A fundamental question in evolutionary genetics concerns the extent to which adaptive phenotypic convergence is attributable to convergent or parallel changes at the molecular sequence level. Here we ...report a comparative analysis of hemoglobin (Hb) function in eight phylogenetically replicated pairs of high- and low-altitude waterfowl taxa to test for convergence in the oxygenation properties of Hb, and to assess the extent to which convergence in biochemical phenotype is attributable to repeated amino acid replacements. Functional experiments on native Hb variants and protein engineering experiments based on site-directed mutagenesis revealed the phenotypic effects of specific amino acid replacements that were responsible for convergent increases in Hb-O2 affinity in multiple high-altitude taxa. In six of the eight taxon pairs, high-altitude taxa evolved derived increases in Hb-O2 affinity that were caused by a combination of unique replacements, parallel replacements (involving identical-by-state variants with independent mutational origins in different lineages), and collateral replacements (involving shared, identical-by-descent variants derived via introgressive hybridization). In genome scans of nucleotide differentiation involving high- and low-altitude populations of three separate species, function-altering amino acid polymorphisms in the globin genes emerged as highly significant outliers, providing independent evidence for adaptive divergence in Hb function. The experimental results demonstrate that convergent changes in protein function can occur through multiple historical paths, and can involve multiple possible mutations. Most cases of convergence in Hb function did not involve parallel substitutions and most parallel substitutions did not affect Hb-O2 affinity, indicating that the repeatability of phenotypic evolution does not require parallelism at the molecular level.
The Atlantic Forest harbors 7% of global biodiversity and possesses high levels of endemism, but many of its component taxa remain unstudied. Due to the importance of tropical forests and the urgency ...to protect them, there is a compelling need to address this knowledge gap. To provide more information on its arthropod fauna, a Malaise trap was deployed for 12 months in a semi-degraded area of the southern Upper Paraná ecoregion of the Atlantic Forest. All specimens were DNA barcoded and the Barcode Index Number (BIN) system was employed to assign each specimen to a species proxy. DNA barcodes were obtained from 75,500 arthropods that included representatives of 8,651 BINs. Nearly 81% of these BINs were first records, highlighting the high rates of endemism and lack of study of arthropods from the Atlantic Forest. Diptera was the most abundant order, followed by Hemiptera, Lepidoptera and Hymenoptera. Diptera was also the most species-rich order, followed by Hymenoptera, Lepidoptera, and Coleoptera, a result consistent with studies in other biogeographic regions. Insects were most abundant in winter and most diverse in autumn and winter. This pattern, however, was caused mainly by the dynamics of dipteran diversity as other orders differed in their seasonal variation. The BIN composition of the insect community varied sharply through the year and also differed between the two consecutive summers included in the sampling period. The study of the 38 commonest BINs showed that seasonal patterns of abundance were not order-specific. Temperature had the strongest impact on seasonal abundance variation. Our results highlight the striking and understudied arthropod diversity of the highly fragmented Atlantic Forest, the predominance of dipterans, and the fact that abundance and richness in this insect community peak in the coolest months. Standardized studies like this generate fast and reliable biodiversity inventories and unveil ecological patterns, thus providing valuable information for conservation programs.
Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern ...South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.
Behavioral isolation can catalyze speciation and permit the slow accumulation of additional reproductive barriers between co-occurring organisms. We illustrate how this process occurs by examining ...the genomic and behavioral bases of pre-mating isolation between two bird species (
and the recently discovered
) that belong to the southern capuchino seedeaters, a recent, rapid radiation characterized by variation in male plumage coloration and song. Although these two species co-occur without obvious ecological barriers to reproduction, we document behaviors indicating species recognition by song and plumage traits and strong assortative mating associated with genomic regions underlying male plumage patterning. Plumage differentiation likely originated through the reassembly of standing genetic variation, indicating how novel sexual signals may quickly arise and maintain species boundaries.
The Neotropical avifauna is more diverse than that of any other biogeographic region, but our understanding of patterns of regional divergence is limited. Critical examination of this issue is ...currently constrained by the limited genetic information available. This study begins to address this gap by assembling a library of mitochondrial COI sequences, or DNA barcodes, for Argentinian birds and comparing their patterns of genetic diversity to those of North American birds.
