Giant taxon‐character matrices: the future of morphological systematics

Simões et al. ( 2016 ) argued that large matrices are linked to the construction of “problematic” characters, and that those characters negatively affect tree topology. In their re‐evaluation of two squamate datasets, however, Simões et al. ( 2016 ) simply eliminated what they termed “problematic” characters, rather than recode them. This practice ignores potential sources of phylogenetic information and, if it were to be more widely followed, would inhibit the advancement of the field of systematics. Here, we defend the necessity and inevitability of large morphological (phenomic) datasets and discuss best practices for morphological data collection in contemporary phylogenetics.     

Combining taxon‐by‐trait and taxon‐by‐site matrices for analysing trait patterns of macroinvertebrate communities: a rejoinder to Monaghan & Soares ()

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Development of taxon‐specific markers for high‐throughput screening of microbial‐feeding nematodes

In an effort to assess the taxonomic identity of large‐scale samplings of nematodes from the Konza Tallgrass Prairie, we sequenced a portion of the 18S rRNA gene and its associated internally transcribed spacer (ITS1) from 74 nematodes encompassing four taxonomic families. From these sequences, we have developed a series of molecular probes to distinguish 16 distinct microbivorous nematode taxa. Using a combination of low power microscopy and taxon‐specific real‐time probes, the 74 nematodes were correctly assigned to their respective taxonomic groups. This optimized method provides a high‐throughput assay to determine nematode identities across larger data sets.     

Strong but taxon‐specific responses of termites and wood‐nesting ants to forest regeneration in Borneo

Land use change is accelerating globally at the expense of biodiversity and ecosystem functioning. Invertebrates are numerically dominant and functionally important in old growth tropical rain forests but highly susceptible to the adverse effects of forest degradation and fragmentation. Ants (Formicidae) and termites (Blattodea: Termitoidae) perform crucial ecosystem services. Here, the potential effects of anthropogenic disturbance on ant and termite communities in dead wood are investigated. Community composition, generic richness, and occupancy rates of ants and termites were compared among two old growth sites (Danum Valley and Maliau Basin) and one twice‐logged site (the Stability of Altered Forest Ecosystems’ (SAFE) Project), in Sabah, Malaysian Borneo. Occupancy was measured as the number of ant or termite encounters (1) per deadwood items, and (2) per deadwood volume, and acts as surrogates for relative abundance (or generic richness). Termites had a lower wood‐occupancy per volume in logged forest. In contrast, there were more ant encounters, and more ant genera, in logged sites and there was a community shift (especially, there were more Crematogaster encounters). The disruption of soil and canopy structure in logged forest may reduce both termite and fungal decay rates, inducing increased deadwood residence times and therefore favoring ants that nest in dead wood. There is an anthropogenic‐induced shift of dead wood in ants and termites in response to disturbance in tropical rain forests and the nature of that shift is taxon‐specific.     

Egg size and offspring quality: a meta‐analysis in birds

Parents affect offspring fitness by propagule size and quality, selection of oviposition site, quality of incubation, feeding of dependent young, and their defence against predators and parasites. Despite many case studies on each of these topics, this knowledge has not been rigorously integrated into individual parental care traits for any taxon. Consequently, we lack a comprehensive, quantitative assessment of how parental care modifies offspring phenotypes. This meta‐analysis of 283 studies with 1805 correlations between egg size and offspring quality in birds is intended to fill this gap. The large sample size enabled testing of how the magnitude of the relationship between egg size and offspring quality depends on a number of variables. Egg size was positively related to nearly all studied offspring traits across all stages of the offspring life cycle. Not surprisingly, the relationship was strongest at hatching but persisted until the post‐fledging stage. Morphological traits were the most closely related to egg size but significant relationships were also found with hatching success, chick survival, and growth rate. Non‐significant effect sizes were found for egg fertility, chick immunity, behaviour, and life‐history or sexual traits. Effect size did not depend on whether chicks were raised by their natural parents or were cross‐fostered to other territories. Effect size did not depend on species‐specific traits such as developmental mode, clutch size, and relative size of the egg, but was larger if tested in captive compared to wild populations and between rather than within broods. In sum, published studies support the view that egg size affects juvenile survival. There are very few studies that tested the relationship between egg size and the fecundity component of offspring fitness, and no studies on offspring survival as adults or on global fitness. More data are also needed for the relationships between egg size and offspring behavioural and physiological traits. It remains to be established whether the relationship between egg size and offspring performance depends on the quality of the offspring environment. Positive effect sizes found in this study are likely to be driven by a causal effect of egg size on offspring quality. However, more studies that control for potential confounding effects of parental post‐hatching care, genes, and egg composition are needed to establish firmly this causal link.     

