Browsing by Subject "Birds"

Now showing 1 - 20 of 59

Open Access
A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis.
(BMC Evol Biol, 2015-06-30) Ribeiro, Ângela M; Zepeda-Mendoza, M Lisandra; Bertelsen, Mads F; Kristensen, Annemarie T; Jarvis, Erich D; Gilbert, M Thomas P; da Fonseca, Rute R
BACKGROUND: Hemostasis is a defense mechanism that enhances an organism's survival by minimizing blood loss upon vascular injury. In vertebrates, hemostasis has been evolving with the cardio-vascular and hemodynamic systems over the last 450 million years. Birds and mammals have very similar vascular and hemodynamic systems, thus the mechanism that blocks ruptures in the vasculature is expected to be the same. However, the speed of the process varies across vertebrates, and is particularly slow for birds. Understanding the differences in the hemostasis pathway between birds and mammals, and placing them in perspective to other vertebrates may provide clues to the genetic contribution to variation in blood clotting phenotype in vertebrates. We compiled genomic data corresponding to key elements involved in hemostasis across vertebrates to investigate its genetic basis and understand how it affects fitness. RESULTS: We found that: i) fewer genes are involved in hemostasis in birds compared to mammals; and ii) the largest differences concern platelet membrane receptors and components from the kallikrein-kinin system. We propose that lack of the cytoplasmic domain of the GPIb receptor subunit alpha could be a strong contributor to the prolonged bleeding phenotype in birds. Combined analysis of laboratory assessments of avian hemostasis with the first avian phylogeny based on genomic-scale data revealed that differences in hemostasis within birds are not explained by phylogenetic relationships, but more so by genetic variation underlying components of the hemostatic process, suggestive of natural selection. CONCLUSIONS: This work adds to our understanding of the evolution of hemostasis in vertebrates. The overlap with the inflammation, complement and renin-angiotensin (blood pressure regulation) pathways is a potential driver of rapid molecular evolution in the hemostasis network. Comparisons between avian species and mammals allowed us to hypothesize that the observed mammalian innovations might have contributed to the diversification of mammals that give birth to live young.
Open Access
Avian brains and a new understanding of vertebrate brain evolution.
(Nat Rev Neurosci, 2005-02) Jarvis, Erich D; Güntürkün, Onur; Bruce, Laura; Csillag, András; Karten, Harvey; Kuenzel, Wayne; Medina, Loreta; Paxinos, George; Perkel, David J; Shimizu, Toru; Striedter, Georg; Wild, J Martin; Ball, Gregory F; Dugas-Ford, Jennifer; Durand, Sarah E; Hough, Gerald E; Husband, Scott; Kubikova, Lubica; Lee, Diane W; Mello, Claudio V; Powers, Alice; Siang, Connie; Smulders, Tom V; Wada, Kazuhiro; White, Stephanie A; Yamamoto, Keiko; Yu, Jing; Reiner, Anton; Butler, Ann B; Avian Brain Nomenclature Consortium
We believe that names have a powerful influence on the experiments we do and the way in which we think. For this reason, and in the light of new evidence about the function and evolution of the vertebrate brain, an international consortium of neuroscientists has reconsidered the traditional, 100-year-old terminology that is used to describe the avian cerebrum. Our current understanding of the avian brain - in particular the neocortex-like cognitive functions of the avian pallium - requires a new terminology that better reflects these functions and the homologies between avian and mammalian brains.
Open Access
Avian Distribution Patterns and Conservation in Amazonia
(2007-10-19) Vale, Mariana M
In this dissertation, I address the distribution and conservation of the Amazonian avifauna at several different scales. In Chapter 1, I looked at how the spatial bias in ornithological collections affects our understanding of the patterns of diversity in Amazonia. I showed that Amazonia is massively under-collected, that biological collection sites cluster around points of access, and that the richness at collection localities is higher than would be expected at random. This greater richness in collected areas was associated with a higher proportion of species with small geographical ranges as compared to uncollected areas. These small range species are relevant for conservation, as they are especially prone to extinction. I concluded that the richness of the uncollected areas of Amazonia is seriously underestimated, and that current knowledge gaps preclude accurate selection of areas for conservation in Amazonia. With this in mind, I modeled the impacts of continued deforestation on the Amazonian endemic avifauna. To overcome knowledge gaps, I complemented bird range maps with a "bird-ecoregions." I identified several taxa and bird-ecoregions likely to face great threat in the near future, most of them associated with riverine habitats. To evaluate these predictions, I conducted a detailed study on two riverine species: the Rio Branco Antbird (Cercomacra carbonaria) and the Hoary-throated Spinetail (Synallaxis kollari). Both are threatened and endemic to the gallery forests of Roraima, Brazil. I predicted that both would lose critical habitat in the near future. I concluded that neither is categorized correctly in by The World Conservation Union and recommend the down-listing of the Rio-Branco-Antbird and the up-listing of the Hoary-throated Spinetail. I also explored the importance of indigenous reserves for the conservation of both species and emphasized the need for greater involvement of conservation biologists in the social issues related to their study organisms.
