Jonathan A. Coddington

CLADISTIC TESTS OF ADAPTATIONAL HYPOTHESES

Abstract— A cladistic viewpoint provides an historical definition of adaptation and an operational ecological test for evolutionary adaptations. Adaptation is apomorphic function promoted by natural selection, as compared with plesiomorphic function. Adaptation is thus a conditional, hierarchical, comparative term, like homology. Hypotheses of adaptation that do not specify levels of apomorphy are weak; they should refer to and explain the function at the level at which it is apomorphic with respect to the plesiomorphic (outgroup) condition. The adaptational hypothesis serves as a prior prediction in the comparison of the apomorphic function of the derived trait with the plesiomorphic function of the plesiomorphic trait serving as the null hypothesis. It is useful to distinguish whether hypotheses about characters identify selection as facilitating: 1) the origin of a character; 2) its maintenance; 3) neither; or 4) both. The latter two are uniformitarian and testable in a strong sense. The former two possibilities use ancillary arguments to protect the hypothesis of the role of natural selection in one way or another, but might still be tested by the weak criterion of plausibility. Given an hypothesis of both origin and maintenance due to selection, the test of adaptation may still be thwarted because only certain kinds of cladistic structure allow feasible tests. Few of the really classic and common examples of supraspecific adaptation survive this kind of cladistic test.

ON MISSING ENTRIES IN CLADISTIC ANALYSIS

Abstract The exact algorithms of two commonly used parsimony programs, Hennig86 by J. S. Farris and PAUP by D. Swofford, sometimes produce different solutions, and sometimes produce resolutions that are not supported by the data being analysed. The discrepancies apparently involve the treatment of missing entries, which can currently represent unknown data, inapplicable character and/or polymorphic taxa. Each of those potential sources of ambiguity is logically (if not computationally) different; with regard to binary characters, unknown data could be either 0 or 1, inapplicable characters are neither 0 nor 1 and polymorphisms are both 0 and 1. Resolutions that cannot be supported by any possible combination of known state attributions should either be flagged as such or suppressed entirely.

Reconstructing web evolution and spider diversification in the molecular era

The evolutionary diversification of spiders is attributed to spectacular innovations in silk. Spiders are unique in synthesizing many different kinds of silk, and using silk for a variety of ecological functions throughout their lives, particularly to make prey-catching webs. Here, we construct a broad higher-level phylogeny of spiders combining molecular data with traditional morphological and behavioral characters. We use this phylogeny to test the hypothesis that the spider orb web evolved only once. We then examine spider diversification in relation to different web architectures and silk use. We find strong support for a single origin of orb webs, implying a major shift in the spinning of capture silk and repeated loss or transformation of orb webs. We show that abandonment of costly cribellate capture silk correlates with the 2 major diversification events in spiders (1). Replacement of cribellate silk by aqueous silk glue may explain the greater diversity of modern orb-weaving spiders (Araneoidea) compared with cribellate orb-weaving spiders (Deinopoidea) (2). Within the “RTA clade,” which is the sister group to orb-weaving spiders and contains half of all spider diversity, >90% of species richness is associated with repeated loss of cribellate silk and abandonment of prey capture webs. Accompanying cribellum loss in both groups is a release from substrate-constrained webs, whether by aerially suspended webs, or by abandoning webs altogether. These behavioral shifts in silk and web production by spiders thus likely played a key role in the dramatic evolutionary success and ecological dominance of spiders as predators of insects.

Undersampling bias: the null hypothesis for singleton species in tropical arthropod surveys

1. Frequency of singletons - species represented by single individuals - is anomalously high in most large tropical arthropod surveys (average, 32%). 2. We sampled 5965 adult spiders of 352 species (29% singletons) from 1 ha of lowland tropical moist forest in Guyana. 3. Four common hypotheses (small body size, male-biased sex ratio, cryptic habits, clumped distributions) failed to explain singleton frequency. Singletons are larger than other species, not gender-biased, share no particular lifestyle, and are not clumped at 0.25-1 ha scales. 4. Monte Carlo simulation of the best-fit lognormal community shows that the observed data fit a random sample from a community of approximately 700 species and 1-2 million individuals, implying approximately 4% true singleton frequency. 5. Undersampling causes systematic negative bias of species richness, and should be the default null hypothesis for singleton frequencies. 6. Drastically greater sampling intensity in tropical arthropod inventory studies is required to yield realistic species richness estimates. 7. The lognormal distribution deserves greater consideration as a richness estimator when undersampling bias is severe.

