Integrated analysis of three newly sequenced fern chloroplast genomes: Genome structure and comparative analysis

BackgroundSome ferns have medicinal properties and are used in therapeutic interventions. However, the classification and phylogenetic relationships of ferns remain incompletely reported. Considering that chloroplast genomes provide ideal information for species identification and evolution, in this study, three unpublished and one published ferns were sequenced and compared with other ferns to obtain comprehensive information on their classification and evolution.Materials and MethodsThe complete chloroplast genomes of Dryopteris goeringiana (Kunze) Koidz, D. crassirhizoma Nakai, Athyrium brevifrons Nakai ex Kitagawa, and Polystichum tripteron (Kunze) Presl were sequenced using the Illumina HiSeq 4,000 platform. Simple sequence repeats (SSRs), nucleotide diversity analysis, and RNA editing were investigated in all four species. Genome comparison and inverted repeats (IR) boundary expansion and contraction analyses were also performed. The relationships among the ferns were studied by phylogenetic analysis based on the whole chloroplast genomes.ResultsThe whole chloroplast genomes ranged from 148,539 to 151,341 bp in size and exhibited typical quadripartite structures. Ten highly variable loci with parsimony informative (Pi) values of > 0.02 were identified. A total of 75–108 SSRs were identified, and only six SSRs were present in all four ferns. The SSRs contained a higher number of A + T than G + C bases. C‐to‐U conversion was the most common type of RNA editing event. Genome comparison analysis revealed that single‐copy regions were more highly conserved than IR regions. IR boundary expansion and contraction varied among the four ferns. Phylogenetic analysis showed that species in the same genus tended to cluster together with and had relatively close relationships.ConclusionThe results provide valuable information on fern chloroplast genomes that will be useful to identify and classify ferns, and study their phylogenetic relationships and evolution.     

Habitat occupancy of sloth bear Melursus ursinus in Chitwan National Park,Nepal

Mammals have experienced a massive decline in their populations and geographic ranges worldwide. The sloth bear, Melursus ursinus (Shaw, 1791), is one of many species facing conservation threats. Despite being endangered in Nepal, decades of inattention to the situation have hindered their conservation and management. We assessed the distribution and patterns of habitat use by sloth bears in Chitwan National Park (CNP), Nepal. We conducted sign surveys from March to June, 2020, in 4 × 4 km grids (n = 45). We collected detection/non‐detection data along a 4‐km trail that was divided into 20 continuous segments of 200 m each. We obtained environmental, ecological, and anthropogenic covariates to understand determinants of sloth bear habitat occupancy. The data were analyzed using the single‐species single‐season occupancy method, with a spatially correlated detection. Using repeated observations, these models accounted for the imperfect detectability of the species to provide robust estimates of habitat occupancy. The model‐averaged occupancy estimate for the sloth bear was 69% and the detection probability was 0.25. The probability of habitat occupancy by sloth bears increased with the presence of termites and fruits and in rugged, dry, open, undisturbed habitats. Our results indicate that the sloth bear is elusive, functionally unique, and widespread in CNP. Future conservation interventions and action plans aimed at sloth bear management must adequately consider their habitat requirements.     

Dispersal,niche, and isolation processes jointly explain species turnover patterns of nonvolant small mammals in a large mountainous region of China

