Multiple losses of sex within a single genus of Microsporidia

Background  

Most asexual eukaryotic lineages have arisen recently from sexual ancestors and contain few ecologically distinct species, providing evidence for long-term advantages of sex. Ancient asexual lineages provide rare exceptions to this rule and so can yield valuable information relating to the evolutionary forces underlying the maintenance of sex. Microsporidia are parasitic, unicellular fungi. They include many asexual species which have traditionally been grouped together into large, presumably ancient taxonomic groups. However, these putative ancient asexual lineages have been identified on the basis of morphology, life cycles and small subunit ribosomal RNA (16S rRNA) gene sequences, all of which hold questionable value in accurately inferring phylogenetic relationships among microsporidia.     

Phylogenetic taxonomy in Drosophila: Problems and prospects

The genus Drosophila is one of the best-studied model systems in modern biology, with twelve fully sequenced genomes available. In spite of the large number of genetic and genomic resources, little is known concerning the phylogenetic relationships, ecology, and evolutionary history of all but a few species. Recent molecular systematic studies have shown that this genus is comprised of at least three independent lineages and that several other genera are actually embedded within Drosophila. This genus accounts for over 2000 described, and many more undescribed, species. While some Drosophila researchers are advocating dividing this genus into three or more separate genera, others favor maintaining Drosophila as a single large genus. With the recent sequencing of the genomes of multiple Drosophila species and their expanding use in comparative biology, it is critical that the Drosophila research community understands the taxonomic framework underlying the naming and relationships of these species. The subdivision of this genus has significant biological implications, ranging from the accurate annotation of single genes to understanding how ecological adaptations have occurred over the history of the group.     

Integrating data‐deficient species in analyses of evolutionary history loss

There is an increasing interest in measuring loss of phylogenetic diversity and evolutionary distinctiveness which together depict the evolutionary history of conservation interest. Those losses are assessed through the evolutionary relationships between species and species threat status or extinction probabilities. Yet, available information is not always sufficient to quantify the threat status of species that are then classified as data deficient. Data‐deficient species are a crucial issue as they cause incomplete assessments of the loss of phylogenetic diversity and evolutionary distinctiveness. We aimed to explore the potential bias caused by data‐deficient species in estimating four widely used indices: HEDGE, EDGE, PDloss, and Expected PDloss. Second, we tested four different widely applicable and multitaxa imputation methods and their potential to minimize the bias for those four indices. Two methods are based on a best‐ vs. worst‐case extinction scenarios, one is based on the frequency distribution of threat status within a taxonomic group and one is based on correlates of extinction risks. We showed that data‐deficient species led to important bias in predictions of evolutionary history loss (especially high underestimation when they were removed). This issue was particularly important when data‐deficient species tended to be clustered in the tree of life. The imputation method based on correlates of extinction risks, especially geographic range size, had the best performance and enabled us to improve risk assessments. Solving threat status of DD species can fundamentally change our understanding of loss of phylogenetic diversity. We found that this loss could be substantially higher than previously found in amphibians, squamate reptiles, and carnivores. We also identified species that are of high priority for the conservation of evolutionary distinctiveness.     

Phylogenetic relationships of the globally distributed freshwater prawn genus Macrobrachium (Crustacea: Decapoda: Palaemonidae): biogeography, taxonomy and the convergent evolution of abbreviated larval development

There has hitherto been little research into evolutionary and taxonomic relationships amongst species of the freshwater prawn genus Macrobrachium Bate across its global distribution. Previous work by the authors demonstrated that the endemic Australian species did not evolve from a single ancestral lineage. To examine whether other regional Macrobrachium faunas also reflect this pattern of multiple origins, the phylogeny of 30 Macrobrachium species from Asia, Central/South America and Australia was inferred from mitochondrial 16S rRNA sequences. Phylogenetic relationships demonstrate that, despite some evidence for regional diversification, Australia, Asia and South America clearly contain Macrobrachium species that do not share a common ancestry, suggesting that large-scale dispersal has been a major feature of the evolutionary history of the genus. The evolution of abbreviated larval development (ALD), associated with the transition from an estuarine into a purely freshwater lifecycle, was also mapped onto the phylogeny and was shown to be a relatively homoplasious trait and not taxonomically informative. Other taxonomic issues, as well as the evolutionary origins of Macrobrachium , are also discussed.     

