Species Limits and Phylogenomic Relationships of Darwin's Finches Remain Unresolved: Potential Consequences of a Volatile Ecological Setting.

Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin's finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin's finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies of prior data and analytic methods explained different proposed classifications, we were surprised to observe that three new phylogenetic hypotheses derived mostly from the same genomics data were topologically inconsistent. We found that the differences between some of these genomics trees were as great as one would expect between two random trees with the same number of taxa. Thus, the phylogeny of Darwin's finches remains unresolved, as it has for more than a century. A component of phylogenetic uncertainty comes from unclear species limits, under any species concept, in the ground finches (Geospiza) and tree finches (Camarhynchus). We suggest that past authors should have tested the species limits of Lack, rather than uncritically accepting them. In fact, the impressive amount of genomics data do not provide unambiguous hypotheses of the number of species of Geospiza or Camarhynchus, although they imply greater species diversity than Lack's taxonomy. We suggest that insufficient sampling of species populations across islands (35.6% for morphometrics and 20.4% for genomics) prevents accurate diagnoses of species limits. However, it is unknown whether samples from a greater number of islands might result in bridging differences between species, or reveal many new ones. We conclude that attempts to interpret patterns of variation among the finches under standard evolutionary paradigms have obscured some major messages, most specifically the ongoing reciprocal interactions between geographic isolation and lineage divergence, and dispersal and gene flow caused by the volatile ecological conditions in the islands. Although the finches provide textbook examples of natural selection, better understanding of species limits and a robust phylogenetic hypothesis are required to corroborate past hypotheses of speciation and adaptive radiation in the finches of the Galapagos.

The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch.

BACKGROUND: Darwin's finches are a clade of 19 species of passerine birds native to the Galápagos Islands, whose biogeography, specialized beak morphologies, and dietary choices-ranging from seeds to blood-make them a classic example of adaptive radiation. While these iconic birds have been intensely studied, the composition of their gut microbiome and the factors influencing it, including host species, diet, and biogeography, has not yet been explored. RESULTS: We characterized the microbial community associated with 12 species of Darwin's finches using high-throughput 16S rRNA sequencing of fecal samples from 114 individuals across nine islands, including the unusual blood-feeding vampire finch (Geospiza septentrionalis) from Darwin and Wolf Islands. The phylum-level core gut microbiome for Darwin's finches included the Firmicutes, Gammaproteobacteria, and Actinobacteria, with members of the Bacteroidetes at conspicuously low abundance. The gut microbiome was surprisingly well conserved across the diversity of finch species, with one exception-the vampire finch-which harbored bacteria that were either absent or extremely rare in other finches, including Fusobacterium, Cetobacterium, Ureaplasma, Mucispirillum, Campylobacter, and various members of the Clostridia-bacteria known from the guts of carnivorous birds and reptiles. Complementary stable isotope analysis of feathers revealed exceptionally high δ15N isotope values in the vampire finch, resembling top marine predators. The Galápagos archipelago is also known for extreme wet and dry seasons, and we observed a significant seasonal shift in the gut microbial community of five additional finch species sampled during both seasons. CONCLUSIONS: This study demonstrates the overall conservatism of the finch gut microbiome over short (< 1 Ma) divergence timescales, except in the most extreme case of dietary specialization, and elevates the evolutionary importance of seasonal shifts in driving not only species adaptation, but also gut microbiome composition.

Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins.

