Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic data in population viability analysis: case studies with ambystomatid salamanders

Parameterization of population viability models is a complicated task for most types of animals, as knowledge of population demography, abundance and connectivity can be incomplete or unattainable. Here I illustrate several ways in which genetic data can be used to inform population viability analysis, via the parameterization of both initial abundance and dispersal matrices. As case studies, I use three ambysomatid salamander datasets to address the following question: how do population viability predictions change when dispersal estimates are based on genetic assignment test data versus a general dispersal–distance function? Model results showed that no local population was large enough to ensure long‐term persistence in the absence of immigration, suggesting a metapopulation structure. Models parameterized with a dispersal–distance function resulted in much more optimistic predictions than those incorporating genetic data in the dispersal estimates. Under the dispersal–distance function scenario all local populations persisted; however, using genetic assignments to infer dispersal revealed local populations at risk of extinction. Viability estimates based on dispersal–distance functions should be interpreted with caution, especially in heterogeneous landscapes. In these situations I promote the idea of model parameterization using genetic assignment tests for a more accurate portrayal of real‐world dispersal patterns.
Does tree size influence timing of flowering in Cerberiopsis candelabra (Apocynaceae), a long-lived monocarpic rain-forest tree?

Cerberiopsis candelabra is a long-lived monocarpic rain-forest tree endemic to New Caledonia that shows mass flowering across a substantial proportion of a population, and across a substantial number of populations. We investigated the relationship between tree size and flowering (and subsequent dying) across 18 populations from the flowering event of 2003 in order to understand the role of possible size thresholds for flowering in the life history and regeneration ecology of this monocarpic species. There was a strong positive correlation between trunk diameter and the incidence of flowering when population data were combined. However, the relationship between size and flowering was complex in that flowering occurred across a wide range of tree sizes, with almost complete overlap in size between flowering (5–79 cm dbh) and non-flowering trees (5–64 cm dbh), and with large trees in both the flowering and non-flowering state in the same population. In about half the populations studied there was no significant difference in mean trunk diameter of flowering and non-flowering trees. Nonetheless, we suggest that tree size may play a fundamental role in the life history and regeneration ecology of this species. The seedlings appear to be relatively shade-intolerant and dependent on large canopy gaps for recruitment. A significant effect of mass flowering and subsequent death of multiple large trees is the potential to form large canopy gaps and enhance seedling survival, as the gap is temporally linked with seed germination. However, it is unclear why there is such a large size range of flowering trees, i.e. whether this is just a consequence of the proximate cue, or whether the optimal size for flowering does indeed vary among individuals.
The evolution of song structure in southern African birds: an assessment of the acoustic adaptation hypothesis

Song is critical to territory defence, mate attraction, and both species and individual recognition. According to the Acoustic Adaptation Hypothesis (AAH), habitat structure may exercise a selective force on vocal evolution such that song evolves to minimise the degradation and attenuation of acoustic signals in the particular habitat in which a species has evolved. We conducted a comparative survey of the songs of 40 South African passerine species to test the generality of the AAH. We compared pairs of congenerics, one from closed and one from grassland habitats, for seven different song attributes, including frequency, bandwidth, structure and temporal parameters. We controlled for phylogenetic effects by assessing differences between pairs of related individuals. The survey did not support the predictions of the AAH.
Reproductive biology of racer goby Neogobius gymnotrachelus in the Włocławski Reservoir (Vistula River, Poland)

Summary Initial studies on the reproductive parameters and spawning behaviour of racer goby Neogobius gymnotrachelus, one of three Ponto-Caspian gobiid species recently invading Polish waters, were carried out in Wloclawski Reservoir (lower River Vistula, Poland), where spawning lasted from April to August. Males were on average about 23.3% longer and 53.8% heavier than females. The smallest female with mature gonads was 58 mm TL (estimated age 2+ years), and males were sexually mature at 59 mm TL (age of 1+ years). Gonado-somatic index at the beginning of spawning was seven times larger in females (mean = 8.4) than that in males (mean = 1.2). Mean absolute fecundity was 952 eggs per female (361–2236). Egg diameter ranged from 0.140 to 1.558 mm, being of bi-modal distribution, which suggests two or three spawning bouts. Length–frequency analysis of juveniles revealed a multimodal distribution. Specialized reproductive behaviour (nest construction and parental care of eggs) and an extended spawning period increase the probability that racer goby can successfully establish self-sustaining populations in novel environments.
The effect of hypochlorite on spores of Bacillus subtilis lacking small acid‐soluble proteins

