite DNA loci. The genetic diversity between populations was indicated by the mean number of alleles per locus and mean observed heterozygosity, which ranged from 7.4 to 8.6 and from 0.241 to 0.388, respectively. Significant departures from Hardy-Weinberg equilibrium were found at most locations at each locus, with the exception Guatemala at Pvan0013, and were caused by high heterozygote deficiencies. Genetic differences between localities were detected by pairwise comparison based on allelic and genotypic frequencies, with the exception of locus Pvan1003. Significant pairwise F _ST values between locations and total F _ST showed that the white shrimp population is structured into subpopulations. However, population differentiation does not follow an isolation-by-distance model. Knowledge of the genetic diversity and structure of L.vannamei populations will be of interest for aquaculture and fisheries management to utilize and preserve aquatic biodiversity.     

Pre‐dispersal seed predators and fungi differ in their effect on Luehea seemannii capsule development,seed germination,and dormancy across two Panamanian forests

Pre‐dispersal seed predation can greatly reduce crop size affecting recruitment success. In addition, non‐fatal damage by seed predators may allow infection by fungi responsible for post‐dispersal seed losses. The objectives of this study were (1) to quantify pre‐dispersal seed predation and fungal infection in a Neotropical tree species, Luehea seemannii, that produces dehiscent fruits and wind‐dispersed seeds, and (2) to link pre‐dispersal effects on seed quality to seed survival in the soil. To examine how seed predators and fungi influence seed losses, mesh exclosures, fungicide, and the combination of both treatments were applied to separate branches in the canopy of trees in Gamboa and Parque Natural Metropolitano (PNM), Panama. To determine if treatments affect seed viability and survival in the soil, half of the seeds collected from each treatment were buried for 4 weeks in forest soils and subsequently allowed to germinate before and after the breaking of dormancy. Overall, 24 percent of developing fruit were lost to insect attack. In contrast, fungi infected only 3 percent of seeds at the pre‐dispersal stage. For seeds germinated directly after collection, fungicide significantly increased germination in the wetter site (Gamboa) but decreased germination in the drier site (PNM). The pre‐dispersal insect exclosure treatment increased the fraction of seeds that remained dormant after burial in the soil. This result suggests that exposure to insect predators may cause physical damage to seeds that results in the loss of physical dormancy but does not necessarily increase the susceptibility of seeds to pathogen attack in the soil.     

DNA barcoding of echinopluteus larvae uncovers cryptic diversity in neotropical echinoids

Surveys of larval diversity consistently increase biodiversity estimates when applied to poorly documented groups of marine invertebrates such as phoronids and hemichordates. However, it remains to be seen how helpful this approach is for detecting unsampled species in well‐studied groups. Echinoids represent a large, robust, well‐studied macrofauna, with low diversity and low incidence of cryptic species, making them an ideal test case for the efficacy of larval barcoding to discover diversity in such groups. We developed a reference dataset of DNA barcodes for the shallow‐water adult echinoids from both coasts of Panama and compared them to DNA sequences obtained from larvae collected primarily on the Caribbean coast of Panama. We sequenced mitochondrial cytochrome c oxidase subunit I (COI) for 43 species of adult sea urchins to expand the number and coverage of sequences available in GenBank. Sequences were successfully obtained for COI and 16S ribosomal DNA from 272 larvae and assigned to 17 operational taxonomic units (OTUs): 4 from the Pacific coast of Panama, where larvae were not sampled as intensively, and 13 from the Caribbean coast. Of these 17 OTUs, 13 were identified from comparisons with our adult sequences and belonged to species well documented in these regions. Another larva was identified from comparisons with unpublished sequences in the Barcode of Life Database (BOLD) as belonging to Pseudoboletia, a genus scarcely known in the Caribbean and previously unreported in Panama. Three OTUs remained unidentified. Based on larval morphology, at least two of these OTUs appeared to be spatangoids, which are difficult to collect and whose presence often goes undetected in standard surveys of benthic diversity. Despite its ability to capture unanticipated diversity, larval sampling failed to collect some species that are locally common along the Caribbean coast of Panama, such as Leodia sexiesperforata, Diadema antillarum, and Clypeaster rosaceus.     

Skeletal Pathologies in a Population of Alouatta palliata: Behavioral, Ecological, and Evolutionary Implications

We examined the pathological conditions in a sample of 200 skulls of Alouatta palliata recovered from Barro Colorado Island (BCI), Panama, to investigate the prevalence of disease and injury in a free-ranging monkey population. Forty-five individuals (22.5%) have some type of nondental pathological condition, indicating that illness and injury are relatively common in this population. Ten individuals, all older adult males, exhibit clear signs of antemortem trauma in the form of healed fractures. We attribute the trauma primarily to fighting, and its frequency (16.4% of adult males) contradicts previous assertions that BCI howlers are nonaggressive. Nine of the 37 scorable immature individuals (24%) have signs of a larval infestation, supporting the suggestion that ectoparasites play an important role in BCI howler mortality. Other pathological conditions in the sample include shifted muscle attachments, periostitis, arthritis, neoplasm, periapical abscesses, and facial deformity, as well as various dental abnormalities.     

