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1.  The water flea Daphnia - a 'new' model system for ecology and evolution? 
Journal of Biology  2010;9(2):21.
Daphnia pulex is the first crustacean to have its genome sequenced. Availability of the genome sequence will have implications for research in aquatic ecology and evolution in particular, as addressed by a series of papers published recently in BMC Evolutionary Biology and BMC Genomics.
See research articles http://www.biomedcentral.com/1471-2148/9/78, http://www.biomedcentral.com/1471-2164/10/527, http://www.biomedcentral.com/1471-2148/9/79, http://www.biomedcentral.com/1471-2164/10/175, http://www.biomedcentral.com/1471-2164/10/172, http://www.biomedcentral.com/1471-2164/10/169, http://www.biomedcentral.com/1471-2164/10/170 and http://www.biomedcentral.com/1471-2148/9/243.
doi:10.1186/jbiol212
PMCID: PMC2871515  PMID: 20478012
2.  Tunicates push the limits of animal evo-devo 
BMC Biology  2011;9:3.
The phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated.
See research article: http://www.biomedcentral.com/1471-2148/11/21
doi:10.1186/1741-7007-9-3
PMCID: PMC3024270  PMID: 21251298
3.  Colonization, mouse-style 
BMC Biology  2010;8:131.
Several recent papers, including one in BMC Evolutionary Biology, examine the colonization history of house mice. As well as background for the analysis of mouse adaptation, such studies offer a perspective on the history of movements of the humans that accidentally transported the mice.
See research article: http://www.biomedcentral.com/1471-2148/10/325
doi:10.1186/1741-7007-8-131
PMCID: PMC2964602  PMID: 20977781
4.  An expanded evolutionary role for flower symmetry genes 
Journal of Biology  2009;8(10):90.
CYCLOIDEA (CYC)-like TCP genes are critical for flower developmental patterning. Exciting recent breakthroughs, including a study by Song et al. published in BMC Evolutionary Biology, demonstrate that CYC-like genes have also had an important role in the evolution of flower form.
See research article http://www.biomedcentral.com/1471-2148/9/244.
doi:10.1186/jbiol193
PMCID: PMC2790833  PMID: 19895716
5.  Computational and phylogenetic validation of nematode horizontal gene transfer 
BMC Biology  2011;9:9.
Sequencing of expressed genes has shown that nematodes, particularly the plant-parasitic nematodes, have genes purportedly acquired from other kingdoms by horizontal gene transfer. The prevailing orthodoxy is that such transfer has been a driving force in the evolution of niche specificity, and a recent paper in BMC Evolutionary Biology that presents a detailed phylogenetic analysis of cellulase genes in the free-living nematode Pristionchus pacificus at the species, genus and family levels substantiates this hypothesis.
See research article: http://www.biomedcentral.com/1471-2148/11/13
doi:10.1186/1741-7007-9-9
PMCID: PMC3042989  PMID: 21342537
6.  Expanding networks of RNA virus evolution 
BMC Biology  2012;10:54.
In a recent BMC Evolutionary Biology article, Huiquan Liu and colleagues report two new genomes of double-stranded RNA (dsRNA) viruses from fungi and use these as a springboard to perform an extensive phylogenomic analysis of dsRNA viruses. The results support the old scenario of polyphyletic origin of dsRNA viruses from different groups of positive-strand RNA viruses and additionally reveal extensive horizontal gene transfer between diverse viruses consistent with the network-like rather than tree-like mode of viral evolution. Together with the unexpected discoveries of the first putative archaeal RNA virus and a RNA-DNA virus hybrid, this work shows that RNA viral genomics has major surprises to deliver.
See research article: http://www.biomedcentral.com/1471-2148/12/91
doi:10.1186/1741-7007-10-54
PMCID: PMC3379944  PMID: 22715894
7.  Diversity lost: are all Holarctic large mammal species just relict populations? 
BMC Biology  2010;8:46.
Population genetic analyses of Eurasian wolves published recently in BMC Evolutionary Biology suggest that a major genetic turnover took place in Eurasian wolves after the Pleistocene. These results add to the growing evidence that large mammal species surviving the late Pleistocene extinctions nevertheless lost a large share of their genetic diversity.
See research article http://www.biomedcentral.com/1471-2148/10/104
doi:10.1186/1741-7007-8-46
PMCID: PMC2858106  PMID: 20409351
8.  Time is of the essence for ParaHox homeobox gene clustering 
BMC Biology  2013;11:72.
ParaHox genes, and their evolutionary sisters the Hox genes, are integral to patterning the anterior-posterior axis of most animals. Like the Hox genes, ParaHox genes can be clustered and exhibit the phenomenon of colinearity - gene order within the cluster matching gene activation. Two new instances of ParaHox clustering provide the first examples of intact clusters outside chordates, with gene expression lending weight to the argument that temporal colinearity is the key to understanding clustering.
