BMC Evolutionary Biology - Latest articles

Genetic evidence links invasive monk parakeet populations in the United States to the international pet trade

Michael A Russello, Michael L Avery and Timothy F Wright — 2008-07-24

Background: Severe ecological and economic impacts caused by some invasive species make it imperative to understand the attributes that permit them to spread. A notorious crop pest across its native range in South America, the monk parakeet (Myiopsitta monachus) has become established on four other continents, including growing populations in the United States. As a critical first step to studying mechanisms of invasion success in this species, here we elucidated the geographical and taxonomic history of the North American invasions of the monk parakeet. Specifically, we conducted a genetic assessment of current monk parakeet taxonomy based on mitochondrial DNA control region sequences from 73 museum specimens. These data supported comparative analyses of mtDNA lineage diversity in the native and naturalized ranges of the monk parakeet and allowed for identification of putative source populations. Results: There was no molecular character support for the M. m. calita, M. m. cotorra, and M. m. monachus subspecies, while the Bolivian M. m. luchsi was monophyletic and diagnosably distinct. Three haplotypes sampled in the native range were detected within invasive populations in Florida, Connecticut, New Jersey and Rhode Island, the two most common of which were unique to M. m. monachus samples from eastern Argentina and bordering areas in Brazil and Uruguay. Conclusions: The lack of discrete morphological character differences in tandem with the results presented here suggest that M. m. calita, M. m. cotorra and M. m. monachus are in need of formal taxonomic revision. The genetic distinctiveness of M. m. luchsi is consistent with previous recommendations of allospecies status for this taxon. The geographic origins of haplotypes sampled in the four U.S. populations are concordant with trapping records from the mid-20th century and suggest that propagule pressure exerted by the international pet bird trade contributed to the establishment of invasive populations in the United States.

Correction: Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset

Jeff W Higdon, Olaf RP Bininda-Emonds, Robin MD Beck and Steven H Ferguson — 2008-07-24

After publication of our article [1], we discovered that one of the programs used to date the supertree, relDate v2.2 [2], contained a bug that can lead to errors in the date estimates it provides. The precise effect of the bug is dependent on tree shape, but it generally results in overestimates of divergence-time estimates, particularly for nodes that are closer topologically to the tips of the tree. It can potentially, however, affect every date estimate on a tree. Fortunately, the impact of the bug on date estimates in the pinniped supertree was minimal. Only 14 of the 35 nodes were affected, with the mean and median absolute errors for the dates of these 14 nodes being 0.19 and 0.10 million years (= 8.9% and 6.1% relative to the corrected date). All but one error (that for node 14) were overestimates. The largest difference was 0.5 million years (for node 6), and the two sets of dates are perfectly correlated with one another (correlation coefficient = 1.000, Z = 28.508, P < 0.0001). Corrected dates and 95% confidence-interval dates for all nodes in the pinniped supertree can be found in Table 1 and should be used in place of those reported in the original publication [1]. We apologize for any inconvenience this error might cause.

Mitogenomic evaluation of the historical biogeography of cichlids toward reliable dating of teleostean divergences

2008-07-23

Background: Recent advances in DNA sequencing and computation offer the opportunity for reliable estimates of divergence times between organisms based on molecular data. Bayesian estimations of divergence times that do not assume the molecular clock use time constraints at multiple nodes, usually based on fossil records, as major boundary conditions. However, fossil records of bony fishes may not adequately provide effective time constraints at multiple nodes. We explored an alternative source of time constraints in teleostean phylogeny by evaluating a biogeographic hypothesis concerning freshwater fishes from the family Cichlidae (Perciformes: Labroidei). Results: We added new mitogenomic sequence data from six cichlid species and conducted phylogenetic analyses using a large mitogenomic data set. We found a reciprocal monophyly of African and Neotropical cichlids and their sister group relationship to some Malagasy taxa (Ptychochrominae sensu Sparks and Smith). All of these taxa clustered with a Malagasy + Indo/Sri Lankan clade (Etroplinae sensu Sparks and Smith). The results of the phylogenetic analyses and divergence time estimations between continental cichlid clades were much more congruent with a Gondwanaland origin and Cretaceous vicariant divergences than with Cenozoic transmarine dispersal between major continents. Conclusions: We propose to add the biogeographic assumption of cichlid divergences by continental fragmentation as effective time constraints in dating teleostean divergence times. We conducted divergence time estimations among teleosts by incorporating these additional time constraints and achieved a considerable reduction in credibility intervals in the estimated divergence times.

