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Diversification of the cullin familyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Most of the known types of cullin-containing ubiquitin ligase complexes are ancient. The available data suggest that, since the origin of eukaryotes, complex diversity has been mostly generated by combining closely related subunits, while radical innovations, giving rise to novel types of complexes, have been scarce. However, several protist groups not examined so far contain highly divergent cullins, indicating that additional types of complexes may exist. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - November 19, 2009 Category: Molecular Biology Authors: Ignacio Marin Source Type: journals

Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study challenges the current view on the classification, origin and evolution of the cystatin superfamily and provides valuable insights into their functional diversification. The findings of this comprehensive study provide guides for future structural and evolutionary studies of the cystatin superfamily as well as of other protease inhibitors and proteases. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - November 18, 2009 Category: Molecular Biology Authors: Dusan KordisVito Turk Source Type: journals

Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Despite the fact that there are now over 20 mitochondrial genome sequences for land plants and green algae, this gene has remained unidentified and largely undetected until now because of the unlikely coincidence that most of the earlier sequences were from the few lineages that lack the intact gene. These results illustrate the power of comparative sequencing to identify novel genomic features. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - November 16, 2009 Category: Molecular Biology Authors: Jeffrey MowerLinda Bonen Source Type: journals

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - November 9, 2009 Category: Molecular Biology Authors: Ferran PaleroJoao LopesPere AbelloEnrique MacphersonMarta PascualMark Beaumont Source Type: journals

Plant chemical defence: a partner control mechanism stabilising plant - seed-eating pollinator mutualisms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Adonivernith accumulation and larval predation intensity appear to be both the reciprocal cause and effect. Adonivernith not only constitutes an effective chemical means of partner control, but may also play a role in the sympatric diversification of the Chiastocheta genus. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - November 3, 2009 Category: Molecular Biology Authors: Sebastien IbanezChristiane GalletFanny DommangetLaurence Despres Source Type: journals

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe SileneaeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The patterns of phylogenetic divergence within Sileneae suggest enormous variability in plant mitochondrial mutation rates and reveal a complex interaction of gene and species effects. The variation in rates across genomic and phylogenetic scales raises questions about the mechanisms responsible for the evolution of mutation rates in plant mitochondrial genomes. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 31, 2009 Category: Molecular Biology Authors: Daniel SloanBengt OxelmanAnja RautenbergDouglas Taylor Source Type: journals

Relatedness facilitates cooperation in the subsocial spider, Stegodyphus tentoriicolaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The combination of our results with those from previous studies indicates that the conflict between individual interests and group interests may be reduced by nepotism and that the latter promote the maintenance of the social community. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 27, 2009 Category: Molecular Biology Authors: Jasmin RuchLisa HeinrichTrine BildeJutta Schneider Source Type: journals

Estimating the phylogeny and divergence times of primates using a supermatrix approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We present an up-to-date, comprehensive estimate of the structure and tempo of primate evolutionary history. Although considerable gaps remain in our knowledge of the primate phylogeny, increased data sampling, particularly from nuclear loci, will be able to provide further resolution. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 27, 2009 Category: Molecular Biology Authors: Helen ChatterjeeSimon HoIan BarnesColin Groves Source Type: journals

Nme protein family evolutionary history, a vertebrate perspectiveEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This work offers an evolutionary framework that will pave the way for future studies on vertebrate Nme proteins and provides a unified vertebrate Nme nomenclature that is consistent with the nomenclature in use in mammals. Based on protein structure and expression data, we also provide new insight into molecular functions of Nme proteins among vertebrates and raise intriguing questions on the roles of Nme proteins in gonads. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 22, 2009 Category: Molecular Biology Authors: Thomas DesvignesPierre PontarottiChristian FauvelJulien Bobe Source Type: journals

Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions The temporal lag between pharyngeal jaw modifications and changes in diversification rates casts doubt on the key innovation hypothesis as a simple explanation for much of the richness seen in labrids and scarines. Although the possession of a secondarily modified PJA was correlated with increased diversification rates, this pattern is better explained by the evolution of extreme dichromatism (and other social and behavioral characters relating to sexual selection) within Scarus and Chlorurus. The PJA-innovation hypothesis also fails to explain the most dominant aspect of labrid lineage diversification, the rad...
Source: BMC Evolutionary Biology - Latest articles - October 21, 2009 Category: Molecular Biology Authors: Michael AlfaroChad BrockBarbara BanburyPeter Wainwright Source Type: journals

Hsp-90 and the biology of nematodesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Hsp-90 is a multi-functional protein and the rapid evolution of the hsp-90 gene presumably correlates with other key cellular functions. Factors other than primary amino acid sequence may influence the ability of Hsp-90 to bind to Geldanamycin. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 21, 2009 Category: Molecular Biology Authors: Nik HimVictoria GillanRichard EmesKirsty MaitlandEileen Devaney Source Type: journals

Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastidsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The phylogenetic studies using concatenated plastid proteins still do not resolve the question of the monophyly of all chromist plastids. However, these results support both the monophyly of heterokont plastids and that of cryptophyte and haptophyte plastids, in agreement with nuclear phylogenies. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 15, 2009 Category: Molecular Biology Authors: Gildas Le CorguilleGareth PearsonMarta ValenteCarla ViegasBernhard GschloesslErwan CorreXavier BaillyAkira PetersClaire JubinBenoit VacherieJ. Mark CockCatherine Leblanc Source Type: journals

Positive selection for the male functionality of a co-retroposed gene in the hominoidsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Therefore, this set of analyses showed that PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in the male functions of humans and its close relatives. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 14, 2009 Category: Molecular Biology Authors: Yong Edward ZhangShujuan LuShuqi ZhaoXiaofeng ZhengManyuan LongLiping Wei Source Type: journals

Cooperative social clusters are not destroyed by dispersal in a ciliateEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: High dispersal among aggregative strains may not destroy group stability in T. thermophila because the dispersal polymorphism allows social strains to more readily escape kin groups than less aggregative strains, yet still benefit from stable group membership among sedentary morphs. Such dispersal polymorphisms should be common in other social organisms, serving to alter the nature of the negative impact of dispersal on social evolution. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 13, 2009 Category: Molecular Biology Authors: Nicolas SchtickzelleElse FjerdingstadAlexis ChaineJean Clobert Source Type: journals

Polyploid evolution in Oryza officinalis complex of the genus OryzaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: C-genome, shared by all polyploid species in the complex, had experienced different evolutionary history particularly after polyploidization, e.g., inter-genomic exchange in BBCC and genomic invasion in CCDD tetraploids. It diverged from B-genome at 4.8 Mya, then participated the tetraploid formation span from 0.9 to 0.3 Mya, and spread into tropics of the disjunct continents by transcontinentally long-distance dispersal, instead of vicariance, as proposed by this study, given that the continental splitting was much earlier than the C-genome species radiation. We also find reliable evidence indicated that an e...
Source: BMC Evolutionary Biology - Latest articles - October 13, 2009 Category: Molecular Biology Authors: Baosheng WangZhuoya DingWei LiuJin PanChangbao LiSong GeDaming Zhang Source Type: journals

Origin and evolution of the Notch signalling pathway: an overview from eukaryotic genomesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The Notch signalling pathway emerged in Metazoa via a diversity of molecular mechanisms, incorporating both novel and ancient protein domains during eukaryote evolution. Thus, a functional Notch signalling pathway was probably present in Urmetazoa. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 12, 2009 Category: Molecular Biology Authors: Eve GazavePascal LapebieGemma RichardsFrederic BrunetAlexander EreskovskyBernard DegnanCarole BorchielliniMichel VervoortEmmanuelle Renard Source Type: journals

Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plant-pollinator associationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: As hypothesized, we discovered evidences of past hybridization in Ficus section Galoglychia. Further, introgression was only detected in subsections presenting incongruence between plant and pollinator phylogenies and taxonomy. This supports the hypothesis that host shift is the cause for plant-pollinator incongruence. Moreover, small fig size could facilitate host shifts. Eventually, this study demonstrates that non-coding chloroplast markers are valuable to resolve deep nodes in Ficus phylogeny. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 11, 2009 Category: Molecular Biology Authors: Julien RenoultFinn KjellbergCinderella GroutSylvain SantoniBouchaib Khadari Source Type: journals