Open Access
Avian genomes. A flock of genomes. Introduction.
(Science, 2014-12-12) Zhang, Guojie; Jarvis, Erich D; Gilbert, M Thomas P
Open Access
Avianbase: a community resource for bird genomics.
(Genome Biol, 2015-01-29) Eöry, Lél; Gilbert, M Thomas P; Li, Cai; Li, Bo; Archibald, Alan; Aken, Bronwen L; Zhang, Guojie; Jarvis, Erich; Flicek, Paul; Burt, David W
Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released by the Avian Phylogenomics Consortium.
Open Access
Batch-produced, GIS-informed range maps for birds based on provenanced, crowd-sourced data inform conservation assessments.
(PloS one, 2021-01) Huang, Ryan M; Medina, Wilderson; Brooks, Thomas M; Butchart, Stuart HM; Fitzpatrick, John W; Hermes, Claudia; Jenkins, Clinton N; Johnston, Alison; Lebbin, Daniel J; Li, Binbin V; Ocampo-Peñuela, Natalia; Parr, Mike; Wheatley, Hannah; Wiedenfeld, David A; Wood, Christopher; Pimm, Stuart L
Accurate maps of species ranges are essential to inform conservation, but time-consuming to produce and update. Given the pace of change of knowledge about species distributions and shifts in ranges under climate change and land use, a need exists for timely mapping approaches that enable batch processing employing widely available data. We develop a systematic approach of batch-processing range maps and derived Area of Habitat maps for terrestrial bird species with published ranges below 125,000 km2 in Central and South America. (Area of Habitat is the habitat available to a species within its range.) We combine existing range maps with the rapidly expanding crowd-sourced eBird data of presences and absences from frequently surveyed locations, plus readily accessible, high resolution satellite data on forest cover and elevation to map the Area of Habitat available to each species. Users can interrogate the maps produced to see details of the observations that contributed to the ranges. Previous estimates of Areas of Habitat were constrained within the published ranges and thus were, by definition, smaller-typically about 30%. This reflects how little habitat within suitable elevation ranges exists within the published ranges. Our results show that on average, Areas of Habitat are 12% larger than published ranges, reflecting the often-considerable extent that eBird records expand the known distributions of species. Interestingly, there are substantial differences between threatened and non-threatened species. Some 40% of Critically Endangered, 43% of Endangered, and 55% of Vulnerable species have Areas of Habitat larger than their published ranges, compared with 31% for Near Threatened and Least Concern species. The important finding for conservation is that threatened species are generally more widespread than previously estimated.
Open Access
Behaviourally driven gene expression reveals song nuclei in hummingbird brain.
(Nature, 2000-08-10) Jarvis, ED; Ribeiro, S; da Silva, ML; Ventura, D; Vielliard, J; Mello, CV
Hummingbirds have developed a wealth of intriguing features, such as backwards flight, ultraviolet vision, extremely high metabolic rates, nocturnal hibernation, high brain-to-body size ratio and a remarkable species-specific diversity of vocalizations. Like humans, they have also developed the rare trait of vocal learning, this being the ability to acquire vocalizations through imitation rather than instinct. Here we show, using behaviourally driven gene expression in freely ranging tropical animals, that the forebrain of hummingbirds contains seven discrete structures that are active during singing, providing the first anatomical and functional demonstration of vocal nuclei in hummingbirds. These structures are strikingly similar to seven forebrain regions that are involved in vocal learning and production in songbirds and parrots--the only other avian orders known to be vocal learners. This similarity is surprising, as songbirds, parrots and hummingbirds are thought to have evolved vocal learning and associated brain structures independently, and it indicates that strong constraints may influence the evolution of forebrain vocal nuclei.
Open Access
Bird extirpations and community dynamics in an Andean cloud forest over 100 years of land-use change.