Understanding the mechanisms that govern the spatial patterns of species turnover (beta diversity) has been one of the fundamental issues in biogeography. Species turnover is generally recognized as strong in mountainous regions, but the way in which different processes (dispersal, niche, and isolation) have shaped the spatial turnover patterns in mountainous regions remains largely unexplored. Here, we explore the directional and elevational patterns of species turnover for nonvolant small mammals in the Hengduan Mountains of southwest China and distinguish the relative roles of geographic distance, environmental distance, and geographic isolation on the patterns. The spatial turnover was assessed using the halving distance (km), which was the geographic distance that halved the similarity (Jaccard similarity) from its initial value. The halving distance was calculated for the linear, logarithmic, and exponential regression models between Jaccard similarity and geographic distance. We found that the east–west turnover is generally faster than the south–north turnover for high‐latitudinal regions in the Hengduan Mountains and that this pattern corresponds to the geographic structure of the major mountain ranges and rivers that mainly extend in a south–north direction. There is an increasing trend of turnover toward the higher‐elevation zones. Most of the variation in the Jaccard similarity could be explained by the pure effect of geographic distance and the joint effects of geographic distance, environmental distance, and average elevation difference. Our study indicates that dispersal, niche, and isolation processes are all important determinants of the spatial turnover patterns of nonvolant small mammals in the Hengduan Mountains. The spatial configuration of the landscape and geographic isolation can strongly influence the rate of species turnover in mountainous regions at multiple spatial scales.     

Habitat heterogeneity,temperature, and primary productivity drive elevational gradients in avian species diversity

AimAnticipating and mitigating the impacts of climate change on species diversity in montane ecosystems requires a mechanistic understanding of drivers of current patterns of diversity. We documented the shape of elevational gradients in avian species richness in North America and tested a suite of a priori predictions for each of five mechanistic hypotheses to explain those patterns.LocationUnited StatesMethodsWe used predicted occupancy maps generated from species distribution models for each of 646 breeding birds to document elevational patterns in avian species richness across the six largest U.S. mountain ranges. We used spatially explicit biotic and abiotic data to test five mechanistic hypotheses proposed to explain geographic variation in species richness.ResultsElevational gradients in avian species richness followed a consistent pattern of low elevation plateau‐mid‐elevation peak (as per McCain, 2009). We found support for three of the five hypotheses to explain the underlying cause of this pattern: the habitat heterogeneity, temperature, and primary productivity hypotheses.Main ConclusionsSpecies richness typically decreases with elevation, but the primary cause and precise shape of the relationship remain topics of debate. We used a novel approach to study the richness‐elevation relationship and our results are unique in that they show a consistent relationship between species richness and elevation among 6 mountain ranges, and universal support for three hypotheses proposed to explain the underlying cause of the observed relationship. Taken together, these results suggest that elevational variation in food availability may be the ecological process that best explains elevational gradients in avian species richness in North America. Although much attention has focused on the role of abiotic factors, particularly temperature, in limiting species’ ranges, our results offer compelling evidence that other processes also influence (and may better explain) elevational gradients in species richness.     

The inventory of bryophytes at sites: completeness and survey effort

Abstract

Knowledge of the species present within a site is often used to inform decisions that have significant implications for biodiversity conservation. This study surveyed eight woodland sites in north-west England for bryophytes. Searches for species within each site continued until all areas had been approached to within a minimum of 50 m and at least 60 minutes had elapsed since the discovery of a new species. Survey data were used to build predictive models that provided an estimate of the total number of species present at each site and the time required to compile a complete inventory. The ‘50 m 60 minutes stopping rule’ consistently produced comprehensive inventories for sites, judging by the numbers of species found and model predictions of the total number of species present. The study suggests that a minor alteration to conventional survey practice and a small amount of data analysis can provide useful assessments of the completeness of bryophyte inventories for sites.     

Camera trap reveals the co‐occurrence patterns of two sympatric muntjac species in southern Anhui Province,China: No spatial segregation

