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July 4, 2015

06:00
Background: Identifying orthologous molecular markers that potentially resolve relationships at and below species level has been a major challenge in molecular phylogenetics over the past decade. Non-coding regions of nuclear low- or single-copy markers are a vast and promising source of data providing information for shallow-scale phylogenetics. Taking advantage of public transcriptome data from the One Thousand Plant Project (1KP), we developed a genome-scale mining strategy for recovering potentially orthologous single-copy markers to address low-scale phylogenetics. Our marker design targeted the amplification of intron-rich nuclear single-copy regions from genomic DNA. As a case study we used Hydrangea section Cornidia, one of the most recently diverged lineages within Hydrangeaceae (Cornales), for comparing the performance of three of these nuclear markers to other “fast” evolving plastid markers. Results: Our data mining and filtering process retrieved 73 putative nuclear single-copy genes which are potentially useful for resolving phylogenetic relationships at a range of divergence depths within Cornales. The three assessed nuclear markers showed considerably more phylogenetic signal for shallow evolutionary depths than conventional plastid markers. Phylogenetic signal in plastid markers increased less markedly towards deeper evolutionary divergences. Potential phylogenetic noise introduced by nuclear markers was lower than their respective phylogenetic signal across all evolutionary depths. In contrast, plastid markers showed higher probabilities for introducing phylogenetic noise than signal at the deepest evolutionary divergences within the tribe Hydrangeeae (Hydrangeaceae). Conclusions: While nuclear single-copy markers are highly informative for shallow evolutionary depths without introducing phylogenetic noise, plastid markers might be more appropriate for resolving deeper-level divergences such as the backbone relationships of the Hydrangeaceae family and deeper, at which non-coding parts of nuclear markers could potentially introduce noise due to elevated rates of evolution. The herein developed and demonstrated transcriptome based mining strategy has a great potential for the design of novel and highly informative nuclear markers for a range of plant groups and evolutionary scales.
06:00
Background: Hybridization between two species usually leads to inviable or infertile offspring, due to endogenous or exogenous selection pressures. Yet, hybrid taxa are found in several plant and animal genera, and some of these hybrid taxa are ecologically and evolutionarily very successful. One example of such a successful hybrid is the water frog, Pelophylax esculentus which originated from matings between the two species P. ridibundus (genotype RR) and P. lessonae (LL). At the northern border of the distribution all-hybrid populations consisting of diploid (LR) and one or two triploid (LLR, LRR) frog types have been established. Here, the hybrid has achieved reproductive independence from its sexual ancestors and forms a self-sustaining evolutionary unit. Based on the gamete production of these hybrids, certain mating combinations should lead to LL and RR offspring, but these parental forms are absent among the adults. Results: In order to investigate the mechanisms that maintain such an all-hybrid system, we performed a field study and a crossing experiment. In the field we sampled several ponds for water frog larvae at different developmental stages. Genotype compositions were then analysed and life-history differences between the genotypes examined. In the experiment we crossed diploid and triploid males and females from different ponds and determined fertilization success as well as development speed and survival rates of the offspring under high, medium and low food availability. In both parts of the study, we found numerous LL and RR offspring during the egg and early larval stages; but the frequency of these parental genotypes decreased drastically during later stages. In natural ponds almost all of them had disappeared already before metamorphosis; under the more benign experimental conditions the last ones died as juveniles during the following year. Conclusions: From the combined results we conclude that the absence of parental genotypes in all-hybrid populations is due to post-zygotic selection against them, rather than to pre-zygotic mechanisms that might prevent their formation in the first place. For this post-zygotic selection, genetic mechanisms resulting from low genetic diversity and fixation of deleterious mutations seem to be a more likely explanation than ecological factors.
00:54
This November we hold our biannual PhD course on the Ecology of Animal Migration. PhD students working on animal migration and related animal movement topics are encouraged to apply. Ecology of Animal Migration International PhD Course, November 2nd - 13th, 2015 Lund University, Sweden. Animals move across different spatial and temporal scales either as part of their daily life or as part of seasonal migrations to exploit resources in the environment. Well known examples are the global scale seasonal migrations in birds, sea turtles, fish and mammals, such as whales and wildebeests. Also movements at smaller scales occur, such as the vertical movements in plankton, the dispersal in soil collembolans and movements of pollinating insects. But what are the ecological causes and evolutionary consequences of animal movements? During this two-week course you will get insight in a number of different methods and approaches to study the migration of birds, insects, fish, amphibians and mammals, ranging from experimental studies in the laboratory to tracking long-distance migration in wild animals. Lectures will be given by international authorities in the field as well as by researchers in the CAnMove Group at Lund University. For further details and to apply for the course visit: http://bit.ly/1FZZhjH /Tom Evans - tom.evans@biol.lu.se - Student coordinator Tom Evans via Gmail
Source: EVOLDIR
00:27
Re-posting: I am looking for a postdoctoral researcher to join my lab at the University of Missouri V St. Louis. The project involves constructing a species-level phylogeny for the Neotropical genus Burmeistera (Campanulaceae) using next-generation sequencing approaches (Hyb-Seq, targeting low-copy nuclear regions with enrichment probes and genome- skimming for plastomes). Results will be used to test the relative roles of pollinator-mediated reproductive isolation and gametic isolation (post-pollination yet prezygotic) in the diversification of Burmeistera. Candidates should have experience with plant molecular phylogenetics, including labwork and bioinformatics analysis of next-gen data, and an interest in plant speciation and/or pollination biology. Successful applicants will also be encouraged to also carry out his or her own research projects related to work done in the Muchhala Lab (see http://bit.ly/1JSD39j). The start date for the position is flexible, from August of 2015 to January 2016. Funding is available for one year with renewal for a second year given satisfactory progress. St. Louis is a vibrant Midwestern city that boasts an exceptional quality of life, combining a low cost of living with a variety of cultural attractions including parks, museums, and lively music and art scenes. The University of Missouri V St. Louis has strong local ties with the Missouri Botanical Garden, the Saint Louis Zoo, Washington University, St. Louis University, and the Donald Danforth Plant Science Center, and annual retreats (sleec.weebly.com) bring together ecologists and evolutionary biologists from these and other local institutions. The Department also houses the Whitney R. Harris World Ecology Center, established to promote international research, particularly in tropical regions. Review of applications will begin on July 15th. Informal inquiries should be emailed to muchhalan@umsl.edu (I will also be at Evolution 2015 in Brazil if you want to discuss in person). Submission online at http://www.umsl.jobs. Applicants must combine application materials, including 1) a short statement (one to two pages) on previous experience, research interest, and motivation for applying, and 2) a curriculum vitae, into a single PDF or Microsoft Word document and upload as a resume attachment. Additionally, have three recommendation letters sent to muchhalan@umsl.edu. For questions about how to apply, please call (314) 516-5258, or if you are experiencing technical problems, please email pshrsupport@umsystem.edu. UMSL is an Equal Opportunity/Access/Affirmative Action/Pro Disabled & Veteran Employer – Nathan Muchhala, Ph.D. Assistant Professor Department of Biology University of Missouri -St Louis One University Blvd, R428 Research Hall St Louis, Missouri 63121 (314) 516-6672 http://bit.ly/16AFv3j “Muchhala, Nathan” via Gmail
Source: EVOLDIR
00:01