Phylogeny and evolutionary history of Leymus (Triticeae; Poaceae) based on a single-copy nuclear gene encoding plastid acetyl-CoA carboxylaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Leymus species have allopolyploid origin. It is hypothesized that the adaptive radiation of Leymus species might have been triggered by the recent upliftings of the Qinghai-Tibetan plateau and subsequent climatic oscillations. Adaptive radiation may have promoted the rapid speciation, as well as the fixation of unique morphological characters in Leymus. Our results shed new light on our understanding of the origin of Xm genome, the polyploidization events and evolutionary history of Leymus that could account for the rich diversity and ecological adaptation of Leymus species. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 7, 2009 Category: Molecular Biology Authors: Xing FanLi-Na ShaRui-Wu YangHou-Yang KangYou-Liang ZhengCun-Bang DingLi ZhangHai-Qin ZhangYong-Hong Zhou Source Type: journals

Poly-paraphyly of Hirudinidae: many lineages of medicinal leeches.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: : The family Hirudinidae must be refined to include only the clade containing Hirudo medicinalis (European medicinal leech) and related leeches irrespective of bloodfeeding behavior. A second clade containing Macrobdella decora (North American medicinal leech) and its relatives is recognized as Semiscolecidae in order to avoid paraphyly. The African distribution of species from each of the divergent hirudinid clades suggests that a deep divergence took place in the history of the medicinal leeches hundreds of millions of years ago. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 6, 2009 Category: Molecular Biology Authors: Anna PhillipsMark Siddall Source Type: journals

Expressions of ECE-CYC2 clade genes relating to abortion of both dorsal and ventral stamens in Opithandra (Gesneriaceae)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: These results suggest that ECE-CYC2 clade TCP genes are not only functionally conserved in the dorsal stamen repression, but also involved in arresting ventral stamens, a genetic mechanism underlying the establishment of zygomorphy with abortion of both the dorsal and ventral stamens evolved in angiosperms, especially within Lamiales s.l. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 6, 2009 Category: Molecular Biology Authors: Chun-Feng SongQi-Bing LinRong-Hua LiangYin-Zheng Wang Source Type: journals

Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 6, 2009 Category: Molecular Biology Authors: Sarah KingstonLara AdamsPatricia Rosel Source Type: journals

The genome sequence of the protostome Daphnia pulex encodes respective orthologues of a neurotrophin, a Trk and a p75NTR: Evolution of neurotrophin signaling components and related proteins in the bilateria.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: It appears that a neurotrophin, Trk and p75NTR existed at the protostome/deuterostome split. In protostomes, a "neurotrophin superfamily" includes Spzs and neurotrophins which respectively form two paralogous families. Trks and Trkl proteins also form closely related paralogous families within the protostomian RTKs, whereby Trkls are absent in deuterostomes. The finding of p75NTR in several protostomes suggests that death domain TNFR superfamily proteins appeared early in evolution. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - October 5, 2009 Category: Molecular Biology Authors: Karen Wilson Source Type: journals

Amphioxus (Branchiostoma floridae) has orthologs of vertebrate odorant receptorsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Here, we show that amphioxus has orthologs of vertebrate ORs. This conclusion demonstrates that the receptors, and perhaps other components of vertebrate olfaction, evolved at least 550 million years ago. We have also identified highly conserved amino acid motifs that may be important for maintaining receptor conformation or regulating receptor activity. We anticipate that the identification of vertebrate OR orthologs in amphioxus will lead to an improved understanding of OR gene family evolution, OR gene function, and the mechanisms that control cell-specific expression, axonal guidance, signal transduction a...
Source: BMC Evolutionary Biology - Latest articles - October 4, 2009 Category: Molecular Biology Authors: Allison ChurcherJohn Taylor Source Type: journals

