Data from: Female-biased gape and body-size dimorphism in the New World watersnakes (tribe: Thamnophiini) oppose predictions from Rensch’s Rule
Contributors: Burbrink, Frank, Futterman, India
... 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
Data from: Sex-biased dispersal obscures species boundaries in integrative species delimitation approaches
Contributors: Eberle, Jonas, Bazzato, Erika, Fabrizi, Silvia, Rossini, Michele, Colomba, Mariastella, Cillo, Davide, Uliana, Marco, Sparacio, Ignazio, Sabatinelli, Guido, Warnock, Rachel
... 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: Ng, Julienne, Smith, Stacey D.
... Traits that have arisen multiple times yet still remain rare present a curious paradox. A number of these rare traits show a distinct tippy pattern, where they appear widely dispersed across a phylogeny, are associated with short branches, and differ between recently diverged sister species. This phylogenetic pattern has classically been attributed to the trait being an evolutionary dead end, where the trait arises due to some short‐term evolutionary advantage, but it ultimately leads species to extinction. While the higher extinction rate associated with a dead end trait could produce such a tippy pattern, a similar pattern could appear if lineages with the trait speciated slower than other lineages, or if the trait was lost more often that it was gained. In this study, we quantify the degree of tippiness of red flowers in the tomato family, Solanaceae, and investigate the macroevolutionary processes that could explain the sparse phylogenetic distribution of this trait. Using a suite of metrics, we confirm that red‐flowered lineages are significantly overdispersed across the tree and form smaller clades than expected under a null model. Next, we fit 22 alternative models using HiSSE (Hidden State Speciation and Extinction), which accommodates asymmetries in speciation, extinction and transition rates that depend on observed and unobserved (hidden) character states. Results of the model fitting indicated significant variation in diversification rates across the family, which is best explained by the inclusion of hidden states. Our best fitting model differs between the maximum clade credibility tree and when incorporating phylogenetic uncertainty, suggesting that the extreme tippiness and rarity of red Solanaceae flowers makes it difficult to distinguish among different underlying processes. However, both of the best models strongly support a bias towards the loss of red flowers. The best fitting HiSSE model when incorporating phylogenetic uncertainty lends some support to the hypothesis that lineages with red flowers exhibit reduced diversification rates due to elevated extinction rates. Future studies employing simulations or targeting population‐level processes may allow us to determine whether red flowers in Solanaceae or other angiosperms clades are rare and tippy due to a combination of processes, or asymmetrical transitions alone.
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Contributors: Oaks, Jamie
... A challenge to understanding biological diversification is accounting for community-scale processes that cause multiple, co-distributed lineages to co-speciate. Such processes predict non-independent, temporally clustered divergences across taxa. Approximate-likelihood Bayesian computation (ABC) approaches to inferring such patterns from comparative genetic data are very sensitive to prior assumptions and often biased toward estimating shared divergences. We introduce a full-likelihood Bayesian approach, ecoevolity, which takes full advantage of information in genomic data. By analytically integrating over gene trees, we are able to directly calculate the likelihood of the population history from genomic data, and efficiently sample the model-averaged posterior via Markov chain Monte Carlo algorithms. Using simulations, we find that the new method is much more accurate and precise at estimating the number and timing of divergence events across pairs of populations than existing approximate-likelihood methods. Our full Bayesian approach also requires several orders of magnitude less computational time than existing ABC approaches. We find that despite assuming unlinked characters (e.g., unlinked single-nucleotide polymorphisms), the new method performs better if this assumption is violated in order to retain the constant characters of whole linked loci. In fact, retaining constant characters allows the new method to robustly estimate the correct number of divergence events with high posterior probability in the face of character-acquisition biases, which commonly plague loci assembled from reduced-representation genomic libraries. We apply our method to genomic data from four pairs of insular populations of Gekko lizards from the Philippines that are not expected to have co-diverged. Despite all four pairs diverging very recently, our method strongly supports that they diverged independently, and these results are robust to very disparate prior assumptions.
