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opencc-zeroDec 2015View details →

Data from: Diet and birdsong: short-term nutritional enrichment improves songs of adult Bengalese finch males

Song is a notable sexual signal of birds, and serves as an honest indicator of male quality. Condition dependence of birdsong has been well examined from the viewpoint of the developmental stress hypothesis, which posits that complex songs assure fitness because learned acoustic features of songs are especially susceptible to early-life stress that young birds experience in song learning periods. The effect of early stress on song phenotypes should be crucial, especially in age-limited song learners which sing stereotyped songs throughout life. However, little attention has been paid to non-learned song features that can change plastically even in adulthood of age-limited song-learners. Although it has been shown that food availability affects song rate in wild songbirds, there is limited evidence of the link between favorable nutritional conditions and song phenotypes other than song rate. Under the prediction that singing behavior reflects an individual's recent life history, we kept adult Bengalese finch males under high-nutrition or normal diet for a short term, and examined changes in body mass and songs. We found that birds on a high-nutrition diet showed higher song output (e.g. song rate and length) compared with those of the control group, while changes in body mass were moderate. In addition, note repertoire became more consistent and temporal structures got faster in both nutrition and control groups, which indicates that songs were subject to other factors than nutrition. Considering that female estrildid finches, including Bengalese and zebra finches, show a preference toward complex songs as well as longer songs and higher song rate, it is plausible that different aspects of singing behavior signal different male qualities, and provide multifaceted clues to females that choose mates.

opencc-zeroDec 2014View details →

Data from: Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment

Background: The past decade has witnessed remarkable progress towards resolution of the Tree of Life. However, despite the increased use of genomic scale datasets, some phylogenetic relationships remain difficult to resolve. Here we employ anchored phylogenomics to capture 107 nuclear loci in 29 species of acanthomorph teleost fishes, with 25 of these species sampled from the recently delimited clade Ovalentaria. Previous studies employing multilocus nuclear exon datasets have not been able to resolve the nodes at the base of the Ovalentaria tree with confidence. Here we test whether a phylogenomic approach will provide better support for these nodes, and if not, why this may be. Results: After using a novel method to account for paralogous loci, we estimated phylogenies with maximum likelihood and species tree methods using DNA sequence alignments of over 80,000 base pairs. Several key relationships within Ovalentaria are well resolved, including 1) the sister taxon relationship between Cichlidae and Pholidichthys, 2) a clade containing blennies, grammas, clingfishes, and jawfishes, and 3) monophyly of Atherinomorpha (topminnows, flyingfishes, and silversides). However, many nodes in the phylogeny associated with the early diversification of Ovalentaria are poorly resolved in several analyses. Through the use of rarefaction curves we show that limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny does not appear to be due to a deficiency of data, as average global node support ceases to increase when only 1/3rd of the sampled loci are used in analyses. Instead this lack of resolution may be driven by model misspecification as a Bayesian mixed model analysis of the amino acid dataset provided good support for parts of the base of the Ovalentaria tree.Conclusions: Although it does not appear that the limited phylogenetic resolution among the earliest nodes in the Ovalentaria phylogeny is due to a deficiency of data, it may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.

opencc-zeroDec 2018View details →

Data from: Plastic changes in brain morphology in relation to learning and environmental enrichment in the guppy (Poecilia reticulata)

Despite the common assumption that the brain is mainly malleable to surrounding conditions during ontogeny, plastic neural changes can occur also in adulthood. One of the driving forces responsible for alterations in brain morphology is increasing environmental complexity that may demand for enhanced cognitive abilities (e.g. attention, memory and learning). However, studies looking at the relationship between brain morphology and learning are scarce. Here, we tested the effects of both learning and environmental enrichment on neural plasticity in guppies (Poecilia reticulata), by means of either a reversal-learning test or a spatial-learning test. Given considerable evidence supporting environmentally-induced plastic alterations, two separate control groups that were not subjected to any cognitive test were included to account for potential changes induced by the experimental setup alone. We did not find any effect of learning on any of our brain measurements. However, we found strong evidence for an environmental effect, where fish given access to the spatial-learning environment had larger relative brain size and optic tectum size in relation to those exposed to the reversal-learning environment. Our results demonstrate the plasticity of the adult brain to respond adaptively mainly to environmental conditions, providing support for the environmental enhancement theory.

opencc-zeroDec 2014View details →

Data from: Identification of habitat-specific biomes of aquatic fungal communities using a comprehensive nearly full-length 18S rRNA dataset enriched with contextual data

Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.

opencc-zeroOct 2021View details →

Data from: Compensatory dynamics of lotic algae break down nonlinearly with increasing nutrient enrichment

<p>One important mechanism governing the temporal maintenance of biodiversity is asynchrony in cooccurring competitors due to fluctuating environments (i.e. compensatory dynamics). Temporal niche partitioning has evolved in response to predictable oscillations in environmental conditions so that species may offset competition, but we do not yet have a clear understanding of how novel anthropogenic stressors alter seasonal patterns of succession. Many primary producers are nutrient-limited, and enrichment may decrease the importance of environmental fluctuations that govern which species are effective competitors under naturally low nutrient regimes. Consequently, elevated nutrient concentrations may synchronize species responses to seasonality. By studying benthic algal assemblages over two years from 35 streams that spanned a wide gradient of nutrient enrichment, we found that compensatory dynamics characterizing seasonal succession under natural nutrient regimes broke down at relatively low levels of total phosphorus (P) enrichment (~ 25 μg L<sup>-1</sup>). With increasing P more species were able to coexist at any given time, and seasonal variation in assemblage composition was characterized by synchronous swings in species biovolumes. We also observed much higher instability in assemblage biovolumes with declines in compensatory dynamics, which indicates that anthropogenic alteration of nutrient regimes can affect community stability by changing the dominant mode of seasonal succession. Our findings indicate that compensatory fluctuations of stream algae are driven by seasonality, and provide insight about how nutrient enrichment alters evolved drivers of species coexistence.</p>

FIGURE 32 Occulta ocnus comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)

FIGURE 32 Occulta ocnus comb.n. Locality records.

FIGURE 29 Trico tricolor comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)

FIGURE 29 Trico tricolor comb.n. Locality records.

FIGURE 25 Xenovena murrayae comb.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)

FIGURE 25 Xenovena murrayae comb.n. Locality records.

FIGURE 22 Taguaiba gen.n in Combining target enrichment and Sanger sequencing data to clarify the systematics of the diverse Neotropical butterfly subtribe Euptychiina (Nymphalidae, Satyrinae)

FIGURE 22 Taguaiba gen.n. Species diversity mapped on a 2 degree grid.