Molecular evolution of three avian neurotrophin genes: implications for proregion functional constraints

Diversity, distribution, and methodological considerations of haemosporidian infections among Galliformes in Alaska

Using samples spanning 10-degrees of latitude in Alaska, we provide the first comparative assessment of avian haemosporidia distribution of Arctic Alaska with subarctic host populations for four species of grouse and three species of ptarmigan (Galliformes). We found a high overall prevalence for at least one haemospordian genus (88%; N = 351/400), with spruce grouse (Canachites canadensis) showing the highest prevalence (100%; N = 54/54). Haemoproteus and Plasmodium lineages were only observed within grouse, while Leucocytozoon species were found within both grouse and ptarmigan. Further, different Leucocytozoon lineages were obtained from blood and tissue samples from the same individual, potentially due to the differential timing and duration of blood and tissue stages. Using different primer sets, we were able to identify different Leucocytozoon lineages within 55% (N = 44/80) of sequenced individuals, thereby detecting coinfections that may have otherwise gone undetected. The commonly used Haemoproteus/Plasmodium primers amplified Leucocytozoon for 90% (N = 103/115) of the products sequenced, highlighting the potential value of alternate primers to identify intra-genus coinfections and the importance of obtaining sequence information rather than relying solely on PCR amplification to assess parasite diversity. Overall, this dataset provides baseline information on parasite lineage distributions to assess the range expansion associated with climate change into Arctic regions and underscores methodological considerations for future studies.

Prevalence and diversity of avian haemosporidian parasites across islands of Milne Bay Province, Papua New Guinea

The taxonomically diverse and relatively understudied avifauna of Papua New Guinea’s (PNG) island archipelagos provide a unique ecological framework for studying haemosporidian parasite differentiation and geographic structure. We implemented molecular and phylogenetic analyses of partial mitochondrial DNA sequences to assess the host distribution of 3 genera of vector-transmitted avian blood parasites (Plasmodium, Leucocytozoon and Haemoproteus) across a range of islands off the southeastern tip of PNG. We identified 40 new lineages of haemosporidians, including five lineages belonging to Leucocytozoon, a genus not previously described in this region. Leucocytozoon infections were only observed on the larger, human-inhabited islands. Lineages belonging to Haemoproteus were diverse and had broad geographic distribution. Compared to the mainland, Haemoproteus parasites on the smaller, more distant islands had greater host specificity and lower infection prevalence. The black sunbird (Leptocoma aspasia), a commonly caught species, was shown to be a rare host for Haemoproteus spp. infections. Moreover, although birds of the genus Pitohui harbor a neurotoxin (homobatrachotoxin), they demonstrated an infection prevalence comparable to other bird species. The islands of PNG display heterogeneous patterns of haemosporidian diversity, distribution and host-specificity and serve as a valuable model system for studying host-parasite-vector interactions.

Description and molecular characterization of novel Leucocytozoon parasite (Apicomplexa: Haemosporida: Leucocytozoidae), Leucocytozoon polynuclearis n. sp. found in North American woodpeckers

We describe Leucocytozoon polynuclearis n. sp. (Haemosporida: Leucocytozoidae) from two North American woodpeckers, the northern flicker (Colaptes auratus Linnaeus) and white-headed woodpecker (Dryobates albolarvatus Boie, 1826), based on the morphology of its blood stages and portions of the mitochondrial cytochrome b gene. The most distinctive features of Leucocytozoon polynuclearis n. sp. development are the triangular-shaped host cell nuclei and position of host cell nuclei above gametocytes. This parasite inhabits thrombocytes. Leucocytozoon squamatus Nandi, 1986, the only other Leucocytozoon species detected from Picidae birds, lacks features that are commonly found with L. polynuclearis n. sp. infections. Phylogenetic analysis identified DNA lineages associated with L. polynuclearis n. sp. and showed that this parasite is more closely related to other North American Leucocytozoon species than to L. squamatus, whose initial description was from infected Old World Picidae species. Although there are reports of L. squamatus in North American Picidae species, these detections were based only on microscopic examinations, remain genetically non-characterized, and might be misidentifications with regards to L. polynuclearis n. sp. Available parasite distribution data indicate that L. polynuclearis n. sp. infects Picidae species throughout North America and L. squamatus distribution probably is restricted to Old World Piciformes birds.