Population structure and genetic variability of pearl oyster Pinctada mazatlanica along Pacific coasts from Mexico to Panama

Populations of the Calafia pearl oyster Pinctada mazatlanica ofthe American Pacific coasts have been considered endangeredbecause of overfishing and/or alteration to coastal areas. Weassessed genetic variability and the pattern of populationstructure among 9 samples collected from Mexico to Panama, usingmtDNA RFLP analysis of two genes: 12S rRNA and subunit one ofCytochrome oxydase (COI). Haplotype diversity varied from 0.000to 0.856. The Panama population appeared to be monomorphic, whilethe other samples exhibited a level of haplotypic variabilitysimilar to those reported in the literature for the same kind ofanalysis on other bivalves species. A test for the impact ofdemographic history on genetic diversity was applied on thesequence data, and the results were congruent with a recentdecline of population sizes. Genetic differentiation was shown tofollow a scheme of isolation by distance, with low levels ofdifferentiation at the scales of ten to one hundred kilometres,whereas stronger and significant genetic structure was detectedat a larger scale. Three significantly distinct groups could thenbe defined, which correspond to Northern Mexico, Southern Mexico,and Panama.     

An integrative approach to reveal speciation and species richness in the genus Diasporus (Amphibia: Anura: Eleutherodactylidae) in eastern Panama

We have applied an integrative taxonomic approach, including bioacoustics, ecology, morphology, and molecular genetics (barcoding and phylogeography), to explore species richness in the genus Diasporus in eastern Panama, from where only Diasporus quidditus (Lynch, 2001) was previously known. During fieldwork in eastern Panama in 2011 and 2012 we found six additional species, four of which we are describing here as new to science, plus two species that are new for this region. We have evaluated the presence of Diasporus diastema (Cope, 1875) in eastern Panama by comparing morphological, genetic, and bioacoustic characters of specimens from near the type locality in central Panama with specimens from eastern Panama. We further describe and compare male advertisement calls of most Diasporus species. The phylogeographic analysis suggests the allopatric speciation of Diasporus species in eastern Panama following the completion of the Panamanian isthmus in the middle Miocene. Subsequent geological events concur with the vicariant evolution of different lineages in situ, suggesting eastern Panama to be a centre of endemism for this group of frogs. We present an integrative analysis of the species from eastern Panama and include an identification key for all species of the genus.     

Isolation and characterization of microsatellite loci in the tropical tree Jacaranda copaia (Bignoniaceae)

We isolated 10 microsatellite loci for Jacaranda copaia for direct measurement of seed and pollen movement within the 50 ha Forest Dynamics Plot on Barro Colorado Island, Panama, and for studies of population genetic structure and gene flow across the Isthmus of Panama. Enriched repeat libraries were screened for microsatellite repeats and polymorphic primer pairs were developed. A total of 110 adult individuals were screened for allelic diversity and loci showed high levels of heterozygosity. These loci show both high maternal and paternal exclusion probabilities.     

Conservation of the Lake Kasumigaura population of Nymphoides indica (L.) Kuntze based on genetic evaluation using microsatellite markers

We compared the genetic diversity of the Lake Kasumigaura population of Nymphoides indica with that of pond populations in Hyogo and Kagawa Prefectures, which are thought to maintain high genetic diversity, to elucidate the current genetic diversity and occurrence of distinctive alleles in the Lake Kasumigaura population. The genetic diversity, as measured by the mean number of alleles per polymorphic locus, effective number of alleles per locus, mean observed heterozygosity, mean expected heterozygosities, total gene diversity, and number of multilocus genotypes was lower in the Lake Kasumigaura population than in the Hyogo and Kagawa populations. In addition, the inbreeding coefficient suggests that random mating does not occur in the Lake Kasumigaura population. The degree of genetic differentiation between the Lake Kasumigaura population and the Hyogo and Kagawa populations suggests that the Lake Kasumigaura population is largely genetically distinct. We found five genotypes in the Lake Kasumigaura population that were absent from the Hyogo and Kagawa populations. These results demonstrate that the Lake Kasumigaura population is an important component of the overall genetic diversity of N. indica in Japan.     

