The historical biogeography of Mammalia

Palaeobiogeographic reconstructions are underpinned by phylogenies, divergence times and ancestral area reconstructions, which together yield ancestral area chronograms that provide a basis for proposing and testing hypotheses of dispersal and vicariance. Methods for area coding include multi-state coding with a single character, binary coding with multiple characters and string coding. Ancestral reconstruction methods are divided into parsimony versus Bayesian/likelihood approaches. We compared nine methods for reconstructing ancestral areas for placental mammals. Ambiguous reconstructions were a problem for all methods. Important differences resulted from coding areas based on the geographical ranges of extant species versus the geographical provenance of the oldest fossil for each lineage. Africa and South America were reconstructed as the ancestral areas for Afrotheria and Xenarthra, respectively. Most methods reconstructed Eurasia as the ancestral area for Boreoeutheria, Euarchontoglires and Laurasiatheria. The coincidence of molecular dates for the separation of Afrotheria and Xenarthra at approximately 100 Ma with the plate tectonic sundering of Africa and South America hints at the importance of vicariance in the early history of Placentalia. Dispersal has also been important including the origins of Madagascar's endemic mammal fauna. Further studies will benefit from increased taxon sampling and the application of new ancestral area reconstruction methods.     

Gene flow between species of Lake Victoria haplochromine fishes

The haplochromine cichlid fishes of Lake Victoria (LV), East Africa, are a textbook example of adaptive radiation-a rapid divergence of multiple morphologically distinguishable forms from a few founding lineages. The forms are generally believed to constitute a "flock" of several hundred reproductively isolated species in a dozen or so genera. This belief has, until now, not been subjected to a test, however. Here, we compare genetic variation at 11 loci in 10 haplochromine populations of 6 different species. Although the genetic diversity in the populations is quite high, using a variety of statistical tests, we find no evidence of genetic differentiation among the populations of LV haplochromines. On genetic distance trees, populations of the same species intermingle with those of different species. At the molecular level, the species are indistinguishable from one another. Genetic comparisons with closely related species in 2 crater lakes indicate that the species within LV continue exchanging genes. These observations have important implications for phylogenetic reconstruction. The approach used in this study is applicable to other instances of adaptive radiation.     

Reconstitution of ancestral green visual pigments of zebrafish and molecular mechanism of their spectral differentiation

We previously reported that zebrafish have four tandemly duplicated green (RH2) opsin genes (RH2-1, RH2-2, RH2-3, and RH2-4). Absorption spectra vary widely among the four photopigments reconstituted with 11-cis retinal, with their peak absorption spectra (lambda(max)) being 467, 476, 488, and 505 nm, respectively. In this study, we inferred the ancestral amino acid (aa) sequences of the zebrafish RH2 opsins by likelihood-based Bayesian statistics and reconstituted the ancestral opsins by site-directed mutagenesis. The ancestral pigment (A1) to the four zebrafish RH2 pigments and that (A3) to RH2-3 and RH2-4 showed lambda(max) at 506 nm, while that (A2) to RH2-1 and RH2-2 showed a lambda(max) at 474 nm, indicating that a spectral shift had occurred toward the shorter wavelength on the evolutionary lineages A1 to A2 by 32 nm, A2 to RH2-1 by 7 nm, and A3 to RH2-3 by 18 nm. Pigment chimeras and site-directed mutagenesis revealed a large contribution (approximately 15 nm) of glutamic acid to glutamine substitution at residue 122 (E122Q) to the A1 to A2 and A3 to RH2-3 spectral shifts. However, the remaining spectral differences appeared to result from complex interactive effects of a number of aa replacements, each of which has only a minor spectral contribution (1-3 nm). The four zebrafish RH2 pigments cover nearly an entire range of lambda(max) distribution among vertebrate RH2 pigments and provide an excellent model to study spectral tuning mechanisms of RH2 in vertebrates.     

Genetic continuity of brood-parasitic indigobird species

Speciation in brood-parasitic indigobirds (genus Vidua) is a consequence of behavioural imprinting in both males and females. Mimicry of host song by males and host fidelity in female egg laying result in reproductive isolation of indigobirds associated with a given host species. Colonization of new hosts and subsequent speciation require that females occasionally lay eggs in the nests of novel hosts but the same behaviour may lead to hybridization when females parasitize hosts already associated with other indigobird species. Thus, retained ancestral polymorphism and ongoing hybridization are two alternative explanations for the limited genetic differentiation among indigobird species. We tested for genetic continuity of indigobird species using mitochondrial sequences and nuclear microsatellite data. Within West Africa and southern Africa, allopatric populations of the same species are generally more similar to each other than to sympatric populations of different species. Likewise, a larger proportion of genetic variation is explained by differences between species than by differences between locations in alternative hierarchical AMOVAS, suggesting that the rate of hybridization is not high enough to homogenize sympatric populations of different species or prevent genetic differentiation between species. Broad sharing of genetic polymorphisms among species, however, suggests that some indigobird species trace to multiple host colonization events in space and time, each contributing to the formation of a single interbreeding population bound together by songs acquired from the host species.     

Are residues in a protein folding nucleus evolutionarily conserved?

