Sexual selection and natural selection in bird speciation

The role of sexual selection in speciation is investigated, addressing two main issues. First, how do sexually selected traits become species recognition traits? Theory and empirical evidence suggest that female preferences often do not evolve as a correlated response to evolution of male traits. This implies that, contrary to runaway (Fisherian) models of sexual selection, premating isolation will not arise as an automatic side effect of divergence between populations in sexually selected traits. I evaluate premating isolating mechanisms in one group, the birds. In this group premating isolation is often a consequence of sexual imprinting, whereby young birds learn features of their parents and use these features in mate choice. Song, morphology and plumage are known recognition cues. I conclude that perhaps the main role for sexual selection in speciation is in generating differences between populations in traits. Sexual imprinting then leads to these traits being used as species recognition mechanisms. The second issue addressed in this paper is the role of sexual selection in adaptive radiation, again concentrating on birds. Ecological differences between species include large differences in size, which may in themselves be sufficient for species recognition, and differences in habitat, which seem to evolve frequently and at all stages of an adaptive radiation. Differences in habitat often cause song and plumage patterns to evolve as a result of sexual selection for efficient communication. Therefore sexual selection is likely to have an important role in generating premating isolating mechanisms throughout an adaptive radiation. It is also possible that sexual selection, by creating more allopatric species, creates more opportunity for ecological divergence to occur. The limited available evidence does not support this idea. A role for sexual selection in accelerating ecological diversification has yet to be demonstrated.

The evolution of diversity in ancient ecosystems: a review

On a perfect planet, such as might be acceptable to a physicist, one might predict that from its origin the diversity of life would grow exponentially until the carrying capacity, however defined, was reached. The fossil record of the Earth, however, tells a very different story. One of the most striking aspects of this record is the apparent evolutionary longueur, marked by the Precambrian record of prokaryotes and primitive eukaryotes, although our estimates of microbial diversity may be seriously incomplete. Subsequently there were various dramatic increases in diversity, including the Cambrian ‘explosion’ and the radiation of Palaeozoic–style faunas in the Ordovician. The causes of these events are far from resolved. It has also long been appreciated that the history of diversity has been punctuated by important extinctions. The subtleties and nuances of extinction as well as the survival of particular clades have to date, however, received rather too little attention, and there is still a tendency towards blanket assertions rather than a dissection of these extraordinary events. In addition, some but perhaps not all mass extinctions are characterized by long lag–times of recovery, which may reflect the slowing waning of extrinsic forcing factors or alternatively the incoherence associated with biological reassembly of stable ecosystems. The intervening periods between the identified mass extinctions may be less stable and benign than popularly thought, and in particular the frequency of extraterrestrial impacts leads to predictions of recurrent disturbance on timescales significantly shorter than the intervals separating the largest extinction events. Even at times of quietude it is far from clear whether biological communities enjoy stability and interlocked stasis or are dynamically reconstituted at regular intervals. Finally, can we yet rely on the present depictions of the rise and falls in the levels of ancient diversity? Existing data is almost entirely based on Linnean taxa, and the application of phylogenetic systematics to this problem is still in its infancy. Not only that, but even more intriguingly the pronounced divergence in estimates of origination times of groups as diverse as angiosperms, diatoms and mammals in terms of the fossil record as against molecular data point to the possibilities of protracted intervals of geological time with a cryptic diversity. If this is correct, and there are alternative explanations, then some of the mystery of adaptive radiations may be dispelled, in as much as the assembly of key features in the stem groups could be placed in a gradualistic framework of local adaptive response punctuated by intervals of opportunity.

Species-range size distributions: products of speciation, extinction and transformation

One basic summary of the spatial pattern of biodiversity across the surface of the Earth is provided by a species–range size distribution, the frequency distribution of the numbers of species exhibiting geographic ranges of different sizes. Although widely considered to be approximately lognormal, increasingly it appears that across a variety of groups of organisms this distribution systematically departs from such a form. Whatever its detailed shape, however, the distribution must arise as a product of three processes, speciation, extinction and transformation (the temporal dynamics of the range sizes of species during their life times). Considering the role potentially played by each of these processes necessitates drawing on information from a diverse array of research fields, and highlights the possible role of geographic range size as a common currency uniting them.

From genes to individuals: developmental genes and the generation of the phenotype

The success of the genetic approach to developmental biology has provided us with a suite of genes that are involved in the regulation of ontogenetic pathways. It is therefore time to ask whether and how such genes might be involved in the generation of adaptive phenotypes. Unfortunately, the current results do not provide a clear answer. Most of the genes that have been studied by developmental biologists affect early embryonic traits with significant effects on the whole organism. These genes are often highly conserved which allows us to do comparative studies even across phyla. However, whether the same genes are also involved in short-term ecological adaptations remains unclear. The suggestion that early acting ontogenetic genes may also affect late phenotypes comes from the genetic analysis of quantitative traits like bristle numbers in Drosophila. A rough mapping of the major loci affecting these traits shows that these loci might correspond to well known early acting genes. On the other hand, there are also many minor effect loci that are as yet uncharacterized. We suggest that these minor loci might correspond to a different class of genes. In comparative studies of randomly drawn cDNAs from Drosophila we find that there is a large group of genes that evolve fast and that are significantly under-represented in normal genetic screens. We speculate that these genes might provide a large, as yet poorly understood, reservoir of genes that might be involved in the evolution of quantitative traits and short-term adaptations.