Genetic introgression among closely related species is a widespread phenomenon across the Tree of Life and could be an important source of adaptive variation during early stages of diversification. In particular, genomic studies have revealed that many rapidly radiating clades tend to have complex, reticulate evolutionary histories. Although rapid radiations appear to be susceptible to introgression, they present special challenges for its detection because formal tests require accurate phylogenies, and paradoxically, introgression itself may obscure evolutionary relationships. To address this methodological challenge, we assessed introgression in a recent, rapid avian radiation in the Andes, the South American siskins (Spinus). Using ~45,000 SNPs, we estimated the Spinus phylogeny using multiple analytical approaches and recovered four strongly conflicting topologies. We performed a series of complimentary introgression tests that included valid tests for each of the likely species trees. From the consilience of test results, we inferred multiple introgression events among Andean Spinus in a way that was robust to phylogenetic uncertainty in the species tree. Positive tests for introgression were corroborated by independent population structure and ancestral assignment analyses, as well as a striking geographic pattern of mitochondrial haplotype sharing among species. The methodological approach we describe could be applied using any genomewide data, including SNP data, for clades without fully resolvable species trees. Our discovery of multiple introgression events within the Andean radiation of Spinus siskins is consistent with an emerging paradigm, that introgression tends to accompany the early stages of diversification.

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches.

Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.

A beak size locus in Darwin's finches facilitated character displacement during a drought.

Ecological character displacement is a process of morphological divergence that reduces competition for limited resources. We used genomic analysis to investigate the genetic basis of a documented character displacement event in Darwin's finches on Daphne Major in the Galápagos Islands: The medium ground finch diverged from its competitor, the large ground finch, during a severe drought. We discovered a genomic region containing the HMGA2 gene that varies systematically among Darwin's finch species with different beak sizes. Two haplotypes that diverged early in the radiation were involved in the character displacement event: Genotypes associated with large beak size were at a strong selective disadvantage in medium ground finches (selection coefficient s = 0.59). Thus, a major locus has apparently facilitated a rapid ecological diversification in the adaptive radiation of Darwin's finches.

Striped-tailed Yellow-finch nesting success in abandoned mining pits from central Brazilian cerrado.

Suitability of degraded areas as breeding habitats can be tested through assessment of nest predation rates. In this study we estimated nest success in relation to several potential predictors of nest survival in the Stripe-tailed Yellow-finch (Sicalis citrina) breeding in abandoned mining pits at Brasília National Park. We monitored 73 nests during the 2007-breeding season. Predation was the main cause of nest failure (n = 48, 66%); while six nests were abandoned (8%) and 19 nests produced young (26%). Mayfield's daily survival rates and nest success were 0.94 and 23%, respectively. Our results from nest survival models on program MARK indicated that daily survival rates increase linearly towards the end of the breeding season and decrease as nests aged. None of the nest individual covariates we tested - nest height, nest size, nest substrate, and edge effect - were important predictors of nest survival; however, nests placed on the most common plant tended to have higher survival probabilities. Also, there was no observer effect on daily survival rates. Our study suggests that abandoned mining pits may be suitable alternative breeding habitats for Striped-tailed Yellow-finches since nest survival rates were similar to other studies in the central cerrado region.

Phylogeny and biogeography of the New World siskins and goldfinches: rapid, recent diversification in the Central Andes.

Time-calibrated molecular phylogenies can help us to understand the origins of the diverse and unique Andean avifauna. Previous studies have shown that the tempo of diversification differed between the Andes and adjacent lowland regions of South America. Andean taxa were found to have speciated more recently and to have avoided the decelerated diversification that is typical of Neotropical lowland clades. The South American siskins, a Pleistocene finch radiation, may typify this Andean pattern. We investigated the phylogenetic biogeography of all the New World siskins and goldfinches in new detail. To understand the specific role of the Andes in siskin diversification, we asked: (1) Was diversification faster in Andean siskin lineages relative to non-Andean ones? (2) Did siskin lineages move into and out of the Andes at different rates? We found that siskin lineages in the Andes had higher diversification rates and higher outward dispersal rates than siskin lineages outside the Andes. We conclude that páramo expansion and contraction in response to Pleistocene climatic cycles caused accelerated diversification and outward dispersal in Andean siskins. The younger average age of bird species in the Andes compared to lowland South America may be attributable to bursts of recent diversification in siskins and several other vagile, open-habitat clades.

