Contributors: Burbrink, Frank T., Gehara, Marcelo
... Most phylogenies are typically represented as purely bifurcating. However, as genomic data has become more common in phylogenetic studies, it is not unusual to find reticulation among terminal lineages or among internal nodes (deep time reticulation; DTR). In these situations, gene flow must have happened in the same or adjacent geographic areas for these DTRs to have occurred and therefore biogeographic reconstruction should provide similar area estimates for parental nodes, provided extinction or dispersal has not eroded these patterns. We examine the phylogeny of the widely distributed New World kingsnakes (Lampropeltis), determine if DTR is present in this group, and estimate the ancestral area for reticulation. Importantly, we develop a new method that uses coalescent simulations in a machine learning framework to show conclusively that this phylogeny is best represented as reticulating at deeper time. Using joint probabilities of ancestral area reconstructions on the bifurcating parental lineages from the reticulating node, we show that this reticulation likely occurred in northwestern Mexico/southwestern US and subsequently led to the diversification of the Mexican kingsnakes. This region has been previously identified as an area important for understanding speciation and secondary contact with gene flow in snakes and other squamates. This research shows that phylogenetic reticulation is common, even in well-studied groups, and that the geographic scope of ancient hybridization is recoverable.
Data from: Field evaluation of the safety, acceptability, and feasibility of early infant male circumcision using the AccuCirc device
Contributors: Bailey, Robert C., Nyaboke, Irene, Mackesy-Amiti, Mary E., Okello, Erick, Pengo, Valentine, Ochomo, Betha, Ouma, Mary Emmaculate, Were, Simon, Ojuok, Stella, Adoyo, Evelyne
... Background: As countries scale up adult voluntary medical male circumcision (VMMC) for HIV prevention, they are looking ahead to long term sustainable strategies, including introduction of early infant male circumcision (EIMC). Although a number of devices for EIMC are prequalified by the World Health Organization, evaluation of additional devices can provide policy-makers and clinicians the information required to make informed decisions. We undertook a field evaluation of the safety and acceptability of the AccuCirc device in Kisumu County, Kenya. Methods: Procedures were performed by four trained clinicians in two public facilities. Participants were recruited from surrounding public health facilities through informational talks at antenatal clinics, maternity wards, and maternal neonatal child health clinics. Healthy infants ages 0-60 days, with no penile abnormality, without a family history of bleeding disorder, with current weight-for-age within -2 Z-scores of WHO growth standards, and whose mother was at least 16 years of age were eligible for EIMC. The procedure was performed after administration of a penile dorsal nerve block using 2% lidocaine and administration of Vitamin K. The mother was given post-operative instructions on wound care and asked to remain in the clinic with the baby for an observational period of one hour, during which a face-to-face questionnaire was administered. Results: Of 1259 babies screened, 704 were enrolled and circumcised. Median age of the infants was 16 days (IQR: 7-32.5) and of the mothers was 26 years (IQR: 22-30). Median time for the procedure was 19 minutes (IQR: 15-23). There were no serious adverse events (AE), and 20 (2.8%) moderate AEs, all of which were due to bleeding that required application of one to three sutures. There were 22 (3.8%) procedures in which the device did not fully incise the entire circumference of the foreskin and had to be completed using sterile scissors. 89.9% of mothers had knowledge of EIMC, but few (8.1%) had any knowledge of devices used for EIMC. Protection against HIV/AIDS was the most cited reason to circumcise a baby (65.3%), while the baby being ill (38.1%) and pain (34.4%) were the most cited barriers to uptake. 99% of mothers were "very satisfied" or "completely satisfied" with the procedure. Conclusions: This evaluation of the AccuCirc device is the largest to date and indicates that the device is safe and acceptable, achieving high levels of parental satisfaction. The AccuCirc device should be considered for WHO prequalification to increase options for safe and sustainable provision of EIMC.
Contributors: Faust, Ellika, Halvorsen, Kim T, Andersen, Per, Knutsen, Halvor, Carl, André
... The genetic impact of farmed fish escaping aquaculture is a highly debated issue. However, non-target species, such as cleaner fish used to remove sea lice from farmed fish, are rarely considered. Here we report that wild corkwing wrasse (Symphodus melops), which are transported long distances to be used as cleaner fish in salmon farms, escape and hybridize with local populations. Recently, increasing numbers of corkwing wrasse have been reported in Flatanger in Norway, north of its described distribution range, an area heavily relying on import of cleaner fish from Skagerrak. Using genetic markers identified with 2bRAD sequencing, we show that, although the Flatanger population largely is a result of a northwards range expansion, there is also evidence of considerable gene flow from southern populations in Skagerrak and Kattegat. Out of 40 corkwing wrasses sampled in Flatanger, we discovered two individuals with clear southern genotypes, one first generation hybrid, and twelve potential second-generation hybrids. In summary, we provide evidence that corkwing wrasse escape from fish farms and hybridize with local populations at the leading edge of an ongoing range expansion. Although the magnitude and significance of escapees warrants further investigation, these results should be taken in consideration in the use of translocated cleaner fish.
