Tropical deforestation is a progressive process resulting in the conversion of rain forest into a mosaic of mature forest fragments, pasture, and degraded habitat. Understanding the long-term effects ...of habitat fragmentation on tropical plant community structure is critical to predicting how alterations to the landscape will impact tropical biodiversity. The objective of this study was to examine fragmentation effects on the composition, abundance, and species richness of epiphyllous (leaf-inhabiting) bryophytes. I conducted this research in an experimentally fragmented forest reserve in central Amazonia where data on the distribution and abundance of 65 bryophyte taxa were analyzed from 16 1-ha sample plots located in continuous forest and fragments. Epiphyll communities inhabiting small (1- and 10-ha) fragments exhibited lower species richness, abundance, and among-site compositional variation than those from 100-ha fragments and continuous forest plots. Reduced epiphyll diversity in small fragments is not simply a statistical artifact of low epiphyll densities, but rather due to a disproportionate loss of regionally common taxa. In contrast, rare taxa responded marginally to fragmentation, and in most cases were more abundant in fragments than in continuous forest habitat. Because epiphyllous bryophytes rapidly establish species-rich communities on spatially discrete habitat patches, they are an ideal plant group for addressing the long-term (multigeneration) impact of habitat fragmentation on plant communities.
In the past decade, floristic studies have rebounded as checklists are fundamental for executing meta-analyses which address ecological, biogeographic and evolutionary questions of broad geographic ...scope. Despite the importance of checklists as baseline records of local diversity and distributions, few attempts have been made to quantify sampling effort and species detectability within and among study sites. Quantitative floristics, which combines the use of checklists with statistical methods for estimating local richness, is a promising method for characterizing the completeness of checklists especially for cryptic components of biodiversity. For bryophytes, quantifying levels of detectability among substrate types is of central importance, especially in tropical forests where much of their diversity is harbored in difficult to access habitats such as the tree canopy. In light of the need to establish quantifiable protocols of detectability in poorly studied tropical regions, we present a bryophyte checklist for the Jaú National Park (JNP), located in the heart of the Amazon, and estimate local species richness and detectability as it relates to five substrate types (epiphytes, epiphylls, epixylic, epipetric and soil). Identifications from 712 collections made during four excursions over the past decade to JNP revealed 150 species consisting of two new country records and five new state records, along with 20 rarely collected Amazonian endemics. Despite our intensive sampling, which included systematic canopy collections during one of the excursions, Chao richness index estimated that ca. 46 species (nearly one-third of those presently observed) remain undetected from JNP. Furthermore, levels of detectability among substrates varied widely, where observed epiphyte richness, in contrast to the other substrates types, most closely approximated the estimates. Our results illustrate the need for quantitative richness estimates as a means to increase the accuracy of checklist data, particularly when used in meta-analyses addressing global-scale questions.
In theory, habitat fragmentation alters plant community dynamics by influencing both local (within patch) and regional (among patch) processes. However, the lengthy generation times of plant taxa ...relative to the short duration of most experiments has precluded studies from assessing the impact of fragmentation at both local and regional scales. Due to their accelerated life cycles, high rates of local extinction, and naturally patchy substrates, epiphyllous bryophyte assemblages are an appropriate plant guild for empirically testing metacommunity-based predictions associated with habitat fragmentation. By examining the local abundance and regional distribution patterns of 67 epiphyllous (leaf-inhabiting) bryophyte species in an experimentally fragmented landscape in Amazonia, we demonstrate that changes in local abundance wrought by habitat fragmentation are best explained by fragment size rather than proximity to forest edge. Furthermore, evidence of a simultaneous inter-specific decline in epiphyll local abundance and regional distribution in small (1- and 10-ha) forest fragments corroborate with metapopulation-based predictions highlighting the importance of immigration in buffering from patch extinction risk (i.e., the rescue effect). Collectively, these results provide indirect evidence that dispersal limitation, rather than compromised habitat quality attributable to edge effects, likely account for species loss from small tropical forest fragments. Whether dispersal limitation is due to increased insularity from regional sources for epiphyll recolonization or rather to lowered within-fragment dispersal potential is unknown; nonetheless, the long-term persistence of these microscopic plant metacommunities depends on the preservation of rain forest reserves of at least 100-ha in size.