M.Z. H. SABLI, P. SETLOW AND W.M. WAITES. 1996. α/β‐Type small acid‐soluble proteins (SASP) bind to spore DNA and protect it against ultraviolet light, heat, hydrogen peroxide and freeze drying, making the spores much more resistant than vegetative cells to these agents. Spores of a mutant of Bacillus subtilis lacking the two major α/β‐type SASP were almost 30 000‐fold less resistant to hypochlorite than were wild‐type spores. After treatment with hypochlorite, surviving spores of the mutant, but not those of the wild type, showed higher levels of mutation, suggesting that SASP contribute to hypochlorite resistance by protecting spore DNA.
Variations and Trade‐offs in Functional Traits of Tree Seedlings during Secondary Succession in a Tropical Lowland Rain Forest

The seedling stage is generally the most important bottleneck for the successful regeneration of trees in forests. The traits of seedlings, particularly biomass allocation and root traits, are more easily quantified than the traits of adults. In this study, we tested the hypothesis that seedling traits vary and trade‐off tracking the changing environment during secondary succession. We measured the major morphological traits of 27 dominant species and the major environmental factors in a chronosequence (30‐yr‐old fallow, 60‐yr‐old fallow, and old growth forest) after shifting cultivation in a tropical lowland rain forest on Hainan Island, China. The 30‐yr‐old fallow had higher light and nutrient availability, and the older forests had higher soil water content. Redundancy analysis based on species abundance and environmental factors revealed groups of seedlings that dominate in different stages of succession. Seedlings in different stages of succession had different strategies of biomass allocation for harvesting resources that varied in availability. Species characteristic of younger forest had higher allocation to roots and higher specific leaf area, while species characteristic of older forest had higher allocation to leaves. Our study suggests that the variations and trade‐offs in the major functional traits of tree seedlings among successional classes may reflect changes in environmental conditions during succession.
Growth and survival of selected aquatic animals in two saline groundwater evaporation basins: an Australian case study

Evaluation trials were undertaken in two evaporation basins filled with saline groundwater to identify finfish and shellfish that have the potential to survive and grow in these conditions. Test animals were reared in replicate culture units in each of two basins filled with saline groundwater located in the Goulburn–Murray Irrigation District (GMID), south-eastern Australia. Salinity in basin 2 (9.5–24.6 p.p.t., mean 16.8 p.p.t.) was significantly higher than in basin 1 (8.8–15.2 p.p.t., mean 11.6 p.p.t.). Some differences were observed between the ionic concentrations in the groundwater and sea water (at 10 p.p.t.) and may have affected growth and survival of some species. Survival and growth for oysters (Crassostrea gigas and Saccostrea glomerata) in the basins were low. Shrimps (Penaeus monodon and Marsupenaeus japonicus) did not survive beyond 3 weeks. Of the eight species of fish stocked into the basins, Salmo salar, Macquaria novemaculeata and Acanthopagrus butcheri survived and grew in both basins. Oncorhynchus mykiss did not survive in the low-salinity basin, whereas Bidyanus bidyanus did not survive in the high-salinity basin. These results indicate that some species of fish in particular can be cultured in saline groundwaters within the GMID.
Trehalose Changes Hydraulic Conductance of Tissue-cultured Soybean Embryos

