Nuclear locus divergence at the early stages of speciation in the Orchard Oriole complex

As two lineages diverge from one another, mitochondrial DNA should evolve fixed differences more rapidly than nuclear DNA due to its smaller effective population size and faster mutation rate. As a consequence, molecular systematists have focused on the criteria of reciprocal monophyly in mitochondrial DNA for delimiting species boundaries. However, mitochondrial gene trees do not necessarily reflect the evolutionary history of the taxa in question, and even mitochondrial loci are not expected to be reciprocally monophyletic when the speciation event happened very recently. The goal of this study was to examine mitochondrial paraphyly within the Orchard Oriole complex, which is composed of Icterus spurius (Orchard Oriole) and Icterus fuertesi (Fuertes' Oriole). We increased the geographic sampling, added four nuclear loci, and used a range of population genetic and coalescent methods to examine the divergence between the taxa. With increased taxon sampling, we found evidence of clear structure between the taxa for mitochondrial DNA. However, nuclear loci showed little evidence of population structure, indicating a very recent divergence between I. spurius and I. fuertesi. Another goal was to examine the genetic variation within each taxon to look for evidence of a past founder event within the I. fuertesi lineage. Based on the high amounts of genetic variation for all nuclear loci, we found no evidence of such an event – thus, we found no support for the possible founding of I. fuertesi through a change in migratory behavior, followed by peripheral isolates speciation. Our results demonstrate that these two taxa are in the earliest stages of speciation, at a point when they have fixed differences in plumage color that are not reflected in monophyly of the mitochondrial or nuclear DNA markers in this study. This very recent divergence makes them ideal for continued studies of species boundaries and the earliest stages of speciation.     

Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, <Emphasis Type="Italic">Buteo jamaicensis harlani</Emphasis>

Background  

Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations.     

THE GEOGRAPHY OF MITOCHONDRIAL DNA VARIATION,POPULATION STRUCTURE,HYBRIDIZATION, AND SPECIES LIMITS IN THE FOX SPARROW (PASSERELLA ILIACA)

Geographic variation in mitochondrial DNA (mtDNA) restriction sites was studied in the fox sparrow (Passerella iliaca). Seventy-eight haplotypes were found. Haplotypes fall into four phylogeographic groups that correspond to groups defined by plumage characters. The geographic distribution of these four groups does not appear congruent with mtDNA patterns in other vertebrates. Within each group, there is little geographic variation in mtDNA restriction sites, although there is geographic variation in plumage coloration and body size. The evolution of mtDNA diversity in fox sparrows seems best explained by vicariant events rather than isolation by distance. The mtDNA evidence suggests that Passerella megarhyncha and Passerella schistacea, two nonsister taxa that occur in western North America, have independently undergone bottlenecks. Hybridization is limited between all pairs of taxa except P. megarhyncha and P. schistacea, where mtDNA evidence suggests a narrow contact zone along the interface of the Great Basin and Sierra Nevada/Cascades. Morphometric characters intergrade over a broader area, suggesting that different processes are responsible for the two gradients. The occurrence of limited backcrossing among taxa suggests that cytoplasmic-nuclear incompatibility is lacking. The number of biological species would range from one to four, depending on the degree of hybridization tolerated. The mtDNA and plumage characters suggest four phylogenetic species: P. iliaca, P. megarhyncha, P. unalaschcensis, and P. schistacea.     