An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animalsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The molecular phylogenetic trees including the P. lamarckii sequences extend early observations that polychaetes tend to have relatively short branches in such trees, and hence are useful taxa with which to reconstruct gene family evolution. Also, with the availability of lophotrochozoan data such as that of P. lamarckii, it is now possible to make much more accurate reconstructions of the gene complement of the ancestor of the bilaterians than was previously possible from comparisons of ecdysozoan and deuterostome genomes to non-bilaterian outgroups. It is clear that the traditional molecular model systems fo...
Source: BMC Evolutionary Biology - Latest articles - September 24, 2009 Category: Molecular Biology Authors: Tokiharu TakahashiCarmel McDougallJolyon TrosciankoWei-Chung ChenAhamarshan Jayaraman-NagarajanSebastian ShimeldDavid Ferrier Source Type: journals

Intra-individual polymorphism in diploid and apomictic polyploid hawkweeds (Hieracium, Lactuceae, Asteraceae): disentangling phylogenetic signal, reticulation, and noiseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The high level of intra-individual ETS polymorphism prevented straightforward phylogenetic analysis. Characterization of this variation as additive, shared informative, homoplasious, or unique made it possible to uncover the phylogenetic signal and to reveal the hybrid origin of 29 out of 60 accessions. Contrary to expectation, diploid sexuals and polyploid apomicts did not differ in their molecular patterns. The basic division of the genus into two major clades had not previously been intimated on morphological grounds. Both major groups are thought to have survived in different glacial refugia and to have hy...
Source: BMC Evolutionary Biology - Latest articles - September 21, 2009 Category: Molecular Biology Authors: Judith FehrerKarol KrakJindrich Chrtek Source Type: journals

Evidence for a rapid rate of molecular evolution at the hypervariable and immunogenic Mycobacterium tuberculosis PPE38 gene regionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Our results show that this antigen-encoding region of the M. tuberculosis genome is hypervariable. The observation that numerous different mutations have become fixed within specific lineages demonstrates that this genomic region is undergoing rapid molecular evolution and that further lineage-specific evolutionary expansion and diversification has occurred subsequent to the lineage-defining mutational events. The affected genes are not essential to the organism's virulence and we predict that their functional loss could aid immune evasion. Finally, we also show that the PPE38 region of the published M. tubercu...
Source: BMC Evolutionary Biology - Latest articles - September 20, 2009 Category: Molecular Biology Authors: Christopher McEvoyPaul van HeldenRobin WarrenNicolaas Gey van Pittius Source Type: journals

Brain structure evolution in a basal vertebrate clade: evidence from phylogenetic comparative analysis of cichlid fishesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results favor a mosaic model of brain evolution, as certain structures are evolving in a modular fashion, with a small but non-negligible influence of concerted evolution in cichlid fishes. Interestingly, one of the structures presenting distinct evolutionary patterns within cichlids, the olfactory bulbs, has also been shown to evolve differently from other structures in mammals. Hence, our results for a basal vertebrate clade also point towards a conserved developmental plan for all vertebrates. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 20, 2009 Category: Molecular Biology Authors: Alejandro Gonzalez-VoyerSvante WinbergNiclas Kolm Source Type: journals

Conserved repertoire of orthologous vomeronasal type 1 receptor genes in ruminant species.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our results suggest that, compared with rodents, the repertoire of orthologous V1R genes is remarkably conserved among the ruminants cow, sheep and goat. We predict that these orthologous V1Rs can detect the same or closely related chemical compound(s) within each orthologous set/pair. Furthermore, all identified goat V1Rs are expressed in the vomeronasal organ and the main olfactory epithelium, suggesting that V1R-mediated ligand information can be detected and processed by both the main and accessory olfactory systems. The fact that ruminant and rodent V1Rs have distinct features suggests that ruminant and r...
Source: BMC Evolutionary Biology - Latest articles - September 14, 2009 Category: Molecular Biology Authors: Hiromi OharaMasato NikaidoAtsuko Date-ItoKazutaka MogiHiroaki OkamuraNorihiro OkadaYukari TakeuchiYuji MoriKimiko Hagino-Yamagishi Source Type: journals