Rates of speciation in the fossil record

Data from palaeontology and biodiversity suggest that the global biota should produce an average of three new species per year. However, the fossil record shows large variation around this mean. Rates of origination have declined through the Phanerozoic. This appears to have been largely a function of sorting among higher taxa (especially classes), which exhibit characteristic rates of speciation (and extinction) that differ among them by nearly an order of magnitude. Secular decline of origination rates is hardly constant, however; many positive deviations reflect accelerated speciation during rebounds from mass extinctions. There has also been general decline in rates of speciation within major taxa through their histories, although rates have tended to remain higher among members in tropical regions. Finally, pulses of speciation appear sometimes to be associated with climate change, although moderate oscillations of climate do not necessarily promote speciation despite forcing changes in species' geographical ranges.

Gnathostomulida--an enigmatic metazoan phylum from both morphological and molecular perspectives

On the basis of few and contentious morphological characters Gnathostomulids have been thought to be the sister-group of either the Platyhelminthes or the Syndermata (Rotifera + Acanthocephala). We provide a full 18S rDNA sequence for a species of Gnathostomula and attempt to resolve its position among the Metazoa, on the basis of molecular evidence. Sixty sequences, representing 30 nominal phyla and including new entoproct and gastrotrich sequences, were used to reconstruct phylogenies using maximum-parsimony, neighbor-joining, and minimum evolution models. We were unable to support either of the morphological hypotheses outright and, moreover, our data supported more strongly a third possible relationship with the gnathostomulids as a member of the Nematoda + Chaetognatha clade. Superficially, as active benthic, vermiform creatures with sclerotized cuticular jaws, they fit a predicted ancestral form of the Nematoda + Chaetognatha clade and, as such, would arguably be members of the Ecdysozoa. The molecular data at least call for a reevaluation of the morphological data and a denser sampling of the lesser phyla. Data from morphology and molecules act synergistically in estimating phylogeny; morphology alone provided limited phylogenetic signal and alternative phylogenetic hypotheses, whereas the molecular solution suggested an alternative topology which, when interpreted in the light of comparative anatomy, may suggest previously unconsidered possibilities.

Phylogenetics of social behavior in Australian gall-forming thrips: evidence from mitochondrial DNA sequence, adult morphology and behavior, and gall morphology

Six species of Australian gall-forming thrips (Insecta: Thysanoptera) on Acacia exhibit soldier castes, individuals with reduced wings and enlarged forelegs that defend their gall against interspecific invaders. We used data from two mitochondrial genes (cytochrome oxidase I and 16S rDNA), adult morphology and behavior, and gall morphology to infer a phylogeny for Acacia gall-forming thrips with and without soldiers, and we used this phylogeny to evaluate hypotheses concerning soldier evolution. Phylogenies inferred from each data set analyzed separately yielded large numbers of most-parsimonious trees and weak support for most nodes. However, when analyzed together the data sets complemented and reinforced one another in such a way as to yield a well-resolved phylogeny. Our phylogeny implies that soldiers originated once or twice early in the history of this clade, that soldiers were lost once or twice, and that soldiers evolved from winged dispersers rather than from nonsoldier within-gall reproductive offspring of foundresses. The phylogeny also provides evidence for long-term morphological stasis, an ancient split between eastern and western gall thrips species, and a high degree of conservatism in host-plant affiliations.

Molecular phylogeny of Acipenserinae

The family Acipenseridae consists of 25 extant sturgeon species (19 species of Acipenserinae and 6 species of Scaphirhynchinae). Together with two extant paddlefish species, Polyodon spathula and Psephurus gladius (Polyodontidae), it composes the order Acipenseriformes, the most numerous of all living "fossil" fishes. This paper presents results of sequencing of three regions of the cytochrome b gene (650 bp), and fragments of 12S (150 bp) and 16S (350 bp) rRNA genes, from all extant species of Acipenserinae (species of Acipenser and Huso) and Scaphirhynchus albus (Scaphirhynchinae). The phylogenetic tree obtained for combined data is the first comprehensive treatment of phylogeny within the Acipenserinae. Three general conclusions are inferred from the tree: (1) The pallid sturgeon, S. albus, is the sister-species of all species of Acipenser and Huso. (2) The two species of Huso are embedded within the genus Acipenser. It also appears that Huso is not a separate taxonomic unit. (3) There are at least three main clades within Acipenser: A. sturio-A. oxyrinchus, A. schrenckii-A. transmontanus, and all Ponto-Caspian species plus A. dabryanus and A. brevirostrum. There is congruence between ploidy and the branching patterns of the sturgeon species. A hypothetical evolutionary history of the Acipenseriformes based on the paleontological, geological, and molecular data is discussed.