Phylogenetic analyses suggest multiple changes of substrate specificity within the Glycosyl hydrolase 20 family

Jari Intra, Giulio Pavesi and David S Horner — 2008-07-22

Background: Beta-N-acetylhexosaminidases belonging to the glycosyl hydrolase 20 (GH20) family are involved in the removal of terminal beta-glycosidacally linked N-acetylhexosamine residues. These enzymes, widely distributed in microorganisms, animals and plants, are involved in many important physiological and pathological processes, such as cell structural integrity, energy storage, pathogen defence, viral penetration, cellular signalling, fertilization, development of carcinomas, inflammatory events and lysosomal storage diseases. Nevertheless, only limited analyses of phylogenetic relationships between GH20 genes have been performed until now. Results: Careful phylogenetic analyses of 233 inferred protein sequences from eukaryotes and prokaryotes reveal a complex history for the GH20 family. In bacteria, multiple gene duplications and lineage specific gene loss (and/or horizontal gene transfer) are required to explain the observed taxonomic distribution. The last common ancestor of extant eukaryotes is likely to have possessed at least one GH20 family member. At least one gene duplication before the divergence of animals, plants and fungi as well as other lineage specific duplication events have given rise to multiple paralogous subfamilies in eukaryotes. Phylogenetic analyses also suggest that a second, divergent subfamily of GH20 family genes present in animals derive from an independent prokaryotic source. Our data suggest multiple convergent changes of functional roles of GH20 family members in eukaryotes. Conclusions: This study represents the first detailed evolutionary analysis of the glycosyl hydrolase GH20 family. Mapping of data concerning physiological function of GH20 family members onto the phylogenetic tree reveals that apparently convergent and highly lineage specific changes in substrate specificity have occurred in multiple GH20 subfamilies.

Genetic origin, admixture, and asymmetry in maternal and paternal human lineages in Cuba

2008-07-21

Background: Before the arrival of Europeans to Cuba, the island was inhabited by two Native American groups, the Tainos and the Ciboneys. Most of the present archaeological, linguistic and ancient DNA evidence indicates a South American origin for these populations. In colonial times, Cuban Native American people were replaced by European settlers and slaves from Africa. It is still unknown however, to what extent their genetic pool intermingled with and was 'diluted' by the arrival of newcomers. In order to investigate the demographic processes that gave rise to the current Cuban population, we analyzed the hypervariable region I (HVS-I) and five single nucleotide polymorphisms (SNPs) in the mitochondrial DNA (mtDNA) coding region in 245 individuals, and 40 Y-chromosome SNPs in 132 male individuals. Results: The Native American contribution to present-day Cubans accounted for 33% of the maternal lineages, whereas Africa and Eurasia contributed 45% and 22% of the lineages, respectively. This Native American substrate in Cuba cannot be traced back to a single origin within the American continent, as previously suggested by ancient DNA analyses. Strikingly, no Native American lineages were found for the Y-chromosome, for which the Eurasian and African contributions were around 80% and 20%, respectively. Conclusions: While the ancestral Native American substrate is still appreciable in the maternal lineages, the extensive process of population admixture in Cuba has left no trace of the paternal Native American lineages, mirroring the strong sexual bias in the admixture processes taking place during colonial times.

