Conodonts Meet Cladistics: Recovering Relationships and Assessing the Completeness of the Conodont Fossil Record

A numerical cladistic analysis of the conodont family Palmatolepidae has been undertaken to determine the applicability of the technique to group-wide systematic revision. Results suggest a new hypothesis of relationships that is considerably more parsimonious than trees compatible with existing hypotheses of relationships, or trees that are even loosely constrained stratigraphically. This may occur either because the fossil record is incomplete, because taxon sampling for the cladistic analysis is low, or because the most parsimonious trees approximate the true tree less well than do stratigraphically-constrained trees (or because of a combination of these factors). Although more taxa and more characters would be preferable in choosing between these possibilities, the tree derived solely from morphological data is adopted. Thus, stratigraphic data can be used to test hypotheses of relationships and construct phylogenies; hypotheses of relationships can be used to test the completeness of the conodont fossil record. Existing schemes of classification within the Palmatolepidae are rejected because most groups within them are either polyphyletic or paraphyletic. A new scheme is presented. Character changes suggest correlated, progressive and mosaic evolution within the Palmatolepidae. Parsimony analysis of partitioned datasets indicates that more phylogenetic information can be recovered from S rather than P or M element positions, although data from all three positional groups are preferable to data from just one. Thus, multielement taxonomy is essential to the resolution of conodont interrelationships.     

ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE

Abstract — Randomization routines have quickly gained wide usage in phylogenetic systematies. Introduced a decade ago, the jackknife has rarely been applied in cladistic methodology. This data resampling technique was re-investigated here as a means to discover the effect that taxon removal may have on the stability of the results obtained from parsimony analyses. This study shows that the removal of even a single taxon in an analysis can cause a solution of relatively few multiple equally parsimonious trees in an inclusive matrix to result in hundreds of equally parsimonious trees with the single removal of a taxon. On the other hand, removal of other taxa can stabilize the results to fewer trees. An index of clade stability, the Jackknife Monophyly Index (JMI) is developed which, like the bootstrap, applies a value to each clade according to its frequency of occurrence in jackknife pseudoreplicates. Unlike the bootstrap and earlier application of the jackknife, alternative suboptimal hypotheses are not forwarded by this method. Only those clades in the most parsimonious tree(s) are given JMI values. The behaviour of this index is investigated both in relation to a hypothetical and a real data set, as well as how it performs in comparison to the bootstrap. The JMI is found to not be influenced by uninformative characters or relative synapomorphy number, unlike the bootstrap.     

Revisiting the ants of Melanesia and the taxon cycle: historical and human-mediated invasions of a tropical archipelago

Understanding the historical evolution of biotas and the dynamics of contemporary human-mediated species introductions are two central tasks of biology. One hypothesis may address both-the taxon cycle. Taxon cycles are phases of range expansion and contraction coupled to ecological and evolutionary niche shifts. These historical invasion processes resemble human-mediated invasions in pattern and possibly mechanism, but both the existence of historical cycles and the roles of recent introductions are in question. We return to the system that originally inspired the taxon cycle-Melanesian ants-and perform novel tests of the hypothesis. We analyze (i) the habitat distributions of Fiji's entire ant fauna (183 species), (ii) ecological shifts associated with the in situ radiation of Fijian Pheidole in a phylogenetic context, and (iii) the ecological structure of a massive exotic ant invasion of the archipelago. Our analyses indicate lineages shift toward primary habitats, higher elevation, rarity, and ecological specialization with increasing level of endemism, consistent with taxon cycle predictions. The marginal habitats that historically formed a dispersal conduit in the Pacific are now mostly replaced by human-modified habitats dominated by a colonization pulse of exotic species. We propose this may represent the first phase of an incipient global cycle of human-mediated colonization, ecological shifts, and diversification.     