Immunological and virological analyses of persons infected by human immunodeficiency virus type 1 while participating in trials of recombinant gp120 subunit vaccines

We have studied 18 participants in phase I/II clinical trials of recombinant gp120 (rgp120) subunit vaccines (MN and SF-2) who became infected with human immunodeficiency virus type 1 (HIV-1) during the course of the trials. Of the 18 individuals, 2 had received a placebo vaccine, 9 had been immunized with MN rgp120, and seven had been immunized with SF-2 rgp120. Thirteen of the 18 infected vaccinees had received three or four immunizations prior to becoming infected. Of these, two were placebo recipients, six had received MN rgp120, and five had received SF-2 rgp120. Only 1 of the 11 rgp120 recipients who had multiple immunizations failed to develop a strong immunoglobulin G antibody response to the immunogen. However, the antibody response to rgp120 was transient, typically having a half-life of 40 to 60 days. No significant neutralizing activity against the infecting strain was detected in any of the infected individuals at any time prior to infection. Antibody titers in subjects infected despite vaccination and in noninfected subjects were not significantly different. Envelope-specific cytotoxic T-lymphocyte responses measured after infection were infrequent and weak in the nine vaccinees who were tested. HIV-1 was isolated successfully from all 18 individuals. Sixteen of these strains had a non-syncytium-inducing (NSI) phenotype, while two had a syncytium-inducing (SI) phenotype. NSI strains used the CCR5 coreceptor to enter CD4+ cells, while an SI strain from one of the vaccinees also used CXCR4. Viruses isolated from the blood of rgp120 vaccinees were indistinguishable from viruses isolated from control individuals in terms of their inherent sensitivity to neutralization by specific monoclonal antibodies and their replication rates in vitro. Furthermore, genetic sequencing of the env genes of strains infecting the vaccinees did not reveal any features that clearly distinguished these viruses from contemporary clade B viruses circulating in the United States. Thus, despite rigorous genetic analyses, using various breakdowns of the data sets, we could find no evidence that rgp120 vaccination exerted selection pressure on the infecting HIV-1 strains. The viral burdens in the infected rgp120 vaccine recipients were also determined, and they were found to be not significantly different from those in cohorts of placebo-vaccinated and nonvaccinated individuals. In summary, we conclude that vaccination with rgp120 has had,to date, no obvious beneficial or adverse effects on the individuals we have studied.

Two nuclear genes yield concordant relationships within Attacini (Lepidoptera: Saturniidae)

To extend initial characterizations of their phylogenetic utility, sequences from the nuclear genes for elongation factor-1 alpha (EF-1 alpha) and dopa decarboxylase (DDC) are tested for phylogenetic concordance with each other and with previous morphological evidence within the giant silk moth tribe Attacini (Lepidoptera: Saturniidae). The sampling of DDC is expanded from the 690 basepairs of previous studies to 1051 basepairs in the current study. All nine attacine genera are sampled. EF-1 alpha and DDC agree in the placement of seven of nine genera, with placement of the other two not in strong conflict. Combination of the gene sequences results in a nearly fully resolved tree that is consistent with EF-1 alpha alone and agrees with morphology in five of eight groups. Conflict between molecules and morphology is confined to deeper-level relationships within Attacini, where node support for the molecular hypotheses, but not the morphological hypotheses, is generally very strong. A strong signal is contributed by synonymous substitutions in both genes, and by nonsynonymous change particularly in DDC. The molecular phylogeny supports a revision of attacine biogeography in that neither East Asian nor New World genera form monophyletic groups.

Phylogenetic relationships and geographic structure in pocket gophers in the genus Thomomys

Phylogenetic relationships among pocket gophers were examined based on the complete sequence for the mitochondrial cytochrome b gene (1140 base pairs). The tribe Geomyini (Geomys, Orthogeomys, Cratogeomys, and Pappogeomys) was well differentiated from the tribe Thomomyini (Thomomys), using the heteromyid genera Dipodomys and Perognathus as the out-group. Within the genus Thomomys, the species in the subgenus Thomomys (T. talpoides, T. monticola, and T. mazama) differed from those in the subgenus Megascapheus (T. bottae, T. townsendii, and T. umbrinus) by an average of 19.3% uncorrected sequence divergence. Extensive sampling within one species, T. bottae, revealed strongly differentiated geographic units, with a maximum difference among localities of 15.7%. The geographic units within T. bottae coincided with geographic regions based on allozyme data in some areas, but not at all boundaries. The geographic units within currently recognized species in the bottae group (subgenus Megascapheus) were not grouped together with a high level of confidence. The pattern suggests a rapid radiation of the bottae group, followed by geographic subdivision.

Details of gastropod phylogeny inferred from 18S rRNA sequences

Some generally accepted viewpoints on the phylogenetic relationships within the molluscan class Gastropoda are reassessed by comparing complete 18S rRNA sequences. Phylogenetic analyses were performed using the neighbor-joining and maximum parsimony methods. The previously suggested basal position of Archaeogastropoda, including Neritimorpha and Vetigastropoda, in the gastropod clade is confirmed. The present study also provides new molecular evidence for the monophyly of both Caenogastropoda and Euthyneura (Pulmonata and Opisthobranchia), making Prosobranchia paraphyletic. The relationships within Caenogastropoda and Euthyneura data turn out to be very unstable on the basis of the present 18S rRNA sequences. The present 18S rRNA data question, but are insufficient to decide on, muricacean (Neogastropoda), neotaenioglossan, pulmonate, or stylommatophoran monophyly. The analyses also focus on two systellommatophoran families, namely, Veronicellidae and Onchidiidae. It is suggested that Systellommatophora are not a monophyletic unit but, due to the lack of stability in the euthyneuran clade, their affinity to either Opisthobranchia or Pulmonata could not be determined.