Haemosporidia of grey crowned cranes in Rwanda

Grey crowned cranes (Balearica regulorum) have been facing significant and long-term population declines in East Africa. Studies of Haemosporidian infections are essential to gain insight into pathogenic threats and help infer vector-host relationships, resolve parasite relationships, and support conservation efforts. As part of a program to reintroduce captive cranes in Rwanda back to their natural habitats, through health checks and initial microscopic examination, 120 grey crowned cranes were selected under suspicion of harboring Haemosporidian infections following initial peripheral blood smear examinations. Of these, 104 were infected with Haemoproteus and 3 were coinfected with Leucocytozoon as detected by PCR and microscopy. Sequencing allowed us to identify 2 distinct unreported lineages of Haemoproteus antigonis and one lineage of Leucocytozoon in the subspecies of Grey Crowned Cranes endemic to East Africa, B. r. gibbericeps. Molecularly, our two lineages of Haemoproteus antigonis differ by 32 base pairs and matched with about 95 percent identity to previously reported sequences of H. antigonis found in other species of cranes. No visible morphologic differences were found when compared to images of H. antigonis from previous studies. Our work demonstrates not only a need for increased testing within the family Gruidae, but also to investigate the possibility of cryptic speciation within the morphospecies Haemoproteus antigonis.

A combined evolutionary and structural approach to disclose the primary structural determinants essential for proneurotrophins biological functions

The neurotrophins, i.e., Nerve Growth Factor (NGF), Brain-Derived Neurotrophic Factor (BDNF), Neurotrophin 3 (NT3) and Neurotrophin 4 (NT4), are known to play a range of crucial functions in the developing and adult peripheral and central nervous systems. Initially synthesized as precursors, i.e., proneurotrophins (proNTs), that are cleaved to release C-terminal mature forms, they act through two types of receptors, the specific Trk receptors (Tropomyosin-related kinases) and the pan-neurotrophin receptor p75NTR, to initiate survival and differentiative responses. Recently, all the proNTs but proNT4 have been demonstrated to be not just inactive precursors, but signaling ligands that mediate opposing actions in fundamental aspects of the nervous system with respect to the mature counterparts through dual-receptor complexes formation with a member of the VPS10 family and p75NTR. Despite the functional relevance, the molecular determinants underpinning the interactions between the pro-domains and their receptors are still elusive probably due to their intrinsically disordered nature. Here we present an evolutionary approach coupled to an experimental study aiming to uncover the structural and dynamical basis of the biological function displayed by proNGF, proBDNF and proNT3 but missing in proNT4. A bioinformatic analysis allowed to elucidate the functional adaptability of the proNTs family in vertebrates, identifying conserved key structural features. The combined biochemical and SAXS experiments shed lights on the structure and dynamic behavior of the human proNTs in solution, giving insights on the evolutionary conserved structural motifs, essential for the multifaceted roles of proNTs in physiological as well as in pathological contexts.

Effect of deforestation on prevalence of avian haemosporidian parasites and mosquito abundance in a tropical rainforest of Cameroon

Habitat change caused by deforestation can modify the interactions of many biotic and abiotic factors, and in turn influence patterns of diseases in wild birds. Whether deforestation directly or indirectly affects the prevalence of avian haemosporidian parasites through their hosts and/or vectors is still not well understood. We sampled understory bird communities (insectivorous, frugivorous, granivorous and nectarivorous birds) and mosquitoes in three habitats showing a gradient of deforestation (pristine forest, fragmented forest, and young palm oil plantation), to assess the effects of habitat changes on avian haemosporidian (Plasmodium and Haemoproteus) prevalence and its relationship to bird feeding guilds and mosquito abundance. Blood samples of 845 individual birds belonging to 85 species and 27 families were collected in the three habitat types and screened using microscopy and PCR. Plasmodium infections were detected in 136 individuals (16.09%) and varied significantly among habitat types while Haemoproteus infections were detected in 98 individuals (11.60%) and did not vary significantly among habitat types. However, the prevalence of Plasmodium and Haemoproteus in bird feeding groups varied significantly among habitats. Nectarivorous and granivorous birds had the highest Plasmodium and Haemoproteus prevalence, respectively. The abundance of mosquitoes varied significantly among habitat types and the prevalence of Plasmodium significantly and positively correlated with mosquito abundance in fragmented forest. This study highlights the importance of host and mosquito determinants in the transmission dynamics of avian Plasmodium and Haemoproteus infections following habitat changes. Selective logging favored an increase in the prevalence of Plasmodium in insectivores, the prevalence of Haemoproteus in nectarivores and the abundance of female mosquitoes while, the establishment of the palm oil plantation favored an increase in the prevalence of Plasmodium in granivores and Haemoproteus in nectarivores. Species feeding behavior is also an important determinant to consider for a better understanding of patterns of parasite infections in a changing environment.