Striped-tailed Yellow-finch nesting success in abandoned mining pits from central Brazilian cerrado / Sucesso reprodutivo de Sicalis citrina em cascalheiras abandonadas, região central do Cerrado

Suitability of degraded areas as breeding habitats can be tested through assessment of nest predation rates. In this study we estimated nest success in relation to several potential predictors of nest survival in the Stripe-tailed Yellow-finch (Sicalis citrina) breeding in abandoned mining pits at Brasília National Park. We monitored 73 nests during the 2007-breeding season. Predation was the main cause of nest failure (n = 48, 66%); while six nests were abandoned (8%) and 19 nests produced young (26%). Mayfield’s daily survival rates and nest success were 0.94 and 23%, respectively. Our results from nest survival models on program MARK indicated that daily survival rates increase linearly towards the end of the breeding season and decrease as nests aged. None of the nest individual covariates we tested - nest height, nest size, nest substrate, and edge effect - were important predictors of nest survival; however, nests placed on the most common plant tended to have higher survival probabilities. Also, there was no observer effect on daily survival rates. Our study suggests that abandoned mining pits may be suitable alternative breeding habitats for Striped-tailed Yellow-finches since nest survival rates were similar to other studies in the central cerrado region.

A adequação de habitats degradados para reprodução de aves pode ser testada por meio de avaliação das taxas de predação de ninhos. Neste estudo nós estimamos o sucesso de nidificação do canário-rasteiro (Sicalis citrina) e o relacionamos, por meio de modelagem no programa MARK, com diversos fatores que potencialmente afetam a sobrevivência dos ninhos da espécie em antigas áreas de extração de solo (cascalheiras), no Parque Nacional de Brasília, Distrito Federal. Nós monitoramos 73 ninhos da espécie durante a estação reprodutiva de 2007. Predação foi a principal causa da perda de ninhos (n = 48, 66%), enquanto seis foram abandonados (8%) e 19 produziram ao menos um filhote (26%). A taxa diária de sobrevivência e o sucesso total de Mayfield foram 0,94 and 23%, respectivamente. Nossos resultados, obtidos da modelagem de sobrevivência, indicaram que as taxas de sobrevivência diária dos ninhos aumenta linearmente à medida que avança a estação reprodutiva, ao passo que diminui conforme a idade do ninho aumenta. Nenhum dos fatores que testamos – altura do ninhos, tamanho dos ninhos, planta suporte e distância até a borda dos ambientes de cascalheira – mostraram-se importantes como fatores determinantes do sucesso dos ninhos. Entretanto, ninhos construídos nas plantas mais comuns na área de estudo (samambaias) apresentaram maior tendência de sucesso que os demais. Adicionalmente, não houve interferência do observador nas estimativas de sobrevivência dos ninhos. Nossos resultados sugerem que as antigas áreas de cascalheira podem ser adequadas para a reprodução do canário-rasteiro, uma vez que as taxas de sobrevivência que encontramos neste estudo são similares às encontradas em estudos com outras espécies na região central do Cerrado.

Striped-tailed Yellow-finch nesting success in abandoned mining pits from central Brazilian cerrado / Sucesso reprodutivo de Sicalis citrina em cascalheiras abandonadas, região central do Cerrado

Suitability of degraded areas as breeding habitats can be tested through assessment of nest predation rates. In this study we estimated nest success in relation to several potential predictors of nest survival in the Stripe-tailed Yellow-finch (Sicalis citrina) breeding in abandoned mining pits at Brasília National Park. We monitored 73 nests during the 2007-breeding season. Predation was the main cause of nest failure (n = 48, 66%); while six nests were abandoned (8%) and 19 nests produced young (26%). Mayfields daily survival rates and nest success were 0.94 and 23%, respectively. Our results from nest survival models on program MARK indicated that daily survival rates increase linearly towards the end of the breeding season and decrease as nests aged. None of the nest individual covariates we tested - nest height, nest size, nest substrate, and edge effect - were important predictors of nest survival; however, nests placed on the most common plant tended to have higher survival probabilities. Also, there was no observer effect on daily survival rates. Our study suggests that abandoned mining pits may be suitable alternative breeding habitats for Striped-tailed Yellow-finches since nest survival rates were similar to other studies in the central cerrado region.(AU)