Five hundred Argentinian species were examined, making this the first major examination of DNA barcodes for South American birds. Our results indicate that most southern Neotropical bird species show deep sequence divergence from their nearest-neighbour, corroborating that the high diversity of this fauna is not based on an elevated incidence of young species radiations. Although species ages appear similar in temperate North and South American avifaunas, patterns of regional divergence are more complex in the Neotropics, suggesting that the high diversity of the Neotropical avifauna has been fueled by greater opportunities for regional divergence. Deep genetic splits were observed in at least 21 species, though distribution patterns of these lineages were variable. The lack of shared polymorphisms in species, even in species with less than 0.5M years of reproductive isolation, further suggests that selective sweeps could regularly excise ancestral mitochondrial polymorphisms.
These findings confirm the efficacy of species delimitation in birds via DNA barcodes, even when tested on a global scale. Further, they demonstrate how large libraries of a standardized gene region provide insight into evolutionary processes.
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.
The riverine barrier hypothesis proposes that large rivers represent geographical barriers to gene flow for terrestrial organisms, leading to population differentiation and ultimately allopatric ...speciation. Here we assess for the first time if the subtropical Paraná–Paraguay River system in the Del Plata basin, second in size among South American drainages, acts as a barrier to gene flow for birds. We analysed the degree of mitochondrial and nuclear genomic differentiation in seven species with known subspecies divided by the Paraná–Paraguay River axis. Only one species showed genetic differentiation concordant with the current river channel, but another five species have an east/west genetic split broadly coincident with the Paraná River's dynamic palaeochannel, suggesting this fluvial axis has had a past role in shaping present‐day genetic structure. Moreover, dating analyses show that these splits have been asynchronous, with species responding differently to the riverine barrier. Comparisons informed by the geological history of the Paraná River and its influence on the ecological and climatic differences among ecoregions in the study area further bolster the finding that responses to this geographical barrier have been species‐specific.
see also the Perspective by Luciano N. Naka and Maria W. Pil.
The evolution of complex behavior is driven by the interplay of morphological specializations and neuromuscular control mechanisms 1–3, and it is often difficult to tease apart their respective ...contributions. Avian vocal learning and associated neural adaptations are thought to have played a major role in bird diversification 4–8, whereas functional significance of substantial morphological diversity of the vocal organ remains largely unexplored. Within the most species-rich order, Passeriformes, “tracheophones” are a suboscine group that, unlike their oscine sister taxon, does not exhibit vocal learning 9 and is thought to phonate with tracheal membranes 10, 11 instead of the two independent sources found in other passerines 12–14. Here we show tracheophones possess three sound sources, two oscine-like labial pairs and the unique tracheal membranes, which collectively represent the largest described number of sound sources for a vocal organ. Birds with experimentally disabled tracheal membranes were still able to phonate. Instead of the main sound source, the tracheal membranes constitute a morphological specialization, which, through interaction with bronchial labia, contributes to different acoustic features such as spectral complexity, amplitude modulation, and enhanced sound amplitude. In contrast, these same features arise in oscines from neuromuscular control of two labial sources 15–17. These findings are supported by a modeling approach and provide a clear example for how a morphological adaptation of the tracheophone vocal organ can generate specific, complex sound features. Morphological specialization therefore constitutes an alternative path in the evolution of acoustic diversity to that of oscine vocal learning and complex neural control.
•The tracheophone syrinx is the first documented vocal organ with three sources•A tracheal membrane pair interacts with the main dual bronchial sound source•Interactions of the three sources generate various spectral and amplitude features•This morphological novelty facilitated the evolution of diverse vocalizations
Garcia et al. show direct videoscopic evidence for the first three-source vocal organ in tracheophones. They confirm through experimental manipulation and mathematical modeling that the bronchial sources are the main sound generators and that the tracheal membranes serve to enhance acoustic features (spectral complexity and amplitude features).
Aim
The Neotropics constitute the most biodiverse region of the world, yet its patterns of diversification and speciation differ among Neotropical areas and are not equally well understood. ...Particularly, avian evolutionary processes are understudied in the open habitats of temperate South America, where the role of glacial cycles is not clear. We analysed the evolutionary history of a Neotropical widespread bird species as a case study to evaluate its continental‐scale patterns and processes of diversification, with a focus on Patagonia.
Location
Open habitats of the Neotropics.
Taxon
Vanellus chilensis (Aves, Charadriiformes).
Methods
We obtained reduced representation genomic and mitochondrial data from the four subspecies of V. chilensis to perform a phylogenetic/phylogeographical analysis and study the evolutionary history of the species. We complemented these analyses with the study of vocalizations, a reproductive signal in birds.