Evolution Meeting Coding Project - Poster Invite System The organizing committee for the annual Evolution Meetings (the joint annual meeting of the ASN/SSB/SSE) is looking to develop a poster-invite system for future meetings and we’re therefore searching for someone (graduate student, pdf, or faculty) who would be we willing to do some coding to develop this for us. We’re after a simple yet reliable system that looks nice, works well, that can easily be implemented across meetings (i.e. plug in a new database and go), and that can also be modified by others if needed (meaning open source with well annotated code). For those not familiar, the basic idea of the poster invite system is that a week or two before the meeting everyone that is presenting a poster gets an email explaining that they can have a personal invite to their poster sent to up to 3 meeting attendees of their choice. The email directs them to a website where they can browse a list of attendees (names and institutions) and select up to three. Any given attendee can only receive a maximum of 5 invites, after which they are no longer available for selection by subsequent poster presenters (it’s first come-first serve). After a few days, the system closes and emails get sent to every attendee that received one or more invites (up to the max of 5 per attendee). Each email indicates the name of the person that invited them, the title of their poster, and the date and time it is being presented. Past experience indicates that the majority of people visit posters to which they are invited, and this system can therefore dramatic ally alter the benefits of giving a poster compared to a talk. We’re willing to offer some financial compensation, and/or funds towards attending the next Evolution meeting in Austin, TX in 2016. However, this should be considered as much a volunteer service as a job. The ideal candidate would therefore be a member of one or more of these societies who values these meetings and would be interested in improving them. If you’re interested, or would like additional details, please contact me at hrundle@uottawa.ca. Those interested are asked to provide some evidence that they have the appropriate skills. Sincerely, Howard Rundle, Chief Meeting Officer Evolution Conferences howard.rundle@uottawa.ca via Gmail

