Phylogeny and classification of the avian superfamily Sylvioidea

Alström, Per; Ericson, Per G. P.; Olsson, Urban; Sundberg, Per

doi:10.1016/j.ympev.2005.05.015

Cited by 147 publications

(203 citation statements)

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“…Ambiguous base pairs and indels were treated as missing data, but indels were plotted on the trees a posteriori. Panurus biarmicus and Prinia bairdii were chosen as outgroups based on the results of Alström et al (2006), Johansson et al (2008) and Fregin et al (2012), except in the SLA of 16S, for which Cisticola brachyptera, Prinia bairdii, Acrocephalus arundinaceus and Aegithalos concinnus were used as outgroups (three latter downloaded from GenBank), as no 16S sequences were available for P. biarmicus. Default priors in MrBayes were used.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

“…del Hoyo et al, 2004;Peters, 1960), whereas based on DNA-DNA hybridization they were placed in the superfamily Passeroidea (Sibley and Ahlquist, 1990;Sibley and Monroe, 1990). However, recent studies based on sequence data have unanimously shown them to be part of the superfamily Sylvioidea, and together with the morphologically and ecologically radically different monotypic genus Panurus (Panuridae) forming a sister clade to the rest of the Sylvioidea (Alström et al, 2006;Ericson and Johansson, 2003;Fregin et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

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Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity

Alström

Barnes

Olsson

et al. 2013

Molecular Phylogenetics and Evolution

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The Alaudidae (larks) is a large family of songbirds in the superfamily Sylvioidea. Larks are cosmopolitan, although species-level diversity is by far largest in Africa, followed by Eurasia, whereas Australasia and the New World have only one species each. The present study is the first comprehensive phylogeny of the Alaudidae. It includes 83.5% of all species and representatives from all recognised genera, and was based on two mitochondrial and three nuclear loci (in total 6.4 kbp, although not all loci were available for all species). In addition, a larger sample, comprising several subspecies of some polytypic species was analysed for one of the mitochondrial loci. There was generally good agreement in trees inferred from different loci, although some strongly supported incongruences were noted. The tree based on the concatenated multilocus data was overall well resolved and well supported by the data.We stress the importance of performing single gene as well as combined data analyses, as the latter may obscure significant incongruence behind strong nodal support values. The multilocus tree revealed many unpredicted relationships, including some non-monophyletic genera (Calandrella, Mirafra, Melanocorypha, Spizocorys). The tree based on the extended mitochondrial data set revealed several unexpected deep divergences between taxa presently treated as conspecific (e.g. within Ammomanes cinctura, Ammomanes deserti, Calandrella brachydactyla, Eremophila alpestris), as well as some shallow splits between currently recognised species (e.g. Certhilauda brevirostris-C. semitorquata-C. curvirostris; Calendulauda barlowi-C. erythrochlamys; Mirafra cantillans-M. javanica). Based on our results, we propose a revised generic classification, and comment on some species limits. We also comment on the extraordinary morphological adaptability in larks, which has resulted in numerous examples of parallel evolution (e.g.

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Section: Phylogenetic Analysesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity

Alström

Barnes

Olsson

et al. 2013

Molecular Phylogenetics and Evolution

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“…To that end, we searched the taxonomic literature (e.g. Alstroem et al (2006)) and 'Tree of Life' servers (such as The Tree of Life Web Project in Maddison et al (2007)). A conservative consensus tree was generated depicting relationships between the 39 warbler species as in Figure 7.…”

Section: Phylogenetic Distance Analysismentioning

confidence: 99%

Inferring species interaction networks from species abundance data: A comparative evaluation of various statistical and machine learning methods

Faisal

Dondelinger

Husmeier

et al. 2010

Ecological Informatics

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The complexity of ecosystems is staggering, with hundreds or thousands of species interacting in a number of ways from competition and predation to facilitation and mutualism. Understanding the networks that form the systems is of growing importance, e.g. to understand how species will respond to climate change, or to predict potential knock-on effects of a biological control agent. In recent years, a variety of summary statistics for characterising the global and local properties of such networks have been derived, which provide a measure for gauging the accuracy of a mathematical model for network formation processes. However, the critical underlying assumption is that the true network is known. This is not a straightforward task to accomplish, and typi- * Corresponding author. Tel: +44 (0) cally requires minute observations and detailed field work. More importantly, knowledge about species interactions is restricted to specific kinds of interactions. For instance, while the interactions between pollinators and their host plants are amenable to direct observation, other types of species interactions, like those mentioned above, are not, and might not even be clearly defined from the outset. To discover information about complex ecological systems efficiently, new tools for inferring the structure of networks from field data are needed. In the present study, we investigate the viability of various statistical and machine learning methods recently applied in molecular systems biology: graphical Gaussian models, L1-regularised regression with least absolute shrinkage and selection operator (LASSO), sparse Bayesian regression and Bayesian networks. We have assessed the performance of these methods on data simulated from food webs of known structure, where we combined a niche model with a stochastic population model in a 2-dimensional lattice.We assessed the network reconstruction accuracy in terms of the area under the receiver operator characteristics (ROC) curve, which was typically in the range between 0.75 and 0.9, corresponding to the recovery of about 60% of the true species interactions at a false prediction rate of 5%. We also applied the models to presence/absence data for 39 European warblers, and found that the inferred species interactions showed a weak yet significant correlation with phylogenetic similarity scores, which tended to weakly increase when including bio-climate covariates and allowing for spatial autocorrelation. Our findings demonstrate that relevant patterns in ecological networks can be identified from large-scale spatial data sets with machine learning methods, and that these methods have the potential to contribute novel important tools for gaining deeper insight into the structure and stability of ecosystems.

