Phylogenetic incongruence and the evolutionary origins of cardenolide-resistant forms of Na(+) ,K(+) -ATPase in Danaus butterflies

Selection Shapes the Genomic Landscape of Introgressed Ancestry in a Pair of Sympatric Sea Urchin Species

A growing number of recent studies have demonstrated that introgression is common across the tree of life. However, we still have a limited understanding of the fate and fitness consequence of introgressed variation at the whole-genome scale across diverse taxonomic groups. Here, we implemented a phylogenetic hidden Markov model to identify and characterize introgressed genomic regions in a pair of well-diverged, nonsister sea urchin species: Strongylocentrotus pallidus and Strongylocentrotus droebachiensis. Despite the old age of introgression, a sizable fraction of the genome (1% to 5%) exhibited introgressed ancestry, including numerous genes showing signals of historical positive selection that may represent cases of adaptive introgression. One striking result was the overrepresentation of hyalin genes in the identified introgressed regions despite observing considerable overall evidence of selection against introgression. There was a negative correlation between introgression and chromosome gene density, and two chromosomes were observed with considerably reduced introgression. Relative to the nonintrogressed genome-wide background, introgressed regions had significantly reduced nucleotide divergence (dXY) and overlapped fewer protein-coding genes, coding bases, and genes with a history of positive selection. Additionally, genes residing within introgressed regions showed slower rates of evolution (dN, dS, dN/dS) than random samples of genes without introgressed ancestry. Overall, our findings are consistent with widespread selection against introgressed ancestry across the genome and suggest that slowly evolving, low-divergence genomic regions are more likely to move between species and avoid negative selection following hybridization and introgression.

Genome sequence of Ophryocystis elektroscirrha, an apicomplexan parasite of monarch butterflies: cryptic diversity and response to host-sequestered plant chemicals

Apicomplexa are ancient and diverse organisms which have been poorly characterized by modern genomics. To better understand the evolution and diversity of these single-celled eukaryotes, we sequenced the genome of Ophryocystis elektroscirrha, a parasite of monarch butterflies, Danaus plexippus. We contextualize our newly generated resources within apicomplexan genomics before answering longstanding questions specific to this host-parasite system. To start, the genome is miniscule, totaling only 9 million bases and containing fewer than 3,000 genes, half the gene content of two other sequenced invertebrate-infecting apicomplexans, Porospora gigantea and Gregarina niphandrodes. We found that O. elektroscirrha shares different orthologs with each sequenced relative, suggesting the true set of universally conserved apicomplexan genes is very small indeed. Next, we show that sequencing data from other potential host butterflies can be used to diagnose infection status as well as to study diversity of parasite sequences. We recovered a similarly sized parasite genome from another butterfly, Danaus chrysippus, that was highly diverged from the O. elektroscirrha reference, possibly representing a distinct species. Using these two new genomes, we investigated potential evolutionary response by parasites to toxic phytochemicals their hosts ingest and sequester. Monarch butterflies are well-known to tolerate toxic cardenolides thanks to changes in the sequence of their Type II ATPase sodium pumps. We show that Ophryocystis completely lacks Type II or Type 4 sodium pumps, and related proteins PMCA calcium pumps show extreme sequence divergence compared to other Apicomplexa, demonstrating new avenues of research opened by genome sequencing of non-model Apicomplexa.

Genomic evidence of speciation by fusion in a recent radiation of grasshoppers

Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.

