Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

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PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.

Section 1. Diversity and Evolution: Introduction Species: their nature and number How many species of insects? Reconstructing evolutionary history Section 2. Fossil Insects: Insect fossilization Dating and ages Major fossil Insect deposits Section 3. Arthropods and the Origin of Insects: Onychophora: the velvet-worms Tardigrada: the water-bears Arthropoda: the jointed animals Hexapoda: the six-legged arthropods Section 4. The insects: Morphology of insects Relationships among the insect orders Section 5. Earliest insects: Archaeognatha: the bristletails Zygentoma: the silverfish +Rhyniognatha Section 6. Insects Take to the Skies: Pterygota, Wings, and flight Ephemeroptera: the mayflies +Palaeodictyopterida: extinct beaked insects Odonatoptera: dragonflies and early relatives Neoptera Section 7. The Polyneopterous Orders: Plecopterida Orthopterida Plecoptera: the stoneflies Embiodea: the webspinners Zoraptera: the Zorapterans Orthoptera: the grasshoppers, crickets, and kin Phasmatodea: the stick- and leaf insects +Titanoptera: the titanic crawlers +Caloneurodea: the Caloneurodeans Dermaptera: the earwigs Grylloblattodea: the ice crawlers Mantophasmatodea: the African rock crawlers Dictyoptera Blattodea: the roaches Citizen roach: the termites Mantodea: the mantises Section 8. The Paraneopteran Orders: Psocoptera: the 'bark'lice Phthiraptera: the true lice Fringe wings: Thysanoptera (thrips) The sucking bugs: Hemiptera Section 9. The Holometabola: problematic fossil orders The origins of complete metamorphosis On wings of lace: Neuropterida Section 10. Coleoptera: early fossils and overview of past diversity Archostemata Adephaga Myxophaga Polyphaga Strepsiptera: the enigmatic order Section 11. Hymenoptera: Ants, Bees, and Other Wasps: The Euhymenoptera and parasitism Aculeata Evolution of insect sociality Section 12. Antliophora: Scorpionflies, Flies, and Fleas: Mecopterida: mecopterans and relatives Siphonaptera: the fleas Evolution of ectoparasites and blood-feeders Diptera: the true flies Section 13. Amphiesmenoptera: The Caddisflies and Lepidoptera: Trichoptera: the caddisflies Lepidoptera: the moths and butterflies Section 14. Insects Become Modern: Cretaceous and Tertiary Periods: The Cretaceous flowering of the world: the Angiosperm Radiations Plant sex and insects: insect pollination Radiations of Phytophagous insects Austral arthropods: remnants of Gondwana? Insects, mass extinctions, and the K/T boundary The tertiary Mammalian radiations Pleistocene dispersal and species lifespans Island faunas Section 15. Epilogue: Why so many insect species? The future Glossary References Index.

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Evolution of the insects

Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.

https://science.sciencemag.org/content/sci/298/5591/129.full.pdf

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

https://science.sciencemag.org/content/sci/346/6210/763.full.pdf

Phylogenomics resolves the timing and pattern of insect evolution

Data from: Phylogenomics resolves the timing and pattern of insect evolution

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Brian M. Wiegmann

Papers

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Linking Evolution, Ecology, and Health: TriCEM

The phylogeny and divergence times of leaf-mining flies (Diptera: Agromyzidae) from anchored phylogenomics.