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2.
Nature ; 587(7833): 252-257, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-33177665

RESUMO

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.


Assuntos
Aves/classificação , Aves/genética , Genoma/genética , Genômica/métodos , Genômica/normas , Filogenia , Animais , Galinhas/genética , Conservação dos Recursos Naturais , Conjuntos de Dados como Assunto , Tentilhões/genética , Humanos , Seleção Genética/genética , Sintenia/genética
3.
Zootaxa ; 4747(1): zootaxa.4747.1.7, 2020 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-32230123

RESUMO

A new classification is proposed for the subfamily Fluvicolinae in the New World Flycatchers (Tyrannidae), based on the results of a previously published phylogeny including more than 90% of the species. In this classification we propose one new family level name (Ochthoecini) and one new generic name (Scotomyias). We also resurrect three genera (Heteroxolmis, Pyrope and Nengetus) and subsume five (Tumbezia, Lathrotriccus, Polioxolmis, Neoxolmis and Myiotheretes) into other genera to align the classification with the current understanding of phylogenetic relationships in Fluvicolinae.


Assuntos
Passeriformes , Aves Canoras , Animais , Filogenia
4.
Science ; 367(6474): 140-141, 2020 01 10.
Artigo em Inglês | MEDLINE | ID: mdl-31919205
5.
J Anim Ecol ; 89(4): 1094-1108, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31873967

RESUMO

Strong relationships between morphological and ecological characters are commonly predicted to reflect the association between form and function, with this hypothesis being well supported in restricted taxonomic and geographical contexts. Conversely, among broader sets of species, ecological variables have been shown to have limited power to explain morphological variation. To understand these apparent discrepancies, for a large and globally distributed passerine radiation, we test whether (a) the character states of four ecological variables (foraging mode, diet, strata and habitat) have different morphological optima, (b) ecological variables explain substantial variance in morphology and (c) ecological character states can be accurately predicted from morphology. We collected 10 linear morphological measurements for 782 species of corvoid passerines, and assessed (a) the fit of models of continuous trait evolution with different morphological optima for each ecological character state, (b) variation in morphological traits among ecological character states using phylogenetically corrected regressions and (c) the accuracy of morphological traits in predicting species-level membership of ecological character states using linear discriminant analysis (LDA). Models of morphological evolution with different ecological optima were well supported across numerous morphological axes, corresponding with significant differences in trait distributions among ecological character states. LDA also showed that membership of the ecological categories can be predicted with relatively high accuracy by morphology. In contrast to these findings, ecological variables explain limited amounts of variation in morphological traits. For a global radiation of passerine birds, we confirm that the generation of morphological variation is generally consistent with ecological selection pressures, but that ecological characters are of limited utility in explaining morphological differences among species. Although selection towards different optima means that membership of ecological character states tend to be well predicted by morphology, the overall morphospace of individual ecological character states tend to be broad, implying that morphology can evolve in multiple ways in response to similar selection pressures. Extensive variation in morphological adaptations among similar ecological strategies is likely to be a widespread phenomenon across the tree of life.


Assuntos
Ecossistema , Passeriformes , Adaptação Fisiológica , Animais , Evolução Biológica , Fenótipo , Filogenia
6.
Elife ; 82019 11 26.
Artigo em Inglês | MEDLINE | ID: mdl-31767056

RESUMO

The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation.


Assuntos
Charadriiformes/genética , DNA Antigo/análise , Extinção Biológica , Dinâmica Populacional , Animais , DNA Mitocondrial , Variação Genética , Genoma Mitocondrial/genética , Humanos , Filogenia
7.
Ecol Evol ; 9(17): 9609-9623, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31534679

