Oligo-barcode illuminates holocentric karyotype evolution in Rhynchospora (Cyperaceae).

Holocentric karyotypes are assumed to rapidly evolve through chromosome fusions and fissions due to the diffuse nature of their centromeres. Here, we took advantage of the recent availability of a chromosome-scale reference genome for Rhynchospora breviuscula, a model species of this holocentric genus, and developed the first set of oligo-based barcode probes for a holocentric plant. These probes were applied to 13 additional species of the genus, aiming to investigate the evolutionary dynamics driving the karyotype evolution in Rhynchospora. The two sets of probes were composed of 27,392 (green) and 23,968 (magenta) oligonucleotides (45-nt long), and generated 15 distinct FISH signals as a unique barcode pattern for the identification of all five chromosome pairs of the R. breviuscula karyotype. Oligo-FISH comparative analyzes revealed different types of rearrangements, such as fusions, fissions, putative inversions and translocations, as well as genomic duplications among the analyzed species. Two rounds of whole genome duplication (WGD) were demonstrated in R. pubera, but both analyzed accessions differed in the complex chain of events that gave rise to its large, structurally diploidized karyotypes with 2n = 10 or 12. Considering the phylogenetic relationships and divergence time of the species, the specificity and synteny of the probes were maintained up to species with a divergence time of ~25 My. However, karyotype divergence in more distant species hindered chromosome mapping and the inference of specific events. This barcoding system is a powerful tool to study chromosomal variations and genomic evolution in holocentric chromosomes of Rhynchospora species.

Direct links between resource availability and activity budget better reveal ecological patterns of endangered Coimbra-Filho's titi monkey.

Many primatological studies do not assess direct indexes of food availability to make inferences about behavioral strategies. We related the diet and behavior of a group of Callicebus coimbrai in northeastern Brazil to fruit availability indexes and compared this pattern between seasons (direct and indirect assessment of food availability) to assess whether direct and indirect approaches detect similar ecological patterns. We monitored the study group for 33 months (5 days/month) via scan sampling. The monthly availability of fruits and new leaves was recorded in phenological transects. Fruit availability varied across years based on fruit prevalence, and timing and duration of the abundant seasons. We did not find evidence of a time-minimizing strategy, since C. coimbrai did not change its activity levels according to food availability. However, the negative relationship between foraging and fruit availability indicates that C. coimbrai can compensate for the lower fruit availability by increasing the search for alternative food sources. Monthly fruit consumption was positively correlated to fruit availability and negatively related to the consumption of other food items. However, the behavioral and feeding profiles did not vary between seasons and were not related to rainfall levels. Primate studies should directly relate behavioral and feeding profiles to fruit availability indices, thus avoiding using seasons as proxies of food availability.

Chromosome size matters: genome evolution in the cyperid clade.

BACKGROUND AND AIMS: While variation in genome size and chromosome numbers and their consequences are often investigated in plants, the biological relevance of variation in chromosome size remains poorly known. Here, we examine genome and mean chromosome size in the cyperid clade (families Cyperaceae, Juncaceae and Thurniaceae), which is the largest vascular plant lineage with predominantly holocentric chromosomes. METHODS: We measured genome size in 436 species of cyperids using flow cytometry, and augment these data with previously published datasets. We then separately compared genome and mean chromosome sizes (2C/2n) amongst the major lineages of cyperids and analysed how these two genomic traits are associated with various environmental factors using phylogenetically informed methods. KEY RESULTS: We show that cyperids have the smallest mean chromosome sizes recorded in seed plants, with a large divergence between the smallest and largest values. We found that cyperid species with smaller chromosomes have larger geographical distributions and that there is a strong inverse association between mean chromosome size and number across this lineage. CONCLUSIONS: The distinct patterns in genome size and mean chromosome size across the cyperids might be explained by holokinetic drive. The numerous small chromosomes might function to increase genetic diversity in this lineage where crossovers are limited during meiosis.

Mixed pollination system and floral signals of Paepalanthus (Eriocaulaceae): insects and geitonogamy ensure high reproductive success.