(Conservation biology : the journal of the Society for Conservation Biology, 2020-06) Palacio, Ruben D; Kattan, Gustavo H; Pimm, Stuart L
Long-term studies to understand biodiversity changes remain scarce-especially so for tropical mountains. We examined changes from 1911 to 2016 in the bird community of the cloud forest of San Antonio, a mountain ridge in the Colombian Andes. We evaluated the effects of past land-use change and assessed species vulnerability to climate disruption. Forest cover decreased from 95% to 50% by 1959, and 33 forest species were extirpated. From 1959 to 1990, forest cover remained stable, and an additional 15 species were lost-a total of 29% of the forest bird community. Thereafter, forest cover increased by 26% and 17 species recolonized the area. The main cause of extirpations was the loss of connections to adjacent forests. Of the 31 (19%) extirpated birds, 25 have ranges peripheral to San Antonio, mostly in the lowlands. Most still occurred regionally, but broken forest connections limited their recolonization. Other causes of extirpation were hunting, wildlife trade, and water diversion. Bird community changes included a shift from predominantly common species to rare species; forest generalists replaced forest specialists that require old growth, and functional groups, such as large-body frugivores and nectarivores, declined disproportionally. All water-dependent birds were extirpated. Of the remaining 122 forest species, 19 are vulnerable to climate disruption, 10 have declined in abundance, and 4 are threatened. Our results show unequivocal species losses and changes in community structure and abundance at the local scale. We found species were extirpated after habitat loss and fragmentation, but forest recovery stopped extirpations and helped species repopulate. Land-use changes increased species vulnerability to climate change, and we suggest reversing landscape transformation may restore biodiversity and improve resistance to future threats.
Open Access
Brain evolution by brain pathway duplication.
(Philos Trans R Soc Lond B Biol Sci, 2015-12-19) Chakraborty, Mukta; Jarvis, Erich D
Understanding the mechanisms of evolution of brain pathways for complex behaviours is still in its infancy. Making further advances requires a deeper understanding of brain homologies, novelties and analogies. It also requires an understanding of how adaptive genetic modifications lead to restructuring of the brain. Recent advances in genomic and molecular biology techniques applied to brain research have provided exciting insights into how complex behaviours are shaped by selection of novel brain pathways and functions of the nervous system. Here, we review and further develop some insights to a new hypothesis on one mechanism that may contribute to nervous system evolution, in particular by brain pathway duplication. Like gene duplication, we propose that whole brain pathways can duplicate and the duplicated pathway diverge to take on new functions. We suggest that one mechanism of brain pathway duplication could be through gene duplication, although other mechanisms are possible. We focus on brain pathways for vocal learning and spoken language in song-learning birds and humans as example systems. This view presents a new framework for future research in our understanding of brain evolution and novel behavioural traits.
Open Access
Brain gene regulation by territorial singing behavior in freely ranging songbirds.
(Neuroreport, 1997-05-27) Jarvis, ED; Schwabl, H; Ribeiro, S; Mello, CV
To investigate the ecological relevance of brain gene regulation associated with singing behavior in songbirds, we challenged freely ranging song sparrows with conspecific song playbacks within their breeding territories. Males responded by approaching the speaker, searching for an intruder and actively singing. In situ hybridization of brain sections revealed significantly higher expression of the transcriptional regulator ZENK in challenged birds than in unstimulated controls in several auditory structures and song control nuclei. We conclude that singing behavior in the context of territorial defense is associated with gene regulation in brain centers that control song perception and production, and that behaviorally regulated gene expression can be used to investigate brain areas involved in the natural behaviors of freely ranging animals.
Open Access
China's endemic vertebrates sheltering under the protective umbrella of the giant panda.