Source: EVOLDIR

July 3, 2015

23:35

A postdoc position is open at the University of Iceland - Compensatory regulatory evolution and transcriptional cooption Which principles influence the rewiring and tuning of gene regulatory networks? How do those network react to genetic perturbations? We are seeking a post-doc to tackle those and related questions in project utilizing populations of Drosophila (fruit flies) that have undergone compensatory adaptation using experimental evolution and artificial selection. The project involves the analysis of tissue specific RNA-seq and numerical analyses. The ideal candidate is strong in evolutionary genetics, statistical and bioinformatic analyses and with capable hands for molecular biology. Excellent communication skills, main focus on writing, are required, as is a solid publication record. The candidate will be encouraged (and given time) to develop their own research program. The project is a collaboration between University of Iceland and McMaster University, mostly conducted in Iceland. Those interested are asked to send a cover letter detailing research interests and experience, a current CV, and contact details for three professional references by July 31th. Anticipated start date is Fall 2015, but this is flexible. The position is funded by the Icelandic Research fund (for 3 years), salary commensurate with qualifications. The University of Iceland is the leading research institute in the country, and groups at the Institute of biology (http://bit.ly/1CR2FgA) and Biomedical Center (lifvisindi.hi.is) study genomics, evolutionary, developmental, cellular and molecular biology. The shared facilities include High throughput sequencers, various specialized molecular biology equipment and computer clusters. The University is an equal opportunity workplace with strong combination of international and domestic scientists. Learn more about the work in the Palsson (uni.hi.is/apalsson) and Dworkin (http://bit.ly/1LNK11x) labs. Please send applications and/or inquiries to apalsson@hi.is. via Gmail

Source: EVOLDIR
06:00
Background: Entoprocta (Kamptozoa) is an enigmatic, acoelomate, tentacle-bearing phylum with indirect development, either via a swimming- or a creeping-type larva and still debated phylogenetic position within Lophotrochozoa. Recent morphological and neuro-anatomical studies on the creeping-type larva support a close relationship of Entoprocta and Mollusca, with a number of shared apomorphies including a tetraneurous nervous system and a complex serotonin-expressing apical organ. However, many morphological traits of entoproct larvae, in particular of the putative basal creeping-type larva, remain elusive. Results: Applying fluorescent markers and 3D modeling, we found that this larval type has the most complex musculature hitherto described for any lophotrochozoan larva. The muscle systems identified include numerous novel and most likely creeping-type larva-specific structures such as frontal organ retractors, several other muscle fibers originating from the frontal organ, and longitudinal prototroch muscles. Interestingly, we found distinct muscle sets that are also present in several mollusks. These include paired sets of dorso-ventral muscles that intercross ventrally above the foot sole and a paired enrolling muscle that is distinct from the musculature of the body wall. Conclusion: Our data add further morphological support for an entoproct-mollusk relationship (Tetraneuralia) and strongly argue for the presence of an enrolling musculature as well as seriality (but not segmentation) in the last common tetraneuralian ancestor. The evolutionary driving forces that have led to the emergence of the extraordinarily complex muscular architecture in this short-lived, non-feeding entoproct larval type remain unknown, as are the processes that give rise to the highly different and much simpler muscular bodyplan of the adult entoproct during metamorphosis.

