Genes,development, and evolvability in primate evolution

Development is the process whereby a fertilized cell becomes a mature individual. In metazoans, this complex process involves the differentiation of somatic cells into committed cell and tissue types; the organization and migration of cells, tissues, and anatomical structures relative to one another; and growth. 1 Development matters to evolution in two ways. First, development carries out heritable genetic instructions contained in zygotes to produce functioning yet phenotypically varied individuals. At the population level, this variation in form and function among individuals provides the “raw material” for evolution. Second, the mechanisms of development influence the magnitude, direction, and interdependence of heritable phenotypic variation among traits. Together with phenomena such as genetic drift, organismal development determines the raw material available to selection and thus influences the rate and direction of phenotypic evolution. 2 , 3     

Hydra and the evolution of stem cells

Hydra are remarkable because they are immortal. Much of immortality can be ascribed to the asexual mode of reproduction by budding, which requires a tissue consisting of stem cells with continuous self‐renewal capacity. Emerging novel technologies and the availability of genomic resources enable for the first time to analyse these cells in vivo. Stem cell differentiation in Hydra is governed through the coordinated actions of conserved signaling pathways. Studies of stem cells in Hydra, therefore, promise critical insights of general relevance into stem cell biology including cellular senescence, lineage programming and reprogramming, the role of extrinsic signals in fate determination and tissue homeostasis, and the evolutionary origin of these cells. With these new facts as a backdrop, this review traces the history of studying stem cells in Hydra and offers a view of what the future may hold.     

The uropygial gland of the monk parakeet Myiopsitta monachus: Histology,morphogenesis, and evolution within Psittaciformes (Aves)

We describe the morphology, histology, and histochemical characteristics of the uropygial gland (UG) of the monk parakeet Myiopsitta monachus. The UG has a heart‐shape external appearance and adenomers extensively branched with a convoluted path, covered by a stratified epithelium formed by different cellular strata and divided into three zones (based on the epithelial height and lumen width), a cylindrical papilla with an internal structure of delicate type and two excretory pores surrounded by a feather tuft. Histochemical and lectin‐histochemical techniques performed showed positivity against PAS, AB pH 2.5, AB‐PAS, and some lectines, likely related to the granivorous feeding habits. Also, we describe the morphogenesis of the UG of the monk parakeet, which appears at embryological stage 34 as a pair of ectodermal invaginations. Heterochronic events in the onset development of the UG when compared with other birds could be recognized. Finally, to examine the phylogenetic occurrence of the UG within the Psittaciformes and infer its evolutionary history, we mapped its presence/absence over a molecular phylogeny. The reconstruction of the characters states at ancestral nodes revealed that the presence of the UG was the plesiomorphic feature for Psittaciformes and its loss evolved independently more than once.     

Conserved synteny between the Ciona genome and human paralogons identifies large duplication events in the molecular evolution of the insulin-relaxin gene family

The aims of the study were to outline the sequence of eventsthat gave rise to the vertebrate insulin-relaxin gene familyand the chromosomal regions in which they reside. We analyzedthe gene content surrounding the human insulin/relaxin geneswith respect to what family they belonged to and if the duplicationhistory of investigated families parallels the evolution ofthe insulin-relaxin family members. Markov Clustering and phylogeneticanalysis were used to determine family identity. More than 15%of the genes belonged to families that have paralogs in theregions, defining two sets of quadruplicate paralogy regions.Thereby, the localization of insulin/relaxin genes in humansis in accordance with those regions on human chromosomes 1,11, 12, 19q (insulin/insulin-like growth factors) and 1, 6p/15q,9/5, 19p (insulin-like factors/relaxins) were formed duringtwo genome duplications. We compared the human genome with thatof Ciona intestinalis, a species that split from the vertebratelineage before the two suggested genome duplications. Two insulin-likeorthologs were discovered in addition to the already describedCi-insulin gene. Conserved synteny between the Ciona regionshosting the insulin-like genes and the two sets of human paralogonsimplies their common origin. Linkage of the two human paralogons,as seen in human chromosome 1, as well as the two regions hostingthe Ciona insulin-like genes suggests that a segmental duplicationgave rise to the region prior to the genome doublings. Thus,preserved gene content provides support that genome duplication(s)in addition to segmental and single-gene duplications shapedthe genomes of extant vertebrates.     

Roles for modularity and constraint in the evolution of cranial diversity among Anolis lizards

Complex organismal structures are organized into modules, suites of traits that develop, function, and vary in a coordinated fashion. By limiting or directing covariation among component traits, modules are expected to represent evolutionary building blocks and to play an important role in morphological diversification. But how stable are patterns of modularity over macroevolutionary timescales? Comparative analyses are needed to address the macroevolutionary effect of modularity, but to date few have been conducted. We describe patterns of skull diversity and modularity in Caribbean Anolis lizards. We first diagnose the primary axes of variation in skull shape and then examine whether diversification of skull shape is concentrated to changes within modules or whether changes arose across the structure as a whole. We find no support for the hypothesis that cranial modules are conserved as species diversify in overall skull shape. Instead we find that anole skull shape and modularity patterns independently converge. In anoles, skull modularity is evolutionarily labile and may reflect the functional demands of unique skull shapes. Our results suggest that constraints have played little role in limiting or directing the diversification of head shape in Anolis lizards.     