基于SSR标记探讨三种金花茶植物的遗传多样性和遗传结构

薄叶金花茶、小花金花茶和小瓣金花茶是三种濒危金花茶植物,为了解珍稀濒危植物遗传多样性和遗传结构,该研究利用微卫星标记对他们的7个种群共184个个体进行了遗传多样性和遗传结构分析。结果表明:11个位点共检测到等位基因92个。在物种水平上,小瓣金花茶平均等位基因数(N_A)为3.9、有效等位基因数(N_E)为2.328、观测杂合度(H_o)为0.520、期望杂合度(H_e)为0.501,高于薄叶金花茶和小花金花茶。在种群水平上,有效等位基因数(N_E)在1.788～2.466之间,期望杂合度(H_e)在0.379～0.543之间;种群间遗传分化系数(FST)在0.143 7～0.453 3之间,种群间基因流(N_m)在0.301 5～1.488 9之间。AMOVA分子变异分析显示65.72%的变异存在于种群内。三种金花茶具有较低水平的遗传多样性和高水平的种群间遗传分化。STRUCTURE和PCoA种群遗传结构分析结果将取样种群分为2组,即薄叶金花茶和小花金花茶大部分个体分为一组,小瓣金花茶大部分个体分为一组。现存所有种群应根据实际情况尽快采取就地保护或迁地保护措施。     

GENETIC CONSEQUENCES OF AUTOPOLYPLOIDY IN TOLMIEA (SAXIFRAGACEAE)

Although there is an extensive literature on the genetic attributes of allopolyploids, very little information is available regarding the genetic consequences of autopolyploidy in natural populations. We therefore addressed the major predicted genetic consequences of autopolyploidy using diploid and tetraploid populations of Tolmiea menziesii. Individual autotetraploid plants frequently maintain three or four alleles at single loci: 39% of the 678 tetraploid plants exhibited three or four alleles for at least one locus. Heterozygosity was also significantly higher in autotetraploid populations than in diploid populations: H_° = 0.070 and 0.237 in diploid and tetraploid Tolmiea, respectively. Most of the genetic diversity in T. menziesii is maintained within populations (ratio of gene diversity within populations to mean total genetic diversity = 0.636). The total genetic diversity due to differentiation between the two cytotypes is only 0.055. Such a low degree of differentiation between cytotypes would be expected between a diploid and its autotetraploid derivative. Most diploid and all tetraploid populations examined are in genetic equilibrium. Diploid and tetraploid Tolmiea share three or four alleles at six of eight polymorphic loci. This suggests that either autotetraploid Tolmiea was formed via crossing of genetically different diploids (perhaps via a triploid intermediate) or autopolyploidy occurred more than once in separate individual plants, followed by later crossing of autotetraploids.     

Unexpected high genetic diversity in small populations suggests maintenance by associative overdominance

The effective population size (N_e) is a central factor in determining maintenance of genetic variation. The neutral theory predicts that loss of variation depends on N_e, with less genetic drift in larger populations. We monitored genetic drift in 42 Drosophila melanogaster populations of different adult census population sizes (10, 50 or 500) using pooled RAD sequencing. In small populations, variation was lost at a substantially lower rate than expected. This observation was consistent across two ecological relevant thermal regimes, one stable and one with a stressful increase in temperature across generations. Estimated ratios between N_e and adult census size were consistently higher in small than in larger populations. The finding provides evidence for a slower than expected loss of genetic diversity and consequently a higher than expected long‐term evolutionary potential in small fragmented populations. More genetic diversity was retained in areas of low recombination, suggesting that associative overdominance, driven by disfavoured homozygosity of recessive deleterious alleles, is responsible for the maintenance of genetic diversity in smaller populations. Consistent with this hypothesis, the X‐chromosome, which is largely free of recessive deleterious alleles due to hemizygosity in males, fits neutral expectations even in small populations. Our experiments provide experimental answers to a range of unexpected patterns in natural populations, ranging from variable diversity on X‐chromosomes and autosomes to surprisingly high levels of nucleotide diversity in small populations.     

The Importance of Where to Dump the Refuse: Seed Banks and Fine Roots in Nests of the Leaf‐Cutting Ants Atta cephalotes and A. colombica1

The location of the nutrient‐rich organic refuse produced by a leaf‐cutting ant colony varies among ant species. Atta cephalotes locate their organic refuse in subterranean chambers, whereas A. colombica place their organic refuse on the soil surface near the nest. We studied the effect of the absence or presence of external organic refuse on the abundance of fine roots and seed bank composition in the superficial horizons of ant nests. We sampled soils from ant nests or dumps and adjacent areas of 15 adult nests of A. cephalotes at La Selva (LS), Costa Rica, and of 15 of A. colombica nests on Barro Colorado Island (BCI), Panama. Soils from A. cephalotes nests did not differ from adjacent soils in abundance of fine‐root and seed diversity. In contrast, organic refuse from A. colombica nests was less diverse in seed composition (due to the great abundance of Miconia argentea) and had a greater abundance of fine roots than adjacent areas. Thus the external location of the ant‐nest organic refuse is potentially important in determining the different types of plant recolonization in abandoned or dead ant nests. The relative abundance of these Atta species may influence the structure and/or composition of tropical forests.