Comparative Immunology

Comparative Immunology includes an evolutionary approach toimmunity revealing the immune system as widespread and necessaryfor survival. Although many immunology textbooks and coursesare often oriented solely toward medicine orallied professions,comparative immunology is a unique beginning for advanced undergraduatestudents of biology, zoology, and immunology. A more biologicapproach to immune competence causes mammalian immunologiststo view comparative immunology as an introduction to numerousectothermic vertebrates and invertebrates. Such exotic animalsare sources of meaningful facts important for anyone viewingsignificant breakthroughs in immunology in phylogenetic perspective.Animals preserve their unique individuality by distinguishingbetween self and non-self to protect against infection and possibleextinction. The earliest beginnings of immune reactions arebest exemplified among the invertebrates by recognition, phagocytosis,graft rejection accompanied by specificity and weak memory,and the induction of agglutinins and lectins. Although vertebratesshare these same responses, the main differences include moreextensive evidence of specificity and memory and the uniquecapacity to synthesize immunoglobulins. Acknowledging the problemof recognition as the common basis for the immune response,certain members of the Ig superfamily, notably Thy-1 and ß₂-microglobulin,will help our attempts to define evolutionary pressures thatcaused the development of immunity.     

Comparative immunology

Comparative immunology, derived from zoology and immunology,examines immune systems during evolution. We now know that invertebrateshave molecules that share homology with some of those in vertebrates.Acquired immunity first appeared in the vertebrates, but beforethen innate immune systems had been successfully defending invertebratesand plants against microbial infections for hundreds of millionsof years. The germline-encoded receptors of innate systems arerelatively limited in diversity and unable to make fine distinctionsbetween closely related structures. Nevertheless, they can recognizecertain chemical features shared by groups of microorganisms(e.g., pattern recognition receptors) but not by the host, suchas lipopolysaccharide of Gram-negative bacterial cell walls.This capability enables innate immunity to detect the presenceof an infection, if not the precise cause—it is thus abiological rather than a structural distinction. Because ofits evolutionary success, innate immunity is no longer consideredprimarily a stopgap measure, a temporary expedient for hostdefense. It no longer seems to matter that there is an absenceof genetic-recombination mechanisms to generate neither specificitynor ‘memory’, because first and second exposuresto a microbial substance elicit similar responses. Comparativeimmunology has enriched the parent field of immunology.     

Phylogenetic and compositional diversity are governed by different rules: a study of fleas parasitic on small mammals in four biogeographic realms

We studied patterns of phylogenetic and compositional diversity of fleas parasitic on small mammals and asked whether these patterns are affected by environmental variation or evolutionary/historical processes. We considered environmental variation via both off‐host (air temperature, precipitation, the amount of green vegetation, latitude) and host‐associated (phylogenetic and species composition) environments. The indicators of evolutionary/historical processes were phylogenetic and compositional uniqueness estimated via phylogenetic or compositional, respectively, β‐diversity of either fleas or hosts. We found that phylogenetic uniqueness of flea assemblages was the main predictor of their phylogenetic diversity in all realms. In addition, host phylogenetic diversity and uniqueness played also some role in the Palearctic, whereas the effect of the off‐host environment was either extremely weak or absent. Compositional diversity of fleas was consistently affected by compositional diversity of hosts in all realms except the Neotropics. The effect of the off‐host environment on compositional flea diversity was substantial in all realms except the Palearctic. No effect of latitude on either metric of flea diversity was found. We conclude that phylogenetic diversity of fleas is driven mainly by evolutionary/historical processes, whereas drivers of their compositional diversity are associated with current ecological conditions.     

Phylogeny, ecology, and the coupling of comparative and experimental approaches

Recent progress in the development of phylogenetic methods and access to molecular phylogenies has made comparative biology more popular than ever before. However, determining cause and effect in phylogenetic comparative studies is inherently difficult without experimentation and evolutionary replication. Here, we provide a roadmap for linking comparative phylogenetic patterns with ecological experiments to test causal hypotheses across ecological and evolutionary scales. As examples, we consider five cornerstones of ecological and evolutionary research: tests of adaptation, tradeoffs and synergisms among traits, coevolution due to species interactions, trait influences on lineage diversification, and community assembly and composition. Although several scenarios can result in a lack of concordance between historical patterns and contemporary experiments, we argue that the coupling of phylogenetic and experimental methods is an increasingly revealing approach to hypothesis testing in evolutionary ecology.     

