Richard Baker

American Museum of Natural History · Sackler Institute for Comparative Genomics

Orb-weaver spiders produce upwards of seven different types of silk, each with unique material properties. We focus on the adhesive within orb-weaving spider webs, aggregate glue silk. These droplets are composed of three main components: water, glycoproteins, and a wide range of low molecular mass compounds (LMMCs). These LMMCs are known to play a...

Net-casting spiders (Deinopidae) are cribellate spiders that spin a rectangular, sticky net that is held stretched between the claws of their first two pairs of legs. Deinopids produce eight distinct silk types, but knowledge of the silk-producing morphologies is mostly limited to the spigots associated with different fibers. As there have been no...

Stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio meiotic drive (SR) and impact the fitness of male and female carriers. Here, we assemble and describe a chromosome-level genome assembly of the stalk-eyed fly, Teleopsis dalmanni, to elucidate patterns of divergence associated with SR. The genome contains t...

Arthropod silk is vital to the evolutionary success of hundreds of thousands of species. The primary proteins in silks are often encoded by long, repetitive gene sequences. Until recently, sequencing and assembling these complex gene sequences has proven intractable given their repetitive structure. Here, using high-quality long-read sequencing, we...

Introduction Orb web and cobweb weaving spiders in the superfamily Araneoidea are distinguished by their ability to make a chemically sticky aqueous glue in specialized aggregate silk glands. Aggregate glue is an environmentally responsive material that has evolved to perform optimally around the humidity at which a spider forages. Protein componen...

Arthropod silk is vital to the evolutionary success of hundreds of thousands of species. The primary proteins in silks are often encoded by long, repetitive gene sequences. Until recently, sequencing and assembling these complex gene sequences has proven intractable given their repetitive structure. Here, using high-quality long-read sequencing, we...

The evolutionary diversification of orb-web weaving spiders is closely tied to the mechanical performance of dragline silk. This proteinaceous fiber provides the primary structural framework of orb web architecture, and its extraordinary toughness allows these structures to absorb the high energy of aerial prey impact. The dominant model of draglin...

Background Spiders have evolved two types of sticky capture threads: one with wet adhesive spun by ecribellate orb-weavers and another with dry adhesive spun by cribellate spiders. The evolutionary history of cribellate capture threads is especially poorly understood. Here, we use genomic approaches to catalog the spider-specific silk gene family (...

Spider dragline fibers exhibit incredible mechanical properties, outperforming many synthetic polymers in toughness assays, and possess desirable properties for medical and other human applications. These qualities make dragline fibers popular subjects for biomimetics research. The enormous diversity of spiders presents both an opportunity for the...

Morphological structures and extended phenotypes are made possible by materials that are encoded by the genome. Nearly all biomaterials are viscoelastic, which means that to understand performance, one must understand the strain rate-dependent properties of these materials in relevant ecological interactions, as the behavior of a material can vary...

The origin of aggregate silk glands and their production of wet adhesive silks is considered a key innovation of the Araneoidea, a superfamily of spiders that build orb-webs and cobwebs. Orb-web weavers place aggregate glue on an extensible capture spiral, whereas cobweb weavers add it to the ends of strong, stiff fibers, called gumfoot lines. Here...

Some stalk-eyed flies in the genus Teleopsis carry selfish genetic elements that induce sex ratio (SR) meiotic drive and impact the fitness of male and female carriers. Here, we produce a chromosome-level genome assembly of the stalk-eyed fly, T. dalmanni , to elucidate the pattern of genomic divergence associated with the presence of drive element...

Many species of stalk-eyed flies have a sex-ratio system where some males sire nearly all-female broods due to an X-linked meiotic drive system. Importin aKap genes have been implicated in meiotic drive systems in Drosophila, where some genes show non-Mendelian inheritance because some genotypes of sperm die or are dysfunctional. Importins mediate...

Background Collective animal behavior, such as the flocking of birds or the shoaling of fish, has inspired a class of algorithms designed to optimize distance-based clusters in various applications, including document analysis and DNA microarrays. In a flocking model, individual agents respond only to their immediate environment and move according...

We report the extraction of a bed bug mitogenome from high-throughput sequencing projects originally focused on the nuclear genome of Cimex lectularius. The assembled mitogenome has a similar AT nucleotide composition bias found in other insects. Phylogenetic analysis of all protein-coding genes indicates that C. lectularius is clearly a member of...

