BMC Evolutionary Biology (BMC EVOL BIOL)

Publications in this journal

• Article: Comparative molecular phylogeography of two otters (Pteronura brasiliensis and Lontra longicaudis, Mustelidae) in the Western Amazon by means of mt DNA genes

  M. Ruiz-Garcia, B. Thoisy, A. Lavergne
  BMC Evolutionary Biology 11/2013;
• Article: Arthroaspis n, gen., a common element of the Sirius Passet Lagerstatte (Cambrian, North Greenland), sheds light on trilobite ancestry.

  Martin Stein, Graham E Budd, John S Peel, David At Harper
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  ABSTRACT: BACKGROUND: Exceptionally preserved Palaeozoic faunas have yielded a plethora of trilobite-like arthropods, often referred to as lamellipedians. Among these, Artiopoda is supposed to contain taxa united by a distinctive appendage structure. This includes several well supported groups, Helmetiida, Nektaspida, and Trilobita, as well as a number of problematic taxa. Interrelationships remain unclear, and the position of the lamellipedian arthropods as a whole also remains the subject of debate. RESULTS: Arthroaspis bergstroemi n. gen. n. sp., a new arthropod from the early Cambrian Sirius Passet Lagerstatte of North Greenland shows a striking combination of both dorsal and ventral characters of Helmetiida, Nektaspida, and Trilobita. Cladistic analysis with a broad taxon sampling of predominantly early Palaeozoic arthropods yields a monophyletic Lamellipedia as sister taxon to the Crustacea or Tetraconata. Artiopoda is resolved as paraphyletic, giving rise to the Marrellomorpha. Within Lamellipedia, a clade of pygidium bearing taxa is resolved that can be shown to have a broadly helmetiid-like tergite morphology in its ground pattern. This morphology is plesiomorphically retained in Helmetiida and in Arthroaspis, which falls basally into a clade containing Trilobita. The trilobite appendages, though similar to those of other lamellipedians in gross morphology, have a unique outward rotation of the anterior trunk appendages, resulting in a 'hard wired' lateral splay, different to that observed in other Lamellipedia. CONCLUSIONS: The combination of helmetiid, trilobite, and nektaspid characters in Arthroaspis gives important hints concerning character polarisation within the trilobite-like arthropods. The distinctive tergite morphology of trilobites, with its sophisticated articulating devices, is derived from flanged edge-to-edge articulating tergites forming a shield similar to the helmetiids, previously considered autapomorphic for that group. The stereotypical lateral splay of the appendages of lamellipedians is a homoplastic character shown to be achieved by several groups independently.
  BMC Evolutionary Biology 05/2013; 13(1):99.
• Article: Babes in the wood -- a unique window into sea scorpion ontogeny.

  James C Lamsdell, Paul A Selden
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  ABSTRACT: BACKGROUND: Few studies on eurypterids have taken into account morphological changes that occur throughout postembryonic development. Here two species of eurypterid are described from the Pragian Beartooth Butte Formation of Cottonwood Canyon in Wyoming, and included in a phylogenetic analysis. Both species comprise individuals from a number of instars, and this allows for changes that occur throughout their ontogeny to be documented, and how ontogenetically variable characters can influence phylogenetic analysis to be tested. RESULTS: The two species of eurypterid are described as Jaekelopterus howelli (Kjellesvig-Waering and St[latin small letter o with stroke]rmer, 1952) and Strobilopterus proteus sp. nov. Phylogenetic analysis places them within the Pterygotidae and Strobilopteridae respectively, both families within the Eurypterina. Jaekelopterus howelli shows positive allometry of the cheliceral denticles throughout ontogeny, while a number of characteristics including prosomal appendage length, carapace shape, lateral eye position, and relative breadth all vary during the growth of Strobilopterus proteus. CONCLUSIONS: The ontogeny of Strobilopterus proteus shares much in common with that of modern xiphosurans, however certain characteristics including apparent true direct development suggest a closer affinity to arachnids. The ontogenetic development of the genital appendage also supports the hypothesis that the structure is homologous to the endopods of the trunk limbs of other arthropods. Including earlier instars in the phylogenetic analysis is shown to destabilise the retrieved topology. Therefore, coding juveniles as individual taxa in an analysis is shown to be actively detrimental and alternative ways of coding ontogenetic data into phylogenetic analyses should be explored.
  BMC Evolutionary Biology 05/2013; 13(1):98.
• Article: The expression and evolution of virulence in multiple infections: the role of specificity, relative virulence and relative dose.

