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Tapping the Woodpecker Tree for Evolutionary Insight
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... The specific evolutionary relationships, however, among various taxa within the family Picidae still lack clarity. For many years, several efforts have been devoted to elucidating the evolutionary relationships within the family Picidae; the study of Shakya et al. (2017) is an example. This family is typically categorized into three subfamilies. ...
... Here, the genus Picumnus represents rare species with a localized distribution and many species have been omitted from molecular phylogenetic investigations. The task of establishing relationships in these birds is further complicated by significant instances of hybridization among these species (Dickinson and Remsen 2013;Dufort 2016;Shakya et al. 2017). ...
... According to the phylogeny described by Shakya et al. (2017), P. nebulosus is the most basal, followed by C. campestris, V. spilogaster, and M. candidus is the most derived. Based on this information, we can observe that the family Picidae possibly had an ancestor with higher diploid number than the PAK (2n = 80, Griffin et al. 2007), given that Jynix torquila (2n = 90), a more basal species than P. nebulosus, also presents this characteristic. ...
The genome organization of woodpeckers has several distinctive features e.g., an uncommon accumulation of repetitive sequences, enlarged Z chromosomes, and atypical diploid numbers. Despite the large diversity of species, there is a paucity of detailed cytogenomic studies for this group and we thus aimed to rectify this. Genome organization patterns and hence evolutionary change in the microchromosome formation of four species ( Colaptes campestris, Veniliornis spilogaster, Melanerpes candidus, and Picumnus nebulosus) was established through fluorescence in situ hybridization using bacterial artificial chromosomes originally derived from Gallus gallus and Taeniopygia guttata. Findings suggest that P. nebulosus (2 n = 110), which was described for the first time, had the most basal karyotype among species of Picidae studied here, and probably arose as a result of fissions of avian ancestral macrochromosomes. We defined a new chromosomal number for V. spilogaster (2 n = 88) and demonstrated microchromosomal rearrangements involving C. campestris plus a single, unique hitherto undescribed rearrangement in V. spilogaster. This comprised an inversion after a fusion involving the ancestral microchromosome 12 (homologous to chicken microchromosome 12). We also determined that the low diploid number of M. candidus is related to microchromosome fusions. Woodpeckers thus exhibit significantly rearranged karyotypes compared to the putative ancestral karyotype.
... We specified a genome range of 16,500-19,000 bp, a K-mer size of k = 39 and an insert size of 300 bp. As a seed, we used an ATP6 sequence from another P. viridis viridis individual (MF766578, Shakya et al. 2017). When the genome was not circularized, we used the BWA algorithm, as implemented in Ugene (Okonechnikov et al. 2012) using the default option except the number of differences that we set to 4. We performed a mitochondrial genome analysis using all Piciformes sequences that are available on Genbank (cutoff date 2023 Jul 15). ...
... The topology recovered from the partitioned concatenated analysis of 12 mitochondrial protein-coding loci (Fig. 3) was in strong agreement with current phylogenetic hypotheses for family-level and genus-level relationships in Piciformes (e.g. Prum et al. 2015;Shakya et al. 2017). ...
... auratus, P. viridis) are part of the Picini subclade, whereas the 2 higher scores belong to the Dendropicini (D. pubescens) and Melanerpini (M. aurifrons) clades(Shakya et al. 2017). Genome fragmentation, especially the number of microchromosomes, could explain this pattern as they could be more difficult to assemble. ...
The European green woodpecker, Picus viridis, is a widely distributed species found in the Western Palearctic region. Here, we assembled a highly contiguous genome assembly for this species using a combination of short- and long-read sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37 Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a ∼30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the P. viridis genome when compared to the chicken (Gallus gallus). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers. Five historical and seven contemporary samples have been resequenced and may give insights on the population history of this species.
... They have typically been grouped in the subfamily Picumninae (e.g. Peters 1948, Winkler et al. 1995, Dickinson 2003, although most authors have removed Nesoctites from this subfamily and placed it either in Picinae (Dickinson & Remsen 2013) or in its own subfamily, Nesoctitinae (Wolters 1976, Benz et al. 2006, Gaudin 2022. In contrast, Sasia, Verreauxia and Picumnus have always been placed in Picumninae (e.g. ...
... In contrast, Sasia, Verreauxia and Picumnus have always been placed in Picumninae (e.g. Peters 1948, Wolters 1976, Winkler et al. 1995, Dickinson 2003, Dickinson & Remsen 2013. ...
... A sixth multilocus study placed Sasia and Verreauxia sister to Picumnus, but again separated by a deep divergence (Dufort 2016). More recently, a multilocus study by Shakya et al. (2017) placed Sasia and Verreauxia closer to Picinae than to Picumnus. Analyses of the two mitochondrial rRNA and 13 protein-coding genes again recovered a deep split between Sasia/Verreauxia and Picumnus but failed to unambiguously resolve the relationships between these taxa and Nesoctites/Picinae (JF et al. unpubl. ...
Summary.— A review of eight molecular phylogenetic studies supports the
distinctiveness of the genera Sasia/Verreauxia from Picumnus and casts doubt on the
monophyly of Picumninae. We propose to restrict Picumninae to Picumnus and to
place Sasia and Verreauxia in a new subfamily, Sasiinae.
Résumé.-Un examen de huit études phylogénétiques moléculaires soutient la
distinctivité des genres Sasia/Verreauxia de Picumnus et jette un doute sur la
monophylie des Picumninae. Nous proposons de restreindre Picumninae à Picumnus et de
placer Sasia et Verreauxia dans une nouvelle sous-famille, Sasiinae.
... For backbone relationships among Piciformes, we used the higher-level tree from Prum et al. (2015). To this tree, we grafted branches following published topologies for woodpeckers (Shakya et al., 2017) and Old World barbets (Moyle, 2004). For the passerine species, we downloaded phylogenetic information for all the species in the focal group from BirdTree (Jetz et al., 2012(Jetz et al., , 2014, and then extracted the subtree corresponding to the passerines. ...
... ancestor with the North American Picoides dorsalis by long-distance recent (~2 mya) dispersal across Beringia from North America to Eurasia (Shakya et al., 2017). This date (~2 mya) also matches the split we inferred between the louse P. arcticus and its closest relative in the New World. ...
... These two sapsucker species have a broad hybrid zone (Winkler and Christie, 2002), which might provide a mechanism for louse transmission between them, as has been found in mammal lice (Hafner et al., 2019) and feather mites (Doña et al., 2019). The genus Chloropicos is not phylogenetically closely related to Sphyrapicus (Shakya et al., 2017), and thus neither host phylogeny nor biogeography can explain the very close relationship between the lice from this African woodpecker and those from New World sapsuckers. We also took special effort to assess whether contamination or other lab error could explain these results, and the COI sequences generated via Sanger sequencing of additional specimens from the original field collection vial were identical across three different sequencing attempts of three different louse individuals from this C. goertae host sample (recent genome and Sanger sequence from this study and the Sanger sequence from Johnson et al. [2001]). ...
Parasite diversification is influenced by many of the same factors that affect speciation of free-living organisms, such as biogeographic barriers. However, the ecology and evolution of the host lineage also has a major impact on parasite speciation. Here we explore the interplay between biogeography and host-association on the pattern of diversification in a group of ectoparasitic lice (Insecta: Phthiraptera: Penenirmus) that feeds on the feathers of woodpeckers, barbets, and honeyguides (Piciformes) and some songbirds (Passeriformes). We use whole genome sequencing of 41 ingroup and 12 outgroup samples to develop a phylogenomic dataset of DNA sequences from a reference set of 2,395 single copy ortholog genes, for a total of nearly four million aligned base positions. The phylogenetic trees resulting from both concatenated and gene-tree/species-tree coalescent analyses were nearly identical and highly supported. These trees recovered the genus Penenirmus as monophyletic and identified several major clades, which tended to be associated with one major host group. However, cophylogenetic analysis revealed that host-switching was a prominent process in the diversification of this group. This host-switching generally occurred within single major biogeographic regions. We did, however, find one case in which it appears that a rare dispersal event by a woodpecker lineage from North America to Africa allowed its associated louse to colonize a woodpecker in Africa, even though the woodpecker lineage from North America never became established there.
... For backbone relationships among Piciformes, we used the higher-level tree from Prum et al. (2015). To this tree, we grafted branches following published topologies for woodpeckers (Shakya et al., 2017) and Old World barbets (Moyle, 2004). For the passerine species, we downloaded phylogenetic information for all the species in the focal group from BirdTree (Jetz et al., 2012(Jetz et al., , 2014, and then extracted the subtree corresponding to the passerines. ...
... The first of these, P. arcticus, appears to have been facilitated by host dispersal and speciation. The host of P. arcticus, Picoides tridactylus, was inferred to have speciated from its common ancestor with the North American Picoides dorsalis by long-distance recent (~2 mya) dispersal across Beringia from North America to Eurasia (Shakya et al., 2017). This date (~2 mya) also matches the split we inferred between the louse P. ...
... These two sapsucker species have a broad hybrid zone (Winkler and Christie, 2002), which might provide a mechanism for louse transmission between them, as has been found in mammal lice (Hafner et al., 2019) and feather mites (Doña et al., 2019). The genus Chloropicos is not phylogenetically closely related to Sphyrapicus (Shakya et al., 2017), and thus neither host phylogeny nor biogeography can explain the very close relationship . CC-BY-NC-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. ...
Parasite diversification is influenced by many of the same factors that affect speciation of free-living organisms, such as biogeographic barriers. However, the ecology and evolution of the host lineage also has a major impact on parasite speciation. Here we explore the interplay between biogeography and host-association on the pattern of diversification in a group of ectoparasitic lice (Insecta: Phthiraptera: Penenirmus) that feeds on the feathers of woodpeckers, barbets, and honeyguides (Piciformes) and some songbirds (Passeriformes). We use whole genome sequencing of 41 ingroup and 12 outgroup samples to develop a phylogenomic dataset of DNA sequences from a reference set of 2,395 single copy ortholog genes, for a total of nearly four million aligned base positions. The phylogenetic trees resulting from both concatenated and gene-tree/species-tree coalescent analyses were nearly identical and highly supported. These trees recovered the genus Penenirmus as monophyletic and identified several major clades, which tended to be associated with one major host group. However, cophylogenetic analysis revealed that host-switching was a prominent process in the diversification of this group. This host-switching generally occurred within single major biogeographic regions. We did, however, find one case in which it appears that a rare dispersal event by a woodpecker lineage from North America to Africa allowed its associated louse to colonize a woodpecker in Africa, even though the woodpecker lineage from North America never became established there.
... Drumming is an exaptation 46,47 , which derived through ritualization (exaggerated amplitude, rhythm stereotypy 48,49 ) from pecking on tree trunks, a foraging behaviour typical of woodpeckers 43 (Fig. 1a). A phylogenetic reconstruction of drumming suggests that this was the ancestral behaviour in this family (95% probability of being present in the common ancestor, 22.5 million years ago 50 -see 'Methods' and Fig. 1b). Drumming is an innate behaviour 51 , whose divergence has been relatively limited during woodpecker radiation 52 , potentially given the strong constraints inherent to its production mechanism 53 . ...
... The lack of a direct fossil record for drumming behaviour (as is the case for most behavioural traits) is of course a limit here. Should future research clearly identify strong anatomical correlates of drumming acoustic features, valuable insights could be added to the picture of drumming evolution we provide here (note, however, that this will in any case be particularly challenging given the scarcity of woodpecker fossils in general 50,65 ). ...
... While evaluating the likelihood that drumming was already present at an early stage of woodpecker's phylogeny, we tried to represent the most complete tree of the family, based on very recent molecular data 50 . Note that strictly speaking, we evaluate the state at the root but at the next internal node, i.e. at the node including Picumninae and Picinae (the largest pie-chart in our Fig. ...
Communicating species identity is a key component of many animal signals. However, whether selection for species recognition systematically increases signal diversity during clade radiation remains debated. Here we show that in woodpecker drumming, a rhythmic signal used during mating and territorial defense, the amount of species identity information encoded remained stable during woodpeckers’ radiation. Acoustic analyses and evolutionary reconstructions show interchange among six main drumming types despite strong phylo- genetic contingencies, suggesting evolutionary tinkering of drumming structure within a constrained acoustic space. Playback experiments and quantification of species discrimin- ability demonstrate sufficient signal differentiation to support species recognition in local communities. Finally, we only find character displacement in the rare cases where sympatric species are also closely related. Overall, our results illustrate how historical contingencies and ecological interactions can promote conservatism in signals during a clade radiation without impairing the effectiveness of information transfer relevant to inter-specific discrimination.