RESUMO

Aim: To document the species richness patterns of breeding birds along elevational gradients and explore its drivers in the Horn of Africa region. Location: Horn of Africa region. Taxon: Breeding birds. Methods: Distributional data for breeding birds were collected. Elevational distribution data were extracted, interpolated, and assembled for all birds, passerines, and nonpasserines. In order to tease apart how different environmental factors contributed to the variation in species richness, we found it is necessary to divide the area into four subregions with different climatic regimes and topographic structure, namely western slope, eastern slope, wet side, and dry side. Then, the species richness in each 100-m elevational band was counted along the elevational gradients of each subregion. Pearson's correlation analyses and ordinary least squares (OLS) regressions were used to examine the relationships between species richness and factors. Results: The variation in species richness followed hump-shaped patterns for all subregions, although with peak values at different elevations. The bird species groups on the western and eastern slopes showed low and high plateaus with mid-elevation peaks, respectively, but very low species diversities at the highest elevations. Species richness was significantly correlated with temperature range and productivity in each subregion. The temperature range, area, and productivity explained 82% of the species richness variations for all birds on the western slope. Main conclusions: The separate analyses of four area subdivisions provide strong indications of how various factors interact. Productivity and temperature range were the major driving factors for shaping the richness patterns, but deviations from expected patterns suggest modifying roles of mist formation zones in the valleys that deeply intersect the large highlands in the west and rich riparian vegetation where water from cool and humid environments at high elevation reaches lower elevations in the arid east. Conservation is recommended in each subregion based on the elevational richness scenarios.

8.
Science ; 365(6458): 1108-1113, 2019 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-31515383

RESUMO

Mountains contribute disproportionately to the terrestrial biodiversity of Earth, especially in the tropics, where they host hotspots of extraordinary and puzzling richness. With about 25% of all land area, mountain regions are home to more than 85% of the world's species of amphibians, birds, and mammals, many entirely restricted to mountains. Biodiversity varies markedly among these regions. Together with the extreme species richness of some tropical mountains, this variation has proven challenging to explain under traditional climatic hypotheses. However, the complex climatic characteristics of rugged mountain regions differ fundamentally from those of lowland regions, likely playing a key role in generating and maintaining diversity. With ongoing global changes in climate and land use, the role of mountains as refugia for biodiversity may well come under threat.


Assuntos
Altitude , Biodiversidade , Ecossistema , Anfíbios , Animais , Aves , Conservação dos Recursos Naturais , Insetos , Mamíferos , Plantas , Clima Tropical
9.
Science ; 365(6458): 1114-1119, 2019 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-31515384

RESUMO

Mountain regions are unusually biodiverse, with rich aggregations of small-ranged species that form centers of endemism. Mountains play an array of roles for Earth's biodiversity and affect neighboring lowlands through biotic interchange, changes in regional climate, and nutrient runoff. The high biodiversity of certain mountains reflects the interplay of multiple evolutionary mechanisms: enhanced speciation rates with distinct opportunities for coexistence and persistence of lineages, shaped by long-term climatic changes interacting with topographically dynamic landscapes. High diversity in most tropical mountains is tightly linked to bedrock geology-notably, areas comprising mafic and ultramafic lithologies, rock types rich in magnesium and poor in phosphate that present special requirements for plant physiology. Mountain biodiversity bears the signature of deep-time evolutionary and ecological processes, a history well worth preserving.


Assuntos
Altitude , Biodiversidade , Evolução Biológica , Ecossistema , Geologia , Clima
10.
Evolution ; 73(6): 1226-1240, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31012491

RESUMO

The accumulation of exceptional ecological diversity within a lineage is a key feature of adaptive radiation resulting from diversification associated with the subdivision of previously underutilized resources. The invasion of unoccupied niche space is predicted to be a key determinant of adaptive diversification, and this process may be particularly important if the diversity of competing lineages within the area, in which the radiation unfolds, is already high. Here, we test whether the evolution of nectarivory resulted in significantly higher rates of morphological evolution, more extensive morphological disparity, and a heightened build-up of sympatric species diversity in a large adaptive radiation of passerine birds (the honeyeaters, about 190 species) that have diversified extensively throughout continental and insular settings. We find that a large increase in rates of body size evolution and general expansion in morphological space followed an ancestral shift to nectarivory, enabling the build-up of large numbers of co-occurring species that vary greatly in size, compared to related and co-distributed nonnectarivorous clades. These results strongly support the idea that evolutionary shifts into novel areas of niche space play a key role in promoting adaptive radiation in the presence of likely competing lineages.