Haemoproteosis lethality in a woodpecker, with molecular and morphological characterization of Haemoproteus velans (Haemosporida, Haemoproteidae)

A juvenile White-headed woodpecker (Dryobates albolarvatus) fitted with a radio tag was located dead at approximately 22-days post-fledging in Yakima county in central Washington in July 2015. Postmortem examination revealed an enlarged liver and spleen plus evidence of iron sequestration. Microscopic examination observed young gametocytes within the cytoplasm of erythrocytes, and exo-erythrocytic meronts within the cytoplasm of capillary endothelial cells, hepatocytes, and myocytes, and free in the tissues. These attributes implicated a haemosporidian infection that likely resulted in mortality. Subsequent sampling results of local woodpecker species in the same area during the breeding season in June-July 2016 and May-July 2017 showed other individuals infected with Haemoproteus parasites. Nested Polymerase Chain Reaction (PCR), sequencing, and microscopic analyses for avian haemosporidians revealed infections with Haemoproteus velans (Haemosporida, Haemoproteidae). This parasite was characterized molecularly and morphologically. This is the first report of a haemosporidian infection in a White-headed woodpecker anywhere in its range, and the first reported suspected mortality from haemoproteosis for a woodpecker (Piciformes, Picidae). The use of radio-tagged birds is an asset in wildlife haemosporidian studies because the effect of the pathogen can be monitored in real time. Additionally, this methodology provides opportunities to collect fresh material for microscopic and histological examination from wild birds that have died from natural causes.

Genetic sequence data reveals widespread sharing of Leucocytozoon lineages in corvids

Leucocytozoon, a widespread hemosporidian blood parasite that infects a broad group of avian families, has been studied in corvids (family: Corvidae) for over a century. Current taxonomic classification indicates that Leucocytozoon sakharoffi infects crows and related Corvus spp., while Leucocytozoon berestneffi infects magpies (Pica spp.) and blue jays (Cyanocitta sp.). This intrafamily host specificity was based on the experimental transmissibility of the parasites, as well as slight differences in their morphology and life cycle development. Genetic sequence data from Leucocytozoon spp. infecting corvids is scarce, and until the present study, sequence data has not been analyzed to confirm the current taxonomic distinctions. Here, we predict the phylogenetic relationships of Leucocytozoon cytochrome b lineages recovered from infected American Crows (Corvus brachyrhynchos), yellow-billed magpies (Pica nuttalli), and Steller's jays (Cyanocitta stelleri) to explore the host specificity pattern of L. sakharoffi and L. berestneffi. Phylogenetic reconstruction revealed a single large clade containing nearly every lineage recovered from the three host species, while showing no evidence of the expected distinction between L. sakharoffi and L. berestneffi. In addition, five of the detected lineages were recovered from both crows and magpies. This absence of the previously described host specificity in corvid Leucocytozoon spp. suggests that L. sakharoffi and L. berestneffi be reexamined from a taxonomic perspective.