A adequação de habitats degradados para reprodução de aves pode ser testada por meio de avaliação das taxas de predação de ninhos. Neste estudo nós estimamos o sucesso de nidificação do canário-rasteiro (Sicalis citrina) e o relacionamos, por meio de modelagem no programa MARK, com diversos fatores que potencialmente afetam a sobrevivência dos ninhos da espécie em antigas áreas de extração de solo (cascalheiras), no Parque Nacional de Brasília, Distrito Federal. Nós monitoramos 73 ninhos da espécie durante a estação reprodutiva de 2007. Predação foi a principal causa da perda de ninhos (n = 48, 66%), enquanto seis foram abandonados (8%) e 19 produziram ao menos um filhote (26%). A taxa diária de sobrevivência e o sucesso total de Mayfield foram 0,94 and 23%, respectivamente. Nossos resultados, obtidos da modelagem de sobrevivência, indicaram que as taxas de sobrevivência diária dos ninhos aumenta linearmente à medida que avança a estação reprodutiva, ao passo que diminui conforme a idade do ninho aumenta. Nenhum dos fatores que testamos altura do ninhos, tamanho dos ninhos, planta suporte e distância até a borda dos ambientes de cascalheira mostraram-se importantes como fatores determinantes do sucesso dos ninhos. Entretanto, ninhos construídos nas plantas mais comuns na área de estudo (samambaias) apresentaram maior tendência de sucesso que os demais. Adicionalmente, não houve interferência do observador nas estimativas de sobrevivência dos ninhos. Nossos resultados sugerem que as antigas áreas de cascalheira podem ser adequadas para a reprodução do canário-rasteiro, uma vez que as taxas de sobrevivência que encontramos neste estudo são similares às encontradas em estudos com outras espécies na região central do Cerrado.(AU)

Evolution of Darwin's finches and their beaks revealed by genome sequencing.

Darwin's finches, inhabiting the Galápagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives. Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis), a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin's finches and, thereby, to an expanded utilization of food resources.

Sisyphean evolution in Darwin's finches.

The trajectory of speciation involves geographic isolation of ancestral populations followed by divergence by natural selection, genetic drift or sexual selection. Once started, the process may experience fits and starts, as sometimes diverging populations intermittently reconnect. In theory populations might cycle between stages of differentiation and never attain species status, a process we refer to as Sisyphean evolution. We argue that the six putative ground finch species (genus Geospiza) of the Galápagos Islands represent a dramatic example of Sisyphean evolution that has been confused with the standard model of speciation. The dynamic environment of the Galápagos, closely spaced islands, and frequent dispersal and introgression have prevented the completion of the speciation process. We suggest that morphological clusters represent locally adapted ecomorphs, which might mimic, and have been confused with, species, but these ecomorphs do not form separate gene pools and are ephemeral in space and time. Thus the pattern of morphological, behavioural and genetic variation supports recognition of a single species of Geospiza, which we suggest should be recognized as Darwin's ground finch (Geospiza magnirostris). We argue that instead of providing an icon of insular speciation and adaptive radiation, which is featured in nearly every textbook on evolutionary biology, Darwin's ground finch represents a potentially more interesting phenomenon, one of transient morphs trapped in an unpredictable cycle of Sisyphean evolution. Instead of revealing details of the origin of species, the mechanisms underlying the transient occurrence of ecomorphs provide one of the best illustrations of the antagonistic effects of natural selection and introgression.