Assuntos
Comportamento Alimentar , Especiação Genética , Aves Canoras/fisiologia , Animais , Evolução Biológica , Dieta , Aves Canoras/genética
11.
Mol Phylogenet Evol ; 130: 346-356, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30321696

RESUMO

The babblers are a diverse group of passerine birds comprising 452 species. The group was long regarded as a "scrap basket" in taxonomic classification schemes. Although several studies have assessed the phylogenetic relationships for subsets of babblers during the past two decades, a comprehensive phylogeny of this group has been lacking. In this study, we used five mitochondrial and seven nuclear loci to generate a dated phylogeny for babblers. This phylogeny includes 402 species (ca. 89% of the overall clade) from 75 genera (97%) and all five currently recognized families, providing a robust basis for taxonomic revision. Our phylogeny supports seven major clades and reveals several non-monophyletic genera. Divergence time estimates indicate that the seven major clades diverged around the same time (18-20 million years ago, Ma) in the early Miocene. We use the phylogeny in a consistent way to propose a new taxonomy, with seven families and 64 genera of babblers, and a new linear sequence of names.


Assuntos
Passeriformes/classificação , Filogenia , Animais , DNA Mitocondrial/genética , Funções Verossimilhança , Passeriformes/genética , Fatores de Tempo
12.
Zootaxa ; 4438(1): 105-127, 2018 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-30313158

RESUMO

We describe a new species of drongo in the Square-tailed Drongo (Dicrurus ludwigii) complex using a combination of biometric and genetic data. The new species differs from previously described taxa in the Square-tailed Drongo complex by possessing a significantly heavier bill and via substantial genetic divergence (6.7%) from its sister-species D. sharpei. The new species is distributed across the gallery forests of coastal Guinea, extending to the Niger and Benue Rivers of Nigeria. We suspect that this taxon was overlooked by previous avian systematists because they either lacked comparative material from western Africa or because the key diagnostic morphological character (bill characteristics) was not measured. We provide an updated taxonomy of the Square-tailed Drongo species complex.


Assuntos
Deriva Genética , Passeriformes , África Ocidental , Animais , Florestas , Nigéria , Filogenia
13.
Mol Phylogenet Evol ; 127: 367-375, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-29625229

RESUMO

The widespread Old World avian family Locustellidae ('grassbirds and allies') comprises 62 extant species in 11 genera. In the present study, we used one mitochondrial and, for most species, four nuclear loci to infer the phylogeny of this family. We analysed 59 species, including the five previously unsampled genera plus two genera that had not before been analysed in a densely sampled dataset. This study revealed extensive disagreement with current taxonomy; the genera Bradypterus, Locustella, Megalurus, Megalurulus and Schoenicola were all found to be non-monophyletic. Non-monophyly was particularly pronounced for Megalurus, which was widely scattered across the tree. Three of the five monotypic genera (Amphilais, Buettikoferella and Malia) were nested within other genera; one monotypic genus (Chaetornis) formed a clade with one of the two species of Schoenicola; whereas the position of the fifth monotypic genus (Elaphrornis) was unresolved. Robsonius was confirmed as sister to the other genera. We propose a phylogenetically informed revision of genus-level taxonomy, including one new generic name. Finally, we highlight several non-monophyletic species complexes and deep intra-species divergences that point to conflict in taxonomy and suggest an underestimation of current species diversity in this group.


