A phylogenetic approach to cultural evolution

There has been a rapid increase in the use of phylogenetic methods to study the evolution of languages and culture. Languages fit a tree model of evolution well, at least in their basic vocabulary, challenging the view that blending, or admixture among neighbouring groups, was predominant in cultural history. Here, we argue that we can use language trees to test hypotheses about not only cultural history and diversification, but also bio-cultural adaptation. Phylogenetic comparative methods take account of the non-independence of cultures (Galton's problem), which can cause spurious statistical associations in comparative analyses. Advances in phylogenetic methods offer new possibilities for the analysis of cultural evolution, including estimating the rate of evolution and the direction of coevolutionary change of traits on the tree. They also enable phylogenetic uncertainty to be incorporated into the analyses, so that one does not have to treat phylogenetic trees as if they were known without error.     

A phylogenetic approach to the evolution of fish behaviour

Summary WHAT HAVE WE LEARNED?As I indicated in the introduction, this is a non-traditional review. I have not asked What generalizations can we draw about the evolution of fish behaviour based upon information gleaned from phylogenetically based studies? Instead, I have presented detailed discussions of those studies. The reason for this approach is quite simple: if all studies in such a wide area of investigation can be discussed at length in one relatively short paper, then the database is not large enough to warrant the move from information collection to information synthesis. The purpose of this review, then, has been to capture the enthusiasm of the phylogenetically orientated fish ethologists and to highlight their discoveries, in the hopes that this will stimulate further research. If successful, the next review of phylogeny and the evolution of fish behaviour will follow a more familiar pathway.Although the database does not allow us to draw generalizations about the evolution of specific behavioural characters in fishes, the studies to date have uncovered a number of more general evolutionary insights. First, phylogenetic conservatism is evident at all levels of analysis, from the muscle activity patterns that underlie behavioural characters (Lauder 1986; Westneat and Wainwright, 1989; Westneat 1991; Wainwright and Lauder, 1992) through foraging preferences (Winterbottom and McLennan, 1993) and egg deposition strategies (Johnston and Page, 1992) to parental care (Stiassney and Gerstner, 1992). This conservatism forms the backbone against which the appearance of novel behaviours (apomorphies) can be highlighted. Each species' behavioural repertoire is thus a unique combination of very old (plesiomorphic), relatively old (synapomorphic) and recently derived (autapomorphic) characters. Second, phylogenetic analysis has allowed us to investigate models of behavioural evolution that were constructed from a variety of microevolutionary fitness parameters. The macroevolutionary patterns have corroborated some parts of those models (transition from biparental to female-only care: Gross and Sargent, 1985; Stiassney and Gerstner, 1992; transition from fresh water to anadromy: Gross et al., 1988; Stearley, 1992) and highlighted other parts of the models that would benefit from a re-examination of the basic assumptions (transition from biparental or female-only to male-only care: Gross and Sargent, 1985; Stiassney and Gerstner, 1992). Third, expanding our evolutionary perspective to include clades of organisms has allowed researchers to formulate new theories of behavioural evolution incroporating information about the patterns of character origin and diversification as well as information about character maintenance (Ryan, 1900a; Ryan and Rand, 1990; Ryan et al., 1990a). And finally, examination of macroevolutionary correlations between the origin and diversification of behavioural characters has allowed us to make predictions about the forces influencing the evolution of those characters that can then be tested experimentally (McLennan et al., 1988; Basolo, 1990a,b, 1991; McLennan, 1991). The studies presented in this paper have spanned a wide theoretical arena. They have revealed a number of interesting insights about the evolution of behaviour, and in so doing, have demonstrated the hybrid vigour of a research programme based upon integrating phylogeny and experimental ethology, phylogeny and functional morphology, and phylogeny and behavioural ecology. The question to be answered now is:WHERE DO WE GO FROM HERE?If this fledgling research programme is to remain vigorous, we need to do two things. First, channels of communication must be re-opened between systematists and ethologists. Specifically, we need to encourage systematists to construct robust phylogenetic trees for groups of fish that either have already been well studied behaviourally and ecologically, or would be of interest to ethologists if a phylogeny existed (the belontiids, poeciliids, and rivulines come to mind, to name just a few). In the absence of such critical information, behavioural ecologists are faced with the option of investigating their ethological data based upon trees reconstructed from old classification schemes or phenograms, neither of which produces a robust phylogenetic hypothesis of genealogy. Researchers who have opted for this approach preface their investigations with the caveat that the analysis and conclusions are only preliminary because of the unsatisfactory nature of the phylogenetic hypotheses available to them. The importance of a preliminary analysis cannot be understimated for researchers who are frustrated by their inability to apply the phylogenetic approach to their burgeoning data sets. It is, however, critical to remember that a preliminary analysis can, at best, produce only tentative results. If the data themselves are both incomplete and ambiguous, this will compound the problems arising from the absence of a rigorous phylogenetic framework, which will produce a confusing picture of behavioural evolution. It is also important to realize that even the most robust phylogenetic tree is still only a hypothesis of genealogical relationships, a hypothesis that may change with the discovery of new data.Second, links must be forged between comparative ethology and behavioural ecology. All of the examples discussed in this paper uncovered a phylogenetic component in patterns of behavioural origin and diversification. The discovery of this phylogenetic influence, however, is only the first step in developing a comprehensive evolutionary picture because phylogenetic patterns can tell us very little about the processes underlying those patterns. In order to explore questions of process, we must incorporate information about the fitness parameters of behavioural characters into our evolutionary picture. For example, optimizing such parameters onto a phylogenetic tree may allow us to investigate whether there are any macroevolutionary correlations between the origin and divergence of a behaviour and a change in one (or more) of the fitness components. We must also incorporate information about the genetic, developmental and physiological control of behaviour into our comparative framework (Brooks and McLennan, 1991; Willis et al., 1991; Lauder et al., 1993). This is perhaps the most neglected aspect of comparative ethology and will thus be the most difficult to remedy. Details of the genetic and developmental systems underlying behaviour are known for only a handful of taxa and for only a handful of behaviours within those taxa. The physiological control of behaviour is better studied, but has yet to be placed within a phylogenetic context (but see e.g. Stearley, 1992, for an example of the insights that can be gained from such a study). The results of such a multilevel approach will be a more robust estimate of the relative roles for the effects of both phylogenetic heritage and environmental factors in the evolution of behaviour in fishes.     