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the worlds terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard operating procedures, and training of students and career scientists. With university, governmental, and industry support, the i5K Consortium aspires to deliver sequences and analytical tools for each of the arthropod branches and each of the species having beneficial and negative effects on humankind.

Inventorying and Estimating Subcanopy Spider Diversity Using Semiquantitative Sampling Methods in an Afromontane Forest

Abstract We investigated the effect of plot-based and unrestricted (plot-less) sampling on an inventory of a megadiverse taxon, spiders, in an Afrotropical forest for the purpose of species richness estimates. We also investigated the efficiency of human-based sampling methods and the effect of allocation of sampling effort to different sampling methods to cover as many microhabitats as possible. In the 10-d sampling period in the montane forest of the Uzungwa Scarp Forest Reserve in Tanzania, eight collectors sampled spiders for 350 h and 800 pitfall “trap-days.” Two hundred hours of sampling were restricted to a 1-ha plot and 150 h of sampling took place outside the plot. The sampling team included both experienced and inexperienced collectors using five different hand collecting methods during day and night sampling periods. Sampling yielded 9,096 adult spiders representing 170 species in total. Number of species and adult spiders per sample and overall species composition depended mainly on the sampling methods used and time of day. Whether the sampling took place within or at random outside the plot did not affect species composition or number of species per sample. Collector experience did affect the number of species collected per hour and thereby overall species composition of the sample but was less important than sampling methods used and time of day.

Global Patterns of Guild Composition and Functional Diversity of Spiders

The objectives of this work are: (1) to define spider guilds for all extant families worldwide; (2) test if guilds defined at family level are good surrogates of species guilds; (3) compare the taxonomic and guild composition of spider assemblages from different parts of the world; (4) compare the taxonomic and functional diversity of spider assemblages and; (5) relate functional diversity with habitat structure. Data on foraging strategy, prey range, vertical stratification and circadian activity was collected for 108 families. Spider guilds were defined by hierarchical clustering. We searched for inconsistencies between family guild placement and the known guild of each species. Richness and abundance per guild before and after correcting guild placement were compared, as were the proportions of each guild and family between all possible pairs of sites. Functional diversity per site was calculated based on hierarchical clustering. Eight guilds were discriminated: (1) sensing, (2) sheet, (3) space, and (4) orb web weavers; (5) specialists; (6) ambush, (7) ground, and (8) other hunters. Sixteen percent of the species richness corresponding to 11% of all captured individuals was incorrectly attributed to a guild by family surrogacy; however, the correlation of uncorrected vs. corrected guilds was invariably high. The correlation of guild richness or abundances was generally higher than the correlation of family richness or abundances. Functional diversity was not always higher in the tropics than in temperate regions. Families may potentially serve as ecological surrogates for species. Different families may present similar roles in the ecosystems, with replacement of some taxa by other within the same guild. Spiders in tropical regions seem to have higher redundancy of functional roles and/or finer resource partitioning than in temperate regions. Although species and family diversity were higher in the tropics, functional diversity seems to be also influenced by altitude and habitat structure.

The functional significance of silk decorations of orb-web spiders: a critical review of the empirical evidence

A number of taxonomically diverse species of araneoid spiders adorn their orb‐webs with conspicuous silk structures, called decorations or stabilimenta. The function of these decorations remains controversial and several explanations have been suggested. These include:(1)stabilising and strengthening the web;(2) hiding and concealing the spider from predators;(3) preventing web damage by larger animals, such as birds;(4) increasing foraging success; or (5) providing a sunshield. Additionally, they may have no specific function and are a consequence of stress or silk regulation. This review evaluates the strength of these explanations based on the evidence. The foraging function has received most supporting evidence, derived from both correlative field studies and experimental manipulations. This contrasts with the evidence provided for other functional explanations, which have not been tested as extensively. A phylogenetic analysis of the different decoration patterns suggests that the different types of decorations are as evolutionary labile as the decorations themselves: the analysis shows little homology and numerous convergences and independent gains. Therefore, it is possible that different types of decorations have different functions, and this can only be resolved by improved species phylogenies, and a combination of experimental and ultimately comparative analyses.