The hydraulic properties of tissue-cultured soybean (Glycine max [L.] Merr.) embryos grown on trehalose-containing culture media were investigated. Water potentials of culture media ranged from -0.13 to -0.65MPa when sucrose and/or trehalose concentrations were altered. The wall extensibility was greatly larger than hydraulic conductance, and the size of the effective turgor was much smaller than that of the growth-induced water potential, indicating that hydraulic conductance and the growth-induced water potential were predominantly regulating growth of soybean embryos under tissue culture conditions. The hydraulic conductance of soybean embryos grown on trehalose-containing media became smaller than that in sucrose-containing media. When both sucrose and trehalose were added to the culture media, the hydraulic conductance became an intermediate between only sucrose-containing and only trehalose-containing treatments. It is suggested that trehalose might reduce hydraulic conductance in soybean embryos, resulting in growth retardation of soybean embryos.
Long‐term effects of agri‐environment schemes on breeding passerine populations in a lowland hay‐meadow system

Capsule Mowing postponement in 25% of a meadow system may lead to improved but instable population dynamics in meadow birds. Aim To monitor the long‐term effects of mowing postponement on the abundance and territory density of meadow passerines in 25% of a 3000‐ha hay‐meadow area in the Saône Valley (eastern France). Methods From 1993 to 2009, passerine abundance was measured annually in 78 plots using point counts and territory density was assessed in two study areas by Territory Mapping. Results The programme of mowing postponement led to substantially increased passerine abundance and territory density, with the highest increase detected in Whinchats Saxicola rubetra. No positive trend was observed in Corn Buntings Emberiza calandra. Immediately after the increase in abundance, bird distribution within the study area was not influenced by the timing of mowing. The hatching success, assessed by the systematic observation of food carrying, was negatively influenced by early mowing (<40% recorded when >60% of the meadow area was already harvested on 1 July) or, in late mown areas, by high meadow passerine territory density (<40% when territory density was >10 per 10 ha). Hatching rate was usually higher in Whinchats than in Corn Buntings. Conclusion By improving meadow passerine breeding outputs and density, mowing postponement led to instable population dynamics with dominance of certain species and density‐dependent breeding success.
Self-renewal and differentiation of spermatogonial stem cells

differentiation, dedifferentiation, and transdifferentiation of SSCs and their potential applications in regenerative and reproductive medicine. Spermatogonial stem cells undergo self-renewal to maintain the stem cell pool while they differentiate into sperm in mammalian testis. Spermatogonia are classified into three types, including type A, intermediate, and type B cells, based upon their morphological characteristics. 19 Type A spermatogonia can be subdivided into A single (A s), A paired (A pr) and A aligned (A al) cells. SSCs are very rare, with only approximately 0.02%–0.03% of all germ cells in adult testis; 22 nevertheless, thousands of spermatids are produced each day, reflecting an unlimited potential of SSC division and differentiation. We illustrated the self-renewal and differentiation of the rodent and human SSCs in Figure 1. In rodents, A s spermatogonia can divide symmetrically to produce new A s stem cells or they divide asymmetrically to give rise to A s spermatogonia and A pr spermatogonia that are characterized by an intercellular cytoplasmic bridge. The A pr spermatogonia continue to divide and form chains of A al spermatogonia (4, 8, 16, and 32 cells) that are able to differentiate into type A 1 to A 4 , intermediate (In) and B spermatogonia. Type B spermatogonia further differentiate to primary spermatocytes, secondary spermatocytes, and eventually spermatids via two meiotic divisions. There are distinct cell types and biochemical phenotypes between rodent and human male germline stem (GS) cells. INTRODUCTION The pluripotent properties of stem cells have attracted considerable interest in both basic research and clinical applications.
Natural Incidence of Metarhizium flavoviride Infection in Two Grasshopper Communities in Northern Benin

The infection of grasshoppers by naturally occurring entomopathogenic fungi was monitored at two sites in Malanville, northern Benin, Africa. Grasshoppers were collected during the monsoon seasons of 1993, 1994 and 1995. At the first site, 982 individuals of 38 grasshopper species were incubated. At the second site, 899 individuals of 33 grasshopper species were incubated. Two hyphomycete fungi (Deuteromycotina: Hyphomycetes), Metarhizium flavoviride Gams and Rozsypal and Sorosporella sp. , were found infecting grasshoppers. The mean incidence of M. flavoviride infection was 0.3-1.7% at the first site and 1.2-3.2% at the second site for all grasshopper species. Sorosporella sp. was only collected from two grasshopper individuals in 1993. The majority of infected species had adult quiescence or continuously reproducing life cycles, and were either arboricolous or terricolous. Comparisons are made with a previous study of the two sites performed during 1992.
The Possible function of Buttresses in Caryocar Nuciferum (Caryocaraceae) in Guyana: Ecological and Wood Anatomical Observations