Taxonomy of squirrel monkeys genus Saimiri (Cebidae,platyrrhini): A preliminary report with description of a hitherto unnamed form

Two groups of squirrel monkeys, genus Saimiri, are distinguished by external characters. The first, or Roman type, contains Saimiri boliviensis of upper Amazonia south of the Rio Marañón-Amazonas, with two subspecies of which S. boliviensis peruviensis is described as new. The second group, or Gothic type, contains three species: Saimiri sciureus with four subspecies distributed over much of tropical South America, Saimiri ustus of Brazil between the south bank Amazonian Rios Purús and Xingu, and S. oerstedi isolated on a Pacific coastal area straddling Costa Rica and Panamá. The geographic range of S. sciureus overlaps parts of those of S. ustus and S. boliviensis. Incomplete karyotypic data indicate that the diploid number of chromosomes for the genus is 44. Geographic variation is characterized by reduction from seven to six or five paired acrocentric autosomes through pericentric inversion with reciprocal increase in number of paired submetacentric or subtelocentric autosomes. Geographic distribution, behavior, sexual dimorphism including dichromatism, and hybridization are discussed. Ventral guide hairs for orientation of subprecocial newborn toward the maternal mammae are described. Distinguishing characters of species and subspecies are provided in a key. The taxons are listed with the taxonomy of each discussed, their geographic distribution plotted and mapped.     

Uacaries,new world monkeys of the genus Cacajao(Cebidae,Platyrrhini): A preliminary taxonomic review with the description of a new subspecies

The two known species of uacaries, inhabitants of the upper Amazonian region, are the black head Cacajao melanocephalus with subspecies C. m. melanocephalus Humboldt and C. m. ouakary Spix, and the larger bald head uacari C. calvus with subspecies C. c. ucayalii Thomas, C. c. rubicundus I. Geoffroy and Deville, C. c. calvus I. Geoffroy, and C. c. novaesi described as new. The diagnostic generic characters described are the external, cranial, dental, some postcranial, and cytogenetic. The species are described and compared and their geographic distribution plotted with those of their subspecies delimited. Sexual differences are outlined. Apart from size-related characters, the species and subspecies are distinguished by pelage pattern of head and coloration in general. It is shown that both species could have diverged from a hairy-headed melanistic ancestral form. Pelage divergence in the descendants was expressed by the more pilose head of C. melanocephalus, and less pilose of C. calvus. Coloration differentiation was geographic and followed metachromic lines with mutation from eumelanism to partial pheomelanism (reddish or golden) in C. melanocephalus and to virtually complete pheomelanism in C. calvus. The subspecies of each species are distinguished by color patterns resulting from selective bleaching or dilution of the pheomelanin fields. The most saturate pheomelanic subspecies of C. calvus is C. c. ucayalii and the most dilute is the albinotic C. c. calvus. Correlation between coloration and environment is not evident. A gazetteer identifies all locality records plotted by numbers on the geographic distribution maps.     

Taxonomy of squirrel monkeys genus Saimiri (cebidae,platyrrhini): A preliminary report with description of a hitherto unnamed form

Two groups of squirrel monkeys, genus Saimiri, are distinguished by external characters. The first, or Roman type, contains Saimiri boliviensis of upper Amazonia south of the Rio Marañón-Amazonas, with two subspecies of which S. boliviensis peruviensis is described as new. The second group, or Gothic type, contains three species: Saimiri sciureus with four subspecies distributed over much of tropical South America, Saimiri ustus of Brazil between the south bank Amazonian Rios Purús and Xingu, and S. oerstedi isolated on a Pacific coastal area straddling Costa Rica and Panamá. The geographic range of S. sciureus overlaps parts of those of S. ustus and S. boliviensis. Incomplete karyotypic data indicate that the diploid number of chromosomes for the genus is 44. Geographic variation is characterized by reduction from seven to six or five paired acrocentric autosomes through pericentric inversion with reciprocal increase in number of paired submetacentric or subtelocentric autosomes. Geographic distribution, behavior, sexual dimorphism including dichromatism, and hybridization are discussed. Ventral guide hairs for orientation of subprecocial newborn toward the maternal mammae are described. Distinguishing characters of species and subspecies are provided in a key. The taxons are listed with the taxonomy of each discussed, their geographic distribution plotted and mapped.     

Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic forest

The open vegetation corridor of South America is a region dominated by savanna biomes. It contains forests (i.e. riverine forests) that may act as corridors for rainforest specialists between the open vegetation corridor and its neighbouring biomes (i.e. the Amazonian and Atlantic forests). A prediction for this scenario is that populations of rainforest specialists in the open vegetation corridor and in the forested biomes show no significant genetic divergence. We addressed this hypothesis by studying plumage and genetic variation of the Planalto woodcreeper Dendrocolaptes platyrostris Spix (1824) (Aves: Furnariidae), a forest specialist that occurs in both open habitat and in the Atlantic forest. The study questions were: (1) is there any evidence of genetic continuity between populations of the open habitat and the Atlantic forest and (2) is plumage variation congruent with patterns of neutral genetic structure or with ecological factors related to habitat type? We used cytochrome b and mitochondrial DNA control region sequences to show that D. platyrostris is monophyletic and presents substantial intraspecific differentiation. We found two areas of plumage stability: one associated with Cerrado and the other associated with southern Atlantic Forest. Multiple Mantel tests showed that most of the plumage variation followed the transition of habitats but not phylogeographical gaps, suggesting that selection may be related to the evolution of the plumage of the species. The results were not compatible with the idea that forest specialists in the open vegetation corridor and in the Atlantic forest are linked at the population level because birds from each region were not part of the same genetic unit. Divergence in the presence of gene flow across the ecotone between both regions might explain our results. Also, our findings indicate that the southern Atlantic forest may have been significantly affected by Pleistocene climatic alteration, although such events did not cause local extinction of most taxa, as occurred in other regions of the globe where forests were significantly affected by global glaciations. Finally, our results neither support plumage stability areas, nor subspecies as full species. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 801–820.     

Systematic and ecological wood anatomy of Neotropical Schefflera (Araliaceae), with an emphasis on the Didymopanax group

Wood anatomy has been investigated from 35 species belonging to the Neotropical clade of the polyphyletic genus Schefflera (Araliaceae), representing three of the five subgroups (Didymopanax, Crepinella and Sciodaphyllum). The species examined are rather uniform in their wood structure, sharing the presence of scalariform and simple perforation plates, septate fibres and scanty paratracheal axial parenchyma. The observed variation in many wood characters showed statistically significant differences relative to latitude, climate and, especially, vegetation types. In particular, the intervessel pits are larger in species from higher latitudes and in seasonally dry habitats than those from lower latitudes and rainforests. Latitudinal and ecological trends in the variation of vessel element lengths, bar numbers on perforation plates, intervessel pit sizes and ray widths may be at least partially explained as effects of adaptation to drier environments in the course of dispersal outside the Amazonian region and diversification in the Atlantic Forest subclade and the Savannic subclade within the Didymopanax group. The occurrence of a granular annulus on the intervessel pit membranes in S. chimantensis and S. sprucei (both of the Crepinella group) is the first record of this feature in Araliaceae. In comparisons of Neotropical Schefflera with the other major clades of Schefflera sensu lato, wood anatomical diversity is consistent with the polyphyly of this genus based on molecular phylogenetic analyses. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 452–475.     

Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae)

Hypotheses on the taxonomic status of two Bolivian Pristimantis with taxonomic problems are assessed by an integrative taxonomic approach that integrates three independent lines of evidence: external morphology, prezygotic reproductive barriers (advertisement calls) and reciprocal monophyly (phylogenetic analyses of partial 16S mtDNA sequences). Central Andean Bolivian populations previously assigned to either P. peruvianus or P. dundeei, and lowland Amazonian populations from southern Peru and northern Bolivia previously considered P. peruvianus do not correspond to these species. Indeed, multivariate analyses of qualitative and quantitative morphological and bioacoustic characters, and phylogenetic analyses support the hypothesis that they represent different, previously unknown, cryptic lineages. They are herein described as new species. The former is a sibling species of P. fenestratus that inhabits the Amazonian and semideciduous forests of the Andean foothills in central Bolivia. The latter is sibling to the Andean species P. danae and is parapatric to it in the Amazonian lowland forests and adjacent foothills of northern Bolivia, southern Peru and adjacent Brazil. Most species of Neotropical frogs, and especially Pristimantis, have been described by using external qualitative morphological characters only. An extended integrative taxonomic approach, as exemplified herein, may lead to the discovery of many other cryptic and sibling lineages that would increase the species numbers of tropical areas. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 97–122.     

