Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

The multi-species coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. Practical applications of the multi-species coalescent model are, however, limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation, effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms (SNPs), and we have implemented it in SNAPP, a Markov chain Monte-Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism (AFLP) loci in 69 individuals sampled from six species of {\em Ourisia} (New Zealand native foxglove)

Ecological Drivers of Song Evolution in Birds: Disentangling the Effects of Habitat and Morphology

Environmental differences influence the evolutionary divergence of mating signals through selection acting either directly on signal transmission (“sensory drive”) or because morphological adaptation to different foraging niches causes divergence in “magic traits” associated with signal production, thus indirectly driving signal evolution. Sensory drive and magic traits both contribute to variation in signal structure, yet we have limited understanding of the relative role of these direct and indirect processes during signal evolution. Using phylogenetic analyses across 276 species of ovenbirds (Aves: Furnariidae), we compared the extent to which song evolution was related to the direct influence of habitat characteristics and the indirect effect of body size and beak size, two potential magic traits in birds. We find that indirect ecological selection, via diversification in putative magic traits, explains variation in temporal, spectral, and performance features of song. Body size influences song frequency, whereas beak size limits temporal and performance components of song. In comparison, direct ecological selection has weaker and more limited effects on song structure. Our results illustrate the importance of considering multiple deterministic processes in the evolution of mating signals

High dispersal ability inhibits speciation in a continental radiation of passerine birds

Dispersal can stimulate speciation byfacilitating geographical expansion across barriers or inhibit speciation by maintaining gene flow among populations. Therefore, the relationship between dispersal ability and speciation rates can be positive or negative. Furthermore, an \u27intermediate dispersal\u27 model that combines positive and negative effects predicts a unimodal relationship between dispersal and diversification. Because both dispersal ability and speciation rates are difficult to quantify, empirical evidence for the relationship between dispersal and diversification remains scarce. Using a surrogate for flight performance and a species-level DNA-based phylogeny of a large South American bird radiation (the Furnariidae), we found that lineages with higher dispersal ability experienced lower speciation rates. We propose that the degree of fragmentation or permeability of the geographical setting together with the intermediate dispersal model are crucial in reconciling previous, often contradictory findings regarding the relationship between dispersal and diversification. © 2011 The Royal Society

Lineage diversification and morphological evolution in a large-scale continental radiation: The neotropical ovenbirds and woodcreepers (aves: furnariidae)

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution

The Effects of Landscape Urbanization on the Gut Microbiome: An Exploration Into the Gut of Urban and Rural White-Crowned Sparrows

Urban habitats present new ecological and evolutionary challenges for animals. Noise and infrastructure often change behavior and community composition, with potential physical costs such as decreased condition. However, the underlying mechanisms driving these patterns are virtually unknown. One potential driver of condition within a species is the diversity of the gut microbiome. Here, we investigate how the urban habitat affects the gut microbiome of White-crowned Sparrows (Zonotrichia leucophrys) males using spatial analyses of land cover (impervious, scrub, grass, and trees) at the regional level and territory level in urban San Francisco, CA and nearby rural Point Reyes, California. We hypothesized that urbanization of habitats affects gut microbial composition and diversity, potentially through direct effects on diet and/or indirect environmental effects. We measured gut microbial community diversity from 16s rRNA sequences amplified from cloacal swabs. We find that the urban and rural male gut microbiomes are significantly different, such that the urban gut microbiome is more diverse than the rural gut microbiome. This relationship may be due to more variable land cover types in urban habitats as compared to rural habitats, which are mainly composed of native scrub. We do not find support for regional impervious cover affecting the gut microbiome, but the more precise territory level analyses show that higher tree cover correlates with increased alpha diversity and impervious cover correlates with relative abundances of gut microbial taxa (Unifrac beta diversity). Although some studies show that gut diversity affects physiology, our measures of body condition do not indicate a strong relationship. Our results highlight how changes in the landscape may affect the gut microbiome of animals in an ever-urbanizing world, and provide a baseline for future studies of how anthropogenic change affects communities at multiple levels

Behavioural response to song and genetic divergence in two subspecies of white-crowned sparrows (Zonotrichia leucophrys)

© 2016 John Wiley & Sons Ltd Divergence in sexual signals may drive reproductive isolation between lineages, but behavioural barriers can weaken in contact zones. Here, we investigate the role of song as a behavioural and genetic barrier in a contact zone between two subspecies of white-crowned sparrows (Zonotrichia leucophrys). We employed a reduced genomic data set to assess population structure and infer the history underlying divergence, gene flow and hybridization. We also measured divergence in song and tested behavioural responses to song using playback experiments within and outside the contact zone. We found that the subspecies form distinct genetic clusters, and demographic inference supported a model of secondary contact. Song phenotype, particularly length of the first note (a whistle), was a significant predictor of genetic subspecies identity and genetic distance along the hybrid zone, suggesting a close link between song and genetic divergence in this system. Individuals from both parental and admixed localities responded significantly more strongly to their own song than to the other subspecies song, supporting song as a behavioural barrier. Putative parental and admixed individuals were not significantly different in their strength of discrimination between own and other songs; however, individuals from admixed localities tended to discriminate less strongly, and this difference in discrimination strength was explained by song dissimilarity as well as genetic distance. Therefore, we find that song acts as a reproductive isolating mechanism that is potentially weakening in a contact zone between the subspecies. Our findings also support the hypothesis that intraspecific song variation can reduce gene flow between populations

Corrigendum to “Phylogeography of the Variable Antshrike (Thamnophilus caerulescens), a South American passerine distributed along multiple environmental gradients” [Mol. Phylogenet. Evol. 148 (2020) 106810](S1055790320300828)(10.1016/j.ympev.2020.106810)

© 2020 Elsevier Inc. The authors regret: (a) The information of Table 2 has incorrect values in column 6. The following table has the correct values. (b) Also, there is a minor typo in the section ‘Data accessibility’, in the word: ‘alignmentsare’. The correct words are: ‘alignments are’. The authors would like to apologize for any inconvenience caused