Widely used, short 16S rRNA mitochondrial gene fragments yield poor and erratic results in phylogenetic estimation and species delimitation of amphibians.

BACKGROUND The 16S mitochondrial rRNA gene is the most widely sequenced molecular marker in amphibian systematic studies, making it comparable to the universal CO1 barcode that is more commonly used in other animal groups. However, studies employ different primer combinations that target different lengths/regions of the 16S gene ranging from complete gene sequences (~ 1500 bp) to short fragments (~ 500 bp), the latter of which is the most ubiquitously used. Sequences of different lengths are often concatenated, compared, and/or jointly analyzed to infer phylogenetic relationships, estimate genetic divergence (p-distances), and justify the recognition of new species (species delimitation), making the 16S gene region, by far, the most influential molecular marker in amphibian systematics. Despite their ubiquitous and multifarious use, no studies have ever been conducted to evaluate the congruence and performance among the different fragment lengths. RESULTS Using empirical data derived from both Sanger-based and genomic approaches, we show that full-length 16S sequences recover the most accurate phylogenetic relationships, highest branch support, lowest variation in genetic distances (pairwise p-distances), and best-scoring species delimitation partitions. In contrast, widely used short fragments produce inaccurate phylogenetic reconstructions, lower and more variable branch support, erratic genetic distances, and low-scoring species delimitation partitions, the numbers of which are vastly overestimated. The relatively poor performance of short 16S fragments is likely due to insufficient phylogenetic information content. CONCLUSIONS Taken together, our results demonstrate that short 16S fragments are unable to match the efficacy achieved by full-length sequences in terms of topological accuracy, heuristic branch support, genetic divergences, and species delimitation partitions, and thus, phylogenetic and taxonomic inferences that are predicated on short 16S fragments should be interpreted with caution. However, short 16S fragments can still be useful for species identification, rapid assessments, or definitively coupling complex life stages in natural history studies and faunal inventories. While the full 16S sequence performs best, it requires the use of several primer pairs that increases cost, time, and effort. As a compromise, our results demonstrate that practitioners should utilize medium-length primers in favor of the short-fragment primers because they have the potential to markedly improve phylogenetic inference and species delimitation without additional cost

Sex-specific routes to independent breeding in a polygynous cooperative breeder

How can individuals obtain a breeding position and what are the benefits associated with philopatry compared to dispersal? These questions are particularly intriguing in polygamous cooperative breeders, where dispersal strategies reflect major life history decisions, and routes to independent breeding may utterly differ between the sexes. We scrutinized sex-dependent life-history routes by investigating dispersal patterns, growth rates and mortality in a wild colony of the cooperatively breeding cichlid Neolamprologus savoryi. Our data reveal that female helpers typically obtain dominant breeding positions immediately after reaching sexual maturity, which is associated with strongly reduced growth. In contrast, males obtain breeder status only at twice the age of females. After reaching sexual maturity, males follow one of two strategies: (i) they may retain their subordinate status within the harem of a dominant male, which may provide protection against predators but involves costs by helping in territory maintenance, defence and brood care; or (ii) they may disperse and adopt a solitary status, which diminishes survival chances and apparently reflects a best-of-a-bad-job strategy, as there are no obvious compensating future fitness benefits associated with this pathway. Our study illustrates that sex-dependent life history strategies strongly relate to specific social structures and mating patterns, with important implications for growth rates, the age at which breeding status is obtained, and survival

Ecological variation drives morphological differentiation in a highly social vertebrate

Animals may respond to ecological heterogeneity by genetic differentiation or phenotypic plasticity. Responses of organisms to their ecology can include adaptation at various levels of organization, including morphology, behaviour and social structure. Adaptations at one level might constrain or enhance adaptations on other levels, which highlights the importance of understanding their interactions. In highly social animals, understanding the influence of their ecological niche on the evolution and maintenance of complex social organization poses an intriguing challenge. Predation risk and habitat characteristics determine social structure in the cooperatively breeding cichlid Neolamprologus pulcher. Here we examine how varying combinations of these ecological factors across eight distinct populations influence morphological differentiation. We investigated the relationship between body shape and ecological parameters for 137 wild-caught individuals from eight distinct populations. Furthermore, we examined the genetic structure and differentiation among these populations using microsatellites. Finally, to disentangle heritable from plastic responses, we raised two successive generations from six populations in the laboratory under common garden conditions and screened 188 individuals for morphological differentiation. We found that body shape of N. pulcher strongly correlates with the measured ecological parameters. Low predation risk, low habitat structure and small shelter size favoured shallow bodies, whereas at the opposite end of these environmental gradients deep body shapes prevail. These consistent morphological differences persisted over two laboratory-reared generations, revealing a heritable basis. In contrast to the significant effect of local ecology on morphological differentiation between populations, both geographical and genetic distance had little explanatory power, suggesting that morphological differentiation between populations is not a simple by-product of genetic isolation. Remarkably, the largest difference in body depth emerged between the two populations located closest to each other, but differing strongly in their ecological niche. These results highlight that morphological variation is a key component of local adaptation in neighbouring populations of a highly social species. Such morphological differentiation has the potential to influence individual cooperative behaviour, which will eventually feed back on group structure and mediate the evolution and maintenance of complex social systems

Ecological variation drives morphological differentiation in a highly social vertebrate