(Conservation biology : the journal of the Society for Conservation Biology, 2016-04) Li, Binbin V; Pimm, Stuart L
The giant panda attracts disproportionate conservation resources. How well does this emphasis protect other endemic species? Detailed data on geographical ranges are not available for plants or invertebrates, so we restrict our analyses to 3 vertebrate taxa: birds, mammals, and amphibians. There are gaps in their protection, and we recommend practical actions to fill them. We identified patterns of species richness, then identified which species are endemic to China, and then which, like the panda, live in forests. After refining each species' range by its known elevational range and remaining forest habitats as determined from remote sensing, we identified the top 5% richest areas as the centers of endemism. Southern mountains, especially the eastern Hengduan Mountains, were centers for all 3 taxa. Over 96% of the panda habitat overlapped the endemic centers. Thus, investing in almost any panda habitat will benefit many other endemics. Existing panda national nature reserves cover all but one of the endemic species that overlap with the panda's distribution. Of particular interest are 14 mammal, 20 bird, and 82 amphibian species that are inadequately protected. Most of these species the International Union for Conservation of Nature currently deems threatened. But 7 mammal, 3 bird, and 20 amphibian species are currently nonthreatened, yet their geographical ranges are <20,000 km(2) after accounting for elevational restriction and remaining habitats. These species concentrate mainly in Sichuan, Yunnan, Nan Mountains, and Hainan. There is a high concentration in the east Daxiang and Xiaoxiang Mountains of Sichuan, where pandas are absent and where there are no national nature reserves. The others concentrate in Yunnan, Nan Mountains, and Hainan. Here, 10 prefectures might establish new protected areas or upgrade local nature reserves to national status.
Open Access
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.
(Mol Ecol, 2010-03) Künstner, Axel; Wolf, Jochen BW; Backström, Niclas; Whitney, Osceola; Balakrishnan, Christopher N; Day, Lainy; Edwards, Scott V; Janes, Daniel E; Schlinger, Barney A; Wilson, Richard K; Jarvis, Erich D; Warren, Wesley C; Ellegren, Hans
Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with approximately 1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.
Open Access
Comparative genomics reveals insights into avian genome evolution and adaptation.
(Science, 2014-12-12) Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M; Lee, Chul; Storz, Jay F; Antunes, Agostinho; Greenwold, Matthew J; Meredith, Robert W; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S; Gatesy, John; Hoffmann, Federico G; Opazo, Juan C; Håstad, Olle; Sawyer, Roger H; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A; Green, Richard E; O'Brien, Stephen J; Griffin, Darren; Johnson, Warren E; Haussler, David; Ryder, Oliver A; Willerslev, Eske; Graves, Gary R; Alström, Per; Fjeldså, Jon; Mindell, David P; Edwards, Scott V; Braun, Edward L; Rahbek, Carsten; Burt, David W; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Avian Genome Consortium; Jarvis, Erich D; Gilbert, M Thomas P; Wang, Jun
Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
Open Access
Complex evolutionary trajectories of sex chromosomes across bird taxa.
(Science, 2014-12-12) Zhou, Qi; Zhang, Jilin; Bachtrog, Doris; An, Na; Huang, Quanfei; Jarvis, Erich D; Gilbert, M Thomas P; Zhang, Guojie
Sex-specific chromosomes, like the W of most female birds and the Y of male mammals, usually have lost most genes owing to a lack of recombination. We analyze newly available genomes of 17 bird species representing the avian phylogenetic range, and find that more than half of them do not have as fully degenerated W chromosomes as that of chicken. We show that avian sex chromosomes harbor tremendous diversity among species in their composition of pseudoautosomal regions and degree of Z/W differentiation. Punctuated events of shared or lineage-specific recombination suppression have produced a gradient of "evolutionary strata" along the Z chromosome, which initiates from the putative avian sex-determining gene DMRT1 and ends at the pseudoautosomal region. W-linked genes are subject to ongoing functional decay after recombination was suppressed, and the tempo of degeneration slows down in older strata. Overall, we unveil a complex history of avian sex chromosome evolution.
Open Access
Convergent differential regulation of parvalbumin in the brains of vocal learners.
(PLoS One, 2012) Hara, Erina; Rivas, Miriam V; Ward, James M; Okanoya, Kazuo; Jarvis, Erich D
Spoken language and learned song are complex communication behaviors found in only a few species, including humans and three groups of distantly related birds--songbirds, parrots, and hummingbirds. Despite their large phylogenetic distances, these vocal learners show convergent behaviors and associated brain pathways for vocal communication. However, it is not clear whether this behavioral and anatomical convergence is associated with molecular convergence. Here we used oligo microarrays to screen for genes differentially regulated in brain nuclei necessary for producing learned vocalizations relative to adjacent brain areas that control other behaviors in avian vocal learners versus vocal non-learners. A top candidate gene in our screen was a calcium-binding protein, parvalbumin (PV). In situ hybridization verification revealed that PV was expressed significantly higher throughout the song motor pathway, including brainstem vocal motor neurons relative to the surrounding brain regions of all distantly related avian vocal learners. This differential expression was specific to PV and vocal learners, as it was not found in avian vocal non-learners nor for control genes in learners and non-learners. Similar to the vocal learning birds, higher PV up-regulation was found in the brainstem tongue motor neurons used for speech production in humans relative to a non-human primate, macaques. These results suggest repeated convergent evolution of differential PV up-regulation in the brains of vocal learners separated by more than 65-300 million years from a common ancestor and that the specialized behaviors of learned song and speech may require extra calcium buffering and signaling.
