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May 31, 2015
With consequences for disease severity, resistance or clearance of a pathogen infection by an individual can be enhanced by a previous exposure to that pathogen, occurring either within an individual or even in its parents. This form of immune memory, traditionally thought the province of the vertebrate adaptive immune response, can also arise from innate immune pathways of vertebrates and invertebrates, and through distinct pathways in plants and bacteria. Researchers studying this phenomenon rarely interact across taxonomic boundaries, however, and use a preponderance of disparate terms to describe this innate immune mediated memory, including immune memory, immune priming, trained immunity, and systemic acquired resistance. This catalysis meeting will facilitate a synthesis of disparate researchers to better understand commonalities among these different forms of innate immune memory and key consequences for disease. We will use this opportunity to produce a broad interest synthesis manuscript elaborating upon specific avenues by which an improved understanding of innate immune memory will inspire future research, with direct and indirect benefits for human health. First, better understanding of how vertebrate immune memory works in retaining specific memory stands to improve vaccine design and delivery. Second, the specificity of immune memory could be manipulated to leave harmful pests, vectors, and human parasites susceptible to pathogen mediated biocontrol, while improving the health of beneficial organisms such as agricultural plants, animals, and pollinators that ensure human food security. Our approach aims to identify model systems functionally analogous to human innate immune memory that maximize our flexibility to interrogate the genetics, constraints, and functional manipulations of innate immune memory. Finally, this synthesis will elucidate fundamental concepts underlying host-pathogen evolution and the limits of immunological plasticity.
May 21, 2015
In the last two decades, models from evolutionary biology have made important contributions to demographic research on human fertility change. Within this evolutionary framework, two distinct traditions have focused on different processes of adaptation and time scales of change: (1) behavioral ecological perspectives have focused on how individual fertility decisions are shaped by local ecological circumstances, while (2) cultural evolutionary approaches have emphasized the role of socially transmitted information and changing social norms in shaping fertility behavior. While each tradition has made independent progress, research that integrates these approaches is necessary to improve our understanding of real fertility behavior, which results from a feedback between individual fertility decisions and social change. This approach requires combined attention to immediate ecological determinants of fertility decisions as well as the long-term processes that shape costs and benefits in a given environment. This workshop will bring together an international team of evolutionary behavioral scientists with complementary methodological and theoretical expertise in anthropology, psychology, and demography to develop (a) a synthetic article which proposes how these approaches can be integrated methodologically and theoretically, (b) an empirical article which applies our new synthetic framework to the study of fertility change in a particular fieldsite, demonstrating how the new methodological approach will work in practice and what we can learn through employing it, and (c) a multi-site grant proposal (UK, US, Bangladesh, Ethiopia, Bolivia, Poland) aimed at integrating and empirically testing these diverse evolutionary models of human fertility change.
May 17, 2015
Human cultural diversity is expressed in myriad ways (from social and marital norms to languages and religious practices), but what factors shape this diversity? Dating back to Darwin, multiple disciplines have debated the degree to which cultural diversity patterns are influenced by different factors, including history, demographics, and ecology. Over recent years an emerging set of studies have showcased how phylogenetic comparative methods from evolutionary biology can help resolve these long-held debates and revolutionize the field of cultural evolution. Now the major barrier to advances lies in the location of necessary data, which are spread across multiple disparate sources in linguistics, biogeography and anthropology. To overcome this challenge we will create D-PLACE (a Database of Phylogenies of Languages for the study of Cultural Evolution), a publicly available and expandable web-portal that will map over 100 cultural features onto language phylogenies and link these to ecological and environmental variables, empowering a whole new line of investigation into the drivers of cultural change and patterns of cultural diversity. We will produce a paper to introduce D-PLACE and outline the many types of questions in comparative anthropology the database can answer. Finally, we will demonstrate the power of this new resource by using D-PLACE to examine two long-standing and fundamental questions from comparative anthropology: (i) What drives the diversity of incest taboos (i.e. how human societies regulate who can mate and marry)? (ii) Can we characterize recurrent âhuman nichesâ, or are societies just arbitrary bundles of cultural features?
