Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti.

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.

Birds are islands for parasites.

Understanding the mechanisms driving the extraordinary diversification of parasites is a major challenge in evolutionary biology. Co-speciation, one proposed mechanism that could contribute to this diversity is hypothesized to result from allopatric co-divergence of host-parasite populations. We found that island populations of the Galápagos hawk (Buteo galapagoensis) and a parasitic feather louse species (Degeeriella regalis) exhibit patterns of co-divergence across variable temporal and spatial scales. Hawks and lice showed nearly identical population genetic structure across the Galápagos Islands. Hawk population genetic structure is explained by isolation by distance among islands. Louse population structure is best explained by hawk population structure, rather than isolation by distance per se, suggesting that lice tightly track the recent population histories of their hosts. Among hawk individuals, louse populations were also highly structured, suggesting that hosts serve as islands for parasites from an evolutionary perspective. Altogether, we found that host and parasite populations may have responded in the same manner to geographical isolation across spatial scales. Allopatric co-divergence is likely one important mechanism driving the diversification of parasites.

110 years of Avipoxvirus in the Galapagos Islands.

The role of disease in regulating populations is controversial, partly owing to the absence of good disease records in historic wildlife populations. We examined birds collected in the Galapagos Islands between 1891 and 1906 that are currently held at the California Academy of Sciences and the Zoologisches Staatssammlung Muenchen, including 3973 specimens representing species from two well-studied families of endemic passerine birds: finches and mockingbirds. Beginning with samples collected in 1899, we observed cutaneous lesions consistent with Avipoxvirus on 226 (6.3%) specimens. Histopathology and viral genotyping of 59 candidate tissue samples from six islands showed that 21 (35.6%) were positive for Avipoxvirus, while alternative diagnoses for some of those testing negative by both methods were feather follicle cysts, non-specific dermatitis, or post mortem fungal colonization. Positive specimens were significantly nonrandomly distributed among islands both for mockingbirds (San Cristobal vs. Espanola, Santa Fe and Santa Cruz) and for finches (San Cristobal and Isabela vs. Santa Cruz and Floreana), and overall highly significantly distributed toward islands that were inhabited by humans (San Cristobal, Isabela, Floreana) vs. uninhabited at the time of collection (Santa Cruz, Santa Fe, Espanola), with only one positive individual on an uninhabited island. Eleven of the positive specimens sequenced successfully were identical at four diagnostic sites to the two canarypox variants previously described in contemporary Galapagos passerines. We conclude that this virus was introduced late in 1890's and was dispersed among islands by a variety of mechanisms, including regular human movements among colonized islands. At present, this disease represents an ongoing threat to the birds on the Galapagos Islands.

Molecular and morphological divergence in a pair of bird species and their ectoparasites.

In an evolutionary context, parasites tend to be morphologically conservative relative to their hosts. However, the rate of neutral molecular evolution across many parasite lineages is faster than in their hosts. Although this relationship is apparent at the macroevolutionary scale, insight into the processes underpinning it may be gained through investigations at the microevolutionary scale. Birds and their ectoparasitic lice have served as important natural experiments in co-evolution. Here, we compared mitochondrial and morphological divergence in 2 recently diverged avian host lineages and their parasites. Gálapagos hawks (Buteo galapagoensis) are phenotypically divergent from their closest mainland relatives, the Swainson's hawk (Buteo swainsoni). Both species are host to a feather louse species of Craspedorrhynchus (Insecta: Phthiraptera: Ischnocera, Philopteridae). We sequenced the 5' end of the mitochondrial gene cytochrome oxidase c subunit I (COI) from a set of hawks and lice. Although this fragment allowed unambiguous identification of host and parasite lineages on the islands and the mainland, only a single variable site was present in the 2 hosts, but 2 major Craspedorrhynchus clades divergent by ~10% were recovered that sorted perfectly with host species. We found significant population genetic structure within the Galápagos Craspedorrhynchus lineage. While the host species are highly differentiated phenotypically, the 2 Craspedorrhynchus louse lineages are phenotypically overlapping, although subtle but significant morphological differences exist.

Patterns of parasite abundance and distribution in island populations of Galápagos endemic birds.

Parasite life-history characteristics, the environment, and host defenses determine variation in parasite population parameters across space and time. Parasite abundance and distribution have received little attention despite their pervasive effects on host populations and community dynamics. We used analyses of variance to estimate the variability of intensity, prevalence, and abundance of 4 species of lice (Insecta: Phthiraptera) infecting Galápagos doves and Galápagos hawks and 1 haemosporidian parasite (Haemosporida: Haemoproteidae) infecting the doves across island populations throughout their entire geographic ranges. Population parameters of parasites with direct life cycles varied less within than among parasite species, and intensity and abundance did not differ significantly across islands. Prevalence explained a proportion of the variance (34%), similar to infection intensity (33%) and parasite abundance (37%). We detected a strong parasite species-by-island interaction, suggesting that parasite population dynamics is independent among islands. Prevalence (up to 100%) and infection intensity (parasitemias up to 12.7%) of Haemoproteus sp. parasites varied little across island populations.