This paper describes the microscopic structure and morphology of stern and buttresses of swamp-grown Caryocar nuciferum L. and discusses the function of buttresses. Buttresses are mainly found at the opposite side of the leaning direction of a tree and thus could function as tension members. In contrast to the stern wood, which exhibits a moderate amount of tension wood fibres with a gelatinous layer, the wood of the buttresses on the tension side and the compression side of the leaning tree is characterised by thick-walled tension wood fibres. In addition, the number of vessels in the buttresses is substantially higher than that in the stern wood. The preferential direction of the buttresses and the anatomical differences in the various parts of the tree are discussed.
Host microtubules in the Hartig net region of ectomycorrhizas, ectendomycorrhizas, and monotropoid mycorrhizas

Various categories of mycorrhizas are recognized primarily by the structural changes that occur between fungi and roots. In all mycorrhiza categories, cytological modifications of root cells accompany the establishment of the functional symbiosis, and among these are alterations in the organization of the cytoskeleton. Using immuno- labelling combined with confocal scanning laser microscopy, this study documents changes in microtubules (MTs) in root cells of ectendomycorrhizas and monotropoid mycorrhizas; in addition, ectomycorrhizas were reinvestigated to de- termine the effect of fungal colonization on host root cells. In Pinus banksiana L. - Laccaria bicolor (Maire) Orton ectomycorrhizas, MTs were present in epidermal and cortical cells adjacent to the Hartig net. The remaining cortical MTs had a different organization when compared with those of cortical cells of control roots. MTs were present in Hartig net hyphae. In ectendomycorrhizas formed when roots of P. banksiana were colonized by the ascomycete, Wilcoxina mikolae var. mikolae Yang & Korf, MTs were present adjacent to intracellular hyphae and host nuclei, but few cortical MTs were present. MTs were present within Hartig net and intracellular hyphae. In field-collected roots of Monotropa uniflora L. , MTs were associated with fungal pegs, intracellular extensions of inner mantle hyphae within epidermal cells. The close association between MTs and fungal pegs may be related to the formation of the highly branched host-derived wall that envelops each fungal peg. The development of exchange interfaces in the three systems studied involve changes in the organization of microtubules.
Uncoupling of Somatic and Otolith Growth Rates in Arctic Char (Salvelinus alpinus) as an Effect of Differences in Temperature Response

Experiments were conducted to study the effect of temperature, fish size, and somatic growth rate on mean daily otolith growth rate in Arctic char (Salvelinus alpinus) fry fed maximum rations. Long-term experiments at two different temperatures (8 and 13 °C) showed exponential relationships between otolith weight and fish wet weight, with the exponent of wet weight for the higher temperature being significantly higher than for the lower temperature. Increasing exponents at each sampling date indicated a difference in growth rates of the char and its otoliths. Short-term experiments showed that specific growth rate of the fry at six different temperatures was that of an optimum curve whereas the otolith growth rate continued to increase with increasing temperatures. A clear uncoupling between otolith growth rate and fish growth rate was demonstrated whereas temperature and fish wet weight modeled otolith growth rate reasonably well. It was found that otolith growth rate expressed as daily increase in weigh.
Mini-Reviews : Current Status of Phytoplasmas and their Related Diseases in Korea