Extensive intraspecific chloroplast DNA (cpDNA) variation in the alpine Draba aizoides L. (Brassicaceae): haplotype relationships and population structure

Chloroplast DNA (cpDNA) sequence variation is currently the most widely used tool for the inference of phylogenetic relationships among plants at all taxonomic levels. Generally, noncoding regions tend to evolve faster than coding sequences and have recently been applied to the study of phylogenetic relationships among closely related taxa. An implicit assumption of many of these studies is that intraspecific cpDNA variation is either absent or low and therefore will not interfere with the reconstruction of interspecific relationships. A survey of cpDNA sequence variation in the common alpine plant species Draba aizoides L. was undertaken to assess levels of intraspecific cpDNA sequence variation. These levels were compared to levels of interspecific sequence divergence between D. aizoides and related alpine Draba species. Intraspecific cpDNA sequence divergence was extensive in D. aizoides, and intraspecific differences were often larger than interspecific differences. cpDNA haplotype relationships were explored using a maximum parsimony approach and minimum-spanning networks. Results from both methods were largely congruent but comparisons provided interesting insights into the presumed evolutionary history of cpDNA haplotypes. A combined effect of cpDNA introgression and complex lineage sorting was inferred to explain the pattern of cpDNA variation found in D. aizoides. Our results suggest that intraspecific cpDNA variation can be extensive and that intraspecific variation needs to be taken into account when inferring phylogenetic relationships among closely related taxa.     

ISLAND BIOGEOGRAPHY AND PALAEOBIOLOGY: IN SEARCH FOR EVOLUTIONARY EQUILIBRIA

1. The concept of evolutionary equilibrium has been derived from the theory of island biogeography via an ecological rationale for increase in species extinction rate and decrease in speciation rate with increasing diversity of the system.
2. This concept is theoretically plausible at the species level and at a regional scale but, in spite of several empirical tests in the fossil record, it has thus far remained unsupported by empirical evidence. In order to test it conclusively, one has to analyze not only the pattern of species number through time but also its relationship to speciation and species extinction rates; independent evidence for perturbations must also be available.
3. The concept of evolutionary equilibrium at the global scale must be extrapolated over higher levels of taxonomic hierarchy, for reliable species-level data are unavailable at this scale. A theoretical justification for this concept cannot, then, be derived from the theory of island biogeography.
4. The rates of family extinction and origination in the Phanerozoic show no evidence for diversity-dependence, which undermines most quantitative models of biotic diversification based on the concept of global evolutionary equilibrium. Rigorous testing of these models cannot be done at the present state of knowledge because of the uncertainty about the empirical pattern (sampling and taxonomic biases, absolute time scale).     

Evolutionary and organismic constraints on the relationship between spacer length and environmental conditions in clonal plants

The rate of lateral spread of clonal plants is considered a plastic trait that responds directly to environmental conditions. However, this response is likely constrained by evolutionary history and other species attributes. Here we ask how the relationships between lateral spread and the distribution of herbaceous plant species in different environments are influenced by the type of spacer (epigeogenous versus hypogeogenous rhizome), its persistence (integrator versus splitter), and the height and phylogeny of the plant. Analysis of spacer length of 367 species from temperate to arctic Europe revealed that other plant characteristics modulate the relationship between spacer length and environmental conditions. While plants with epigeogenous rhizomes, which have usually shorter spacers than hypogeogenous rhizomes, were associated with illuminated habitats, plants with hypogeogenous rhizomes were associated with warm habitats. These relationships were also shown within the specific rhizome type, as within the group of species with epigeogenous rhizomes, those having short spacers were associated with more light. The trend toward long spacers in warm environment was detected within both epigeogenous and hypogeogenous rhizome bearing species. Splitters were found to be associated with wet, nutrient rich habitats irrespective of rhizome type. When plant height was accounted for by using the ratio of spacer length to plant height (L:H) instead of absolute spacer length, no relationship with environmental variables was found until phylogenetic relationships among the species were taken into account. This implies that overall variability in L:H ratio in the dataset masked trends common for different taxonomic groups. Future comparative studies relating particular clonal growth forms or individual traits to environmental conditions should consider the constraints arising from other growth characteristics and evolutionary history of the subject species.     