1. Animals may respond to ecological heterogeneity by genetic differentiation or phenotypic plasticity. Responses of organisms to their ecology can include adaptation at various levels of organization, including morphology, behaviour and social structure. Adaptations at one level might constrain or enhance adaptations on other levels, which highlights the importance of understanding their interactions. 2. In highly social animals, understanding the influence of their ecological niche on the evolution and maintenance of complex social organization poses an intriguing challenge. Predation risk and habitat characteristics determine social structure in the cooperatively breeding cichlid Neolamprologus pulcher. Here we examine how varying combinations of these ecological factors across eight distinct populations influence morphological differentiation. 3. We investigated the relationship between body shape and ecological parameters for 137 wild-caught individuals from eight distinct populations. Furthermore, we examined the genetic structure and differentiation among these populations using microsatellites. Finally, to disentangle heritable from plastic responses, we raised two successive generations from six populations in the laboratory under common garden conditions and screened 188 individuals for morphological differentiation. 4. We found that body shape of N. pulcher strongly correlates with the measured ecological parameters. Low predation risk, low habitat structure and small shelter size favoured shallow bodies, whereas at the opposite end of these environmental gradients deep body shapes prevail. These consistent morphological differences persisted over two laboratory-reared generations, revealing a heritable basis. In contrast to the significant effect of local ecology on morphological differentiation between populations, both geographical and genetic distance had little explanatory power, suggesting that morphological differentiation between populations is not a simple by-product of genetic isolation. Remarkably, the largest difference in body depth emerged between the two populations located closest to each other, but differing strongly in their ecological niche. 5. These results highlight that morphological variation is a key component of local adaptation in neighbouring populations of a highly social species. Such morphological differentiation has the potential to influence individual cooperative behaviour, which will eventually feed back on group structure and mediate the evolution and maintenance of complex social systems

Unexpectedly high levels of genetic diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)

One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world’s so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace’s Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognitio

Inflammation and convergent placenta gene co-option contributed to a novel reproductive tissue

Highlights: • Pelvic brooding induces tissue-specific changes in gene expression • Inflammatory signaling characterizes transcriptome of the egg-anchoring plug • Similar to embryo implantation, the plug likely evolved from an inflammatory response • Mammalian placenta genes were independently co-opted into the plug Summary: The evolution of pregnancy exposes parental tissues to new, potentially stressful conditions, which can trigger inflammation.1 Inflammation is costly2,3 and can induce embryo rejection, which constrains the evolution of pregnancy.1 In contrast, inflammation can also promote morphological innovation at the maternal-embryonic interface as exemplified by co-option of pro-inflammatory signaling for eutherian embryo implantation.1,4,5 Given its dual function, inflammation could be a key process explaining how innovations such as pregnancy and placentation evolved many times convergently. Pelvic brooding ricefishes evolved a novel “plug” tissue,6,7 which forms inside the female gonoduct after spawning, anchors egg-attaching filaments, and enables pelvic brooders to carry eggs externally until hatching.6,8 Compared to pregnancy, i.e., internal bearing of embryos, external bearing should alleviate constraints on inflammation in the reproductive tract. We thus hypothesized that an ancestral inflammation triggered by the retention of attaching filaments gave rise to pathways orchestrating plug formation. In line with our hypothesis, histological sections of the developing plug revealed signs of gonoduct injuries by egg-attaching filaments in the pelvic brooding ricefish Oryzias eversi. Tissue-specific transcriptomes showed that inflammatory signaling dominates the plug transcriptome and inflammation-induced genes controlling vital processes for plug development such as tissue growth and angiogenesis were overexpressed in the plug. Finally, mammalian placenta genes were enriched in the plug transcriptome, indicating convergent gene co-option for building, attaching, and sustaining a transient tissue in the female reproductive tract. This study highlights the role of gene co-option and suggests that recruiting inflammatory signaling into physiological processes provides a fast-track to evolutionary innovation

Содержание. Секция 07 - Оптика и спектроскопия

The remarkable complexity of soil and its importance to a wide range of ecosystem services presents major challenges to the modeling of soil processes. Although major progress in soil models has occurred in the last decades, models of soil processes remain disjointed between disciplines or ecosystem services, with considerable uncertainty remaining in the quality of predictions and several challenges that remain yet to be addressed. First, there is a need to improve exchange of knowledge and experience among the different disciplines in soil science and to reach out to other Earth science communities. Second, the community needs to develop a new generation of soil models based on a systemic approach comprising relevant physical, chemical, and biological processes to address critical knowledge gaps in our understanding of soil processes and their interactions. Overcoming these challenges will facilitate exchanges between soil modeling and climate, plant, and social science modeling communities. It will allow us to contribute to preserve and improve our assessment of ecosystem services and advance our understanding of climate-change feedback mechanisms, among others, thereby facilitating and strengthening communication among scientific disciplines and society. We review the role of modeling soil processes in quantifying key soil processes that shape ecosystem services, with a focus on provisioning and regulating services. We then identify key challenges in modeling soil processes, including the systematic incorporation of heterogeneity and uncertainty, the integration of data and models, and strategies for effective integration of knowledge on physical, chemical, and biological soil processes. We discuss how the soil modeling community could best interface with modern modeling activities in other disciplines, such as climate, ecology, and plant research, and how to weave novel observation and measurement techniques into soil models. We propose the establishment of an international soil modeling consortium to coherently advance soil modeling activities and foster communication with other Earth science disciplines. Such a consortium should promote soil modeling platforms and data repository for model development, calibration and intercomparison essential for addressing contemporary challenges