Open Access
Convergent differential regulation of SLIT-ROBO axon guidance genes in the brains of vocal learners.
(J Comp Neurol, 2015-04-15) Wang, Rui; Chen, Chun-Chun; Hara, Erina; Rivas, Miriam V; Roulhac, Petra L; Howard, Jason T; Chakraborty, Mukta; Audet, Jean-Nicolas; Jarvis, Erich D
Only a few distantly related mammals and birds have the trait of complex vocal learning, which is the ability to imitate novel sounds. This ability is critical for speech acquisition and production in humans, and is attributed to specialized forebrain vocal control circuits that have several unique connections relative to adjacent brain circuits. As a result, it has been hypothesized that there could exist convergent changes in genes involved in neural connectivity of vocal learning circuits. In support of this hypothesis, expanding on our related study (Pfenning et al. [2014] Science 346: 1256846), here we show that the forebrain part of this circuit that makes a relatively rare direct connection to brainstem vocal motor neurons in independent lineages of vocal learning birds (songbird, parrot, and hummingbird) has specialized regulation of axon guidance genes from the SLIT-ROBO molecular pathway. The SLIT1 ligand was differentially downregulated in the motor song output nucleus that makes the direct projection, whereas its receptor ROBO1 was developmentally upregulated during critical periods for vocal learning. Vocal nonlearning bird species and male mice, which have much more limited vocal plasticity and associated circuits, did not show comparable specialized regulation of SLIT-ROBO genes in their nonvocal motor cortical regions. These findings are consistent with SLIT and ROBO gene dysfunctions associated with autism, dyslexia, and speech sound language disorders and suggest that convergent evolution of vocal learning was associated with convergent changes in the SLIT-ROBO axon guidance pathway.
Open Access
Convergent transcriptional specializations in the brains of humans and song-learning birds.
(Science, 2014-12-12) Pfenning, Andreas R; Hara, Erina; Whitney, Osceola; Rivas, Miriam V; Wang, Rui; Roulhac, Petra L; Howard, Jason T; Wirthlin, Morgan; Lovell, Peter V; Ganapathy, Ganeshkumar; Mouncastle, Jacquelyn; Moseley, M Arthur; Thompson, J Will; Soderblom, Erik J; Iriki, Atsushi; Kato, Masaki; Gilbert, M Thomas P; Zhang, Guojie; Bakken, Trygve; Bongaarts, Angie; Bernard, Amy; Lein, Ed; Mello, Claudio V; Hartemink, Alexander J; Jarvis, Erich D
Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes of song-learning birds and humans relative to vocal nonlearners identified convergent gene expression specializations in specific song and speech brain regions of avian vocal learners and humans. The strongest shared profiles relate bird motor and striatal song-learning nuclei, respectively, with human laryngeal motor cortex and parts of the striatum that control speech production and learning. Most of the associated genes function in motor control and brain connectivity. Thus, convergent behavior and neural connectivity for a complex trait are associated with convergent specialized expression of multiple genes.
Open Access
Differential expression of glutamate receptors in avian neural pathways for learned vocalization.
(J Comp Neurol, 2004-08-09) Wada, Kazuhiro; Sakaguchi, Hironobu; Jarvis, Erich D; Hagiwara, Masatoshi
Learned vocalization, the substrate for human language, is a rare trait. It is found in three distantly related groups of birds-parrots, hummingbirds, and songbirds. These three groups contain cerebral vocal nuclei for learned vocalization not found in their more closely related vocal nonlearning relatives. Here, we cloned 21 receptor subunits/subtypes of all four glutamate receptor families (AMPA, kainate, NMDA, and metabotropic) and examined their expression in vocal nuclei of songbirds. We also examined expression of a subset of these receptors in vocal nuclei of hummingbirds and parrots, as well as in the brains of dove species as examples of close vocal nonlearning relatives. Among the 21 subunits/subtypes, 19 showed higher and/or lower prominent differential expression in songbird vocal nuclei relative to the surrounding brain subdivisions in which the vocal nuclei are located. This included relatively lower levels of all four AMPA subunits in lMAN, strikingly higher levels of the kainite subunit GluR5 in the robust nucleus of the arcopallium (RA), higher and lower levels respectively of the NMDA subunits NR2A and NR2B in most vocal nuclei and lower levels of the metabotropic group I subtypes (mGluR1 and -5) in most vocal nuclei and the group II subtype (mGluR2), showing a unique expression pattern of very low levels in RA and very high levels in HVC. The splice variants of AMPA subunits showed further differential expression in vocal nuclei. Some of the receptor subunits/subtypes also showed differential expression in hummingbird and parrot vocal nuclei. The magnitude of differential expression in vocal nuclei of all three vocal learners was unique compared with the smaller magnitude of differences found for nonvocal areas of vocal learners and vocal nonlearners. Our results suggest that evolution of vocal learning was accompanied by differential expression of a conserved gene family for synaptic transmission and plasticity in vocal nuclei. They also suggest that neural activity and signal transduction in vocal nuclei of vocal learners will be different relative to the surrounding brain areas.
Open Access
Differential introgression of a female competitive trait in a hybrid zone between sex-role reversed species.
(Evolution; international journal of organic evolution, 2019-02) Lipshutz, Sara E; Meier, Joana I; Derryberry, Graham E; Miller, Matthew J; Miller, Matthew J; Seehausen, Ole; Derryberry, Elizabeth P
Mating behavior between recently diverged species in secondary contact can impede or promote reproductive isolation. Traditionally, researchers focus on the importance of female mate choice and male-male competition in maintaining or eroding species barriers. Although female-female competition is widespread, little is known about its role in the speciation process. Here, we investigate a case of interspecific female competition and its influence on patterns of phenotypic and genetic introgression between species. We examine a hybrid zone between sex-role reversed, Neotropical shorebird species, the northern jacana (Jacana spinosa) and wattled jacana (J. jacana), in which female-female competition is a major determinant of reproductive success. Previous work found that females of the more aggressive and larger species, J. spinosa, disproportionately mother hybrid offspring, potentially by monopolizing breeding territories in sympatry with J. jacana. We find a cline shift of female body mass relative to the genetic center of the hybrid zone, consistent with asymmetric introgression of this competitive trait. We suggest that divergence in sexual characteristics between sex-role reversed females can influence patterns of gene flow upon secondary contact, similar to males in systems with more typical sex roles.
Open Access
Dynamic evolution of base composition: causes and consequences in avian phylogenomics.
(Mol Biol Evol, 2011-08) Nabholz, Benoit; Künstner, Axel; Wang, Rui; Jarvis, Erich D; Ellegren, Hans
Resolving the phylogenetic relationships among birds is a classical problem in systematics, and this is particularly so when it comes to understanding the relationships among Neoaves. Previous phylogenetic inference of birds has been limited to mitochondrial genomes or a few nuclear genes. Here, we apply deep brain transcriptome sequencing of nine bird species (several passerines, hummingbirds, dove, parrot, and emu), using next-generation sequencing technology to understand features of transcriptome evolution in birds and how this affects phylogenetic inference, and combine with data from two bird species using first generation technology. The phylogenomic data matrix comprises 1,995 genes and a total of 0.77 Mb of exonic sequence. First, we find an unexpected heterogeneity in the evolution of base composition among avian lineages. There is a pronounced increase in guanine + cytosine (GC) content in the third codon position in several independent lineages, with the strongest effect seen in passerines. Second, we evaluate the effect of GC content variation on phylogenetic reconstruction. We find important inconsistencies between the topologies obtained with or without taking GC variation into account, each supporting different conclusions of past studies and also influencing hypotheses on the evolution of the trait of vocal learning. Third, we demonstrate a link between GC content evolution and recombination rate and, focusing on the zebra finch lineage, find that recombination seems to drive GC content. Although we cannot reveal the causal relationships, this observation is consistent with the model of GC-biased gene conversion. Finally, we use this unparalleled amount of avian sequence data to study the rate of molecular evolution, calibrated by fossil evidence and augmented with data from alligator transcriptome sequencing. There is a 2- to 3-fold variation in substitution rate among lineages with passerines being the most rapidly evolving and ratites the slowest. This study illustrates the potential of next-generation sequencing for phylogenomic studies but also the pitfalls when using genome-wide data with heterogeneous base composition.

Browsing by Subject "Birds"

Results Per Page

Sort Options