July 2, 2015

18:00
Background: Long-distance dispersal events have the potential to shape species distributions and ecosystem diversity over large spatial scales, and to influence processes such as population persistence and the pace and scale of invasion. How such dispersal strategies have evolved and are maintained within species is, however, often unclear. We have studied long-distance dispersal in a range of pest-controlling terrestrial spiders that are important predators within agricultural ecosystems. These species persist in heterogeneous environments through their ability to re-colonise vacant habitat by repeated long-distance aerial dispersal (“ballooning”) using spun silk lines. Individuals are strictly terrestrial, are not thought to tolerate landing on water, and have no control over where they land once airborne. Their tendency to spread via aerial dispersal has thus been thought to be limited by the costs of encountering water, which is a frequent hazard in the landscape. Results: In our study we find that ballooning in a subset of individuals from two groups of widely-distributed and phylogenetically distinct terrestrial spiders (linyphiids and one tetragnathid) is associated with a hitherto undescribed ability of those same individuals to survive encounters with both fresh and marine water. Individuals that showed a high tendency to adopt ‘ballooning’ behaviour adopted elaborate postures to seemingly take advantage of the wind current whilst on the water surface. Conclusions: The ability of individuals capable of long-distance aerial dispersal to survive encounters with water allows them to disperse repeatedly, thereby increasing the pace and spatial scale over which they can spread and subsequently exert an influence on the ecosystems into which they migrate. The potential for genetic connectivity between populations, which can influence the rate of localized adaptation, thus exists over much larger geographic scales than previously thought. Newly available habitat may be particularly influenced given the degree of ecosystem disturbance that is known to follow new predator introductions.
06:00
Background: Only a handful of signaling pathways are major actors of development and responsible for both the conservation and the diversification of animal morphologies. To explain this twofold nature, gene duplication and enhancer evolution were predominantly put forth as tinkering mechanisms whereas the evolution of alternative isoforms has been, so far, overlooked. We investigate here the role of gain and loss of isoforms using Edaradd, a gene of the Ecodysplasin pathway, implicated in morphological evolution. A previous study had suggested a scenario of isoform gain and loss with an alternative isoform (A) newly gained in mammals but secondarily lost in mouse lineage. Results: For a comprehensive view of A and B Edaradd isoforms history during mammal evolution, we obtained sequences for both isoforms in representative mammals and performed in vitro translations to support functional predictions. We showed that the ancestral B isoform is well conserved, whereas the mammal-specific A isoform was lost at least 7 times independently in terminal lineages throughout mammal phylogeny. Then, to gain insights into the functional relevance of this evolutionary pattern, we compared the biological function of these isoforms: i) In cellulo promoter assays showed that they are transcribed from two alternative promoters, only B exhibiting feedback regulation. ii) RT-PCR in various tissues and ENCODE data suggested that B isoform is systematically expressed whereas A isoform showed a more tissue-specific expression. iii) Both isoforms activated the NF-κB pathway in an in cellulo reporter assay, albeit at different levels and with different dynamics since A isoform exhibited feedback regulation at the protein level. Finally, only B isoform could rescue a zebrafish edaradd knockdown. Conclusions: These results suggest that the newly evolved A isoform enables modulating EDA signaling in specific conditions and with different dynamics. We speculate that during mammal diversification, A isoform regulation may have evolved rapidly, accompanying and possibly supporting the diversity of ectodermal appendages, while B isoform may have ensured essential roles. This study makes the case to pay greater attention to mosaic loss of evolutionarily speaking “young” isoforms as an important mechanism underlying phenotypic diversity and not simply as a manifestation of neutral evolution.

July 1, 2015

06:00
Background: Peripatric speciation and peripheral isolation have uncertain importance in species accumulation, and are largely overshadowed by assumed dominance of allopatric modes of speciation. Understanding the role of different speciation mechanisms within biodiversity hotspots is central to understanding the generation of biological diversity. Here, we use a phylogeographic analysis of the spiny-throated reed frogs and examine sister pairings with unbalanced current distributional ranges for characteristics of peripatric speciation. We further investigate whether forest/grassland mosaic adapted species are more likely created through peripatric speciation due to instability of this habitat type. Results: We reconstructed a multi-locus molecular phylogeny of spiny-throated reed frogs which we then combined with comparative morphologic data to delimit species and analyze historical demographic change; identifying three new species. Three potential peripatric speciation events were identified along with one case of allopatric speciation. Peripatric speciation is supported through uneven potential and realized distributions and uneven population size estimates based on field collections. An associated climate shift was observed in most potentially peripatric splits. Morphological variation was highest in sexually dimorphic traits such as body size and gular shape, but this variation was not limited to peripatric species pairs as hypothesized. The potentially allopatric species pair showed no niche shifts and equivalent effective population sizes, ruling out peripatry in that speciation event. Two major ecological niche shifts were recovered within this radiation, possibly as adaptations to occupy areas of grassland that became more prevalent in the last 5 million years. Restricted and fluctuating grassland mosaics within forests might promote peripatric speciation in the Eastern Arc Biodiversity Hotspot (EABH). Conclusions: In our case study, peripatric speciation appears to be an important driver of diversity within the EABH biodiversity hotspot, implying it could be a significant speciation mechanism in highly fragmented ecosystems. Extensive peripatric speciation in this montane archipelago may explain the abundance of discrete lineages within the limited area of the EABH, as inferred in remote island archipelagos. Future phylogenetic studies incorporating demographic and spatial analyses will clarify the role of peripatric speciation in creating biodiversity hotspots.