Evolution of adaptive immunity

The current state of the problem of emergence and evolution of adaptive immunity in different taxonomic groups of animals is analyzed. Special attention is given to the emergence and phylogenetic development of the lymphocyte, the key component of immune response, as well as to the evolutionary development of T- and B-cell immune systems, adaptive immune responses and their molecular regulators (cytokines), and antigen-recognition structures.     

Curious parallels and curious connections--phylogenetic thinking in biology and historical linguistics

In The Descent of Man (1871), Darwin observed "curious parallels" between the processes of biological and linguistic evolution. These parallels mean that evolutionary biologists and historical linguists seek answers to similar questions and face similar problems. As a result, the theory and methodology of the two disciplines have evolved in remarkably similar ways. In addition to Darwin's curious parallels of process, there are a number of equally curious parallels and connections between the development of methods in biology and historical linguistics. Here we briefly review the parallels between biological and linguistic evolution and contrast the historical development of phylogenetic methods in the two disciplines. We then look at a number of recent studies that have applied phylogenetic methods to language data and outline some current problems shared by the two fields.     

Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group,the Neotropical Pristimantis leaf litter frogs

The Neotropical leaf litter frog genus Pristimantis is very species-rich, with 526 species described to date, but the full extent of its diversity is much higher and remains unknown. This study explores the phylogenetic processes and resulting evolutionary patterns of diversification in Pristimantis. Given the well-recognised failure of morphology- and community-based species groups to describe diversity within the genus, we apply a new test for the presence and phylogenetic distribution of higher evolutionary units. We developed a phylogeny based on 260 individuals encompassing 149 Pristimantis presumed species, sampled at mitochondrial and nuclear genes (3718 base pair alignment), combining new and available sequence data. Our phylogeny broadly agrees with previous studies, both in topology and age estimates, with the origin of Pristimantis at 28.97 (95% HDP =21.59 – 37.33) million years ago (MYA). New taxa that we add to the genus, which had not previously been included in Pristimantis phylogenies, suggest considerable diversity remains to be described. We assessed patterns of lineage origin and recovered 14 most likely (95% CI: 13–19) phylogenetic clusters or higher evolutionary significant units (hESUs) within Pristimantis. Diversification rates decrease towards the present following a density-dependent pattern for Pristimantis overall and for most hESU clusters, reflecting historical evolutionary radiation. The timing of diversification suggests that geological events in the Miocene, such as Andes orogenesis and Pebas system formation and drainage, may have had a direct or indirect impact on the evolution of Pristimantis and thus contributed to the origins of evolutionary independent phylogenetic clusters.     

FACTORS DETERMINING THE ACCURACY OF CLADOGRAM ESTIMATION: EVALUATION USING COMPUTER SIMULATION

We developed a simulation model of phylogenesis with which we generated a large number of phylogenies and associated data matrices. We examined the characteristics of these and evaluated the success of three taxonomic methods (Wagner parsimony, character compatibility, and UPGMA clustering) as estimators of phylogeny, paying particular attention to the consequences of changes in certain evolutionary assumptions: relative rate of evolution in three different evolutionary contexts (phyletic, parent lineage, and daughter lineage); relative rate of evolution in different directions (novel forward, convergent forward, or reverse); variation of evolutionary rates; and topology of the phylogenetic tree. Except for variation of evolutionary rates, all the evolutionary parameters that we controlled had significant effects on accuracy of phylogenetic reconstructions. Unexpectedly, the topology of the phylogeny was the most important single factor affecting accuracy; some phylogenies are more readily estimated than others for simply historical reasons. We conclude that none of the three estimation methods is very accurate, that the differences in accuracy among them are rather small, and that historical effects (the branching pattern of a phylogeny) may outweigh biological effects in determining the accuracy with which a phylogeny can be reconstructed.     