A consensus tree approach for reconstructing human evolutionary history and detecting population substructure

The random accumulation of variations in the human genome over time implicitly encodes a history of how human populations have arisen, dispersed, and intermixed since we emerged as a species. Reconstructing that history is a challenging computational and statistical problem but has important applications both to basic research and to the discovery of genotype-phenotype correlations. We present a novel approach to inferring human evolutionary history from genetic variation data. We use the idea of consensus trees, a technique generally used to reconcile species trees from divergent gene trees, adapting it to the problem of finding robust relationships within a set of intraspecies phylogenies derived from local regions of the genome. Validation on both simulated and real data shows the method to be effective in recapitulating known true structure of the data closely matching our best current understanding of human evolutionary history. Additional comparison with results of leading methods for the problem of population substructure assignment verifies that our method provides comparable accuracy in identifying meaningful population subgroups in addition to inferring relationships among them. The consensus tree approach thus provides a promising new model for the robust inference of substructure and ancestry from large-scale genetic variation data.     

Regional variation in the historical components of global avian species richness

Aim Using a global data base of the distribution of extant bird species, we examine the evidence for spatial variation in the evolutionary origins of contemporary avian diversity. In particular, we assess the possible role of the timing of mountain uplift in promoting diversification in different regions. Location Global. Methods We mapped the distribution of avian richness at four taxonomic levels on an equal‐area 1° grid. We examined the relationships between richness at successive taxonomic levels (e.g. species richness vs. genus richness). We mapped the residuals from linear regressions of these relationships to identify areas that are exceptional in the number of lower taxa relative to the number of higher taxa. We use generalized least squares models to test the influence of elevation range and temperature on lower‐taxon richness relative to higher‐taxon richness. Results Peaks of species richness in the Neotropics were congruent with patterns of generic richness, whilst peaks in Australia and the Himalayas were congruent with patterns of both genus and family richness. Hotspots in the Afrotropics did not reflect higher‐taxon patterns. Regional differences in the relationship between richness at successive taxonomic levels revealed variation in patterns of taxon co‐occurrence. Species and genus co‐occurrence was positively associated with elevational range across much of the world. Taxon occurrence in the Neotropics was associated with a positive interaction between elevational range and temperature. Conclusions These results demonstrate that contemporary patterns of richness show different associations with higher‐taxon richness in different regions, which implies that the timing of historical effects on these contemporary patterns varies across regions. We suggest that this is due to dispersal limitation and phylogenetic constraints on physiological tolerance limits promoting diversification. We speculate that diversification rates respond to long‐term changes in the Earth's topography, and that the role of tropical mountain ranges is implicated as a correlate of contemporary diversity, and a source of diversification across avian evolutionary history.     