BACKGROUND AND AIMS: Eriocaulaceae exhibit a great variety of floral traits associated with insect (e.g. nectariferous structures) and wind pollination (unisexual flowers, exposed sexual organs and small pollen grains), as well as the 'selfing syndrome' (small flowers, short distance between stigma and anthers, and temporal overlap of male and female phases). Paepalanthus bifidus, P. subtilis and P. tortilis are related species that differ in form, size and colour of floral structures. We aimed to investigate the pollination and reproductive biology of these three species. METHODS: We analysed the floral biology, floral visitors, pollinator behaviour, and the contribution of insects, wind and spontaneous geitonogamy to fruit set. We also evaluated the floral colour and scent of the species. Colour reflectance of capitula of each species was measured and plotted in models of insect vision. Floral scent samples were extracted and the compounds were compared to vegetative scent samples. KEY RESULTS: In all species, the staminate and pistillate flowers are arranged in alternating cycles with a temporal overlap between these phases. Ants were the most frequent floral visitors and were effective pollinators in P. bifidus and P. tortilis, while flies were occasional pollinators in P. tortilis. Floral visitors were not observed in P. subtilis. In all species, fruits were produced by spontaneous geitonogamy, with no evidence of wind pollination. According to the models of insect vision, the colours of the capitula of P. bifidus and P. subtilis are the most inconspicuous for ants and flies. We found no difference between the emission of volatiles of inflorescences and vegetative structures. CONCLUSIONS: This study suggests that ant pollination might be more widespread in Eriocaulaceae than currently assumed. Furthermore, for small monocarpic plants, mixed mating strategies are most favourable, by ensuring reproduction either by outcrossing when pollinators are abundant or by spontaneous geitonogamy when pollinations are scarce/absent.

Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA.

BACKGROUND AND AIMS: With the advance of high-throughput sequencing, reduced-representation methods such as target capture sequencing (TCS) emerged as cost-efficient ways of gathering genomic information, particularly from coding regions. As the off-target reads from such sequencing are expected to be similar to genome skimming (GS), we assessed the quality of repeat characterization in plant genomes using these data. METHODS: Repeat composition obtained from TCS datasets of five Rhynchospora (Cyperaceae) species were compared with GS data from the same taxa. In addition, a FISH probe was designed based on the most abundant satellite found in the TCS dataset of Rhynchospora cephalotes. Finally, repeat-based phylogenies of the five Rhynchospora species were constructed based on the GS and TCS datasets and the topologies were compared with a gene-alignment-based phylogenetic tree. KEY RESULTS: All the major repetitive DNA families were identified in TCS, including repeats that showed abundances as low as 0.01 % in the GS data. Rank correlations between GS and TCS repeat abundances were moderately high (r = 0.58-0.85), increasing after filtering out the targeted loci from the raw TCS reads (r = 0.66-0.92). Repeat data obtained by TCS were also reliable in developing a cytogenetic probe of a new variant of the holocentromeric satellite Tyba. Repeat-based phylogenies from TCS data were congruent with those obtained from GS data and the gene-alignment tree. CONCLUSIONS: Our results show that off-target TCS reads can be recycled to identify repeats for cyto- and phylogenomic investigations. Given the growing availability of TCS reads, driven by global phylogenomic projects, our strategy represents a way to recycle genomic data and contribute to a better characterization of plant biodiversity.

Successional, spatial, and seasonal changes in seed rain in the Atlantic forest of southern Bahia, Brazil.

Seed arrival is a limiting factor for the regeneration of diverse tropical forests and may be an important mechanism that drives patterns of tree species' distribution. Here we quantify spatial and seasonal variation in seed rain of secondary forests in southern Bahia, Brazil. We also examine whether secondary forest age enhances seed dispersal and whether seed rain density and diversity in secondary forests decay with distance from mature forest. Across a chronosequence of 15 pairs of mature and secondary forests, 105 seed traps were installed and monitored for one year. We tested the effects of secondary forest age, distance from mature forest, and seasonality on monthly seed rain density, diversity, seed dispersal mode, and diaspore size. We found that secondary forest age had strong, positive effects on the diversity of seed rain, which was generally higher during the wet season. Moreover, contrasting patterns among diversity indices revealed that seeds of rare species occurred more often in 40 yr old secondary forests and mature forests. While the proportion of biotically and abiotically dispersed seeds did not change significantly with distance from mature forest across all forest age classes, we found that biotically dispersed seeds contributed disproportionately more to seed rain diversity. Our results emphasize the importance of biotic dispersal to enhance diversity during secondary succession and suggest that changes in secondary forest structure have the potential to enhance the diversity of tropical secondary forests, principally by increasing dispersal of rare species.

Testing the monophyly of Simaba (Simaroubaceae): Evidence from five molecular regions and morphology.