Genomic evidence suggests further changes of butterfly names

Further genomic sequencing of butterflies by our research group expanding the coverage of species and specimens from different localities, coupled with genome-scale phylogenetic analysis and complemented by phenotypic considerations, suggests a number of changes to the names of butterflies, mostly those recorded from the United States and Canada. Here, we present evidence to support these changes. The changes are intended to make butterfly classification more internally consistent at the genus, subgenus and species levels. I.e., considering all available evidence, we attempt to assign similar taxonomic ranks to the clades of comparable genetic differentiation, which on average is correlated with the age of phylogenetic groups estimated from trees. For species, we use criteria devised by genomic analysis of the genetic differentiation across suture zones and comparison of sympatric populations of closely related species. As a result, we resurrect 4 genera and 1 subgenus from subgeneric status or synonymy, change the rank of 8 currently used genera to subgenus, synonymize 7 genus-group names, summarize evidence to support 19 taxa as species instead of subspecies and 1 taxon as subspecies instead of species, along with a number of additional changes. One new genus and one new subspecies are described. Namely, the following taxa are treated as genera Tharsalea Scudder, 1876, Helleia Verity, 1943, Apangea Zhdanko, 1995, and Boldenaria Zhdanko, 1995. Tetracharis Grote, 1898 is a valid subgenus (not a synonym of Anthocharis Boisduval, Rambur, [Duménil] & Graslin, [1833]) that consists of Anthocharis cethura C. Felder & R. Felder, 1865 (Müller, 1764), Anthocharis midea (Hübner, [1809]), and Anthocharis limonea (A. Butler, 1871). The following are subgenera: Speyeria Scudder, 1872 of Argynnis Fabricius, 1807; Aglais Dalman, 1816 and Polygonia Hübner, [1819] of Nymphalis Kluk, 1780; Palaeonympha Butler, 1871 of Megisto Hübner, [1819]; Hyponephele Muschamp, 1915 of Cercyonis Scudder, 1875; Pyronia Hübner, [1819] and Aphantopus Wallengren, 1853 of Maniola Schrank, 1801 and Pseudonymphidia Callaghan, 1985 of Pachythone. Lafron Grishin, gen. n. (type species Papilio orus Stoll, [1780], parent subfamily Lycaeninae [Leach], [1815]) is described. Dipsas japonica Murray, 1875 is fixed as the type species of Neozephyrus Sibatani & Ito, 1942. The following taxa are junior subjective synonyms: Falcapica Klots, 1930 of Tetracharis Grote, 1898; Habrodais Scudder, 1876, Favonius Sibatani & Ito, 1942, Neozephyrus Sibatani & Ito, 1942, Quercusia Verity, 1943, Chrysozephyrus Shirôzu & Yamamoto, 1956, and Sibataniozephyrus Inomata, 1986 of Hypaurotis Scudder, 1876; Plesioarida Trujano & García, 2018 of Roeberella Strand, 1932; Papilio temenes Godart, 1819 (lectotype designated herein) of Heraclides aristodemus (Esper, 1794), Speyeria hydaspe conquista dos Passos & Grey, 1945 of Argynnis hesperis tetonia (dos Passos & Grey, 1945), and Erycides imbreus Plötz, 1879 of Phocides polybius polybius (Fabricius, 1793). The following are revised genus-species combinations: Pachythone lencates (Hewitson, 1875) Pachythone flocculus (Brévignon & Gallard, 1993), Pachythone floccus (Brévignon, 2013), Pachythone heberti (P. Jauffret & J. Jauffret, 2007), Pachythone marajoara (P. Jauffret & J. Jauffret, 2007) and Cissia cleophes (Godman & Salvin, 1889). The following species are transferred between subgenera: Anthocharis lanceolata Lucas, 1852 belongs to