Linking self-fertilization, dispersal and distribution traits of species: Is Bakerâs law an exception to the rule?
Bakerâs Law (hereafter BL) states that self-compatible organisms are more likely to be successful colonizers after long-distance dispersal than self-incompatible organisms. This simple prediction draws a link between mating-system evolution and diverse fields of ecology and evolution such as dispersal biology and colonization, the evolution of range size and range limits, demography and Allee effect, and invasion biology. However, after >60 years of experimental research and theory development, the accumulated data yield varying, and often contradictory, support of BL. Our working group brings together a diverse array of researchers to assess predictions and assumptions of BL and elucidate ecological, evolutionary, and demographic parameters likely to determine the relationships between mating system, dispersal, and colonization success. To accomplish these goals we will: 1) Compile the voluminous literature on BL. 2) Link the BL data with two extensive databases gathered by prior NESCent support (seed germination and seed traits data; mating system data) and a NCEAS pollen limitation database. These expanded databases will include dispersal, range size, and life-history traits, thereby creating a powerful tool for testing various aspects of the relationship between mating-system and colonization success. 3) Employ macroevolutionary tools to map mating-system and dispersal traits onto the angiosperm phylogeny to assess evolutionary patterns and phylogenetically-corrected trait correlations. 4) Formalize BL using current population genetic theory and dispersal theory. Synthetic products of our working group should elucidate the links between dispersal and mating-system in colonization success, and will influence multiple fields of research in evolution for the foreseeable future.
May 10, 2015
Building non-model species genome curation communities
May 6, 2015
Primates are highly charismatic and often serve as flagship species in conservation efforts. They are also the closest living relatives of humans, and therefore hold the keys to resolving many questions about human evolution and ecology. However, the slow life histories of primates, combined with their complex social systems, their behavioral plasticity, and the challenging field conditions in which primate researchers must work, have severely limited analyses of mortality and fertility in wild, unprovisioned primate populations. This in turn limits comparative analyses that can shed light on the population dynamics and the social and ecological adaptations that have shaped both human and nonhuman primate evolution. We propose a Primate Life Histories Working Group to compare mortality and fertility schedules across taxa, to evaluate a set of hypotheses about the roles that phylogeny, ecology, and behavior play in shaping primate mortality and fertility patterns, and to examine whether life history theory predicts which vital rates are most variable across species. Using unique, individual-based life history data that have been collected from wild populations by nine working group participants over a minimum of 19 years, we will develop age-specific mortality and fertility schedules and create population projection matrices for each species. Our immediate goals are to test current hypotheses about the evolution of life histories in order to advance our understanding of primate evolution. Our longer-term goal is to move toward a collaborative, shared databank allowing analyses of irreplaceable life history data on wild primates.
May 3, 2015
April 28, 2015
A number of independent efforts have compiled global plant databases on functionally important traits of leaves, stems, seeds, and flowers. These databases are comprised of 1000's to tens of 1000's of species. With a few notable exceptions, they have not been analyzed in an evolutionary or phylogenetic context. However, when synthesized with a modern molecular phylogeny, these data could tell a comprehensive, multivariate story of the evolution of plant functional diversity. In this working group, we will merge multiple databases to explore the rate (tempo, sensu GG Simpson) of evolution of these traits and the best fit evolutionary model(s) (mode) underlying the trait diversification of land plants. We will ask 1. whether important divergences in trait space occurred along similar branches for different traits, 2. whether there were periods of evolution when trait diversification was especially rapid, and 3. whether there were interactions between trait evolution and rates of speciation and extinction. This work will lead to a new community resource of great interestâan internally synced trait matrixâmatched with the current state-of-the-art phylogeny. These data can then be synthesized with fossil evidence to explore whether the tempo and mode of trait evolution in extant and extinct taxa provide similar stories. Furthermore, these data will provide a powerful view into the coordinated (or lack thereof) evolution of ecologically important traits across vascular plantsâone of the most diverse and important lineages in the world today.
