We evaluated the potential effects of homoplasy, ancestral polymorphism, and hybridization as obstacles to resolving phylogenetic relationships within Nomonyx-Oxyura stiff-tailed ducks (Oxyurinae; subtribe Oxyurina). Mitochondrial DNA (mtDNA) control region sequences from 94 individuals supported monophyly of mtDNA haplotypes for each of the six species and provided no evidence of extant incomplete lineage sorting or inter-specific hybridization. The ruddy ducks (O. j. jamaicensis,O. j. andina, O. j. ferruginea) are each others' closest relatives, but the lack of shared haplotypes between O. j. jamaicensis and O. j. ferruginea suggests long-standing historical isolation. In contrast, O. j. andina shares haplotypes with O. j. jamaicensis and O. j. ferruginea, which supports Todd's (1979) and Fjeldså's (1986) hypothesis that O. j. andina is an intergrade or hybrid subspecies of O. j. jamaicensis and O. j. ferruginea. Control region data and a much larger data set composed of approximately 8800 base pairs of mitochondrial and nuclear sequence for each species indicate that the two New World species, O. vittata and O. jamaicensis, branch basally within Oxyura. A clade of three Old World species (O. australis, O. maccoa, O. leucocephala) is well supported, but different loci and also different characters within the mtDNA data support three different resolutions of the Old World clade, yielding an essentially unresolved trichotomy. Fundamentally different factors limited the resolution of the mtDNA and nuclear gene trees. Gene trees for most nuclear loci were unresolved due to slow rates of mutation and a lack of informative variation, whereas uncertain resolution of the mtDNA gene tree was due to homoplasy. Within the mtDNA, approximately equal numbers of characters supported each of three possible resolutions. Parametric and nonparametric bootstrap analyses suggest that resolution of the mtDNA tree based on ~4300 bp per taxon is uncertain but that complete mtDNA sequences would yield a fully resolved gene tree. A short internode separating O. leucocephala from (O. australis, O. maccoa) in the best mtDNA tree combined with long terminal branches and substantial rate variation among nucleotide sites allowed the small number of changes occurring on the internode to be obscured by homoplasy in a significant portion of simulated data sets. Although most nuclear loci were uninformative, two loci supported a resolution of the Old World clade (O. maccoa, O. leucocephala) that is incongruent with the best mtDNA tree. Thus, incongruence between nuclear and mtDNA trees may be due to random sorting of ancestral lineages during the short internode, homoplasy in the mtDNA data, or both. The Oxyura trichotomy represents a difficult though likely common problem in molecular systematics. Given a short internode, the mtDNA tree has a greater chance of being congruent with the history of speciation because its effective population size (N(e)) is one-quarter that of any nuclear locus, but its resolution is more likely to be obscured by homoplasy. In contrast, gene trees for more slowly evolving nuclear loci will be difficult to resolve due to a lack of substitutions during the internode, and when resolved are more likely to be incongruent with the species history due to the stochastic effects of lineage sorting. We suggest that researchers consider first whether independent gene trees are adequately resolved and then whether those trees are congruent with the species history. In the case of Oxyura, the answer to both questions may be no. Complete mtDNA sequences combined with data from a very large number of nuclear loci may be the only way to resolve such trichotomies.
