“Home Again”: The Contrasting Experiences of Richard D. Dunphy and Lewis A. Horton

Union veterans returning home from the war in 1865 faced a myriad of experiences and reacted to the return to civilian life in a variety of ways. Richard D. Dunphy and Lewis A. Horton, both double-arm amputee veterans of the Navy, ably demonstrate the differences in experience and reaction to the war and life afterwards. [excerpt

A Target Restricted Assembly Method (TRAM) for Phylogenomics

While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications. Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes. This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon

Biology, ecology, and evolution of chewing lice

Book ChapterChewing lice are small, dorsoventrally compressed insects and are parasites of virtually all birds (Fig. 1) and some mammals (Fig. 2). Many chewing lice are host specific, being found on only a single species of host. All chewing lice are permanent ectoparasites and complete their entire life cycle on the body of the host, where they feed mainly on feathers, dead skin, blood, or secretions. Chewing lice on mammals apparently do not ingest hair, rather they feed on skin and skin products (Waterhouse 1953). Some species of lice feed on the eggs and molting stages of mites and other lice, including members of their own species (Nelson and Murray 1971). Lice also ingest microbes, such as bacteria and fungi, which are of unknown nutritive value

Swiftlets on islands: genetics and phylogeny of the Seychelles and Mascarene swiftlets

Journal ArticlePopulations on islands are isolated from mainland populations and are thus expected to diverge and speciate from mainland relatives. We investigated die phylogenetic position and taxonomic rank of the Seychelles and Mascarene swiftlets using nuclear (fibrinogen intron 7) and mitochondrial (cytochrome b) DNA sequences. Both sequences recovered a placement for these two swiftlets within a group of other echolocating swiftlets (Aerodramus)

Testing species limits of non-echolocating Philippine swiftlets (Collocalia spp.) using molecular genetic data

Journal ArticleSwiftlets are small, insectivorous birds that are distributed from the Indian Ocean, through southeast Asia and north Australia, to the Pacific. About 22 species of swiflets nest in caves or other dark places, where they navigate using a crude form of echolocation (Chantler and Driessens 1995). Three additional species, which are incapable of echolocation, do not nest in the dark. The 25 species of swiftlets are considered by many authors to represent the most difficult problem in the taxonomy of birds (e.g., Mayr 1937). This is because swiftlets show extreme morphological similarity, making species limits extremely difficult to decipher. Lee et a/. (1996) used DNA sequence data to show that morphologically-based species concepts are seriously flawed for swiftlets. They also showed that the echolocating species (Aerodramus spp.) are not closely related to the non-echolocating species (Collocalia spp.)

Molecular phylogeny of the dove genus Zenaida: mitochondrial and nuclear DNA sequences

Journal ArticleWe reconstructed a phylogeny for the seven species of doves in the genus Zenaida on the basis of a combined analysis of mitochondria (ND2 and cytochrome b) and nuclear (fibrinogen intron 7) DNA sequences. This phylogeny, which is completely resolved, is well supported with all nodes showing greater than 50% bootstrap support. There was no significant conflict between trees based on each gene independently, although trees produced from fibrinogen intron 7 did not resolve relationships among five of the Zenaida species. The species status of Z. graysoni, as well as that of Z. meloda, is suggested based on their divergence from sister taxa (about 1% and 4%, respectively) and other differences. Zenaida can be divided into two major groups: Zenaida asiatica and Z. meloda versus Z. aurita, Z. galapagoensis, Z. auriculata, Z. graysoni, and Z. macrour

Molecular phylogeny of the dove genera Streptopelia and Columba

Journal ArticleEvolutionary history of the dove genus Streptopelia has not been examined with rigorous phylogenetic methods. We present a study of phylogenetic relationships of Streptopelia based on over 3,600 base pairs of nuclear and mitochondrial gene sequences

Host body size, not host population size, predicts genome-wide effective population size of parasites

Funding was provided by US NSF DEB-1342604, DEB-1925487 and DEB-1926919 grant awards to K.P.J., and European Commission grant H2020-MSCA-IF-2019 (INTROSYM:886532) to JD.The effective population size (N-e) of an organism is expected to be generally proportional to the total number of individuals in a population. In parasites, we might expect the effective population size to be proportional to host population size and host body size, because both are expected to increase the number of parasite individuals. However, among other factors, parasite populations are sometimes so extremely subdivided that high levels of inbreeding may distort these predicted relationships. Here, we used whole-genome sequence data from dove parasites (71 feather louse species of the genus Columbicola) and phylogenetic comparative methods to study the relationship between parasite effective population size and host population size and body size. We found that parasite effective population size is largely explained by host body size but not host population size. These results suggest the potential local population size (infrapopulation or deme size) is more predictive of the long-term effective population size of parasites than is the total number of potential parasite infrapopulations (i.e., host individuals).National Science Foundation (NSF) DEB-1342604, DEB-1925487, DEB-1926919European Commission Joint Research Centre H2020-MSCA-IF-2019 (INTROSYM:886532

Genetic and phylogenetic consequences of island biogeography

Journal ArticleIsland biogeography theory predicts that the number of species on an island should increase with island size and decrease with island distance to the mainland. These predictions are generally well supported in comparative and experimental studies. These ecological, equilibrium predictions arise as a result of colonization and extinction processes