Background Collective animal behavior such as the flocking of birds or the shoaling of fish has inspired a class of algorithms designed to optimize distance-based clusters in various applications including document analysis and DNA microarrays. In the flocking model, individual agents respond only to their immediate environment and move according t...

Throughout their evolutionary history, genomes acquire new genetic material that facilitates phenotypic innovation and diversification. Developmental processes associated with reproduction are particularly likely to involve novel genes. Abundant gene creation impacts the evolution of chromosomal gene content and general regulatory mechanisms such a...

The common bed bug (Cimex lectularius) has been a persistent pest of humans for thousands of years, yet the genetic basis of the bed bug's basic biology and adaptation to dense human environments is largely unknown. Here we report the assembly, annotation and phylogenetic mapping of the 697.9-Mb Cimex lectularius genome, with an N50 of 971 kb, usin...

Insects are the most diverse group of organisms on the planet. Variation in gene expression lies at the heart of this biodiversity and recent advances in sequencing technology have spawned a revolution in researchers' ability to survey tissue-specific transcriptional complexity across a wide range of insect taxa. Increasingly, studies are using a c...

Table S1. Recent transcriptome studies in non-model insects.

Although sex chromosome meiotic drive has been observed in a variety of species for over 50 years, the genes causing drive are only known in a few cases, and none of these cases cause distorted sex-ratios in nature. In stalk-eyed flies (Teleopsis dalmanni), driving X chromosomes are commonly found at frequencies approaching 30% in the wild, but the...

Stalk-eyed flies (family Diopsidae) are a model system for studying sexual selection due to the elongated and sexually dimorphic eye-stalks found in many species. These flies are of additional interest because their X chromosome is derived largely from an autosomal arm in other flies. To identify candidate genes required for development of dimorphi...

Exaggerated male ornaments are predicted to be costly to their bearers, but these negative effects may be offset by the correlated evolution of compensatory traits. However, when locomotor systems, such as wings in flying species, evolve to decrease such costs, it remains unclear whether functional changes across related species are achieved via th...

Gene duplication provides an essential source of novel genetic material to facilitate rapid morphological evolution. Traits involved in reproduction and sexual dimorphism represent some of the fastest evolving traits in nature, and gene duplication is intricately involved in the origin and evolution of these traits. Here, we review genomic research...

Protein alignment of bHLH and Bearded genes. Alignment file of the E(spl)-C proteins for all dipteran species used to generate phylogenies in Figure 3. and Figure 4.

In Drosophila, the Enhancer of split complex (E(spl)-C) comprises 11 bHLH and Bearded genes that function during Notch signaling to repress proneural identity in the developing peripheral nervous system. Comparison with other insects indicates that the basal state for Diptera is a single bHLH and Bearded homolog and that the expansion of the gene c...

Recent whole-genome approaches to microbial phylogeny have emphasized partitioning genes into functional classes, often focusing on differences between a stable core of genes and a variable shell. To rigorously address the effects of partitioning and combining genes in genome-level analyses, we developed a novel technique called Random Addition Con...

Summary of gene movement for Teleopsis species. Gene designations are explained in Table S1 legend. ‘Duplicate set’ refers to whether a duplication event was inferred for that gene within stalk-eyed flies based on an analysis of EST consensus sequences. For each gene, the inferred chromosomal locations (A-autosomal, X-X chromosome, and {AX}-unknown...

Gene CGH log ratio values for the four Teleopsis species. In the majority of cases, gene names and IDs correspond to the annotation used for the Drosophila melanogaster genes that are homologous to the Teleopsis ESTs that were the source of the CGH probes. A few genes, that had no significant hit to D. melanogaster, use the gene names for their hom...

Summary information on genotyped loci in T. dalmanni. Sample sizes and heterozygosity (Ho) for each sex, average CGH values, and linkage mapping in relation to chromosomal arm location in D. melanogaster (Dm) are provided. ‘Inf chr.’ provides the chromosomal location based on genotyping, while ‘CGH chr.’ provides the chromosomal location based on C...

Chromosomal location has a significant effect on the evolutionary dynamics of genes involved in sexual dimorphism, impacting both the pattern of sex-specific gene expression and the rate of duplication and protein evolution for these genes. For nearly all non-model organisms, however, knowledge of chromosomal gene content is minimal and difficult t...