Inferring speciation modes in a clade of Iberian chafers from rates of morphological evolution in different character systemsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: Structural morphological characters, often used for species recognition, have evolved at a rate proportional to that of the mtDNA, with no evidence of selection according to our measures. The change in body morphospace seem to have evolved neutrally at short term, but the overall change is different from that expected under a pure random drift, reflecting either selection or developmental constraints. Changes in paramere shape were not neutral at short term, possibly reflecting sexual selection, but their overall amount of change over longer evolutionary periods was neutral, possibly reflecting their lack of fu...
Source: BMC Evolutionary Biology - Latest articles - September 14, 2009 Category: Molecular Biology Authors: Dirk AhrensIgnacio Ribera Source Type: journals

Evolutionary conservation and changes in insect TRP channelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: The total number of insect TRP family members is 13-14, approximately half that of mammalian TRP family members. As shown for mammalian TRP channels, this may suggest that single TRP channels are responsible for integrating diverse sensory inputs to maintain the insect sensory systems. The above results demonstrate that there are both evolutionary conservation and changes in insect TRP channels. In particular, the evolutionary processes have been accelerated in the TRPA subfamily, indicating divergence in the mechanisms that insects use to detect environmental temperatures. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 9, 2009 Category: Molecular Biology Authors: Hironori MatsuuraTakaaki SokabeKeigo KohnoMakoto TominagaTatsuhiko Kadowaki Source Type: journals

Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteinsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our analysis suggests that SECIS binding proteins arose once in evolution but diverged significantly in multiple lineages. In addition, likely due to a gene duplication event in the early vertebrate lineage, SBP2 an SBP2L are paralogous in vertebrates. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 9, 2009 Category: Molecular Biology Authors: Jesse DonovanPaul Copeland Source Type: journals

Nuclear receptor complement of the cnidarian Nematostella vectensis: phylogenetic relationships and developmental expression patternsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: N. vectensis contains a diverse complement of nuclear receptors including orthologs of several bilaterian nuclear receptors. Novel nuclear receptors in N. vectensis may be ancient genes lost from triploblastic lineages or may represent cnidarian-specific radiations. Nuclear receptors exhibited distinct developmental expression patterns, which are consistent with diverse regulatory roles for these genes. Understanding the evolutionary relationships and developmental expression of the N. vectensis nuclear receptor complement provides insight into the evolution of the nuclear receptor superfamily and a foundation ...
Source: BMC Evolutionary Biology - Latest articles - September 9, 2009 Category: Molecular Biology Authors: Adam ReitzelAnn Tarrant Source Type: journals

FGFRL1 is a neglected putative actor of the FGF signalling pathway present in all major metazoan phylaEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Our work sheds light on the existence of a putative FGF signalling pathway actor present in the ancestor of probably all metazoans, the function of which has received little attention until now. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 8, 2009 Category: Molecular Biology Authors: Stephanie BertrandIldiko SomorjaiJordi Garcia-FernandezThomas LamonerieHector Escriva Source Type: journals

Fast optimization of statistical potentials for structurally constrained phylogenetic modelsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Due to its computational speed, the optimization method we propose offers an attractive alternative for the design and empirical evaluation of alternative forms of potentials, using large data sets and high-dimensional parameterizations. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 8, 2009 Category: Molecular Biology Authors: Cecile BonnardClaudia KleinmanNicolas RodrigueNicolas Lartillot Source Type: journals

The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor familyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We conclude that the GluR genes did not undergo drastic changes such as accelerated evolution in the human lineage after the divergence of chimpanzees. However, there remains a possibility that two human-specific "fixed" amino acid substitutions, D71G in GRIN3A and R727H in GRIN3B, are related to human-specific brain function. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 7, 2009 Category: Molecular Biology Authors: Hiroki GotoKazunori WatanabeNaozumi AraragiRui KageyamaKunika TanakaYoko KurokiAtsushi ToyodaMasahira HattoriYoshiyuki SakakiAsao FujiyamaYasuyuki FukumakiHiroki Shibata Source Type: journals

PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Covarion models implemented in PROCOV may be especially useful for phylogenetic estimation when ancient divergences between sequences have occurred and rates of evolution at sites are likely to have changed over the tree. It can also be used to study lineage-specific functional shifts in protein families that result in changes in the patterns of site variability among subtrees. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 7, 2009 Category: Molecular Biology Authors: Huai-Chun WangEdward SuskoAndrew Roger Source Type: journals

FoxO gene family evolution in vertebratesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: We present a phylogeny describing the evolutionary history of the FoxO gene family and show that the genes have evolved through duplications followed by purifying selection except for four sites in FoxO6 fixed by positive selection lie mostly within the non-conserved optimal PKB motif in the C-terminal part. Relaxed selection may play important roles in the process of functional differentiation evolved through gene duplications as well. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 6, 2009 Category: Molecular Biology Authors: Minghui WangXiangzhe ZhangHongbo ZhaoQishan WangYuchun Pan Source Type: journals

Quaternary history and contemporary patterns in a currently expanding speciesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: In regions that were not prone to marked glaciations, recent moth introductions/expansions could be detected due to the existence of a strong spatial genetic structure. In contrast, in regions that experienced the most intense Quaternary climatic oscillations, the natural populations are not genetically structured, and contemporary patterns of population expansion remain undetected. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 3, 2009 Category: Molecular Biology Authors: Carole KerdelhueLorenzo ZaneMauro SimonatoPaola SalvatoJerome RousseletAlain RoquesAndrea Battisti Source Type: journals

Differential transcriptional modulation of duplicated fatty acid-binding protein genes by dietary fatty acids in zebrafish (Danio rerio): evidence for subfunctionalization and neofunctionalization of duplicated genesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Differential induction of only one of the sister pair of duplicated fabp genes by FAs provides evidence to support the DDC model for retention of duplicated genes in the zebrafish genome by either subfunctionalization or neofunctionalization. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - September 1, 2009 Category: Molecular Biology Authors: Santhosh KaranthSantosh LallEileen Denovan-WrightJonathan Wright Source Type: journals

The small heat shock protein (sHSP) genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusion: B. mori has the largest number of insect sHSP genes characterized to date, including 16 genes. The inference that most species-specific sHSPs might have diverged in function across insects investigated will help us understand the adaptability of these insects to diverse environments. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - August 27, 2009 Category: Molecular Biology Authors: Zi-Wen LiXue LiQuan-You YuZhong-Huai XiangHirohisa KishinoZe Zhang Source Type: journals

Inferring polyploid phylogenies from multiply-labeled gene treesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We illustrate the applicability of our method using two collections of trees for plants of the genusSilene, that involve several allopolyploids at different levels. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - August 27, 2009 Category: Molecular Biology Authors: Martin LottAndreas SpillnerKatharina HuberAnna PetriBengt OxelmanVincent Moulton Source Type: journals

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMCEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/ (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - August 27, 2009 Category: Molecular Biology Authors: Rahul SatijaAdam NovakIstvan MiklosRune LyngsoJotun Hein Source Type: journals

Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of DscamEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Analyses of the multiple ASEs of Dscam allowed direct tests of the effect of splice-related factors on synonymous codon usage and provided clear evidence that synonymous codon usage bias is restricted by exonic splicing signals near the intron-exon boundary. A similar synonymous divergence level between the different exonic regions suggests that the intensity of splice-related selection is generally weak and comparable to that of translational selection. Finally, the leveling off of differences in codon bias over time in retrotransposed genes meets the direct prediction of the trade-off model that invokes conf...
Source: BMC Evolutionary Biology - Latest articles - August 26, 2009 Category: Molecular Biology Authors: Aya Takahashi Source Type: journals

Correction: Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hairEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Correction to Wu DD, Irwin DM, Zhang YP: Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair. BMC Evol Biol 2008, 8:241 (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - August 24, 2009 Category: Molecular Biology Authors: Dong-Dong WuDavid IrwinYa-Ping Zhang Source Type: journals

Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolutionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Reconstruction of the phylogenetic history of beetle-associated Diplogastridae yields four distinct subclades, whose deep phylogenetic divergence, as indicated by short internal branch lengths, shows evidence for evolution by successions of ancient rapid radiation events. The stem species of the Diplogastridae existed at the same time period when the major radiations of the beetles occurred. Comparison of nematode and beetle phylogenies provides, however, no evidence for long-term coevolution of diplogastrid nematodes and their beetle hosts. Instead, frequent host switching is observed. The molecular phylogeny...
Source: BMC Evolutionary Biology - Latest articles - August 23, 2009 Category: Molecular Biology Authors: Werner MayerMatthias HerrmannRalf Sommer Source Type: journals

Phylogenetic inference under varying proportions of indel-induced alignment gapsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: When gaps in an alignment are a consequence of indel events in the evolution of the sequences, the accuracy of phylogenetic analysis is likely to improve if: (1) alignment gaps are categorized as arising from insertion events or deletion events and then treated separately in the analysis, (2) the evolutionary signal provided by indels is harnessed in the phylogenetic analysis, and (3) methods that utilize the phylogenetic signal in indels are developed for distance methods too. When the true homology is known and the amount of gaps is 20 percent of the alignment length or less, the methods used in this study a...
Source: BMC Evolutionary Biology - Latest articles - August 22, 2009 Category: Molecular Biology Authors: Bhakti DwivediSudhindra Gadagkar Source Type: journals

Multiple gains of spliceosomal introns in a superfamily of vertebrate protease inhibitor genesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: Multiple intron acquisition events were detected in a group of actinopterygian fishes, but not in other vertebrates, suggesting that insertion rates for introns may be episodically increased. The co-occurrence of non-standard introns points to the possibility of parallel or rapidly consecutive gain of introns. The sequences flanking the insertion points correspond to the consensus sequence MAG[arrow up]N, revealing relaxed conditions for proto-splice sites. Association of intron gain events with a group of fishes that underwent genome compaction may indicate that breakage/repair processes related to DNA loss m...
Source: BMC Evolutionary Biology - Latest articles - August 21, 2009 Category: Molecular Biology Authors: Hermann RaggAbhishek KumarKatharina KosterCaterina BenteleYunjie WangMarc-Andre FreseNatalie PribOlaf Kruger Source Type: journals

Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from riceEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We provide a thorough analysis of comparative genome evolution between barley and rice. A barley genetic map of approximately 2000 non-redundant EST sequences provided sufficient density to allow a detailed view of shared synteny with the rice genome. Using an indirect approach that included the localization of WGD-derived duplicated genome segments in the rice genome, we determined the current extent of shared WGD-derived genome duplications that occurred prior to species divergence. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - August 21, 2009 Category: Molecular Biology Authors: Thomas ThielAndreas GranerRobbie WaughIvo GrosseTimothy CloseNils Stein Source Type: journals

Whole genome duplications and expansion of the vertebrate GATA transcription factor gene familyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: From our analysis, we infer the evolutionary birth order and relationships among vertebrate GATA transcription factors, and define their expansion via multiple rounds of whole genome duplication events. As the genomes of four independent invertebrate deuterostome lineages contain single copy GATA123 and GATA456 genes, we infer that the 0R (pre-genome duplication) invertebrate deuterostome ancestor also had two GATA genes, one of each class. Our analysis identifies the duplications of paralogous chromosomal regions (paralogons), from single ancestral vertebrate GATA123 and GATA456 chromosomes to four paralogons...
Source: BMC Evolutionary Biology - Latest articles - August 19, 2009 Category: Molecular Biology Authors: William GillisJohn JohnBruce BowermanStephan Schneider Source Type: journals

Evolutionary rate patterns of the Gibberellin pathway genesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study suggests that significant heterogeneity of evolutionary rate of the GA pathway genes is mainly ascribed to differential constraint relaxation rather than the positive selection and supports the pathway flux theory that predicts that natural selection primarily targets enzymes that have the greatest control on fluxes. (Source: BMC Evolutionary Biology - Latest articles)
Source: BMC Evolutionary Biology - Latest articles - August 17, 2009 Category: Molecular Biology Authors: Yan-hua YangFu-min ZhangSong Ge Source Type: journals