Microfilariae in Galápagos penguins (Spheniscus mendiculus) and flightless cormorants (Phalacrocorax harrisi): genetics, morphology, and prevalence.

Galapagos penguins (Spheniscus mendiculus) and flightless cormorants (Phalacrocorax harrisi) live in small, isolated populations on the westernmost islands of Isabela and Fernandina in the Galápagos Islands, Ecuador. Between August 2003 and February 2005, 4 field trips, 2 in the cool, dry season (August 2003 and August 2004) and 2 in the hot, rainy season (March 2004 and February 2005), were undertaken; 298 Galápagos penguins and 380 cormorants were sampled for prevalence and intensity of hemoparasites. Microfilariae were found in both the penguins and the cormorants. Blood smears were negative for the presence of other species of hemoparasites. Overall prevalence of microfilariae across seasons was 42.0% in cormorants and 13.8% in the penguins. Intensity of infection was generally low (mean = 3.2-31.7 in 25 fields across seasons and species) with the exception of a few individuals with markedly high intensities of parasites (>300 in 25 fields in 1 cormorant). Prevalence of microfilariae increased significantly over the 4 sampling periods for cormorants, but not for penguins. Prevalences were significantly higher in cormorants than in penguins for 3 of the 4 collecting trips. Male penguins had higher prevalences than females; however, there were no gender differences in cormorants. No relation was detected between body mass and either presence or intensity of parasitism. Morphological characteristics of the microfilariae are also described and specimens from each host species were similar in all characters measured. DNA sequence data from the mitochondrial cytochrome c oxidase subunit I gene were consistent with the morphological evidence and together demonstrate that the penguins and cormorants are likely to be infected with the same species of microfilariae.

Disease ecology in the Galápagos Hawk (Buteo galapagoensis): host genetic diversity, parasite load and natural antibodies.

An increased susceptibility to disease is one hypothesis explaining how inbreeding hastens extinction in island endemics and threatened species. Experimental studies show that disease resistance declines as inbreeding increases, but data from in situ wildlife systems are scarce. Genetic diversity increases with island size across the entire range of an extremely inbred Galápagos endemic bird, providing the context for a natural experiment examining the effects of inbreeding on disease susceptibility. Extremely inbred populations of Galápagos hawks had higher parasite abundances than relatively outbred populations. We found a significant island effect on constitutively produced natural antibody (NAb) levels and inbred populations generally harboured lower average and less variable NAb levels than relatively outbred populations. Furthermore, NAb levels explained abundance of amblyceran lice, which encounter the host immune system. This is the first study linking inbreeding, innate immunity and parasite load in an endemic, in situ wildlife population and provides a clear framework for assessment of disease risk in a Galápagos endemic.

Phylogeography of the Galápagos hawk (Buteo galapagoensis): a recent arrival to the Galápagos Islands.

Galápagos hawks (Buteo galapagoensis) are one of the most inbred bird species in the world, living in small, isolated island populations. We used mitochondrial sequence and nuclear minisatellite data to describe relationships among Galápagos hawk populations and their colonization history. We sampled 10 populations (encompassing the entire current species range of nine islands and one extirpated population), as well as the Galápagos hawk's closest mainland relative, the Swainson's hawk (B. swainsoni). There was little sequence divergence between Galápagos and Swainson's hawks (only 0.42% over almost 3kb of data), indicating that the hawks colonized Galápagos very recently, likely less than 300,000 years ago, making them the most recent arrivals of the studied taxa. There were only seven, closely related Galápagos hawk haplotypes, with most populations being monomorphic. The mitochondrial and minisatellite data together indicated a general pattern of rapid population expansion followed by genetic isolation of hawk breeding populations. The recent arrival, genetic isolation, and phenotypic differentiation among populations suggest that the Galápagos hawk, a rather new species itself, is in the earliest stages of further divergence.

Cryptic host specificity of an avian skin mite (Epidermoptidae) vectored by louseflies (Hippoboscidae) associated with two endemic Galapagos bird species.