Anthocharis Boisduval, Rambur, [Duménil] & Graslin, [1833] instead of Paramidea Kuznetsov, 1929 and Danaus eresimus (Cramer, 1777) belongs to Danaus Kluk, 1780, and not to Anosia Hübner, 1816. The following taxa are distinct species rather than subspecies (of species shown in parenthesis): Heraclides ponceana (Schaus, 1911) (not Heraclides aristodemus (Esper, 1794)), Colias elis Strecker, 1885 (not Colias meadii W. H. Edwards, 1871), Argynnis irene Boisduval, 1869 and Argynnis nausicaa W. H. Edwards, 1874 (not Argynnis hesperis W. H. Edwards, 1864), Coenonympha california Westwood, [1851] (not Coenonympha tullia (Müller, 1764)), Dione incarnata N. Riley, 1926 (not Dione vanillae (Linnaeus, 1758)), Chlosyne coronado (M. Smith & Brock, 1988) (not Chlosyne fulvia (W. H. Edwards, 1879)), Chlosyne chinatiensis (Tinkham, 1944) (not Chlosyne theona (Ménétriés, 1855)), Phocides lilea (Reakirt, [1867]) (not Phocides polybius (Fabricius, 1793)), Cecropterus nevada (Scudder, 1872) and Cecropterus dobra (Evans, 1952) (not Cecropterus mexicana (Herrich-Schäffer, 1869)), Telegonus anausis Godman & Salvin, 1896, (not Telegonus anaphus (Cramer, 1777)), Epargyreus huachuca Dixon, 1955 (not Epargyreus clarus (Cramer, 1775)), Nisoniades bromias (Godman & Salvin, 1894) (not Nisoniades rubescens (Möschler, 1877)), Pholisora crestar J. Scott & Davenport, 2017 (not Pholisora catullus (Fabricius, 1793)), Carterocephalus mandan (W. H. Edwards, 1863) and Carterocephalus skada (W. H. Edwards, 1870) (not Carterocephalus palaemon (Pallas, 1771)), Amblyscirtes arizonae H. Freeman, 1993 (not Amblyscirtes elissa Godman, 1900), and Megathymus violae D. Stallings & Turner, 1956 (not Megathymus ursus Poling, 1902). Resulting from these changes, the following are revised species-subspecies combinations: Heraclides ponceana bjorndalae (Clench, 1979), Heraclides ponceana majasi L. Miller, 1987, Argynnis irene dodgei Gunder, 1931, Argynnis irene cottlei J. A. Comstock, 1925, Argynnis irene hanseni (J. Emmel, T. Emmel & Mattoon, 1998), Argynnis nausicaa elko (Austin, 1984), Argynnis nausicaa greyi (Moeck, 1950), Argynnis nausicaa viola (dos Passos & Grey, 1945), Argynnis nausicaa tetonia (dos Passos & Grey, 1945), Argynnis nausicaa chitone W. H. Edwards, 1879, Argynnis nausicaa schellbachi (Garth, 1949), Argynnis nausicaa electa W. H. Edwards, 1878, Argynnis nausicaa dorothea (Moeck, 1947), and Argynnis nausicaa capitanensis (R. Holland, 1988), Argynnis zerene atossa W. H. Edwards, 1890, Dione incarnata nigrior (Michener, 1942), Chlosyne coronado pariaensis (M. Smith & Brock, 1988), Cecropterus nevada aemilea (Skinner, 1893), Cecropterus nevada blanca (J. Scott, 1981), Telegonus anausis annetta (Evans, 1952), Telegonus anausis anoma (Evans, 1952), Telegonus anausis aniza (Evans, 1952), Epargyreus huachuca profugus Austin, 1998, Carterocephalus mandan mesapano (Scudder, 1868) and Carterocephalus skada magnus Mattoon & Tilden, 1998. American Coenonympha subspecies placed under C. tullia other than Coenonympha tullia kodiak W. H. Edwards, 1869, Coenonympha tullia mixturata Alpheraky, 1897 and Coenonympha tullia yukonensis W. Holland, 1900 belong to C. california. Heraclides ponceana latefasciatus Grishin, ssp. n. is described from Cuba. Argynnis coronis carolae dos Passos & Grey, 1942 is considered a subspecies-level taxon. Unless stated otherwise, all subgenera, species, subspecies and synonyms of mentioned genera and species are transferred together with their parent taxa, and others remain as previously classified.