"ALL TREE HISTOGRAMS" AND THE EVALUATION OF CLADISTIC EVIDENCE: SOME AMBIGUITIES

Abstract— Inspection of trees of varying lengths (by the option ALL TREES, which produces a histogram for tree lengths in PAUP 3.0) has been used to evaluate cladistic data and results. For example, a result may be judged more effective if the groups supported in the most parsimonious tree are preserved in trees that require increasingly greater amounts of homoplasy. Evaluation of grouping purely on the basis of this stability criterion ignores other highly relevant aspects of cladistic results. In particular, some data sets may incorporate additional taxa that introduce homoplasy to the shortest tree in a manner that concurrently allows for a revised understanding of character optimization patterns. These taxa may render groups preserved in the shortest tree less stable, but this result is not necessarily deficient if the homoplasy underlying such instability reveals possible character state changes for the given taxa irretrievable from the original matrix. The hypothetical example described here is relevant to so called "stem", "basal" or "plesiomorphic sister" taxa that are commonly considered in studies of both fossil and extant taxa.     

Habitat preferences and diet in the predatory Coccinellidae (Coleoptera): an evolutionary perspective

Coccinellids (ladybird beetles) exhibit considerable diversity in habitat and dietary preference and specificity. This is evident even when comparing species within some coccinellid genera. Resource limitation and competition are suggested as of greatest importance in the evolution of coccinellid habitat preferences. Dietary and habitat specialization has probably occurred in some lineages within broader preferences possessed by generalist ancestors, to avoid the costs associated with migration between habitats and prey switching. Feeding in atypical habitats, on alternative food, when optimal prey are scarce, is likely to have been of great importance in facilitating evolutionary shifts to novel diets and habitats. The broad host ranges of many coccinellid parasitoids and observed interspecific differences in parasitoid prevalence resulting from physiological differences between coccinellid species argue that enemy free space has been of limited importance in habitat and prey shifts in this group. Rapid change may occur in coccinellid foraging patterns, perhaps due to conditioning, and coccinellids may swiftly adapt to new habitats through selection acting on the expression pre-existing traits. Diet, as a determinant of coccinellid migration and gene flow, is likely to affect probable modes of speciation in different coccinellid groups. Parapatric speciation and possibly sympatric speciation are suggested as of possible importance in the genesis of new coccinellid species through prey and habitat shifts.     

Forum – Taxonomic Stability is Ignorance

Absolute nomenclatural stability is undesirable in phylogenetic classifications because they reflect changing hypotheses of cladistic relationships. De Queiroz and Gauthier's (1990: Syst. Zool. 39, 307–322; 1992: A. Rev. Ecol. Syst. 23, 449–480; 1994: Trends Ecol. Evol. 9, 27–31) alternative to Linnaean nomenclature is concluded to provide stable names for unstable concepts. In terms of communicating either characters shared by species of a named taxon or elements (species) included in a taxon, de Queiroz and Gauthier's system is less stable than the Linnaean system. Linnaean ranks communicate limited information about inclusivity of taxa, but abandonment of ranks results in the loss of such information. As cladistic hypotheses advance, taxa named under de Queiroz and Gauthier's system can change their level of generality radically, from being part of a group to including it, without any indicative change in its spelling. The Linnaean system has been retained by taxonomists because its hierarchic ranks are logically compatible with nested sets of species, monophyletic groups, and characters. Other authors have offered conventions to increase the cladistic information content of Linnaean names or to replace them with names that convey cladistic knowledge in greater detail; de Queiroz and Gauthier sacrifice the meaning of taxon names and categorical ranks in favor of spelling stability.     

Does ecological specialization transcend scale? Habitat partitioning among individuals and species of Anolis lizards

Ecological specialization is common across all levels of biological organization, raising the question of whether the evolution of specialization at one scale in a taxon is linked to specialization at other scales. Anolis lizards have diversified repeatedly along axes of habitat use, but it remains unknown if this diversification into habitat use specialists is underlain by individual specialization. From repeated observations of individuals in a population of Anolis sagrei in Florida, we show that the extent of habitat use specialization among individuals is comparable to the extent of specialization in the same traits among ten sympatric Anolis habitat specialist species in Cuba. However, the adaptive correlations between habitat use and morphology commonly seen across species of Anolis were not observed across individuals in the sampled population. Our results therefore suggest that while patterns of ecological specialization can transcend scale, these parallels are the consequence of distinct ecological processes acting at microevolutionary and macroevolutionary scales.     