Generic circumscriptions in the mostly pantropical family Simaroubaceae are somewhat controversial. Simaba is the largest genus, currently defined as exclusively neotropical, with around 25 species of trees and shrubs, but both its limits and infrageneric classification have been a matter of discussion and divergence. Traditionally, species of the genus have been treated in three sections: Simaba sect. Tenuiflorae, S. sect. Floribundae and S. sect. Grandiflorae, but a phylogenetic analysis suggested that the latter two may not be monophyletic. To test the monophyly of Simaba and its infrageneric classification, we used a molecular approach based on DNA sequence data from two nuclear ribosomal spacer regions (ITS and ETS) and three plastid regions (rps16 intron, and intergenic spacers psbA-trnH and trnL-trnF), including a comprehensive sampling of species from Simaba and closely related genera. We also performed ancestral character reconstructions to identify morphological characters that could serve as synapomorphies for major clades and to explore patterns of homoplasy in the morphological dataset. Our results show Simaba as traditionally circumscribed is not monophyletic, with taxa segregated into two strongly supported but distinct clades, one of which is more closely related to Simarouba. The three main clades that emerged in the phylogeny include a mostly Amazonian Simaba clade (which includes the type species of Simaba and the remaining species of S. sect. Tenuiflorae, here proposed to be recognized as Simaba sensu stricto), a mostly extra-Amazonian Simaba clade (a distinct lineage that will be recognized as Homalolepis, a genus currently treated in synonymy and equivalent to Simaba sections Grandiflorae and Floribundae), and the Simarouba clade (including all of its current species). These three clades are characterized by a combination of morphological characters, described in detail herein, some of which are novel features for Simaba not previously reported in the literature. Mapping character-states on the phylogenetic tree provides tests for evolutionary hypotheses. For example, our reconstruction of habit and geographic distribution suggests that the diversification of several shrubby species within the extra-Amazonian lineage in the South American cerrados probably occurred from ancestors inhabiting tropical forests, involving transitions in morphological and ecological traits.

Angiospermas em remanescentes de floresta montana no sul da Bahia, Brasil / Angiosperms of Montane Forest areas in southern Bahia, Brazil

Foi realizado um levantamento florístico de três remanescentes de floresta montana localizados na Mata Atlântica do sul da Bahia. Durante os anos de 2004 a 2008 foram feitas coletas periódicas de material botânico, principalmente ao longo de trilhas no interior dos fragmentos das áreas: Reserva Serra da Pedra Lascada - SPL, Reserva Serra das Lontras - SLO e Reserva Particular do Patrimônio Natural Serra Bonita - SBO. A riqueza florística em cada área foi comparada entre si e com outras áreas de Mata Atlântica na Bahia e no Sudeste do Brasil. Foi registrado um total de 1.129 espécies em 467 gêneros e 124 famílias. O hábito arbóreo representou 46,9 por cento das espécies, seguido de herbáceas (20,1 por cento), epífitas (19,5 por cento) e trepadeiras (13,5 por cento). As famílias Araceae, Asteraceae, Bromeliaceae, Fabaceae, Lauraceae, Melastomataceae, Myrtaceae, Orchidaceae, Piperaceae, Poaceae, Rubiaceae e Solanaceae apresentaram a maior riqueza florística nas três áreas em conjunto. O gênero Psychotria (Rubiaceae) apresentou o maior número de espécies em todas as áreas (21 spp.), destacando-se também Miconia (20 spp.), Solanum (20 spp.), Piper (19 spp.), Ocotea (16 spp.), Leandra (16 spp.), Peperomia (15 spp.) e Myrcia (14 spp.). Os resultados confirmam a elevada riqueza de angiospermas no sul da Bahia e evidenciam, pela primeira vez, a ocorrência de espécies características de regiões montanhosas da Mata Atlântica do Sudeste do Brasil nessa região.

A floristic study of three areas of montane Atlantic forest in southern Bahia, Brazil, was carried out. From 2004 to 2008 regular botanical collections were made, principally along trails in the interior of the forest fragments at: the Reserva Serra da Pedra Lascada (SPL), the Reserva Serra das Lontras (SLO) and the Reserva Particular do Patrimônio Natural Serra Bonita (SBO). The species richness of each area was compared to that of the other two, and together to other areas of Atlantic coastal forest in Bahia and southeastern Brazil. For all three areas, a total of 1129 species in 467 genera and 124 families were found. Trees represented 46.9 percent of the species, followed by herbs (20.1 percent), epiphytes (19.5 percent), and vines and lianas (13.5 percent). The families Araceae, Asteraceae, Bromeliaceae, Fabaceae, Lauraceae, Melastomataceae, Myrtaceae, Orchidaceae, Piperaceae, Poaceae, Rubiaceae, and Solanaceae showed the highest species richness for the three areas together. The genus Psychotria (Rubiaceae) had the highest number of species for all three areas (21 spp.), followed by Miconia (20 spp.), Solanum (20 spp.), Piper (19 spp.), Ocotea (16 spp.), Leandra (16 spp.), Peperomia (15 spp.), and Myrcia (14 spp.). The results confirm the high species diversity of angiosperms in southern Bahia and demonstrate for the first time the presence of species characteristic of montane regions of southeastern Brazil in this region.