  Frida Ben-Ami, Jarkko Routtu
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  ABSTRACT: BACKGROUND: Multiple infections of the same host by different strains of the same microparasite species are believed to play a crucial role during the evolution of parasite virulence. We investigated the role of specificity, relative virulence and relative dose in determining the competitive outcome of multiple infections in the Daphnia magna-Pasteuria ramosa host-parasite system. RESULTS: We found that infections by P. ramosa clones (single genotype) were less virulent and produced more spores than infections by P. ramosa isolates (possibly containing multiple genotypes). We also found that two similarly virulent isolates of P. ramosa differed considerably in their within-host competitiveness and their effects on host offspring production when faced with coinfecting P. ramosa isolates and clones. Although the relative virulence of a P. ramosa isolate/clone appears to be a good indicator of its competitiveness during multiple infections, the relative dose may alter the competitive outcome. Moreover, spore counts on day 20 post-infection indicate that the competitive outcome is largely decided early in the parasite's growth phase, possibly mediated by direct interference or apparent competition. CONCLUSIONS: Our results emphasize the importance of epidemiology as well as of various parasite traits in determining the outcome of within-host competition. Incorporating realistic epidemiological and ecological conditions when testing theoretical models of multiple infections, as well as using a wider range of host and parasite genotypes, will enable us to better understand the course of virulence evolution.
  BMC Evolutionary Biology 05/2013; 13(1):97.
• Article: Evolution of MHC class I genes in the endangered loggerhead sea turtle (Caretta caretta) revealed by 454 amplicon sequencing.

  Victor A Stiebens, Sonia E Merino, Frédéric J Chain, Christophe Eizaguirre
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  ABSTRACT: BACKGROUND: In evolutionary and conservation biology, parasitism is often highlighted as a major selective pressure. To fight against parasites and pathogens, genetic diversity of the immune genes of the major histocompatibility complex (MHC) is particularly important. However, the extensive degree of polymorphism observed in these genes makes it difficult to conduct thorough population screening. METHODS: We utilized a genotyping protocol that uses 454 amplicon sequencing to characterize the MHC class I in the endangered loggerhead sea turtle (Caretta caretta) and to investigate their evolution at multiple relevant levels of organization. RESULTS: MHC class I genes revealed signatures of trans-species polymorphism across several reptile species. In the studied loggerhead turtle individuals, it results in the maintenance of two ancient allelic lineages. We also found that individuals carrying an intermediate number of MHC class I alleles are larger than those with either a low or high number of alleles. CONCLUSIONS: Multiple modes of evolution seem to maintain MHC diversity in the loggerhead turtles, with relatively high polymorphism for an endangered species.
  BMC Evolutionary Biology 04/2013; 13(1):95.
• Article: Global climate changes drive ecological specialization of mammal faunas: trends in rodent assemblages from the Iberian Plio-Pleistocene.

  Ana R Gómez Cano, Juan L Cantalapiedra, Aurora Mesa, Ana Moreno Bofarull, Manuel Hernández Fernández
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  ABSTRACT: BACKGROUND: Several macroevolutionary hypotheses propose a synchrony between climatic changes and variations in the structure of faunal communities. Some of them focus on the importance of the species ecological specialization because of its effects on evolutionary processes and the resultant patterns. Particularly, Vrba's turnover pulse hypothesis and resource-use hypothesis revolve around the importance of biome inhabitation. In order to test these hypotheses, we used the Biomic Specialization Index, which is based on the number of biomes occupied by each species, and evaluated the changes in the relative importance of generalist and specialist rodents in more than forty fossil sites from the Iberian Plio-Pleistocene. RESULTS: Our results indicate that there was a decrease in the specialization degree of rodent faunas during the Pliocene due to the global cooling that triggered the onset of the glacial events of the Cenozoic (around 2.75 Ma). The subsequent faunal transition after this critical paleoenvironmental event was characterized by an increase of specialization related to the adaptation to the new environmental conditions, which was mainly associated with the Pleistocene radiation of Arvicolinae (voles). CONCLUSIONS: The pattern of faunal turnover is correlated with the development of the modern glaciations in the Northern Hemisphere around 2.75 Ma, and represents a reorganization of the rodent communities, as suggested by the turnover pulse hypothesis. Our data also support the resource-use hypothesis, which presumes the role of the degree of specialization in resources specifically related to particular biomes as a driver of differential speciation and extinction rates. These results stress the intimate connection between ecological and evolutionary changes.
  BMC Evolutionary Biology 04/2013; 13(1):94.
• Article: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes.