Colonize,radiate, decline: Unraveling the dynamics of island community assembly with Fijian trap-jaw ants

The study of island community assembly has been fertile ground for developing and testing theoretical ideas in ecology and evolution. The ecoevolutionary trajectory of lineages after colonization has been a particular interest, as this is a key component of understanding community assembly. In this system, existing ideas, such as the taxon cycle, posit that lineages pass through a regular sequence of ecoevolutionary changes after colonization, with lineages shifting toward reduced dispersal ability, increased ecological specialization, and declines in abundance. However, these predictions have historically been difficult to test. Here, we integrate phylogenomics, population genomics, and X-ray microtomography/3D morphometrics, to test hypotheses for whether the ecomorphological diversity of trap-jaw ants (Strumigenys) in the Fijian archipelago is assembled primarily through colonization or postcolonization radiation, and whether species show ecological shifts toward niche specialization, toward upland habitats, and decline in abundance after colonization. We infer that most Fijian endemic Strumigenys evolved in situ from a single colonization and have diversified to fill a large fraction of global morphospace occupied by the genus. Within this adaptive radiation, lineages trend to different degrees toward high elevation, reduced dispersal ability, and demographic decline, and we find no evidence of repeated colonization that displaces the initial radiation. Overall these results are only partially consistent with taxon cycle and associated ideas, while highlighting the potential role of priority effects in assembling island communities.     

PHYLOGENETIC RELATIONSHIPS OF THE CAMAENIDAE (PULMONATA: STYLOMMATOPHORA: HELICOIDEA)

The land snail family Camaenidae is defined by the lack of characters,such as dart sac and glands, which are present in related familiesAlthough the Camaenidae is regarded as monophyletic, no synapomorphiesunite the family It is possible that the Camaenidae is para-or polyphyletic This was investigated using a cladistic analysisof the super-family Helicoidea which was based on anatomicalcharacters from previous studies by Tilher (1989) Camaenidaewas split into two geographical groups (American and Australasian).Successive weighting generated a single most parsimonious cladogram(length 198, c.i. 0.61, r.i. 0.64), which suggested that theCamaenidae is a polyphyletic taxon. Evidence from this analysisdemonstrated that the American component of the Camaenidae isclosely related to the Hehcidae and Helminthoglyptidae, andthe Australasian component is sister group to the Bradybaenidae ^*Current address Department oJ Zoology. James Cook Universityof North Queensland. Townsville. Queensland 4811, Australia (Received 30 July 1994; accepted 20 June 1995)     

Molecular phylogenetics of the bee-eaters (Aves: Meropidae) based on nuclear and mitochondrial DNA sequence data

The bee-eaters (family Meropidae) comprise a group of brightly colored, but morphologically homogeneous, birds with a wide variety of life history characteristics. A phylogeny of bee-eaters was reconstructed using nuclear and mitochondrial DNA sequence data from 23 of the 25 named bee-eater species. Analysis of the combined data set provided a well-supported phylogenetic hypothesis for the family. Nyctiornis is the sister taxon to all other bee-eaters. Within the genus Merops, we recovered two well-supported clades that can be broadly separated into two groups along geographic and ecological lines, one clade with mostly African resident species and the other clade containing a mixture of African and Asian taxa that are mostly migratory species. The clade containing resident African species can be further split into two groups along ecological lines by habitat preference into lowland forest specialists and montane forest and forest edge species. Intraspecific sampling in several of the taxa revealed moderate to high (3.7-6.5%, ND2) levels of divergence in the resident taxa, whereas the lone migratory taxon showed negligible levels of intraspecific divergence. This robust molecular phylogeny provides the phylogenetic framework for future comparative tests of hypotheses about the evolution of plumage patterns, sociality, migration, and delayed breeding strategies.     