A phylogenetic approach to assessing the targets of microbial warfare

Bacteriocins are the most abundant and diverse defense systems in bacteria. As a result of the specific mechanisms of bacteriocin recognition and translocation into the target cell it is assumed that these toxins mediate intra-specific or population-level interactions. However, no published studies specifically address this question. We present here a survey of bacteriocin production in a collection of enteric bacteria isolated from wild mammals in Australia. A subset of the bacteriocin-producing strains was assayed for the ability to kill a broad range of enteric bacteria from the same bacterial collection. A novel method of estimating killing breadth was developed and used to compare the surveyed bacteriocins in terms of the phylogenetic range over which they kill. The most striking result is that although bacteriocin-producers kill members of their own species most frequently, some kill phylogenetically distant taxa more frequently than they kill closer relatives. This study calls into question the role these toxins play in natural populations. A significant number of bacteriocins are highly effective in killing inter-specific strains and thus bacteriocins may serve to mediate bacterial community interactions.     

A graph theoretic approach to the development of minimal phylogenetic trees

Summary The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistically-sized Steiner problems in reasonable computing time. A heuristic method of approaching the phylogenetic problem is presented, together with a worked example with 7 mammalian cytochrome c sequences. It is shown in this case that the method develops a phylogenetic tree that has the smallest possible number of amino acid replacements. The potential and limitations of the method are discussed. It is stressed that objective methods must be used for comparing different trees. In particular it should be determined how close a given tree is to a mathematically determined lower bound. A theorem is proved which is used to establish a lower bound on the length of any tree and if a tree is found with a length equal to the lower bound, then no shorter tree can exist.     

A molecular biological approach to the phylogenetic position of the genus Hyperamoeba

In 1923 Alexeieff described a new amoebic species within a new genus and named it Hyperamoeba flagellata. This amoeba exhibits three life cycle stages, an amoeboid trophozoite, a flagellated stage, and a cyst-like the heteroloboseans, the mastigamoebae, and several slime moulds. Since then more strains have been isolated and relationships to the protostelids and cercomonads and to the myxogastrid plasmodial slime moulds have been suggested. However, up to now the classification and phylogenetic position of the hyperamoebae has remained unclear. The aim of our study was to make an approach to the phylogeny of the genus Hyperamoeba with combined morphological and molecular biological data. Since 1988 we have isolated and collected Hyperamoeba-like strains from different aquatic and terrestrial sources. The 18S rDNA-sequences of 8 new Hyperamoeba strains isolated from various habitats were analysed and a cluster analysis was performed including all other available hyperamoebae. Altogether, the results of our study corroborate the relatedness of Hyperamoeba to various slime moulds. However, the hyperamoebae do not seem to be a monophyletic group, clearly putting the validity of the genus Hyperamoeba into question.     