... Given this, plus the fact that option 1 would obscure the distinctiveness of the two species in Gecinulus and option 2 would negate that of D. rafflesii, we here propose that D. rafflesii be moved to another genus. This is not, however, to pretend that anomalies might not result as a consequence: in the phylogenetic trees generated by Shakya et al. (2017) Unfortunately, the second species of Gecinulus, Blyth, 1845, G. viridis (Bamboo Woodpecker) was not sampled by Shakya et al. (2017), but a close relationship between these congeners has long been assumed, with conspecificity sometimes proposed (Short 1982, Dickinson 2003, in part doubtless because a narrow hybrid zone between them exists in northern Thailand and, presumably, northern Laos (Round et al. 2012). The risk that the absence of molecular data for G. viridis might complicate the scenario recovered by Shakya et al. (2017) therefore appears remote. ...
... Given this, plus the fact that option 1 would obscure the distinctiveness of the two species in Gecinulus and option 2 would negate that of D. rafflesii, we here propose that D. rafflesii be moved to another genus. This is not, however, to pretend that anomalies might not result as a consequence: in the phylogenetic trees generated by Shakya et al. (2017) Unfortunately, the second species of Gecinulus, Blyth, 1845, G. viridis (Bamboo Woodpecker) was not sampled by Shakya et al. (2017), but a close relationship between these congeners has long been assumed, with conspecificity sometimes proposed (Short 1982, Dickinson 2003, in part doubtless because a narrow hybrid zone between them exists in northern Thailand and, presumably, northern Laos (Round et al. 2012). The risk that the absence of molecular data for G. viridis might complicate the scenario recovered by Shakya et al. (2017) therefore appears remote. ...
... This is not, however, to pretend that anomalies might not result as a consequence: in the phylogenetic trees generated by Shakya et al. (2017) Unfortunately, the second species of Gecinulus, Blyth, 1845, G. viridis (Bamboo Woodpecker) was not sampled by Shakya et al. (2017), but a close relationship between these congeners has long been assumed, with conspecificity sometimes proposed (Short 1982, Dickinson 2003, in part doubtless because a narrow hybrid zone between them exists in northern Thailand and, presumably, northern Laos (Round et al. 2012). The risk that the absence of molecular data for G. viridis might complicate the scenario recovered by Shakya et al. (2017) therefore appears remote. ...
A recent comprehensive molecular phylogeny of the Picidae recovered the genus Dinopium as paraphyletic, with Olive-backed Woodpecker D. rafflesii sister to Pale-headed Woodpecker Gecinulus grantia. Of the available taxonomic responses, we favour assigning D. rafflesii to its own genus, in line with the modern trend to recognise more and smaller genera. Several genus names were used for rafflesii between the mid-19th and early 20th centuries, of which Chloropicoides Malherbe, 1849, is the oldest. Available information suggests, however, that it was not Malherbe's intention to designate rafflesii as the type of his new genus, but that in near-simultaneously publishing two works on the Picidae he inadvertently introduced Chloropicoides first in combination solely with rafflesii, making it the type species by monotypy. Should it be proven that his other, more detailed paper was in fact published first, then another Malherbe genus, Gauropicoides, could be used by those who seek to recognise the distinctiveness of rafflesii.
... The topology recovered from the partitioned concatenated analysis of twelve mitochondrial protein coding loci (Figure 3) was in strong agreement with current phylogenetic hypotheses for family-level and genus-level relationships in Piciformes (e.g. Prum et al. 2015, Shakya et al. 2017. ...
... Melanerpini (Melanerpes aurifrons) clades (Shakya et al. 2017). Genome fragmentation, especially the number of microchromosomes, could explain this pattern as they could be more difficult to ...
The European Green Woodpecker, Picus viridis , is a widely distributed species found in the Western Palearctic region. Here we assembled a highly contiguous genome assembly for this species using a combination of short and long reads sequencing and scaffolded with chromatin conformation capture (Hi-C). The final genome assembly was 1.28 Gb and features a scaffold N50 of 37Mb and a scaffold L50 of 39.165 Mb. The assembly incorporates 89.4% of the genes identified in birds in OrthoDB. Gene and repetitive content annotation on the assembly detected 15,805 genes and a 30.1% occurrence of repetitive elements, respectively. Analysis of synteny demonstrates the fragmented nature of the Picus viridis genome when compared to the chicken ( Gallus gallus ). The assembly and annotations produced in this study will certainly help for further research into the genomics of P. viridis and the comparative evolution of woodpeckers.
... The family contains 230-250 species in 37 genera (Fuchs & Pons 2015, Shakya et al. 2017) but their taxonomy is complex and the exact relationships the axact relationships between species are still not calrified (Benz et al. 2006). In addition, the phylogenetic tree of the family is rather complicated due to hybridization between some species (Cracraft et al. 2004, Fuchs et al. 2013, Seneviratne et al. 2016. ...
... The habitat preferences of each woodpecker species corresponds with their cranial attributes, because these species are mostly non-migratory (Pasinelli 2006) and their home ranges are linked to certain trees and forests (Michalczuk et al. 2018, Vadász et al. 2022. Climatic changes and changes in flora elements through glacial and interglacial periods most likely had major effects on closely related species (like the Dendrocopos) and worked as a significant factor during speciation (Varga 2009, Horsák et al. 2015, Szatmári 2015, Shakya et al. 2017. It is also possible that some unique attributes may have evolved in isolated populations. ...
The woodpecker family (Picidae) includes numerous species that vary in size and plumage colouration, but which share many easily recognisable external features. These birds possess pronounced anatomical adaptions that enable them to exploit arboreal habitats and live in niches that are inaccessible to most other birds. The aim of this study was to increase our knowledge on the relationships between skull shape, habitat preference, pecking abilities and foraging habits of 10 European woodpecker species. A geometric morphometric approach was used to analyse two-dimensional cranial landmarks. We used principal component (PC) analyses on those measurements that may be related to habitat preference and foraging habits. The PCs resulted in descriptions of the relative length and width of the bill, variation in its relative size, orientation of the nostrils variation in the elongation of the neurocranium, the relative size and position of the palatine bone, length of the rostrum , and the thickness of the mandible bone. The analysis showed and confirmed the presence of some cranial elements that are strongly associated with habitat preference, pecking behaviour and excavation abilities.
... [p. 332] Nuclear and mitochondrial DNA sequences (Benz et al. 2006, Dufort 2016, Shakya et al. 2017 indicate that Nesoctites micromegas belongs to the Picinae rather than to the Picumninae. Delete the headings Tribe PICUMNINI: Typical Piculets and Tribe NESOCTITINI: Antillean Piculets. ...
... Notes.-Formerly (e.g., AOU 1983AOU , 1998) placed in the subfamily Picumninae, but genetic data (Benz et al. 2006, Dufort 2016, Shakya et al. 2017 show that this species is sister to the rest of the Picinae and is not part of the Picumninae, as anticipated by the anatomical study of Goodge (1972). ...
... Moreover, hybridization might be less common in genera that belong to a mimicry complex (and vice versa). We tested these predictions in woodpeckers, a bird group in which interspecific mimicry has convergently evolved several times (Benz et al. 2015, Shakya et al. 2017, Miller et al. 2019) and which shows a relatively high incidence of hybridization (ca 25%, Ottenburghs et al. 2015). We compiled an extensive database of reliable hybrid records in woodpeckers and compared the divergence times between hybridizing species and species that belong to mimicry complex. ...
The evolution of interspecific mimicry does not always result in perfect resemblance between mimics and models. Differences between members of a mimicry complex can be explained by genetic or developmental constraints. Alternatively, imperfect mimicry might be the outcome of a tradeoff between multiple selective pressures. In this study, we explored the evolutionary conflict between mimicry and hybridization in woodpeckers. Based on the selective tradeoff hypothesis, we expected that mimicry complexes will start to evolve once the constraint of maladaptive hybridization is relaxed. Hence, we predicted limited overlap in the divergence times between hybridizing species pairs and members of a mimicry complex. This prediction was supported by clear tipping point in the probability of hybridization and mimicry at ca 9 million years of divergence. Around this timepoint, the probability of hybridization approaches zero while the probability of belonging to a mimicry complex increases. This finding is only correlational and remains to be confirmed in other taxonomic groups. Nonetheless, our results suggest a selective tradeoff between evolving interspecific mimicry and avoiding maladaptive hybridization in woodpeckers.
... Despite this dynamic demographic history, Downy and Hairy Woodpeckers were able to maintain very large effective population sizes, which might have prevented erosion of adaptive variation by genetic drift and therefore facilitated the action of natural selection (18). Moreover, although they belong to different clades, separating more than eight million years ago (19,20), Downy and Hairy Woodpeckers resemble each other more closely than other species of their clades (21). This plumage convergence is hypothesized to result from interspecies social dominance mimicry, where a smaller animal mimics a larger one to scare off competitors and gain access to resources (22). ...
Convergent local adaptation offers a glimpse into the role of constraint and stochasticity in adaptive evolution, in particular the extent to which similar genetic mechanisms drive adaptation to common selective forces. Here, we investigated the genomics of local adaptation in two nonsister woodpeckers that are codistributed across an entire continent and exhibit remarkably convergent patterns of geographic variation. We sequenced the genomes of 140 individuals of Downy (Dryobates pubescens) and Hairy (Dryobates villosus) woodpeckers and used a suite of genomic approaches to identify loci under selection. We showed evidence that convergent genes have been targeted by selection in response to shared environmental pressures, such as temperature and precipitation. Among candidates, we found multiple genes putatively linked to key phenotypic adaptations to climate, including differences in body size (e.g., IGFPB) and plumage (e.g., MREG). These results are consistent with genetic constraints limiting the pathways of adaptation to broad climatic gradients, even after genetic backgrounds diverge.
... (R Core Team, 2022), using comparative methods that account for the shared ancestry (nondependence) of the data points (species). As such, we based our analyses on a woodpecker phylogeny (Miles et al., 2020) that combines two recent well-resolved phylogenies for this clade (Dufort, 2016;Shakya et al., 2017). ...
... and the two Crypturellus(Barker et al., 2015;Chaves et al., 2013;DaCosta & Klicka, 2008;Harvey et al., 2020;Mann et al., 2006;McGuire et al., 2014;Shakya et al., 2017;Sorenson & Payne, 2005;Wink et al., 2004). ...
Understanding the factors that govern variation in genetic structure across species is key to the study of speciation and population genetics. Genetic structure has been linked to several aspects of life history, such as foraging strategy, habitat association, migration distance, and dispersal ability, all of which might influence dispersal and gene flow. Comparative studies of population genetic data from species with differing life histories provide opportunities to tease apart the role of dispersal in shaping gene flow and population genetic structure. Here, we examine population genetic data from sets of bird species specialized on a series of Amazonian habitat types hypothesized to filter for species with dramatically different dispersal abilities: stable upland forest, dynamic floodplain forest, and highly dynamic riverine islands. Using genome-wide markers, we show that habitat type has a significant effect on population genetic structure, with species in upland forest, floodplain forest, and riverine islands exhibiting progressively lower levels of structure. Although morphological traits used as proxies for individual-level dispersal ability did not explain this pattern, population genetic measures of gene flow are elevated in species from more dynamic riverine habitats. Our results suggest that the habitat in which a species occurs drives the degree of population genetic structuring via its impact on long-term fluctuations in levels of gene flow, with species in highly dynamic habitats having particularly elevated gene flow. These differences in genetic variation across taxa specialized in distinct habitats may lead to disparate responses to environmental change or habitat-specific diversification dynamics over evolutionary time scales.
... Woodpeckers are represented by one fossil from the Oligocene (Mayr, 2001), but the morphology of that fossil was intermediate between trunk-climbing and non-climbing Piciformes, making it difficult to assign a date to the origin of climbing in woodpeckers. Molecular dating Shakya et al., 2017) suggests a divergence of the non-climbing wryneck (Jynx torquilla) from other woodpeckers during the early Miocene or Oligocene-Miocene transition, but insufficient data exist to determine when vertical climbing evolved relative to this divergence. That multiple lineages appear to have independently evolved vertical foraging on trees during or close to the early Miocene may potentially be attributed to the expansion of temperate deciduous forest during the Oligocene-Miocene transition (Jiménez-Moreno, 2006). ...