DISRUPTIVE SELECTION ON HABITAT PREFERENCE AND THE EVOLUTION OF REPRODUCTIVE ISOLATION: AN EXPLORATORY EXPERIMENT

A. pair of replicate experiments was carried out to examine the role of habitat specialization in the process of sympatric speciation. The rationale of the experimental design was that disruptive selection for habitat preference can facilitate the process of sympatric speciation by reducing an antagonistic interaction between the processes of recombination and selection. Replicate populations of Drosophila melanogaster were subjected to disruptive selection for habitat preference and simultaneous selection for positive assortative mating, for a period of 46 generations. The experimental protocol simulated the introduction of a frugivorous fly population into a new environment that contained a mosaic of eight equally abundant habitats. Only two habitats were suitable to the flies, and these required opposite patterns of geotaxis, phototaxis, chemotaxis, and developmental time to be successfully located. At the beginning of each generation, flies were placed as pupae into the middle of a maze containing eight discrete habitats. To produce disruptive selection on habitat preference, only those flies that chose one or the other of two selected habitats were permitted to contribute gametes to the next generation. Flies from each of the selected habitats were cultured separately to simulate independent carrying capacities within each habitat. Because flies rarely mated until they assorted themselves into the available habitats, genes affecting habitat preference pleiotropically produced assortative mating between flies with similar habitat preference. A genetic marker was used to continuously monitor the level of potential gene flow between the flies derived from the two selected habitats. During the course of the experiment, there was a gradual increase in the philopatry of the flies, indicating the development of habitat specialization. The evolution of habitat specialization resulted in substantial reproductive isolation between the subpopulations utilizing each habitat resource.     

Morphological phylogenetics of termites (Isoptera)

Isoptera (termites) are an ecologically important order, with both a high abundance and biomass in tropical ecosystems. However, there have been few phylogenetic hypotheses for termites, and we present here the first comprehensive cladistic analysis for the group. We analysed relationships between all seven termite families, including representatives of all known feeding group, plus a number of systematically critical taxa. Termite species richness is biased towards the higher termites (Termitidae), and our taxon sampling reflects this. Our analysis was based essentially on morphological characters (96 workers, 93 soldiers) plus seven biological characters. The cladistic analysis gave four equally parsimonious trees, representing two islands of topologies. The strict consensus tree is fully resolved for the higher termites, but less so for the lower termites. Overall there is low statistical support for the suggested topology, and this can be explained by the high incongruence between the data sets (worker, soldier and biological). This study highlights the particular problems of coding morphological characters in social insects with multiple castes. Without the input of additional data sets, e.g. alates, biological, behavioural and molecular, it will not be possible to obtain a well-supported termite phylogeny.     

Parallelism,parsimony, and the phytogeny of the lemuridae

In spite of the increasing popularity of cladistic methods in studies of primate systematics, few authors have investigated the effects of parallel evolution when such methods are applied to empirical data. To counter the effects of parallelism, cladistic techniques rely on the principle of evolutionary parsimony. When parsimony procedures are used to reconstruct the phylogeny of the Lemuridae, nine highly parsimonious phylogenies can be deduced. Further choice among these competing hypotheses of relationship is determined by the extent to which one embraces the parsimony principle. The phylogeny obtained by the most rigorous adherence to the parsimony principle is one which is wholly consistent with traditional evolutionary classifications of the Lemuridae. Moderate levels of parallelism can lead to the generation of several plausible, alternative phylogenetic hypotheses; less than 25% of the characters analyzed here need have evolved in parallel, yet they are largely responsible for the ambiguity of the nine different lemurid phylogenies. This suggests that phylogeny reconstructions based entirely on cladistic methods do not provide a suitable basis for the construction of classifications for groups such as the order Primates, where the degree of parallelism is likely to be quite high.     