Phenotypic evolution of an Atlantic Forest passerine (Xiphorhynchus fuscus): biogeographic and systematic implications

We studied the phenotypic variation of the Atlantic Forest passerine Xiphorhynchus fuscus (Aves: Dendrocolaptidae) with the broad aim of addressing whether the history and type of forest affected the evolution of endemic taxa. We also tested whether the different subspecies and genetic lineages of X. fuscus could be considered full species. We collected plumage and body size measurements and, in combination with genetic data, used multivariate tests to evaluate the working hypotheses. Our results, combined with previous biogeographic analyses, indicate that vicariant events have been important determinants in the evolution of phenotypic characters of X. fuscus, once genetic isolation was complete. Our analysis also suggests that forest heterogeneity and ecotones are important factors in the early evolution of Atlantic Forest taxa, perhaps via divergent selection. Forest instability during the Pleistocene was critical in the evolution of phenotypic traits. We confirm that the subspecies atlanticus should be considered a full species. Other lineages or populations are also phenotypically differentiated but we do not suggest considering them as full species. They share high levels of gene flow and are part of a continuous latitudinal cline of phenotypic variation. Our study suggests that not all the historic events in the Atlantic Forest that affected the evolution of genetic lineages also influenced the evolution of phenotypic characters in the same direction and intensity. Undoubtedly, natural selection played a major role in the evolution of Atlantic Forest organisms. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 1047–1066.     

Genetic divergence in the superspecies Manacus

The bearded manakins in the genus Manacus are lekking, neotropical passerines. Male plumage colour varies with geographical location and classification is based solely on these plumage patterns. It has recently been suggested that in this group of birds, plumage patterns may be a misleading taxonomic character. In this study we used microsatellite variation in a collection of museum samples to establish the amount of genetic divergence between the previously described bearded manakin species/subspecies. We found substantial genetic substructuring between species/subspecies and that plumage patterns indeed may be a misleading taxonomic character because the presence of yellow in male nuptial plumage is found in most divergent forms. We did not detect a significant isolation by distance relationship although the P -value was close to significance. Physical barriers such as rivers and mountains may affect gene flow and play a role in shaping genetic structure of the genus Manacus . Accordingly, boundaries between species/subspecies often coincide with large rivers, mountains and seas.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 439–447.     

The evolution of black plumage from blue in Australian fairy‐wrens (Maluridae): genetic and structural evidence

Genetic variation in the melanocortin‐1 receptor (MC1R) locus is responsible for color variation, particularly melanism, in many groups of vertebrates. Fairy‐wrens, Maluridae, are a family of Australian and New Guinean passerines with several instances of dramatic shifts in plumage coloration, both intra‐ and inter‐specifically. A number of these color changes are from bright blue to black plumage. In this study, we examined sequence variation at the MC1R locus in most genera and species of fairy‐wrens. Our primary focus was subspecies of the white‐winged fairy‐wren Malurus leucopterus in which two subspecies, each endemic to islands off the western Australian coast, are black while the mainland subspecies is blue. We found fourteen variable amino acid residues within M. leucopterus, but at only one position were alleles perfectly correlated with plumage color. Comparison with other fairy‐wren species showed that the blue mainland subspecies, not the black island subspecies, had a unique genotype. Examination of MC1R protein sequence variation across our sample of fairy‐wrens revealed no correlation between plumage color and sequence in this group. We thus conclude that amino acid changes in the MC1R locus are not directly responsible for the black plumage of the island subspecies of M. leucopterus. Our examination of the nanostructure of feathers from both black and blue subspecies of M. leucopterus and other black and blue fairy‐wren species clarifies the evolution of black plumage in this family. Our data indicate that the black white‐winged fairy‐wrens evolved from blue ancestors because vestiges of the nanostructure required for the production of blue coloration exist within their black feathers. Based on our phylogeographic analysis of M. leucopterus, in which the two black subspecies do not appear to be each other's closest relatives, we infer that there have been two independent evolutionary transitions from blue to black plumage. A third potential transition from blue to black appears to have occurred in a sister clade.     