Protein is the working molecule of the cell, and evolution is the hallmark of life. It is important to understand how protein folding and evolution influence each other. Several studies correlating experimental measurement of residue participation in folding nucleus and sequence conservation have reached different conclusions. These studies are based on assessment of sequence conservation at folding nucleus sites using entropy or relative entropy measurement derived from multiple sequence alignment. Here we report analysis of conservation of folding nucleus using an evolutionary model alternative to entropy-based approaches. We employ a continuous time Markov model of codon substitution to distinguish mutation fixed by evolution and mutation fixed by chance. This model takes into account bias in codon frequency, bias-favoring transition over transversion, as well as explicit phylogenetic information. We measure selection pressure using the ratio omega of synonymous versus non-synonymous substitution at individual residue site. The omega-values are estimated using the PAML method, a maximum-likelihood estimator. Our results show that there is little correlation between the extent of kinetic participation in protein folding nucleus as measured by experimental phi-value and selection pressure as measured by omega-value. In addition, two randomization tests failed to show that folding nucleus residues are significantly more conserved than the whole protein, or the median omega value of all residues in the protein. These results suggest that at the level of codon substitution, there is no indication that folding nucleus residues are significantly more conserved than other residues. We further reconstruct candidate ancestral residues of the folding nucleus and suggest possible test tube mutation studies for testing folding behavior of ancient folding nucleus.     

Distribution-abundance relationship for passerines breeding in Tunisian oases: test of the sampling hypothesis

The positive relationship between local abundance and distribution of species is a widely recognized pattern in community ecology. However, it has been suggested that this relationship can simply be an artefact of sampling because locally rare species are less detectable then locally abundant ones, and hence their distribution can easily be underestimated. Here, we use count data to investigate the relationship between distribution and abundance of passerines breeding in a sample of oases from southern Tunisia, and we provide a test of the sampling artefact hypothesis. In particular, we checked for a difference in detection probability between localized and widespread species, and we tested if increasing the sampling effort affects the significance of the relationship. A significant positive relationship between the average local abundance of passerine species and the proportion of occupied oases was found. The use of a capture-recapture approach allowed us to estimate and to compare the detection probabilities of localized and widespread species subsets. We found that localized species were locally less detectable than widespread species, which is consistent with the main assumption of the sampling artefact hypothesis. However, increasing the detection probability of species by conducting more counts did not affect the significance of the relationship, which did not give support to the sampling artefact hypothesis. Our work implies that sampling contributed to the distribution-abundance relationship we found, but that it is unlikely that such a relationship could entirely be explained by an artefact of sampling. It also underlines the insight that can be gained by using probabilistic approaches of estimating species number and detection probability when attempting to disentangle sampling from ecological effects in community ecology studies.     

Estimating Orangutan Densities Using the Standing Crop and Marked Nest Count Methods: Lessons Learned for Conservation

Reliable estimates of great ape abundance are needed to assess distribution, monitor population status, evaluate conservation tactics, and identify priority populations for conservation. Rather than using direct counts, surveyors often count ape nests. The standing crop nest count (SCNC) method converts the standing stock of nests into animal densities using a set of parameters, including nest decay rate. Nest decay rates vary greatly over space and time, and it takes months to calculate a site-specific value. The marked nest count (MNC) method circumvents this issue and only counts new nests produced during a defined period. We compared orangutan densities calculated by the two methods using data from studies in Sumatra and Kalimantan, Indonesia. We show how animal densities calculated using nest counts should be cautiously interpreted when used to make decisions about management or budget allocation. Even with site-specific decay rates, short studies using the SCNC method may not accurately reflect the current population unless conducted at a scale sufficient to include wide-ranging orangutan movement. Density estimates from short studies using the MNC method were affected by small sample sizes and by orangutan movement. To produce reliable results, the MNC method may require a similar amount of effort as the SCNC method. We suggest a reduced reliance on the traditional line transect surveys in favor of feasible alternative methods when absolute abundance numbers are not necessary or when site-specific nest decay rates are not known. Given funding constraints, aerial surveys, reconnaissance walks, and interview techniques may be more cost-effective means of accomplishing some survey goals.     

Estimating the timing of growth rings in Atlantic cod otoliths using stable oxygen isotopes

A technique involving micro‐scale sampling of otolith carbonate and analyses of stable oxygen isotope composition was used to relate the zone appearance of the otolith to the seasonal temperature cycle. Otolith opacity could then be related to the timing of zone formation. Otoliths from two groups of Atlantic cod Gadus morhua held under known temperature conditions over a period of 4 and 6 years were examined. The otolith translucency followed the same pattern as the estimated temperature (from otolith δ¹⁸O values) in the yearly increments three and four, meaning that the translucent zones were deposited at the seasonal highest temperature in late summer and early autumn. The relative light intensities of otolith yearly increments five and six of older fish (deposited in the same years), however, were not significantly correlated to the estimated temperatures since increased otolith translucency also occurred at low temperatures. This might have been caused by stress in connection with gonad development or starvation during the spawning period. The results showed that this method of coupling otolith opacity and stable oxygen isotope composition can be used to estimate the timing of zone formations in otoliths.     

Using evolutionary information and ancestral sequences to understand the sequence-function relationship in GLP-1 agonists

Glucagon-like peptide-1 (GLP-1) is an incretin hormone with therapeutic potential for type 2 diabetes. A variety of GLP-1 sequences are known from amphibian species, and some of these have been tested here and found to be able to bind and activate the human GLP-1 receptor. While little difference was observed for the in vitro potency for the human GLP-1 receptor, larger differences were found in the enzymatic stability of these peptides. Two peptides showed increased enzymatic stability, and they group together phylogenetically, though they originate from Amphibia and Reptilia. We have used ancestral sequence reconstruction to analyze the evolution of these GLP-1 molecules, including the synthesis of new peptides. We find that the increased stability could not be observed in the resurrected peptides from the common ancestor of frogs, even though they maintain the ability to activate the human GLP-1 receptor. Another method, using residue mapping on evolutionary branches yielded peptides that had maintained potency towards the receptor and also showed increased stability. This represents a new approach using evolutionary data in protein engineering.