June 30, 2015

22:30
There are several processes that create reticulate phylogenetic topologies, including hybridization, introgression (or admixture) and horizontal gene transfer (HGT). Biologically, introgression operates via the same mechanism as does hybridization (ie. during sexual reproduction), but it results in only a small amount of genetic material entering the recipient genome, making an admixed genome that is similar to the end result of HGT.

Constructing phylogenetic networks in situations where introgression or HGT have occurred has been somewhat different in practice to that used for hybridization. Hybridization has usually been tackled by merging incongruent tree topologies, based on the idea that the different topologies represent the phylogenetic history of the different genomes of the hybrid taxon. Introgression and HGT have usually been tackled by adding reticulation edges to a phylogenetic tree, on the basis that the tree represents the phylogenetic history of the main part of the genome.

So, the study of introgression (and HGT) involves (a) constructing a phylogenetic tree from some genomic sample, and (b) detecting the introgressed (or HGT) parts of the genome. This is potentially a problematic procedure, because how do we construct a phylogenetic tree from data that already contain non-tree components? Apparently, the expectation is that a single tree will be supported by the majority of the data, and the remainder will represent the introgressed (or HGT) pathways(s), plus whatever other components have created the observed genomic variability (such as incomplete lineage sorting, gene duplication-loss, and stochastic mutations).

Recently, there have been quite a few studies published that have adopted a specific protocol for this procedure, usually under the rubric of admixture. Most of these have involved the study of ancient human DNA, but there have also been studies of contemporary humans, as well as ancient non-humans, An example of the latter is shown in the next two figures, which represent parts (a) and (b), respectively. They are taken from this study of the relatives of horses: Hákon Jónsson, et alia (2014) Speciation with gene flow in equids despite extensive chromosomal plasticity. Proceedings of the National Academy of Sciences of the USA 111: 18655-18660.



The phylogenetic tree (step a) was constructed using "maximum likelihood inference and 20,374 protein-coding genes ... based on a relaxed molecular clock." So, only stochastic mutations were accounted for when constructing the tree, and not incomplete lineage sorting or gene duplication-loss.

The detection of introgression (step b) used "the D statistics approach, which tests for an excess of shared polymorphisms between one of two closely related lineages (E1 or E2) and a third lineage (E3)". The reticulations representing the detected gene flow were then added to the tree manually.

The D-statistic is also known as the ABBA-BABA test (see: Patterson NJ et alia. 2012. Ancient admixture in human history. Genetics 192: 1065-1093). It operates as follows for sets of four taxa, applied to character data.

Let the species tree be this, where E1–E3 are the three taxa being compared, and O is the outgroup:


There are three possible allele trees for each binary character (ie. single nucleotide polymorphism) in which states are shared pairwise:


In the first tree, E3 shares the ancestral character state with the outgroup, which is expected to be the most common pattern in the absence of gene flow. E1 and E2 share the ancestral state with the outgroup in the second and third trees, respectively.

The admixture test compares the ABBA tree to the BABA tree. The expectation is that if there has been no introgression then the data support for these two trees should be equal. That is, under the null hypothesis that there is no gene flow between the species (and the underlying species tree is correct), the difference in the expected number of occurrences of the ABBA and BABA patterns should be zero. Deviation from this expectation is statistically evaluated using a jackknife procedure.

When there are more than three ingroup taxa, they are tested in groups of three (plus the outgroup). No correction for multiple hypothesis testing seems ever to be applied. Recently, the test has been extended to five taxa (Pease JB, Hahn MW. 2015. Detection and polarization of introgression in a five-taxon phylogeny. Systematic Biology 64: 651-662).

Note that this test assumes that:
  • the "excess of shared polymorphisms" arises solely from gene flow, with or without incomplete lineage sorting, rather than from any other tree-like processes such as gene duplication-loss or ancestral population structure
  • there are no other sources of co-ordinated polymorphisms, such as character-state reversals due to adaptation / selection
  • any gene flow that does exist is due to introgression, rather than to hybridization or HGT.
How realistic these assumptions are is not immediately obvious.

