Decoupled evolution of display morphology and display behaviour in phrynosomatid lizards

A widespread trend in animals is the evolution of morphological ornaments and behaviours that are involved in aggressive and courtship displays. These display traits are important from the standpoint of communication, sexual selection, and speciation. Previous authors have suggested that the evolution of display morphology and display behaviour should be closely linked. In this study, I tested for this association with behavioural and morphological data for 59 taxa of phrynosomatid lizards using phylogenetic comparative methods (Mad-dison's concentrated changes test and Felsenstein's independent contrasts). The results showed little significant association between features of display morphology and behaviour, suggesting that the evolution of these traits is not tightly coupled. This decoupling is particularly evident in the genus Sceloporus , in which several species have lost the display coloration but retain unmodified display behaviour. The results also suggest that display morphology is more evolutionarily labile than display behaviour in this group.     

Chromosome numbers in African and Madagascan Loranthaceae and Viscaceae

Eighty-five chromosome numbers representing about 63 species and 23 genera are reported for African and Madagascan Loranthaceae. The base chromosome number of all genera studied is χ= 9. This chromosome number also typifies all other Old World genera of the tribe Lorantheae, and thus supports the previously suggested thesis that the Asian and African Loranthaceae are relatively closely related. Seventy-six chromosome numbers, representing three genera ( Arceuthobium, Korthalsella, Viscum ) and 40 species are reported for African and Madagascan Viscaceae. Most of the data are for Viscum. The number χ= 14 is suggested as the base chromosome number for both Viscum and the family as a whole. The Madagascan Visca , however, have a modal chromosome number of χ= 13. Aneuploid chromosome numbers of χ= 12, 11 and 10 occur in Viscum at the north-south distributional extremes in southern Africa and Europe and, with the addition χ= 13, in all the species with eastward distributions in Madagascar, Asia and Australia. Polyploidy is rare in African and Madagascan members of both families, as is generally also true for other parts of the world where they have been studied. Translocation heterozygosity is reported for a number of species in Viscum.     

Habitat fragmentation: island v landscape perspectives on bird conservation

Fragments of habitat are often viewed as islands and are managed as such; however, habitat fragmentation includes a wide range of spatial patterns of environments that may occur on many spatial scales. Fragments exist in a complex landscape mosaic, and dynamics within a fragment are affected by external factors that vary as the mosaic structure changes. The simple analogy of fragments to islands, therefore, is unsatisfactory. Understanding how birds respond to these complexities of fragmentation requires mechanistic studies focused on habitat selection and movement behaviour. Conservation efforts must be based on viewing fragmentation as a range of conditions that occurs in a landscape mosaic, and management should be directed toward the mosaics rather than focusing solely on reserves.     

Discordant mitochondrial and nuclear gene phylogenies in emydid turtles: implications for speciation and conservation

Do phylogenies and branch lengths based on mitochondrial DNA (mtDNA) provide a reasonable approximation to those based on multiple nuclear loci? In the present study, we show widespread discordance between phylogenies based on mtDNA (two genes) and nuclear DNA (nucDNA; six loci) in a phylogenetic analysis of the turtle family Emydidae. We also find an unusual type of discordance involving the unexpected homogeneity of mtDNA sequences across species within genera. Of the 36 clades in the combined nucDNA phylogeny, 24 are contradicted by the mtDNA phylogeny, and six are strongly contested by each data set. Two genera (Graptemys, Pseudemys) show remarkably low mtDNA divergence among species, whereas the combined nuclear data show deep divergences and (for Pseudemys) strongly supported clades. These latter results suggest that the mitochondrial data alone are highly misleading about the rate of speciation in these genera and also about the species status of endangered Graptemys and Pseudemys species. In addition, despite a strongly supported phylogeny from the combined nuclear genes, we find extensive discordance between this tree and individual nuclear gene trees. Overall, the results obtained illustrate the potential dangers of making inferences about phylogeny, speciation, divergence times, and conservation from mtDNA data alone (or even from single nuclear genes), and suggest the benefits of using large numbers of unlinked nuclear loci. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 445–461.     