The ability of feathers to perform many functions either simultaneously or at different times throughout the year or life of a bird is integral to the evolutionary history of birds. Many studies focus on single functions of feathers, but any given feather performs many functions over its lifetime. These functions necessarily interact with each other throughout the evolution and development of birds, so our knowledge of avian evolution is incomplete without understanding the multifunctionality of feathers, and how different functions may act synergistically or antagonistically during natural selection. Here, we review how feather functions interact with avian evolution, with a focus on recent technological and discovery‐based advances. By synthesising research into feather functions over hierarchical scales (pattern, arrangement, macrostructure, microstructure, nanostructure, molecules), we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into an astounding array of environments and life‐history strategies. We suggest that future research into avian evolution involving feather function should consider multiple aspects of a feather, including multiple functions, seasonal wear and renewal, and ecological or mechanical interactions. With this more holistic view, processes such as the evolution of avian coloration and flight can be understood in a broader and more nuanced context.
... Non-phylogenetic analyses assume independence among data points, but this assumption can be violated by ancestral relatedness among taxa in comparative studies [64]. Thus, we accounted for the shared history of woodpeckers through analyses informed by recently published maximum clade credibility supermatrix tree (based on nuclear and mitochondrial genes), which is time-calibrated to fossil and biogeographic data [65]. We then added a time calibration and taxon name adjustment based on previous work [66]. ...
Sexual selection drives the evolution of many spectacular animal displays that we see in nature. Yet, how selection combines and elaborates different signal traits remains unclear. Here, we investigate this issue by testing for correlated evolution between head plumage colour and drumming behaviour in woodpeckers. These signals function in the context of mate choice and male–male competition, and they may appear to a receiver as a single multimodal display. We test for such correlations in males of 132 species using phylogenetic linear models, while considering the effect of habitat. We find that the plumage chromatic contrast is positively correlated with the speed of the drum, supporting the idea that species evolving more conspicuous plumage on their head also evolve faster drum displays. By contrast, we do not find evidence of correlated evolution between drum speed and head colour diversity, size of the head's red patch, or extent of the plumage achromatic contrast. Drum length was not correlated with any of the plumage coloration metrics. Lastly, we find no evidence that habitat acts as a strong selective force driving the evolution of head coloration or drumming elaboration. Coevolution between different signal modalities is therefore complex, and probably depends on the display components in question.
... Using receptor profiling and behavioral tests, we uncover both an early gain and an unexpected subsequent loss of sugar sensing in woodpeckers, a primarily insectivorous family of landbirds. 8,9 Our analyses show that, similar to hummingbirds 10 and songbirds, 4 the ancestors of woodpeckers repurposed their T1R1-T1R3 savory receptor to detect sugars. Importantly, whereas woodpeckers seem to have broadly retained this ability, our experiments demonstrate that wrynecks (an enigmatic ant-eating group sister to all other woodpeckers) selectively lost sugar sensing through a novel mechanism involving a single amino acid change in the T1R3 transmembrane domain. ...
Sensory receptors evolve, and changes to their response profiles can directly impact sensory perception and affect diverse behaviors, from mate choice to foraging decisions.1, 2, 3 Although receptor sensitivities can be highly contingent on changes occurring early in a lineage’s evolutionary history,⁴ subsequent shifts in a species’ behavior and ecology may exert selective pressure to modify and even reverse sensory receptor capabilities.5, 6, 7 Neither the extent to which sensory reversion occurs nor the mechanisms underlying such shifts is well understood. Using receptor profiling and behavioral tests, we uncover both an early gain and an unexpected subsequent loss of sugar sensing in woodpeckers, a primarily insectivorous family of landbirds.⁸,⁹ Our analyses show that, similar to hummingbirds¹⁰ and songbirds,⁴ the ancestors of woodpeckers repurposed their T1R1-T1R3 savory receptor to detect sugars. Importantly, whereas woodpeckers seem to have broadly retained this ability, our experiments demonstrate that wrynecks (an enigmatic ant-eating group sister to all other woodpeckers) selectively lost sugar sensing through a novel mechanism involving a single amino acid change in the T1R3 transmembrane domain. The identification of this molecular microswitch responsible for a sensory shift in taste receptors provides an example of the molecular basis of a sensory reversion in vertebrates and offers novel insights into structure-function relationships during sensory receptor evolution.
... In addition, juvenile dispersal appears to occur over several hundred kilometres, and eruptive movements are well-documented for this species (del Hoyo et al. 2018), suggesting strong dispersal abilities and high genetic connectivity of populations. Middle and great spotted woodpeckers are not closely related and have been suggested to belong to different clades (Fuchs & Pons 2015;Shakya et al 2017), and no evidence of interbreeding has been reported. ...
Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.
... The DFA showed us that although the vocalizations of each subspecies can be easily confused with other subspecies within their own vocal group, they can be reliably Acorn Woodpeckers present moderate geographic variation in genetic structure, coloration, and body size as compared to other woodpeckers with a similar distribution but wider variation patterns (e.g., Dryobates villosus; Weibel and Moore 2005, Klicka et al. 2011). Furthermore, vocal attributes have very rarely been used in evolutionary studies in woodpeckers (e.g., Popp andFicken 1991, Benz andRobbins 2011), perhaps because complex patterns of differentiation, hybridization, and convergence are more easily detected using plumage attributes (e.g., Navarro-Sigüenza et al. 2017, Shakya et al. 2017, and vocal variation apparently has lower complexity (e.g., Winkler andShort 1978, Benz andRobbins 2011), but without having any investigations about vocal geographic variation between subspecies or populations. ...
Studies of geographic variation of bird vocalizations facilitate the understanding of species' divergence and evolutionary histories, as vocal traits vary in response to different factors including the environment, morphology, culture, and inheritance. The Acorn Woodpecker (Melanerpes formicivorus) is a non-passerine species of the family Picidae, and therefore its vocalizations are not acquired through learning. It is widely distributed throughout the Americas and exhibits distinctive morphological and genetic differences among the 7 allopatric subspecies, but little is known about geographic variation in the structure of its vocalizations and whether vocal variation corresponds with their genetic differences. We collected recordings throughout the species' range and assessed the frequency and temporal features of their most common calls to study geographic variation in vocalizations. Specifically, we tested whether divergence in vocal traits mirrored subspecies limits. Our results showed the formation of 2 vocal groups that do not reflect subspecies limits. The genetic divergence described in previous studies coincides with the vocal divergence found in this study, with 2 areas promoting the greatest divergence: the Isthmus of Tehuantepec and the Gulf of California. Previously described morphological variation in bill sizes also coincides with the vocal groups found in this study, in which large and small sizes are grouped separately.
... A molecular phylogeny of the Picidae (Shakya et al. 2017) found the genus Dinopium paraphyletic, because Olive-backed Woodpecker D. rafflesii (Plate 18) was recovered as sister to Pale-headed Woodpecker Gecinulus grantia. Thus either (1) Gecinulus should be merged in Dinopium; ...
Pakistan’s avifauna was well documented in the two-volume
work ‘The Birds of Pakistan’ (Roberts 1991, 1992), thanks to the
numerous ornithologists and birdwatchers who visited, many
of them stationed as civil service officers. Pakistan’s bird list was
added to by Roberts (2002), and Grimmett et al. (2008) published
the first modern field guide to the country, providing a more
contemporary country list in the process.
Since this time birdwatching and ornithology across the
country have grown and, as a consequence, numerous new and
interesting bird records have come to light. This article highlights
and classifies the notable records in two categories from mid-
2013 to mid-2021: (1) records which constitute an addition to the
checklist of Pakistan, in some cases presenting substantial range
extensions; and (2) vagrant species with five or fewer previous
records. In total, we document 23 new species for Pakistan and
discuss 17 vagrant species.
... We suspect that sexual selection by male-male competition drives the evolutionary elaboration of drum speed and length, at least in downy woodpeckers. This idea is based on recent studies that suggest that elaborate displays produced through FIGURE 2 | Cladogram of the woodpeckers (Picidae) from Shakya et al. (2017). Colors within the phylogenetic tree illustrate the five main woodpecker tribes and non-drumming old world woodpeckers (e.g., wrynecks). ...
Understanding how and why behavioral traits diversify during the course of evolution is a longstanding goal of organismal biologists. Historically, this topic is examined from an ecological perspective, where behavioral evolution is thought to occur in response to selection pressures that arise through different social and environmental factors. Yet organismal physiology and biomechanics also play a role in this process by defining the types of behavioral traits that are more or less likely to arise. Our paper explores the interplay between ecological, physiological, and mechanical factors that shape the evolution of an elaborate display in woodpeckers called the drum. Individuals produce this behavior by rapidly hammering their bill on trees in their habitat, and it serves as an aggressive signal during territorial encounters. We describe how different components of the display—namely, speed (bill strikes/beats sec–1), length (total number of beats), and rhythm—differentially evolve likely in response to sexual selection by male-male competition, whereas other components of the display appear more evolutionarily static, possibly due to morphological or physiological constraints. We synthesize research related to principles of avian muscle physiology and ecology to guide inferences about the biomechanical basis of woodpecker drumming. Our aim is to introduce the woodpecker as an ideal study system to study the physiological basis of behavioral evolution and how it relates to selection born through different ecological factors.
... Woodpeckers are represented by one fossil from the Oligocene (Mayr 2001), but the morphology of that fossil was intermediate between trunk-climbing and non-climbing Piciformes, and so it is difficult to assign a date to the origin of climbing in woodpeckers. Molecular dating , Shakya et al. 2017) suggests a divergence of the non-climbing Wryneck (Jynx torquilla) from other woodpeckers during the early Miocene or Oligocene-Miocene transition, but not enough data exists to determine when vertical climbing evolved relative to this divergence. That multiple lineages appear to have independently evolved vertical foraging on trees during or close to the early Miocene may potentially be attributed to the expansion of temperate deciduous forest during the Oligocene-Miocene transition (Jiménez-Moreno 2006). ...
The ability feathers have to perform many functions simultaneously and at different times is integral to the evolutionary history of all birds. Many studies focus on single functions of feathers; but any given feather performs many functions over its lifetime. Here, we review the known functions of feathers and discuss the interactions of these functions with avian evolution. Recent years have seen an increase in research on the evolution and development of feather functions because of an increase in high quality fossils with preserved feathers, new tools for understanding genetic mechanisms of feather development, new tools for measuring and analyzing feather color, availability of phylogenies and phylogenetic comparative methods, and an increase in interest in feather molt. Here, we aim to review how feather functions interact with avian evolution, with a focus on recent technological and discovery-based advances. By synthesizing research into feather functions over hierarchical scales, we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into the astounding array of environments and life-history strategies. Overall, we suggest research into avian evolution that involves feather function in any way should consider all aspects of a feathers’ functionality, including multiple functions, molt patterns, ecological/mechanical interactions, and feather wear over time. With this more holistic view, processes such as the evolution of avian coloration and flight can be understood in a broader and more nuanced context.
... First, the species must be reasonably closely related to apply the integrative approach. Downy and hairy woodpeckers are congeners or are at least in the same clade (Shakya et al. 2017;Miles et al. 2018) and are thus sufficiently closely related so that a comparison is reasonable. ...
Phylogenetic comparative methods represent a major advance in integrative and comparative biology and have allowed researchers to rigorously test for adaptation in a macroevolutionary framework. However, phylogenetic comparative methods require trait data for many species, which is impractical for certain taxonomic groups and trait types. We propose that the philosophical principle of severity can be implemented in an integrative framework to generate strong inference of adaptation in studies that compare only a few populations or species. This approach requires (1) ensuring that the study system contains species that are relatively closely related; (2) formulating a specific, clear, overarching hypothesis that can be subjected to integrative testing across levels of biological organization (e.g., ecology, behavior, morphology, physiology, and genetics); (3) collecting data that avoid statistical underdetermination and thus allow severe tests of hypotheses; and (4) systematically refining and refuting alternative hypotheses. Although difficult to collect for more than a few species, detailed, integrative data can be used to differentiate among several potential agents of selection. In this way, integrative studies of small numbers of closely related species can complement and even improve on broadscale phylogenetic comparative studies by revealing the specific drivers of adaptation.
... These sites are described as "anvils". Food items such as nuts, seeds, cones, fruits, and even insects, are wedged by woodpecker species of the genera Dendrocopos, Dryobates and Melanerpes of the tribe Melanerpini (Winkler et al. 1995;Bondo et al. 2008;Leonard and Heath 2010;Shakya et al. 2017). In some species, anvils are used only once, with a woodpecker processing a food item in an available site, and then leaving the remains in place (e.g. ...