A review of the relationships between human population density and biodiversity

To explore the impacts of increasing human numbers on nature, many studies have examined relationships between human population density (HPD) and biodiversity change. The implicit assumption in many of these studies is that as population density increases so does the threat to biodiversity. The implications of this assumption are compounded by recent research showing that species richness for many taxonomic groups is often highest in areas with high HPD. If increasing HPD is a threat to conservation, this threat may be magnified owing to the spatial congruence between people and species richness. Here, I review the relationships between HPD and measures of biodiversity status focussing in particular on evidence for the spatial congruence between people and species richness and the threat that increasing HPD may pose to biodiversity conservation. The review is split into two major sections: (i) a quantitative assessment of 85 studies covering 401 analyses, including meta-analyses on discrete relationships; and (ii) a discussion of the implications of the quantitative analyses and major issues raised in the literature. Our understanding of the relationships between HPD and biodiversity is skewed by geographic and taxonomic biases in the literature. Most research has been conducted in the Northern Hemisphere and focussed primarily on birds and mammals, largely ignoring relationships with other taxonomic groups. A total of 127 analyses compared HPD with the species richness of particular taxonomic groups. A meta-analysis of these results found a significant positive population correlation indicating that, on average, species-rich regions and human settlements co-occur. However, there was substantial unexplained heterogeneity in these data. Some of this heterogeneity was explained by the size of the sampling unit used by researchers - as this increased so did the strength of the correlation between HPD and species richness. The most convincing result for a taxonomic group was a significant positive population correlation between HPD and bird species richness. Significant positive population correlations were also found for HPD versus the richness of threatened and geographically restricted species. Hence, there is reasonably good evidence for spatial congruence between people and species-rich regions. The reasons for this congruence are only just beginning to be explored, but key mutual drivers appear to include available energy and elevation. The evidence for increasing HPD as a threat to conservation was weak, owing primarily to the extreme heterogeneity in the approaches used to address this issue. There was some suggestion of a positive relationship between HPD and species extinction, but this result should be interpreted with caution owing to the wide diversity of approaches used to measure extinction. Identifying strong links between human development and species extinction is hampered in part by the difficulty of recording extinction events. The most convincing indication of the negative impact of increasing HPD was a significant negative population correlation between density and the size of protected areas. The magnitude and implications of spatial congruence between people and biodiversity are now being explored using the principles of complementarity and irreplaceability. Human development as a threat to conservation is usually assessed within a complex, interdisciplinary modelling framework, although population size is still considered a key factor. Future population growth and expansion of human settlements will present increasing challenges for conserving species-rich regions and maximising the benefits humans gain from nature.     

The phylogeny of Old World monkeys

The living Old World monkeys, family Cercopithecidae, are the most successful group of nonhuman primates alive today. Overall, they account for over one quarter of the extant genera of primates and approximately 40% of the species. They have an extensive fossil record extending back to the early and middle Miocene of Africa.^1,2 Despite this specific diversity and a long evolutionary history, it is commonly argued that the group is relatively uniform in both its skeletal³ and dental⁴ anatomy, suggesting that much of the current taxonomic diversity is a relatively recent phenomenon. In such a species group, it is perhaps not surprising that the taxonomy of Old World monkeys is subject to many differing classifications. Thus, in recent years, authors have recognized as few as 10 and as many as 22 different genera within the family. Although some of this greater-than-two-fold difference in the number of genera can be attributed to the “splitting” versus “lumping” philosophies of different researchers, much of it is based on major disagreements over phylogenetic relationships. Recent studies of the genetics and chromosomes of this group have illuminated Old World monkey phylogeny in many ways. Some of these studies have resolved longstanding debates based on morphological data; others have revealed phylogenetic relationships that morphologists had never suspected.     