The competitive relationship and coexistence pattern among close related species have long been one of the hot issues in ecological research. Interspecies interactions can exert important influences on the local distribution of rare species. Black muntjac Muntiacus crinifrons is an endemic species to eastern China, currently restricted to limited regions. In contrast, Chinese muntjac Muntiacus reevesi is the most common and widespread deer in southern China. Both species co‐occur in southern Anhui and western Zhejiang Province. Little is known about the interaction of these two sympatric‐related species. In this study, to investigate the site use determinants and co‐occurrence pattern of the two sympatric muntjac species, we conducted a camera trap survey across about 250 km² in mountainous area of southern Anhui Province, China. We adopted a multistep approach to incorporate habitat preferences while modeling occupancy and detection. We found that the two species did not separate along elevation gradient (range from 400 m to 1,400 m) as described in previous studies. Results of single‐species occupancy models indicated that elevation had positive effects on the site use of both species, while slope had an opposite influence on their site use. Positive effects of elevation on the site use implied that both species try to avoid human interference at low elevations. Significant negative effect of slope on the site use of black muntjac suggested that the species prefer habitat with gentle slope and avoided steep. Co‐occurrence models and species interaction factors provided evidence that the two muntjac species had an independent occupancy (ψ ^{BM CM} = ψ ^{BM cm}, SIF = 1) and exhibited a positive species interaction in detection probability (p ^BM < r ^{BM CM}). Combined with the results of previous studies, we suggested that it was fine differentiation in microhabitats and food resources utilization rather spatial or temporal segregation that allowed the two species co‐occurrence. The site use determinants revealed in our study would be useful for the habitat conservation and restoration for the rare black muntjac, and the co‐occurrence pattern of the two sympatric muntjac species could provide useful information for deep understanding of the coexistence mechanism among forest‐dwelling ungulates.     

A specialized new species of Ashicaulis (Osmundaceae,Filicales) from the Jurassic of Liaoning,NE China

A new species of structurally preserved fern rhizome, Ashicaulis plumites (Osmundaceae, Filicales), is described from the Middle Jurassic Tiaojishan Formation in western Liaoning Province, NE China. The new species is characterized by a peculiar sclerenchyma mass in the petiolar vascular bundle concavity. This sclerenchyma mass varies from a linear-shape to a mushroom-like shape with a remarkable outward protuberance, which distinguishes the present new species from other Ashicaulis species. Such a protuberance is very rare among osmundaceous ferns, and should represent a unique type for sclerenchymatous tissue in the osmundaceous vascular bundle concavity. Recognition of the peculiar structure of this new fossil species enriches anatomical diversity of permineralized osmundaceous ferns, indicating that the family Osmundaceae might have experienced a remarkable diversification during the Middle Jurassic in NE China. The new species show anatomical similarities to Osmunda pluma Miller from the Palaeocene of North America. The occurrence of A. plumites in the Middle Jurassic of China provides a new clue for understanding the evolution of some members of the living subgenus Osmunda.     

Calcicole–calcifuge plant strategies limit restoration potential in a regional semi‐arid flora

AimTo examine calcicole and calcifuge plant strategies, as well as nutrient‐acquisition strategies, as drivers of the distribution of species in response to edaphic factors, and the degree to which these strategies may act as filters to species establishment in ecological restoration on heavily altered or reconstructed substrates.LocationAn 82,000‐ha area within a major mining province in the Mid‐West region of Western Australia, harboring vegetation communities ranging from species‐poor halophytic scrub on saline flats to dense biodiverse shrubland on the skeletal soils of ancient Banded Ironstone Formations (BIF).MethodsUnivariate and multivariate analyses were employed to examine how variation in soil chemistry and landscape position (undulating plains, slopes, and BIF crests and ridges) influenced patterns of floristic diversity, calcifuge plant strategies, and nutrient‐acquisition strategies in 538 plant species from 830 relevés.ResultsLandscape position was the strongest driver of species richness and vegetation functional composition. Soils became increasingly acidic and P‐impoverished along an increasing elevational gradient. Vegetation from different landscape positions was not compositionally dissimilar, but vegetation of BIF crests and ridges was up to twice as biodiverse as vegetation from adjacent lower‐relief areas and harbored higher proportions of calcifuge species and species with mycorrhizal associations.Main conclusionsTopographic and edaphic complexity of BIF landforms in an otherwise relatively homogenous landscape has likely facilitated species accumulation over long time periods. They represent musea of regional floristic biodiversity, excluding only species that cannot establish or are inferior competitors in heavily weathered, acidic, skeletal, and nutrient‐impoverished soils. Plant strategies likely represent a major filter in establishing biodiverse, representative vegetation on postmining landforms in geologically ancient regions.     