  Robert Alexander Pyron, Frank T Burbrink, John J Wiens
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  ABSTRACT: BACKGROUND: The extant squamates (>9400 known species of lizards and snakes) are one of the most diverse and conspicuous radiations of terrestrial vertebrates, but no studies have attempted to reconstruct a phylogeny for the group with large-scale taxon sampling. Such an estimate is invaluable for comparative evolutionary studies, and to address their classification. Here, we present the first large-scale phylogenetic estimate for Squamata. RESULTS: The estimated phylogeny contains 4161 species, representing all currently recognized families and subfamilies. The analysis is based on up to 12896 base pairs of sequence data per species (average = 2497 bp) from 12 genes, including seven nuclear loci (BDNF, c-mos, NT3, PDC, R35, RAG-1, and RAG-2), and five mitochondrial genes (12S, 16S, cytochrome b, ND2, and ND4). The tree provides important confirmation for recent estimates of higher-level squamate phylogeny based on molecular data (but with more limited taxon sampling), estimates that are very different from previous morphology-based hypotheses. The tree also includes many relationships that differ from previous molecular estimates and many that differ from traditional taxonomy. CONCLUSIONS: We present a new large-scale phylogeny of squamate reptiles that should be a valuable resource for future comparative studies. We also present a revised classification of squamates at the family and subfamily level to bring the taxonomy more in line with the new phylogenetic hypothesis. This classification includes new, resurrected, and modified subfamilies within gymnophthalmid and scincid lizards and boid, colubrid, and lamprophiid snakes.
  BMC Evolutionary Biology 04/2013; 13(1):93.
• Article: Bayesian species delimitation reveals generalist and specialist parasitic wasps on Galerucella beetles (Chrysomelidae): sorting by herbivore or plant host.

  Peter A Hambäck, Elisabet Weingartner, Lars Ericson, Lisa Fors, Anna Cassel-Lundhagen, Johan A Stenberg, Johannes Bergsten
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  ABSTRACT: BACKGROUND: To understand the ecological and evolutionary consequences of species interactions in food webs necessitates that interactions are properly identified. Genetic analyses suggest that many supposedly generalist parasitoid species should rather be defined as multiple species with a more narrow diet, reducing the probability that such species may mediate indirect interactions such as apparent competition among hosts. Recent studies showed that the parasitoid Asecodes lucens mediate apparent competition between two hosts, Galerucella tenella and G. calmariensis, affecting both interaction strengths and evolutionary feedbacks. The same parasitoid was also recorded from other species in the genus Galerucella, suggesting that similar indirect effect may also occur for other species pairs. METHODS: To explore the possibility of such interactions, we used mitochondrial and nuclear genetic markers to resolve the phylogeny of both host and parasitoid and to test the number of parasitoid species involved. We thus collected 139 Galerucella larvae from 8 host plant species and sequenced 31 adult beetle and 108 parasitoid individuals. RESULTS: The analysis of the Galerucella data, that also included sequences from previous studies, verified the five species previously documented as reciprocally monophyletic, but the Bayesian species delimitation for A. lucens suggested 3--4 cryptic taxa with a more specialised host use than previously suggested. The gene data analyzed under the multispecies coalescent model allowed us to reconstruct the species tree phylogeny for both host and parasitoid and we found a fully congruent coevolutionary pattern suggesting that parasitoid speciation followed upon host speciation. CONCLUSION: Using multilocus sequence data in a Bayesian species delimitation analysis we propose that hymenoptera parasitoid of the genus Asecodes that infest Galerucella larvae constitute at least three species with narrow diet breath. The evolution of parasitoid Asecodes and host Galerucella show a fully congruent coevolutionary pattern. This finding strengthens the hypothesis that the parasitoid in host search uses cues of the host rather than more general cues of both host and plant.
  BMC Evolutionary Biology 04/2013; 13(1):92.
• Article: Genetic and environmental factors affecting cryptic variations in gene regulatory networks.