The mechanism of background extinction

Following publication of On the Origin of Species, biologists concentrated on and resolved the mechanisms of adaptation and speciation, but largely ignored extinction. Thus, extinction remained essentially a discipline of palaeontology. Adequate language is not available to describe extinction phenomena because they must be discussed in the passive voice, wherein populations simply ‘go extinct’ without reference to process, specifics, effects, or causality. Extinction is also described typically in terms of its dynamics (including rate or risk), and although correlative variables enhance our ability to predict extinction, they do not necessarily enable an understanding of process. Yet background extinction, like evolution, is a process requiring a functional explanation, without which it is impossible to formulate mechanisms. We define the mechanism of background extinction as a typically long‐term, multi‐generational loss of reproductive fitness. This simple concept has received little credence because of a perception that excess generation of progeny ensures population sustainability, and perhaps the misconception that the loss of reproductive fitness somehow constitutes selection against reproduction itself. During environmental shifts, reproductive fitness is compromised when biotic or abiotic extremes consistently exceed existing norms of reaction. Subsequent selection will now favour individual survival over reproductive fitness, initiating long‐term negative selection pressure and population decline. Background extinction consists typically of two intergrading phases: habitat attenuation and habitat dissolution. These processes generate the relict populations that characterize many species undergoing background extinction. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 255–268.     

缺失数据和贝叶斯系统发育分析精确度之探索

The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that incomplete taxa can be accurately placed as long as the overall number of characters in the analysis is large. However, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses.     

Riverine landscapes: taking landscape ecology into the water

1. Landscape ecology deals with the influence of spatial pattern on ecological processes. It considers the ecological consequences of where things are located in space, where they are relative to other things, and how these relationships and their consequences are contingent on the characteristics of the surrounding landscape mosaic at multiple scales in time and space. Traditionally, landscape ecologists have focused their attention on terrestrial ecosystems, and rivers and streams have been considered either as elements of landscape mosaics or as units that are linked to the terrestrial landscape by flows across boundaries or ecotones. Less often, the heterogeneity that exists within a river or stream has been viewed as a `riverscape' in its own right.
2. Landscape ecology can be unified about six central themes: (1) patches differ in quality (2) patch boundaries affect flows, (3) patch context matters, (4) connectivity is critical, (5) organisms are important, and (6) the importance of scale. Although riverine systems differ from terrestrial systems by virtue of the strong physical force of hydrology and the inherent connectivity provided by water flow, all of these themes apply equally to aquatic and terrestrial ecosystems, and to the linkages between the two.
3. Landscape ecology therefore has important insights to offer to the study of riverine ecosystems, but these systems may also provide excellent opportunities for developing and testing landscape ecological theory. The principles and approaches of landscape ecology should be extended to include freshwater systems; it is time to take the `land' out of landscape ecology.     

Reproductive Responses of Northern Goshawks to Variable Prey Populations

ABSTRACT Developing comprehensive conservation strategies requires knowledge of factors influencing population growth and persistence. Although variable prey resources are often associated with fluctuations in raptor demographic parameters, the mechanisms of food limitation are poorly understood, especially for a generalist predator like the northern goshawk (Accipiter gentilis). To determine the reproductive responses of goshawks to variable prey populations, we evaluated 823 goshawk breeding opportunities on the Kaibab Plateau, Arizona, USA, during 1994–2002. Concurrently, density was estimated for 4 prey species (2 avian, 2 mammalian). We explored the relationship between goshawk reproduction and prey density at one temporal scale (year) and 2 spatial scales (study area, forest type). Prey density for all 4 species combined accounted for 89% of the variation in goshawk reproduction within the entire study area (P < 0.001), 74% in mixed conifer forest (P = 0.003) and 85% in ponderosa pine (Pinus ponderosa) forest (P < 0.001). We found that an incremental increase in prey density resulted in a greater increase in goshawk reproduction in ponderosa pine forest than in mixed conifer forest, suggesting that the denser structural conditions of mixed conifer forest may have reduced prey availability. Red squirrel (Tamiasciurus hudsonicus) density explained more annual variation in goshawk reproduction within the study area (r² = 0.87, P < 0.001), mixed conifer forest (r² = 0.80, P = 0.001), and ponderosa pine forest (r² = 0.85, P < 0.001) than did any other individual species. Although certain prey species were more strongly correlated with fluctuations in goshawk reproduction than were others, the high model selection uncertainty and the strong relationship between total prey density and number of goshawk fledglings produced indicated that alternate prey species were readily substituted for one another. Therefore, conservation strategies concerned with the status of goshawk populations should incorporate forest management practices that increase the abundance, diversity, and availability of prey resources.