Molecular and chromosomal phylogeny in the obscura group of Drosophila inferred from sequences of the rp49 gene region

A region of approximately 1.6 kb encompassing the ribosomal protein 49 gene (rp49) has been sequenced and compared in nine species of the obscura group of Drosophila: four species belonging to the obscura subgroup, three to the pseudoobscura subgroup, and two to the affinis subgroup. Our data provide strong support that the nearctic species (pseudoobscura and affinis subgroups) are monophyletic and place D. bifasciata with the other species of the obscura subgroup. Nucleotide sequence information at the rp49 gene region (located very close to one of the breakpoints of inversion O3) has also been used to infer the phylogeny of the O chromosome in the subobscura species cluster. Analysis based both on parsimony-informative sites and on genetic distances confirms that the O3 gene arrangement, present in D. guanche (together with inversion g) and in D. madeirensis, is ancestral to gene arrangements O3 + 4 and Ost present in extant populations of D. subobscura.

Population biology of an endangered butterfly, Lycaeides melissa samuelis (Lepidoptera; Lycaenidae): genetic variation, gene flow, and taxonomic status

We present data from 34 allozyme loci to test whether the Karner Blue butterfly is specifically differentiated from the Melissa Blue. Furthermore, as the Karner Blue is an endangered organism of low vagility that occurs predominantly in small, widely separated populations, we investigated (i) whether the Karner Blue is depauperate in genetic variation and (ii) whether gene flow between sampled populations is unusually low. Genetic identities between New York and Wisconsin populations of the Karner Blue and a sample of Melissa Blue from Minnesota are all statistically indistinguishable. Neither genetic identity data nor application of the phylogenetic species concept support formal recognition of the Karner Blue as a species separate from the Melissa Blue. Nonetheless, the data indicate that gene flow among the samples was very low compared with that among populations of other Lepidoptera. Heterozygosity estimates for all three samples were comparable to data for other Lepidoptera and indicate that the Karner Blue populations surveyed are not under immediate threat of extirpation due to loss of genetic diversity. Although the available data are limited, if the Karner Blue is to be managed as an evolutionarily significant unit, then the eastern and western populations should probably be treated independently and each should receive high conservation priority.

The molecular phylogenetics of tuco-tucos (genus Ctenomys, Rodentia: Octodontidae) suggests an early burst of speciation

Variation in the nucleotide sequence of the entire mitochondrial cytochrome b gene (1140 bp) was examined for 27 individuals representing 13 species of South American rodents of the genera Ctenomys, Octodontomys, Tympanoctomys, and Spalacopus. Representatives of the family Echimyidae, Euryzygomatomys and Mesomys, were used as outgroups to test the monophyly of the Octodontinae and Ctenomyinae. Relationships among species of tuco-tucos (genus Ctenomys) were also examined including representatives of the three described subgenera and the two sperm morphs. Reciprocal monophyly of the Octodontinae and Ctenomyinae is strongly supported. Several basal relationships among species of the genus Ctenomys are poorly resolved, suggesting the possibility of a hard polytomy due to a rapid and potentially simultaneous radiation early in the history of the genus. In other cases, clades within the Ctenomyinae previously identified on the basis of allozymes, chromosomes, parasites, or skull morphology were supported. Calibrations based on the fossil record suggest that the mitochondrial cytochrome b of these caviomorphs has evolved at a rapid rate, comparable to those proposed for Mus-Rattus, and three to four times higher than ungulate rates.

Phylogeny of leeches (Hirudinea) based on mitochondrial cytochrome c oxidase subunit I

The phylogenetic relationships of leeches were investigated for the first time using molecular data. Twenty-one species were examined representing 7 of the 10 conventionally recognized euhirudinean families. In addition, Acanthobdella peledina, a branchiobdellid, four oligochaetes, and two polychaetes were included. Cladistic analysis of the mitochondrial cytochrome c oxidase subunit I gene yielded one most-parsimonious tree. Contemporary taxonomic groupings of leeches into higher categories were found to be largely consistent with monophyletic groups identified in the analysis. Unusual relationships for which there is some precedent include a sister-group relationship between the piscicolids and Arhynchobdellida, as well as the grouping of the haemopids within Hirudinidae.