See research articles: http://www.biomedcentral.com/1741-7007/11/68 and http://www.biomedcentral.com/1471-2148/13/129
doi:10.1186/1741-7007-11-72
PMCID: PMC3694477  PMID: 23803337
9.  The coming and going of Batesian mimicry in a Holarctic butterfly clade 
BMC Biology  2010;8:122.
A study using phylogenetic hypothesis testing, published in BMC Evolutionary Biology, suggests that non-mimetic forms of the North American white admiral butterfly evolved from a mimetic ancestor. This case might provide one of the first examples in which mimicry was gained and then lost again, emphasizing the evolutionary lability of Batesian mimicry.
See research article http://www.biomedcentral.com/1471-2148/10/239
doi:10.1186/1741-7007-8-122
PMCID: PMC2939503  PMID: 20887635
10.  Hybridization and speciation in angiosperms: a role for pollinator shifts? 
BMC Biology  2010;8:45.
The majority of convincingly documented cases of hybridization in angiosperms has involved genetic introgression between the parental species or formation of a hybrid species with increased ploidy; however, homoploid (diploid) hybridization may be just as common. Recent studies, including one in BMC Evolutionary Biology, show that pollinator shifts can play a role in both mechanisms of hybrid speciation.
See research article http://www.biomedcentral.com/1471-2148/10/103
doi:10.1186/1741-7007-8-45
PMCID: PMC2858105  PMID: 20409350
11.  A modern circadian clock in the common angiosperm ancestor of monocots and eudicots 
BMC Biology  2010;8:55.
The circadian clock enhances fitness through temporal organization of plant gene expression, metabolism and physiology. Two recent studies, one in BMC Evolutionary Biology, demonstrate through phylogenetic analysis of the CCA1/LHY and TOC1/PRR gene families that the common ancestor of monocots and eudicots had components sufficient to construct a circadian clock consisting of multiple interlocked feedback loops.
See research article http://www.biomedcentral.com/1471-2148/10/126
doi:10.1186/1741-7007-8-55
PMCID: PMC2867782  PMID: 20459860
12.  The gene complement of the ancestral bilaterian - was Urbilateria a monster? 
Journal of Biology  2009;8(10):89.
Expressed sequence tag analyses of the annelid Pomatoceros lamarckii, recently published in BMC Evolutionary Biology, are consistent with less extensive gene loss in the Lophotrochozoa than in the Ecdysozoa, but it would be premature to generalize about patterns of gene loss on the basis of the limited data available.
See research article http://www.biomedcentral.com/1471-2148/9/240.
doi:10.1186/jbiol192
PMCID: PMC2790832  PMID: 19939290
13.  As you weed, so shall you reap: on the origin of algaculture in damselfish 
BMC Biology  2010;8:81.
Within their territories, damselfish cultivate particular algae for consumption. A recent study in BMC Evolutionary Biology shows extensive variation among and within fish species in the composition of these algal 'gardens', varying from monocultures to cultures of mixed species, and in the mode of cultivation. This fish-algal agriculture may provide insight into the early stages of domestication.
See research article http://www.biomedcentral.com/1471-2148/10/185
doi:10.1186/1741-7007-8-81
PMCID: PMC2887784  PMID: 20594375
14.  Losing the desire: selection can promote obligate asexuality 
BMC Biology  2010;8:101.
Whilst parthenogenesis has evolved multiple times from sexual invertebrate and vertebrate lineages, the drivers and consequences of the sex-asex transition remain mostly uncertain. A model by Stouthamer et al. recently published in BMC Evolutionary Biology shows a pathway by which obligate asexuality could be selected for following endosymbiont infection.
See research article http://www.biomedcentral.com/1471-2148/10/229
doi:10.1186/1741-7007-8-101
PMCID: PMC2911426  PMID: 20687906
15.  A little bit is better than nothing: the incomplete parthenogenesis of salamanders, frogs and fish 
BMC Biology  2010;8:78.
A re-examination of the mitochondrial genomes of unisexual salamander lineages, published in BMC Evolutionary Biology, shows them to be the oldest unisexual vertebrates known, having been around for 5 million years. This presents a challenge to the prediction that lack of genetic recombination is a fast track to extinction.
See research article http://www.biomedcentral.com/1471-2148/10/238
doi:10.1186/1741-7007-8-78
PMCID: PMC2914643  PMID: 20687905
16.  Making progress in genetic kin recognition among vertebrates 
Journal of Biology  2010;9(2):13.