Taxonomy and conservation: a tale of two tinamou species groups (Tinamidae,Crypturellus)

Species delimitation has important consequences for the management of endangered species. Species‐level taxonomy in the genus Crypturellus (Tinamidae) has been based largely on plumage characters and species limits in several groups have been difficult to establish. Because some of the forms of uncertain taxonomic status are currently threatened with extinction, a basic understanding of species limits is crucial not only for taxonomists but also for conservation biologists and managers. We analysed vocal variation to assess species limits in two Crypturellus species‐groups, the red‐legged complex (Crypturellus erythropus and allied forms) and the brown tinamou Crypturellus obsoletus. In the red‐legged complex, where several species‐level taxa have been recognized by some authors, there is no obvious geographic variation in vocalizations and populations appear mostly continuously distributed, with plumage variation largely explicable in terms of environmental conditions. In the brown group, a single species is recognized, but we found marked geographic variation in vocalizations and populations have disjunct distributions; we propose that at least one of the populations in this group likely merits recognition as a separate species. We conclude that incomplete knowledge of patterns of variation in relevant traits in addition to the momentum carried by traditional taxonomy may potentially mislead conservation actions.     

Geographic variation in the plumage coloration of willow flycatchers Empidonax traillii

The ability to identify distinct taxonomic groups of birds (species, subspecies, geographic races) can advance ecological research efforts by determining connectivity between the non‐breeding and breeding grounds for migrant species, identifying the origin of migrants, and helping to refine boundaries between subspecies or geographic races. Multiple methods are available to identify taxonomic groups (e.g., morphology, genetics), and one that has played an important role for avian taxonomists over the years is plumage coloration. With the advent of electronic devices that can quickly and accurately quantify plumage coloration, the potential of using coloration as an identifier for distinct taxonomic groups, even when differences are subtle, becomes possible. In this study, we evaluated the degree to which plumage coloration differs among the four subspecies of the willow flycatcher Empidonax traillii, evaluated sources of variation, and considered the utility of plumage coloration to assign subspecies membership for individuals of unknown origin. We used a colorimeter to measure plumage coloration of 374 adult willow flycatchers from 29 locations across their breeding range in 2004 and 2005. We found strong statistical differences among the mean plumage coloration values of the four subspecies; however, while individuals tended to group around their respective subspecies’ mean color value, the dispersion of individuals around such means overlapped. Mean color values for each breeding site of the three western subspecies clustered together, but the eastern subspecies’ color values were dispersed among the other subspecies, rather than distinctly clustered. Additionally, sites along boundaries showed evidence of intergradation and intermediate coloration patterns. We evaluated the predictive power of colorimeter measurements on flycatchers by constructing a canonical discriminant model to predict subspecies origin of migrants passing through the southwestern U.S. Considering only western subspecies, we found that individuals can be assigned with reasonable certainty. Applying the model to migrants sampled along the Colorado River in Mexico and the U.S. suggests different migration patterns for the three western subspecies. We believe that the use of plumage coloration, as measured by electronic devices, can provide a powerful tool to look at ecological questions in a wide range of avian species.     