June 29, 2015

18:00
Background: Sexual dimorphism in brain size is common among primates, including humans, apes and some Old World monkeys. In these species, the brain size of males is generally larger than that of females. Curiously, this dimorphism has persisted over the course of primate evolution and human origin, but there is no explanation for the underlying genetic controls that have maintained this disparity in brain size. Results: In the present study, we tested the effect of the female hormone (estradiol) on seven genes known to be related to brain size in both humans and nonhuman primates, and we identified half estrogen responsive elements (half EREs) in the promoter regions of four genes (MCPH1, ASPM, CDK5RAP2 and WDR62). Likewise, at sequence level, it appears that these half EREs are generally conserved across primates. Later testing via a reporter gene assay and cell-based endogenous expression measurement revealed that estradiol could significantly suppress the expression of the four affected genes involved in brain size. More intriguingly, when the half EREs were deleted from the promoters, the suppression effect disappeared, suggesting that the half EREs mediate the regulation of estradiol on the brain size genes. We next replicated these experiments using promoter sequences from chimpanzees and rhesus macaques, and observed a similar suppressive effect of estradiol on gene expression, suggesting that this mechanism is conserved among primate species that exhibit brain size dimorphism. Conclusions: Brain size dimorphism among certain primates, including humans, is likely regulated by estrogen through its sex-dependent suppression of brain size genes during development.
18:00
Background: The classification of royal ferns (Osmundaceae) has long remained controversial. Recent molecular phylogenies indicate that Osmunda is paraphyletic and needs to be separated into Osmundastrum and Osmunda s.str. Here, however, we describe an exquisitely preserved Jurassic Osmunda rhizome (O. pulchella sp. nov.) that combines diagnostic features of both Osmundastrum and Osmunda, calling molecular evidence for paraphyly into question. We assembled a new morphological matrix based on rhizome anatomy, and used network analyses to establish phylogenetic relationships between fossil and extant members of modern Osmundaceae. We re-analysed the original molecular data to evaluate root-placement support. Finally, we integrated morphological and molecular data-sets using the evolutionary placement algorithm. Results: Osmunda pulchella and five additional Jurassic rhizome species show anatomical character suites intermediate between Osmundastrum and Osmunda. Molecular evidence for paraphyly is ambiguous: a previously unrecognized signal from spacer sequences favours an alternative root placement that would resolve Osmunda s.l. as monophyletic. Our evolutionary placement analysis identifies fossil species as probable ancestral members of modern genera and subgenera, which accords with recent evidence from Bayesian dating. Conclusions: Osmunda pulchella is likely a precursor of the Osmundastrum lineage. The recently proposed root placement in Osmundaceae—based solely on molecular data—stems from possibly misinformative outgroup signals in rbcL and atpA genes. We conclude that the seemingly conflicting evidence from morphological, anatomical, molecular, and palaeontological data can instead be elegantly reconciled under the assumption that Osmunda is indeed monophyletic.
18:00
Background: Sympatric speciation is today generally viewed as plausible, and some well-supported examples exist, but its relative contribution to biodiversity remains to be established. We here quantify geographic overlap of sister species of heliconiine butterflies, and use age-range correlations and spatial simulations of the geography of speciation to infer the frequency of sympatric speciation. We also test whether shifts in mimetic wing colour pattern, host plant use and climate niche play a role in speciation, and whether such shifts are associated with sympatry. Results: Approximately a third of all heliconiine sister species pairs exhibit near complete range overlap, and analyses of the observed patterns of range overlap suggest that sympatric speciation contributes 32 %–95 % of speciation events. Müllerian mimicry colour patterns and host plant choice are highly labile traits that seem to be associated with speciation, but we find no association between shifts in these traits and range overlap. In contrast, climatic niches of sister species are more conserved. Conclusions: Unlike birds and mammals, sister species of heliconiines are often sympatric and our inferences using the most recent comparative methods suggest that sympatric speciation is common. However, if sister species spread rapidly into sympatry (e.g. due to their similar climatic niches), then assumptions underlying our