Julie Feinstein

Sailing through the Late Pleistocene: unusual historical demography of an East Asian endemic, the Chinese Hwamei (Leucodioptron canorum canorum), during the last glacial period

Pleistocene climate fluctuations shaped the patterns of genetic diversity observed in extant species. In contrast to Europe and North America where the effects of recent glacial cycles on genetic diversity have been well studied, the genetic legacy of the Late Pleistocene for East Asia, a region of great topographical complexity and presumably milder historical climate, remains poorly understood. We analysed 3.86 kb of the mitochondrial genome of 186 Chinese Hwamei birds, Leucodioptron canorum canorum, and found that contrary to the conventional expectation of population decline during cold periods (stadials), the demographic history of this species shows continuous population growth since the penultimate glacial period (about 170 000 years ago). Refugia were identified in the south, coastal regions, and northern inland areas, implying that topographic complexity played a substantial role in providing suitable habitats for the Chinese Hwamei during cold periods. Intermittent gene flow between these refugia during the warmer periods (interstadials) might have resulted in a large effective population of this bird through the last glacial period.

CHAPTER 7 – The Phylogeny of Ratite Birds: Resolving Conflicts between Molecular and Morphological Data Sets

The chapter attempts to investigate paleognath interrelationships and further augments both morphological and molecular data sets. It describes several new postcranial characters and adds new characters to the osteological database, based on an examination of cranial morphology. Within the framework of paleognath monophyly, the debate has shifted to controversies over the interrelationships among the ratites. At the heart of this debate are apparent conflicts over, first, what morphological characters appear to tell us about those interrelationships, and second, the seemingly disparate relationships implied by several different molecular data sets, on the one hand, and morphology, on the other. Because DNA hybridization distances suggest that the relative rates in the nuclear genome are essentially parallel to those in the mitochondrial genome, there is at least some reason to predict that any long-branch artifacts of clustering arising within one data set might also be present in the other. Thus, the fact that there is congruence in results from DNA hybridization studies and those based on mitochondrial gene sequences does not necessarily constitute a sufficient reason for believing that molecular data is producing a robust estimate of relationships.

What is not a bird of paradise? Molecular and morphological evidence places Macgregoria in the Meliphagidae and the Cnemophilinae near the base of the corvoid tree

The cnemophiline ‘birds of paradise’ (Cnemophilinae) and Macgregors ‘bird of paradise’ (Macgregoria) have traditionally been included in the Paradisaeidae although their relationships within the group have been enigmatic and subject to repeated discussion in the literature. Here we use sequences from two mitochondrial genes, cytochrome b and cytochrome oxidase I, along with a suite of morphological characters, to investigate their relationships to paradisaeids and other members of the passerine Parvorder Corvida. The combined data strongly support the removal of both groups from the birds of paradise: the cnemophilines are basal members of the Corvoidea and Macgregoria is a member of the Meliphagoidea and embedded in the honeyeaters (Meliphagidae) close to the genus Melipotes. The amount of sequence divergence among basal passeriforms and members of the Corvida, as well as available fossil evidence for Australian corvidans, suggest that cnemophilines represent an ancient lineage within the corvoid radiation. Because cnemophilines and Macgregoria have been placed at the base of the paradisaeid tree, hypotheses of morphological, behavioural and ecological character–state transformations within the family will require reanalysis.

DNA sequence from butterfly frass and exuviae

The early instar larvae of many butterflies are cryptic and minute. Identification often requires microscopy. One cannot simultaneously prepare samples for microscopy (Peterson 1967) and optimal DNA preservation (Reiss et al. 1995). Insect tissue storage in DNA isolation buffer, in fact, works best when the insect material is homogenized (Reiss et al. 1995). These issues become critical in the case of tropical insects, where, for many species, male and female forms have not yet been linked, where larval and adult forms have not yet been associated, and where new species are likely to be found. Field collectors face a dilemma of mutually exclusive options. A non-destructive method of DNA isolation that would leave specimens intact for collection or alive for observation and rearing would be useful. Most caterpillars consume high bulk plant material throughout their larval stages, growing rapidly and producing large amounts of frass relative to their size. Molecular scatology may prove fruitful in their study. Additionally, butterflies are holometabolic, undergoing periodic ecdyses. Their shed skins (exuviae) may be viewed as another reservoir of DNA. Two species of butterfly were investigated in this study: Vanessa cardui L., the “Painted Lady”, and Pieris rapae L., the “Cabbage Butterfly”. A mating pair of P. rapae plus two gravid females, (designated females f1, f2 and f3) were caught wild in Palisades Park, Bergen Co., New Jersey, and caged, individually, with the wild host plant, “garlic mustard” (Alliaria officinalis). The females oviposited on and under the leaves during three days of captivity. Eggs were removed and reared on cabbage leaves following standard protocols of butterfly culture (Pyle 1984). P. rapae exuviae were not found in the cages of the growing larvae. Presumably, they were eaten, as is commonly the case (Aiello 1993). Five P. rapae caterTable 1. Primers for PCR and sequencing of P. rapae ND5 (pieND5n) and V. cardui ND1 (vanND1n) designed for this study

The mitochondrial genome of Cygnus columbianus, the Whistling Swan

The nucleotide sequence of the mitochondrial genome of the Whistling Swan, Cygnus columbianus, is reported. Many of the features common to avian mitochondrial genomes are present in C. columbianus and are described here. The gene order is the same as in Gallus gallus. The sequence of this mitochondrial genome allows relationships within the family Anatidae (swans, geese and ducks) to be reconsidered in the light of a large suite of mitochondrial characters. Protein-coding gene sequences of C. columbianus were concatenated to form a supergene, which was analyzed phylogenetically with similar constructs from previously published avian genomes. Relationships within Anatidae and between the Anatidae and the galliform birds were addressed. Three independent phylogenetic methods confirmed traditional classifications and the existence of the Galloanseres clade.

Solving a sequencing problem in the vertebrate mitochondrial control region using phylogenetic comparisons.

The mitochondrial control region (mtCR) of the bird-of-paradise, Phonygammus keraudrenii, the Trumpet Manucode, contains a unique arrangement of homopolymers and short tandem repeats. Homopolymers occur within a few hundred bases of each other, trapping sequence information between unsequenceable barriers. A comparative strategy, involving other manucode species, allowed the prediction of primer sites in the inaccessible region. The method is suggested for similar sequencing problems.