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"abbe (1990, ABO (2000) and McMullan & Donegan (2014) drew attention to subspecies andina of Colombia being intermediate in its plumage features between jamaicensis and ferruginea. Birds with white cheeks similar to jamaicensis, entirely black cheeks similar to ferruginea and mixed black/white cheeks are all found in the Bogotá region (e.g.Fig. 21). McCracken & Sorenson (2005)'s molecular study of the group concluded that "the lack of shared haplotypes between O. j. jamaicensis and O. j. ferruginea suggests long-standing historical isolation. In contrast, O. j. andina shares haplotypes with O. j. jamaicensis and O. j. ferruginea, which supports Todd's (1979) and Fjeldså's (1986) hypothesis that O. j. andina i"
[Show abstract][Hide abstract]ABSTRACT: Subtropical Pygmy-Owl Glaucidium parkeri, Fiery-tailed Awlbill Avocettula recurvirostris and Pale-rumped Swift Chaetura egregia are added to Colombia's bird checklist based on photographic records. Band-rumped Storm-Petrel Oceanodroma castro, Golden-spangled Piculet Picumnus exilis, Yellow-bellied Flycatcher Empidonax flaviventris and Yellow-throated Tanager Iridisornis analis are all elevated to the status of confirmed species occurring on the mainland, also following photographic records. We considered taxonomic proposals by del Hoyo & Collar (2014) using Tobias et al. (2010)'s "species scoring system". We studied possible changes relevant to Colombia in detail, based on new studies of vocalisations, our own fieldwork data and published molecular studies. We conclude that the following proposed Trochilidae (hummingbird) splits are supported by differentiation in voice: White-throated Wedgebill Schistes albogularis from Geoffroy's Wedgebill S. geoffroyi (Wedge-billed Hummingbird); Longuemare's Sunangel Heliangelus clarisse and Merida Sunangel H. spencei from Amethystine Sunangel Heliangelus amethysticollis; White-tailed Hillstar Urochroa leucura from Rufous-gaped Hillstar U. bougeri; and Humboldt's Sapphire Amazilia humboldtii from Gray's Sapphire A. grayi. In light of these positive assessments, we accepted proposed splits of morphologically distinctive hummingbirds in a little-vocalising genus: Perija Starfrontlet Coeligena consita and Golden Starfrontlet C. eos from Golden-bellied Starfrontlet C. bonapartei and Green Inca C. conradii from Collared Inca C. torquata. We adopt the proposed split of Double-banded Puffbird Hypnelus bicinctus from Rufous-throated Puffbird H. ruficollis, highlighting vocal differences. We suggest transfer of subspecies striaticollis to the bicinctus group. We split Splendid Woodpecker Campephilus splendens from C. haematogaster based on differences in voice, plumage, distribution and drumming behaviour. Carribean Coot Fulica caribaea is lumped with American Coot F. americana on account of widely reported intergradation. After studying vocal differentiation in three genera, we reject 10 proposed splits in Ramphastidae (toucans) of forms which either intergrade with one another or which are not as vocally distinct as sympatric toucans. Our vocal analyses instead suggest that the Groove-billed Toucanet subspecies Aulacorhynchus sulcatus erythrognatus of Venezuela may merit species rank. The widely adopted split of Andean Duck Oxyura ferruginea from Ruddy Duck O. jamaicensis is again rejected, due to well-documented intergradation in Colombia. We conclude that del Hoyo & Collar (2014)'s taxonomy has been useful and worthwhile in drawing attention to novel taxonomic situations, especially in Trochilidae. However, we suggest using the Tobias et al. (2010) system as a point of reference and not a sole criterion to determine taxonomic rank. After analysis of sound recordings of putative related species, we conclude that Providencia Vireo V. approximans merits species rank. We split the Blossomcrowns Anthocephala. Several amendments to genus and species names, English names and linear order are made, following recent publications. The Colombian checklist increases again to 1,921 species (excluding escapes), of which 1,846 are documented by 'confirmed' records on the mainland.
"These data suggest that many sub-haplogroups were already present among the bezoar populations and, therefore, that many lineages were included in the domesticated stocks. Previous studies on livestock species showed that phylogenies based on short mitochondrial sequences can be heavily affected by the confounding effects of homoplasies18192021 and mitochondrial pseudo- genes222324, which blur the real extent of lineage divergences/similarities. The available goat sequencing data are usually restricted to a few hundreds of controlregion base pairs (bps), spanning from np 15431 to np 16643. "
[Show abstract][Hide abstract]ABSTRACT: Background: The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results: We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ∼460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ∼12-10 ka ago. Conclusions: Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (∼130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.
"In hamsters, males are the migrating sex, as was shown for Tscherskia triton (Song et al. 2005) and also suggested for Cricetus cricetus on the basis of relatedness analysis (Banaszek and Ziomek 2012). Populations with mixed mtDNA haplotypes could become mtDNA pure quite quickly through lineage sorting (McCracken and Sorenson 2005). Rapid loss of haplotypes is quite possible in common hamster populations which are naturally often bottlenecked (Neumann et al. 2004, 2005). "