methods would be violated. Furthermore, although we find some evidence for the role of ecology in speciation, ecological shifts did not show the associations with range overlap expected under sympatric speciation. We delimit species of heliconiines in three different ways, based on “strict and ” “relaxed” biological species concepts (BSC), as well as on a surrogate for the widely-used “diagnostic” version of the phylogenetic species concept (PSC). We show that one reason why more sympatric speciation is inferred in heliconiines than in birds may be due to a different culture of species delimitation in the two groups. To establish whether heliconiines are exceptional will require biogeographic comparative studies for a wider range of animal taxa including many more invertebrates.
18:00
Background: Hemostasis is a defense mechanism that enhances an organism’s survival by minimizing blood loss upon vascular injury. In vertebrates, hemostasis has been evolving with the cardio-vascular and hemodynamic systems over the last 450 million years. Birds and mammals have very similar vascular and hemodynamic systems, thus the mechanism that blocks ruptures in the vasculature is expected to be the same. However, the speed of the process varies across vertebrates, and is particularly slow for birds. Understanding the differences in the hemostasis pathway between birds and mammals, and placing them in perspective to other vertebrates may provide clues to the genetic contribution to variation in blood clotting phenotype in vertebrates. We compiled genomic data corresponding to key elements involved in hemostasis across vertebrates to investigate its genetic basis and understand how it affects fitness. Results: We found that: i) fewer genes are involved in hemostasis in birds compared to mammals; and ii) the largest differences concern platelet membrane receptors and components from the kallikrein-kinin system. We propose that lack of the cytoplasmic domain of the GPIb receptor subunit alpha could be a strong contributor to the prolonged bleeding phenotype in birds. Combined analysis of laboratory assessments of avian hemostasis with the first avian phylogeny based on genomic-scale data revealed that differences in hemostasis within birds are not explained by phylogenetic relationships, but more so by genetic variation underlying components of the hemostatic process, suggestive of natural selection. Conclusions: This work adds to our understanding of the evolution of hemostasis in vertebrates. The overlap with the inflammation, complement and renin-angiotensin (blood pressure regulation) pathways is a potential driver of rapid molecular evolution in the hemostasis network. Comparisons between avian species and mammals allowed us to hypothesize that the observed mammalian innovations might have contributed to the diversification of mammals that give birth to live young.
18:00
Background: Retraction is among the most important basic behaviors of anthozoan Cnidaria polyps and is achieved through the coordinated contraction of at least six different muscle groups. Across the Anthozoa, these muscles range from unrecognizable atrophies to massive hypertrophies, producing a wide diversity of retraction abilities and functional morphologies. The marginal musculature is often the single largest component of the retraction mechanism and is composed of a diversity of muscular, attachment, and structural features. Although the arrangements of these features have defined the higher taxonomy of Zoanthidea for more than 100 years, a decade of inferring phylogenies from nucleotide sequences has demonstrated fundamental misconceptions of their evolution. Results: Here we expand the diversity of known marginal muscle forms from two to at least ten basic states and reconstruct the evolution of its functional morphology across the most comprehensive molecular phylogeny available. We demonstrate that the evolution of these forms follows a series of transitions that are much more complex than previously hypothesized and converge on similar forms multiple times. Evolution of the marginal musculature and its attachment and support structures are partially scaled according to variation in polyp and muscle size, but also vary through evolutionary allometry. Conclusions: Although the retraction mechanisms are diverse and their evolutionary histories complex, their morphologies are largely reflective of the evolutionary relationships among Zoanthidea higher taxa and may offer a key feature for integrative systematics. The convergence on similar forms across multiple linages of Zoanthidea mirrors the evolution of the marginal musculature in another anthozoan order (Actiniaria). The marginal musculature varies through evolutionary allometry of functional morphologies in response to requirements for additional force and resistance, and the specific ecological and symbiotic functions of individual taxa.