Neurotrophin-4 in the brain of adult Nothobranchius furzeri

Neurotrophin-4 (NT-4) is a member of the well-known family of neurotrophins that regulate the development of neuronal networks by participating in neuronal survival and differentiation, the growth of neuronal processes, synaptic development and plasticity, as well as myelination. NT-4 interacts with two distinct receptors: TrkB, high affinity receptor and p75 low-affinity neurotrophin receptor (p75(NTR)). In the present survey, we identified the gene encoding NT-4 in the teleost Nothobranchius furzeri, a model species for aging research. The identified gene shows a similarity of about 72% with medaka, the closest related species. The neuroanatomical localization of NT-4 mRNA is obtained by using an LNA probe. NT-4 mRNA expression is observed in neurons and glial cells of the forebrain and hindbrain, with very low signal found in the midbrain. This survey confirms that NT-4 is expressed in the brain of N. furzeri during adulthood, suggesting that it could also be implicated in the maintenance and regulation of neuronal functions.

Coevolutionary patterns and diversification of avian malaria parasites in African sunbirds (Family Nectariniidae)

The coevolutionary relationships between avian malaria parasites and their hosts influence the host specificity, geographical distribution and pathogenicity of these parasites. However, to understand fine scale coevolutionary host–parasite relationships, robust and widespread sampling from closely related hosts is needed. We thus sought to explore the coevolutionary history of avianPlasmodiumand the widespread African sunbirds, family Nectariniidae. These birds are distributed throughout Africa and occupy a variety of habitats. Considering the role that habitat plays in influencing host-specificity and the role that host-specificity plays in coevolutionary relationships, African sunbirds provide an exceptional model system to study the processes that govern the distribution and diversity of avian malaria. Here we evaluated the coevolutionary histories using a multi-gene phylogeny for Nectariniidae and avianPlasmodiumfound in Nectariniidae. We then assessed the host–parasite biogeography and the structuring of parasite assemblages. We recoveredPlasmodiumlineages concurrently in East, West, South and Island regions of Africa. However, severalPlasmodiumlineages were recovered exclusively within one respective region, despite being found in widely distributed hosts. In addition, we inferred the biogeographic history of these parasites and provide evidence supporting a model of biotic diversification in avianPlasmodiumof African sunbirds.

Distribution, diversity and drivers of blood-borne parasite co-infections in Alaskan bird populations

Avian species are commonly infected by multiple parasites, however few studies have investigated the environmental determinants of the prevalence of co-infection over a large scale. Here we believe that we report the first, detailed ecological study of the prevalence, diversity and co-infections of four avian blood-borne parasite genera: Plasmodium spp., Haemoproteus spp., Leucocytozoon spp. and Trypanosoma spp. We collected blood samples from 47 resident and migratory bird species across a latitudinal gradient in Alaska. From the patterns observed at collection sites, random forest models were used to provide evidence of associations between bioclimatic conditions and the prevalence of parasite co-infection distribution. Molecular screening revealed a higher prevalence of haematozoa (53%) in Alaska than previously reported. Leucocytozoons had the highest diversity, prevalence and prevalence of co-infection. Leucocytozoon prevalence (35%) positively correlated with Trypanosoma prevalence (11%), negatively correlated with Haemoproteus prevalence (14%) and had no correlation with Plasmodium prevalence (7%). We found temperature, precipitation and tree cover to be the primary environmental drivers that show a relationship with the prevalence of co-infection. The results provide insight into the impacts of bioclimatic drivers on parasite ecology and intra-host interactions, and have implications for the study of infectious diseases in rapidly changing environments.

Resolving deep lineage divergences in core corvoid passerine birds supports a proto-Papuan island origin

It is well established that the global expansion of songbirds (Oscines) originated in East Gondwana (present day Australo-Papua), and it has been postulated that one of the main constituent groups, the "core Corvoidea", with more than 750 species, originated in the first islands that emerged where New Guinea is now located. However, several polytomous relationships remained within the clade, obstructing detailed biogeographical interpretations. This study presents a well-resolved family-level phylogeny, based on a dataset of 22 nuclear loci and using a suite of partitioning schemes and Maximum Likelihood and Bayesian inference methods. Resolving the relationships within the core Corvoidea provides evidence for three well-supported main clades, which are in turn sister to the New Zealand genus Mohoua. Some monotypic lineages, which have previously been considered Incertae sedis, are also placed in a phylogenetic context. The well-resolved phylogeny provides a robust framework for biogeographical analyses, and provides further support for the hypothesis that core corvoids originated in the proto-Papuan island region that emerged north of Australia in the late Oligocene/early Miocene. Thus, the core Corvoidea appear to represent a true island radiation, which successfully colonized all continents except Antarctica.