Is Psammophily an Evolutionary Dead End? A Phylogenetic Test in the Genus Willemia (Collembola: Hypogastruridae)

The law of the unspecialized states that specialized taxa have evolved from more generalized ancestors. Moreover, it is usually assumed that ecological specialization is irreversible and hence leads to extinction. This study aims to test these assumptions using a phylogenetic framework in a case study within the springtail genus Willemia and its diverse life habits. This genus is represented mostly by loam-dwelling species (generalized condition), but some species are psammophilous, living in sandy habitats (specialized condition). Fifty-two morphological characters were examined in 34 of the 36 species of the genus and in three outgroups. The cladistic analysis yielded two most parsimonious trees (tree length 124 steps; consistency index 0.56; retention index 0.86). The evolution of psammophily versus loam-confined life is compared to the cladogram: unexpectedly, psammophily is not an evolutionary innovation that occurred once in a monophyletic group; the evolutionary scenario that parsimoniously fits the phylogeny suggests that psammophily is ancestral to the genus Willemia and reversed twice to loam-confined life. These results demonstrate that habitat generalists can evolve from habitat specialists and therefore that habitat specializations are not necessarily an evolutionary dead end. Many other seemingly specialized characters may be shown to be equally malleable.     

Taxon‐biased diet preference in the ‘generalist’ beetle‐hunting wasp Cerceris rubida provides insights on the evolution of prey specialization in apoid wasps

Opportunism and specialization appear to be widespread in apoid wasps, although the factors affecting the diet preference (and thus explaining the degree of specialization) are still largely unknown. Four hypotheses that stressed the importance of the size, sex, habitat, and taxonomic identity of prey of the beetle‐hunting digger wasp, Cerceris rubida, were formulated and tested. The wasp population hunted for phytophagous beetles belonging to abundant families around the wasp nesting site. In practice, the prey appeared to be hunted only in two cultivated fields, thus habitat accounted for a majority of the observed diet. The size of wasps was furthermore correlated with the size of their prey, and thus this also accounted for the frequencies of hunted prey and the strong individual specialization for both taxa and size. However, in the exploited habitat, some species were significantly over‐hunted than expected and some other significantly avoided by the wasps, causing an unexpected major role of prey taxon on the probability of being hunted, over the other explanatory variables (body size, body shape, sex, availability). This contrasts to that found in other wasp species, which appear to select prey basing essentially on their ecology and size or their relative abundance (opportunism). The results obtained in the present study show that even an apparent ‘generalist’ predator may turn out to be taxonomically specialized. Together with a re‐evaluation of previous studies, our results further suggest that the effect of size constraints and the developmental plan of prey (holometaboulous versus hemimetabolous) may have promoted either taxonomic opportunism or specialization in different lineages of apoid wasps. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 544–558.     

Flatworm phylogeny from partial 18S rDNA sequences

Partial 18S rDNA sequences from 29 flatworms and 2 outgroup taxa were used in a cladistic analysis of the Platyhelminthes. Support for the clades in the resulting single most parsimonious tree was estimated through bootstrap analysis, jack-knife analysis and decay indices. The Acoelomorpha (Acoela and Nemertodermatida) were absent from the most parsimonious tree. The Acoela and the Fecampiidae form a strongly supported clade, the sister group of which may be the Tricladida. There is some support for monophyly of the rhabdocoel taxon Dalyellioida, previously regarded as paraphyletic. The sister group of the Neodermata remains unresolved. This revised version was published online in July 2006 with corrections to the Cover Date.     