Organization of the vascular system in the stems of Diplazium and Blechnum (Filicales)

Detailed analysis of the three-dimensional vascular organization in species of Diplazium and Blechnum indicates that these ferns possess reticulate (dictyostelic) vascular systems that closely reflect the helical phyllotaxis of the shoot. In each species, the vascular pattern shows a specific relationship to the phyllotaxis, so that the phyllotactic fraction can be determined by examination of the number of cauline vascular bundles (meristeles) in cross section of the stem. The number of meristeles in a cross section equals the denominator of the phyllotactic fraction, i.e., the number of foliar orthostichies on the stem. The same numerical relationship also exists in the eusteles of seed plants between the number of axial (sympodial) stem bundles and the phyllotaxis. There is a further parallel between the three-dimensional reticulate pattern of fern dictyosteles and the reticulate patterns that characterize some herbaceous dicotyledons. However, the hypothesized separate origins of seed plant eusteles and fern dictyosteles from protostelic precursors preclude any direct homologies between these similar patterns. The parallel evolution of presumably more physiologically efficient reticulate systems in herbaceous seed plants and in ferns that have only a primary plant body is noteworthy. The similar relationships between the primary stem vascular patterns and phyllotaxy in both ferns and seed plants further emphasize the likely similarity of the morphogenetic events that occur at the shoot apex in these taxonomically disparate groups.     

Geographic patterns of Lucanus (Coleoptera: Lucanidae) species diversity and environmental determinants in China

Clarifying the geographic patterns of species diversity and the determinant factors can provide essential information for species conservation and management. Stag beetles (Coleoptera: Lucanidae) of Lucanus are important saproxylic insects and can be used for biomonitoring forests. Most of Lucanus species are facing conservation concerns due to their limited distribution and fragmented habitats, particularly in China, which has the richest species diversity of this genus. The distribution patterns of species diversity of Lucanus at large spatial scales remain portly understood. We studied the distribution patterns of Lucanus and its environmental and geographic determinants in China. Distribution data for 72 species and subspecies were examined. All these species are distributed in southern China except for Lucanus maculifemoratus dybowskyi, which is mainly distributed in north China. The hotspot for Lucanus in China is southeastern Tibet. Our study indicated that the species richness of Lucanus in China was shaped by the precipitation of the wettest and driest month, net primary productivity, digital elevation model, and latitude at a large scale. These variables collectively explained 56.2% of the variation in species richness; precipitation contributed the most (44.1%). Our results provide valuable insights to improve the conservation of Lucanus and can contribute to furthering our understanding of the biogeography of stag beetles in China.

We describe the diversity of the stag beetle species and further explore its formation. The result indicated that the variables of geography vegetation, temperature, and precipitation collectively shaped the distributed pattern, and geographical variables are most important.     

GBIF information is not enough: national database improves the inventory completeness of Amazonian epiphytes

Distribution data sharing in global databases (e.g. GBIF) allowed the knowledge synthesis in several biodiversity areas. However, their Wallacean shortfalls still reduce our capacity to understand distribution patterns. Including exclusive records from other databases, such as national ones (e.g. SpeciesLink), could mitigate these shortfall problems, but it remains not evaluated. Therefore, we assessed whether (i) the inventory completeness, (ii) taxonomic contribution and (iii) spatial biases could be improved when integrating both global and national biodiversity databases. Using Amazonian epiphytes as a model, we compared the available taxonomic information spatially between GBIF and SpeciesLink databases using a species contribution index. We obtained the inventory completeness from sources using species accumulation curves and assessed their spatial biases by constructing spatial autoregressive models. We found that both databases have a high amount of exclusive records (GBIF: 36.7%; SpeciesLink: 21.7%) and species (17.8%). Amazonia had a small epiphyte inventory completeness, but it was improved when we analyzed both databases together. Individually, both database records were biased to sites with higher altitude, population and herbarium density. Together, river density appeared as a new predictor, probably due to the higher species contribution of SpeciesLink along them. Our findings provide strong evidence that using both global and national databases increase the overall biodiversity knowledge and reduce inventory gaps, but spatial biases may persist. Therefore, we highlight the importance of aggregating more than one database to understand biodiversity patterns, to address conservation decisions and direct shortfalls more efficiently in future studies.

