Contributors: Burbrink, Frank, Futterman, India

Date: 2019-08-25

... Sexual size dimorphism (SSD) is ubiquitous across animals with female bias most prominent in snakes and other ectothermic organisms. To understand how SSD evolves across species, Rensch’s Rule predicts that in taxa where males are larger, SSD increases with body size. In contrast, where females are larger, SSD decreases with body size. While this rule holds for many taxa, it may be ambiguous for others, particularly ectothermic vertebrates. Importantly, this rule suggests that the outcomes of SSD over phylogenetic time scales depends on the direction of dimorphism predicated on the difference in reproductive efforts between males and females. Here we examine SSD in the context of Rensch’s Rule in Thamnophiini, the garter and waternsakes, a prominent group composing the North American snake biota. Using a dated phylogeny, measurements of gape, body and tail size, we show that these snakes do not follow Rensch’s Rule, but rather female-biased SSD increases with body size. We in turn find that this allometry is most pronounced with gape and is correlated with both neonate and litter size, suggesting that acquiring prey of increased size may be directly related to fecundity selection. These changes in SSD are not constrained to any particular clade; we find no evidence of phylogenetic shifts in those traits showing SSD. We suggest several ways forward to better understand the anatomical units of selection for SSD and modularity

Contributors: Franz, Nico M., Musher, Lukas J., Brown, Joseph W., Shizhuo, Yu, Ludäscher, Bertram

Date: 2019-02-18

... Phylogenomic research is accelerating the publication of landmark studies that aim to resolve deep divergences of major organismal groups. Meanwhile, systems for identifying and integrating the products of phylogenomic inference–such as newly supported clade concepts–have not kept pace. However, the ability to verbalize node concept congruence and conflict across multiple, in effect simultaneously endorsed phylogenomic hypotheses, is a prerequisite for building synthetic data environments for biological systematics and other domains impacted by these conflicting inferences. Here we develop a novel solution to the conflict verbalization challenge, based on a logic representation and reasoning approach that utilizes the language of Region Connection Calculus (RCC–5) to produce consistent alignments of node concepts endorsed by incongruent phylogenomic studies. The approach employs clade concept labels to individuate concepts used by each source, even if these carry identical names. Indirect RCC–5 modeling of intensional (property-based) node concept definitions, facilitated by the local relaxation of coverage constraints, allows parent concepts to attain congruence in spite of their differentially sampled children. To demonstrate the feasibility of this approach, we align two recent phylogenomic reconstructions of higher-level avian groups that entail strong conflict in the "neoavian explosion" region. According to our representations, this conflict is constituted by 26 instances of input "whole concept" overlap. These instances are further resolvable in the output labeling schemes and visualizations as "split concepts", which provide the labels and relations needed to build truly synthetic phylogenomic data environments. Because the RCC–5 alignments fundamentally reflect the trained, logic-enabled judgments of systematic experts, future designs for such environments need to promote a culture where experts routinely assess the intensionalities of node concepts published by our peers–even and especially when we are not in agreement with each other.

Contributors: Eliason, Chad, Andersen, Michael, Hackett, Shannon

Date: 2019-02-15

... Color is among the most striking features of organisms, varying not only in spectral properties like hue and brightness, but also in where and how it is produced on the body. Different combinations of colors on a bird’s body are important in both environmental and social contexts. Previous comparative studies have treated plumage patches individually or derived plumage complexity scores from color measurements across a bird’s body. However, these approaches do not consider the multivariate nature of plumages (allowing for plumage to evolve as a whole) or account for interpatch distances. Here, we leverage a rich toolkit used in historical biogeography to assess color pattern evolution in a cosmopolitan radiation of birds, kingfishers (Aves: Alcedinidae). We demonstrate the utility of this approach and test hypotheses about the tempo and mode of color evolution in kingfishers. Our results highlight the importance of considering interpatch distances in understanding macroevolutionary trends in color diversity and demonstrate how historical biogeography models are a useful way to model plumage color pattern evolution. Furthermore, they show that distinct color mechanisms (pigments or structural colors) spread across the body in different ways and at different rates. Specifically, net rates are higher for structural colors than pigment-based colors. Together, our study suggests a role for both development and selection in driving extraordinary color pattern diversity in kingfishers. We anticipate this approach will be useful for modeling other complex phenotypes besides color, such as parasite evolution across the body.

Contributors: Self Davies, Zoe, Spence, Andrew, Wilson, Alan

Date: 2019-02-12

... Horse locomotion is remarkably economical. Here we measure external mechanical work of the galloping horse and relate it to published measurements of metabolic cost. Seven Thoroughbred horses were galloped (ridden) over force plates, under a racing surface. Twenty-six full strides of force data were recorded and used to calculate external mechanical work of galloping. The mean sum of decrements of mechanical energy was -876J (± 280J) per stride and increments were 2163J (± 358J) per stride as horses were accelerating. Combination with published values for internal work and metabolic costs for galloping yield an apparent muscular efficiency of 37-46% for galloping which would be reduced by energy storage in leg tendons. Knowledge about external work of galloping provides further insight into the mechanics of galloping from both an evolutionary and performance standpoint.