A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification?

2008-07-19

Background: The order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated into various habitats such as freshwater, brackish and coastal waters, open seas, and deep waters along continental shelves and slopes. Despite extensive studies based on both morphology and molecule, there has been no clear resolution except for monophylies of each family and sister-group relationships of Diodontidae + Tetraodontidae and Balistidae + Monacanthidae. To address phylogenetic questions of tetraodontiform fishes, we used whole mitochondrial genome (mitogenome) sequences from 27 selected species (data for 11 species were newly determined during this study) that fully represent all families and subfamilies of Tetraodontiformes (except for Hollardinae of the Triacanthodidae). Partitioned maximum likelihood (ML) and Bayesian analyses were performed on two data sets comprising concatenated nucleotide sequences from 13 protein-coding genes (all positions included; third codon positions converted into purine [R] and pyrimidine [Y]), 22 transfer RNA and two ribosomal RNA genes (total positions = 15,084). Results: The resultant tree topologies from the two data sets were congruent, with many internal branches showing high support values. The mitogenomic data strongly supported monophyly of all families and subfamilies (except the Tetraodontinae) and sister-group relationships of Balistidae + Monacanthidae and Tetraodontidae + Diodontidae, confirming the results of previous studies. However, we also found two unexpected basal splits into Clade A (Triacanthidae + Balistidae + Monacanthidae + Tetraodontidae + Diodontidae + Molidae) and Clade B (Ostraciidae + Triodontidae + Triacanthodidae). Conclusion: This split into two basal clades has never been reported and challenges previously proposed hypotheses based on both morphology and nuclear gene sequences. It is likely that the basal split had involved ecological diversification, because most members of Clade A exclusively occur in shallow waters (freshwater, brackish and coastal waters, and open seas), while those of Clade B occur mainly in relatively deep waters along continental shelves and slopes except for more derived ostraciids. This suggests that the basal split between the two clades led to subsequent radiation into the two different habitats.

The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses

Xuhua Xia — 2008-07-19

Background: Fungal and animal mitochondrial genomes typically have one tRNA for each synonymous codon family. The codon-anticodon adaptation hypothesis predicts that the wobble nucleotide of a tRNA anticodon should evolve towards maximizing Watson-Crick base pairing with the most frequently used codon within each synonymous codon family, whereas the wobble versatility hypothesis argues that the nucleotide at the wobble site should be occupied by a nucleotide most versatile in wobble pairing, i.e., the tRNA wobble nucleotide should be G for NNY codon families, and U for NNR and NNN codon families (where Y stands for C or U, R for A or G and N for any nucleotide). Results: We here integrate these two traditional hypotheses on tRNA anticodons into a unified model based on an analysis of the wobble costs associated with different wobble base pairs. This novel approach allows the relative cost of wobble pairing to be qualitatively evaluated. A comprehensive study of 36 fungal genomes suggests very different costs between two kinds of U:G wobble pairs, i.e., (1) between a G at the wobble site of a tRNA anticodon and a U at the third codon position (designated MU3:G) and (2) between a U at the wobble site of a tRNA anticodon and a G at the third codon position (designated MG3:U). Conclusions: In general, MU3:G is much smaller than MG3:U, suggesting no selection against U-ending codons in NNY codon families with a wobble G in the tRNA anticodon but strong selection against G-ending codons in NNR codon families with a wobble U at the tRNA anticodon. This finding resolves several puzzling observations in fungal genomics and corroborates previous studies showing that U3:G wobble is energetically more favorable than G3:U wobble.