A recent study in BMC Evolutionary Biology has shown that genetically similar individual ring-tailed lemurs are also more similar in their scent composition, suggesting a possible mechanism of kin recognition. Theoretical and experimental studies reveal challenges ahead in achieving a true systems-level understanding of this process and its outcomes.
See research article http://www.biomedcentral.com/1471-2148/9/281.
doi:10.1186/jbiol221
PMCID: PMC2871517  PMID: 20236486
17.  Evolution underground: shedding light on the diversification of subterranean insects 
Journal of Biology  2010;9(3):17.
A recent study in BMC Evolutionary Biology has reconstructed the molecular phylogeny of a large Mediterranean cave-dwelling beetle clade, revealing an ancient origin and strong geographic structuring. It seems likely that diversification of this clade in the Oligocene was seeded by an ancestor already adapted to subterranean life.
See research article http://www.biomedcentral.com/1471-2148/10/29
doi:10.1186/jbiol227
PMCID: PMC2871511  PMID: 20236467
18.  A climate for contemporary evolution 
BMC Biology  2010;8:136.
A new study of divergence in freshwater fish provides strong evidence of rapid, temperature-mediated adaptation. This study is particularly important in the ongoing debate over the extent and significance of evolutionary response to climate change because divergence has occurred in relatively few generations in spite of ongoing gene flow and in the aftermath of a significant genetic bottleneck, factors that have previously been considered obstacles to evolution. Climate change may thus be more likely to foster contemporary evolutionary responses than has been anticipated, and I argue here for the importance of investigating their possible occurrence.
See Research article: http://www.biomedcentral.com/1471-2148/10/350/abstract
doi:10.1186/1741-7007-8-136
PMCID: PMC2984389  PMID: 21070684
19.  Ecological genomics: steps towards unraveling the genetic basis of inducible defenses in Daphnia 
BMC Biology  2010;8:51.
Little is known about the genetic mechanisms underlying inducible defenses. Recently, the genome of Daphnia pulex, a model organism for defense studies, has been sequenced. Building on the genome information, recent preliminary studies in BMC Developmental Biology and BMC Molecular Biology have assessed gene response profiles in Daphnia under predation pressure. We review the significance of the findings and highlight future research perspectives.
See research articles http://www.biomedcentral.com/1471-2164/10/527, http://www.biomedcentral.com/1471-2105/6/45, http://www.biomedcentral.com/1471-213X/10/45
doi:10.1186/1741-7007-8-51
PMCID: PMC2867779  PMID: 20529235
20.  Different noses for different mice and men 
BMC Biology  2012;10:75.
Chemosensory receptor genes encode G protein-coupled receptors with which animals sense their chemical environment. The large number of chemosensory receptor genes in the genome and their extreme genetic variability pose unusual challenges for understanding their evolution and function. Two articles in BMC Genomics explore the genetic variation of chemosensory receptor gene repertoires in humans and mice and provide unparalleled insight into the causes and consequences of this variability.
See research articles http://www.biomedcentral.com/1471-2164/13/414 and http://www.biomedcentral.com/1471-2164/13/415
doi:10.1186/1741-7007-10-75
PMCID: PMC3424162  PMID: 22908960
21.  Prospects for automated diagnosis of verbal autopsies 
BMC Medicine  2014;12:18.
Verbal autopsy is a method for assessing probable causes of death from lay reporting of signs, symptoms and circumstances by family members or caregivers of a deceased person. Several methods of automated diagnoses of causes of death from standardized verbal autopsy questionnaires have been developed recently (Inter-VA, Tariff, Random Forest and King-Lu). Their performances have been assessed in a series of papers in BMC Medicine. Overall, and despite high specificity, the current strategies of automated computer diagnoses lead to relatively low sensitivity and positive predictive values, even for causes which are expected to be easily assessed by interview. Some methods have even abnormally low sensitivity for selected diseases of public health importance and could probably be improved. Ways to improve the current strategies are proposed: more detailed questionnaires; using more information on disease duration; stratifying for large groups of causes of death by age, sex and main category; using clusters of signs and symptoms rather than quantitative scores or ranking; separating indeterminate causes; imputing unknown cause with appropriate methods.
Please see related articles: http://www.biomedcentral.com/1741-7015/12/5; http://www.biomedcentral.com/1741-7015/12/19; http://www.biomedcentral.com/1741-7015/12/20; http://www.biomedcentral.com/1741-7015/12/21; http://www.biomedcentral.com/1741-7015/12/22; http://www.biomedcentral.com/1741-7015/12/23.
doi:10.1186/1741-7015-12-18
PMCID: PMC3912493  PMID: 24495788
Cause of death; Verbal autopsy; Automated diagnosis; Health information system; Evaluation of health programs; Public health
22.  Sometimes one just isn't enough: do vertebrates contain an H2A.Z hyper-variant? 
Journal of Biology  2010;9(1):3.