  Watal M Iwasaki, Masaki E Tsuda, Masakado Kawata
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  ABSTRACT: BACKGROUND: Cryptic genetic variation (CGV) is considered to facilitate phenotypic evolution by producing visiblevariations in response to changes in the internal and/or external environment. Several mechanismsenabling the accumulation and release of CGVs have been proposed. In this study, we focused on generegulatory networks (GRNs) as an important mechanism for producing CGVs, and examined howinteractions between GRNs and the environment influence the number of CGVs by using individualbasedsimulations. RESULTS: Populations of GRNs were allowed to evolve under various stabilizing selections, and we then measuredthe number of genetic and phenotypic variations that had arisen. Our results showed that CGVswere not depleted irrespective of the strength of the stabilizing selection for each phenotype, whereasthe visible fraction of genetic variation in a population decreased with increasing strength of selection.On the other hand, increasing the number of different environments that individuals encounteredwithin their lifetime (i.e., entailing plastic responses to multiple environments) suppressed theaccumulation of CGVs, whereas the GRNs with more genes and interactions were favored in suchheterogeneous environments. CONCLUSIONS: Given the findings that the number of CGVs in a population was largely determined by the size (order)of GRNs, we propose that expansion of GRNs and adaptation to novel environments are mutuallyfacilitating and sustainable sources of evolvability and hence the origins of biological diversity andcomplexity.
  BMC Evolutionary Biology 04/2013; 13(1):91.
• Article: Large variation in mitochondrial DNA of sexual and parthenogenetic Dahlica triquetrella (Lepidoptera: Psychidae) shows multiple origins of parthenogenesis.

  Jelmer A Elzinga, Jukka Jokela, Lisa Ns Shama
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  ABSTRACT: BACKGROUND: Obligate parthenogenesis is relatively rare in animals. Still, in some groups it is quite common and has evolved and persisted multiple times. These groups may provide important clues to help solve the 'paradox of sex'. Several species in the Psychidae (Lepidoptera) have obligate parthenogenesis. Dahlica triquetrella is one of those species where multiple transitions to parthenogenesis are postulated based on intensive cytological and behavioural studies. This has led to the hypothesis that multiple transitions from sexuals to diploid parthenogens occurred during and after the last glacial period, followed by transitions from parthenogenetic diploids to parthenogenetic tetraploids. Our study is the first to test these hypotheses using a molecular phylogeny based on mtDNA from multiple sexual and parthenogenetic populations from a wide geographic range. RESULTS: Parthenogenetic (and sexual) D. triquetrella are not monophyletic, and considerable sequence variation is present suggesting multiple transitions to parthenogenesis. However, we could not establish ancestral sexual haplotypes from our dataset. Our data suggest that some parthenogenetic clades have evolved, indicating origins of parthenogenesis before the last glacial period. CONCLUSIONS: Multiple transitions to parthenogenesis have taken place in Dahlica triquetrella, confirming previous hypotheses. The number of different parthenogenetic clades, haplotypes and their apparent evolutionary age, clearly show that parthenogenesis has been a very successful reproductive strategy in this species over a long period.
  BMC Evolutionary Biology 04/2013; 13(1):90.
• Article: Phylogenomics of strongylocentrotid sea urchins.