Realism in systematics through biogeographical consilience

There is an overlooked gap between any phylogenetic hypothesis and the natural world shaped by historical evolutionary processes, since the main concern during phylogenetic analyses is solely the search for congruence among characters under a defined criterion. Given a scientific realistic view, however, phylogenetic hypotheses are scientific theories that try to depict the historical series of cladogenetic events among biological entities. In this sense, the challenge is to establish a form of measuring the degree of truthfulness of our phylogenetic hypotheses. Here, we advocate the use of consilient biogeographical hypotheses to recognize the biological meaning of a phylogenetic inference apart from its instrumentalist value. Our proposal is based on the assumption that robust biogeographical hypotheses allows us to be close to the real evolutionary history of taxa. © The Willi Hennig Society 2011.     

Environmental and topographic drivers of amphibian phylogenetic diversity and endemism in the Iberian Peninsula

Understanding the ecological and evolutionary processes driving biodiversity patterns and allowing their persistence is of utmost importance. Many hypotheses have been proposed to explain spatial diversity patterns, including water-energy availability, habitat heterogeneity, and historical climatic refugia. The main goal of this study is to identify if general spatial drivers of species diversity patterns of phylogenetic diversity (PD) and phylogenetic endemism (PE) at the global scale are also predictive of PD and PE at regional scales, using Iberian amphibians as a case study. Our main hypothesis assumes that topography along with contemporary and historical climate are drivers of phylogenetic diversity and endemism, but that the strength of these predictors may be weaker at the regional scale than it tends to be at the global scale. We mapped spatial patterns of Iberian amphibians' phylogenetic diversity and endemism, using previously published phylogenetic and distribution data. Furthermore, we compiled spatial data on topographic and climatic variables related to the water-energy availability, topography, and historical climatic instability hypotheses. To test our hypotheses, we used Spatial Autoregressive Models and selected the best model to explain diversity patterns based on Akaike Information Criterion. Our results show that, out of the variables tested in our study, water-energy availability and historical climate instability are the most important drivers of amphibian diversity in Iberia. However, as predicted, the strength of these predictors in our case study is weaker than it tends to be at global scales. Thus, additional drivers should also be investigated and we suggest caution when interpreting these predictors as surrogates for different components of diversity.     

I. I. Mechnikoff's contribution to immunology

I. I. Mechnikoff's contribution to various aspects of immunology is evaluated. The 25 years' struggle of this scientist for the existence of phagocytosis theory is briefly described. Works of I. I. Mechnikoff dealing with several factors of humoral immunity and cytotoxins are reviewed. The significance of I. I. Mechnikoff's studies providing analysis of immune processes in the phylogenetic sense as well as his ideas about the nervous system role in immunity processes is stressed.     

The road less traveled: Phylogenetic perspectives in primatology

Interest in phylogeny is increasing in many areas of evolutionary biology. One area of evolutionary anthropology that has not yet fully embraced this growth in phylogenetic thinking, however, is the study of primate behavior and ecology.¹ The predominant framework for behavioral studies of primates over the last three decades has been socioecological. The goals have been to identify broad correlations between species' behaviors and current environmental conditions. As such, the socioecological approach has been largely nonhistorical, taking little account of phylogeny. In contrast, phylogenetic approaches view the behavior of contemporary taxa within an explicitly historical framework. Although socioecology has proven extremely productive, there are many reasons to think that research in primatology could be profitably supplemented by a phylogenetic perspective.^2,3     

Phylogeny and evo-devo: characters, homology, and the historical analysis of the evolution of development

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.     

Adaptations and history

The historical definition of adaptations has come into wide use as comparative biologists have applied methods of phylogenetic analysis to a variety of evolutionary problems. Here we point out a number of difficulties in applying historical methods to the study of adaptation, especially in cases where a trait has arisen but once. In particular, the potential complexity of the genetic correlations among phenotypic traits, performance variables and fitness makes inferring past patterns of selection from comparative data difficult. A given pattern of character distribution may support many alternative hypotheses of mechanism. While phylogenetic data are limited in their ability to reveal evolutionary mechanisms, they have always been an important source of adaptive hypotheses and will continue to be so.     

