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Birds in a bush : Toward an avian phylogenetic network
Ottenburghs, Jente ; Hooft, Pim van; Wieren, Sipke E. van; Ydenberg, Ronald C. ; Prins, Herbert H.T. - \ 2016
The Auk : a quarterly journal of ornithology 133 (2016)4. - ISSN 0004-8038 - p. 577 - 582.
adaptive radiation - genomics - hybridization - phylogenetic networks - Phylogenetics

Reconstructing the avian tree of life has become one of the major goals in ornithology. The use of genomic tools seemed a promising approach to reach this goal, but, instead, phylogenetic analyses of large numbers of genes uncovered high levels of incongruence between the resulting gene trees. This incongruence can be caused by several biological processes, such as recombination, hybridization, and rapid speciation (which can lead to incomplete lineage sorting). These processes directly or indirectly amount to deviations from tree-like patterns, thereby thwarting the use of phylogenetic trees. Phylogenetic networks provide an ideal tool to deal with these difficulties. We illustrate the usefulness of phylogenetic networks to capture the complexity and subtleties of diversification processes by discussing several recent genomic analyses of birds in general and the well-known radiation of Darwin's finches. With the increasing amount of genomic data in avian phylogenetic studies, capturing the evolutionary history of a set of taxa in a phylogenetic tree will become increasingly difficult. Moreover, given the widespread occurrence of hybridization and the numerous adaptive radiations in birds, phylogenetic networks provide a powerful tool to display and analyse the evolutionary history of many bird groups. The genomic era might thus result in a paradigm shift in avian phylogenetics from trees to bushes.

Species delimitation and DNA barcoding of Atlantic Ensis (Bivalvia, Pharidae)
Vierna, J. ; Cuperus, J. ; Martinez-lage, A. ; Jansen, J.M. ; Perina, A. ; Pelt-Heerschap, H.M.L. van; Gonzalez-Tizon, A.M. - \ 2014
Zoologica Scripta 43 (2014)2. - ISSN 0300-3256 - p. 161 - 171.
pcr-rflp analysis - phylogenetic networks - maximum-likelihood - mollusca-bivalvia - 5s rdna - siliqua - directus - macha - population - taxonomy
Ensis Schumacher, 1817 razor shells occur at both sides of the Atlantic and along the Pacific coasts of tropical west America, Peru, and Chile. Many of them are marketed in various regions. However, the absence of clear autapomorphies in the shell and the sympatric distributions of some species often prevent a correct identification of specimens. As a consequence, populations cannot be properly managed, and edible species are almost always mislabelled along the production chain. In this work, we studied whether the currently accepted Atlantic Ensis morphospecies are different evolutionary lineages, to clarify their taxonomic status and enable molecular identifications through DNA barcoding. For this, we studied 109 specimens sampled at 27 sites, which were identified as belonging to nine of those morphospecies. We analysed nucleotide variation at four nuclear (18S, 5.8S, ITS1, and ITS2) and two mitochondrial (COI and 16S) regions, although the 18S and 5.8S regions were not informative at the species level and were not further considered. The phylogenetic trees and networks obtained supported all morphospecies as separately evolving lineages. Phylogenetic trees recovered Ensis at each side of the Atlantic as reciprocally monophyletic. Remarkably, we confirm the co-occurrence of the morphologically similar E. minor (Chenu, 1843) and E. siliqua (Linné, 1758) along the NW Iberian coast, a fact that has been often overlooked. In South America, a relevant divergence between E. macha (Molina, 1792) individuals from Chile and Argentina was unveiled and suggests incipient speciation. We also confirm the occurrence of the North American species E. directus (Conrad, 1843) as far south as north-eastern Florida. Among the genomic regions analysed, we suggest COI as the most suitable DNA barcode for Atlantic Ensis. Our results will contribute to the conservation and management of Ensis populations and will enable reliable identifications of the edible species, even in the absence of the valves. The name Ensis coseli Vierna nom. nov. is proposed to replace E. minor Dall, 1899 non (Chenu, 1843).
Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms
Kraus, R.H.S. ; Hooft, W.F. van; Megens, H.J.W.C. ; Tsvey, A. ; Fokin, S.Y. ; Ydenberg, R.C. ; Prins, H.H.T. - \ 2013
Molecular Ecology 22 (2013)1. - ISSN 0962-1083 - p. 41 - 55.
maximum-likelihood-estimation - mallard anas-platyrhynchos - influenza-a viruses - population-structure - mitochondrial-dna - phylogenetic networks - coalescent approach - genetic-structure - biased dispersal - white sharks
Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual-based structuring algorithms discern geographical structuring. Model-based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.
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