Evolutionary theory and systematics: relationships between process and patterns

The relevance of the Modern Evolutionary Synthesis to the foundations of taxonomy (the construction of groups, both taxa and phyla) is reexamined. The nondimensional biological species concept, and not the multidimensional, taxonomic, species notion which is based on it, represents a culmination of an evolutionary understanding. It demonstrates how established evolutionary mechanisms acting on populations of sexually reproducing organisms provide the testable ontological basis of the species category. We question the ontology and epistemology of the phylogenetic or evolutionary species concept, and find it to be a fundamentally untenable one. We argue that at best, the phylogenetic species is a taxonomic species notion which is not a theoretical concept, and therefore should not serve as foundation for taxonomic theory in general, phylogenetics, and macroevolutionary reconstruction in particular. Although both evolutionary systematists and cladists are phylogeneticists, the reconstruction of the history of life is fundamentally different in these two approaches. We maintain that all method, including taxonomic ones, must fall out of well corroborated theory. In the case of taxonomic methodology the theoretical base must be evolutionary. The axiomatic assumptions that all phena, living and fossil, must be holophyletic taxa (species, and above), resulting from splitting events, and subsequently that evaluation of evolutionary change must be based on a taxic perspective codified by the Hennig ian taxonomic species notion, are not testable premises. We discuss the relationship between some biologically, and therefore taxonomically, significant patterns in nature, and the process dependence of these patterns. Process-free establishment of deductively tested “genealogies” is a contradiction in terms; it is impossible to “recover” phylogenetic patterns without the investment of causal and processual explanations of characters to establish well tested taxonomic properties of these (such as homologies, apomorphies, synapomorphies, or transformation series). Phylogenies of either characters or of taxa are historical-narrative explanations (H-N Es), based on both inductively formulated hypotheses and tested against objective, empirical evidence. We further discuss why construction of a “genealogy”, the alleged framework for “evolutionary reconstruction”, based on a taxic, cladistic outgroup comparison and a posteriori weighting of characters is circular. We define how the procedure called null-group comparison leads to the noncircular testing of the taxonomic properties of characters against which the group phylogenies must be tested. This is the only valid rooting procedure for either character or taxon evolution. While the Hennig -principle is obviously a sound deduction from the theory of descent, cladistic reconstruction of evolutionary history itself lacks a valid methodology for testing transformation hypotheses of both characters and species. We discuss why the paleontological method is part of comparative biology with a critical time dimension ana why we believe that an “ontogenetic method” is not valid. In our view, a merger of exclusive (causal and interactive, but best described as levels of organization) and inclusive (classificatory) hierarchies has not been accomplished by a taxic scheme of evolution advocated by some. Transformational change by its very nature is not classifiable in an inclusive hierarchy, and therefore no classification can fully reflect the causal and interactive chains of events constituting phylogeny, without ignoring and contradicting large areas of corroborated evolutionary theory. Attempts to equate progressive evolutionary change with taxic schemes by Haeckel were fundamentally flawed. His ideas found 19th century expression in a taxic perception of the evolutionary process (“phylogenesis”), a merger of typology, hierarchic and taxic notions of progress, all rooted in an ontogenetic view of phylogeny. The modern schemes of genealogical hierarchies, based on punctuation and a notion of “species” individuality, have yet to demonstrate that they hold promise beyond the Haeckel ian view of progressive evolution.     

A phylogenomic perspective on diversity,hybridization and evolutionary affinities in the stickleback genus Pungitius

Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome‐anchored single nucleotide polymorphisms and de novo assembled RAD‐tag loci were constructed with RAD‐seq data. Both data sets yielded topologically identical and well‐supported species trees. Incongruence between nuclear and mitochondrial DNA‐based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology‐based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius‐complex, including suggestion of several trans‐Arctic invasions of Europe from the Northern Pacific. The well‐resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.     

Molecular Phylogenetics of the Genus Neoconocephalus (Orthoptera,Tettigoniidae) and the Evolution of Temperate Life Histories

Background

The katydid genus Neoconocephalus (25+ species) has a prominent acoustic communication system and occurs in large parts of the Neotropics and Nearctic. This group has been subject of numerous behavioral, physiological, and evolutionary studies of its acoustic communication system. Two distinct life histories occur in this group: The tropical life history incorporates multiple generations/year and direct egg development without environmental triggers. Temperate life history is characterized by overwintering in the egg stage, cold trigger of egg development, and one generation/year. This study reconstructs the phylogenetic relationships within the genus to (1) determine the evolutionary history of the temperate life history, and (2) to support comparative studies of evolutionary and physiological problems in this genus.

Methodology/Principal Findings

We used Amplified Fragment Length Polymorphisms (AFLP), and sequences of two nuclear loci and one mitochondrial locus to reconstruct phylogenetic relationships. The analysis included 17 ingroup and two outgroup species. AFLP and mitochondrial data provided resolution at the species level while the two nuclear loci revealed only deeper nodes. The data sets were combined in a super-matrix to estimate a total evidence tree. Seven of the temperate species form a monophyletic group; however, three more temperate species were placed as siblings of tropical species.