Assuntos
Passeriformes/classificação , Filogenia , Animais , Teorema de Bayes , Núcleo Celular , Citocromos b/genética , Espectrografia do Som , Especificidade da Espécie , Vocalização Animal
14.
Mol Phylogenet Evol ; 124: 100-105, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29526804

RESUMO

Detailed knowledge of species limits is an essential component of the study of biodiversity. Although accurate species delimitation usually requires detailed knowledge of both genetic and phenotypic variation, such variation may be limited or unavailable for some groups. In this study, we reconstruct a molecular phylogeny for all currently recognized species and subspecies of Australasian shrikethrushes (Colluricincla), including the first sequences of the poorly known C. tenebrosa. Using a novel method for species delimitation, the multi-rate Poisson Tree Process (mPTP), in concordance with the phylogenetic data, we estimate species limits in this genetically diverse, but phenotypically subtly differentiated complex of birds. In line with previous studies, we find that one species, the little shrikethrush (C. megarhyncha) is characterized by deep divergences among populations. Delimitation results suggest that these clades represent distinct species and we consequently propose a new classification. Furthermore, our findings suggest that C. megarhyncha melanorhyncha of Biak Island does not belong in this genus, but is nested within the whistlers (Pachycephala) as sister to P. phaionota. This study represents a useful example of species delimitation when phenotypic variation is limited or poorly defined.


Assuntos
Passeriformes/classificação , Filogenia , Pigmentação/genética , Animais , Austrália , Teorema de Bayes , DNA Mitocondrial/genética , Geografia , Passeriformes/genética , Fenótipo , Especificidade da Espécie , Fatores de Tempo
15.
Proc Biol Sci ; 285(1893): 20182181, 2018 Dec 19.
Artigo em Inglês | MEDLINE | ID: mdl-30963909

RESUMO

Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.


Assuntos
Distribuição Animal , Especiação Genética , Aves Canoras/anatomia & histologia , Aves Canoras/fisiologia , Animais , Filogenia
16.
Mol Phylogenet Evol ; 118: 172-183, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28834700

RESUMO

The Long-billed Tailorbird (Artisornis moreaui), one of Africa's rarest birds, has a strikingly disjunct distribution, the origin of which has long puzzled biogeographers. One small population (subspecies moreaui) occurs in sub-montane forest in the East Usambara Mountains, a sky island near the coast of northern Tanzania, and another (subspecies sousae) on Serra Jeci in northwestern Mozambique, 950km away. The African Tailorbird, the putative sister-species of Long-billed Tailorbird, also occurs in the East Usambara Mountains and on Serra Jeci, but in addition occupies all the Eastern Arc Mountain forests between these disjunct sites. Stuart (1981) hypothesized that the two tailorbird distributions could be explained by strong ecological competition, with African Tailorbird populations having eliminated Long-billed Tailorbird populations via competitive exclusion in montane forests between the East Usambara and Serra Jeci. If such competitive exclusion explains these geographic distributions, the co-occurrence of the two species in the East Usambara and at Serra Jeci may be ephemeral, with the status of Long-billed Tailorbird especially in doubt. We sought to (1) determine whether the two species of African tailorbirds are indeed sister-species, and (2) test predictions from Stuart's (1981) competitive exclusion hypothesis using genetic data. Phylogenetic analyses of our seven gene dataset (3 mtDNA, 4 introns; 4784bp) indeed place these two species together in the genus Artisornis. Instead of finding shallow divergence among African Tailorbird populations and deep divergence between Long-billed Tailorbird populations as expected from Stuart's hypothesis, we recover deep genetic divergence and geographic structure among populations of both tailorbird species. This result is consistent with long-term co-existence of the two species at East Usambara and Serra Jeci. Observational data from both the East Usambara and Serra Jeci suggest that the two species have diverged in use of forest canopy strata. From a conservation standpoint, our results suggest that extinction of the Long-billed Tailorbird as a function of competition with African Tailorbird is highly unlikely, and should not be viewed as imminent. Threats to its survival are instead anthropogenic, and conservation measures should take this into account. Finally, our empirical results suggest that mis-specification of the branch-length prior in Bayesian analyses of mitochondrial DNA data can have a profound effect on the overall tree-length (sum of branch-lengths), whereas the topology and support values tend to remain more stable. In contrast, mis-specification of the branch-length prior had a lesser impact on all aspects of the nuclear-only DNA analyses. This problem may be exacerbated when mitochondrial and nuclear DNA analyses are combined in a total evidence approach.