HISTORICAL VERSUS SELECTIONIST EXPLANATIONS IN EVOLUTIONARY BIOLOGY

Abstract— Evolutionary changes require historical explanations, yet these are limited by the evolutionary processes we entertain and investigate. Using phylogenetic analysis, adaptation and natural selection can be tested as historical claims, but this is appropriate only in those special cases where change follows the scheme of one character-one function, singled out in new environmental circumstances. Systematic treatment of the evolutionary origin of characters (in particular, origin through ecological and developmental flexibility) lies outside the scope of selectionist explanations. Structural hypotheses about regularities in the directions of change, also analyzed phylogenetically, expand the scope of historical explanation to include the origin of characters, yet retain the view of organisms as passive and constrained objects of evolutionary change. Historical biology needs to encompass both the active responses of organisms and the construction by organisms of their own environments. For this to be realized will require changes in the concepts and practices of evolutionary biology, including a re-examination of the Lamarckian theme that the active responses of organisms have evolutionary significance—the rarity of individual-to-individual transmission of "acquired" characters does not disprove the possibility of their frequency increasing in a population.     

Phylogenetic perspective on ecological niche evolution in american blackbirds (Family Icteridae)

Analysis of ecological characters on phylogenetic frameworks has only recently appeared in the literature, with several studies addressing patterns of niche evolution, generally over relatively recent time frames. In the present study, we examined patterns of niche evolution for a broad radiation of American blackbird species (Family Icteridae), exploring more deeply into phylogenetic history. Within each of three major blackbird lineages, overlap of ecological niches in principal components analysis transformed environmental space varied from high to none. Comparative phylogenetic analyses of ecological niche characteristics showed a general pattern of niche conservatism over evolutionary time, with differing degrees of innovation among lineages. Although blackbird niches were evolutionarily plastic over differing periods of time, they diverged within a limited set of ecological possibilities, resulting in examples of niche convergence among extant blackbird species. Hence, an understanding of the patterns of ecological niche evolution on broad phylogenetic scales sets the stage for framing questions of evolutionary causation, historical biogeography, and ancestral ecological characteristics more appropriately.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 869–878.     

Mosaics of convergences and noise in morphological phylogenies: what's in a viverrid-like carnivoran?

Adaptive convergence in morphological characters has not been thoroughly investigated, and the processes by which phylogenetic relationships may be misled by morphological convergence remains unclear. We undertook a case study on the morphological evolution of viverrid-like feliformians (Nandinia, Cryptoprocta, Fossa, Eupleres, Prionodon) and built the largest morphological matrix concerning the suborder Feliformia to date. A total of 349 characters grouped into four anatomical partitions were used for all species of Viverridae and viverrid-like taxa plus representatives of the Felidae, Hyaenidae, Herpestidae, and one Malagasy mongoose. Recent molecular phylogenetic analyses suggest that viverrid-like morphotypes appeared independently at least three times during feliformian evolution. We thus used a synthetic molecular tree to assess morphological evolutionary patterns characterizing the viverrid-like taxa. We examined phylogenetic signal, convergence and noise in morphological characters using (a) tree-length distribution (g1), (b) partitioned Bremer support, (c) RI values and their distribution, (d) respective contributions of diagnostic synapomorphies at the nodes for each partition, (e) patterns of shared convergences among viverrid-like taxa and other feliformian lineages, (f) tree-length differences among alternative hypotheses, and (g) the successive removal of convergent character states from the original matrix. In addition, the lability of complex morphological structures was assessed by mapping them onto the synthetic molecular tree. The unconstrained morphological analysis yielded phylogenetic groupings that closely reflected traditional classification. The use of a synthetic molecular tree (constraint) combined with our thorough morphological investigations revealed the mosaics of convergences likely to have contributed to part of the historical uncertainty over viverrid classification. It also showed that complex morphological structures could be subjected to reversible evolutionary trends. The morphological matrix proved useful in characterizing several feliformian clades with diagnostic synapomorphies. These results support the removal from the traditionally held Viverridae of several viverrid-like taxa into three distinct families: Nandiniidae (Nandinia), Prionodontidae (Prionodon), and the newly defined Eupleridae (including Cryptoprocta, Fossa, Eupleres plus all "mongoose-like" Malagasy taxa). No clearly "phylogenetically misleading" data subsets could be identified, and the great majority of morphological convergences appeared to be nonadaptive. The multiple approaches used in this study revealed that the most disruptive element with regards to morphological phylogenetic reconstruction was noise, which blured the expression of phylogenetic signal. This study demonstrates the crucial need to consider independent (molecular) phylogenies in order to produce reliable evolutionary hypotheses and should promote a new approach to the definition of morphological characters in mammals. [Constrained analysis; convergence; evolutionary scenario; Feliformia; morphology; noise; phylogenetic signal; phylogeny; Viverridae.].     