The animal sialyltransferases and sialyltransferase-related genes: a phylogenetic approach

The animal sialyltransferases are Golgi type II transmembrane glycosyltransferases. Twenty distinct sialyltransferases have been identified in both human and murine genomes. These enzymes catalyze transfer of sialic acid from CMP-Neu5Ac to the glycan moiety of glycoconjugates. Despite low overall identities, they share four conserved peptide motifs [L (large), S (small), motif III, and motif VS (very small)] that are hallmarks for sialyltransferase identification. We have identified 155 new putative genes in 25 animal species, and we have exploited two lines of evidence: (1) sequence comparisons and (2) exon-intron organization of the genes. An ortholog to the ancestor present before the split of ST6Gal I and II subfamilies was detected in arthropods. An ortholog to the ancestor present before the split of ST6GalNAc III, IV, V, and VI subfamilies was detected in sea urchin. An ortholog to the ancestor present before the split of ST3Gal I and II subfamilies was detected in ciona, and an ortholog to the ancestor of all the ST8Sia was detected in amphioxus. Therefore, single examples of the four families (ST3Gal, ST6Gal, ST6GalNAc, and ST8Sia) have appeared in invertebrates, earlier than previously thought, whereas the four families were all detected in bony fishes, amphibians, birds, and mammals. As previously hypothesized, sequence similarities among sialyltransferases suggest a common genetic origin, by successive duplications of an ancestral gene, followed by divergent evolution. Finally, we propose predictions on these invertebrates sialyltransferase-related activities that have not previously been demonstrated and that will ultimately need to be substantiated by protein expression and enzymatic activity assays.     

A feature selection approach for identification of signature genes from SAGE data

Background  

One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed using microarray technique. Due to important differences in the probabilistic models of microarray and SAGE technologies, it is important to develop suitable techniques to select specific genes from SAGE measurements.     

A chemocentric approach to the identification of cancer targets

A novel chemocentric approach to identifying cancer-relevant targets is introduced. Starting with a large chemical collection, the strategy uses the list of small molecule hits arising from a differential cytotoxicity screening on tumor HCT116 and normal MRC-5 cell lines to identify proteins associated with cancer emerging from a differential virtual target profiling of the most selective compounds detected in both cell lines. It is shown that this smart combination of differential in vitro and in silico screenings (DIVISS) is capable of detecting a list of proteins that are already well accepted cancer drug targets, while complementing it with additional proteins that, targeted selectively or in combination with others, could lead to synergistic benefits for cancer therapeutics. The complete list of 115 proteins identified as being hit uniquely by compounds showing selective antiproliferative effects for tumor cell lines is provided.     

On a functional-morphological approach to phylogenetic reconstruction: A critique

A method of phylogenetic reconstruction as proposed by a number of scientists of the Senckenberg Research Institute is discussed. The method is based on functional-morphological studies, the evolutionary adaptation principle of Bock and Von Wahlert (1965) and so-called model reconstruction. It is argued in this paper that direction of the adaptation process cannot be determined because of lack of knowledge about particular selective forces and that theories of model reconstruction are not open to contradiction in the sense of Popperian falsification. Although it has been claimed that the method provides the only valid directional argument for morphoclines in cladistic studies, it remains unclear how to proceed when morphoclines show contradictory polarities. Moreover, it is doubtful whether polarities of morphoclines can be determined independently of phylogenetic hypotheses, and also whether the use of multistate morphoclines is methodologically valid. By relying on a particular evolutionary theory, i.e. the neo-Darwinian theory, and consequently assigning natural selection as the major agent of directional progress, the Senckenburg method of phylogenetic reconstruction restricts itself to microevolutionary change and, therefore, cannot be used when other hypotheses on the evolutionary process appear to explain the speciation process more plausibly, i.e. hypotheses on macroevolution. Furthermore, it is an unproved statement that evolution always proceeds according to the principle of economy.     

A phylogenetic approach to total evaporative water loss in mammals

Abstract Maintaining appropriate water balance is a constant challenge for terrestrial mammals, and this problem can be exacerbated in desiccating environments. It has been proposed that natural selection has provided desert-dwelling mammals physiological mechanisms to reduce rates of total evaporative water loss. In this study, we evaluated the relationship between total evaporative water loss and body mass in mammals by using a recent phylogenetic hypothesis. We compared total evaporative water loss in 80 species of arid-zone mammals to that in 56 species that inhabit mesic regions, ranging in size from 4 g to 3,500 kg, to test the hypothesis that mammals from arid environments have lower rates of total evaporative water loss than mammals from mesic environments once phylogeny is taken into account. We found that arid species had lower rates of total evaporative water loss than mesic species when using a dichotomous variable to describe habitat (arid or mesic). We also found that total evaporative water loss was negatively correlated with the average maximum and minimum environmental temperature as well as the maximum vapor pressure deficit of the environment. Annual precipitation and the variable Q (a measure of habitat aridity) were positively correlated with total evaporative water loss. These results support the hypothesis that desert-dwelling mammals have lower rates of total evaporative water loss than mesic species after controlling for body mass and evolutionary relatedness regardless of whether categorical or continuous variables are used to describe habitat.     