Plant Secondary Metabolites Modulate Insect Behavior-Steps Toward Addiction?

Plants produce a diversity of secondary metabolites (PSMs) that serve as defense compounds against herbivores and microorganisms. In addition, some PSMs attract animals for pollination and seed dispersal. In case of pollinating insects, PSMs with colors or terpenoids with fragrant odors attract pollinators in the first place, but when they arrive at a flower, they are rewarded with nectar, so that the pollinators do not feed on flowers. In order to be effective as defense chemicals, PSMs evolved as bioactive substances, that can interfere with a large number of molecular targets in cells, tissues and organs of animals or of microbes. The known functions of PSMs are summarized in this review. A number of PSMs evolved as agonists or antagonists of neuronal signal transduction. Many of these PSMs are alkaloids. Several of them share structural similarities to neurotransmitters. Evidence for neuroactive and psychoactive PSMs in animals will be reviewed. Some of the neuroactive PSMs can cause addiction in humans and other vertrebrates. Why should a defense compound be addictive and thus attract more herbivores? Some insects are food specialists that can feed on plants that are normally toxic to other herbivores. These specialists can tolerate the toxins and many are stored in the insect body as acquired defense chemicals against predators. A special case are pyrrolizidine alkaloids (PAs) that are neurotoxic and mutagenic in vertebrates. PAs are actively sequestered by moths of the family Arctiidae and a few other groups of arthropods. In arctiids, PAs are not only used for defense, but also serve as morphogens for the induction of male coremata and as precursors for male pheromones. Caterpillars even feed on filter paper impregnated with pure PAs (that modulate serotonin receptors in vertebrates and maybe even in insects) and thus show of behavior with has similarities to addiction in vertebrates. Not only PA specialists, but also many monophagous herbivores select their host plants according to chemical cues i.e., PSMs) and crave for plants with a particular PSMs, again a similarity to addiction in vertebrates.

Missing data, clade support and "reticulation": the molecular systematics of Heliconius and related genera (Lepidoptera: Nymphalidae) re-examined

Kozak et al. (2015, Syst. Biol., 64: 505) portrayed the inference of evolutionary history among Heliconius and allied butterfly genera as a particularly difficult problem for systematics due to prevalent gene conflict caused by interspecific reticulation. To control for this, Kozak et al. conducted a series of multispecies coalescent phylogenetic analyses that they claimed revealed pervasive conflict among markers, but ultimately chose as their preferred hypothesis a phylogenetic tree generated by the traditional supermatrix approach. Intrigued by this seemingly contradictory set of conclusions, we conducted further analyses focusing on two prevalent aspects of the data set: missing data and the uneven contribution of phylogenetic signal among markers. Here, we demonstrate that Kozak et al. overstated their findings of reticulation and that evidence of gene-tree conflict is largely lacking. The distribution of intrinsic homoplasy and incongruence homoplasy in their data set does not follow the pattern expected if phylogenetic history had been obscured by pervasive horizontal gene flow; in fact, noise within individual gene partitions is ten times higher than the incongruence among gene partitions. We show that the patterns explained by Kozak et al. as a result of reticulation can be accounted for by missing data and homoplasy. We also find that although the preferred topology is resilient to missing data, measures of support are sensitive to, and strongly eroded by too many empty cells in the data matrix. Perhaps more importantly, we show that when some taxa are missing almost all characters, adding more genes to the data set provides little or no increase in support for the tree.

Mutational Biases Influence Parallel Adaptation

While mutational biases strongly influence neutral molecular evolution, the role of mutational biases in shaping the course of adaptation is less clear. Here we consider the frequency of transitions relative to transversions among adaptive substitutions. Because mutation rates for transitions are higher than those for transversions, if mutational biases influence the dynamics of adaptation, then transitions should be overrepresented among documented adaptive substitutions. To test this hypothesis, we assembled two sets of data on putatively adaptive amino acid replacements that have occurred in parallel during evolution, either in nature or in the laboratory. We find that the frequency of transitions in these data sets is much higher than would be predicted under a null model where mutation has no effect. Our results are qualitatively similar even if we restrict ourself to changes that have occurred, not merely twice, but three or more times. These results suggest that the course of adaptation is biased by mutation.