Resurrection in Carapa (Meliaceae): a reassessment of morphological variation and species boundaries using multivariate methods in a phylogenetic context

The taxonomy of the amphi‐Atlantic tree genus Carapa (Meliaceae) has long been controversial. Of the three species currently recognized in the genus, two are known to present substantial morphological variation that has been used in the past to distinguish several taxa, most of which are currently placed in synonymy. Here, a combination of field observations, univariate analyses of leaf, floral and seed characters and principal coordinate analyses of floral characters in the context of a molecular phylogenetic analysis was used to investigate the patterns of variation and delimit morphological species anew in the genus. These results support the recognition of 27 species in Carapa, of which 16 are previously described and 11 are new. In general, phylogenetically related species occurred in the same geographical area, but were morphologically distinct. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 186–221.     

Phylogeny and species limits in the Palaearctic chiffchaff Phylloscopus collybita complex: mitochondrial genetic differentiation and bioacoustic evidence*

Nucleotide sequences of the mitochondrial cytochrome b gene (1041 bp), analysis of vocalizations and behavioural evidence from zones of contact were used to reassess the species limits and phylogenetic relationships at the species and subspecies levels in the Phylloscopus collybita complex. A new classification is proposed which recognizes four biological species. Phylloscopus brehmii (Iberia) and P. canariensis (Canary Islands) are genetically and bioacoustically highly distinct. There is no mitochondrial gene flow between them or with P. collybita. The Mountain Chiffchaff P. sindianus (with subspecies sindianus and Iorenzii) is equally distinct genetically from southwest Asian subspecies of P. collybita (caucasicus, brevirostris). The status of the Siberian form tristis, which shares potentially synapomorphic characters with the Mountain Chiffchaff (ascending song notes, grey-brown adult plumage) but genetically closely resembles P. c. collybita and P. c. abietinus, remains uncertain. In two zones of secondary contact between taxa with “greenish” (P. collybita) and brownish plumage, hybridization is either unrecorded (caucasicus v lorenzii, Caucasus Mountains) or its extent is insufficiently known (abietinus v tristis, west of Ural Mountains). A phylogeny reconstructed from nucleotide sequences agrees with one based on song and some morphological characters in identifying P. brehmii as the oldest branch within the chiffchaff group. Of the remaining taxa, four fall into a clade with greenish plumage (P. collybita ssp.), two into one with brownish plumage (P. s. sindianus, P. s. lorenzii), while the position of P. canariensis with respect to these two clades is uncertain. Molecular and phenotypic phylogenies contradict each other regarding the affinities of P. (ssp.?) tristis.     

Differentiation and phylogeny of the olivaceous warbler Hippolais pallida species complex

The pattern of phenotypic and molecular variation within the polytypic olivaceous warbler H. pallida was examined. This species is distributed in the southern parts of the western Palaearctic, central Asia and in the arid parts of northern Africa, and also in parts of the sub-Saharan Sahel zone. Based on morphology, five subspecies, at times assigned to three groups, have been identified. By comparing morphological, behavioural, vocal and molecular variation, we investigated the phenotypic and phylogenetic relationships within the Hippolais pallida group. The morphological and genetic data of the present study support the view of splitting the olivaceous warbler into a western (former subspecies opaca) and an eastern form (former subspecies elaeica, pallida, reiseri and laeneni). Opaca is consistently and significantly larger than the other taxa in all size measurements, even if it does share morphological properties with elaeica in characters associated with migration. The song of the polytypic pallida differs clearly from that of opaca, and is remarkably consistent within its wide range which comprises four subspecies. The molecular analysis, and the resulting phylogenetic pattern, clearly separated opaca on a single branch distant from the other subspecies. The eastern form consists of two non-overlapping haplotype groups: elaeica with relatively diverse mtDNA variation, and the three African subspecies pallida, reiseri and laeneni, which all share the same or closely related mtDNA haplotypes. It remains open whether the African taxa should be regarded as three valid subspecies of the Eastern olivaceous warbler, or if they are better treated as a single African subspecies.