A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant–microbe interactions and legume evolution

Lupins are important grain legume crops that form a critical part of sustainable farming systems, reducing fertilizer use and providing disease breaks. It has a basal phylogenetic position relative to other crop and model legumes and a high speciation rate. Narrow‐leafed lupin (NLL; Lupinus angustifolius L.) is gaining popularity as a health food, which is high in protein and dietary fibre but low in starch and gluten‐free. We report the draft genome assembly (609 Mb) of NLL cultivar Tanjil, which has captured >98% of the gene content, sequences of additional lines and a dense genetic map. Lupins are unique among legumes and differ from most other land plants in that they do not form mycorrhizal associations. Remarkably, we find that NLL has lost all mycorrhiza‐specific genes, but has retained genes commonly required for mycorrhization and nodulation. In addition, the genome also provided candidate genes for key disease resistance and domestication traits. We also find evidence of a whole‐genome triplication at around 25 million years ago in the genistoid lineage leading to Lupinus. Our results will support detailed studies of legume evolution and accelerate lupin breeding programmes.     

The evolutionary and morphological history of the parasphenoid bone in vertebrates

The parasphenoid is located in the cranium of many vertebrates. When present, it is always an unpaired, dermal bone. While most basal vertebrates have a parasphenoid, most placental mammals lack this element and have an unpaired, dermal vomer in a similar position (i.e. associated with the same bones) and with a similar function. As such, the parasphenoid and the vomer were considered homologous by some early twentieth century researchers. However, others questioned this homology based on comparisons between mammals and reptiles. Here we investigate the parasphenoid bone across the major vertebrate lineages (amphibians, reptiles, mammals and teleosts) including both developmental and evolutionary aspects, which until now have not been considered together. We find that within all the major vertebrate lineages there are organisms that possess a parasphenoid and a vomer, while the parasphenoid is absent within caecilians and most placental mammals. Based on our assessment and Patterson's conjunction tests, we conclude that the non‐mammalian parasphenoid and the vomer in mammals cannot be considered homologous. Additionally, the parasphenoid is likely homologous between sarcopterygian and actinopterygian lineages. This research attempts to resolve the issue of the parasphenoid homology and highlights where gaps in our knowledge are still present.     

Spatio‐temporal patterns of genome evolution in allotetraploid species of the genus Oryza

Despite knowledge that polyploidy is widespread and a major evolutionary force in flowering plant diversification, detailed comparative molecular studies on polyploidy have been confined to only a few species and families. The genus Oryza is composed of 23 species that are classified into ten distinct ‘genome types’ (six diploid and four polyploid), and is emerging as a powerful new model system to study polyploidy. Here we report the identification, sequence and comprehensive comparative annotation of eight homoeologous genomes from a single orthologous region (Adh1–Adh2) from four allopolyploid species representing each of the known Oryza genome types (BC, CD, HJ and KL). Detailed comparative phylogenomic analyses of these regions within and across species and ploidy levels provided several insights into the spatio‐temporal dynamics of genome organization and evolution of this region in ‘natural’ polyploids of Oryza. The major findings of this study are that: (i) homoeologous genomic regions within the same nucleus experience both independent and parallel evolution, (ii) differential lineage‐specific selection pressures do not occur between polyploids and their diploid progenitors, (iii) there have been no dramatic structural changes relative to the diploid ancestors, (iv) a variation in the molecular evolutionary rate exists between the two genomes in the BC complex species even though the BC and CD polyploid species appear to have arisen <2 million years ago, and (v) there are no clear distinctions in the patterns of genome evolution in the diploid versus polyploid species.     

A developmental staging series for the lizard genus Anolis: a new system for the integration of evolution, development, and ecology

Vertebrate developmental biologists typically rely on a limited number of model organisms to understand the evolutionary bases of morphological change. Unfortunately, a typical model system for squamates (lizards and snakes) has not yet been developed leaving many fundamental questions about morphological evolution unaddressed. New model systems would ideally include clades, rather than single species, that are amenable to both laboratory studies of development and field-based analyses of ecology and evolution. Combining an understanding of development with an understanding of ecology and evolution within and between closely related species has the potential to create a seamless understanding of how genetic variation underlies ecologically and evolutionarily relevant variation within populations and between species. Here we briefly introduce a new model system for the integration of development, evolution, and ecology, the lizard genus Anolis, a diverse group of lizards whose ecology and evolution is well understood, and whose genome has recently been sequenced. We present a developmental staging series for Anolis lizards that can act as a baseline for later comparative and experimental studies within this genus.     