April 23, 2015
The identification and explanation of long-term evolutionary trends in higher taxa and biological communities is an important goal of biological research. Body size is the single most important ecological characteristic of metazoa and the variable most easily applied to analysis of evolutionary trends across distantly related taxa. The proposed working group will bring together paleobiologists studying body size evolution in deep time and across higher taxa with biologists studying the distribution of body sizes in living organisms from the community to global scale. The working group will initiate a community-wide database of body sizes through the Phanerozoic, an effort that requires standardized data on body size across higher taxa. The working group will also catalyze collaborations between paleobiologists and biologists to develop the theory necessary to investigate long-term dynamics in body-size evolution across diverse living and extinct metazoan lineages. The workshop will provide a venue for members to address the relationships between the pattern of body size evolution and the distribution of body sizes in extant organisms. How well can macroevolutionary patterns be inferred from macroecological ones? How well do those patterns reflect evolutionary mechanisms, whether driven or passive? Ultimately, the resulting database will become a broadly applicable and dynamic resource for macroevolutionary research, with real potential to help future workers shed light on the forces that have shaped the evolutionary trajectory of animal life on Earth.
Phylogeography and evolutionary history of the Crocidura olivieri complex (Mammalia, Soricomorpha): from a forest origin to broad ecological expansion across Africa
Background: This study aims to reconstruct the evolutionary history of African shrews referred to the Crocidura olivieri complex. We tested the respective role of forest retraction/expansion during the Pleistocene, rivers (allopatric models), ecological gradients (parapatric model) and anthropogenic factors in explaining the distribution and diversification within this species complex. We sequenced three mitochondrial and four nuclear markers from 565 specimens encompassing the known distribution of the complex, i.e. from Morocco to Egypt and south to Mozambique. We used Bayesian phylogenetic inference, genetic structure analyses and divergence time estimates to assess the phylogenetic relationships and evolutionary history of these animals. Results: The C. olivieri complex (currently composed of C. olivieri, C. fulvastra, C. viaria and C. goliath) can be segregated into eight principal geographical clades, most exhibiting parapatric distributions. A decrease in genetic diversity was observed between central and western African clades and a marked signal of population expansion was detected for a broadly distributed clade occurring across central and eastern Africa and portions of Egypt (clade IV). The main cladogenesis events occurred within the complex between 1.37 and 0.48 Ma. Crocidura olivieri sensu stricto appears polyphyletic and C. viaria and C. fulvastra were not found to be monophyletic. Crocidura somalica is part of the complex. Conclusions: Climatic oscillations over the Pleistocene probably played a major role in shaping the genetic diversity within this species complex. Different factors can explain their diversification, including Pleistocene forest refuges, riverine barriers and differentiation along environmental gradients. The earliest postulated members of the complex originated in central/eastern Africa and the first radiations took place in rain forests of the Congo Basin. A dramatic shift in the ecological requirements in early members of the complex, in association with changing environments, took place sometime after 1.13 Ma. Some lineages then colonized a substantial portion of the African continent, including a variety of savannah and forest habitats. The low genetic divergence of certain populations, some in isolated localities, can be explained by their synanthropic habits. This study underlines the need to revise the taxonomy of the C. olivieri complex.