The molecular basis of color vision in colorful fish: Four Long Wave-Sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites

2008-07-18

Background: Comparisons of functionally important changes at the molecular level in model systems have identified key adaptations driving isolation and speciation. In cichlids, for example, long wavelength-sensitive (LWS) opsins appear to play a role in mate choice and male color variation within and among species. To test the hypothesis that the evolution of elaborate coloration in male guppies (Poecilia reticulata) is also associated with opsin gene diversity, we sequenced long wavelength-sensitive (LWS) opsin genes in six species of the family Poeciliidae. Results: Sequences of four LWS opsin genes were amplified from the guppy genome and from mRNA isolated from adult guppy eyes. Variation in expression was quantified using qPCR. Three of the four genes encode opsins predicted to be most sensitive to different wavelengths of light because they vary at key amino acid positions. This family of LWS opsin genes was produced by a diversity of duplication events. One, an intronless gene, was produced prior to the divergence of families Fundulidae and Poeciliidae. Between-gene PCR and DNA sequencing show that two of the guppy LWS opsins are linked in an inverted orientation. This inverted tandem duplication event occurred near the base of the poeciliid tree in the common ancestor of Poecilia and Xiphophorus. The fourth sequence has been uncovered only in the genus Poecilia. In the guppies surveyed here, this sequence is a hybrid, with the 5' end most similar to one of the tandem duplicates and the 3' end identical to the other. Conclusion: Enhanced wavelength discrimination, a possible consequence of opsin gene duplication and divergence, might have been an evolutionary prerequisite for color-based sexual selection and have led to the extraordinary coloration now observed in male guppies and in many other poeciliids.

Regionally and climatically restricted patterns of distribution of genetic diversity in a migratory bat species, Miniopterus schreibersii (Chiroptera: Vespertilionidae)

2008-07-18

Background: Various mechanisms such as geographic barriers and glacial episodes have been proposed as determinants of intra-specific and inter-specific differentiation of populations, and the distribution of their genetic diversity. More recently, habitat and climate differences, and corresponding adaptations have been shown to be forces influencing the phylogeographic evolution of some vertebrates. In this study, we examined the contribution of these various factors on the genetic differentiation of the bent-winged bat, Miniopterus schreibersii, in southeastern Europe and Anatolia.Results and conclusionOur results showed differentiation in mitochondrial DNA coupled with weaker nuclear differentiation. We found evidence for restriction of lineages to geographical areas for hundreds of generations. The results showed that the most likely ancestral haplotype was restricted to the same geographic area (the Balkans) for at least 6,000 years. We were able to delineate the migration routes during the population expansion process, which followed the coasts and the inland for different nested mitochondrial clades. Hence, we were able to describe a scenario showing how multiple biotic and abiotic events including glacial periods, climate and historical dispersal patterns complemented each other in causing regional and local differentiation within a species.

Differences in evolutionary pressure acting within highly conserved ortholog groups

Teresa M Przytycka, Raja Jothi, L. Aravind and David J Lipman — 2008-07-17

In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions. Using a set of ortholog groups from prokaryotes, with a single representative in each studied organism, we asked the question if this evolutionary pressure is acting similarly on different subgroups of orthologs defined as major lineages (e.g. Proteobacteria or Firmicutes) Results: Using correlations in entropy measures as a proxy for evolutionary pressure, we observed two distinct behaviors within our ortholog collection. The first subset of ortholog groups, called here informational, consisted mostly of proteins associated with information processing (i.e. translation, transcription, DNA replication) and the second, the non-informational ortholog groups, mostly comprised of proteins involved in metabolic pathways. The evolutionary pressure acting on non-informational proteins is more uniform relative to their informational counterparts. The non-informational proteins show higher level of correlation between entropy profiles and more uniformity across subgroups. Conclusion: The low correlation of entropy profiles in the informational ortholog groups suggest that the evolutionary pressure acting on the informational ortholog groups is not uniform across different clades considered this study. This might suggest "fine-tuning" of informational proteins in each lineage leading to lineage-specific differences in selection. This, in turn, could make these proteins less exchangeable between lineages. In contrast, the uniformity of the selective pressure acting on the non-informational groups might allow the exchange of the genetic material via lateral gene transfer.