Conclusions/Significance

Our analyses support the reliability of the current taxonomic treatment of the Neoconocephalus fauna of Caribbean, Central, and North America. Ancestral state reconstruction of life history traits was not conclusive, however at least four transitions between life histories occurred among our sample of species. The proposed phylogeny will strengthen conclusions from comparative work in this group.     

Uncertain branch lengths, taxonomic sampling error, and the egg to body size allometry in temperate butterflies (Lepidoptera)

The allometry of egg to body size in temperate butterflies, and the relationships between egg size and larval host structure, taxonomy, voltinism, and duration of the egg stage, are investigated using cross-species analysis and the comparative analysis of independent contrasts. In addition, the effect of two sources of uncertainty that may affect continuous data when treated under a statistical, comparative, framework, is assessed: (1) unknown evolutionary distances, and (2) taxonomic representativity (proportion of species of a given taxon, from which data are available). It is suggested that the effects of taxonomic under-representation could be important in comparative, quantitative studies, but this problem may be tempered by means of weighted regression. Under the assumption that taxonomy represents butterfly phylogeny, egg and adult body size are related by negative allometry (i.e. the slope of the line fitted to the logarithmically transformed data is lower than 1.0). However, the precise slope (0.2-0.9) depends on the method used, branch lengths, and taxonomic sampling. There is evidence for a relationship between a species' voltinism and the number of days it spends in the egg stage, as well as between adult butterfly size and the gross structure of the plants used as larval hosts (woody plants or herbs). Egg size proves to be related to foodplant taxonomy, voltinism, and duration of the egg stage when the data are analysed using species means, but these relationships become non-significant when the comparative method is employed.     

The phylogenetic significance of colour patterns in marine teleost larvae

Ichthyologists, natural‐history artists, and tropical‐fish aquarists have described, illustrated, or photographed colour patterns in adult marine fishes for centuries, but colour patterns in marine fish larvae have largely been neglected. Yet the pelagic larval stages of many marine fishes exhibit subtle to striking, ephemeral patterns of chromatophores that warrant investigation into their potential taxonomic and phylogenetic significance. Colour patterns in larvae of over 200 species of marine teleosts, primarily from the western Caribbean, were examined from digital colour photographs, and their potential utility in elucidating evolutionary relationships at various taxonomic levels was assessed. Larvae of relatively few basal marine teleosts exhibit erythrophores, xanthophores, or iridophores (i.e. nonmelanistic chromatophores), but one or more of those types of chromatophores are visible in larvae of many basal marine neoteleosts and nearly all marine percomorphs. Whether or not the presence of nonmelanistic chromatophores in pelagic marine larvae diagnoses any major teleost taxonomic group cannot be determined based on the preliminary survey conducted, but there is a trend toward increased colour from elopomorphs to percomorphs. Within percomorphs, patterns of nonmelanistic chromatophores may help resolve or contribute evidence to existing hypotheses of relationships at multiple levels of classification. Mugilid and some beloniform larvae share a unique ontogenetic transformation of colour pattern that lends support to the hypothesis of a close relationship between them. Larvae of some tetraodontiforms and lophiiforms are strikingly similar in having the trunk enclosed in an inflated sac covered with xanthophores, a character that may help resolve the relationships of these enigmatic taxa. Colour patterns in percomorph larvae also appear to diagnose certain groups at the interfamilial, familial, intergeneric, and generic levels. Slight differences in generic colour patterns, including whether the pattern comprises xanthophores or erythrophores, often distinguish species. The homology, ontogeny, and possible functional significance of colour patterns in larvae are discussed. Considerably more investigation of larval colour patterns in marine teleosts is needed to assess fully their value in phylogenetic reconstruction. © 2013 The Authors. Zoological Journal of the Linnean Society published by John Wiley & Sons Ltd on behalf of The Linnean Society of London     

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.     