The use of anvils for foraging allows access to food that cannot be exploited otherwise by most birds or other animals. This may be especially important in habitats where food resources are scarce or fluctuate seasonally and where animals exploit novel and highly nutritional food resources that require unconventional foraging techniques to acquire energy. In dry woodlands of northern Argentina, the White-fronted Woodpecker, Melanerpes cactorum, secures seeds from a shrub species, Sarcotoxicum salicifolium, by wedging the seeds into crevices, holes, or forks within plant structures, where they peck the hard cover of the seeds to extract the embryo. The aim of this study was to evaluate whether the anvil use by the White-fronted Woodpecker conforms to or differs from the anvil use by other woodpecker species. Specifically, we (1) described the behaviour of seed consumption mediated by using anvils in plant structures, and (2) analysed the use of anvils for seed consumption relative to seasonality and food availability in the dry Chaco of Argentina. The woodpecker matched the size of the seed to the anvil, and seeds were positioned mostly with a specific orientation pattern in structures of seven plant species, facilitating opening and extraction of the complete embryo. As in other anvil-using woodpecker species, this pattern of deliberate manipulation and orientation of seeds by the woodpeckers may imply spatial association of the seed and the site used as an anvil, a behaviour that could be cognitively more demanding than simply using an anvil. In contrast with other anvil-using woodpecker species, seed consumption mediated by anvil use was most important in summer (i.e. breeding season), when S. salicifolium seeds were more abundant but also when the availability of food resources was more diverse and abundant. The seed embryos are likely an important source of nutrients and more profitable than other less protected food resources for the White-fronted Woodpecker, particularly during the breeding season when energy demands increase.
... Within this group, the West Indian Woodpecker is most similar in appearance to the Red-bellied Woodpecker (Melanerpes carolinus) (1), and genetic data confirm that it is a member of the group of species that includes Melanerpes carolinus, Melanerpes aurifrons (Golden-fronted Woodpecker), and Melanerpes uropygialis (Gila Woodpecker) (26, 27,28). Surprisingly, however, the genetic data show that West Indian Woodpecker is most closely related to Melanerpes radiolatus (Jamaican Woodpecker), which is also part of this species group (28,29), even though the coloration of M. superciliaris is much more similar to that of continental M. carolinus (30). ...
This conspicuous, vocal woodpecker is resident in a wide variety of habitats on Grand Cayman, Cuba and nearby islands, and San Salvador, Abaco, and (until recently) Grand Bahama in The Bahamas. West Indian Woodpecker is similar to the Red-bellied Woodpecker (Melanerpes carolinus) of eastern North America in appearance and behavior, but it is usually larger. Also, most subspecies of West Indian Woodpecker have a distinctive black mark over and behind the eye (the supercilium of the scientific name).
West Indian Woodpecker frequently is found in areas with tall, smooth-trunked palms, which provide suitable nesting habitat, and this limits its distribution on some islands. It forages solitarily or in pairs on the trunks and branches of trees. Its feeding behavior is exceptionally broad for a woodpecker. It gathers insects, spiders, small frogs, and lizards by pecking on bark, probing into bromeliad leaves, or gleaning vegetation, and also frequently feeds on fruit. Distinct populations on particular islands are recognized as separate subspecies. Although West Indian Woodpecker is common on Cuba and Grand Cayman, some of the subspecies on smaller islands have small populations that are vulnerable to extinction, and the original Grand Bahama population probably has been extirpated.
... Trees were rooted with sequences from Picoides pubescens and Veniliornis mixtus (e.g. Shakya et al., 2017). Detailed information on the sequences included in the analyses is reported in Table S1. ...
We use multilocus molecular data and species distribution modelling to investigate the phylogenetics and the phylogeography of the White-backed Woodpecker (Dendrocopos leucotos), a bird species widely distributed over the entire Palaearctic. Our phylogenetic results reveal three well-supported clades within D. leucotos: the Chinese endemic subspecies (tangi, insularis), the northerly distributed subspecies (leucotos, uralensis) and the four poorly genetically differentiated Japanese sub-species (subcirris, stejnegeri, namiyei, owstoni), and the southwestern Palaearctic lilfordi subspecies. According to our results, the Amami Woodpecker, endemic to Amami Oshima Island (Ryukyu archipelago, Japan) sometimes treated as full species Dendrocopos owstoni, does not deserve a species-level status. Based on the mito-chondrial phylogeographic results, the Japanese archipelago was recently colonized only once by D. leucotos from eastern Eurasia. Our results suggest a split between the leucotos and lilfordi lineages that dates back to mid-Pleistocene (around 0.6 Mya) with likely no gene flow between these two subspecies since then. Our results thus do not support a phylogeographic pattern in which Central Europe and Northern Europe were recolonized from one or several southern glacial refugia where lilfordi populations persisted through several Pleistocene glacial periods. Spatial variation in mitochondrial diversity across leucotos/uralensis populations and niche ecological modelling suggest a possible eastward population expansion from a unique glacial refugium likely located in Central Europe. Molecular species delimitation methods, gene flow analyses and differences in adult and juvenile plumage indicate that the lilfordi subspecies may warrant to be ranked as a valid phylogenetic species. Further studies are nevertheless needed in the Balkans, where leucotos and lilfordi came recently into contact to measure the effectiveness of reproductive barriers and gene flow.
... Interestingly, in the case of woodpeckers, an additional eye-catching aspect of their co-existence is plumage convergence. Proposed mechanisms for phenotypic resemblance include shared ancestry (Short 1982), parallel evolution due to common evolutionary pressures (Winkler et al. 1994), convergence between distantly related taxa (Shakya et al. 2017) and advergent evolution like some types of mimicry (Brower and Brower 1972). Miller et al. (2019) concluded that many woodpecker species form mimicry complexes. ...
Explaining the co-existence of sympatric and ecologically similar species is a central goal in ecology. In woodpeckers (Picidae), co-existence is frequently accompanied by plumage convergence. A particularly striking case concerns three woodpecker species in the Atlantic Forest of South America: Robust Woodpecker (Campephilus robustus), Lineated Woodpecker (Dryocopus lineatus) and Helmeted Woodpecker (Celeus galeatus), which show a remarkable degree of plumage similarity thought to result from convergence due to interspecific social dominance mimicry (ISDM). We studied the foraging ecology and interactions of these three species in old-growth forests and selectively logged forests to test the extent to which these species differ in various aspects of their foraging ecology, and we examined whether particular foraging requirements may help explain the association of the threatened Helmeted Woodpecker with mature forests. The species selected different tree species, tree diameters, foraging heights, decay states of trees and decay states of substrates, resulting in marked niche separation among the three species. Proportionally, the Robust Woodpecker chiselled more, Helmeted Woodpecker used more probing and Lineated Woodpecker used more hammering. Helmeted Woodpecker was the only species that included bamboos as foraging substrates, and it foraged more on dead wood than Lineated or Robust Woodpeckers, but mostly on small dead branches in live trees rather than standing dead trees. Foraging requirements are not the most likely factor explaining the association of Helmeted Woodpecker with mature forests. Limited resource and substrate overlap among the three woodpecker species, lack of interspecific interactions, and rarity of the Helmeted Woodpecker do not match predictions if these species were conforming to a mimicry complex under the hypothesis of ISDM. Instead, plumage convergence may aid in interactions with third species, or impart advantages in intraspecific competition.
... This is not surprising for D. pubescens, given the small number of individuals sampled from a relatively limited geographic area. As expected, based on previous phylogenetic work (Shakya et al. 2017), D. nuttallii and D. scalaris were closely related in the haplotype network ( Figure 3), with ~1-2% uncorrected sequence divergence between individuals of the 2 species. D. pubescens was more FIGURE 2. Demographic and divergence scenarios tested using ∂a∂i. ...
Evolutionary biologists have long used behavioral, ecological, and genetic data from contact zones between closely related species to study various phases of the speciation continuum. North America has several concentrations of avian contact zones, where multiple pairs of sister lineages meet, with or without hybridization. In a southern California contact zone, 2 species of woodpeckers, Nuttall’s Woodpecker (Dryobates nuttallii) and the Ladder-backed Woodpecker (D. scalaris), occasionally hybridize. We sampled these 2 species in a transect across this contact zone and included samples of their closest relative, the Downy Woodpecker (D. pubescens), to obtain large single nucleotide polymorphism panels using restriction-site associated DNA sequencing (RAD-seq). Furthermore, we used whole-genome resequencing data for 2 individuals per species to identify whether patterns of diversity inferred from RAD-seq were representative of whole-genome diversity. We found that these 3 woodpecker species are genomically distinct. Although low levels of gene flow occur between D. nuttallii and D. scalaris across the contact zone, there was no evidence for widespread genomic introgression between these 2 species. Overall patterns of genomic diversity from the RAD-seq and wholegenome datasets appear to be related to distributional range size and, by extension, are likely related to effective population sizes for each species.
... Picumnus limae is believed to be related to P. nebulosus Sundevall, 1866 (Short 1982;Sick 1997;Winkler and Christie 2002), however, morphology and vocal characters support a relationship with P. spilogaster Sundevall, 1866. This is also suggested by molecular analysis, which placed all piculets with trilled voice within the same group (Shakya et al. 2017;Lima 2018). ...
Picumnus limae Snethlage, 1924 and Picumnus fulvescens Stager, 1961 are two similar species of piculets distinguished by their plumage colouration and distribution. We present here a taxonomic reassessment of these two species based on a large sample of museum specimens and photographic material. We show that the two species are highly variable in colouration, showing a clinal colour gradient. Picumnus fulvescens is not diagnosable from P. limae by any morphological features or vocalization. We thus suggest that P. fulvescens should be considered a synonym of P. limae, which presents a large variation in plumage colour.
We present a complete, time-scaled, evolutionary tree of the world’s bird species. This tree unites phylogenetic estimates for 9,239 species from 262 studies published between 1990 and 2024, using the Open Tree synthesis algorithm. The remaining species are placed in the tree based on curated taxonomic information. The tips of this complete tree are aligned to the species in the Clements Taxonomy used by eBird and other resources, and cross-mapped to other taxonomic systems including the Open Tree of Life (Open Tree), National Center for Biotechnology Information (NCBI), and Global Biodiversity Information Facility (GBIF). The total number of named bird species varies between 10,824 and 11,017 across the taxonomy versions we applied (v2021, v2022 and v2023). We share complete trees for each taxonomy version. The procedure, software and data-stores we used to generate this tree are public and reproducible. The tree presented here is Aves v1.2 and can be easily updated with new phylogenetic information as new estimates are published. We demonstrate the types of large scale analyses this data resource enables by linking geographic data with the phylogeny to calculate the regional phylogenetic diversity of birds across the world. We will release updated versions of the phylogenetic synthesis and taxonomic translation tables annually. The procedure we describe here can be applied to developing complete phylogenetic estimates for any taxonomic group of interest.
Significance statement
Birds are charismatic - well loved, and highly studied. Many new phylogenies elucidating avian birds evolutionary relationships are published every year. We have united phylogenetic estimates from hundreds of studies to create a complete evolutionary tree of all birds. While a variety of resources aggregate huge collections of trait, behavior and location data for birds, previously the barriers to linking data between these data resources and bird evolutionary history have limited the opportunities to do exciting large scale analyses. We have bridged that gap, and developed a system that allows us to easily update our understanding of bird evolution as new estimates are generated. We share a workflow and the software needed to create a complete evolutionary tree for any group.
Acoustic communication plays a critical role in the lives of most species of birds. The focus of this chapter is on the ways that birds produce both nonvocal and vocal sounds. The anatomy of the avian syrinx and how it varies among different taxa of birds is discussed. The mechanism by which the syrinx produces sounds is explained and the types and functions of those sounds (calls and songs) are discussed in detail. Different species of birds vary dramatically in the size of their vocal repertoires, including call and song types, and possible explanations for such variation are provided. Many aspects of the singing behavior of birds are discussed, including the mechanisms by which the central nervous system controls singing behavior and differences between the sexes in those mechanisms, variation within and among species in song structure, the various functions of bird song, intra- and interspecific variation in the size of song repertoires, and the process of song learning. Also discussed are vocal mimicry, duetting, group choruses, and the roles of vocalizations in male cooperative courtship.
Plumage patterns of melanerpine (Melanerpes-Sphyrapicus) woodpeckers are strikingly diverse. Understanding the evolution and function of this diversity is challenging because of the difficulty of quantifying plumage patterns. We use a three-dimensional space to characterize the evolution of melanerpine achromatic plumage patterns. The axes of the space are three pattern features (spatial frequency, orientation, and contrast) quantified using two-dimensional fast Fourier transformation of museum specimen images. Mapping plumage in pattern space reveals differences in how species and subclades occupy the space. To quantify these differences, we derive two new measures of pattern: pattern diversity (diversity across plumage patches within a species) and pattern uniqueness (divergence of patterns from those of other species). We estimate that the melanerpine ancestor had mottled plumage and find that pattern traits across patches and subclades evolve at different rates. We also find that smaller species are more likely to display horizontal face patterning. We promote pattern spaces as powerful tools for investigating animal pattern evolution.