Skeletal elements within teleost eyes and a discussion of their homology

Scleral ossicles and scleral cartilages form part of the craniofacial skeleton of many vertebrates. Some vertebrates, including all birds and most reptiles, but excluding most mammals, have scleral cartilages as well as scleral ossicles supporting their eyes. The teleost equivalent of these elements has received little attention in the literature. From radiographic and whole-mount analyses of over 400 individuals from 376 teleost species, we conclude that the teleost scleral skeletal elements (ossicles and cartilage) differ significantly from those of reptiles (including birds). Scleral ossicles in teleosts have different developmental origins, different positions within the eyeball, and different relationships with the scleral cartilaginous element than those in reptiles. From whole-mount staining of a growth series of four species of teleost (Danio rerio, Salmo salar, Esox lucius, and Alosa pseudoharengus), we interpret the development of these elements and show that they arise from within an Alcian blue-staining cartilaginous ring that develops around the eye earlier in development. We present possible scenarios on the evolution of these scleral skeletal elements from a common gnathostome ancestor, and consider that teleost scleral skeletal elements may not be homologous to those in reptiles. Our study indicates that homology cannot be assumed for these elements, despite the fact that they share the same name, scleral ossicles.     

The animal in the genome: comparative genomics and evolution

Comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. Given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. Simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; increased numbers of regulatory non-coding RNAs and increased complexity of the cis-regulatory code. An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components. I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components.     

The location of heart melanocytes is specified and the level of pigmentation in the heart may correlate with coat color

Melanocytes are mainly found in the skin and more rarely in other parts of the body, including the heart. We analyzed the localization of heart melanocytes and their levels of pigmentation in a series of mutant mice presenting different numbers of melanocytes and pigmentation in the skin. We found that melanocytes were localized in the valves (mitral, tricuspid, and aortic) and septa (ventricular and atrial). Moreover, the numbers of melanocytes in the heart appears to reflect that of the skin. Mice having a high or low level of pigmented cells and/or melanin in valves and septa have similar lifespan. In this respect, melanocytes found in the valves and septa of the heart are probably not essential in a healthy and non-stressful environment.     

Functional evolutionary developmental biology (evo‐devo) of morphological novelties in plants

Abstract The origin of morphological and ecological novelties is a long‐standing problem in evolutionary biology. Understanding these processes requires investigation from both the development and evolution standpoints, which promotes a new research field called “evolutionary developmental biology” (evo‐devo). The fundamental mechanism for the origin of a novel structure may involve heterotopy, heterochrony, ectopic expression, or loss of an existing regulatory factor. Accordingly, the morphological and ecological traits controlled by the regulatory genes may be gained, lost, or regained during evolution. Floral morphological novelties, for example, include homeotic alterations (related to organ identity), symmetric diversity, and changes in the size and morphology of the floral organs. These gains and losses can potentially arise through modification of the existing regulatory networks. Here, we review current knowledge concerning the origin of novel floral structures, such as “evolutionary homeotic mutated flowers”, floral symmetry in various plant species, and inflated calyx syndrome (ICS) within Solanaceae. Functional evo‐devo of the morphological novelties is a central theme of plant evolutionary biology. In addition, the discussion is extended to consider agronomic or domestication‐related traits, including the type, size, and morphology of fruits (berries), within Solanaceae.     

The evolution of development in Streptomyces analysed by genome comparisons

There is considerable information about the genetic control of the processes by which mycelial Streptomyces bacteria form spore-bearing aerial hyphae. The recent acquisition of genome sequences for 16 species of actinobacteria, including two streptomycetes, makes it possible to try to reconstruct the evolution of Streptomyces differentiation by a comparative genomic approach, and to place the results in the context of current views on the evolution of bacteria. Most of the developmental genes evaluated are found only in actinobacteria that form sporulating aerial hyphae, with several being peculiar to streptomycetes. Only four (whiA, whiB, whiD, crgA) are generally present in nondifferentiating actinobacteria, and only two (whiA, whiG) are found in other bacteria, where they are widespread. Thus, the evolution of Streptomyces development has probably involved the stepwise acquisition of laterally transferred DNA, each successive acquisition giving rise either to regulatory changes that affect the conditions under which development is initiated, or to changes in cellular structure or morphology.     

Visual pigment evolution in Characiformes: The dynamic interplay of teleost whole‐genome duplication,surviving opsins and spectral tuning

Vision represents an excellent model for studying adaptation, given the genotype‐to‐phenotype map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light, making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we showcase the visual system evolution of neotropical Characiformes and the spectral tuning mechanisms they exhibit to modulate their visual sensitivities. Such mechanisms include gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A₁/A₂‐chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform's entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS‐ and RH1‐duplicates originated from a teleost specific whole‐genome duplication as well as characiform‐specific duplication events. Both LWS‐opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS‐paralogues has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. Furthermore, characiforms' colour vision is based on the expression of both LWS‐paralogues and SWS2. Finally, we found interspecific and intraspecific variation in A₁/A₂‐chromophores proportions, correlating with the light environment. These multiple mechanisms may be a result of the diverse visual environments where Characiformes have evolved.