Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community ...

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Phylogenies and Community Ecology

Whether inbreeding affects the demography and persistence of natural populations has been questioned. However, new pedigree data from field populations and molecular and analytical tools for tracing patterns of relationship and inbreeding have now enhanced our ability to detect inbreeding depression within and among wild populations. This work reveals that levels of inbreeding depression vary across taxa, populations and environments, but are usually substantial enough to affect both individual and population performance. Data from bird and mammal populations suggest that inbreeding depression often significantly affects birth weight, survival, reproduction and resistance to disease, predation and environmental stress. Plant studies, based mostly on comparing populations that differ in size or levels of genetic variation, also reveal significant inbreeding effects on seed set, germination, survival and resistance to stress. Data from butterflies, birds and plants demonstrate that populations with reduced genetic diversity often experience reduced growth and increased extinction rates. Crosses between such populations often result in heterosis. Such a genetic rescue effect might reflect the masking of fixed deleterious mutations. Thus, it might be necessary to retain gene flow among increasingly fragmented habitat patches to sustain populations that are sensitive to inbreeding.

Inbreeding effects in wild populations.

Current global patterns of biodiversity result from processes that operate over both space and time and thus require an integrated macroecological and macroevolutionary perspective. Molecular time trees have advanced our understanding of the tempo and mode of diversification and have identified remarkable adaptive radiations across the tree of life. However, incomplete joint phylogenetic and geographic sampling has limited broad-scale inference. Thus, the relative prevalence of rapid radiations and the importance of their geographic settings in shaping global biodiversity patterns remain unclear. Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective. Overall, whereas constituent clades may exhibit slowdowns, the adaptive zone into which modern birds have diversified since the Cretaceous may still offer opportunities for diversification.

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The global diversity of birds in space and time

A DNA test to sex most birds.

Endangered species often occur in small populations that may have a greater risk of short-term extinction due to the negative effects of inbreeding depression. The eastern massasauga (Sistrurus c. catenatus) is an endangered rattlesnake that is found in isolated populations of varying size throughout its range. Here, we investigate whether variation in an indirect measure of individual fitness (relative body condition) can be explained by genome-wide levels of genetic variation (based on 19 microsatellite loci) and other factors. To do this, we use genetic and phenotypic data from individual snakes sampled from 14 populations throughout the species’ range. We tested for levels of inbreeding by comparing observed mean multi-locus heterozygosity (MLH) for each population (an estimate of average inbreeding) with the expected distribution under random mating. We then looked for evidence of heterozygosity-fitness correlations (HFCs) using a measures of individual MLH and relative body condition. In all but one population, observed MLH values are indistinguishable from those generated under a model of random mating implying low levels of inbreeding in most populations. There was significant variation in both mean MLH and mean body condition within and among populations but evidence for inbreeding depression was equivocal: in support, there were some high (but largely non-significant) HFCs effect sizes within a number populations, including one that showed significant evidence for both inbreeding and a HFC. Overall, however, there was no significant correlation between MLH and body condition across all populations after controlling for non-genetic factors such as sex, season of capture and year of capture. Our results suggest that among-population and individual differences in fitness (measured as body condition) in these snakes are better explained by short-term ecological factors rather than genetic mechanisms, but leave open the possibility that limited undetected effects of inbreeding depression are present.

Inbreeding, body condition, and heterozygosity-fitness correlations in isolated populations of the endangered eastern massasauga rattlesnake (Sistrurus c. catenatus)

Bird song is a prominent example of a trait under inter- and intrasexual selection. Performance-related aspects of bird song have been shown to vary among males and to influence territorial interactions as well as female mate choice. In oscine songbirds, song is different from many other sexually selected traits in that it is learned. As a result of learning, territorial neighbors share songs in some species. Thus, social interactions may be influenced not only by how well a male performs song but also by whom he shares song with. Here, we test the hypothesis that song sharing indicates local song learning and experience from which females may benefit. We examine the prediction that song sharing correlates with reproductive success. During our 4-year field study on white-crowned sparrows Zonotrichia leucophrys pugetensis, we found that yearling males that shared song with at least one territorial neighbor had higher social mating success than nonsharers. At the same time, song performance did not significantly correlate with social mating success but did correlate with paternity loss. Males with high performance were more likely to lose paternity than males with low performance. No song feature correlated with gaining paternity. We conclude that song sharing may be an indicator of male quality and stable social neighborhoods which may be a direct benefit to females. Furthermore, our results may provide a functional explanation for a developmental process where songbirds adjust their song to the local social neighborhood.

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Song sharing correlates with social but not extrapair mating success in the white-crowned sparrow

RAD-Seq Refines Previous Estimates of Genetic Structure in Lake Erie Walleye

Theory predicts that predator–prey interactions can generate reciprocal selection pressures on species pairs, which can result in local adaptation, yet the presence and pattern of local adaptation is poorly studied in vertebrate predator–prey systems Here, we used a reciprocal common garden (laboratory) experimental design involving comparisons between local and foreign populations to determine if local adaptation was present between a generalist predator—the pigmy rattlesnake (Sistrurus miliarius)—and a co-occurring prey—the squirrel treefrog (Hyla squirella) We conducted toxicity trials using snake venom from two populations separated by 340 km tested on prey from sympatric and allopatric populations, resulting in data from four venom origin–frog origin combinations We assessed venom effectiveness using two measures (frog mortality at 24 h and time to frog death) and then used regression analyses to look for a signal of local adaptation with either measure We found evidence for local adaptation for one measure (time to death), but not the other (frog mortality) We argue that in this system, the time to death of a prey item is a more ecologically relevant measure of venom effectiveness than is frog mortality at 24 h Our results document an example of local adaptation between two interacting vertebrates using a whole-organism assay and a local versus foreign criteria and provide evidence that population-level variation in snake venom is adaptive

H. Lisle Gibbs

Papers

Inbreeding, body condition, and heterozygosity-fitness correlations in isolated populations of the endangered eastern massasauga rattlesnake (Sistrurus c. catenatus)

Song sharing correlates with social but not extrapair mating success in the white-crowned sparrow

RAD-Seq Refines Previous Estimates of Genetic Structure in Lake Erie Walleye

Evaluating local adaptation of a complex phenotype: reciprocal tests of pigmy rattlesnake venoms on treefrog prey

Microsatellite DNA loci suitable for parentage analysis in the yellow‐pine chipmunk (Tamias amoenus)