reminder: upcoming deadline PhD positions in Population Genetics Over the past years, Vienna has developed into one of the leading centres of population genetics. The Vienna Graduate School of Population Genetics has been founded to provide a training opportunity for PhD students to build on this excellent on site expertise. We invite applications from highly motivated and outstanding students with a background in one of the following disciplines: bioinformatics, statistics, evolutionary genetics, functional genetics, theoretical and experimental population genetics. Students from related disciplines, such as physics or mathematics are also welcome to apply. Topics include: via Gmail
–_004_51F1C9039AFF3447A20EA4E34EDA40310CF42D51B6ARTEMISpersad_ Content-Type: multipart/alternative; boundary=“_000_51F1C9039AFF3447A20EA4E34EDA40310CF42D51B6ARTEMISpersad_” –_000_51F1C9039AFF3447A20EA4E34EDA40310CF42D51B6ARTEMISpersad_ Content-Type: text/plain; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable Dear Brian, Would you please post the attached Graduate position ad on EvolDir? Sincerely, Kristina Sefc –_000_51F1C9039AFF3447A20EA4E34EDA40310CF42D51B6ARTEMISpersad_ Content-Type: text/html; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable
–_000_D15DD1EC43A49lg8beservicesvirginiaedu_ Content-Type: text/plain; charset=“us-ascii” Content-Transfer-Encoding: quoted-printable The Department of Biology at the University of Virginia invites applications for a postdoctoral Research Associate position in the lab of Dr. Laura Galloway. The position is supported by an NSF-funded project to explore the relationship between biogeography and mating system evolution in American bellflower (Campanulastrum americanum). Mating systems are evolutionarily labile and variation is often explained by hypotheses focusing on the context-dependent benefits of selfing (e.g. reproductive assurance). However, mating system evolution may be driven by historical changes in genetic load. In particular, colonization from glacial refugia to current distributions often entailed bottlenecks and small population sizes that shape population genetic structure and hence potential for mating system evolution. Our goal is to integrate studies of biogeography and mating system using Campanulastrum americanum, a North American herb in which preliminary data indicate reduced inbreeding depression and greater autogamy in sites where phylogeographic data suggest recent colonization. The Research Associate will work with the PI, our collaborator Jeremiah Busch (Washington State Univ), and lab personnel to design and lead research in the lab and field. The Research Associate will conduct greenhouse studies of genetic load and mechanisms of autogamy, field studies of factors that underlie pollen limitation, estimate population selfing rate and interact with collaborators determining population genetic structure. The position also involves data management and dissemination, preparing manuscripts, and mentoring graduate and undergraduate students. The ideal candidate will enjoy working both in a team and independently, and may use the appointment to develop and pursue additional related studies. Finally, this position will coordinate outreach activities at Mountain Lake Biological Station and an Environmental Studies Academy at a local high school. Demonstrated expertise in ecological genetics including field and greenhouse work and strong written and oral communication skills are required. Experience in evolutionary genetics is desirable. The completion of a PhD degree in Biology or related field by the appointment start date is required. Preferred appointment start date is Summer 2015. This is a two-year appointment; the appointment may be renewed for an additional year, contingent upon availability of funds and satisfactory performance. To apply, please submit a candidate profile through Jobs@UVA (http://bit.ly/1ccxWRu) and electronically attach: curriculum vitae with list of publications, a cover letter that summarizes research interests and professional goals, and contact information for three (3) references; search on posting number 0616239. Review of applications will begin May 9, 2015; however, the position will remain open until filled. Questions regarding this position should be directed to: Dr. Laura Galloway (firstname.lastname@example.org) Questions regarding the Candidate Profile process or Jobs@UVA should be directed to: Rich Haverstrom (email@example.com) The University will perform background checks on all new hires prior to making a final offer of employment. The University of Virginia is an Equal Opportunity/Affirmative Action Employer. Women, minorities, veterans and persons with disabilities are encouraged to apply. –_000_D15DD1EC43A49lg8beservicesvirginiaedu_ Content-Type: text/html; charset=“us-ascii” Content-ID: Content-Transfer-Encoding: quoted-printable The Department of Biology at the University of Virginia invites applications for a postdoctoral Research Associate position in the lab of Dr. Laura Galloway. The position is supported by an NSF-funded project to explore the relationship between biogeography and mating system evolution in American bellflower (Campanulastrum americanum). Mating systems are evolutionarily labile and variation is often explained by hypotheses focusing on the context-dependent benefits of selfing (e.g. reproductive assurance). However, mating system evolution may be driven by historical changes in genetic load. In particular, colonization from glacial refugia to current distributions often entailed bottlenecks and small population sizes that shape population genetic structure and hence potential for