Contributors: Espeland, Marianne, Breinholt, Jesse W., Willmott, Keith R., Warren, Andrew D., Vila, Roger, Toussaint, Emmanuel F. A., Maunsell, Sarah C., Aduse-Poku, Kwaku, Talavera, Gerard, Eastwood, Rodney
... Butterflies (Papilionoidea), with over 18,000 described species , have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species representing 98% of tribes, a 35-fold increase in gene sampling and 3-fold increase in taxon sampling over previous studies . Most data were generated with a new anchored hybrid enrichment (AHE)  gene kit (BUTTERFLY1.0) that includes both new and frequently used (e.g., ) informative loci, enabling direct comparison and future dataset merging with previous studies. Butterflies originated around 119 million years ago (mya) in the late Cretaceous, but most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass-extinction 65 mya. Our analyses support swallowtails (Papilionidae) as sister to all other butterflies, followed by skippers (Hesperiidae) + the nocturnal butterflies (Hedylidae) as sister to the remainder, indicating a secondary reversal from diurnality to nocturnality. The whites (Pieridae) were strongly supported as sister to brush-footed butterflies (Nymphalidae) and blues + metalmarks (Lycaenidae and Riodinidae). Ant association independently evolved once in Lycaenidae and twice in Riodinidae. This study overturns prior notions of the taxon’s evolutionary history, as many long-recognized subfamilies and tribes are para- or polyphyletic. It also provides a much-needed backbone for a revised classification of butterflies and for future comparative studies including genome evolution and ecology.
Contributors: Blanchet, F. Guillaume, Roslin, Tomas, Kimura, Masahito T., Huotari, Tea, Kaartinen, Riikka, Gripenberg, Sofia, Tack, Ayco J. M.
... 1.Within natural communities, different taxa display different dynamics in time. Why this is the case we do not fully know. This thwarts our ability to predict changes in community structure, which is important for both the conservation of rare species in natural communities and for the prediction of pest outbreaks in agriculture. 2.Species sharing phylogeny, natural enemies and/or life history traits have been hypothesized to share similar temporal dynamics. We operationalized these concepts into testing whether feeding guild, voltinism, similarity in parasitoid community, and/or phylogenetic relatedness explained similarities in temporal dynamics among herbivorous community members. 3.Focusing on two similar data sets from different geographical regions (Finland and Japan), we used asymmetric eigenvector maps as temporal variables to characterize species- and community-level dynamics of specialist insect herbivores on oak (Quercus). We then assessed whether feeding guild, voltinism, similarity in parasitoid community, and/or phylogenetic relatedness explained similarities in temporal dynamics among taxa. 4.Species-specific temporal dynamics varied widely, ranging from directional decline or increase to more complex patterns. Phylogeny was a clear predictor of similarity in temporal dynamics at the Finnish site, whereas for the Japanese site, the data were uninformative regarding a phylogenetic imprint. Voltinism, feeding guild and parasitoid overlap explained little variation at either location. Despite the rapid temporal dynamics observed at the level of individual species, these changes did not translate into any consistent temporal changes at the community level in either Finland or Japan. 5.Overall, our findings offer no direct support for the notion that species sharing natural enemies and/or life history traits would be characterised by similar temporal dynamics, but reveal a strong imprint of phylogenetic relatedness. As this phylogenetic signal cannot be attributed to guild, voltinism or parasitoids, it will likely derive from shared microhabitat, microclimate, anatomy, physiology or behaviour. This has important implications for predicting insect outbreaks and for informing insect conservation. We hope that future studies will assess the generality of our findings across plant-feeding insect communities and beyond, and establish the more precise mechanism(s) underlying the phylogenetic imprint.
Contributors: Du, Andrew, Zipkin, Andrew M., Hatala, Kevin G., Renner, Elizabeth, Baker, Jennifer L., Bianchi, Serena, Bernal, Kallista H., Wood, Bernard A.
... A large brain is a defining feature of modern humans, yet there is no consensus regarding the patterns, rates, and processes involved in hominin brain size evolution. We use a reliable proxy for brain size in fossils, endocranial volume (ECV), to better understand how brain size evolved at both clade- and lineage-level scales. For the hominin clade overall, the dominant signal is consistent with a gradual increase in brain size. This gradual trend appears to have been generated primarily by processes operating within hypothesized lineages – 64% or 88% depending on whether one uses a more or less speciose taxonomy, respectively. These processes were supplemented by the appearance in the fossil record of larger-brained Homo species and the subsequent disappearance of smaller-brained Australopithecus and Paranthropus taxa. When the estimated rate of within-lineage ECV increase is compared to an exponential model that operationalizes generation-scale evolutionary processes, it suggests that the observed data were the result of episodes of directional selection interspersed with periods of stasis and/or drift; all of this occurs on too fine a time scale to be resolved by the current human fossil record, thus producing apparent gradual trends within lineages. Our findings provide a quantitative basis for developing and testing scale-explicit hypotheses about the factors that led brain size to increase during hominin evolution.