Phytoplasmas have been associated with more than 46 plant species in Korea. Several vegetables, ornamentals, fruit trees and other crop species are affected by phytoplasma diseases. Six 16Sr groups of phytoplasmas have been identified and these phytoplasmas are associated with 63 phytoplasma diseases. Aster yellows phytoplasmas are the most prevalent group and has been associated with more than 25 diseases in Korea. Jujube witches` broom, paulownia witches` broom and mulberry dwarf diseases cause economic losses to host trees throughout the country. So far, Korean phytoplasmas belong to six species of ``Candidatus Phytoplasma``; ``Ca. P. asteris``, ``Ca. P. pruni*``, ``Ca. P. ziziphi``, ``Ca. P. trifolii``, ``Ca. P. solani*`` and ``Ca. P. castaneae``. The diseases are distributed throughout the country and most of them were observed in Gyeongbuk and Chonbuk provinces. At least four insect vectors; Cyrtopeltis tenuis, Hishimonus sellatus, Macrosteles striifrons and Ophiola flavopicta have been identified for phytoplasma transmission.
A morphological study and taxonomic revision of Euptilota (Ceramiaceae, Rhodophyta)

A reassessment of the genus Euptilota reveals that it presently contains four validly published species: E. formosissima (Montagne) Kützing from New Zealand and the islands of the Campbell Plateau, E. articulata (J. Agardh) Schmitz from Australia, India, South Africa and Japan, E. fergusonii Cotton from the Indian Ocean, and E. molle (Wollaston) comb. nov., from the eastern part of South Africa. Euptilota pappeana Kützing from the Western Cape Province, South Africa, and E. mooreana Lindauer from New Zealand are excluded from the genus. Euptilota is characterized by: alternate-distichous branching at the apex, a prominent central axis covered by a small-celled outer cortex and with internal rhizoidal filaments, spermatangia with a terminal nucleus subtended by a single mucilage-containing vesicle, and fertile female periaxial cells borne in the plane of lateral branching. The carpogonium does not divide after fertilization and produces two tubular protuberances that are cut off as connecting cells. Traditionally placed in the tribe Ptiloteae, Euptilota appears to be more closely related to the Callithamnieae. As in the Callithamnieae, periaxial cells are cut off longitudinally in pairs from the fertile axial cell. One of each pair bears a horizontally oriented four-celled carpogonial branch and both cut off auxiliary cells after fertilization. Sterile group cells are absent. Connecting cells mediate transfer of the derivatives of the fertilization nucleus to the auxiliary cells. A diploid nucleus divides at the surface of an auxiliary cell and one daughter nucleus moves to its centre while the other is extruded into a residual cell. The haploid auxiliary cell nucleus is cut off into a foot cell. It is proposed that the closest relatives of Euptilota are Seirospora and Sciurothamnion.
Ancient genetic divergence in bumblebee catfish of the genus Pseudopimelodus (Pseudopimelodidae: Siluriformes) from northwestern South America

Pseudopimelodus is a Neotropical genus of bumblebee catfish, composed of four valid species occurring in both trans- and cis-Andean rivers of South America. The orogeny of the Andes has led to diversification in the genus Pseudopimelodus in Colombia. This study analyzed partial sequences of mitochondrial cox1 and nuclear rag2 genes to test the hypothesis that the species, nominally recognized as P. schultzi and P. bufonius in Colombia, correspond to more than two different evolutionary lineages. Results indicate high levels of genetic divergence among individuals of nominal P. schultzi and P. bufonius, from trans- and cis-Andean basins in Colombia. In addition, five divergent lineages of Pseudopimelodus were confidently delimited by using a single-locus species-discovery approach and confirmed by species tree analyses. Additionally, molecular-clock dating showed that most diversification processes in Pseudopimelodus took place during the Miocene, when Andean tectonic evolution was occurring in northwestern South America. The present study provides, for the first time, phylogeographic insight into this Neotropical genus.
A TECHNIQUE FOR DEPLETION OF BACTERIA ADHERENT TO THE EPITHELIUM OF THE BOVINE RUMEN

Rumens of fistulated cattle were manually emptied, washed with a buffered saline solution, and then filled with buffered saline with or without added antibiotic. After 3 days without feed, cattle were slaughtered and blocks of rumen epithelium were assayed for urease and prepared for scanning electron microscopy. Urease activity in treated animals was less than 3% of that in controls, thus indicating almost complete removal of urease-producing bacteria, and scanning electron microscopy showed a dramatic decrease in the number of adherent bacteria. The technique can thus be used to assess the relative contributions of epithelium and adherent bacteria to various processes known to occur at the epithelial boundary.