  Kord M Kober, Giacomo Bernardi
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  ABSTRACT: BACKGROUND: Strongylocentrotid sea urchins have a long tradition as model organisms for studying many fundamental processes in biology including fertilization, embryology, development and genome regulation but the phylogenetic relationships of the group remain largely unresolved. Although the differing isolating mechanisms of vicariance and rapidly evolving gamete recognition proteins have been proposed, a stable and robust phylogeny is unavailable. RESULTS: We used a phylogenomic approach with mitochondrial and nuclear genes taking advantage of the whole-genome sequencing of nine species in the group to establish a stable (i.e. concordance in tree topology among multiple lies of evidence) and robust (i.e. high nodal support) phylogenetic hypothesis for the family Strongylocentrotidae. We generated eight draft mitochondrial genome assemblies and obtained 13 complete mitochondrial genes for each species. Consistent with previous studies, mitochondrial sequences failed to provide a reliable phylogeny. In contrast, we obtained a very well-supported phylogeny from 2301 nuclear genes without evidence of positive Darwinian selection both from the majority of most-likely gene trees and the concatenated fourfold degenerate sites: ((P. depressus, (M. nudus, M. franciscanus), (H. pulcherrimus, (S. purpuratus, (S. fragilis, (S. pallidus, (S. droebachiensis, S. intermedius)). This phylogeny was consistent with a single invasion of deep-water environments followed by a holarctic expansion by Strongylocentrotus. Divergence times for each species estimated with reference to the divergence times between the two major clades of the group suggest a correspondence in the timing with the opening of the Bering Strait and the invasion of the holarctic regions. CONCLUSIONS: Nuclear genome data contains phylogenetic signal informative for understanding the evolutionary history of this group. However, mitochondrial genome data does not. Vicariance can explain major patterns observed in the phylogeny. Other isolating mechanisms are appropriate to explore in this system to help explain divergence patterns not well supported by vicariance, such as the effects of rapidly evolving gamete recognition proteins on isolating populations. Our findings of a stable and robust phylogeny, with the increase in mitochondrial and nuclear comparative genomic data, provide a system in which we can enhance our understanding of molecular evolution and adaptation in this group of sea urchins.
  BMC Evolutionary Biology 04/2013; 13(1):88.
• Article: Parallel reduction in expression, but no loss of functional constraint, in two opsin paralogs within cave populations of Gammarus minus (Crustacea: Amphipoda).

  David B Carlini, Suma Satish, Daniel W Fong
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  ABSTRACT: BACKGROUND: Gammarus minus, a freshwater amphipod living in the cave and surface streams in the eastern USA, is a premier candidate for studying the evolution of troglomorphic traits such as pigmentation loss, elongated appendages, and reduced eyes. In G. minus, multiple pairs of genetically related, physically proximate cave and surface populations exist which exhibit a high degree of intraspecific morphological divergence. The morphology, ecology, and genetic structure of these sister populations are well characterized, yet the genetic basis of their morphological divergence remains unknown. RESULTS: We used degenerate PCR primers designed to amplify opsin genes within the subphylum Crustacea and discovered two distinct opsin paralogs (average inter-paralog protein divergence [almost equal to] 20%) in the genome of three independently derived pairs of G. minus cave and surface populations. Both opsin paralogs were found to be related to other crustacean middle wavelength sensitive opsins. Low levels of nucleotide sequence variation (< 1% within populations) were detected in both opsin genes, regardless of habitat, and dN/dS ratios did not indicate a relaxation of functional constraint in the cave populations with reduced or absent eyes. Maximum likelihood analyses using codon-based models also did not detect a relaxation of functional constraint in the cave lineages. We quantified expression level of both opsin genes and found that the expression of both paralogs was significantly reduced in all three cave populations relative to their sister surface populations. CONCLUSIONS: The concordantly lowered expression level of both opsin genes in cave populations of G. minus compared to sister surface populations, combined with evidence for persistent purifying selection in the cave populations, is consistent with an unspecified pleiotropic function of opsin proteins. Our results indicate that phototransduction proteins such as opsins may have retained their function in cave-adapted organisms because they may play a pleiotropic role in other important processes that are unrelated to vision.
  BMC Evolutionary Biology 04/2013; 13(1):89.
• Article: Convergent evolution of [D-Leucine1] microcystin-LR in taxonomically disparate cyanobacteria.