Host specificity of vectors is an important but understudied force shaping parasite evolution and the relationship between hosts and parasites. Low vector specificity may allow a vectored parasite to invade new host species, whereas high specificity of vectors may reduce the host range of the parasite and favor specialization. The 'generalist' and widely distributed avian skin mite Myialges caulotoon Speiser (Acari: Epidermoptidae) is unusual because females require an insect vector to complete their life cycle. Myialges caulotoon was previously reported from 2 lousefly (Diptera: Hippoboscidae) species, Olfersia sordida and Icosta nigra, parasitizing flightless cormorants (Phalacrocorax harrisi) and Galápagos hawks (Buteo galapagoensis), respectively, within the Galápagos Islands. This is a surprising distribution, given that the 2 lousefly species involved are relatively host-specific. Mitochondrial DNA sequences revealed 2 reciprocally monophyletic Myialges clades that sorted out perfectly with respect to their vector species, regardless of whether they were in allopatry or sympatry. One clade was restricted to flies of hawks and the other to flies of cormorants. Females of the 2 Myialges groups were also separated consistently by the shape of the sternal surface sclerotization. Mites of hawk flies were more abundant than those of cormorant flies. Within the Myialges clade associated with hawks, genetic differentiation between 2 island populations mirrored its host's patterns of differentiation.

Characterization of canarypox-like viruses infecting endemic birds in the Galápagos Islands.

The presence of avian pox in endemic birds in the Galápagos Islands has led to concern that the health of these birds may be threatened by avipoxvirus introduction by domestic birds. We describe here a simple polymerase chain reaction-based method for identification and discrimination of avipoxvirus strains similar to the fowlpox or canarypox viruses. This method, in conjunction with DNA sequencing of two polymerase chain reaction-amplified loci totaling about 800 bp, was used to identify two avipoxvirus strains, Gal1 and Gal2, in pox lesions from yellow warblers (Dendroica petechia), finches (Geospiza spp.), and Galápagos mockingbirds (Nesomimus parvulus) from the inhabited islands of Santa Cruz and Isabela. Both strains were found in all three passerine taxa, and sequences from both strains were less than 5% different from each other and from canarypox virus. In contrast, chickens in Galápagos were infected with a virus that appears to be identical in sequence to the characterized fowlpox virus and about 30% different from the canarypox/Galápagos group viruses in the regions sequenced. These results indicate the presence of canarypox-like viruses in endemic passerine birds that are distinct from the fowlpox virus infecting chickens on Galápagos. Alignment of the sequence of a 5.9-kb region of the genome revealed that sequence identities among Gal1, Gal2, and canarypox viruses were clustered in discrete regions. This indicates that recombination between poxvirus strains in combination with mutation led to the canarypox-like viruses that are now prevalent in the Galápagos.

Effects of host sociality on ectoparasite population biology.

Theory predicts a positive relationship between parasite infection intensity and host density. However, this generalization is complicated in natural systems by differences in life history among parasite taxa, e.g., transmissibility. Accordingly, predictions relating host density to parasite load should be specific to each parasite taxon. To illustrate this, we studied parasites that differed greatly in life history in the context of the Galapagos hawk's (Buteo galapagoensis) variably cooperative mating system. Two louse (Phthiraptera) species were collected: Colpocephalum turbinatum (Amblycera), with 53 host species, and Degeeriella regalis (Ischnocera), with 10 host species, although B. galapagoensis was the only known Galapagos host. Sixty territorial adult male hawks from 26 groups of 1-6 males were quantitatively sampled for lice. Average abundance and intensity of C. turbinatum but not D. regalis were significantly larger in large groups of hawks than small groups. Males from the same polyandrous group harbored significantly correlated abundances of C. turbinatum but not D. regalis. Prevalence, average abundance, and intensity of C. turbinatum were significantly higher than D. regalis. These are the first results to demonstrate significant differences in a suite of population responses between these louse suborders in the context of host sociality.

Differences in straggling rates between two genera of dove lice (Insecta: Phthiraptera) reinforce population genetic and cophylogenetic patterns.

Differences in dispersal abilities have been implicated for causing disparate evolutionary patterns between Columbicola and Physconelloides lice (Insecta: Phthiraptera). However, no study has documented straggling (when lice are found on atypical hosts) rates within these lineages. We used the fact that the Galapagos Hawk, Buteo galapagoensis (Gould) (Falconiformes) feeds on the Galapagos Dove Zenaida galapagoensis Gould (Columbiformes) within an ecologically simplified setting. The Galapagos Dove is the only typical host of Columbicola macrourae (Wilson) and Physconelloides galapagensis (Kellogg and Huwana) in Galapagos. We quantitatively sampled and found these lice on both bird species. A DNA barcoding approach confirmed that stragglers were derived from Galapagos doves. We also collected a Bovicola sp. louse, likely originating from a goat (Capra hircus). On hawks, C. macrourae was significantly more prevalent than P. galapagensis. On doves, the two lice were equally prevalent and abundant. Differences in prevalence on hawks was a function of differences in straggling rate between lice, and not a reflection of their relative representation within the dove population. This provides further evidence that differences in dispersal abilities may drive differences in the degree of cospeciation in Columbicola and Phyconelloides lice, which have become model systems in evolutionary biology.