Molecular phylogenetic, morphological, and mycotoxin data support reidentification of the Quorn mycoprotein fungus as Fusarium venenatum

Molecular phylogenetic, morphological, and mycotoxin data were obtained in order to investigate the relationships and identity of the Quorn mycoprotein fungus within Fusarium and to examine Quorn strains and commercial Quorn food products for trichothecene mycotoxins. Phylogenetic analyses of aligned DNA sequences obtained via the polymerase chain reaction from the nuclear 28S ribosomal DNA, nuclear ribosomal internal transcribed spacer region, and beta-tubulin gene exons and introns indicate that the Quorn fungus is Fusarium venenatum, rather than F. graminearum as previously reported. All of the Quorn strains examined were morphologically degenerate aconidial colonial mutants except for NRRL 25139, which produced chlamydospores in recurved terminal chains together with mostly 5-septate sporodochial conidia on doliform monophialides diagnostic of F. venenatum. Bootstrap and decay analyses provide strong support for a monophyletic lineage containing F. venenatum and several other type A trichothecene-producing species, while reference strains of F. graminearum were nested in a separate clade of species that produce type B trichothecenes and/or zearalenone. Analysis of mycotoxins from rice cultures inoculated with Quorn strain NRRL 25416 revealed that four type A trichothecenes are produced, but at low levels relative to strain NRRL 22198 of F. venenatum. No trichothecene mycotoxins, however, were detected from the analysis of three commercial Quorn products marketed for human consumption in England.

Body size and species-richness in carnivores and primates

We use complete species-level phylogenies of extant Carnivora and Primates to perform the first thorough phylogenetic tests, in mammals, of the hypothesis that small body size is associated with species-richness. Our overall results, based on comparisons between sister clades, indicate a weak tendency for lineages with smaller bodies to contain more species. The tendency is much stronger within caniform carnivores (canids, procyonids, pinnipeds, ursids and mustelids), perhaps relating to the dietary flexibility and hence lower extinction rates in small, meat-eating species. We find significant heterogeneity in the size-diversity relationship within and among carnivore families. There is no significant association between body mass and species-richness in primates or feliform carnivores. Although body size is implicated as a correlate of species-richness in mammals, much of the variation in diversity cannot be attributed to size differences.

Origin of the metazoan phyla: molecular clocks confirm paleontological estimates

The time of origin of the animal phyla is controversial. Abundant fossils from the major animal phyla are found in the Cambrian, starting 544 million years ago. Many paleontologists hold that these phyla originated in the late Neoproterozoic, during the 160 million years preceding the Cambrian fossil explosion. We have analyzed 18 protein-coding gene loci and estimated that protostomes (arthropods, annelids, and mollusks) diverged from deuterostomes (echinoderms and chordates) about 670 million years ago, and chordates from echinoderms about 600 million years ago. Both estimates are consistent with paleontological estimates. A published analysis of seven gene loci that concludes that the corresponding divergence times are 1,200 and 1,000 million years ago is shown to be flawed because it extrapolates from slow-evolving vertebrate rates to faster-evolving invertebrate rates, as well as in other ways.

Phylogeny and evolution of host-parasitoid interactions in hymenoptera

Recent studies of hymenopteran phylogeny using both comparative morphology and DNA sequence data have greatly enhanced our understanding of the evolution of that order. Resulting phylogenetic hypotheses make possible more rigorous investigations of the evolution of various biological life-styles, among them the parasitoid habit. This paper reviews the current findings from higher-taxon phylogenetic analyses of the order. A "consensus" phylogeny derived from these findings is used to trace the most likely evolutionary pathways leading to the current diversity of parasitoid habits. Taxa and biological phenomena for which our current understanding is fragmentary are highlighted. Based on current evidence, it appears that parasitism arose, from mycophagous ancestors, a single time within the order. Many subsequent elaborations of the parasitic mode of life (e.g. endoparasitism, secondary phytophagy, etc) apparently evolved independently more than once.

Body size and feeding specificity: macrolepidoptera in Britain

Within a geographic assemblage, large-bodied species of macrolepidopteran moths tend, on average, to be less host-specific than small-bodied. Five possible explanations for this pattern are identified, based respectively on (i) phylogenetic relationships between species, (ii) latitudinal gradients in body size and feeding specificity, (iii) the relationship between range size and body size, (iv) larger body size as a buffer from environmental variation, and (v) the relationship between endophagous host associations and small body size. These mechanisms are tested using data for British macrolepidoptera and also evaluated using evidence from the literature at large. Although some of their assumptions are found to be justified, there is no significant support for any single mechanism. This lack of evidence for previously proposed mechanisms is discussed in the light of a recently proposed alternative explanation which combines theories of host quality and host defence mechanisms.Copyright 1998 The Linnean Society of London

Sex determination in plants

The majority of flowering plants produce flowers that are "perfect." These flowers are both staminate (with stamens) and pistillate (with one or more carpels). In a small number of species, there is spatial separation of the sexual organs either as monoecy, where the male and female organs are carried on separate flowers on the same plant, or dioecy, where male and female flowers are carried on separate male (staminate) or female (pistillate) individuals. Sex determination systems in plants, leading to unisexuality as monoecy or dioecy, have evolved independently many times. In dioecious plant species, the point of divergence from the hermaphrodite pattern shows wide variation between species, implying that the genetic bases are very different. This review considers monoecious and dioecious flowering plants and focuses on the underlying genetic and molecular mechanisms. We propose that dioecy arises either from monoecy as an environmentally unstable system controlled by plant growth substances or from hermaphroditism where the underlying mechanisms are highly stable and control does not involve plant growth substances.