  Tânia Keiko Shishido, Ulla Kaasalainen, David P Fewer, Leo Rouhiainen, Jouni Jokela, Matti Wahlsten, Marli de Fiore, João Sarkis Yunes, Jouko Rikkinen, Kaarina Sivonen
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  ABSTRACT: BACKGROUND: Many important toxins and antibiotics are produced by non-ribosomal biosynthetic pathways. Microcystins are a chemically diverse family of potent peptide toxins and the end-products of a hybrid NRPS and PKS secondary metabolic pathway. They are produced by a variety of cyanobacteria and are responsible for the poisoning of humans as well as the deaths of wild and domestic animals around the world. The chemical diversity of the microcystin family is attributed to a number of genetic events that have resulted in the diversification of the pathway for microcystin assembly. RESULTS: Here, we show that independent evolutionary events affecting the substrate specificity of the microcystin biosynthetic pathway have resulted in convergence on a rare [D-Leu1] microcystin-LR chemical variant. We detected this rare microcystin variant from strains of the distantly related genera Microcystis, Nostoc, and Phormidium. Phylogenetic analysis performed using sequences of the catalytic domains within the mcy gene cluster demonstrated a clear recombination pattern in the adenylation domain phylogenetic tree. We found evidence for conversion of the gene encoding the McyA2 adenylation domain in strains of the genera Nostoc and Phormidium. However, point mutations affecting the substrate-binding sequence motifs of the McyA2 adenylation domain were associated with the change in substrate specificity in two strains of Microcystis. In addition to the main [D-Leu1] microcystin-LR variant, these two strains produced a new microcystin that was identified as [Met1] microcystin-LR. CONCLUSIONS: Phylogenetic analysis demonstrated that both point mutations and gene conversion result in functional mcy gene clusters that produce the same rare [D-Leu1] variant of microcystin in strains of the genera Microcystis, Nostoc, and Phormidium. Engineering pathways to produce recombinant non-ribosomal peptides could provide new natural products or increase the activity of known compounds. Our results suggest that the replacement of entire adenylation domains could be a more successful strategy to obtain higher specificity in the modification of the non-ribosomal peptides than point mutations.
  BMC Evolutionary Biology 04/2013; 13(1):86.
• Article: Evolution and variability of Solanum RanGAP2, a cofactor in the incompatible interaction between the resistance protein GPA2 and the Globodera pallida effector Gp-RBP-1.

  Jean Carpentier, Eric Grenier, Magalie Esquibet, Louis-Philippe Hamel, Peter Moffett, Maria J Manzanares-Dauleux, Marie-Claire Kerlan
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  ABSTRACT: BACKGROUND: The Ran GTPase Activating Protein 2 (RanGAP2) was first described as a regulator of mitosis and nucleocytoplasmic trafficking. It was then found to interact with the Coiled-Coil domain of the Rx and GPA2 resistance proteins, which confer resistance to Potato Virus X (PVX) and potato cyst nematode Globodera pallida, respectively. RanGAP2 is thought to mediate recognition of the avirulence protein GP-RBP-1 by GPA2. However, the Gpa2-induced hypersensitive response appears to be relatively weak and Gpa2 is limited in terms of spectrum of efficiency as it is effective against only two nematode populations. While functional and evolutionary analyses of Gp-Rbp-1 and Gpa2 identified key residues in both the resistance and avirulence proteins that are involved in recognition determination, whether variation in RanGAP2 also plays a role in pathogen recognition has not been investigated. RESULTS: We amplified a total of 147 RanGAP2 sequences from 55 accessions belonging to 18 different di-and tetraploid Solanum species from the section Petota. Among the newly identified sequences, 133 haplotypes were obtained and 19.1% of the nucleotide sites were found to be polymorphic. The observed intra-specific nucleotide diversity ranges from 0.1 to 1.3%. Analysis of the selection pressures acting on RanGAP2 suggests that this gene evolved mainly under purifying selection. Nonetheless, we identified polymorphic positions in the protein sequence at the intra-specific level, which could modulate the activity of RanGAP2. Two polymorphic sites and a three amino-acid deletion in RanGAP2 were found to affect the timing and intensity of the Gpa2-induced hypersensitive response to avirulent GP-RBP-1 variants even though they did not confer any gain of recognition of virulent GP-RBP-1 variants. CONCLUSIONS: Our results highlight how a resistance gene co-factor can manage in terms of evolution both an established role as a cell housekeeping gene and an implication in plant parasite interactions. StRanGAP2 gene appears to evolve under purifying selection. Its variability does not seem to influence the specificity of GPA2 recognition but is able to modulate this activity by enhancing the defence response. It seems therefore that the interaction with the plant resistance protein GPA2 (and/or Rx) rather than with the nematode effector was the major force in the evolution of the RanGAP2 locus in potato. From a mechanistic point of view these results are in accordance with a physical interaction of RanGAP2 with GPA2 and suggest that RBP-1 would rather bind the RanGAP2-GPA2 complex than the RanGAP2 protein alone.
  BMC Evolutionary Biology 04/2013; 13(1):87.
• Article: Mitochondrial lineage sorting in action -- historical biogeography of the Hyles euphorbiae complex (Sphingidae, Lepidoptera) in Italy.