Data from: Phylogenomic mining of the mints reveals multiple mechanisms contributing to the evolution of chemical diversity in Lamiaceae
Contributors: Mint Evolutionary Genomics Consortium
... The evolution of chemical complexity has been a major driver of plant diversification, with novel compounds serving as key innovations. The species-rich mint family (Lamiaceae) produces an enormous variety of compounds that act as attractants and defense molecules in nature and are used widely by humans as flavor additives, fragrances, and anti-herbivory agents. To elucidate the mechanisms by which such diversity evolved, we combined leaf transcriptome data from 48 Lamiaceae species and four outgroups with a robust phylogeny and chemical analyses of three terpenoid classes (monoterpenes, sesquiterpenes, iridoids) that share and compete for precursors. Our integrated chemical-genomic-phylogenetic approach revealed that: 1) gene family expansion rather than increased enzyme promiscuity of terpene synthases is correlated with mono- and sesqui-terpene diversity; 2) differential expression of core genes within the iridoid biosynthetic pathway is associated with iridoid presence/absence; 3) generally, production of iridoids and canonical monoterpenes appeared to be inversely correlated; and 4) iridoid biosynthesis was significantly associated with expression of geraniol synthase, which diverts metabolic flux away from canonical monoterpenes, suggesting that competition for common precursors can be a central control point in specialized metabolism. These results suggest that multiple mechanisms contributed to the evolution of chemodiversity in this economically important family. ----------MINT EVOLUTIONARY GENOMICS CONSORTIUM MEMBERS: Benoît Boachon¹, C. Robin Buell², Emily Crisovan², Natalia Dudareva¹, Nicolas Garcia³*, Grant Godden² ³, Laura Henry¹, Mohamed O. Kamileen⁴, Heather Rose Kates³, Matthew B. Kilgore¹, Benjamin R. Lichman⁴, Evgeny V. Mavrodiev³, Linsey Newton², Carlos Rodriguez-Lopez⁴, Sarah E. O’Connor⁴, Douglas Soltis³ ⁵, Pamela Soltis³, Brieanne Vaillancourt², Krystle Wiegert-Rininger², Dongyan Zhao² ---------- ¹Department of Biochemistry, Purdue University, West Lafayette, IN 47907-2063, USA ²Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA ³Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA ⁴The John Innes Centre, Department of Biological Chemistry, Norwich, NR4 7UH, UK ⁵Department of Biology, University of Florida, Gainesville, FL 32611, USA ---------- Current address: *Herbario EIF/Laboratorio de Sistemática y Evolución de Plantas, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Av. Santa Rosa 11315, La Pintana, Santiago, Chile ---------- For Correspondence: C. Robin Buell; firstname.lastname@example.org; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; 517-353-5597
Data from: Finite element analysis of microwave scattering from a three dimensional human head model for brain stroke detection
Contributors: Qureshi, Awais M., Mustansar, Zartasha, Mustafa, Samah
... In this paper, a detailed analysis of microwave scattering from a three dimensional (3-D) anthropomorphic human head model is presented. It is the first time that Finite Element Method (FEM) has been deployed to study the microwave scattering phenomenon of a 3-D realistic head model for brain stroke detection. A major contribution of this paper is to add anatomically more realistic details into the human head model compared to the literature available to-date. Using MRI database, a 3-D numerical head model was developed and segmented into 21 different types through a novel tissue mapping scheme and a mixed-model approach. The heterogeneous and frequency-dispersive dielectric properties to brain tissues were assigned using the same mapping technique. To mimic the simulation setup, an 8-elements antenna array around the head model was designed using dipole antennas. Two types of brain stroke (Hemorrhagic and Ischemic) at various locations inside the head model were then analyzed for possible detection and classification. The transmitted and backscattered signals were calculated by finding out the solution of Helmholtz wave equation in frequency-domain using FEM. FE mesh convergence analysis for electric field values and comparison between different types of iterative solver were also performed to obtain error-free results in a minimum computational time. At the end, a Specific Absorption Rate analysis was conducted to examine the ionization effects of microwave signals to a 3-D human head model. Through computer simulations, it is foreseen that microwave imaging may efficiently be exploited to locate and differentiate two types of brain stroke by detecting abnormal tissue’s dielectric properties. A significant contrast between electric field values of the normal and stroke affected brain tissues was observed at the stroke location. This is a step towards generating microwave scattering information for the development of an efficient image reconstruction algorithm.
Data from: Dispersal is associated with morphological innovation, but not increased diversification, in Cyphostemma (Vitaceae)
Contributors: Hearn, David J, Evans, Margaret, Wolf, Ben, McGinty, Michael, Wen, Jun
... Multiple processes - including dispersal, morphological innovation, and habitat change - are frequently cited as catalysts for increased diversification. We investigate these processes and the causal linkages among them in the genus Cyphostemma (Vitaceae), a clade comprising ~200 species that is unique in the Vitaceae for its diversity of growth habits. We reconstruct time-calibrated evolutionary relationships among 64 species in the genus using five nuclear and chloroplast markers, and infer the group’s morphological and biogeographic history. We test for changes in speciation rate, and evaluate the temporal association and sequencing of events with respect to dispersal, habitat change, and morphological evolution using a Monte Carlo simulation approach. In Cyphostemma, neither dispersal nor morphological evolution is associated with shifts in speciation rate, but dispersal is associated with evolutionary shifts in growth form. Evolution of stem succulence, in particular, is associated with adaptation to local, pre-existing conditions following long-distance dispersal, not habitat change in situ. We suggest that the pattern of association between dispersal, morphological innovation, and diversification may depend on the particular characters under study. Lineages with evolutionarily labile characters, such as stem succulence, do not necessarily conform to the notion of niche conservatism and instead demonstrate remarkable morphological adaptation to local climate and edaphic conditions following dispersal.
Contributors: Dupuis, Julian, Bremer, Forest, Kauwe, Angela, San Jose, Michael, Leblanc, Luc, Rubinoff, Daniel, Geib, Scott
... 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.
Data from: A biting commentary: integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume “killer algae”
Contributors: Berriman, John S., Ellingson, Ryan A., Awbrey, Jaymes D., Rico, Diane M., Valdes, Angel A., Wilson, Nerida G., Aguilar, Andres, Herbert, David G., Hirano, Yayoi M., Trowbridge, Cynthia D.
... Predicting biotic resistance to highly invasive strains of “killer algae” (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe. Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae.
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.