Results
The initial diversification event within V. chilensis, approximately 600,000 years ago, split a Patagonian lineage from one containing individuals from the rest of the Neotropics. We found considerable gene flow between these two lineages and a contact zone in northern Patagonia, and showed that genomic admixture extends to northwestern Argentina. Shallower divergence was detected between the two non‐Patagonian subspecies, which are separated by the Amazon River. Vocalizations were significantly different between the two main lineages and were intermediate in their temporal and frequency characteristics in the contact zone.
Main Conclusions
Patagonian populations of V. chilensis are clearly differentiated from those of the rest of the Neotropics, possibly as a consequence of Pleistocene glaciations. A secondary contact zone in northern Patagonia with extensive gene flow among lineages appears to be the consequence of post‐glacial, northward expansion of the Patagonian populations. Future analyses focused on the dynamics of the contact zone will allow us to establish whether the species continues to diverge or is homogenizing.
Resumen
Objetivo
El Neotrópico constituye la región más biodiversa del mundo pero sus patrones de diversificación y especiación difieren entre distintas áreas neotropicales y no son igualmente bien entendidos. En particular, los procesos evolutivos de las aves han sido poco estudiados en los ambientes abiertos de las zonas templadas de América del Sur, donde el rol de los ciclos glaciales no es del todo claro. Analizamos la historia evolutiva de una especie de ave neotropical de amplia distribución geográfica como caso de estudio, para evaluar sus patrones y procesos de diversificación a escala continental en el Neotrópico, enfocándonos en la Patagonia.
Localidad
Ambientes abiertos del Neotrópico.
Taxón
Vanellus chilensis (Aves, Charadriiformes).
Metodología
Obtuvimos una representación reducida de datos genómicos y datos mitocondriales de las cuatro subespecies de V. chilensis para realizar análisis filogenéticos/filogeográficos y estudiar la historia evolutiva de la especie. Complementamos estos análisis con el estudio de las vocalizaciones, una señal reproductiva en las aves.
Resultados
El evento de diversificación inicial dentro de V. chilensis, hace aproximadamente 600.000 años, separó un linaje Patagónico de uno que contenía individuos del resto del Neotrópico. Encontramos un considerable flujo génico entre estos dos linajes y una zona de contacto en el norte de la Patagonia, y mostramos que el contenido genómico mixto se extiende al noroeste de la Argentina. Se detectó una divergencia menor entre las dos subespecies no patagónicas, que están separadas por el Río Amazonas. Las vocalizaciones fueron significativamente diferentes entre los dos linajes principales y presentaron valores intermedios en sus características temporales y de frecuencia en la zona de contacto.
Conclusiones Principales
Las poblaciones patagónicas de V. chilensis están claramente diferenciadas de aquellas del resto del Neotrópico, posiblemente como consecuencia de las glaciaciones pleistocénicas. La presencia de una zona de contacto secundario en el norte de la Patagonia con un extenso flujo génico entre linajes parece deberse a la expansión post‐glacial de las poblaciones patagónicas hacia el norte. Análisis futuros enfocados en la dinámica de la zona de contacto nos permitirán establecer si la especie continúa divergiendo o se está homogeneizando.
Avian diversity in the Neotropics has been traditionally attributed to the effect of vicariant forces promoting speciation in allopatry. Recent studies have shown that phylogeographical patterns ...shared among codistributed species cannot be explained by a single vicariant event, as species responses to a common barrier depend on the biological attributes of each taxon. The open vegetation corridor (OVC) isolates Amazonia and the Andean forests from the Atlantic Forest, creating a notorious pattern of avian taxa that are disjunctly codistributed in these forests. Here, we studied and compared the evolutionary histories of Ramphotrigon megacephalum and Pipraeidea melanonota, two passerines with allopatric populations east and west of the OVC that represent different subspecies. These species differ in their biological attributes: R. megacephalum is a sedentary, forest specialist mostly confined to bamboo understorey, whereas P. melanonota is a seasonal migrant and generalist species that ranges in a variety of closed and semi‐open environments. We performed genetic and genomic analyses, complemented with the study of coloration and behavioural differentiation, to assess population divergence across the OVC. We found that the evolutionary histories of both R. megacephalum and P. melanonota have been shaped by this environmental barrier. However, these species responded in different and asynchronous manners to the establishment of the OVC and to past connections between the currently isolated South American forests, which can be mostly explained by their distinct ecologies and dispersal abilities. Our results support the fact that the biological attributes of species can make their evolutionary histories idiosyncratic.
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