  Michael B Mende, Anna K Hundsdoerfer
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  ABSTRACT: BACKGROUND: Mitochondrial genes are among the most commonly used markers in studies of species' phylogeography and to draw conclusions about taxonomy. The Hyles euphorbiae complex (HEC) comprises six distinct mitochondrial lineages in the Mediterranean region, of which one exhibits a cryptic disjunct distribution. The predominant mitochondrial lineage in most of Europe, euphorbiae, is also present on Malta; however, it is nowadays strangely absent from Southern Italy and Sicily, where it is replaced by 'italica'. A separate biological entity in Italy is further corroborated by larval colour patterns with a congruent, confined suture zone along the Northern Apennines. By means of historic DNA extracted from museum specimens, we aimed to investigate the evolution of the mitochondrial demographic structure of the HEC in Italy and Malta throughout the Twentieth Century. RESULTS: At the beginning of the Twentieth Century, the European mainland lineages were also present at a moderate frequency in Southern Italy and Sicily. The proportion of 'italica' then steadily increased in this area from below 60 percent to near fixation in about 120 years. Thus, geographical sorting of mitochondrial lineages in the HEC was not as complete then as the current demography suggests. The pattern of an integral 'italica' core region and a disjunct euphorbiae distribution evolved very recently. To explain these strong demographic changes, we propose genetic drift due to anthropogenic habitat loss and fragmentation in combination with an impact from recent climate warming that favoured the spreading of the potentially better adapted 'italica' populations. CONCLUSIONS: The pattern of geographically separated mitochondrial lineages is commonly interpreted as representing long term separated entities. However, our results indicate that such a pattern can emerge surprisingly quickly, even in a widespread and rather common taxon. We thus caution against drawing hasty taxonomic conclusions from biogeographical patterns of mitochondrial markers derived from modern sampling alone.
  BMC Evolutionary Biology 04/2013; 13(1):83.
• Article: Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses.

  Jun-Bo Yang, Min Tang, Hong-Tao Li, Zhi-Rong Zhang, De-Zhu Li
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  ABSTRACT: BACKGROUND: Cymbidium orchids, including some 50 species, are the famous flowers, and they possess high commercial value in the floricultural industry. Furthermore, the values of different orchids are great differences. However, species identification is very difficult. To a certain degree, chloroplast DNA sequence data are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. However, there is no evidence that a short sequence can distinguish all plant species from each other in order to infer phylogenetic relationships. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. RESULTS: The complete nucleotide sequences of eight individuals from a total of five Cymbidium species' chloroplast (cp) genomes were determined using Illumina sequencing technology of the total DNA via a combination of de novo and reference-guided assembly. The length of the Cymbidium cp genome is about 155 kb. The cp genomes contain 123 unique genes, and the IR regions contain 24 duplicates. Although the genomes, including genome structure, gene order and orientation, are similar to those of other orchids, they are not evolutionarily conservative. The cp genome of Cymbidium evolved moderately with more than 3% sequence divergence, which could provide enough information for phylogeny. Rapidly evolving chloroplast genome regions were identified and 11 new divergence hotspot regions were disclosed for further phylogenetic study and species identification in Orchidaceae. CONCLUSIONS: Phylogenomic analyses were conducted using 10 complete chloroplast genomes from seven orchid species. These data accurately identified the individuals and established the phylogenetic relationships between the species. The results reveal that phylogenomics based on organelle genome sequencing lights the species identification---organelle-scale "barcodes", and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium.
  BMC Evolutionary Biology 04/2013; 13(1):84.
• Article: Inferring the evolutionary histories of divergences in Hylobates and Nomascus gibbons through multilocus sequence data.