A genome-wide approach to identifying novel-imprinted genes

Genomic imprinting is an epigenetic process in which the copy of a gene inherited from one parent (maternal or paternal) is consistently silenced or expressed at a significantly lower level than the copy from the other parent. In an effort to begin a systematic genome-wide screen for imprinted genes, we assayed differential allelic expression (DAE) at 3,877 bi-allelic protein-coding sites located in 2,625 human genes in 67 unrelated individuals using genotyping microarrays. We used the presence of both over- and under-expression of the reference allele compared to the alternate allele to identify candidate-imprinted genes. We found 61 genes with at least twofold DAE plus “flipping” of the more highly expressed allele between reference and alternate across heterozygous samples. Sixteen flipping genes were genotyped and assayed for DAE in an independent data set of lymphoblastoid cell lines from two CEPH pedigrees. We confirmed that PEG10 is paternally expressed, identified one gene (ZNF331) with multiple lines of data indicating it is imprinted, and predicted several additional imprinting candidate genes. Our findings suggest that there are at most several hundred genes in the human genome that are universally imprinted. With samples of mRNA from appropriate tissues and a collection of informative cSNPs, a genome-wide search using this methodology could expand the list of genes that undergo genomic imprinting in a tissue- or temporal-specific manner. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A biometric approach to laboratory rodent identification

Individual identification of laboratory rodents typically involves invasive methods, such as tattoos, ear clips, and implanted transponders. Beyond the ethical dilemmas they may present, these methods may cause pain or distress that confounds research results. The authors describe a prototype device for biometric identification of laboratory rodents that would allow researchers to identify rodents without the complications of other methods. The device, which uses the rodent's ear blood vessel pattern as the identifier, is fast, automatic, noninvasive, and painless.     

A frequency distribution approach to hotspot identification

We present a new global method for the identification of hotspots in conservation and ecology. The method is based on the identification of spatial structure properties through cumulative relative frequency distributions curves, and is tested with two case studies, the identification of fish density hotspots and terrestrial vertebrate species diversity hotspots. Results from the frequency distribution method are compared with those from standard techniques among local, partially local and global methods. Our approach offers the main advantage to be independent from the selection of any threshold, neighborhood, or other parameter that affect most of the currently available methods for hotspot analysis. The two case studies show how such elements of arbitrariness of the traditional methods influence both size and location of the identified hotspots, and how this new global method can be used for a more objective selection of hotspots.     

A phylogenetic approach to species delimitation in freshwater Gastrotricha from Sweden

Gastrotricha is a cosmopolitan group of aquatic invertebrates. To date, approximately 765 species have been described. This study is the first to deal with species delimitation and cryptic species of freshwater Gastrotricha. Three commonly encountered species, Heterolepidoderma ocellatum, Lepidochaetus zelinkai, and Lepidodermella squamata, are investigated for cryptic speciation. Most of the material is based on Swedish specimens but closely related species from other parts of the world are also included. Taxonomic revisions are supported by phylogenies based on 18S rRNA, 28S rRNA, and COI mtDNA of freshwater Chaetonotidae from several genera and inferred from Bayesian and maximum likelihood approaches. Heterolepidoderma ocellatum f. sphagnophilum is raised to species level, under the name H. acidophilum n. sp. Moreover, genetic data based on COI indicate large variation between two morphologically very similar groups of Lepidodermella squamata. The extent of cryptic speciation in L. zelinkai appears low. Based on the phylogenetic hypothesis presented in this article, the new species, Lepidodermella intermedia n. sp., from northern Sweden is also described. The phylogenetic hypothesis generated shows that Chaetonotidae is a non-monophyletic group.     

A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora

To critically examine the relationship between species recognized by phylogenetic and reproductive compatibility criteria, we applied phylogenetic species recognition (PSR) to the fungus in which biological species recognition (BSR) has been most comprehensively applied, the well-studied genus Neurospora. Four independent anonymous nuclear loci were characterized and sequenced from 147 individuals that were representative of all described outbreeding species of Neurospora. We developed a consensus-tree approach that identified monophyletic genealogical groups that were concordantly supported by the majority of the loci, or were well supported by at least one locus but not contradicted by any other locus. We recognized a total of eight phylogenetic species, five of which corresponded with the five traditional biological species, and three of which were newly discovered. Not only were phylogenetic criteria superior to traditional reproductive compatibility criteria in revealing the full species diversity of Neurospora, but also significant phylogenetic subdivisions were detected within some species. Despite previous suggestions of hybridization between N. crassa and N. intermedia in nature, and the fact that several putative hybrid individuals were included in this study, no molecular evidence in support of recent interspecific gene flow or the existence of true hybrids was observed. The sequence data from the four loci were combined and used to clarify how the species discovered by PSR were related. Although species-level clades were strongly supported, the phylogenetic relationships among species remained difficult to resolve, perhaps due to conflicting signals resulting from differential lineage sorting.