How much functional specialization can one component histone confer on a single nucleosome? The histone variant H2A.Z seems to be an extreme example. Genome-wide distribution maps show non-random (and evolutionarily conserved) patterns, with localized enrichment or depletion giving a tantalizing suggestion of function. Multiple post-translational modifications on the protein indicate further regulation. An additional layer of complexity has now been uncovered: the vertebrate form is actually encoded by two non-allelic genes that differ by expression pattern and three amino acids.
See research articles http://www.biomedcentral.com/1741-7007/7/86 and http://www.biomedcentral.com/1471-2148/9/31.
doi:10.1186/jbiol214
PMCID: PMC2871525  PMID: 20092611
23.  Host-parasite relationships in the genome 
BMC Biology  2011;9:67.
Transposable elements are best interpreted as genomic parasites, proliferating in genomes through their over-replication relative to the rest of the genome. A new study examining correlations across Drosophila species between transposable element numbers and rates of host evolution has brought into focus one of the most complex questions in transposable element biology-what it is that determines the proportion of the genome that is transposable elements.
See research article: http://www.biomedcentral.com/1471-2148/11/258/
doi:10.1186/1741-7007-9-67
PMCID: PMC3189907  PMID: 21985691
24.  Predicting the evolution of antibiotic resistance 
BMC Biology  2013;11:14.
Mutations causing antibiotic resistance are often associated with a cost in the absence of antibiotics. Surprisingly, a new study found that bacteria adapting to increased temperature became resistant to rifampicin. By studying the consequences of the involved mutations in different conditions and genetic backgrounds, the authors illustrate how knowledge of two fundamental genetic properties, pleiotropy and epistasis, may help to predict the evolution of antibiotic resistance.
See research article http://www.biomedcentral.com/1471-2148/13/50
doi:10.1186/1741-7007-11-14
PMCID: PMC3579749  PMID: 23433262
25.  The genetic basis of modularity in the development and evolution of the vertebrate dentition. 
The construction of organisms from units that develop under semi-autonomous genetic control (modules) has been proposed to be an important component of their ability to undergo adaptive phenotypic evolution. The organization of the vertebrate dentition as a system of repeated parts provides an opportunity to study the extent to which phenotypic modules, identified by their evolutionary independence from other such units, are related to modularity in the genetic control of development. The evolutionary history of vertebrates provides numerous examples of both correlated and independent evolution of groups of teeth. The dentition itself appears to be a module of the dermal exoskeleton, from which it has long been under independent genetic control. Region-specific tooth loss has been a common trend in vertebrate evolution. Novel deployment of teeth and reacquisition of lost teeth have also occurred, although less frequently. Tooth shape differences within the dentition may be discontinuous (referred to as heterodonty) or graded. The occurrence of homeotic changes in tooth shape provides evidence for the decoupling of tooth shape and location in the course of evolution. Potential mechanisms for region-specific evolutionary tooth loss are suggested by a number of mouse gene knockouts and human genetic dental anomalies, as well as a comparison between fully-developed and rudimentary teeth in the dentition of rodents. These mechanisms include loss of a tooth-type-specific initiation signal, alterations of the relative strength of inductive and inhibitory signals acting at the time of tooth initiation and the overall reduction in levels of proteins required for the development of all teeth. Ectopic expression of tooth initiation signals provides a potential mechanism for the novel deployment or reacquisition of teeth; a single instance is known of a gene whose ectopic expression in transgenic mice can lead to ectopic teeth. Differences in shape between incisor and molar teeth in the mouse have been proposed to be controlled by the region-specific expression of signalling molecules in the oral epithelium. These molecules induce the expression of transcription factors in the underlying jaw mesenchyme that may act as selectors of tooth type. It is speculated that shifts in the expression domains of the epithelial signalling molecules might be responsible for homeotic changes in tooth shape. The observation that these molecules are regionally restricted in the chicken, whose ancestors were not heterodont, suggests that mammalian heterodonty may have evolved through the use of patterning mechanisms already acting on skeletal elements of the jaws. In general, genetic and morphological approaches identify similar types of modules in the dentition, but the data are not yet sufficient to identify exact correspondences. It is speculated that modularity may be achieved by gene expression differences between teeth or by differences in the time of their development, causing mutations to have cumulative effects on later-developing teeth. The mammalian dentition, for which virtually all of the available developmental genetic data have been collected, represents a small subset of the dental diversity present in vertebrates as a whole. In particular, teleost fishes may have a much more extensive dentition. Extension of research on the genetic control of tooth development to this and other vertebrate groups has great potential to further the understanding of modularity in the dentition.
doi:10.1098/rstb.2001.0917
PMCID: PMC1088541  PMID: 11604128

Results 1-25 (291246)