Foraging behavior and diet of the vulnerable Cinereous Warbling-finch Poospiza cinerea (Aves, Emberizidae) / Comportamento de forrageamento e dieta do vulnerável capacetinho-do-oco-do-pau Poospiza cinerea (Aves, Emberizidae)

The Cinereous Warbling-finch Poospiza cinerea is a globally vulnerable Emberizidae passerine, patchily distributed and rare in the open savannah of central South America. Attributes of rare species include niche specificity such as feeding habits. To verify possible niche specialization in this species we aimed to describe its foraging habits related to substrate use, foraging and substrate height, attack maneuvers, and consumed food items. We monitored two groups at two study sites and sampled foraging events with intervals of 15 minutes. The substrates used in greater frequency were foliage and reproductive organs. Foraging and substrate height varied widely with study area. The attack maneuver adopted in greater frequency was glean. Most food items attacked were small invertebrates. Big invertebrates included Lepidoptera, Hemiptera, Coleoptera, Hymenoptera and Orthoptera. Poospiza cinerea was also recorded foraging in mixed bird flocks with seven other species. The generalist foraging behavior of the species cannot be associate to its rarity.

O capacetinho-do-oco-do-pau Poospiza cinerea é um passeriforme da família Emberizidae globalmente vulnerável, irregularmente distribuído e raro no Cerrado do centro da América do Sul. Atributos de espécies raras incluem especificidades de nicho tais como hábitos de forrageamento. Para verificar possível especialização de nicho dessa espécie, buscamos descrever seu comportamento de forrageamento relacionado a uso de substrato, altura de forrageamento e do substrato, manobras de ataque e itens alimentares consumidos. Nós monitoramos dois grupos em duas áreas de estudo e amostramos eventos de forrageamento com intervalos de 15 minutos. Os substratos utilizados em maior frequência foram folhagem e órgãos reprodutivos. Alturas de forrageamento e dos substratos variaram amplamente com a área de estudo. A manobra de ataque adotada em maior frequência foi respigar. A maioria dos itens alimentares foi pequenos invertebrados. Grandes invertebrados incluíram Lepidoptera, Hemiptera, Coleoptera, Hymenoptera e Orthoptera. Poospiza cinerea foi registrado forrageando em bandos mistos com outras sete espécies. O comportamento de forrageamento generalista da espécie não pode ser associado com sua raridade.

Foraging behavior and diet of the vulnerable Cinereous Warbling-finch Poospiza cinerea (Aves, Emberizidae) / Comportamento de forrageamento e dieta do vulnerável capacetinho-do-oco-do-pau Poospiza cinerea (Aves, Emberizidae)

The Cinereous Warbling-finch Poospiza cinerea is a globally vulnerable Emberizidae passerine, patchily distributed and rare in the open savannah of central South America. Attributes of rare species include niche specificity such as feeding habits. To verify possible niche specialization in this species we aimed to describe its foraging habits related to substrate use, foraging and substrate height, attack maneuvers, and consumed food items. We monitored two groups at two study sites and sampled foraging events with intervals of 15 minutes. The substrates used in greater frequency were foliage and reproductive organs. Foraging and substrate height varied widely with study area. The attack maneuver adopted in greater frequency was glean. Most food items attacked were small invertebrates. Big invertebrates included Lepidoptera, Hemiptera, Coleoptera, Hymenoptera and Orthoptera. Poospiza cinerea was also recorded foraging in mixed bird flocks with seven other species. The generalist foraging behavior of the species cannot be associate to its rarity.(AU)

O capacetinho-do-oco-do-pau Poospiza cinerea é um passeriforme da família Emberizidae globalmente vulnerável, irregularmente distribuído e raro no Cerrado do centro da América do Sul. Atributos de espécies raras incluem especificidades de nicho tais como hábitos de forrageamento. Para verificar possível especialização de nicho dessa espécie, buscamos descrever seu comportamento de forrageamento relacionado a uso de substrato, altura de forrageamento e do substrato, manobras de ataque e itens alimentares consumidos. Nós monitoramos dois grupos em duas áreas de estudo e amostramos eventos de forrageamento com intervalos de 15 minutos. Os substratos utilizados em maior frequência foram folhagem e órgãos reprodutivos. Alturas de forrageamento e dos substratos variaram amplamente com a área de estudo. A manobra de ataque adotada em maior frequência foi respigar. A maioria dos itens alimentares foi pequenos invertebrados. Grandes invertebrados incluíram Lepidoptera, Hemiptera, Coleoptera, Hymenoptera e Orthoptera. Poospiza cinerea foi registrado forrageando em bandos mistos com outras sete espécies. O comportamento de forrageamento generalista da espécie não pode ser associado com sua raridade.(AU)

Invasive parasites, habitat change and heavy rainfall reduce breeding success in Darwin's finches.