mating system evolution. Our goal is to integrate studies of biogeography and mating system using Campanulastrum americanum, a North American herb in which preliminary data indicate reduced inbreeding depression and greater autogamy in sites where phylogeographic data suggest recent colonization. The Research Associate will work with the PI, our collaborator Jeremiah Busch (Washington State Univ), and lab personnel to design and lead research in the lab and field. The Research Associate will conduct greenhouse studies of genetic load and mechanisms of autogamy, field studies of factors that underlie pollen limitation, estimate population selfing rate and interact with collaborators determining population genetic structure. The position also involves data management and dissemination, preparing manuscripts, and mentoring graduate and undergraduate students. The ideal candidate will enjoy working both in a team and independently, and may use the appointment to develop and pursue additional related studies. Finally, this position will coordinate outreach activities at Mountain Lake Biological Station and an Environmental Studies Academy at a local high school. Demonstrated expertise in ecological genetics including field and greenhouse work and strong written and oral communication skills are required. Experience in evolutionary genetics is desirable. The completion of a PhD degree in Biology or related field by the appointment start date is required. Preferred appointment start date is Summer 2015. This is a two-year appointment; the appointment may be renewed for an additional year, contingent upon availability of funds and satisfactory performance. To apply, please submit a candidate profile through Jobs@UVA (http://bit.ly/1ccxWRu) and electronically attach: curriculum vitae with list of publications, a cover letter that summarizes research interests and professional goals, and contact information for three (3) references; search on posting number 0616239. Review of applications will begin May 9, 2015; however, the position will remain open until filled. Questions regarding this position should be directed to: Dr. Laura Galloway (firstname.lastname@example.org) Questions regarding the Candidate Profile process or Jobs@UVA should be directed to: Rich Haverstrom (email@example.com) The University will perform background checks on all new hires prior to making a final offer of employment. The University of Virginia is an Equal Opportunity/Affirmative Action Employer. Women, minorities, veterans and persons with disabilities are encouraged to apply. –_000_D15DD1EC43A49lg8beservicesvirginiaedu via Gmail
Category: Course Topic: AMUPoznan.Poland.Bioinformatics.RNA.July6-10 Dear colleagues, We are extremely happy to announce 11th edition of Poznan Summer School of Bioinformatics. This meeting takes place at Adam Mickiewicz University in Poznan (Poland) from 6th to 10th July 2015. This year’s course will cover modern approaches to RNA analyses, including subjects like: 1. Introduction to RNA biology 2. Applications of next-generation sequencing in RNA studies 3. Transcriptome sequencing, assembly and gene expression estimation 4. Identification and analysis of microRNAs and other small RNAs 5. long non-coding RNAs 6. Secondary and tertiary structures of RNAs The course is suitable both for beginners and for those who already have some basic knowledge in computational biology and find it necessary and interesting to learn more about bioinformatic applications in RNA studies. Our school consists of lectures and hands-on - this combination should fit best your needs as you have a chance to try out the discussed methods yourself. For further information please visit our website: http://bit.ly/1DDxbdc Please forward this announcement to anyone who might be interested. Best regards, PSSB Organizing Committee Contact: firstname.lastname@example.org Bioinfo School via Gmail
PhD scholarship opportunity Subject title: “Epigenetic inheritance of physiological flexibility in a primate species, the grey mouse lemur” Location: UMR CNRS/MNHN 7179 (MECADEV) 1 avenue du petit château, 91800 Brunoy (France) Main PhD supervisor: Dr Fabienne Aujard Secondary PhD supervisors: Drs Pierre-Yves Henry and Jérémy Terrien The French research unit UMR 7179 is offering an opportunity to defend a PhD scholarship to be attributed by the Museum National d'Histoire Naturelle. The applicant will defend a subject treating on the “Epigenetic inheritance of physiological flexibility in a primate species, the grey mouse lemur”. Briefly, exhibiting high phenotypic flexibility requires fine tuning of all mechanisms involved in the control of metabolism, including regulation of gene expression through epigenetic changes. Epigenetic modifications are a mechanism of regulating gene expression that is reversible, heritable and particularly sensitive to environmental conditions. The role of epigenetic modifications as a way of adjusting phenotypic flexibility in response to environmental change has gained much interest since epigenetic inheritance has been described as a potential mechanism for a specimen to benefit from its parents history. In this project, we propose to evaluate the potential of epigenetic inheritance in a primate species, the grey mouse lemur (Microcebus murinus), characterized by its great phenotypic flexibility adapted to the unpredictability of Madagascar climate. Using the in-house breeding colony resource (~400 individuals), we will mimic periods of food scarcity during key periods of reproduction (spermatogenesis for males and gestation, lactation for females) and evaluate the impacts of such treatment in juveniles and their ability to respond to the same energetic challenge. The student will have to conduct experiments to answer 2 main questions: 1) Which are the epigenetic modifications induced by an energetic challenge in the adult grey mouse lemur, and can we link these changes to metabolic phenotyping characteristics? 