Adaptive evolution via a major gene effect: paedomorphosis in the Mexican axolotl

Although adaptive evolution is thought to depend primarily on mutations of small effect, major gene effects may underlie many of the important differences observed among species in nature. The Mexican axolotl (Ambystoma mexicanum) has a derived mode of development that is characterized by metamorphic failure (paedomorphosis), an adaptation for an entirely aquatic life cycle. By using an interspecific crossing design and genetic linkage analysis, a major quantitative trait locus for expression of metamorphosis was identified in a local map of amplified fragment length polymorphisms. These data are consistent with a major gene hypothesis for the evolution of paedomorphosis in A. mexicanum.

The interphotoreceptor retinoid binding protein gene in therian mammals: implications for higher level relationships and evidence for loss of function in the marsupial mole

The subclass Theria of Mammalia includes marsupials (infraclass Metatheria) and placentals (infraclass Eutheria). Within each group, interordinal relationships remain unclear. One limitation of many studies is incomplete ordinal representation. Here, we analyze DNA sequences for part of exon 1 of the interphotoreceptor retinoid binding protein gene, including 10 that are newly reported, for representatives of all therian orders. Among placentals, the most robust clades are Cetartiodactyla, Paenungulata, and an expanded African clade that includes paenungulates, tubulidentates, and macroscelideans. Anagalida, Archonta, Altungulata, Hyracoidea + Perissodactyla, Ungulata, and the "flying primate" hypothesis are rejected by statistical tests. Among marsupials, the most robust clade includes all orders except Didelphimorphia. The phylogenetic placement of the monito del monte and the marsupial mole remains unclear. However, the marsupial mole sequence contains three frameshift indels and numerous stop codons in all three reading frames. Given that the interphotoreceptor retinoid binding protein gene is a single-copy gene that functions in the visual cycle and that the marsupial mole is blind with degenerate eyes, this finding suggests that phenotypic degeneration of the eyes is accompanied by parallel changes at the molecular level as a result of relaxed selective constraints.

Cross-species comparisons

Cognitive and neural adaptations in animals have been analysed using the comparative method. Comparisons between closely related species that differ in a cognitive or neural character, and comparison between distantly related species that share a cognitive or neural character, can be used to identify adaptations. Recent research has identified adaptive modifications of memory and the hippocampus that have evolved convergently in two clades of food-storing birds, the chickadees and tits (Paridae), and the jays and nutcrackers (Corvidae). Similar modifications of the hippocampus occur in other groups of animals, such as the cowbird brood parasites, in which there has been selection for spatial memory. Three general patterns that emerge from the comparative study of animal cognition provide a framework for research on human psychological adaptations: the existence of both specialized and general cognitive capacities; a clear relation between specialized capacities and specific selective pressures; and evolutionary change in the relative size of brain areas with cognitive functions.

Inferring species trees from gene trees: a phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins

Toward the goal of recovering the phylogenetic relationships among elapid snakes, we separately found the shortest trees from the amino acid sequences for the venom proteins phospholipase A2 and the short neurotoxin, collectively representing 32 species in 16 genera. We then applied a method we term gene tree parsimony for inferring species trees from gene trees that works by finding the species tree which minimizes the number of deep coalescences or gene duplications plus unsampled sequences necessary to fit each gene tree to the species tree. This procedure, which is both logical and generally applicable, avoids many of the problems of previous approaches for inferring species trees from gene trees. The results support a division of the elapids examined into sister groups of the Australian and marine (laticaudines and hydrophiines) species, and the African and Asian species. Within the former clade, the sea snakes are shown to be diphyletic, with the laticaudines and hydrophiines having separate origins. This finding is corroborated by previous studies, which provide support for the usefulness of gene tree parsimony.

Phylogeny of the avian family Ciconiidae (storks) based on cytochrome b sequences and DNA-DNA hybridization distances

This study is a phylogenetic analysis of the avian family Ciconiidae, the storks, based on two molecular data sets: 1065 base pairs of sequence from the mitochondrial cytochrome b gene and a complete matrix of single-copy nuclear DNA-DNA hybridization distances. Sixteen of the nineteen stork species were included in the cytochrome b data matrix, and fifteen in the DNA-DNA hybridization matrix. Both matrices included outgroups from the families Cathartidae (New World vultures) and Threskiornithidae (ibises, spoonbills). Optimal trees based on the two data sets were congruent in those nodes with strong bootstrap support. In the best-fit tree based on DNA-DNA hybridization distances, nodes defining relationships among very recently diverged species had low bootstrap support, while nodes defining more distant relationships had strong bootstrap support. In the optimal trees based on the sequence data, nodes defining relationships among recently diverged species had strong bootstrap support, while nodes defining basal relationships in the family had weak support and were incongruent among analyses. A combinable-component consensus of the best-fit DNA-DNA hybridization tree and a consensus tree based on different analyses of the cytochrome b sequences provide the best estimate of relationships among stork species based on the two data sets.

Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh

The Archaea present in salt marsh sediment samples from a tidal creek and from an adjacent area of vegetative marshland, both of which showed active methanogenesis and sulfate reduction, were sampled by using 16S rRNA gene libraries created with Archaea-specific primers. None of the sequences were the same as reference sequences from cultured taxa, although some were closely related to sequences from methanogens previously isolated from marine sediments. A wide range of Euryarchaeota sequences were recovered, but no sequences from Methanococcus, Methanobacterium, or the Crenarchaeota were recovered. Clusters of closely related sequences were common and generally contained sequences from both sites, suggesting that some related organisms were present in both samples. Recovery of sequences closely related to those of methanogens such as Methanococcoides and Methanolobus, which can use substrates other than hydrogen, provides support for published hypotheses that such methanogens are probably important in sulfate-rich sediments and identifies some likely candidates. Sequences closely related to those of methanogens such as Methanoculleus and Methanogenium, which are capable of using hydrogen, were also discovered, in agreement with previous inhibitor and process measurements suggesting that these taxa are present at low levels of activity. More surprisingly, we recovered a variety of sequences closely related to those from different halophilic Archaea and a cluster of divergent sequences specifically related to the marine group II archaeal sequences recently shown by PCR and probing to have a cosmopolitan distribution in marine samples.

Allometric patterning in the limb skeleton of bats: Implications for the mechanics and energetics of powered flight

Allometric analysis was employed to compare linear dimensions of forelimb and hindlimb bones (humeri, radii, third and fifth metacarpals, third and fifth manual phalanges, femora, and tibiae) of 227 species of bats and 105 species of nonvolant mammals of varying degrees of phylogenetic affinity to bats. After accounting for body size, all forelimb bones are longer in bats than in nonvolant species, with the exception of humeri and radii of a few highly arboreal primates. Hindlimb bones are generally, but not uniformly, shorter in bats than in other mammals. For the humerus, radius, and metacarpals, midshaft diameters are greater in bats than in their comparably sized relatives. Proximal phalangeal midshaft diameters are statistically indistinguishable from those of other mammals, and distal phalanges show significantly reduced outer diameters. The pattern of relative reduction in wing bone diameters along the wing's proximodistal axis parallels the reduction in bone mineralization along the same axis, and a similar pattern of change in cortical thickness from the smallest wall thicknesses among mammals in the humerus and radius to the greatest wall thicknesses among mammals in the phalanges. The combination of altered cross-sectional geometry and mineralization appears significantly to reduce the mass moment of inertia of the bat wing relative to a theoretical condition in which elongated bones preserve primitive mammalian mineralization levels and patterns of scaling of long bone diameters. This intercorrelated suite of skeletal specializations may significantly reduce the inertial power of flight, contributing significant energetic savings to the total energy budgets of the only flying mammals. J. Morphol. 234: 277-294, 1997. © 1997 Wiley-Liss, Inc.

Escaping from the Felsenstein zone by detecting long branches in phylogenetic data

Long branches in a true phylogeny tend to disrupt hierarchical character covariation (phylogenetic signal) in the distribution of traits among organisms. The distortion of hierarchical structure in character-state matrices can lead to errors in the estimation of phylogenetic relationships and inconsistency of methods of phylogenetic inference. Examination of trees distorted by long-branch attraction will not reveal the identities of problematic taxa, in part because the distortion can mask long branches by reducing inferred branch lengths and through errors in branching order. Here we present a simple method for the detection of taxa whose placement in evolutionary trees is made difficult by the effects of long-branch attraction. The method is an extension of a tree-independent conceptual framework of phylogenetic data exploration (RASA). Taxa that are likely to attract are revealed because long branches leave distinct footprints in the distribution of character states among taxa, and these traces can be directly observed in the error structure of the RASA regression. Problematic taxa are identified using a new diagnostic plot called the taxon variance plot, in which the apparent cladistic and phenetic variances contributed by individual taxa are compared. The procedure for identifying long edges employs algorithms solved in polynomial time and can be applied to morphological, molecular, and mixed characters. The efficacy of the method is demonstrated using simulated evolution and empirical evidence of long branches in a set of recently published sequences. We show that the accuracy of evolutionary trees can be improved by detecting and combating the potentially misleading influences of long-branch taxa.

The potential of Betv1 homologues, a nuclear multigene family, as phylogenetic markers in flowering plants

Betv1 homologues are a ubiquitous group of genes in flowering plants encoding a class of highly conserved defense-related proteins and containing open reading frames from 465 to 480 bp. Betv1-like genes consist of two exons interrupted by an intron of 76-359 bp, with the intron position highly conserved. The pairwise p distance ranged from 0 to 0.583 among flowering plants. Within plant families, the ranges of the p distance were 0-0.403, 0-0.253, and 0.011-0.369, for Apiaceae, Betulaceae, and Fabaceae, respectively. The most striking feature of the betv1 gene phylogeny was that the multiple sequences from each plant family formed a monophyletic group and sequences from each species were generally more similar to each other than those from other species. The almost exclusive paralogous relationships of genes from the same species suggested that the genes of the multigene family underwent strong concerted evolution. Phylogenies of Betulaceae and Fabaceae inferred from betv1 gene trees were generally congruent with those based on morphology and other molecules. Betv1 homologues constitute potential phylogenetic markers at the intrafamilial level or among closely related families in flowering plants.