Two new Haemoproteus species (Haemosporida: Haemoproteidae) from columbiform birds

Here we describe Haemoproteus (Haemoproteus) multivolutinus n. sp. from a tambourine dove (Turtur timpanistria) of Uganda and Haemoproteus (Haemoproteus) paramultipigmentatus n. sp. (Haemosporida, Haemoproteidae) from the Socorro common ground dove (Columbina passerina socorroensis) of Socorro Island, Mexico. These parasites are described based on the morphology of their blood stages and segments of the mitochondrial cytochrome b gene that can be used for molecular identification and diagnosis of these species. Gametocytes of H. multivolutinus possess rod-like pigment granules and are evenly packed with volutin, which masks pigment granules and darkly stains both macro- and microgametocytes in the early stages of their development. Based on these 2 characters, H. multivolutinus can be readily distinguished from other species of hemoproteids parasitizing columbiform (Columbiformes) birds. Haemoproteus paramultipigmentatus resembles Haemoproteus multipigmentatus; it can be distinguished from the latter parasite primarily due to the broadly ovoid shape of its young gametocytes and significantly fewer pigment granules in its fully developed gametocytes. We provide illustrations of blood stages of the new species, and phylogenetic analyses identify DNA lineages closely related to these parasites. Cytochrome b lineages of Haemoproteus multivolutinus and H. paramultipigmentatus cluster with hippoboscid-transmitted lineages of hemoproteids; thus these parasites likely belong to the subgenus Haemoproteus. We emphasize the importance of using cytochrome b sequences in conjunction with thorough microscopic descriptions to facilitate future identification of these and other avian hemosporidian species.

Testosterone and brain-derived neurotrophic factor interactions in the avian song control system

Interaction between steroid sex hormones and brain-derived neurotrophic factor (BDNF) is a common feature of vertebrate brain organization. The avian song control system provides an excellent model for studying such interactions in neural circuits that regulate song, a learned sensorimotor behavior that is often sexually dimorphic and restricted to reproductive contexts. Testosterone (T) and its steroid metabolites interact with BDNF during development of the song system and in adult plasticity, including the addition of newborn neurons to the pallial nucleus HVC and seasonal changes in structure and function of these circuits. T and BDNF interact locally within HVC to influence cell proliferation and survival. This interaction may also occur transsynpatically; T increases the synthesis of BDNF in HVC, and BDNF protein is then released on to postsynaptic cells in the robust nucleus of the arcopallium (RA) where it has trophic effects. The interaction between sex steroids and BDNF is an example of molecular exploitation, with the evolutionarily ancient steroid-receptor complex having been captured by the more recently evolved BDNF. The functional linkage of sex steroids to BDNF may be of adaptive value in regulating the trophic effects of the neurotrophin in sexually dimorphic and reproductively relevant contexts.

North American transmission of hemosporidian parasites in the Swainson's thrush (Catharus ustulatus), a migratory songbird

The geographic structuring of parasite communities across the range of a single host species can illuminate patterns of host-population connectivity. To determine the location of parasite transmission in a Neotropical migrant bird species, we sampled adult and hatch-year (HY) birds across the breeding and wintering range of the Swainson's thrush (SWTH), an abundant passerine with a migratory divide. We examined the phylogenetic relationships among cytochrome b lineages of the avian blood parasite genera Haemoproteus, Plasmodium, and Leucocytozoon and determined the transmission location of unique lineages. We found that Haemoproteus and Plasmodium lineages are transmitted on California breeding grounds, whereas Leucocytozoon transmission occurs on Alaskan breeding grounds. The presence of hemosporidians on wintering grounds and shared lineages between the SWTH and resident species suggests that transmission of some of these lineages occurs on both breeding and wintering grounds. We emphasize that the sampling of HY birds and local resident heterospecifics will supplement vector studies to determine the key players in hemosporidian host switching and range-expansion events.

Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora

Turtles are currently the most endangered major clade of vertebrates on earth, and Asian box turtles (Cuora) are in catastrophic decline. Effective management of this diverse turtle clade has been hampered by human-mediated, and perhaps natural hybridization, resulting in discordance between mitochondrial and nuclear markers and confusion regarding species boundaries and phylogenetic relationships among hypothesized species of Cuora. Here, we present analyses of mitochondrial and nuclear DNA data for all 12 currently hypothesized species to resolve both species boundaries and phylogenetic relationships. Our 15-gene, 40-individual nuclear data set was frequently in conflict with our mitochondrial data set; based on its general concordance with published morphological analyses and the strength of 15 independent estimates of evolutionary history, we interpret the nuclear data as representing the most reliable estimate of species boundaries and phylogeny of Cuora. Our results strongly reiterate the necessity of using multiple nuclear markers for phylogeny and species delimitation in these animals, including any form of DNA "barcoding", and point to Cuora as an important case study where reliance on mitochondrial DNA can lead to incorrect species identification.

An improved phylogeny of the Andean tit-tyrants (Aves, Tyrannidae): more characters trump sophisticated analyses

The phylogeny of the flycatcher genus Anairetes was previously inferred using short fragments of mitochondrial DNA and parsimony and distance-based methods. The resulting topology spurred taxonomic revision and influenced understanding of Andean biogeography. More than a decade later, we revisit the phylogeny of Anairetes tit-tyrants using more mtDNA characters, seven unlinked loci (three mitochondrial genes, six nuclear loci), more closely related outgroup taxa, partitioned Bayesian analyses, and two coalescent species-tree approaches (Bayesian estimation of species trees, BEST; Bayesian evolutionary analysis by sampling trees, (*)BEAST). Of these improvements in data and analyses, the fourfold increase in mtDNA characters was both necessary and sufficient to incur a major shift in the topology and near-complete resolution. The species-tree analyses, while theoretically preferable to concatenation or single gene approaches, yielded topologies that were compatible with mtDNA but with weaker statistical resolution at nodes. The previous results that had led to taxonomic and biogeographic reappraisal were refuted, and the current results support the resurrection of the genus Uromyias as the sister clade to Anairetes. The sister relationship between these two genera corresponds to an ecological dichotomy between a depauperate humid cloud forest clade and a diverse dry-tolerant clade that has diversified along the latitudinal axis of the Andes. The species-tree results and the concatenation results each reaffirm the primacy of mtDNA to provide phylogenetic signal for avian phylogenies at the species and subspecies level. This is due in part to the abundance of informative characters in mtDNA, and in part to its lower effective population size that causes it to more faithfully track the species tree.

Host and habitat specialization of avian malaria in Africa

Studies of both vertebrates and invertebrates have suggested that specialists, as compared to generalists, are likely to suffer more serious declines in response to environmental change. Less is known about the effects of environmental conditions on specialist versus generalist parasites. Here, we study the evolutionary strategies of malaria parasites (Plasmodium spp.) among different bird host communities. We determined the parasite diversity and prevalence of avian malaria in three bird communities in the lowland forests in Cameroon, highland forests in East Africa and fynbos in South Africa. We calculated the host specificity index of parasites to examine the range of hosts parasitized as a function of the habitat and investigated the phylogenetic relationships of parasites. First, using phylogenetic and ancestral reconstruction analyses, we found an evolutionary tendency for generalist malaria parasites to become specialists. The transition rate at which generalists become specialists was nearly four times as great as the rate at which specialists become generalists. We also found more specialist parasites and greater parasite diversity in African lowland rainforests as compared to the more climatically variable habitats of the fynbos and the highland forests. Thus, with environmental changes, we anticipate a change in the distribution of both specialist and generalist parasites with potential impacts on bird communities.

Evolution of CDC42, a putative virulence factor triggering meristematic growth in black yeasts

The cell division cycle gene (CDC42) controlling cellular polarization was studied in members of Chaetothyriales. Based on ribosomal genes, ancestral members of the order exhibit meristematic growth in view of their colonization of inert surfaces such as rock, whereas in derived members of the order the gene is a putative virulence factor involved in expression of the muriform cell, the invasive phase in human chromoblastomycosis. Specific primers were developed to amplify a portion of the gene of 32 members of the order with known position according to ribosomal phylogeny. Phylogeny of CDC42 proved to be very different. In all members of Chaetohyriales the protein sequence is highly conserved. In most species, distributed all over the phylogenetic tree, introns and 3^rd codon positions are also invariant. However, a number of species had paralogues with considerable deviation in non-coding exon positions, and synchronous variation in introns, although non-synonomous variation had remained very limited. In some strains both orthologues and paralogues were present. It is concluded that CDC42 does not show any orthologous evolution, and that its paralogues haves the same function but are structurally relaxed. The variation or absence thereof could not be linked to ecological changes, from rock-inhabiting to pathogenic life style. It is concluded that eventual pathogenicity in Chaetothyriales is not expressed at the DNA level in CDC42 evolution.

Phylogenesis of brain-derived neurotrophic factor (BDNF) in vertebrates

Brain-derived neurotrophic factor (BDNF) belongs to neurotrophin family, a class of molecules playing key roles in neuronal development, survival and regeneration, neurite growth and plasticity: memory processes are mainly affected, and mutations of the human BDNF gene are associated to cognitive and behavioural disturbances. All neurotrophins contain a highly conserved C-terminal domain and bind to the same receptor family. Both correct folding and post-translational processing of the entire preproprotein are pivotal for sorting to the extracellular space, dimerization and receptor binding. Evolutionary studies conducted so far demonstrate that a single ancestor gene underwent two independent duplication events at an early stage of vertebrate evolution, leading to the formation of the current neurotrophins. However, works focusing on BDNF evolution are scarce and fragmentary, mainly in lower vertebrates. In this work, we report cloning of eight DNA sequences from amphibians and teleosts, and analysis of the entire coding regions (cDNA sequences) of BDNF from 35 organisms, from teleosts to mammals. A phylogenetic tree was constructed and the analysis of non-synonymous-synonymous substitution rates performed for the different branches. Our results suggest that natural selection is acting on mammals, separating them from other classes. Since preproprotein cleavage and 3D structure of mature protein are important for functional activity of BDNF, we also propose a de novo prediction of the 3D structure of translates in at least one species for each class, in order to get hints about the functional constraints of the protein.

Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence

MOTIVATION

Functional divergence among proteins is often assumed to be strongly influenced by natural selection, as inferred from the ratio of non-synonymous nucleotide divergence (d(N)) to synonymous nucleotide divergence (d(S)). That is, the more a mutation changes protein function, the more likely it is to be either selected against or selectively favored, and because the d(N)/d(S) ratio is a measure of natural selection, this ratio can be used to predict the degree of functional divergence (d(F)). However, these hypotheses have rarely been experimentally tested.

RESULTS

I present a novel method to address this issue, and demonstrate that divergence in bacteria-killing activity among animal antimicrobial peptides is positively correlated with the log of the d(N)/d(S) ratio. The primary cause of this pattern appears to be that positively selected substitutions change protein function more than neutral substitutions do. Thus, the d(N)/d(S) ratio is an accurate estimator of adaptive functional divergence.

CONTACT

tennessj@science.oregonstate.edu

SUPPLEMENTARY INFORMATION

Supplementary data, including GenBank Accession numbers, are available at Bioinformatics online.

Formation and evolution of the chordate neurotrophin and Trk receptor genes

Neurotrophins are structurally related neurotrophic polypeptide factors that regulate neuronal differentiation and are essential for neuronal survival, neurite growth and plasticity. It has until very recently been thought that the neurotrophin system appeared with the vertebrate species, but identification of a cephalochordate neurotrophin receptor (Trk), and more recently neurotrophin sequences in several genomes of deuterostome invertebrates, show that the system already existed at the stem of the deuterostome group. Comparative genomics supports the hypothesis that two whole genome duplications produced many of the vertebrate gene families, among those the neurotrophin and Trk families. It remains to be proven to what extent the whole genome duplications have driven macroevolutionary change, but it appears certain that the formation of the multi-gene copy neurotrophin and Trk receptor families at the stem of vertebrates has provided a foundation from which the various functions and pleiotropic effects produced by each of the four extant neurotrophins have evolved.