2) Can we estimate the epigenetic inheritance in such context, and evaluate the potential of parental history on juvenile physiological capacities? Applicants must be highly motivated and have a strong interest in our scientific area (for more information, please visit our website at http://bit.ly/1yVcfmq). A strong background of basic molecular research methodology (knowledge of epigenetic mechanisms would be highly appreciated) is highly recommended. Given the scope of this subject, a good background in physiology and biology of adaptation would be appreciated. Applications should contain a CV, a short statement of your research interests as well as a recommendation letter. Please send your application to email@example.com before May 20, 2015. Jrmy TERRIEN via Gmail
*Call for candidates to apply for an FCT * *We are looking for* candidates to apply for an FCT (Portuguese Foundation for Science and Technology) doctoral fellowship for a mixed Ph.D at the Centre for Functional Ecology of the University of Coimbra (cfe.uc.pt), and Durham University (http://bit.ly/1DDnOu0). *The successful candidate* will be expected to develop a research project to investigate evolution and adaptation of the invasive weed *Centaurea solstitialis* across broad biogeographical ranges. The research involves laboratory and field-based work and involves the interaction with an international network of collaborators from the USA, Chile, Argentina, Australia, Turkey, Spain, and the UK. The candidate is expected to spend half of the time in Portugal and half in the UK. *The candidate* should have a good scientific background, with an interest into reproductive and evolutionary ecology, and genetics of invasive weeds. A good knowledge of the English language, of ecological statistics, or molecular biology is highly desirable. Candidates should be European or permanent residents, and comply with the conditions to be a candidate for the FCT Doctoral Grants ( http://bit.ly/1EfKF3q). *The doctoral fellowship includes* a monthly payment of 980 euros (tax-free), plus an accident insurance and a monthly contribution to the Portuguese Social Security system (full healthcare and retirement, but no unemployment benefits). During stages in the UK, the scholarship will be topped up to 1710 euros monthly to compensate for differences in the cost of living. The scholarship is renewable for up to four years, at the end of which the candidate is expected to defend his or her PhD. dissertation thesis. *A call for fellowship applications* will open during July and be open until May 11, 2015 (http://bit.ly/VgqPC8), but contacts should be made before *May 1*, at 6pm Greenwich time. Interested candidates should send a one page cover letter describing their research interests and experience, a CV (explicitly including average scores for B.Sc. and/or M.Sc.), and the contact information for up to two referees to Daniel Montesinos (firstname.lastname@example.org) and Adrian Brennan (email@example.com). Informal inquiries are welcome. More information about the groups can be found here: http://bit.ly/1EfKF3u http://bit.ly/1DDnRpD http://bit.ly/VgqMWI Daniel Montesinos Researcher (IF) Centre for Functional Ecology DCV - FCTUC - Universidade de Coimbra Calada Martim de Freitas 3000-456 Coimbra, Portugal T: (+351) 239 855 223 (ext. 156) http://bit.ly/1EfKF3u Editor-in-Chief Web Ecology www.web-ecology.net Daniel Montesinos via Gmail
April 22, 2015
Background: The genomic history of prokaryotic organismal lineages is marked by extensive horizontal gene transfer (HGT) between groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated in lineages that have since gone extinct. Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life. Results: Organisms existing as part of a diverse ecosystem at the time of LUCA likely shared genetic material between lineages. If these other lineages persisted for some time, HGT with the descendants of LUCA could have continued into the bacterial and archaeal lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein families support the hypothesis that the molecular common ancestors of the most ancient gene families did not all coincide in space and time. This is most apparent in the evolutionary histories of seryl-tRNA synthetase and threonyl-tRNA synthetase protein families, each containing highly divergent “rare” forms, as well as the sparse phylogenetic distributions of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of glycyl-tRNA synthetase. These topologies and phyletic distributions are consistent with horizontal transfers from ancient, likely extinct branches of the tree of life. Conclusions: Of all the organisms that may have existed at the time of LUCA, by definition only one lineage is survived by known progeny; however, this lineage retains a genomic record of heterogeneous genetic origins. The evolutionary histories of aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting this signal, as they perform primordial biological functions, have undergone several ancient HGT events, and contain many sites with low substitution rates allowing deep phylogenetic reconstruction. We conclude that some aaRS families contain groups that diverge before LUCA. We propose that these ancient gene variants be described by the term “hypnologs”, reflecting their ancient, reticulate origin from a time in life history that has been all but erased.”