Molecular phylogenetics and the evolution of antarctic notothenioid fishes

The monophyly of the antarctic fish suborder Notothenioidei and the monophyly of its earliest family the Bovichtidae have been investigated with 12S and 16S mitochondrial DNA sequences. New data from Cottoperca, Pseudaphritis, Harpagifer and several outgroups, in addition to available sequences, show that the bovichtids are paraphyletic. Pseudaphritis is the sister group of all the non-bovichtid notothenioids. The same results are found from two independent genetic markers, the nuclear 28S rDNA and the 12S and 16S mitochondrial rDNA. This reliably refutes a previous hypothesis that placed Pseudaphritis as the sister group of all the remaining notothenioids (including Cottoperca and Bovichtus). Bootstrap analyses show that the Notothenioidei are monophyletic (although members of the suborder Trachinoidei have not been surveyed). Subsequent data from hemoglobin composition confirm the present relationships. After discussions between members of the European Science Foundation (ESF) network during its last two meetings, we point out here some fundamental aspects of comparative biology to improve understanding between the physiologist community and phylogeneticists. The most important points are differences in how the concept of homology is used and differences in the consideration of adaptation. When adaptation is evoked or questioned, endless speculations and untestable scenarios are often developed. We strongly advocate the use of phylogenetic trees for testing hypotheses of adaptation (through multiple character mapping). Such a "research program" in comparative biology has the power to improve knowledge because it can potentially lead to new experiments for testing adaptive hypotheses.

Determining divergence times with a protein clock: update and reevaluation

A recent study of the divergence times of the major groups of organisms as gauged by amino acid sequence comparison has been expanded and the data have been reanalyzed with a distance measure that corrects for both constraints on amino acid interchange and variation in substitution rate at different sites. Beyond that, the availability of complete genome sequences for several eubacteria and an archaebacterium has had a great impact on the interpretation of certain aspects of the data. Thus, the majority of the archaebacterial sequences are not consistent with currently accepted views of the Tree of Life which cluster the archaebacteria with eukaryotes. Instead, they are either outliers or mixed in with eubacterial orthologs. The simplest resolution of the problem is to postulate that many of these sequences were carried into eukaryotes by early eubacterial endosymbionts about 2 billion years ago, only very shortly after or even coincident with the divergence of eukaryotes and archaebacteria. The strong resemblances of these same enzymes among the major eubacterial groups suggest that the cyanobacteria and Gram-positive and Gram-negative eubacteria also diverged at about this same time, whereas the much greater differences between archaebacterial and eubacterial sequences indicate these two groups may have diverged between 3 and 4 billion years ago.

Immunocytochemical localization of somatostatin and autoradiographic distribution of somatostatin binding sites in the brain of the African lungfish, Protopterus annectens

The anatomical distribution of somatostatin-immunoreactive structures and the autoradiographic localization of somatostatin binding sites were investigated in the brain of the African lungfish, Protopterus annectens. In general, there was a good correlation between the distribution of somatostatin-immunoreactive elements and the location of somatostatin binding sites in several areas of the brain, particularly in the anterior olfactory nucleus, the rostral part of the dorsal pallium, the medial subpallium, the anterior preoptic area, the tectum, and the tegmentum of the mesencephalon. However, mismatching was found in the mid-caudal dorsal pallium, the reticular formation, and the cerebellum, which contained moderate to high concentrations of binding sites and very low densities of immunoreactive fibers. In contrast, the caudal hypothalamus and the neural lobe of the pituitary exhibited low concentrations of binding sites and a high to moderate density of somatostatin-immunoreactive fibers. The present results provide the first localization of somatostatin in the brain of a dipnoan and the first anatomical distribution of somatostatin binding sites in the brain of a fish. The location of somatostatin-immunoreactive elements in the brain of P. annectens is consistent with that reported in anuran amphibians, suggesting that the general organization of the somatostatin peptidergic systems occurred in a common ancestor of dipnoans and tetrapods. The anatomical distribution of somatostatin-immunoreactive elements and somatostatin binding sites suggests that somatostatin acts as a hypophysiotropic neurohormone as well as a neurotransmitter and/or neuromodulator in the lungfish brain.

Can skull morphology be used to predict ecological relationships between bat species? A test using two cryptic species of pipistrelle

Can ecological relationships between bat species be predicted largely on the basis of morphology? This question was addressed by investigating skull morphology of two cryptic species of the pipistrelle bat. Since 45 Pipistrellus pipistrellus apparently eats larger prey than 55 P. pipistrellus, we predicted that it would have a larger overall skull size, a larger dentary apparatus, and a larger gape. To test these predictions, variables were measured from skulls of the two cryptic species, and comparisons made between them. In accordance with our predictions, overall skull size was larger in 45 P. pipistrellus than in 55 P. pipistrellus, and 45 P. pipistrellus had a longer lower jaw and the distance between the jaws at maximum gape was larger. In addition, 45 P. pipistrellus had longer upper canines, which may allow it to pierce harder prey items than 55 P. pipistrellus. Only some aspects of dietary differences between the two cryptic species could be explained by differences in skull morphology, and we suggest that empirical data, at least on diet and habitat use, are also required to explain mechanisms of resource partitioning among species in bat communities.