Sarawak is Malaysia’s largest state, covering most of northern Borneo. It has a remarkable history of scientific bird study, starting in the 1840s and growing ever since. To set the stage for the gazetteer, which is the core of this paper, we start with a review of this history and discuss various forces that have influenced the direction of bird research in the state. Following this introduction comes the gazetteer, which is an annotated list of c. 865 sites in Sarawak where birds have been collected, studied, or regularly observed. The gazetteer provides the latitude, longitude, and elevation of each site, and it lists publications, reports, and museum collections associated with each site. The purpose of the gazetteer is to help interested parties locate sites and investigate their research history. It is also intended to help museum curators geolocate specimens for various kinds of studies, including the assessment of bird distributions in relation to habitat change over time. A notable byproduct of the historical review and gazetteer is a bibliography of c. 750 references related to Sarawak ornithology. Another is the identification of areas in Sarawak where birds are better known and areas where they are not.
Hairy (Dryobates villosus) and downy (Dryobates pubescens) woodpeckers occur in high densities in residential areas of the eastern United States. In many areas of their range, they cause damage to wooden structures through foraging, excavation of nesting cavities, and drumming behaviors, causing requests for allowable take permits. Both species hold year‐round territories, which could make them vulnerable to local extirpation with excess take. To meet the requirements of the Migratory Bird Treaty act, the United States Fish and Wildlife Service (USFWS) requested scientifically informed evaluation of take to minimize population effects as part of its approach to reduce human–wildlife conflict. We used a prescribed take approach, which uses data from population, demographic, and management parameter estimates to determine the allowable take from Louisiana to Minnesota and all states east. Furthermore, we used 2 different methods of estimating growth rates to control for demographic uncertainties. The resulting estimates provide take at the state and USFWS regional scales to improve stakeholder choices when setting allowable take. Current authorized take (2016–2018) is below the take that could be sustained by current populations, and current rates of take are not likely to cause population‐level effects. These results were largely consistent across methodologies for calculating the rate of growth for both species. Take still needs to be managed to prevent local extirpation of these resident species. Allowable take estimates should be periodically updated to reflect changing management and population needs for both species. Downy and hairy woodpeckers (top panel) cause human‐wildlife conflict when they damage structures with pecking behaviors, and lethal take is sometimes issued. We used a prescribed take level analysis to determine if current levels of lethal take are affecting the population (bottom panel). We found that current take (blue points) is lower than prescribed take (black whisker plots) for all U.S. states containing or east of the Mississippi river.
Species are fundamental to biology, conservation, and environmental legislation; yet, there is often disagreement on how and where species limits should be drawn. Even sophisticated molecular methods have limitations, particularly in the context of geographically isolated lineages or inadequate sampling of loci. With extinction rates rising, methods are needed to assess species limits rapidly but robustly. Tobias et al. devised a points-based system to compare phenotypic divergence between taxa against the level of divergence in sympatric species, establishing a threshold to guide taxonomic assessments at a global scale. The method has received a mixed reception. To evaluate its performance, we identified 397 novel taxonomic splits from 328 parent taxa made by application of the criteria (in 2014‒2016) and searched for subsequent publications investigating the same taxa with molecular and/or phenotypic data. Only 71 (18%) novel splits from 60 parent taxa have since been investigated by independent studies, suggesting that publication of splits underpinned by the criteria in 2014–2016 accelerated taxonomic decisions by at least 33 years. In the evaluated cases, independent analyses explicitly or implicitly supported species status in 62 (87.3%) of 71 splits, with the level of support increasing to 97.2% when excluding subsequent studies limited only to molecular data, and reaching 100% when the points-based criteria were applied using recommended sample sizes. Despite the fact that the training set used to calibrate the criteria was heavily weighted toward passerines, splits of passerines and non-passerines received equally strong support from independent research. We conclude that the method provides a useful tool for quantifying phenotypic divergence and fast-tracking robust taxonomic decisions at a global scale.
To help resolve phylogenetic and phylogeographic relationships of Southeast Asian birds, we have collected specimens in Borneo, Sumatra, and Java for phylogenetic and morphological study. Here, we compare mitochondrial ND2 gene sequences from some of these new specimens to sequences obtained in previous studies to shed light on genealogical relationships in nine passerine clades: Erythropitta venusta/granatina/ussheri (pittas); Dicrurus hottentottus (drongos); Alophoixus bulbuls; Napothera, Turdinus and Pellorneum babblers; Anthipes flycatchers; Brachypteryx shortwings; and Myophonus whistling thrushes. These comparisons resolve or shed substantial light on taxonomic problems in pittas, Alophoixus, Napothera, Dicrurus, Brachypteryx, and Myophonus, and they confirm assumed (but previously unquantified) genetic relationships within Turdinus and Anthipes. The resulting trees also allow us to (1) suggest improved taxonomic arrangements in several groups, (2) confirm the rediscovery of a “lost” species within Napothera, and (3) provide the basis for the description of a new subspecies of Alophoixus.
Abstract We again revise Colombia's checklist based on new records and the literature. Band-tailed Antbird Hypocnemoides maculicauda, Black-tailed Antbird Myrmoborus melanurus and Cave Swallow Petrochelidon fulva are newly added to the Colombian bird checklist, based on photographic records. Christmas Shearwater Puffinus navitatis is returned to the checklist as an unconfirmed species based on a new sight record. A new photographic record allows Scissor-tailed Flycatcher Tyrannus forficatus to be promoted from unconfirmed to confirmed status. Great Frigatebird Fregata minor is promoted to confirmed status, based on a revision of overlooked historical specimens and a new photographic record. Three species are added to the "escaped" category, but which lack evidence of establishment, namely: Turkey Meleagris gallopavo, Swan Goose Anser cygniodes and Egyptian Goose Alopochen aegyptiaca. Splits are accepted of Riparian Antbird Cercomacroides fuscicauda and Campina Thrush Turdus arthuri. Several amendments to genus and species names, English names and linear order are made, following recent publications. The Colombian checklist rises to 1,941 species (excluding escapees).
Resumen Nuevamente revisamos el listado de aves de Colombia, basado en nuevos registros y la literatura. Las especies Hypocnemoides maculicauda, Myrmoborus melanurus y Petrochelidon fulva se agregan al listado de aves de Colombia, basadas en registros fotográficos. Puffinus navitatis vuelve al listado, basada en un nuevo registro visual. Con un registro fotográfico, la especie Tyrannus forficatus es ahora elevada al estado de especie confirmada. La especie Fregata minor, se promociona a estado confirmado, posterior a una revision de especimenes históricos que habían sido pasados por alto, y un nuevo registro fotográfico. Se agregan Meleagris gallopavo, Anser cygniodes y Alopochen aegyptia en la categoría de especies escapadas, pero dichas especies carecen de evidencia sobre su establecimiento. Hemos aceptado las separaciones taxonómicas de Cercomacroides fuscicauda y Turdus arthuri. Finalmente, se realizaron varias modificaciones a los nombres de géneros y especies, nombres en inglés y el orden lineal del listado. El número de especies registradas en el listado de aves de Colombia asciende a 1.941 especies (excluyendo especies exóticas que no han establecido poblaciones). Palabras clave: nuevos registros, especímenes, fotografías, revisión del estado.
The following excerpt from a review by Paul Hamel in the journal Integrative and Comparative Biology serves well as an abstract: "Wow, what a great book! Discretion suggests I stop at that first impression, yet the task of reviewing demands that readers receive more for their interest. Eugene McCarthy, a geneticist interested in hybridization, provides more, too, in this extensive documentation of the literature of avian hybridization. His intent was “to provide basic information about each of the thousands of types of reported avian crosses, to provide access to documenting literature, and to familiarize readers with the nature of avian hybridization.” I give him extremely high marks for achievement of the second goal, high marks for the first, and a better than passing grade for the third. The work is well organized, with 299 pages devoted to cross-referenced accounts of individual summaries of reported hybrids, 157 pages to a bibliography of more than 5000 citations of hybrids, and a 69-page index of common and scientific names conforming to the usage of Sibley and Monroe (1990). The introduction, at 38 pages, is just that, a brief review of the concepts of hybridization, followed by his rationale for, and organization of, the work. Three short appendices complete the book. That dealing with Canary hybrids runs to more than 70 crosses, including two which are considered dubious based on McCarthy's meticulous evaluation of the original accounts. The great strength of this book lies in the careful and extensive presentation of the accounts, which are organized alphabetically by species within genus within family. Families are presented in the order of Sibley and Monroe (1990), an older scheme than those presently in use. Given that the work required many years to compile, it is forgivable that more modern sequences were not employed. McCarthy devised a very compact scheme of codes to present the information, which, after minimal reference to the inside front cover where the scheme is presented, was both logical and easy to follow. I salute him for that, and hope that in future editions this scheme will be presented with the code letters capitalized rather than italicized. The scheme includes information about the nature (captive or natural), extent (extensive or not), and quality of information (reported or inferred) about hybridization. Seven categories identify the extent of fertility of hybrids from exceptionally high to very low fertility, variation between sexes in fertility, as well as the viability of hybrids. Additional categories clarify the relationship of breeding ranges in nature. For biologists interested in hybridization, for conservationists interested in particular species, for ornithologists interested in specific relationships, and for birdwatchers intent on evaluating plumages, this book is a goldmine."
BAMM (Bayesian Analysis of Macroevolutionary Mixtures) is a statistical framework that uses reversible jump MCMC to infer complex macroevolutionary dynamics of diversification and phenotypic evolution on phylogenetic trees. A recent article by Moore and coauthors (MEA) reported a number of theoretical and practical concerns with BAMM. Major claims from MEA are that (1) BAMM's likelihood function is incorrect, because it does not account for unobserved rate shifts; (2) the posterior distribution on the number of rate shifts is overly sensitive to the prior; and (3) diversification rate estimates from BAMM are unreliable. Here, we show that these and other conclusions from MEA are generally incorrect or unjustified. We first demonstrate that MEA's numerical assessment of the BAMM likelihood is compromised by their use of an invalid likelihood function. We then show that "unobserved rate shifts" appear to be irrelevant for biologically-plausible parameterizations of the diversification process. We find that the purportedly extreme prior sensitivity reported by MEA cannot be replicated with standard usage of BAMM v2.5, or with any other version, when conventional Bayesian model selection is performed. Finally, we demonstrate that BAMM performs very well at estimating diversification rate variation across the ∼20% of simulated trees in MEA's dataset for which it is theoretically possible to infer rate shifts with confidence. Due to ascertainment bias, the remaining 80% of their purportedly variable-rate phylogenies are statistically indistinguishable from those produced by a constant-rate birth-death process and were thus poorly-suited for the summary statistics used in their performance assessment. We demonstrate that inferences about diversification rates have been accurate and consistent across all major previous releases of the BAMM software. We recognize an acute need to address the theoretical foundations of rate-shift models for phylogenetic trees, and we expect BAMM and other modeling frameworks to improve in response to mathematical and computational innovations. However, we remain optimistic that that the imperfect tools currently available to comparative biologists have provided and will continue to provide important insights into the diversification of life on Earth.
Significance
We show that Bayesian analysis of macroevolutionary mixtures (BAMM)—a method for identifying lineage-specific diversification rates—is flawed. Exposing the problems with BAMM is important both to empiricists (to avoid making unreliable inferences using this method) and to theoreticians (to focus their efforts on solving the problems that we identify).
During the last 15–20 years, phylogenetic, phylogeographic, paleontological, geological, and habitat
modeling studies have improved our knowledge of Sundaic biogeography dramatically. In light of these advances, we review (or postulate) where Sundaic rainforest birds came from, the causes of their endemism, and the influence of Pleistocene climatic perturbations on their diversification. We suggest that four scenarios make up a coherent, plausible explanation of patterns of extant diversity. First, relictual lineages, which represent hangovers from the warm, wet Eocene, survived the hard climatic times of the colder, drier Oligocene and Pliocene in the mountains and adjacent lowlands of eastern Borneo, where rainforest has existed continuously for the last 20–30 million years. Second, most modern SE Asian genera developed during the Miocene. Third, the rainforest of Sundaland and its avifauna were largely isolated from the rest of SE Asia during the late Miocene and Pliocene by seasonal habitats in southern Indochina and ocean boundaries elsewhere, increasing regional endemism. Finally, the advent of global glaciation in the Pleistocene introduced a different diversification dynamic to Sundaland. Early glacial events caused sufficient
drying in central Sundaland to fragment rainforest and its avifauna into refugia in eastern and western Sundaland and to allow dry-habitat taxa to reach Java from Indochina. More recent glacial events resulted in sufficient perhumid habitat in central Sundaland to reconnect previously vicariated rainforest populations, creating the lowland and elevational parapatry we see today. This Pleistocene dynamic was probably not simply one period of separation and one period of connection, but rather a complex interplay of isolation and colonization, influenced by highly variable population sizes, changing levels of gene flow, and behavioral idiosyncrasies of the species involved. Throughout all of these events, Borneo played a seminal role in rainforest bird evolution by providing the habitat necessary for diversification and the long-term survival of
taxa.