Contributors: Eberle, Jonas, Bazzato, Erika, Fabrizi, Silvia, Rossini, Michele, Colomba, Mariastella, Cillo, Davide, Uliana, Marco, Sparacio, Ignazio, Sabatinelli, Guido, Warnock, Rachel

Date: 2018-10-25

... Accurate delimitation of species is crucial for a stable taxonomy, which provides the foundation for the study of evolutionary biology, ecology and essentially all biological disciplines. Several approaches towards impartial and repeatable taxonomic practices are available but all existing methods have potentially unacceptable shortcomings. In particular, problems can arise when the underlying model assumptions are violated, for instance in the presence of reduced gene flow. This is observed in the context of sex-biased dispersal, which is a common but underappreciated feature in many groups of organisms. Previously, simulations have indicated that sex-biased dispersal may lead to erroneous estimations of the true species numbers. However, this phenomenon has never been examined using empirical data. We evaluate the bias introduced by extreme female philopatry on a range of de novo (GMYC, PTP, ABGD, statistical parsimony, trinomial distribution of triplets model [tr2]) and validation (STACEY, iBPP) approaches to species delimitation in the scarab beetle genus Pachypus. Since female philopatry exhibited in this genus in particular can affect mitochondrial gene flow, we compared the results from analyses of single loci, mitochondrial loci, nuclear loci and combined data, as well as the performance of morphometric data as a secondary data source in a fully integrative Bayesian framework. Large overestimation of species numbers was observed across all analyses of combined and mitochondrial DNA datasets, suggesting specimens from nearly every sampling location as separate species. The use of nuclear data resulted in more reasonable estimations of species boundaries, which were largely supported by morphometrics of linear measurements, while geometric morphometrics of body outlines resulted in stronger splitting. Simulations of population divergence with migration, corresponding to the biology of Pachypus, showed that female philopatry strongly increases reciprocal monophyly of mitochondrial markers and may substantially contribute to over-splitting in species delimitation. Robust results recovered using nuclear DNA and morphological data nevertheless enabled us to reach novel conclusions about species boundaries in Pachypus. Our findings suggest that mitochondrial DNA will be less suited to species delimitation in many cases, in particular in the presence of sex-biased dispersal.

Contributors: Salariato, Diego L., Al-Shehbaz, Ihsan A., Zuloaga, Fernando O.

Date: 2018-05-08

... Stenodraba (Brassicaceae) included a group of eight species distributed along the Andes of South-Central Argentina and Chile. All of its species were subsequently transferred to other genera and are currently treated in Pennellia (Tribe Halimolobeae) and Weberbauera (Tribe Thelypodieae). However, the phylogeny of Stenodraba and its tribal placement were never analyzed using molecular data. The lack of such studies, as well as paucity of herbarium collections suggesting that some species are vulnerable and/or endangered, prompted us to address the molecular phylogeny of Stenodraba. For this purpose, we generated comprehensive molecular phylogenies using nuclear (ITS) and plastid (trnL-F and trnH-psbA) data, and conducted different niche comparisons in the environmental and geographic space using climate data processed both by ordination and species distribution modelling (SDM) techniques. The results demonstrated that Stenodraba belongs to the South American tribe Eudemeae and is related to the genera Aschersoniodoxa, Brayopsis, Dactylocardamum, and Eudema. Stenodraba species formed two, strongly supported clades, and although molecular data did not recover monophyly of the genus, this hypothesis was not significantly rejected. The main clades were differentiated in their climatic niches (both in the environmental and geographical spaces), and niche overlap was greater within than between clades. Systematic implications, including a key distinguishing Stenodraba from the remaining genera of Eudemeae and a synopsis of its species, are also provided.

Contributors: Dupuis, Julian, Bremer, Forest, Kauwe, Angela, San Jose, Michael, Leblanc, Luc, Rubinoff, Daniel, Geib, Scott

Date: 2018-03-21

... High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and post-sequencing consensus calling and alignment. This method is inexpensive and amenable to sequencing a large number (hundreds) of taxa simultaneously, requires minimal hands-on time at the bench (150,000 bp concatenated alignment, ~20% missing character sites across all individuals and amplicons) contained >40,000 phylogenetically informative characters, and although some discordance was observed between analyses, it provided unparalleled resolution of many phylogenetic relationships in this group. Most notably, we found high support for the generic status of Zeugodacus and the sister relationship between Dacus and Zeugodacus. We discuss HiMAP, with regard to its molecular and bioinformatic strengths, and the insight the resulting dataset provides into relationships of this diverse insect group.

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

Date: 2018-02-16

... Butterflies (Papilionoidea), with over 18,000 described species [1], 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 [4]. Most data were generated with a new anchored hybrid enrichment (AHE) [5] gene kit (BUTTERFLY1.0) that includes both new and frequently used (e.g., [6]) 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.

Date: 2018-02-08

... 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.

Date: 2018-02-05

... 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.