Invasive alien parasites and pathogens are a growing threat to biodiversity worldwide, which can contribute to the extinction of endemic species. On the Galápagos Islands, the invasive parasitic fly Philornis downsi poses a major threat to the endemic avifauna. Here, we investigated the influence of this parasite on the breeding success of two Darwin's finch species, the warbler finch (Certhidea olivacea) and the sympatric small tree finch (Camarhynchus parvulus), on Santa Cruz Island in 2010 and 2012. While the population of the small tree finch appeared to be stable, the warbler finch has experienced a dramatic decline in population size on Santa Cruz Island since 1997. We aimed to identify whether warbler finches are particularly vulnerable during different stages of the breeding cycle. Contrary to our prediction, breeding success was lower in the small tree finch than in the warbler finch. In both species P. downsi had a strong negative impact on breeding success and our data suggest that heavy rain events also lowered the fledging success. On the one hand parents might be less efficient in compensating their chicks' energy loss due to parasitism as they might be less efficient in foraging on days of heavy rain. On the other hand, intense rainfalls might lead to increased humidity and more rapid cooling of the nests. In the case of the warbler finch we found that the control of invasive plant species with herbicides had a significant additive negative impact on the breeding success. It is very likely that the availability of insects (i.e. food abundance)is lower in such controlled areas, as herbicide usage led to the removal of the entire understory. Predation seems to be a minor factor in brood loss.

The evolutionary history of Darwin's finches: speciation, gene flow, and introgression in a fragmented landscape.

Many classic examples of adaptive radiations take place within fragmented systems such as islands or mountains, but the roles of mosaic landscapes and variable gene flow in facilitating species diversification is poorly understood. Here we combine phylogenetic and landscape genetic approaches to understand diversification in Darwin's finches, a model adaptive radiation. We combined sequence data from 14 nuclear introns, mitochondrial markers, and microsatellite variation from 51 populations of all 15 recognized species. Phylogenetic species-trees recovered seven major finch clades: ground, tree, vegetarian, Cocos Island, grey and green warbler finches, and a distinct clade of sharp-beaked ground finches (Geospiza cf. difficilis) basal to all ground and tree finches. The ground and tree finch clades lack species-level phylogenetic structure. Interisland gene flow and interspecies introgression vary geographically in predictable ways. First, several species exhibit concordant patterns of population divergence across the channel separating the Galápagos platform islands from the separate volcanic province of northern islands. Second, peripheral islands have more admixed populations while central islands maintain more distinct species boundaries. This landscape perspective highlights a likely role for isolation of peripheral populations in initial divergence, and demonstrates that peripheral populations may maintain genetic diversity through outbreeding during the initial stages of speciation.

Foraging behavior and diet of the vulnerable Cinereous Warbling-finch Poospiza cinerea (Aves, Emberizidae).

The Cinereous Warbling-finch Poospiza cinerea is a globally vulnerable Emberizidae passerine, patchily distributed and rare in the open savannah of central South America. Attributes of rare species include niche specificity such as feeding habits. To verify possible niche specialization in this species we aimed to describe its foraging habits related to substrate use, foraging and substrate height, attack maneuvers, and consumed food items. We monitored two groups at two study sites and sampled foraging events with intervals of 15 minutes. The substrates used in greater frequency were foliage and reproductive organs. Foraging and substrate height varied widely with study area. The attack maneuver adopted in greater frequency was glean. Most food items attacked were small invertebrates. Big invertebrates included Lepidoptera, Hemiptera, Coleoptera, Hymenoptera and Orthoptera. Poospiza cinerea was also recorded foraging in mixed bird flocks with seven other species. The generalist foraging behavior of the species cannot be associate to its rarity.