Determining the timing of diversification of modern birds has been difficult. We combined DNA sequences of clock-like genes for most avian families with 130 fossil birds to generate a new time tree for Neornithes and investigated their biogeographic and diversification dynamics. We found that the most recent common ancestor of modern birds inhabited South America around 95 million years ago, but it was not until the Cretaceous-Paleogene transition (66 million years ago) that Neornithes began to diversify rapidly around the world. Birds used two main dispersion routes: reaching the Old World through North America, and reaching Australia and Zealandia through Antarctica. Net diversification rates increased during periods of global cooling, suggesting that fragmentation of tropical biomes stimulated speciation. Thus, we found pervasive evidence that avian evolution has been influenced by plate tectonics and environmental change, two basic features of Earth's dynamics.
Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves-a clade that encompasses nearly all living bird species-remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10(7) bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades-Columbea and Passerea-were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous-Palaeogene (K-Pg) mass extinction.
A nesting of a pair of Gecinulus woodpeckers in a possible zone of intergradation between the parapatric taxa Pale-headed Woodpecker G. grantia and Bamboo Woodpecker G. viridis is described. While the male looked like a more or less typical G. viridis the female bore plumage characters that appeared intermediate between G. grantia and G. viridis. Additionally a specimen labelled as G. grantia indochinensis, collected in Thailand in 1964 (the only record for that country), also appeared atypical, showing characters somewhat intermediate between G. grantia and G. viridis. It is likely that a narrow hybrid zone between G. grantia and G. viridis exists where the two come into contact in northern Thailand and, presumably, northern Laos. Recommendations for further surveys are made in order to determine the extent of postulated hybridisation, and additionally to investigate the ecological and taxonomic relations of these two taxa.
When two species or subspecies hybridize, the parental taxa may become more similar or follow new directions as alleles from one enter the novel genetic and ecological environment of the other. Here, we document hybridization between two Dinopium woodpeckers in Sri Lanka: two subspecies of Black-rumped Flameback woodpeckers (Dinopium benghalense jaffnense and D. b psarodes, recently considered as a full species Lesser Sri Lanka Flameback Dinopium psarodes). Hybridization has been suspected for 130 years. We describe eight different forms of hybrids, only two of which were known historically, and pairing patterns that indicate hybridization. The species and subspecies along with numerous hybrids have now become a hybrid swarm in northern Sri Lanka. Received 2 May 2014. Accepted 30 December 2014.
During the last 15–20 years, phylogenetic, phylogeographic, paleontological, geological, and habitat modeling studies have improved our knowledge of Sundaic biogeography dramatically. In light of these advances, we review (or postulate) where Sundaic rainforest birds came from, the causes of their endemism, and the influence of Pleistocene climatic perturbations on their diversification. We suggest that four scenarios make up a coherent, plausible explanation of patterns of extant diversity. First, relictual lineages, which represent hangovers from the warm, wet Eocene, survived the hard climatic times of the colder, drier Oligocene and Pliocene in the mountains and adjacent lowlands of eastern Borneo, where rainforest has existed continuously for the last 20–30 million years. Second, most modern SE Asian genera developed during the Miocene. Third, the rainforest of Sundaland and its avifauna were largely isolated from the rest of SE Asia during the late Miocene and Pliocene by seasonal habitats in southern Indochina and ocean boundaries elsewhere, increasing regional endemism. Finally, the advent of global glaciation in the Pleistocene introduced a different diversification dynamic to Sundaland. Early glacial events caused sufficient
drying in central Sundaland to fragment rainforest and its avifauna into refugia in eastern and western Sundaland and to allow dry-habitat taxa to reach Java from Indochina. More recent glacial events resulted in sufficient perhumid habitat in central Sundaland to reconnect previously vicariated rainforest populations, creating the lowland and elevational parapatry we see today. This Pleistocene dynamic was probably not simply one period of separation and one period of connection, but rather a complex interplay of isolation and colonization, influenced by highly variable population sizes, changing levels of gene flow, and behavioral idiosyncrasies of the species involved. Throughout all of these events, Borneo played a seminal
role in rainforest bird evolution by providing the habitat necessary for diversification and the long-term survival of taxa.
Piculus chrysochloros (Vieillot 1818) is a species of woodpecker that ranges from Argentina to Panama, occurring in lowland forests as well as Cerrado, Caatinga and Chaco vegetation. Currently, nine subspecies are accepted, but no study has evaluated individual variation within populations, so the status of these taxa remains uncertain. Here we review the taxonomy and distribution of this species, based on morphological and morphometric data from 267 specimens deposited in ornithological collections. Our results suggest the existence of six unambiguous taxonomic units that can be treated as phylogenetic species: Piculus xanthochloros (Sclater & Salvin 1875), from northwestern South America; Piculus capistratus (Malherbe 1862), from northern Amazonia west to the Branco River; Piculus laemostictus Todd 1937, from southern Amazonia; Piculus chrysochloros (Vieillot 1818), from the Cerrado, Caatinga and Chaco; Piculus paraensis (Snethlage 1907) from the Belém Center of Endemism; and Piculus polyzonus (Valenciennes 1826) from the Atlantic Forest. Both Brazilian endemics (P. polyzonus and P. paraensis) are threatened due to habitat loss. In addition, we found one undescribed form from the Tapajós-Tocantins interfluve, now under study, that may prove to be a valid species once more specimens and other data become available.
To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
Copyright © 2014, American Association for the Advancement of Science.
Volume 1 covers the Non-passerines (4072 spp. in pp. i-l, 1-461). Joel Cracraft provided and explained the sequence of families. Fourteen colleagues participated in this work which draws extensively on recent molecular studies, is very extensively footnoted and includes 2877 references. The reference list is on an accompanying CD which includes maps, a gazetteer and appendices 5 to 9 (the previous four being in the book).
The paper presents a phylogeny of Old World woodpeckers based on mitochondrial (cytochrome b,
12S rRNA). It complements published phylogenies of this group in several important aspects. A species that
was formerly treated as part of the core group of pied woodpeckers of the genus Dendrocopos, turned out to
be the closest relative of the Eurasian lesser spotted woodpecker (Dryobates minor), itself a representative
of an American radiation. We identified the brown-fronted woodpecker, a bird of the Himalayan foothills,
as the closest relative of the predominantly European middle spotted woodpecker. The latter is a close relative
of the yellow-crowned woodpecker, widely distributed over India and other parts of South Asia. We
include these three species in the genus Leiopicus (with species medius, auriceps, and mahrattensis). Further
taxonomic recommendations resulted from analyses based on a short fragment of the cytochrome b gene.
Among these is the inclusion of the genus Mulleripicus into Dryocopus that is represented both in the New
and Old World. We present further details of our suggested taxonomy that covers the whole family Picidae
in Appendix 2. Open questions concern, among others, the exact phylogenetic relationships of the two African
woodpecker clades with Asian woodpeckers, and the phylogeographical and taxonomic structure of the
great spotted woodpecker (Dendrocopos major) and its closest allies.
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.
The increase in species richness from the poles to the tropics, referred to as the latitudinal diversity gradient, is one of the most ubiquitous biodiversity patterns in the natural world. Although understanding how rates of speciation and extinction vary with latitude is central to explaining this pattern, such analyses have been impeded by the difficulty of estimating diversification rates associated with specific geographic locations. Here, we use a powerful phylogenetic approach and a nearly complete phylogeny of mammals to estimate speciation, extinction, and dispersal rates associated with the tropical and temperate biomes. Overall, speciation rates are higher, and extinction rates lower, in the tropics than in temperate regions. The diversity of the eight most species-rich mammalian orders (covering 92% of all mammals) peaks in the tropics, except that of the Lagomorpha (hares, rabbits, and pikas) reaching a maxima in northern-temperate regions. Latitudinal patterns in diversification rates are strikingly consistent with these diversity patterns, with peaks in species richness associated with low extinction rates (Primates and Lagomorpha), high speciation rates (Diprotodontia, Artiodactyla, and Soricomorpha), or both (Chiroptera and Rodentia). Rates of range expansion were typically higher from the tropics to the temperate regions than in the other direction, supporting the "out of the tropics" hypothesis whereby species originate in the tropics and disperse into higher latitudes. Overall, these results suggest that differences in diversification rates have played a major role in shaping the modern latitudinal diversity gradient in mammals, and illustrate the usefulness of recently developed phylogenetic approaches for understanding this famous yet mysterious pattern.
Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.
I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available.
The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML.
Alexandros.Stamatakis@h-its.org.
The chapter explores three fundamental issues: phylogenetic accuracy, adaptation, and phylogenetic constraint. These issues are central to historical ecology and cover a broad range of subjects in the field. The most important step to successful historical ecology is the collection of appropriate, accurate, ecological, and phylogenetic data. Although obvious, this assertion is remarkably underemphasized in ecophylogenetic studies. Emphasis is placed primarily on the quality of ecological data, which are viewed as dependent variables, instead of on the accuracy of phylogeny, which is generally viewed as an independent variable without error. However, phylogenetic estimates have error distributions, but these are commonly ignored because they are too complicated to quantify. Historical ecology is burgeoning because it provides structure to the study of ecological patterns and evolutionary processes. Emphasis on the use of accurate phylogenetic data is crucial because the interpretation of evolutionary patterns obviously changes as relationships among taxa change. Although progress may be limited without knowledge of the quantitative genetics of specific traits, initial hypothesis testing is possible with prudent use of the phylogenetic approach, provided that multiple examples of potential evolutionary phenomena are examined.
Adult and juvenile plumage characters were traced onto a well-resolved molecular based phylogeny for Picoides woodpeckers, and a simple phylogenetic test of homology, parallelism, and convergence of plumage characters was performed. Reconstruction of ancestral character states revealed multiple events of independent evolution of derived character states in most characters studied, and a concentrated changes test revealed that some plumage characters evolved in association with habitat type. For example, there was a statistically significant association between loss of dorsal barring and use of densely vegetated habitats among Picoides species. Two analyses indicated that convergence, as opposed to parallel evolution or shared ancestry, underlies the similarity in plumage patterns between the Downy (Picoides pubescens) and Hairy (P. villosus) Woodpeckers. Possible causal explanations for convergence in plumage patterns may include mimicry and interspecific territoriality.
The hybrid zone between the Red- and Yellow-shafted Flickers has been stable on the United States Great Plains in historical times. This conclusion is based on multivariate comparisons of historical and contemporary collections from 18 locales. Adaptive speciation theory predicts that the hybrid zone should either become broader or narrower as a result of introgressive hybridization or reinforcement of premating isolating mechanisms. Neither of these predictions was borne out. Despite 10,000-13,000 years of hybridization, mating between subspecies remains indiscriminate. The data are also inconsistent with a dynamicequilibrium hypothesis wherein narrow hybrid zones are maintained by hybrid unfitness. According to this hypothesis, the hybrid zone would probably "flow" unless it was trapped by a population density trough. The hybrid zone does not appear to be associated with such a feature. The data are consistent with a bounded hybrid superiority theory of a hybrid zone, but this is more a question of survival in a process of elimination than a resounding corroboration.
Are measurements of quantitative genetic variation useful for predicting long-term adaptive evolution? To answer this question, I focus on gmax , the multivariate direction of greatest additive genetic variance within populations. Original data on threespine sticklebacks, together with published genetic measurements from other vertebrates, show that morphological differentiation between species has been biased in the direction of gmax for at least four million years, despite evidence that natural selection is the cause of differentiation. This bias toward the direction of evolution tends to decay with time. Rate of morphological divergence between species is inversely proportional to θ, the angle between the direction of divergence and the direction of greatest genetic variation. The direction of greatest phenotypic variance is not identical with gmax , but for these data is nearly as successful at predicting the direction of species divergence. I interpret the findings to mean that genetic variances and covariances constrain adaptive change in quantitative traits for reasonably long spans of time. An alternative hypothesis, however, cannot be ruled out: that morphological differentiation is biased in the direction gmax because divergence and gmax are both shaped by the same natural selection pressures. Either way, the results reveal that adaptive differentiation occurs principally along "genetic lines of least resistance."