A phylogenetic perspective on the evolutionary processes of floristic assemblages within a biodiversity hotspot in eastern Asia

Abstract How to maximize the conservation of biodiversity is critical for conservation planning, particularly given rapid habitat loss and global climatic change. The importance of preserving phylogenetic diversity has gained recognition due to its ability to identify some influences of evolutionary history on contemporary patterns of species assemblages that traditional taxonomic richness measures cannot identify. In this study, we evaluate the relationship between taxonomic richness and phylogenetic diversity of angiosperms at genus and species levels and explore the spatial pattern of the residuals of this relationship. We then incorporate data on historical biogeography to understand the process that shaped contemporary floristic assemblages in a global biodiversity hotspot, Yunnan Province, located in southwestern China. We identified a strong correlation between phylogenetic diversity residuals and the biogeographic affinity of the lineages in the extant Yunnan angiosperm flora. Phylogenetic diversity is well correlated with taxonomic richness at both genus and species levels between floras in Yunnan, where two diversity centers of phylogenetic diversity were identified (the northwestern center and the southern center). The northwestern center, with lower phylogenetic diversity than expected based on taxonomic richness, is rich in temperate‐affinity lineages and signifies an area of rapid speciation. The southern center, with higher phylogenetic diversity than predicted by taxonomic richness, contains a higher proportion of lineages with tropical affinity and seems to have experienced high immigration rates. Our results highlight that maximizing phylogenetic diversity with historical interpretation can provide valuable insights into the floristic assemblage of a region and better‐informed decisions can be made to ensure different stages of a region's evolutionary history are preserved.     

Historical range expansion determines the phylogenetic diversity introduced during contemporary species invasion

For a species rapidly expanding its geographic range, such as during biological invasion, most alleles in the introduced range will have their evolutionary origins in the native range. Yet, the way in which historical processes occurring over evolutionary time in the native range contribute to the diversity sampled during contemporary invasion is largely unknown. We used chloroplast DNA (cpDNA) gene genealogies and coalescent methods to study two congeneric plants, Silene latifolia and S. vulgaris. We examined how phylogenetic diversity was shaped by demographic growth and historical range expansions in the native European range, and how this history affected the diversity sampled during their recent invasion of North America. Genealogies from both species depart from neutrality, likely as a result of demographic expansion in the ancestral range, the timing of which corresponds to shortly after each species originated. However, the species differ in the spatial distribution of cpDNA lineages across the native range. Silene latifolia shows a highly significant phylogeographic structure that most likely reflects different avenues of the post-glacial expansion into northern Europe from Mediterranean refugia. By contrast, cpDNA lineages in S. vulgaris have been widely scattered across Europe during, or since, the most recent post-glacial expansion. These different evolutionary histories resulted in dramatic differences in how phylogenetic diversity was sampled during invasion of North America. In S. latifolia, relatively few, discrete invasion events from a structured native range resulted in a rather severe genetic bottleneck, but also opportunities for admixture among previously isolated lineages. In S. vulgaris, lack of genetic structure was accompanied by more representative sampling of phylogenetic diversity during invasion, and reduced potential for admixture. Our results provide clear insights into how historical processes may feed forward to influence the phylogenetic diversity of species invading new geographic ranges.     

谈系统发生树建立的分子标准

随着进化生物学以及生物信息学的发展 ,研究不同物种间进化关系的方法也有了新的进展。其中分子进化方法使得系统发生树的建立更加简便和精确。几种系统发生树的建树方法及相关分子标准目前比较流行。。