Temperature‐size responses match latitudinal‐size clines in arthropods,revealing critical differences between aquatic and terrestrial species

Two major intraspecific patterns of adult size variation are plastic temperature‐size (T‐S) responses and latitude‐size (L‐S) clines. Yet, the degree to which these co‐vary and share explanatory mechanisms has not been systematically evaluated. We present the largest quantitative comparison of these gradients to date, and find that their direction and magnitude co‐vary among 12 arthropod orders (r² = 0.72). Body size in aquatic species generally reduces with both warming and decreasing latitude, whereas terrestrial species have much reduced and even opposite gradients. These patterns support the prediction that oxygen limitation is a major controlling factor in water, but not in air. Furthermore, voltinism explains much of the variation in T‐S and L‐S patterns in terrestrial but not aquatic species. While body size decreases with warming and with decreasing latitude in multivoltine terrestrial arthropods, size increases on average in univoltine species, consistent with predictions from size vs. season‐length trade‐offs.     

Prediction of taxon occurrence: a test on taxon‐specific change point values of stream benthic invertebrates

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Body size and sperm quality in queen‐ And worker‐produced ant males

Workers of many species of social Hymenoptera have functional ovaries and are capable of laying haploid, unfertilized eggs, at least in the absence of a queen. Except for honeybees, it remains largely unknown whether worker‐produced males have the same quality as queen‐produced males and whether workers benefit in direct fitness by producing their sons. Previous studies in the monogynous ant Temnothorax crassispinus revealed that a high proportion of males in natural and laboratory colonies are worker offspring. Here, we compare longevity, body size, sperm length and sperm viability between queen‐ and worker‐produced males. We either split queenright colonies into queenright and queenless halves or removed the queen from a fraction of the queenright colonies and then examined the newly produced males. Male quality traits varied considerably among colonies but differed only slightly between queen‐ and worker‐produced males. Worker‐produced males outnumbered queen‐produced males and also had a longer lifespan, but under certain rearing conditions sperm from queen‐produced males had a higher viability.     

The phylogeography of the Placozoa suggests a taxon‐rich phylum in tropical and subtropical waters

Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. The genetic data also suggest deep phylogenetic branching patterns between clades.     

Autofluorescence excitation‐emission matrices as a quantitative tool for the assessment of meat quality

Commercially produced meat is currently graded by a complex and partly subjective multiparameter methodology; a quantitative method of grading, using small samples would be desirable. Here, we investigate the correlation between commercial grades of beef and spectral signatures of native fluorophores in such small samples. Beef samples of different commercial grades were characterized by fluorescence spectroscopy complemented by biochemical and histological assessment. The excitation‐emission matrices of the specimens reveal five prominent native autofluorescence signatures in the excitation range from 250 to 350 nm, derived mainly from tryptophan and intramuscular fat. We found that these signatures reflect meat grade and can be used for its determination.      

Disentangling the effects of local and regional processes on biodiversity patterns through taxon‐contingent metacommunity network analysis

Metacommunity theory, which has gained a central position in ecology, accounts for the role of migration in patterns of diversity among communities at different scales. Community isolation has a main role in this theory, but is difficult to estimate empirically, partly due to the taxon‐dependent nature of dispersal. Landscapes could be perceived as either fragmented or connected for organisms with contrasting dispersal abilities. Indeed, the dispersal ability of a taxon, and the spatial scale at which eco‐evolutionary processes shape local diversity, determine a taxon‐dependent metacommunity network. In this paper, we introduce a methodology using graph theory to define this taxon‐dependent metacommunity network and then to estimate the isolation of local communities. We analyzed the relative importance of local conditions versus community isolation as determinants of community richness for 25 taxa inhabiting 18 temporary ponds. Although local factors have been the foci of most previous empirical and theoretical considerations, we demonstrate that the metacommunity network is an equally important contributor to local diversity. We also found that the relative effect of local conditions and the metacommunity network depend on body size and taxon abundance. Local diversity of larger species was more affected by patch isolation, while taxon abundances were associated with positive or negative effects of isolation. Our results provide empirical support for the proposed role of metacommunity networks as determinants of community diversity and show the taxon‐dependent nature of these networks.     