Phylogenetic relationships and patterns of evolution within Melanerpes, one of the most diverse groups of New World woodpeckers (22-23 lineages), have been complicated due to complex plumages and morphological adaptations. In an attempt to resolve these issues, we obtained sequence data from four nuclear introns and two mitochondrial protein-coding genes for 22 of the 24 currently recognized species in the genus. We performed phylogenetic analyses involving Maximum Likelihood and Bayesian Inference, species-tree divergence dating, and biogeographic reconstructions. Tree topologies from the concatenated and species-tree analyses of the mtDNA and nDNA showed broadly similar patterns, with three relatively well-supported groups apparent: a) the Sphyrapicus clade (four species); b) the typical Melanerpes clade, which includes temperate and subtropical dry forest black-backed species; and c) the mostly barred-backed species, here referred to as the “Centurus” clade. The phylogenetic position of Melanerpes superciliaris regarding the rest of Melanerpes is ambiguous as it is recovered as sister to the rest of Melanerpes or as sister to a group including Sphyrapicus + Melanerpes. Our species tree estimations recovered the same well-delimited highly-supported clades. Geographic range evolution (estimated in BioGeoBEARS) was best explained by a DIVALIKE + j model, which includes vicariance, founder effect speciation, and anagenetic dispersal (range expansion) as important processes involved in the diversification of the largest radiation of woodpeckers in the New World.
Although reconstruction of the phylogeny of living birds has progressed tremendously in the last decade, the evolutionary history of Neoaves—a clade that encompasses nearly all living bird species—remains the greatest unresolved challenge in dinosaur systematics. Here we investigate avian phylogeny with an unprecedented scale of data: >390,000 bases of genomic sequence data from each of 198 species of living birds, representing all major avian lineages, and two crocodilian outgroups. Sequence data were collected using anchored hybrid enrichment, yielding 259 nuclear loci with an average length of 1,523 bases for a total data set of over 7.8 × 10⁷ bases. Bayesian and maximum likelihood analyses yielded highly supported and nearly identical phylogenetic trees for all major avian lineages. Five major clades form successive sister groups to the rest of Neoaves: (1) a clade including nightjars, other caprimulgiforms, swifts, and hummingbirds; (2) a clade uniting cuckoos, bustards, and turacos with pigeons, mesites, and sandgrouse; (3) cranes and their relatives; (4) a comprehensive waterbird clade, including all diving, wading, and shorebirds; and (5) a comprehensive landbird clade with the enigmatic hoatzin (Opisthocomus hoazin) as the sister group to the rest. Neither of the two main, recently proposed Neoavian clades—Columbea and Passerea—were supported as monophyletic. The results of our divergence time analyses are congruent with the palaeontological record, supporting a major radiation of crown birds in the wake of the Cretaceous–Palaeogene (K–Pg) mass extinction.
Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic datasets can also result in conflicting estimates of phylogeny. Here we use the early divergences in Neoaves, the largest clade of extant birds, as a 'model system' to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [?42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters (?0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more 'biologically-realistic' models is likely to be critical for efforts to reconstruct the tree of life.
The dynamics of species accumulation of African terrestrial vertebrates over time remains underexplored in comparison with those in the New World, despite Africa hosting about 25% of the world’s avian diversity. This lack of knowledge hampers our understanding of the fundamental processes that drive biodiversity and the dynamics of speciation. To begin to address this gap, we reconstructed species-level phylogenies of two unrelated clades of African woodpeckers (12 species of Geocolaptes/Campethera and 13 species of Chloropicus/ Mesopicos/ Dendropicos/Ipophilus) that diverged from their closest Indo-Malayan relatives at similar times. Our results demonstrate that the current taxonomy is misleading: three (Campethera, Dendropicos and Mesopicos) out of four polytpic genera/subgenera are not monophyletic. Our results also show that current estimates of diversity at the species level are significantly understated, as up to 18 species for the ‘Campethera clade’ and 19 for the ‘Dendropicos clade’ could be recognized. The first splits within both clades involve species that are largely restricted to the Guineo-Congolian biogeographic regions, followed by later adaptations to particular habitats (forest versus savannah) and colonisation of other regions (e.g. Southern Africa), each of which occurred multiple times in both clades. Assuming a conservative species delimitation scheme, our results indicate that diversification rates are decreasing through time for both clades. Applying a more extreme species recognition scheme (18 and 19 species for the Campethera and Dendropicos clades, respectively), our results support a decrease in diversification rates only for the Dendropicos clade and thus underline the importance of the number of species included in our diversification analyses. Greater ecological diversity of the Campethera clade where multiple species exhibit either an arboreal or terrestrial foraging strategy might explain the constant diversification rates through time we found under the eighteen species scheme.
Hybrid zones, where two divergent taxa meet and interbreed, offer unique opportunities to investigate how climate contributes to reproductive isolation between closely related taxa and how these taxa may respond to climatic changes. Red-naped (Sphyrapicus nuchalis) and Red-breasted (Sphyrapicus ruber) sapsuckers (Aves: Picidae) hybridize along a narrow contact zone that stretches from northern California to British Columbia. The hybrid zone between these species has been studied extensively for more than 100 years and represents an excellent system for investigations of the evolution of reproductive isolation. Shifts in the proportions of phenotypes at hybrid localities since 1910 that were inferred using specimens from museum collections were confirmed using species distribution models. We predicted the historical, current, and future distributions of parental and hybrid sapsuckers using Random Forests models to quantify how climate change is affecting hybrid zone movement in the Pacific Northwest. We found observed distribution shifts of parental sapsuckers were likely the result of climate change over the past 100 years, with these shifts predicted to continue for both sapsuckers over the next 80 years. We found Red-breasted Sapsuckers are predicted to continue to expand, while Red-naped Sapsuckers are predicted to contract substantially under future climate scenarios. As a result of the predicted changes, the amount of overlap in the distribution of these sapsuckers may decrease. Using hybrid phenotypes, we found the climate niche occupied by the hybrid zone is predicted to disappear under future conditions. The disappearance of this climate niche where the two parental species come into contact and hybridize may lead to a substantial reduction in genetic introgression. Understanding the impacts of global climate change on hybrid zones may help us to better understand how speciation has been shaped by climate in the past, as well as how evolution may respond to climate change in the future.
Philippine bird taxonomy is relatively conservative and in need of re-examination. A number of well-marked subspecies were selected and subjected to a simple system of scoring (Tobias et al. 2010 Ibis 152: 724-746) that grades morphological and vocal differences between allopatric taxa (exceptional character 4, major 3, medium 2, minor 1; minimum score 7 for species status). This results in the recognition or confirmation of species status for (inverted commas where a new English name is proposed) 'Philippine Collared Dove' Streptopelia (bitorquatus) dusumieri, 'Philippine Green Pigeon' Treron (pompadora) axillaris and 'Buru Green Pigeon' T. (p.) aromatica, Luzon Racquet-tail Prioniturus montanus, Mindanao Racquet-tail P. waterstradti, Blue-winged Raquet-tail P. verticalis, Blue-headed Raquet-tail P. platenae, Yellow-breasted Racquet-tail P. flavicans, White-throated Kingfisher Halcyon (smyrnensis) gularis (with White-breasted Kingfisher applying to H. smyrnensis), 'Northern Silvery Kingfisher' Alcedo (argentata) flumenicola, 'Rufous-crowned Bee-eater' Merops (viridis) americanus, 'Spot-throated Flameback' Dinopium (javense) everetti, 'Luzon Flameback' Chrysocolaptes (lucidus) haematribon, 'Buff-spotted Flameback' C. (l.) lucidus, 'Yellow-faced Flameback' C. (l.) xanthocephalus, 'Red-headed Flameback' C. (l.) erythrocephalus, 'Javan Flameback' C. (l.) strictus, Greater Flameback C. (l.) guttacristatus, 'Sri Lankan Flameback' (Crimson-backed Flameback) Chrysocolaptes (l.) stricklandi, 'Southern Sooty Woodpecker' Mulleripicus (funebris) fuliginosus, Visayan Wattled Broadbill Eurylaimus (steerii) samarensis, White-lored Oriole Oriolus (steerii) albiloris, Tablas Drongo Dicrurus (hottentottus) menagei, Grand or Long-billed Rhabdornis Rhabdornis (inornatus) grandis, 'Visayan Rhabdornis' Rhabdornis (i.) rabori, and 'Visayan Shama' Copsychus (luzoniensis) superciliaris. However, Phapitreron leucotis nigrorum and P. l. brevirostris, P. amethystina maculipectus, Ceyx melanurus mindanensis, Orthotomus castaneiceps frontalis and Phylloscopus trivirgatus nigrorum do not quite make species status and require further vocal or other evidence; and Sulu or Black-billed Hanging Parrot Loriculus bonapartei and Camiguin Hanging Parrot L. camiguinensis are here considered to remain part of Philippine Hanging Parrot L. philippensis.
Examples of phenotypic convergence in plumage coloration have been reported in a wide diversity of avian taxonomic groups, yet the underlying evolutionary mechanisms driving this phenomenon have received little scientific inquiry. We document a striking new case of plumage convergence in the Helmeted Woodpecker (Dryocopus galeatus) and explore the possibility of visual mimicry among Atlantic Forest woodpeckers. Our multilocus phylogenetic analyses unequivocally place D. galeatus within Celeus, indicating that the former has subsequently converged in appearance upon the distantly related and syntopic Dryocopus lineatus, to which it bears a remarkable resemblance in plumage coloration and pattern. Although details of the Helmeted Woodpecker's ecology and natural history are only now beginning to emerge, its smaller size and submissive behavior are consistent with predictions derived from evolutionary game-theory models and the hypothesis of interspecific social-dominance mimicry (ISDM). Moreover, estimates of avian visual acuity suggest that size-related mimetic deception is plausible at distances ecologically relevant to Celeus and Dryocopus foraging behavior. In light of our results, we recommend taxonomic transfer of D. galeatus to Celeus and emphasize the need for detailed behavioral studies that examine the social costs and benefits of plumage convergence to explicitly test for ISDM and other forms of mimicry in these Atlantic Forest woodpecker communities. Future field studies examining potential cases of competitive mimicry should also take into account the mimic's acoustic behavior, particularly in the presence of putative model species and other heterospecific competitors, as any discontinuity between morphological and behavioral mimicry would likely preclude the possibility of deception.
The accumulation of DNA sequence data in public repositories allows for phylogenetic inference on unprecedented taxonomic scales using supermatrix approaches. Careful analysis of available data allows strategic augmentation with new sequences in order to maximize taxonomic sampling and coverage of informative loci. I inferred relationships among 179 species (76%) in the avian family Picidae (woodpeckers, piculets, and wrynecks), using publicly available sequence data supplemented with targeted sequencing to increase species-level and locus-level sampling and maximize resolution. Results of these analyses generally corroborate previous molecular studies, with consensus on the membership of most genera and tribes. However, several newly placed taxa show surprising affinities, and several genera as currently delineated appear to be paraphyletic. Relationships among major clades of Picidae remain poorly resolved, particularly among the three lineages of piculets, the unusual woodpecker genus Hemicircus, and the remaining woodpeckers, and among the major groups of true woodpeckers (Picinae). Phylogenomic approaches may be necessary to resolve these deep relationships.
The Helmeted Woodpecker Dryocopus galeatus is a threatened species of the Atlantic Forest in southeastern South America. It has traditionally been placed in the genus Dryocopus, but it shows similarities in plumage and structure with woodpeckers in the genus Celeus. We sequenced mitochondrial and nuclear DNA that was sampled from live captured Helmeted Woodpeckers. We found that the Helmeted Woodpecker has a phylogenetic position embedded within the genus Celeus, and recommend its taxonomic treatment as Celeus galeatus. The Helmeted Woodpecker belongs to a clade within Celeus that includes Kaempfer’s Woodpecker C. obrieni, Rufous-headed Woodpecker C. spectabilis, and Cream-coloured Woodpecker C. flavus. It has the southernmost distribution range of the woodpeckers in this clade. The Helmeted Woodpecker is sympatric throughout its range with Lineated Woodpecker Dryocopus lineatus and Robust Woodpecker Campephilus robustus and these species from three different genera show a remarkable convergence in plumage colours and patterns. With the inclusion of Helmeted Woodpecker in Celeus, this genus has four out of 15 species on the International Union for Conservation of Nature (IUCN) red list, a higher proportion of red listed species than in the woodpecker family overall.