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“…Taylor (1970) proposed that the Verdin is instead related to Bananaquits, and Sibley and Ahlquist (1990) placed it near gnatcatchers (Polioptila). A more thorough genetic study (but with limited outgroups) and two osteological studies have since supported the placement of the Verdin in the Remizidae (Webster 2000, James et al 2003, Gill et al 2005), a family clearly related to and often subsumed within the tits and chickadees (Paridae; James et al 2003, Barker et al 2004, Alström et al 2006, Johansson et al 2008. Besides the Paridae, the family has been thought to be related to the long-tailed tits (Aegithalidae) and a group including flowerpeckers, sunbirds, white-eyes, and honeyeaters (Dicaeidae, Nectariniidae, Zosteropidae, and Meliphagidae; Delacour and Vaurie 1957).…”

Section: October 2009 -Fused Vertebrae In Songbirds -871mentioning

confidence: 99%

Repeated Evolution of Fused Thoracic Vertebrae in Songbirds

James¹

2009

The Auk

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Resumen.-La fusión de dos o más vértebras torácicas, independientemente del sinsacro, es un fenómeno que está más ampliamente distribuido entre los paseriformes que lo que se había documentado previamente. El hueso que se forma de este modo se llama notario. Hice una evaluación de esqueletos de aves paserinas y observé la presencia de un notario con vértebras completamente fusionadas en Leptopterus chabert, algunos Artamidae y Laniidae, Rhipidura leucophrys, Phainopepla nitens, los Remizidae incluyendo a Auriparus flaviceps, varios Alaudidae, Sturnus vulgaris y las especies de los géneros Toxostoma y Loxia. El mapeo de la evolución de este rasgo sobre un superárbol sugiere que un notario completamente fusionado ha evolucionado independientemente al menos 12 veces en los paseriformes oscinos y que notarios con fusión menos completa de las vértebras (por ejemplo, con sólo los procesos espinosos fusionados) están aún más ampliamente distribuidos filogenéticamente. La expresión fenotípica de un notario está fija en algunas especies y grupos taxonómicos mayores, pero varía entre individuos en otras especies. Ontogenéticamente, el notario completamente fusionado se forma cuando el ave es inmadura. El desarrollo evolutivo de los notarios probablemente depende de mutaciones que alteran los patrones de expresión de genes de transición (los genes Pax y Hox son candidatos probables) que controlan la diferenciación embriológica de las vértebras. Entre las implicaciones sistemáticas de este estudio se encuentran el apoyo adicional para la ubicación de Auriparus en la familia Remizidae y para la monofilia de un grupo de mímidos occidentales (Toxostoma spp.) con picos fuertemente decurvados.-862 - Abstract.-The fusion of two or more thoracic vertebrae, independent of the synsacrum, is more widespread in the Passeriformes than has previously been reported. The bone thus formed is known as a "notarium." I surveyed oscine passerine skeletons and found a notarium with fully fused vertebrae in Chabert's Vanga (Leptopterus chabert), certain woodswallows (Artamidae) and shrikes (Laniidae), the Willie Wagtail (Rhipiduridae, Rhipidura leucophrys), the Phainopepla (Bombycillidae, Phainopepla nitens), the penduline tits (Remizidae) including the Verdin (Auriparus flaviceps), various larks (Alaudidae), the Common Starling (Sturnus vulgaris), the sicklebilled thrashers (Toxostoma spp.), and the crossbills (Loxia spp.). Mapping of character evolution on a supertree suggests that a fully fused notarium has evolved independently at least 12 times in the oscine passerines and that notaria with less extensive fusion of the vertebrae (only the spinous processes fused, for example) are even more widespread phylogenetically. Phenotypic expression of a notarium is fixed in some species and higher taxonomic groups but varies within the species in others. Ontogenetically, the fully fused notarium forms when the bird is immature. The evolutionary development of notaria probably depends on mutations that alter expression patterns of transcription genes...

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Phylogeny and classification of the avian superfamily Sylvioidea

Cited by 147 publications

References 45 publications

Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity

Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity

Inferring species interaction networks from species abundance data: A comparative evaluation of various statistical and machine learning methods

Repeated Evolution of Fused Thoracic Vertebrae in Songbirds

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