Evidence from a house finch (Haemorhous mexicanus) spleen transcriptome for adaptive evolution and biased gene conversion in passerine birds.

Identifying genes influenced by natural selection can provide information about lineage-specific adaptations, and transcriptomes generated by next-generation sequencing are a useful resource for identifying such genes. Here, we utilize a spleen transcriptome for the house finch (Haemorhous mexicanus), an emerging model for sexual selection and disease ecology, together with previously sequenced avian genomes (chicken, turkey, and zebra finch), to investigate lineage-specific adaptations within birds. An analysis of 4,398 orthologous genes revealed a significantly higher ratio of nonsynonymous to synonymous substitutions and significantly higher GC content in passerines than in galliforms, an observation deviating from strictly neutral expectations but consistent with an effect of biased gene conversion on the evolutionary rate in passerines. These data also showed that genes exhibiting signs of positive selection and fast evolution in passerines have functional roles related to fat metabolism, neurodevelopment, and ion binding.

A molecular phylogeny of the Sierra-Finches (Phrygilus, Passeriformes): extreme polyphyly in a group of Andean specialists.

The unparalleled avian diversity of the Neotropics has long been argued to be in large part the evolutionary consequence of the incredible habitat diversity and rugged topography of the Andes mountains. Various scenarios have been proposed to explain how the Andean context could have generated lineage diversification (e.g. vicariant speciation or parapatric speciation across vertical ecological gradients), yet further study on Andean taxa is needed to reveal the relative importance of the different processes. Here we use mitochondrial and nuclear DNA sequences to derive the first phylogenetic hypothesis for Phrygilus (Sierra-Finches), one of the most species-rich genera of mainly Andean passerines. We find strong evidence that the genus is polyphyletic, comprising four distantly related clades with at least nine other genera interspersed between them (Acanthidops, Catamenia, Diglossa, Haplospiza, Idiopsar, Melanodera, Rowettia, Sicalis and Xenodacnis). These four Phrygilus clades coincide with groups previously established mainly on the basis of plumage characters, suggesting single evolutionary origins for each of these. We consider the history of diversification of each clade, analyzing the timing of splitting events, ancestral reconstruction of altitudinal ranges and current geographical distributions. Phrygilus species origins date mainly to the Pleistocene, with representatives diversifying within, out of, and into the Andes. Finally, we explored whether Phrygilus species, especially those with broad altitudinal and latitudinal Andean distributions, showed phylogeographic structure. Our best-sampled taxon (Phrygilus fruticeti) exhibited no clear pattern; however, we found deep genetic splits within other surveyed species, with Phrygilus unicolor being the most extreme case and deserving of further research.

Reconstructing the phylogeny of "Buarremon" brush-finches and near relatives (Aves, Emberizidae) from individual gene trees.

Gene trees are often assumed to be equivalent to species trees, but processes such as incomplete lineage sorting can generate incongruence among gene topologies and analyzing multilocus data in concatenated matrices can be prone to systematic errors. Accordingly, a variety of new methods have been developed to estimate species trees using multilocus data sets. Here, we apply some of these methods to reconstruct the phylogeny of Buarremon and near relatives, a group in which phylogenetic analyses of mitochondrial DNA sequences produced results that were inconsistent with relationships implied by a taxonomy based on variation in external phenotype. Gene genealogies obtained for seven loci (one mitochondrial, six nuclear) were varied, with some supporting and some rejecting the monophyly of Buarremon. Overall, our species-tree analyses tended to support a monophyletic Buarremon, but due to lack of congruence between methodologies, resolution of the phylogeny of this group remains uncertain. More generally, our study indicates that the number of individuals sampled can have an important effect on phylogenetic reconstruction, that the use of seven markers does not guarantee obtaining a strongly-supported species tree, and that methods for species-tree reconstruction can produce different results using the same data; these are important considerations for researchers using these new phylogenetic approaches in other systems.