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April 21, 2015
Homology is a concept that is fundamental to biological studies, and yet it is difficult to define. Generally, characters are considered to be homologous among organisms if they have been inherited from a common ancestral character.
Homology is thus at the heart of phylogenetics, as it expresses the historical relationships among characters, whereas a phylogeny expresses the historical relationships among taxa (including individuals). Since the relationships among the taxa are based on pre-existing information about the relationships among the characters, homology must be established first. It is for this reason that multiple sequence alignments, for example, are so valuable.
However, homology is a relative concept; that is, it is context sensitive. It only applies locally, to any one level of the hierarchy of character generalization. The classic example of this idea is bird wings versus bat wings. These structures are homologous as forelimbs but not as wings – birds and bats independently modified their forelimbs into wings. So, homology exists at the more general level (forelimbs) but not at the less general level (wings). Forelimbs developed first in evolutionary history (the common ancestor of animals with four legs is ancient), and later these forelimbs were modified in different descendants, with some developing wings, some flippers, and some arms. Wings, flippers and arms are more recent, and are thus less general.
So, we can conceptualize characters as existing at many hierarchical levels of generality, depending on when they developed. We might have (going from specific to general) nucleotides, amino acids, protein domains, proteins, biosynthetic pathways, developmental origins, and anatomy, among many possible conceptual levels. Lower levels in the hierarchy "control" the upper levels, so that nucleotides code for amino acids, domains consist of strings of amino acids, proteins function as enzymes in biosynthesis, and development is controlled by biosynthetic pathways.
A nucleotide insertion and compensatory deletion results in two amino acid substitutions,
so that simultaneously aligning homologous nucleotides and homologous amino acids is no longer possible
The issue is that homology among characters can only be determined within any one hierarchical level. As noted by Fitch (2000): "Life would have been simple if phylogenetic homology necessarily implied structural homology or either of them had necessarily implied functional homology. However, they map onto each other imperfectly".
For example, homology of amino acids among a group of organisms does not necessarily imply that all of their coding nucleotides are homologous (see the figure above) — originally the nucleotides would also have been homologous, but insertions and deletions through time can break the original relationship between the amino acids and their coding nucleotides. So, one cannot always simultaneously align homologous amino acids and homologous nucleotides.
Similarly, homology of two anatomical features does not necessarily imply that their developmental sequences are homologous. This is an issue that the study of evo-devo has made increasingly obvious. That is, sometimes identity of morphological characters is not the result of identity of the sets of genes that control their development (Meyer 1999; Mindell and Meyer 2001; Wagner 2014) — non-homologous genes and gene networks can produce morphological structures that are usually considered to be homologs, and non-homologous structures can express homologous genes.
Developmental biologists therefore often prefer a process-oriented concept of homology, which they call 'biological homology', where homologous features are those sharing a set of developmental constraints (Wagner 1989). Indeed, the terms 'syngeny' (Butler and Saidel 2000) and 'homocracy' (Nielsen and Martinez 2003) have been coined to describe morphological features that are organized through the expression of homologous gene networks, irrespective of whether those features are evolutionarily homologous or convergent.
Reticulation and homology
This idea can be extended to other evolutionary scenarios. The one I am particularly interested in here is the consequence of reticulation. In the situations discussed above the character modifications (ancestral to derived) come from "within" the lineage (traditional ancestor-descendant gene inheritance), but the modifications can also come from "outside", by gene flow.
For example, Andam and Gogarten (2012) have noted that horizontal gene transfer (HGT) can in fact be used to provide information for the concept of a Tree of Life, because a transferred gene can also be regarded as a shared derived character. That is, HGT of a gene into an ancestor forms a synapomorphy for its descendants. This gene may subsequently diversify among those descendants, even following a simple tree-like pattern of descent.