Brood parasitism causes female‐biased host nestling mortality regardless of parasite species

Inequality in male and female numbers may affect population dynamics and extinction probabilities and so has significant conservation implications. We previously demonstrated that Brown‐headed Cowbird Molothrus ater brood parasitism of Song Sparrows Melospiza melodia results in a 50% reduction in the proportion of female host offspring by day 6 post‐hatch and at fledging, which modelling demonstrated is as significant as nest predation in affecting demography. Many avian brood parasites possess special adaptations to parasitize specific hosts so this sex‐ratio effect could be specific to the interaction between these two species. Alternatively, perturbations associated with brood parasitism per se (e.g. the addition of an extra, larger, unrelated nestling), rather than a Cowbird nestling specifically, may be responsible. We experimentally eliminated the effects of Cowbird‐specific traits by parasitizing nests with a conspecific nestling rather than a Cowbird, while otherwise emulating the circumstances of Cowbird parasitism by adding an extra, larger (2‐day‐older), unrelated Song Sparrow nestling to Song Sparrow nests. Our parasitism treatment led to few host offspring deaths and no evidence of male‐biased sex ratios by day 6 post‐hatch. However, after day 6, female nestling mortality rates increased significantly in experimentally parasitized nests, resulting in a 60% reduction in the proportion of females fledging. Cowbird‐specific traits are thus not necessary to cause female‐biased host nestling mortality and far more general features associated with Cowbird parasitism instead appear responsible. Our results suggest, however, that Cowbird‐specific traits may help accelerate the pace of female host deaths. The conservation implications of our results could be wide reaching. Cowbirds are unrelated to all their hosts, are larger than the great majority, and a Cowbird nestling's presence can mean there is an extra mouth to feed. Thus, sex‐biased mortality in parasitized nests could be occurring across a range of host species.     

Real‐time PCR quantification of Bemisia tabaci (Homoptera: Aleyrodidae) B‐biotype remains in predator guts

The cotton whitefly, Bemisia tabaci (Gennadius) B‐biotype, is fed on by a wide variety of generalist predators, but there is little information on these predator–prey interactions, especially under field conditions. In this study, a real‐time polymerase chain reaction (PCR) assay was developed to quantify B. tabaci B‐biotype remains in predator gut. The B. tabaci B‐biotype genomic DNA copy number was referred to the actual amount of BT1 isolate, the B. tabaci B‐biotype specific DNA fragment. The numbers of BT1 isolate in one B. tabaci B‐biotype egg, individual adult and a single red‐eyed nymph were 2.56 × 10³, 2.56 × 10⁴, and 1.29 × 10⁴ copies, respectively. When Propylaea japonica adults fed on one, two, four, eight or 16 red‐eyed nymphs, the detected numbers of BT1 isolate ranged from 2.77 × 10⁴ to 4.05 × 10⁵ copies, forming a strong linear relationship (R² = 0.9899). Following the consumption of two red‐eyed nymphs, prey DNA was detectable in 100% of P. japonica at t = 0, decreasing to 80.0% and 60.0% after 1–4 h and 8 h of digestion, respectively, with 3.36 × 10⁴–1.25 × 10³ BT1 isolate copies. The predation by field‐collected predators, 26 larvae of P. japonica, and of Harmonia axyridis each, Chrysopa spp. larvae (Chrysopa pallens and C. formosa, 18 individuals in total), and a single adult of Scymnus hoffmanni, 19 adults of Orius sauteri and nine adult spiders (Erigonnidium graminicolum and Neoscona doenitzi), on B. tabaci B‐biotype were quantified. Of the 99 analysed predator individuals, 3.65 × 10²–4.60 × 10⁵ copies of BT1 isolate, equivalent to 0.8–18.8 red‐eyed nymphs were detected. These results suggest that TaqMan real‐time PCR technology may provide a rapid and sensitive method for quantifying B. tabaci B‐biotype remains in predator guts and will be invaluable in assessing the food web relationship between prey and arthropod predators.     