Molecular investigations of pathogenesis-related Bet v 1 homologues in Passiflora (Passifloraceae)

The major birch pollen allergen, Bet v 1, responsible for allergic reactions in many areas of the world, is homologous to a large number of pathogenesis-related proteins (PRs), identified as PR10. As part of a long-range investigation of these types of proteins and of evolution in Passiflora,DNA sequences from eight Bet v 1 homologue isoforms were obtained from five species of this genus in Brazil, and their sequences compared among themselves and with 30 others from 8 different species, classified in different taxonomic units. The objective was a first characterization of these PRs in wild passionflowers, and their use for evolutionary and applied investigations. High interspecific, but low intraspecific variability was observed, as expected from multigenic families subjected to concerted evolution. The relationships obtained both within Passiflora and between it and seven other genera probably best reflect functional similarities than evolutionary history.     

Sequence Analysis of Bitter Taste Receptor Gene Repertoires in Different Ruminant Species

Bitter taste has been extensively studied in mammalian species and is associated with sensitivity to toxins and with food choices that avoid dangerous substances in the diet. At the molecular level, bitter compounds are sensed by bitter taste receptor proteins (T2R) present at the surface of taste receptor cells in the gustatory papillae. Our work aims at exploring the phylogenetic relationships of T2R gene sequences within different ruminant species. To accomplish this goal, we gathered a collection of ruminant species with different feeding behaviors and for which no genome data is available: American bison, chamois, elk, European bison, fallow deer, goat, moose, mouflon, muskox, red deer, reindeer and white tailed deer. The herbivores chosen for this study belong to different taxonomic families and habitats, and hence, exhibit distinct foraging behaviors and diet preferences. We describe the first partial repertoires of T2R gene sequences for these species obtained by direct sequencing. We then consider the homology and evolutionary history of these receptors within this ruminant group, and whether it relates to feeding type classification, using MEGA software. Our results suggest that phylogenetic proximity of T2R genes corresponds more to the traditional taxonomic groups of the species rather than reflecting a categorization by feeding strategy.     

Assessing the utility of conserving evolutionary history

It is often claimed that conserving evolutionary history is more efficient than species‐based approaches for capturing the attributes of biodiversity that benefit people. This claim underpins academic analyses and recommendations about the distribution and prioritization of species and areas for conservation, but evolutionary history is rarely considered in practical conservation activities. One impediment to implementation is that arguments related to the human‐centric benefits of evolutionary history are often vague and the underlying mechanisms poorly explored. Herein we identify the arguments linking the prioritization of evolutionary history with benefits to people, and for each we explicate the purported mechanism, and evaluate its theoretical and empirical support. We find that, even after 25 years of academic research, the strength of evidence linking evolutionary history to human benefits is still fragile. Most – but not all – arguments rely on the assumption that evolutionary history is a useful surrogate for phenotypic diversity. This surrogacy relationship in turn underlies additional arguments, particularly that, by capturing more phenotypic diversity, evolutionary history will preserve greater ecosystem functioning, capture more of the natural variety that humans prefer, and allow the maintenance of future benefits to humans. A surrogate relationship between evolutionary history and phenotypic diversity appears reasonable given theoretical and empirical results, but the strength of this relationship varies greatly. To the extent that evolutionary history captures unmeasured phenotypic diversity, maximizing the representation of evolutionary history should capture variation in species characteristics that are otherwise unknown, supporting some of the existing arguments. However, there is great variation in the strength and availability of evidence for benefits associated with protecting phenotypic diversity. There are many studies finding positive biodiversity–ecosystem functioning relationships, but little work exists on the maintenance of future benefits or the degree to which humans prefer sets of species with high phenotypic diversity or evolutionary history. Although several arguments link the protection of evolutionary history directly with the reduction of extinction rates, and with the production of relatively greater future biodiversity via increased adaptation or diversification, there are few direct tests. Several of these putative benefits have mismatches between the relevant spatial scales for conservation actions and the spatial scales at which benefits to humans are realized. It will be important for future work to fill in some of these gaps through direct tests of the arguments we define here.