     

How well documented is Australia's flora? Understanding spatial bias in vouchered plant specimens

Massive digitization of natural history collections (NHC) has opened the door for researchers to conduct inferential studies on the collection of biological diversity across space and time. The widespread use of NHCs in scientific research makes it essential to characterize potential sources of spatial bias. In this study, we assessed spatial patterns in records from the Australian Virtual Herbarium (AVH), based on >3 000 000 vouchered specimens of around 21 000 native plant species. The AVH is the main database for describing Australia's flora, and identifying its limitations is of paramount interest for the validity of conservation and environmental studies. We characterized how sampling effort is distributed across each Interim Bioregion of Australia (IBRA), then asked: (i) How complete are species inventories for each bioregion? We define completeness (C) as the ratio of observed to estimated species richness, using the Chao 1 estimator, (ii) How is sampling effort related to a commonly used Human Influence Index (HII)? and (iii) What is the probability that additional collections would result in the identification of previously unrecorded species in each bioregion? Sampling effort across bioregions is unequal, which partially reflects the collecting behaviour of naturalists in relation to species richness patterns. The density of records in bioregions ranges from 0.02–8.37 km^?2. At the bioregional scale, completeness is generally high with 79% of bioregions estimated to have records for at least 80% of their species. Completeness is partly explained by sampling effort (r = 0.43, p = 0.01), although some bioregions (e.g. Northern Kimberley and Burt Plain) have high completeness yet relatively low sampling effort. The inventory of Hampton, however, is substantially less complete than other bioregions (C = 0.66). Bioregions with high HII consistently have high completeness, while regions with low HII span the full range of completeness values. We calculated that an additional specimen collected from a bioregion has a 0.33% (Wet Tropics) to 11.7% (Arnhem Coast) probability of representing a new species for that region. Our assessment can assist with directing future systematic survey efforts by identifying bioregions where additional surveying may result in the greatest return, in terms of increasing knowledge of species richness and diversity.     

Reduced genetic diversity associated with the northern expansion of an amphibian species with high habitat specialization,Ascaphus truei,resolved using two types of genetic markers

Reconstruction of historical relationships between geographic regions within a species’ range can indicate dispersal patterns and help predict future responses to shifts in climate. Ascaphus truei (coastal tailed frog) is an indicator species of the health of forests and perennial streams in the Coastal and Cascade Mountains of the Pacific Northwest of North America. We used two genetic techniques—microsatellite and genotype‐by‐sequencing (GBS)—to compare the within‐region genetic diversity of populations near the northern extent of the species’ range (British Columbia, Canada) to two geographic regions in British Columbia and two in Washington, USA, moving toward the core of the range. Allelic richness and heterozygosity declined substantially as latitude increased. The northernmost region had the lowest mean expected heterozygosities for both techniques (microsatellite, M = 0.20, SE = 0.080; GBS, M = 0.025, SE = 0.0010) and the southernmost region had the highest (microsatellite, M = 0.88, SE = 0.054; GBS, M = 0.20, SE = 0.0029). The northernmost regions (NC and MC) clustered together in population structure models for both genetic techniques. Our discovery of reduced diversity may have important conservation and management implications for population connectivity and the response of A. truei to climate change.     