Polymorphisms of single amino acid repeats (SARPs) are a potential source of genetic variation for rapidly evolving morphological traits. Here, we characterize variation in and test for an association between SARPs and head shape, a trait under strong sexual selection, in the stalk-eyed fly, Teleopsis dalmanni. Using an annotated expressed sequence...

Background Many species of stalk-eyed flies (Diopsidae) possess highly-exaggerated, sexually dimorphic eye-stalks that play an important role in the mating system of these flies. Eye-stalks are increasingly being used as a model system for studying sexual selection, but little is known about the genetic mechanisms producing variation in these ornam...

EST Assemblies. Nucleotide sequence, EST reads and Genbank accession numbers are provided for 11,545 consensus sequences (conseqs).

EST Annotation. Detailed annotation of 7,066 cluster sequences. Information is provided for the top hit for each cluster blasted against the protein databases of Drosophila melanogaster, Anopheles gambiae and the D. melanogaster Transposable Element database.

Relative rate of protein evolution in Teleopsis dalmanni. Branch length (BL) data for each branch of the ML tree is provided. Columns with species abbreviations indicate the BL for branches leading to terminal taxa. The 'Dm-Dp' column indicates the BL for the node uniting D. melanogaster and D. pseudoobscura and the 'Dros' column indicates the BL f...

EST dipteran alignments. Amino acid alignment files for Teleopsis dalmanni EST translations and proteins for A. gambiae, D. melanogaster, D. pseudoobscura and D. virilis.

Selection line gene expression values. Normalized intensity values and log ratios are presented for each microarray oligonucleotide probe for all eight replicate hybridizations.

The male ejaculate is made up of two components: sperm and non-sperm. There has been little consideration of how these two basic compartments evolve. If they are subject to trade-offs, theory predicts that when the sperm competition raffle is unfair, when seminal fluid proteins stimulate fecundity and/or when ejaculate components alter fertilizatio...

In the taxonomic congruence approach to systematics, data sets are analyzed separately, and corroboration among data sets is indicated by replicated components in topologies derived from the separate analyses. By contrast, in the total evidence and conditional combination approaches, characters from different data sets are mixed in combined phyloge...

Combined analysis of multiple phylogenetic data sets can reveal emergent character support that is not evident in separate analyses of individual data sets. Previous parsimony analyses have shown that this hidden support often accounts for a large percentage of the overall phylogenetic signal in cladistic studies. Here, reanalysis of a large compar...

Traditionally it was thought that fitness-related traits such as male mating frequency, with a history of strong directional selection, should have little additive genetic variance and thus respond asymmetrically to bidirectional artificial selection. However, recent findings and theory suggest that a balance between selection for increased male ma...

Age at first reproduction is an extremely important life-history trait. Several factors such as nutritional state and age-specific fecundity have been shown to influence time to sexual maturity; however, little work has been done in insects. We addressed this in a stalk-eyed fly (Cyrtodiopsis dalmanni), by testing the hypothesis that time to sexual...

Age at first reproduction is an extremely important life-history trait. Several factors such as nutritional state and age-specific fecundity have been shown to influence time to sexual maturity; however, little work has been done in insects. We addressed this in a stalk-eyed fly (Cyrtodiopsis dalmanni), by testing the hypothesis that time to sexual...

Morphological divergence among species may be constrained by the pattern of genetic variances and covariances among traits within species. Assessing the existence of such a relationship in nature requires information on the stability of intraspecific correlation and covariance structure and the correspondence of this structure to the pattern of evo...

The utility of morphological data in modern systematics has recently been challenged because strong selection pressures are thought to create widespread patterns of convergent evolution at this level. This concern has led to suggestions that morphological data should be excluded either from all analyses or at least from analyses where there is conf...

The results of a cladistic analysis based on a combined character matrix consisting of the morphological data set of Meier & Hilger (2000) and the molecular data set of Baker & al. (2001) is presented. The data set is subjected to an extensive sensitivity analysis and equal character weighting is found to perform best according to character incongr...

Over the past ten years the comparative method has taken a central place in evolutionary biology. Following the seminal paper by Felsenstein [1] and the general treatments of Harvey and Pagel [2] and Brooks and McLennan [3], it is now widely recognized that knowledge of phylogenetic relationships among species is critical to understanding the evolu...