GB‐to‐TNT: facilitating creation of matrices from GenBank and diagnosis of results in TNT

This paper presents a pipeline, implemented in an open‐source program called GB→TNT (GenBank‐to‐TNT), for creating large molecular matrices, starting from GenBank files and finishing with TNT matrices which incorporate taxonomic information in the terminal names. GB→TNT is designed to retrieve a defined genomic region from a bulk of sequences included in a GenBank file. The user defines the genomic region to be retrieved and several filters (genome, length of the sequence, taxonomic group, etc.); each genomic region represents a different data block in the final TNT matrix. GB→TNT first generates Fasta files from the input GenBank files, then creates an alignment for each of those (by calling an alignment program), and finally merges all the aligned files into a single TNT matrix. The new version of TNT can make use of the taxonomic information contained in the terminal names, allowing easy diagnosis of results, evaluation of fit between the trees and the taxonomy, and automatic labelling or colouring of tree branches with the taxonomic groups they represent. © The Willi Hennig Society 2012.     

mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests

SUMMARY: Pairwise comparisons of disagreement in phylogenetic datasets offer a powerful tool for isolating historical incongruence for closer analysis. Statistically significant phylogenetic character incongruence may reflect important differences in evolutionary history, such as horizontal gene transfer. Such testing can also be used to specify possible combinations of datasets for further phylogenetic analysis. The process of comparing multiple datasets can be very time consuming, and it is sometimes unclear how to combine data partitions given the observed patterns of incongruence. Here we present an application that automates the process of making pairwise comparisons between large numbers of phylogenetic datasets using the Incongruence Length Difference (ILD) test. The application also implements strategies for data combination based on the patterns of incongruence observed in pairwise comparisons.     

A perfusion bioreactor system efficiently generates cell‐loaded bone substitute materials for addressing critical size bone defects

Critical size bone defects and non‐union fractions are still challenging to treat. Cell‐loaded bone substitutes have shown improved bone ingrowth and bone formation. However, a lack of methods for homogenously colonizing scaffolds limits the maximum volume of bone grafts. Additionally, therapy robustness is impaired by heterogeneous cell populations after graft generation. Our aim was to establish a technology for generating grafts with a size of 10.5 mm in diameter and 25 mm of height, and thus for grafts suited for treatment of critical size bone defects. Therefore, a novel tailor‐made bioreactor system was developed, allowing standardized flow conditions in a porous poly(L‐lactide‐co‐caprolactone) material. Scaffolds were seeded with primary human mesenchymal stem cells derived from four different donors. In contrast to static experimental conditions, homogenous cell distributions were accomplished under dynamic culture. Additionally, culture in the bioreactor system allowed the induction of osteogenic lineage commitment after one week of culture without addition of soluble factors. This was demonstrated by quantitative analysis of calcification and gene expression markers related to osteogenic lineage. In conclusion, the novel bioreactor technology allows efficient and standardized conditions for generating bone substitutes that are suitable for the treatment of critical size defects in humans.     

Mortality induced by electrofishing and handling in five young‐of‐the‐year cyprinids: effect of the fish size,species and anode size

Immediate mortality induced by electrofishing and handling of young‐of the‐year (YOY) fish of five cyprinid species (bitterling Rhodeus amarus, chub Leuciscus cephalus, bleak Alburnus alburnus, barbel Barbus barbus, roach Rutilus rutilus) was quantified during routine YOY fish monitoring (point abundance sampling with backpack electrofisher, in situ identification and measurement). Sampled, identified and measured fish were held in screened containers immersed in the river for 5 h after electrofishing. Bleak exhibited significantly higher mortality (17%) than all other species (1–3%). Mortality decreased significantly with fish length; fish <35 mm exhibited the highest mortality. Anode size (10, 20, and 30 cm diameter) had no direct effect on mortality. Point abundance electrofishing with in situ identification and measurement is a safe method for sampling riverine YOY cyprinids.     

Effective size of density‐dependent two‐sex populations: the effect of mating systems

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare N_e in short‐lived, density‐dependent animal populations with different mating systems. We study the impact of a fluctuating, density‐dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual N_e/N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male‐biased, density‐dependent sex ratio reduces the rate of genetic drift compared to an equal, density‐independent sex ratio, but a stochastic change towards male bias reduces the N_e/N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes.