Luís Fábio Silveira

Ticks collected on birds in the state of São Paulo, Brazil

The present study reports a collection of Amblyomma spp. ticks in birds from several areas of the state of São Paulo, Brazil. A total of 568 tick specimens (404 larvae, 164 nymphs) were collected from 261 bird specimens. From these ticks, 204 (36%) specimens (94 larvae, 110 nymphs) were reared to the adult stage, being identified as Amblyomma longirostre (94 larvae, 90 nymphs), Amblyomma calcaratum (13 nymphs), Amblyomma nodosum (2 nymphs), and Amblyomma cajennense (5 nymphs). Additionally, 39 larvae reared to the nymphal stage and 8 nymphs that died before reaching the adult stage were identified as A. longirostre according to peculiar characters inherent to the nymphal stage of this species: scutum elongate, and hypostome pointed. The remaining 271 larvae and 46 nymphs were identified as Amblyomma sp. Ticks were collected from 51 species of birds distributed in 22 bird families and 6 orders. The order Passeriformes constituted the vast majority of the records, comprising 253 (97%) out of the 261 infested birds. Subadults of A. longirostre were identified from 35 species of Passeriformes, comprising 11 families (Cardinalidae, Dendrocolaptidae, Fringillidae, Furnariidae, Parulidae, Pipridae, Thamnophilidae, Thraupidae, Turdidae, Tyrannidae, and Vireonidae), and from 1 species of a non-passerine bird, a puffbird (Bucconidae). Subadults of A. calcaratum were identified from 5 species of Passeriformes, comprising 5 families (Cardinalinae, Conopophagidae, Pipridae, Thamnophilidae and Turdidae). Subadults of A. nodosum were identified from 2 species of Passeriformes, comprising two bird families (Thamnophilidae and Pipridae). Subadults of A. cajennense were identified from 2 species of non-passerine birds, belonging to 2 different orders (Ciconiiformes: Threskiornithidae, and Gruiformes: Cariamidae). Birds were usually infested by few ticks (mean infestation of 2.2 ticks per bird; range: 1–16). Currently, 82 bird species are known to be infested by immature stages of A. longirostre, with the vast majority [74 (90%)] being Passeriformes. Our results showed that Passeriformes seems to be primary hosts for subadult stages of A. longirostre, A. calcaratum, and A. nodosum. However, arboreal passerine birds seem to be the most important hosts for A. longirostre whereas ground-feeding passerine birds seem to be the most important for both A. calcaratum and A. nodosum. In contrast, the parasitism of birds by subadults of A. cajennense has been restricted to non-passerine birds.

Estimating abundance of unmarked animal populations: accounting for imperfect detection and other sources of zero inflation

Summary 1. Inference and estimates of abundance are critical for quantifying population dynamics and impacts of environmental change. Yet imperfect detection and other phenomena that cause zero inflation can induce estimation error and obscure ecological patterns. 2. Recent statistical advances provide an increasingly diverse array of analytical approaches for estimating population size to address these phenomena. 3. We examine how detection error and zero inflation in count data inform the choice of analytical method for estimating population size of unmarked individuals that are not uniquely identified. We review two established (GLMs and distance sampling) and nine emerging methods that use N-mixture models (Royle–Nichols model, and basic, zero inflated, temporary emigration, beta-binomial, generalized open-population, spatially explicit, single visit and multispecies) to estimate abundance of unmarked populations, focusing on their requirements and how each method accounts for imperfect detection and zero inflation. 4. Eight of the emerging methods can account for both imperfect detection and additional variation in population size in the forms of non-occupancy, temporary emigration, correlated detection and population dynamics. 5. Methods differ in sampling design requirements (e.g. count vs. detection/non-detection data, single vs. multiple visits, covariate data), and their suitability for a particular study will depend on the characteristics of the study species, scale and objectives of the study, and financial and logistical considerations. 6. Most emerging methods were developed over the past decade, so their efficacy is still under study, and additional statistical advances are likely to occur.

Para que servem os inventários de fauna

Inventarios de fauna acessam diretamente a diversidade de uma localidade, em um determinado espaco e tempo. Os dados primarios gerados pelos inventarios compoem uma das ferramentas mais importantes na tomada de decisoes a respeito do manejo de areas naturais. Entretanto, varios problemas tem sido observados em diversos niveis relacionados aos inventarios de fauna no Brasil e vao desde a formacao de recursos humanos ate a ausencia de padronizacao, de desenho experimental e de selecao de metodos inadequados. Sao apresentados estudos de caso com mamiferos, repteis, anfibios e peixes, nos quais sao discutidos problemas como variabilidade temporal e metodos para deteccao de fauna terrestre, sugerindo que tanto os inventarios quanto os programas de monitoramento devam se estender por prazos maiores e que os inventarios devem incluir diferentes metodologias para que os seus objetivos sejam plenamente alcancados.

Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae).

Buteonine hawks represent one of the most diverse groups in the Accipitridae, with 58 species distributed in a variety of habitats on almost all continents. Variations in migratory behavior, remarkable dispersal capability, and unusual diversity in Central and South America make buteonine hawks an excellent model for studies in avian evolution. To evaluate the history of their global radiation, we used an integrative approach that coupled estimation of the phylogeny using a large sequence database (based on 6411 bp of mitochondrial markers and one nuclear intron from 54 species), divergence time estimates, and ancestral state reconstructions. Our findings suggest that Neotropical buteonines resulted from a long evolutionary process that began in the Miocene and extended to the Pleistocene. Colonization of the Nearctic, and eventually the Old World, occurred from South America, promoted by the evolution of seasonal movements and development of land bridges. Migratory behavior evolved several times and may have contributed not only to colonization of the Holarctic, but also derivation of insular species. In the Neotropics, diversification of the buteonines included four disjunction events across the Andes. Adaptation of monophyletic taxa to wet environments occurred more than once, and some relationships indicate an evolutionary connection among mangroves, coastal and várzea environments. On the other hand, groups occupying the same biome, forest, or open vegetation habitats are not monophyletic. Refuges or sea-level changes or a combination of both was responsible for recent speciation in Amazonian taxa. In view of the lack of concordance between phylogeny and classification, we propose numerous taxonomic changes.

Distinguishing Noise from Signal in Patterns of Genomic Divergence in a Highly Polymorphic Avian Radiation

Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated or that may cross species barriers through introgressive hybridization. Here we use a reduced‐representation genomic approach to explore divergence among six species of southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. For the first time in these taxa, we discovered a small proportion of markers that appeared differentiated among species. However, when assessing the significance of these signatures of divergence, we found that similar patterns can also be recovered from random grouping of individuals representing different species. A detailed demographic inference indicates that genetic differences among Sporophila species could be the consequence of neutral processes, which include a very large ancestral effective population size that accentuates the effects of incomplete lineage sorting. As these neutral phenomena can generate genomic scan patterns that mimic those of markers involved in speciation and phenotypic differentiation, they highlight the need for caution when ascertaining and interpreting differentiated markers between species, especially when large numbers of markers are surveyed. Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans.

Does counting species count as taxonomy? On misrepresenting systematics, yet again

Recent commentary by Costello and collaborators on the current state of the global taxonomic enterprise attempts to demonstrate that taxonomy is not in decline as feared by taxonomists, but rather is increasing by virtue of the rate at which new species are formally named. Having supported their views with data that clearly indicate as much, Costello et al. make recommendations to increase the rate of new species descriptions even more. However, their views appear to rely on the perception of species as static and numerically if not historically equivalent entities whose value lie in their roles as “metrics”. As such, their one‐dimensional portrayal of the discipline, as concerned solely with the creation of new species names, fails to take into account both the conceptual and epistemological foundations of systematics. We refute the end‐user view that taxonomy is on the rise simply because more new species are being described compared with earlier decades, and that, by implication, taxonomic practice is a formality whose pace can be streamlined without considerable resources, intellectual or otherwise. Rather, we defend the opposite viewpoint that professional taxonomy is in decline relative to the immediacy of the extinction crisis, and that this decline threatens not just the empirical science of phylogenetic systematics, but also the foundations of comparative biology on which other fields rely. The allocation of space in top‐ranked journals to propagate views such as those of Costello et al. lends superficial credence to the unsupportive mindset of many of those in charge of the institutional fate of taxonomy. We emphasize that taxonomy and the description of new species are dependent upon, and only make sense in light of, empirically based classifications that reflect evolutionary history; homology assessments are at the centre of these endeavours, such that the biological sciences cannot afford to have professional taxonomists sacrifice the comparative and historical depth of their hypotheses in order to accelerate new species descriptions.

Repeated divergent selection on pigmentation genes in a rapid finch radiation

Selection acted repeatedly on regions that may regulate the expression of genes underlying coloration differences in seedeaters. Instances of recent and rapid speciation are suitable for associating phenotypes with their causal genotypes, especially if gene flow homogenizes areas of the genome that are not under divergent selection. We study a rapid radiation of nine sympatric bird species known as capuchino seedeaters, which are differentiated in sexually selected characters of male plumage and song. We sequenced the genomes of a phenotypically diverse set of species to search for differentiated genomic regions. Capuchinos show differences in a small proportion of their genomes, yet selection has acted independently on the same targets in different members of this radiation. Many divergent regions contain genes involved in the melanogenesis pathway, with the strongest signal originating from putative regulatory regions. Selection has acted on these same genomic regions in different lineages, likely shaping the evolution of cis-regulatory elements, which control how more conserved genes are expressed and thereby generate diversity in classically sexually selected traits.

Checklist das aves do Estado de São Paulo, Brasil

Species lists are essential to understand both temporal and distributional patterns of taxa. Based on data compiled by CEO (Centro de Estudos Ornitologicos), Willis and Oniki (2003), and from a search of more than 50 theses, dissertations, monographs and technical works, we listed all bird species recorded in the State of Sao Paulo. These records are composed of skins and other evidence collected and deposited in collections, and on photographs and voice samples. A total of 793 species were registered, distributed in 25 orders and 85 families, and corresponding to 45% of the Brazilian avifauna. Reasons for this high diversity are related to the environmental diversity found in the state, influenced by altitudinal and geographical ranges, different phytophysiognomies, presence of a coastal region, and areas of contact between forest ecosystems and Cerrado. Results of the Biota project contributed to a better understanding of how birds respond to anthropogenic alterations of the environment, such as habitat fragmentation. The main ornithological research groups are still based in universities and museums. Deficiencies of knowledge concerning bird studies in Sao Paulo are related to the lack of standardization of survey methodologies; paucity in the monitoring of threatened species in the long term; restricted knowledge about species capacity to use matrix; and lack of refinement in the delimitation of evolutionary units and their distribution, which is essential for species reintroduction in regions where they have gone extinct.

The First Occurrence in the Fossil Record of an Aquatic Avian Twig-Nest with Phoenicopteriformes Eggs: Evolutionary Implications

Background We describe the first occurrence in the fossil record of an aquatic avian twig-nest with five eggs in situ (Early Miocene Tudela Formation, Ebro Basin, Spain). Extensive outcrops of this formation reveal autochthonous avian osteological and oological fossils that represent a single taxon identified as a basal phoenicopterid. Although the eggshell structure is definitively phoenicopterid, the characteristics of both the nest and the eggs are similar to those of modern grebes. These observations allow us to address the origin of the disparities between the sister taxa Podicipedidae and Phoenicopteridae crown clades, and traces the evolution of the nesting and reproductive environments for phoenicopteriforms. Methodology/Principal Findings Multi-disciplinary analyses performed on fossilized vegetation and eggshells from the eggs in the nest and its embedding sediments indicate that this new phoenicopterid thrived under a semi-arid climate in an oligohaline (seasonally mesohaline) shallow endorheic lacustine environment. High-end microcharacterizations including SEM, TEM, and EBSD techniques were pivotal to identifying these phoenicopterid eggshells. Anatomical comparisons of the fossil bones with those of Phoenicopteriformes and Podicipediformes crown clades and extinct palaelodids confirm that this avian fossil assemblage belongs to a new and basal phoenicopterid. Conclusions/Significance Although the Podicipediformes-Phoenicopteriformes sister group relationship is now well supported, flamingos and grebes exhibit feeding, reproductive, and nesting strategies that diverge significantly. Our multi-disciplinary study is the first to reveal that the phoenicopteriform reproductive behaviour, nesting ecology and nest characteristics derived from grebe-like type strategies to reach the extremely specialized conditions observed in modern flamingo crown groups. Furthermore, our study enables us to map ecological and reproductive characters on the Phoenicopteriformes evolutionary lineage. Our results demonstrate that the nesting paleoenvironments of flamingos were closely linked to the unique ecology of this locality, which is a direct result of special climatic (high evaporitic regime) and geological (fault system) conditions.

Range extensions and conservation of some threatened or little known Brazilian grassland birds.

Populations of grassland birds are declining in Brazil due to profound alterations to grassland habitats. In this paper, we present recent records and range extensions for 12 threatened or little known Brazilian grassland species: Ocellated Crake Micropygia schomburgkii , Sickle-winged Nightjar Eleothreptus anomalus , Campo Miner Geositta poeciloptera , Rufous-sided Pygmy-tyrant Euscarthmus rufomarginatus , Sharp-tailed Grass-tyrant Culicivora caudacuta , Cock-tailed Tyrant Alectrurus tricolor , Cinereous Warbling-finch Poospiza cinerea , Black-masked Finch Coryphaspiza melanotis , Tawny-bellied Seedeater Sporophila hypoxantha , Marsh Seedeater S . palustris , Chestnut Seedeater S . cinnamomea and Black-bellied Seedeater S . melanogaster . We also comment on the biogeography and conservation of these species.