Females of the stalk-eyed fly, Cyrtodiopsis dalmanni, mate repeatedly during their lifetime and exhibit mating preference for males with large eye span. How these mating decisions affect female fitness is not fully understood. In this study, we examined the effects of multiple mating and male eye span on short-term reproductive output in this speci...

— Eye stalks and their scaling relationship with body size are important features in the mating system of many diopsid species, and sexual selection is a critical force influencing the evolution of this exaggerated morphology. Interspecific variation in eye span suggests there has been significant evolutionary change in this trait, but a robust phy...

A phylogenetic hypothesis of relationships among 33 species of stalk-eyed flies was generated from a molecular data set comprising three mitochondrial and three nuclear gene regions. A combined analysis of all the data equally weighted produced a single most-parsimonious cladogram with relatively strong support at the majority of nodes. The phyloge...

Polytene chromosome banding patterns have long been used by Drosophila evolutionists to infer degree of relatedness among taxa. Recently, nucleotide sequences have preempted this traditional method. We place the classical Drosophila evolutionary biology tools of polytene chromosome inversion analysis in a phylogenetic context and assess their utili...

The species in the repleta group of the genus Drosophila have been placed into five subgroups-the mulleri, hydei, mercatorum, repleta, and fasciola subgroups. Each subgroup has been further subdivided into complexes and clusters. Extensive morphological and cytological analyses of the members of this species group have formed the foundation for the...

Sperm and female reproductive tract morphology are among the most rapidly evolving characters known in insects. To investigate whether interspecific variation in these traits results from divergent coevolution we examined testis size, sperm length and female reproductive tract morphology for evidence of correlated evolution using 13 species of diop...

Data in this study confirm the validity of a species of muntjac, Muntiacus rooseveltorum, that has been controversial for 60 years. Diagnostic DNA characters are presented for each species examined including the M. rooseveltorum holotype. Three specimens of a recently collected small Laos barking deer have identical sequences to the type specimen o...

An adult male gorilla was donated from private ownership in 1994 to Zoo Atlanta and became part of the American Zoo and Aquarium Association's Gorilla Species Survival Plan. This animal, Ivan, was captured as an infant in Africa in 1964. Ambiguity regarding origin and concomitant sub-species designation was resolved by analyzing the cytochrome oxid...

We examined the contribution of morphological and molecular character information for 15 systematics studies in which these two kinds of data were used in combined or simultaneous analyses. Assessment of the disagreement between these data sources, as measured by the incongruence length difference, reveals substantial conflict for the studies surve...

Relationships among representatives of the five major Hawaiian Drosophila species groups were examined using data from eight different gene regions. A simultaneous analysis of these data resulted in a single most-parsimonious tree that (1) places the adiastola picture-winged subgroup as sister taxon to the other picture-winged subgroups, (2) unites...

Sensory exploitation predicts that female mate preferences exist before the evolution of exaggerated male ornaments. We tested this prediction by estimating female preference functions, remating intervals, and copulation durations for three species of stalk-eyed flies. Two species, Cyrtodiopsis whitei and C dalmanni , exhibit extreme sexual dimorph...

As the pioneer natural historian of the Hawaiian entomofauna, R. C. L. Perkins showed a keen interest in the Diptera, in general, and the Drosophilidae, in particular. Perkins described and named two of the most charismatic of the Hawaiian picture-winged drosophilid flies: Idiomyia heteroneura and I. silvestris. These two species are part of a chro...

Our understanding of insect development and evolution has increased greatly due to recent advances in the comparative developmental approach. Modern developmental biology techniques such as in situ hybridization and molecular analysis of developmentally important genes and gene families have greatly facilitated these advances. The role of the compa...

We used the polymerase chain reaction (PCR) to amplify, clone, and sequence 10 engrailed homeodomains from 8 species in the five major molluscan classes, including the serially organized chiton (Polyplacophora) lineage. The Drosophila melanogaster gene engrailed (en) is one of several genes involved in embryonic segment polarity determination. Stud...

Predictions of optimal foraging theory were tested for Peromyscus polionotus in the laboratory and in two field experiments in which seed item-size was manipulated. In the laboratory, handling times for millet, sunflower seeds, and peanuts were determined. Additionally, energy/handling (E/h) time values were calculated and seed preference experimen...