June 28, 2015

16:30

I have noted before that common usage of expressions like "family tree" often extend far beyond actual pedigrees. This particular expression is often used to describe any sort of historical relationship, not just genealogical ones. It is also sometimes used simply to describe any sort of personal inter-connection. All of these usages occurred in a short-lived magazine from 25 years ago called Wigwag.


Wigwag magazine formally debuted in October 1989 (after a test issue in 1988), and published its last issue in February 1991, for a total of 15 issues. It was a sort of cozy version of the New Yorker magazine. Similarly, it had a number of regular features, such as the Road Trip, the Map, and Letters From Home. The one that is of interest to us was called The Family Tree.

This feature mapped cultural relationships, having been described as "a field guide to the genealogy of influence in American life". It included human relationships, but it also included things like cars (the tree of which is reproduced in the book by Nobuhiro Minaka & Kunihiko Sugiyama. 2012. Phylogeny Mandala: Chain, Tree, and Network) and comic-book superheroes.

I have been unable to locate any decent copies, but four of the "trees" are included below.

As you can see, sometimes The Family Tree was actually a genealogical tree, but just as often it was simply a network of pairwise cultural connections. The latter, of course, usually formed a complex network that did not really map historical relationships.





This last Family Tree is from the original trial issue, and shows the inter-relationships of the writers and producers of American TV sitcoms.

You can read a bit more about the magazine, and its history, here:

00:20

–_000_D1B48D7EE0BEdb60standrewsacuk_ Content-Type: text/plain; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable Dear Evoldir, 4273pi is for those wishing to teach, learn or use research-grade bioinformatics on the low-cost Raspberry Pi computer. 4273pi includes Open Access teaching material and a customised Linux operating system for the Raspberry Pi. Coverage of particular interest to Evoldir includes: delimiting gene/protein families; multiple alignment and phylogeny; gene family evolution; looking at species differences; and function and evolution of enzymes. We are happy to announce 4273pi version 1.31. This has the best software and teaching material yet, and may be downloaded at: http://bit.ly/16toIJY For further details on 4273pi, see also: http://bit.ly/1aY6gRa and http://bit.ly/1Nn9QU3 - Daniel via Gmail

Source: EVOLDIR

June 27, 2015

23:54

POSITION TITLE: Clinical Genomics Scientist, AncestryHealth LOCATION: San Francisco, CA AncestryHealth (http://bit.ly/1KicYAJ) is seeking a motivated, collaborative and talented computational biologist with experience in the analysis of clinical and genomic data. Working with a nimble team of geneticists, statisticians, computer scientists and epidemiologists, the Clinical Genomics Scientist will invent algorithms and methods to interpret our singular data set of genotypes, pedigrees and phenotypes. We are seeking applicants who are eager to develop novel ways to extract actionable and accurate clinical genomics discoveries for consumers. Requirements/Qualifications: * The successful candidate for the position will have an M.D. or Ph.D. in Computational Biology, Genetics, Statistics, Computer Science (or a related field). * The candidate must have a passion for using genomic data to advance healthcare, population health, and wellness. * Demonstrated excellence in algorithm development using “- omics” data in clinical applications is important. * The successful applicant will have a strong working knowledge of statistics and proficiency in one or more of Python, Java, C/C++ or R. * Excellent verbal and written communication skills are required. * Strong organizational and interpersonal skills will be needed in our fast-paced team. Interested? Here’s how to apply: Begin your online application http://bit.ly/1ICCZq1 or if you have any problems please submit your CV/resume to careers@ancestryhealth.com Please reference CLINICAL GENOMICS SCIENTIST in the subject field of your e-mail. Ancestry (www.ancestry.com) is a private equity owned company with large US offices in Provo, Utah, and San Francisco, as well as several international offices including London, Dublin, Munich, Toronto, and Sydney. Ancestry is the world’s largest online resource for family history with an extensive collection of over 13 billion historical records that have been digitized, indexed, and made available online over the past 15 years. These digital records and documents enabled Ancestry’s 2.7 million plus paying subscribers and over 12 million registrants to create nearly 60 million family trees. While most of Ancestry’s subscribers are in the US, the company has a strong presence in the UK, Canada, and Australia, and is in the process of a large international expansion into Eastern Europe and Mexico. In 2014, Ancestry had non-GAAP revenue of $619.5 million (up 10.3% YOY) and adjusted EBITDA of $214.8 million. AncestryDNA (www.ancestryDNA.com ) has become the fastest growing direct-to-consumer genomic company by providing consumers insights into their ancestral origins. A team of scientists leverages pedigrees, documents, demographics, and genomes to conduct innovative research in population – via Gmail

Source: EVOLDIR
23:27

Dear All We have recently released the R package LEA that enables users to run genome-wide ecological association studies from the R command line. Genome-wide ecological association studies aim at detecting allele frequencies that exhibit significant statistical association with ecological gradients. Ecological association studies can provide lists of genetic polymorphisms that are potentially involved in local adaptation to environmental conditions through natural selection. The package LEA runs (very fast) STRUCTURE-like analyses of population structure, and performs genome scans for selection from large genomic data sets. It derives advantages from R programming functionalities to adjust significance values for multiple testing issues and to visualize results. The package is available from the Bioconductor resource repository http://bit.ly/1TWf0Ld. Online documentations and tutorials are available from the authors’ webpages http://bit.ly/1NoZ277. See also the application note here: http://bit.ly/1TWeZXK If you have any questions or want to send feedback, do not hesitate to contact us at: olivier.francois@imag.fr Best regards, Olivier via Gmail

Source: EVOLDIR