The hybrid zone between the Red- and Yellow-shafted Flickers has been stable on the United States Great Plains in historical times. This conclusion is based on multivariate comparisons of historical and contemporary collections from 18 locales. Adaptive speciation theory predicts that the hybrid zone should either become broader or narrower as a result of introgressive hybridization or reinforcement of premating isolating mechanisms. Neither of these predictions was borne out. Despite 10,000-13,000 years of hybridization, mating between subspecies remains indiscriminate. The data are also inconsistent with a dynamicequilibrium hypothesis wherein narrow hybrid zones are maintained by hybrid unfitness. According to this hypothesis, the hybrid zone would probably "flow" unless it was trapped by a population density trough. The hybrid zone does not appear to be associated with such a feature. The data are consistent with a bounded hybrid superiority theory of a hybrid zone, but this is more a question of survival in a process of elimination than a resounding corroboration.
Interspecific social dominance mimicry (ISDM) is a proposed form of social parasitism in which a subordinate species evolves to mimic and deceive a dominant ecological competitor in order to avoid attack by the dominant, model species. The evolutionary plausibility of ISDM has been established previously by the Hairy-Downy game (Prum & Samuelson). Psychophysical models of avian visual acuity support the plausibility of visual ISDM at distances ∼>2–3 m for non-raptorial birds, and ∼>20 m for raptors. Fifty phylogenetically independent examples of avian ISDM involving 60 model and 93 mimic species, subspecies, and morphs from 30 families are proposed and reviewed. Patterns of size differences, phylogeny, and coevolutionary radiation generally support the predictions of ISDM. Mimics average 56–58% of the body mass of the proposed model species. Mimics may achieve a large potential deceptive social advantage with <20% reduction in linear body size, which is well within the range of plausible, visual size confusion. Several, multispecies mimicry complexes are proposed (e.g. kiskadee-type flycatchers) which may coevolve through hierarchical variation in the deceptive benefits, similar to Müllerian mimicry. ISDM in birds should be tested further with phylogenetic, ecological, and experimental investigations of convergent similarity in appearance, ecological competition, and aggressive social interactions between sympatric species. Evolutionary explanations of mimicry must consider the possibility that mimics evolve to deceive model species themselves. © 2014 The Linnean Society of London
To analyze our collection we established a phenotypic score for each specimen (Sibley and Short 1964). contact zone between ruber and nuchalis. Lacking extensive series of known S. u. tuber and S. n. nuchalis, we relied heavily on published descriptions METHODS of these races (Ridgway 1914, Howell 1952). We COLLECTING SITES selected nine characters that appeared to distinguish Tuber from nuchalis. The characters and the scores as-Between 14 and 28 June, Jarosch collected 32 adult signed to each phenotype were: (1) Middle pair of sapsuckers, all with broodoatches. at selected localities rectrices: mostly black, 0; intermediate, 1; mostly between Alexandria (21 -km by' air S Kersley) and white, 2, (2) Back: little white, 0; intermediate, 1; Stoner (90 km by air N Kersley). We chose these much white, 2, (3) Subauricular stripe: all red, 0; localities to reexamine the interaction between the some red, 1; no red, 2, (4) Auricular region: all red, taxa in the vicinity of Kersley and to determine the 0; black or tinged with red, 2, (5) Postocular stripe: northern edge of the zone of contact. Collecting sites red, 0; incomplete, 1; complete, 2, (6) Black malar in 1973 and 1974 are listed below in approximate stripe: completely obscured by red, 0; at least partly order from south to north. Co-ordinates given are visible, 2, (7) Red nape: completely confluent with those of the collecting sites, not of the associated red on crown, 0; incompletely separated from red on communities. crown, 1; completely separated from crown by black 1. McLeese Lake (52"23' N, 122"17' W, Canadian border, 2, (8) Pectoral patch: all red, 0; some red, 1; all black, 2, and (9) Rudimentary primary: no white National Topographic Sheet-Soda Creek 93 B/8 W, 1: 50,000).
1. The R package ‘diversitree’ contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE (binary state speciation and extinction), MuSSE (a multistate extension of BiSSE), and QuaSSE (quantitative state speciation and extinction). Diversitree also includes methods for analysing trait evolution and estimating speciation/extinction rates independently.
2. In this note, I describe the features and demonstrate use of the package, using a new method, MuSSE (multistate speciation and extinction), to examine the joint effects of two traits on speciation.
3. Using simulations, I found that MuSSE could reliably detect that a binary trait that affected speciation rates when simultaneously accounting for additional thats that had no effect on speciation rates.
4. Diversitree is an open source and available on the Comprehensive R Archive Network (cran). A tutorial and worked examples can be downloaded from http://www.zoology.ubc.ca/prog/diversitree.
Knowledge of the evolutionary history of crown group birds (Neornithes) has significantly improved through emerging congruence among phylogenetic hypotheses and the description of numerous new Palaeogene stem group representatives. However, controversies still persist about the precise interrelationships of many extant and fossil taxa and about the timing of the diversification of the neornithine crown group. Using the example of Phaethontiformes (tropicbirds) and Psittaciformes (parrots), it is shown how new sequence-based phylogenies may shed light on the relationships of fossils with an unexpected character mosaic, and how such fossils can improve our understanding of character evolution in morphologically disparate avian taxa. The earliest occurrences of neornithine birds are plotted on a current phylogeny. As noted by previous authors, an extensive diversification of neornithine birds before the latest Cretaceous is not supported by the fossil record, and the existence of essentially modern-type representatives of Telluraves (the clade including most arboreal birds) in the Cretaceous, such as suggested from molecular calibrations, is highly unlikely.
Life on Earth is conspicuously more diverse in the tropics. Although this intriguing geographical pattern has been linked to many biotic and abiotic factors, their relative importance and potential interactions are still poorly understood. The way in which latitudinal changes in ecological conditions influence evolutionary processes is particularly controversial, as there is evidence for both a positive and a negative latitudinal gradient in speciation rates. Here, we identify and address some methodological issues (how patterns are analysed and how latitude is quantified) that could lead to such conflicting results. To address these issues, we assemble a comprehensive data set of the environmental correlates of latitude (including climate, net primary productivity and habitat heterogeneity) and combine it with biological, historical and molecular data to explore global patterns in recent divergence events (subspeciation). Surprisingly, we find that the harsher conditions that typify temperate habitats (lower primary productivity, decreased rainfall and more variable and unpredictable temperatures) are positively correlated with greater subspecies richness in terrestrial mammals and birds. Thus, our findings indicate that intraspecific divergence is greater in regions with lower biodiversity, a pattern that is robust to both sampling variation and latitudinal biases in taxonomic knowledge. We discuss possible causal mechanisms for the link between environmental harshness and subspecies richness (faster rates of evolution, greater likelihood of range discontinuities and more opportunities for divergence) and conclude that this pattern supports recent indications that latitudinal gradients of diversity are maintained by simultaneously higher potentials for both speciation and extinction in temperate than tropical regions.
Palaeospiza bella was described as an oscine songbird in the late 19th century. The late Eocene age of the holotype specimen Would make it the oldest Northern Hemisphere record of the Passeriformes. However, few recent workers have accepted the placement-of P. bella within Passeriformes, and the higher relationships of this fossil have remained controversial. We show that P bella is a member of the Coliiformes (mousebirds) and represents the latest North American occurrence of a clade with all exclusively African extant distribution. Coliiformes are now, known from the latest Paleocene to the approach Of the Eocene-Oligocene boundary in North America. We present a redescription of P. bella and a new phylogenetic analysis of fossil and living Coliiformes based on a matrix including 49 characters and 08 ingroup taxa. The results of this analysis place R bella in Colli, the clade comprising taxa more closely related to Coliidae (crown mousebirds) than to the extinct Sandcoleidae. The oldest stem-group Coliiformes are late Paleocene (about 56.2-56.6 Ma) in age. However, no fossil taxon can be confidently placed within the crown clade Coliidae at present. Phylogenetic results imply that a minimum of three mousebird dispersals from Europe to North America occurred during the Early Cenozoic. Review of the early Eocene fossil Eocolius walkeri from the London Clay shows that this taxon lacks Convincing coliiform synapomorphies and should be removed from the clade. Received 22 October 2007, accepted 23,August 2008.
Are measurements of quantitative genetic variation useful for predicting long-term adaptive evolution? To answer this question, I focus on g(max), the multivariate direction of greatest additive genetic variance within populations. Original data on threespine sticklebacks, together with published genetic measurements from other vertebrates, show that morphological differentiation between species has been biased in the direction of g(max) for at least four million years, despite evidence that natural selection is the cause of differentiation. This bias toward the direction of evolution tends to decay with time. Rate of morphological divergence between species is inversely proportional to theta, the angle between the direction of divergence and the direction of greatest genetic variation. The direction of greatest phenotypic variance is not identical with g(max), but for these data is nearly as successful at predicting the direction of species divergence. I interpret the findings to mean that genetic variances and covariances constrain adaptive change in quantitative traits for reasonably long spans of time. An alternative hypothesis, however, cannot be ruled out: that morphological differentiation is biased in the direction g(max) because divergence and g(max) are both shaped by the same natural selection pressures. Either way, the results reveal that adaptive differentiation occurs principally along ''genetic lines of least resistance.''
The Red-breasted Sapsucker (Sphyrapicus tuber daggetti) and Red-naped Sap- sucker (S. nuchalis) are sympatric and hybridize in south-central Oregon, northeastern Cali- fornia, along the California-Nevada border, and in southern Nevada. We examined the overlapping distribution, nature of hybridization, and mate preference in these two taxa. Using a "hybrid index" system, we identified 13 phenotypic classes that represent the range of variation seen in typical parental types and their hybrids. Variation of parental forms in regions of allopatry was used to distinguish parental phenotypes from hybrids in the zone of overlap and hybridization. The percentage representation of various categories of mating (conspecific, 75.8%; backcross, 16.6%; hybrid, 1.4%; and interspecific, 6.2%) shown by 145 nesting pairs in the zone of overlap was used to infer the relative fitness of Fand F= generation hybrids. Although interspecific matings produce fully viable Foffspring in num- bers proportional to expectation, hybrid and backcross matings apparently are selected against. We suspect that Findividuals and various recombinants have partial sterility barriers. In interspecific matings and in backcrosses, the male nearly always is S. r. daggetti or the redder mate. The data agree most closely with the dynamic-equilibrium model (stable-zone hy- pothesis), which has been proposed to explain zones of sympatry and hybridization in which gene flow from the extensive regions of allopatry of parental forms is balanced by selection against hybrids. In view of the preponderance of conspecific matings where S. r. daggetti and S. nuchalis occur together, they are regarded as biologic species. This decision is most appro- priate for these taxa despite their low degree of hybridization and their near genetic identity as shown by electrophoresis. Received 9 March 1984, accepted 5 September 1984.
Adult and juvenile plumage characters were traced onto a well-resolved molecular based phylogeny for Picoides woodpeckers, and a simple phylogenetic test of homology, parallelism, and convergence of plumage characters was performed. Reconstruction of ancestral character states revealed multiple events of independent evolution of derived character states in most characters studied, and a concentrated changes test revealed that some plumage characters evolved in association with habitat type. For example, there was a statistically significant association between loss of dorsal barring and use of densely vegetated habitats among Picoides species. Two analyses indicated that convergence, as opposed to parallel evolution or shared ancestry, underlies the similarity in plumage patterns between the Downy (Picoides pubescens) and Hairy (P. villosus) Woodpeckers. Possible causal explanations for convergence in plumage patterns may include mimicry and interspecific territoriality.
The subfamily Picumninae (piculets) includes 3 genera and 30 species of tiny and short-tailed woodpeckers with a pantropical distribution. Within the Picumninae, two cases of intercontinentally disrupted distributions at the genus level occur. The first one concerns the genus Sasia (one species in Africa and two in southeast Asia) while the second concerns Picumnus (one species in southeast Asia and 25 in South America). These disrupted distributions, as well as several morphological differences, have lead some authors to place the African representative of Sasia and the southeast Asian representative of Picumnus in their own monotypic genera (Verreauxia and Vivia, respectively). To address the taxonomic status and biogeographic history of the piculets, we sequenced 2676 bp of DNA from one mitochondrial (ND2) and two nuclear markers (myoglobin intron 2 and -fibrinogen intron 7). Monophyly of Picumninae could not be recovered with confidence, while monophyly of Sasia and Picumnus were always strongly supported. Molecular dating analyses revealed that the splits both between the African and Indo-Malayan Sasia and between the New World and Old World Picumnus occurred at ca 7.9 Myr BP. This time corresponds to the beginning of the formation of the northern Hemisphere ice sheets and the accompanying expansion of grasslands throughout the world. The spread of open areas in the northern parts of Eurasia and America prevented gene flow between tropical forest birds, such as the piculets, in Africa, southeast Asia and South America, respectively.