Phylogeny of Extant Nephilid Orb-Weaving Spiders (Araneae, Nephilidae): Testing Morphological and Ethological Homologies

The Pantropical spider clade Nephilidae is famous for its extreme sexual size dimorphism, for constructing the largest orb‐webs known, and for unusual sexual behaviors, which include emasculation and extreme polygamy. We synthesize the available data for the genera Nephila, Nephilengys, Herennia and Clitaetra to produce the first species level phylogeny of the family. We score 231 characters (197 morphological, 34 behavioral) for 61 taxa: 32 of the 37 known nephilid species plus two Phonognatha and one Deliochus species, 10 tetragnathid outgroups, nine araneids, and one genus each of Nesticidae, Theridiidae, Theridiosomatidae, Linyphiidae, Pimoidae, Uloboridae and Deinopidae. Four most parsimonious trees resulted, among which successive weighting preferred one ingroup topology. Neither an analysis of an alternative data set based on different morphological interpretations, nor separate analyses of morphology and behavior are superior to the total evidence analysis, which we therefore propose as the working hypothesis of nephilid relationships, and the basis for classification. Ingroup generic relationships are (Clitaetra (Herennia (Nephila, Nephilengys))). Deliochus and Phonognatha group with Araneidae rather than Nephilidae. Nephilidae is sister to all other araneoids (contra most recent literature). Ethological data, although difficult to obtain and thus frequently missing for rare taxa, are phylogenetically informative. We explore the evolution of selected morphological and behavioral characters, discuss and redefine the homology of palpal sclerites, disprove semientelegyny in spiders, trace the newly interpreted evolution of the orb web, and show that nephilid genital morphologies coevolve with sexual behaviors and extreme sexual size dimorphism. Phylogenetic interpretations of behavior suggest new insights into spider biology and avenues for future research.

From a comb to a tree: phylogenetic relationships of the comb-footed spiders (Araneae, Theridiidae) inferred from nuclear and mitochondrial genes.

The family Theridiidae is one of the most diverse assemblages of spiders, from both a morphological and ecological point of view. The family includes some of the very few cases of sociality reported in spiders, in addition to bizarre foraging behaviors such as kleptoparasitism and araneophagy, and highly diverse web architecture. Theridiids are one of the seven largest families in the Araneae, with about 2200 species described. However, this species diversity is currently grouped in half the number of genera described for other spider families of similar species richness. Recent cladistic analyses of morphological data have provided an undeniable advance in identifying the closest relatives of the theridiids as well as establishing the familys monophyly. Nevertheless, the comb-footed spiders remain an assemblage of poorly defined genera, among which hypothesized relationships have yet to be examined thoroughly. Providing a robust cladistic structure for the Theridiidae is an essential step towards the clarification of the taxonomy of the group and the interpretation of the evolution of the diverse traits found in the family. Here we present results of a molecular phylogenetic analysis of a broad taxonomic sample of the family (40 taxa in 33 of the 79 currently recognized genera) and representatives of nine additional araneoid families, using approximately 2.5kb corresponding to fragments of three nuclear genes (Histone 3, 18SrDNA, and 28SrDNA) and two mitochondrial genes (16SrDNA and CoI). Several methods for incorporating indel information into the phylogenetic analysis are explored, and partition support for the different clades and sensitivity of the results to different assumptions of the analysis are examined as well. Our results marginally support theridiid monophyly, although the phylogenetic structure of the outgroup is unstable and largely contradicts current phylogenetic hypotheses based on morphological data. Several groups of theridiids receive strong support in most of the analyses: latrodectines, argyrodines, hadrotarsines, a revised version of spintharines and two clades including all theridiids without trace of a colulus and those without colular setae. However, the interrelationships of these clades are sensitive to data perturbations and changes in the analysis assumptions.