Data from: Bayesian divergence-time estimation with genome-wide SNP data of sea catfishes (Ariidae) supports Miocene closure of the Panamanian isthmus
Contributors: Stange, Madlen, Sánchez-Villagra, Marcelo R., Salzburger, Walter, Matschiner, Michael
... The closure of the Isthmus of Panama has long been considered to be one of the best defined biogeographic calibration points for molecular divergence-time estimation. However, geological and biological evidence has recently cast doubt on the presumed timing of the initial isthmus closure around 3 Ma but has instead suggested the existence of temporary land bridges as early as the Middle or Late Miocene. The biological evidence supporting these earlier land bridges was based either on only few molecular markers or on concatenation of genome-wide sequence data, an approach that is known to result in potentially misleading branch lengths and divergence times, which could compromise the reliability of this evidence. To allow divergence-time estimation with genomic data using the more appropriate multi-species coalescent model, we here develop a new method combining the SNP-based Bayesian species-tree inference of the software SNAPP with a molecular clock model that can be calibrated with fossil or biogeographic constraints. We validate our approach with simulations and use our method to reanalyze genomic data of Neotropical army ants (Dorylinae) that previously supported divergence times of Central and South American populations before the isthmus closure around 3 Ma. Our reanalysis with the multi-species coalescent model shifts all of these divergence times to ages younger than 3 Ma, suggesting that the older estimates supporting the earlier existence of temporary land bridges were artifacts resulting at least partially from the use of concatenation. We then apply our method to a new RAD-sequencing data set of Neotropical sea catfishes (Ariidae) and calibrate their species tree with extensive information from the fossil record. We identify a series of divergences between groups of Caribbean and Pacific sea catfishes around 10 Ma, indicating that processes related to the emergence of the isthmus led to vicariant speciation already in the Late Miocene, millions of years before the final isthmus closure.
Contributors: Pearse, William David, Morales-Castilla, Ignacio, James, Logan S., Farrell, Maxwell, Boivin, Frédéric, Davies, T. Jonathan
... Studying the macroevolution of the songs of Passeriformes (perching birds) has proved challenging. The complexity of the task stems not just from the macroevolutionary and macroecological challenge of modelling so many species, but also from the difficulty in collecting and quantifying birdsong itself. Using machine learning techniques, we extracted songs from a large citizen science dataset, and then analysed the evolution, and biotic and abiotic predictors of variation in birdsong across 578 passerine species. Contrary to expectations, we found few links between life-history traits (monogamy and sexual dimorphism) and the evolution of song pitch (peak frequency) or song complexity (standard deviation of frequency). However, we found significant support for morphological constraints on birdsong, as reflected in a negative correlation between bird size and song pitch. We also found that broad-scale biogeographical and climate factors such as net primary productivity, temperature, and regional species richness were significantly associated with both the evolution and present-day distribution of bird song features. Our analysis integrates comparative and spatial modelling with newly developed data cleaning and curation tools, and suggests that evolutionary history, morphology, and present-day ecological processes shape the distribution of song diversity in these charismatic and important birds.
Data from: Using public surveys to reliably and rapidly estimate the distributions of multiple invasive species on the Andaman archipelago
Contributors: Mohanty, Nitya Prakash, Sachin, A., Selvaraj, Gayathri, Vasudevan, Karthikeyan
... To effectively manage multiple biological invasions, information on their distributions must be generated rapidly and over large spatial scales. Using public surveys in a false-positive occupancy framework, we reliably estimate the distributions of three synanthropic invasive species on the Andaman Islands.
Contributors: Wang, Lu-Yi, Huang, Wen-San, Tang, Hsin-Chieh, Huang, Lung-Chun, Lin, Chung-Ping
... Anti-predator strategies are significant components of adaptation in prey species. Aposematic prey are expected to possess effective defences that have evolved simultaneously with their warning colours. This study tested the hypothesis of the defensive function and ecological significance of the hard body in aposematic Pachyrhynchus weevils pioneered by Alfred Russel Wallace nearly 150 years ago. We used predation trials with Japalura tree lizards to assess the survivorship of ‘hard’ (mature) vs. ‘soft’ (teneral) and ‘clawed’ (intact) vs. ‘clawless’ (surgically removed) weevils. The ecological significance of the weevil's hard body was evaluated by assessing the hardness of the weevils, the local prey insects, and the bite forces of the lizard populations. The existence of toxins or deterrents in the weevil was examined by gas chromatography-mass spectrometry (GC-MS). All ‘hard’ weevils were instantly spat out after being bitten once and survived attacks by the lizards. In contrast, the ‘soft’ weevils were chewed and subsequently swallowed. The results were the same regardless of the presence or absence of the weevil's tarsal claws. The hardness of ‘hard’ Pachyrhynchus weevils was significantly higher than the average hardness of other prey insects in the same habitat and the mean bite forces of the local lizards. The four candidate compounds of the weevil identified by GC-MS had no known toxic or repellent functions against vertebrates. These results reveal that the hardness of aposematic prey functions as an effective secondary defence, and they provide a framework for understanding the spatio-temporal interactions between vertebrate predators and aposematic insect prey.