Assuntos
Passeriformes/classificação , Filogeografia , Estatística como Assunto , Animais , Teorema de Bayes , DNA Mitocondrial/genética , Loci Gênicos , Moçambique , Passeriformes/genética , Filogenia , Tanzânia
17.
Ecol Evol ; 7(16): 6346-6357, 2017 08.
Artigo em Inglês | MEDLINE | ID: mdl-28861238

RESUMO

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino-Himalayan Mountains or these mountains and Central Asia-Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid-Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo-/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials-contrary to the usual view that glacial periods resulted mainly in fragmentations.

18.
Genes (Basel) ; 8(6)2017 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-28617333

RESUMO

One hundred and seventy-three years ago, the last two Great Auks, Pinguinusimpennis, ever reliably seen were killed. Their internal organs can be found in the collections of the Natural History Museum of Denmark, but the location of their skins has remained a mystery. In 1999, Great Auk expert Errol Fuller proposed a list of five potential candidate skins in museums around the world. Here we take a palaeogenomic approach to test which-if any-of Fuller's candidate skins likely belong to either of the two birds. Using mitochondrial genomes from the five candidate birds (housed in museums in Bremen, Brussels, Kiel, Los Angeles, and Oldenburg) and the organs of the last two known individuals, we partially solve the mystery that has been on Great Auk scholars' minds for generations and make new suggestions as to the whereabouts of the still-missing skin from these two birds.

19.
Evolution ; 71(1): 38-50, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27709603

RESUMO

Regional variation in clade richness can be vast, reflecting differences in the dynamics of historical dispersal and diversification among lineages. Although it has been proposed that dispersal into new biogeographic regions may facilitate diversification, to date there has been limited assessment of the importance of this process in the generation, and maintenance, of broad-scale biodiversity gradients. To address this issue, we analytically derive biogeographic regions for a global radiation of passerine birds (the Corvides, c. 790 species) that are highly variable in the geographic and taxonomic distribution of species. Subsequently, we determine rates of historical dispersal between regions, the dynamics of diversification following regional colonization, and spatial variation in the distribution of species that differ in their rates of lineage diversification. The results of these analyses reveal spatiotemporal differences in the build-up of lineages across regions. The number of regions occupied and the rate of transition between regions both predict family richness well, indicating that the accumulation of high clade richness is associated with repeated expansion into new geographic areas. However, only the largest family (the Corvidae) had significantly heightened rates of both speciation and regional transition, implying that repeated regional colonization is not a general mechanism promoting lineage diversification among the Corvides.


Assuntos
Biodiversidade , Especiação Genética , Aves Canoras/fisiologia , Animais , Evolução Biológica , Filogenia , Aves Canoras/classificação , Aves Canoras/genética
20.
Mol Phylogenet Evol ; 107: 516-529, 2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-28017855

RESUMO

With nearly 300 species, the infraorder Meliphagides represents one of the largest and most conspicuous Australasian bird radiations. Although the group has been the focus of a number of recent phylogenetic studies, a comprehensive species-level phylogenetic hypothesis is still lacking. This has impeded the assessment of broad-scale evolutionary, biogeographic and ecological hypotheses. In the present study, we use a supermatrix approach including five mitochondrial and four nuclear markers to infer a time-calibrated phylogeny of the Meliphagides. Our phylogeny, which includes 286 of the 289 (99%) currently recognized species, is largely congruent with previous estimates. However, the addition of 60 newly sequenced species reveals some novel relationships. Our biogeographic analyses suggest an Australian origin for the group in the early Oligocene (31.3Mya, 95% HPD 25.2-38.2Mya). In addition, we find that dispersal events out of Australia have been numerous and frequent, particularly to New Guinea, which has also been the source of multiple back-colonizations to the Australian mainland. The phylogeny provides an important framework for studying a wide variety of macroecological and macroevolutionary themes, including character evolution, origin and timing of diversification, biogeographic patterns and species responses to climate change.


Assuntos
Passeriformes/classificação , Filogenia , Filogeografia , Animais , Sequência de Bases , Teorema de Bayes , Calibragem , Bases de Dados Genéticas , Evolução Molecular , Passeriformes/genética , Fatores de Tempo
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