We synthesize findings to date from the world’s largest and longest-running experimental study of habitat fragmentation, located in central Amazonia. Over the past 32
years, Amazonian forest ...fragments ranging from 1 to 100
ha have experienced a wide array of ecological changes. Edge effects have been a dominant driver of fragment dynamics, strongly affecting forest microclimate, tree mortality, carbon storage, fauna, and other aspects of fragment ecology. However, edge-effect intensity varies markedly in space and time, and is influenced by factors such as edge age, the number of nearby edges, and the adjoining matrix of modified vegetation surrounding fragments. In our study area, the matrix has changed markedly over the course of the study (evolving from large cattle pastures to mosaics of abandoned pasture and regrowth forest) and this in turn has strongly influenced fragment dynamics and faunal persistence. Rare weather events, especially windstorms and droughts, have further altered fragment ecology. In general, populations and communities of species in fragments are hyperdynamic relative to nearby intact forest. Some edge and fragment-isolation effects have declined with a partial recovery of secondary forests around fragments, but other changes, such as altered patterns of tree recruitment, are ongoing. Fragments are highly sensitive to external vicissitudes, and even small changes in local land-management practices may drive fragmented ecosystems in markedly different directions. The effects of fragmentation are likely to interact synergistically with other anthropogenic threats such as logging, hunting, and especially fire, creating an even greater peril for the Amazonian biota.
Although habitat fragmentation is a major threat to global biodiversity, the demographic mechanisms underlying species loss from tropical forest remnants remain largely unexplored. In particular, no ...studies at the landscape scale have quantified fragmentation’s impacts on colonization, extinction, and local population growth simultaneously. In central Amazonia, we conducted a multiyear demographic census of 292 populations of two leaf‐inhabiting (i.e., epiphyllous) bryophyte species transplanted from continuous forest into a network of 10 study sites ranging from 1, 10, and 100 to >10,000 ha in size. All populations experienced significantly positive local growth (
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) and a nearly constant per‐generational extinction probability (15%). However, experimental leaf patches in reserves of ≥100 ha experienced nearly double (48%) the colonization probability observed in small reserves (27%), suggesting that the proximate cause of epiphyll species loss in small fragments (≤10 ha) is reduced colonization. Nonetheless, populations of small fragments exhibit rates of colonization above patch extinction, positive local growth, and low temporal variation, which are features that should theoretically reduce the probability of extinction. This result suggests that for habitat‐tracking metapopulations subject to frequent and stochastic turnover events, including epiphylls, colonization/extinction ratios must be maintained well above unity to ensure metapopulation persistence.
Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher ...data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.
Amazonian forests are extraordinarily diverse, but the estimated species richness is very much debated. Here, we apply an ensemble of parametric estimators and a novel technique that includes ...conspecific spatial aggregation to an extended database of forest plots with up-to-date taxonomy. We show that the species abundance distribution of Amazonia is best approximated by a logseries with aggregated individuals, where aggregation increases with rarity. By averaging several methods to estimate total richness, we confirm that over 15,000 tree species are expected to occur in Amazonia. We also show that using ten times the number of plots would result in an increase to just ~50% of those 15,000 estimated species. To get a more complete sample of all tree species, rigorous field campaigns may be needed but the number of trees in Amazonia will remain an estimate for years to come.
Summary
Nitrogen‐fixing symbiosis is globally important in ecosystem functioning and agriculture, yet the evolutionary history of nodulation remains the focus of considerable debate. Recent evidence ...suggesting a single origin of nodulation followed by massive parallel evolutionary losses raises questions about why a few lineages in the N2‐fixing clade retained nodulation and diversified as stable nodulators, while most did not. Within legumes, nodulation is restricted to the two most diverse subfamilies, Papilionoideae and Caesalpinioideae, which show stable retention of nodulation across their core clades.
We characterize two nodule anatomy types across 128 species in 56 of the 152 genera of the legume subfamily Caesalpinioideae: fixation thread nodules (FTs), where nitrogen‐fixing bacteroids are retained within the apoplast in modified infection threads, and symbiosomes, where rhizobia are symplastically internalized in the host cell cytoplasm within membrane‐bound symbiosomes (SYMs).
Using a robust phylogenomic tree based on 997 genes from 147 Caesalpinioideae genera, we show that losses of nodulation are more prevalent in lineages with FTs than those with SYMs.
We propose that evolution of the symbiosome allows for a more intimate and enduring symbiosis through tighter compartmentalization of their rhizobial microsymbionts, resulting in greater evolutionary stability of nodulation across this species‐rich pantropical legume clade.
Premise
Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and ...mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear.
Methods
Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations.
Results
The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more and propose 10 new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene‐tree topology.
Conclusions
We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.
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