  Yi-Chiao Chan, Christian Roos, Miho Inoue-Murayama, Eiji Inoue, Chih-Chin Shih, Kurtis Jai-Chyi Pei, Linda Vigilant
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  ABSTRACT: BACKGROUND: Gibbons (Hylobatidae) are the most diverse group of living apes. They exist as geographically-contiguous species which diverged more rapidly than did their close relatives, the great apes (Hominidae). Of the four extant gibbon genera, the evolutionary histories of two polyspecific genera, Hylobates and Nomascus, have been the particular focus of research but the DNA sequence data used was largely derived from the maternally inherited mitochondrial DNA (mtDNA) locus. RESULTS: To investigate the evolutionary relationships and divergence processes of gibbon species, particularly those of the Hylobates genus, we produced and analyzed a total of 11.5 kb DNA of sequence at 14 biparentally inherited autosomal loci. We find that on average gibbon genera have a high average sequence diversity but a lower degree of genetic differentiation as compared to great ape genera. Our multilocus species tree features H. pileatus in a basal position and a grouping of the four Sundaic island species (H. agilis, H. klossii, H. moloch and H. muelleri). We conducted pairwise comparisons based on an isolation-with-migration (IM) model and detect signals of asymmetric gene flow between H. lar and H. moloch, between H. agilis and H. muelleri, and between N. leucogenys and N. siki. CONCLUSIONS: Our multilocus analyses provide inferences of gibbon evolutionary histories complementary to those based on single gene data. The results of IM analyses suggest that the divergence processes of gibbons may be accompanied by gene flow. Future studies using analyses of multi-population model with samples of known provenance for Hylobates and Nomascus species would expand the understanding of histories of gene flow during divergences for these two gibbon genera.
  BMC Evolutionary Biology 04/2013; 13(1):82.
• Article: Rapid adaptation to mammalian sociality via sexually selected traits.

  Adam C Nelson, Kevin E Colson, Steve Harmon, Wayne K Potts
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  ABSTRACT: BACKGROUND: Laboratory studies show that the components of sexual selection (e.g. mate choice and intrasexual competition) can profoundly affect the development and fitness of offspring. Less is known, however, about the total effects of sexual selection on offspring in normal social conditions. Complex social networks, such as dominance hierarchies, regulate the opportunity for mating success, and are often missing from laboratory studies. Social selection is an extended view of sexual selection that incorporates competition during sexual and nonsexual interactions, and predicts complex evolutionary dynamics. Whether social selection improves or constrains offspring fitness is controversial. RESULTS: To identify fitness consequences of social selection, wild-derived mice that had bred under laboratory conditions for eight generations were re-introduced to naturalistic competition in enclosures for three consecutive generations (promiscuous line). In parallel, a control lineage bred in cages under random mate assignment (monogamous line). A direct competition experiment using second-generation animals revealed that promiscuous line males had greater reproductive success than monogamous line males (particularly during extra-territorial matings), in spite of higher mortality and equivalent success in social dominance and sperm competition. There were no major female fitness effects (though promiscuous line females had fewer litters than monogamous line females). This result suggested that selection primarily acted upon a sexually attractive male phenotype in the promiscuous line, a hypothesis we confirmed in female odor and mating preference trials. CONCLUSIONS: We present novel evidence for the strength of sexual selection under normal social conditions, and show rapid male adaptation driven largely by sexual trait expression, with tradeoffs in survivorship and female fecundity. Re-introducing wild-derived mice to competition quickly uncovers sexually selected phenotypes otherwise lost in normal colony breeding.
  BMC Evolutionary Biology 04/2013; 13(1):81.