This creates a terminological issue. If diversification occurs, then these genes are homologous in the traditional sense (they are modified descendants of a common ancestral character). However, how do they compare to genes in the descendants of species that did not receive the HGT, and to the genes from which the transfer occurred? In the first case they are not applicable (just as the concept of wings is not applicable to animals with flippers). In the second case our current concept of homology does not apply in any simple sense.
The hierarchical concept of homology is tied to a tree model of evolution. The hierarchical nature of characters results from the nested hierarchy of taxon relationships. If there is no nested hierarchy of taxon relationships then our current concepts of homology are inadequate. We need terms that describe possible reticulate relationships among the characters, not just hierarchical ones.
Thus, along with modifications to the concept of monophyly (see Monophyletic groups in networks ), networks imply that we need modifications to the concept of homology, as well.
It is worth noting that a similar issue applies in other fields that are based on a concept of evolutionary history. For example, in historical linguistics words are considered to descend from ancestral languages and diversify among multiple daughter languages. These words are considered to be cognate (cf. homologous). However, words are also borrowed from unrelated languages, and these are loan words (cf. HGT). Loan words may also diversify among the daughter languages, both in the original language and in the borrowing language.
For example, the Germanic word *rīks (ruler) was borrowed from Celtic *rīxs (king), and it has come down to modern times as German 'Reich', English 'rich' (West Germanic), Swedish 'rike' (North Germanic), and Gothic 'reiks' (East Germanic) (see Wikipedia). This diversification has followed Grimm's Law, a regular phonological change that defines the Germanic family — so, the subsequent development of the loan word allows reconstruction of the evolutionary history, and the descendants are cognate. But are they cognate to the words descended from *rīxs within Celtic?
Andam CP, Gogarten JP (2013) Biased gene transfer contributes to maintaining the Tree of Life. In: Lateral Gene Transfer in Evolution (U Gophna, ed.), pp 263-274. Springer: New York.
Butler AB, Saidel WM (2000) Defining sameness: historical, biological, and generative homology. Bioessays 22: 846-853.
Fitch WM (2000) Homology: a personal view on some of the problems. Trends in Genetics 16: 227-231.
Meyer A (1999) Homology and homoplasy: the retention of genetic programmes. In: Homology (GR Bock, G Cardew, eds), pp. 141-157. Wiley: Chichester.
Mindell DP, Meyer A (2001) Homology evolving. Trends in Ecology and Evolution 16: 434-440.
Nielsen C, Martinez P (2003) Patterns of gene expression: homology or homocracy? Development Genes and Evolution 213: 149-154.
Wagner GP (1989) The biological homology concept. Annual Review of Ecology and Systematics 20: 51-69.
Wagner GP (2014) Homology, Genes, and Evolutionary Innovation. Princeton University Press: Princeton NJ.
Background: The genomes of eukaryotes vary enormously in size, with much of this diversity driven by differences in the abundances of transposable elements (TEs). There is also substantial structural and phylogenetic diversity among TEs, such that they can be classified into distinct classes, superfamilies, and families. Possible relationships between TE diversity (and not just abundance) and genome size have not been investigated to date, though there are reasons to expect either a positive or a negative correlation. This study compares data from 256 species of animals, plants, fungi, and “protists” to determine whether TE diversity at the superfamily level is related to genome size. Results: No simple relationship was found between TE diversity and genome size. There is no significant correlation across all eukaryotes, but there is a positive correlation for genomes below 1,000Mbp and a negative correlation among land plants. No relationships were found across animals or within vertebrates. Some TE superfamilies tend to be present across all major groups of eukaryotes, but there is considerable variance in TE diversity in different taxa. Conclusions: Differences in genome size are thought to arise primarily through accumulation of TEs, but beyond a certain point (~500Mbp), TE diversity does not increase with genome size. Several possible explanations for these complex patterns are discussed, and recommendations to facilitate future analyses are provided.
The Genealogical World of Phylogenetic Networks
BMC Evolutionary Biology
Molecular Biology and Evolution