Ferns and Melastomataceae as indicators of vascular plant composition in rain forests of Colombian Amazonia

In a case-study from Colombian Amazonia, species information from ferns and Melastomataceae was used to explain the compositional patterns of other vascular plant species in 40 widely distributed 0.1-ha plots. Canonical correspondence analysis was applied to regress vascular plant species composition in the forests against information from these two indicator groups (summarized as axes of principal coordinate analyses), together with that from soils, landscape, and the spatial sampling design. In total, 53,941 individuals of 2480 vascular plant species were recorded. Of these, 17,473 individuals and 132 species were from ferns and Melastomataceae. In 19 well-drained upland (tierra firme) plots 19,622 vascular plant individuals and 1716 species were found, with 3793 plants and 91 species from ferns and Melastomataceae. In both the set of all landscapes and the subset of tierra firme forests the principal PCoA axes of the two indicator groups were highly related to the main patterns of forest species composition. In principle, therefore, ferns and Melastomataceae can be used to detect and forecast changes in the forest composition of the study area. However, evidence was not obtained that ferns and Melastomataceae show more potential to predict the main patterns in species composition of forests than soil, landscape, and spatial variables. The partioning of the total variation in forest composition showed that the correlation of ferns and Melastomataceae with other forest plants was quite independent from that of soil, landscape, and space. Direct effects of ferns and Melastomataceae on other plants might be obtained from experimental studies of between-plant interactions, concentrating on the seedling or juvenile stages of trees and lianas, both above-ground as well as in the rooting environment.     

Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections

BackgroundHigh rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage.Conclusions/SignificanceThis study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.     

Spatial patterns in the size of Chinese lizards are driven by multiple factors

BackgroundFor almost two centuries, ecologists have examined geographical patterns in the evolution of body size and the associated determinants. During that time, one of the most common patterns to have emerged is the increase in body size with increasing latitude (referred to as Bergmann''s rule). Typically, this pattern is explained in terms of an evolutionary response that serves to minimize heat loss in colder climates, mostly in endotherms. In contrast, however, this rule rarely explains geographical patterns in the evolution of body size among ectotherms (e.g., reptiles).LocationChina.AimIn this study, we assembled a dataset comprising the maximum sizes of 211 lizard species in China and examined the geographical patterns in body size evolution and its determinants. Specifically, we assessed the relationship between body size and climate among all lizard species and within four major groups at both assemblage and interspecific levels.ResultsAlthough we found that the body size of Chinese lizards was larger in warmer regions, we established that at the assemblage level, size was correlated with multiple climatic factors, and that body size–climate correlations differed within the four major groups. Phylogenetic analysis at the species level revealed that no single climatic factor was associated with body size, with the exception of agamids, for which size was found to be positively correlated with temperature.Main conclusionsGeographical patterns in Chinese lizard body size are driven by multiple factors, and overall patterns are probably influenced by those of the major groups. We suggest that our analyses at two different levels may have contributed to the inconsistent results obtained in this study. Further studies investigating the effects of altitude and ecological factors are needed to gain a more comprehensive understanding of the evolution of ectotherm body size.     

Variation in distribution and abundance of the endemic flora of Juan Fernández Islands, Chile. Pteridophyta

The Juan Fernández Archipelago is located 667 km west of central Chile (33°S) in the Pacific Ocean. It is composed of three islands: Robinson Crusoe (ex-Masatierra), Santa Clara and Marinero Alejandro Selkirk (ex-Masafuera).The first botanical collections were made 250 years after its discovery and colonization. These studies showed the great importance of ferns in the vascular flora of the islands. Of the 53 species described up to the present, 23 are endemic (45%), with one endemic monotypic genus, Thyrsopteris, whose only species is T. elegans Kunze (Dicksoniaceae).During a period of 4 years, I have studied the flora of the islands. There has been surprisingly little change in the distribution of the ferns, considering the devastation of the angiosperm flora. Some species have even increased their abundance, especially the tree ferns. Nevertheless, the more delicate species and those with a more restricted habitat have been reduced in abundance.Ten of the endemic species (43%) are in danger of extinction, such as Asplenium macrosorum and Ophioglossum fernandezianum, four are vulnerable (17%), including Blechnum schottii and Polypodium intermedium, and nine (40%), including Pteris berteroana and Blechnum cycadifolium are not endangered.