THE NATURE OF CLADISTIC DATA

Abstract— Cladistic data are the characters of organisms. Character is defined as a feature that can be evaluated as a variable with two or more mutually exclusive and ordered states. Cladistic characters must be treated as multistate variables, and coded as sequential numbers or in additive binary fashion. Any other interpretation and handling of cladistic data will introduce error into analysis. Character states cannot be treated independently as present or absent, i.e., as nominal variables, because redundancy is introduced into the data and information content is sacrificed. Non-additive binary coding demonstrates that treating cladistic variables as nominal data will lead to multiple, equally parsimonious solutions. Defining characters found universally in a group of organisms, but unknown outside those organisms have no alternative state that can be designated as absent. Absence, however, is valid as a character state if it can be shown to be apomorphic. When two or more character states occur within a taxon, that taxon must be coded as having an unknown state for that character, or the taxon must be split in two or more taxa. Continuously varying quantitative data are not suitable for cladistic analysis because there is no justifiable basis for recognizing discrete states among them. Quantitative data are questionable even when they exhibit mutually exclusive states because the states can be interpreted only in reference to an archetype, i.e., as implied homologies not subject to test.     

The relationships of mammals

A cladistic analysis generates alternative hypotheses regarding both the origin and the interrelationships of mammals to those most widely accepted at the present time. It is proposed that the tritylodontids are more closely related to mammals than is Probainognathus ; that the non-therian mammals do not constitute a monophyletic group; and that the monotremes are related to the modern therians, the ear ossicles among other characters having evolved only once. The multituberculates may be related to the monotremes.
It is argued that the current views are variously based on an overemphasis of superficial dental similarities, misinterpretation of the structure of the mammalianbraincaseand too readyacceptance of parallel evolution amongstthe groups concerned. The hypotheses proposed here are apparently much more parsimonious.     

Ontogenetic patterns of habitat use by fishes within the main channel of an Australian floodplain river

The ontogenetic patterns of habitat use by a community of fishes in the main channel of the Broken River, an Australian lowland river, was investigated. Stratified sampling was conducted fortnightly across six habitat types throughout the spring‐summer period within the main channel. As predicted by the 'low flow recruitment hypothesis', backwaters and still littoral habitats were important nursery habitats for most species. These habitats were found to be used by some species throughout all stages of their life cycle, while other species showed clear ontogenetic shifts in habitat preference. Only one species, Murray cod Maccullochella peelii peelii , was never found in backwaters. This study confirms the significance of main channel habitats in the rearing of larvae of some riverine fish species, and emphasizes the importance of considering the habitat requirements of all stages of a fish's life cycle in the management and restoration of rivers and streams.     

Functional homogenization of bird communities along habitat gradients: accounting for niche multidimensionality

Aim To test whether functional homogenization of bird communities is promoted by anthropogenic landscape transformation, using specialization and habitat preference indices that account for the multidimensionality of niches. Location Catalonia, north‐east Iberian Peninsula. Methods We used data on bird species occurrences and landscape features in 2834 1‐km² squares. Three orthogonal landscape gradients, which were taken as niche dimensions, were defined by means of principal components analysis (PCA). Specialization and habitat preference indices were created for 103 terrestrial bird species on the basis of their frequency of occurrence variation along the landscape gradients. These indices, together with species rarity, were then averaged for bird communities. We then analysed the patterns of variation of communities’ mean specialization, mean rarity and mean habitat preference values along a gradient of agricultural–forest habitat mosaics. Results Wherever we found a significant variation in the degree of specialization along the agricultural–forest gradient, agricultural habitats held more specialized bird communities than did forest ones and bore, on average, rarer species. Thus, results contradicted our initial hypothesis that humanized areas would bear more functionally homogenized bird communities. Higher α‐diversity values tended to be associated with generalist communities and with those having rarer species. Main conclusions Estimations of bird community specialization for different niche dimensions can behave differently along certain landscape gradients, and some of these differences can be explained by the variation of mean habitat preferences. Thus, we argue that a multidimensional approach to assess average niche breadth of communities can be more informative than a unidimensional measure. Our results suggest that widespread land abandonment and current secondary forest expansion throughout the Mediterranean area are promoting functional homogenization of bird communities. It would be desirable to construct larger‐scale indicators of functional homogenization in order to monitor communities’ responses to widespread landscape changes.