Insights into mammalian TE diversity through the curation of 248 genome assemblies.

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree.

Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size.

Species with low effective population sizes are at greater risk of extinction because of reduced genetic diversity. Such species are more vulnerable to chance events that decrease population sizes (e.g.

Taxonomic and functional components of avian metacommunity structure along an urban gradient.

Identifying biological processes that structure natural communities has long interested ecologists. Community structure may be determined by various processes, including differential responses of species to environmental characteristics, regional-level spatial influences such as dispersal, or stochasticity generated from ecological drift. Few studies have used the metacommunity paradigm (interacting communities linked by dispersal) to investigate avian community composition along an urban gradient, yet such a theoretical construct may provide insights into species turnover even in unnatural settings such as rural to urban gradients.

SINE-Based Phylogenomics Reveal Extensive Introgression and Incomplete Lineage Sorting in .

Using presence/absence data from over 10,000 Ves SINE insertions, we reconstructed a phylogeny for 11 species. With nearly one-third of individual Ves gene trees discordant with the overall species tree, phylogenetic conflict appears to be rampant in this genus. From the observed conflict, we infer that ILS is likely a major contributor to the discordance.

Broad-scale gradients of resource utilization by phyllostomid bats in Atlantic Forest: patterns of dietary overlap, turnover and the efficacy of ecomorphological approaches.

Identifying mechanisms that promote coexistence at the local level is enigmatic for many organisms. Numerous studies have indirectly demonstrated that biotic interactions may not cause deterministic patterns reflective of the coexistence of interacting bat species. Nonetheless, demonstration of the partitioning of resources by phyllostomid bats by directly examining diet matrices may illuminate a mechanism of coexistence.

Diets Containing Egg or Whey Protein and Inulin Fiber Improve Energy Balance and Modulate Gut Microbiota in Exercising Obese Rats.

Scope: Dietary protein, prebiotic fiber, and exercise individually have been shown to aid in weight loss; however less is known of their combined effects on energy balance. The effects of diets high in protein and fiber, with exercise, on energy balance, hormones, and gut microbiota, were determined.

Methods And Results: Obese male rats were fed high-fat diets with high protein and fiber contents from egg protein and cellulose, egg protein and inulin, whey protein and cellulose, or whey protein and inulin, together with treadmill exercise.

NeoBat Interactions: A data set of bat-plant interactions in the Neotropics.

Data papers and open databases have revolutionized contemporary science, as they provide the long-needed incentive to collaborate in large international teams and make natural history information widely available. Nevertheless, most data papers have focused on species occurrence or abundance, whereas interactions have received much less attention. To help fill this gap, we have compiled a georeferenced data set of interactions between 93 bat species of the family Phyllostomidae (Chiroptera) and 501 plant species of 68 families.

Relative contributions of ecological drift and selection on bat community structure in interior Atlantic Forest of Paraguay.

Despite extensive focus on numerous mechanisms that potentially structure Neotropical bat communities, understanding of the relative importance of any is still illusive. Recently, it has been demonstrated that all mechanisms used to explain community organization can be conceptualized as one or a combination of the few higher-level processes of dispersal, drift, selection and speciation. These four higher-level processes have not been addressed equally by Neotropical bat community ecologists.

A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae.

Crocodilians are an economically, culturally, and biologically important group. To improve researchers' ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.

Insights into the assembly rules of a continent-wide multilayer network.

How are ecological systems assembled? Identifying common structural patterns within complex networks of interacting species has been a major challenge in ecology, but researchers have focused primarily on single interaction types aggregating in space or time. Here, we shed light on the assembly rules of a multilayer network formed by frugivory and nectarivory interactions between bats and plants in the Neotropics. By harnessing a conceptual framework known as the integrative hypothesis of specialization, our results suggest that phylogenetic constraints separate species into different layers and shape the network's modules.

Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats.

The rapid diversification of Myotis bats into more than 100 species is one of the most extensive mammalian radiations available for study. Efforts to understand relationships within Myotis have primarily utilized mitochondrial markers and trees inferred from nuclear markers lacked resolution. Our current understanding of relationships within Myotis is therefore biased towards a set of phylogenetic markers that may not reflect the history of the nuclear genome.

ATLANTIC BATS: a data set of bat communities from the Atlantic Forests of South America.

Bats are the second most diverse mammal order and they provide vital ecosystem functions (e.g., pollination, seed dispersal, and nutrient flux in caves) and services (e.

Threshold effect of habitat loss on bat richness in cerrado-forest landscapes.

Understanding how animal groups respond to contemporary habitat loss and fragmentation is essential for development of strategies for species conservation. Until now, there has been no consensus about how landscape degradation affects the diversity and distribution of Neotropical bats. Some studies demonstrate population declines and species loss in impacted areas, although the magnitude and generality of these effects on bat community structure are unclear.

Human-modified habitats change patterns of population genetic structure and group relatedness in Peter's tent-roosting bats.

Although coloniality is widespread among mammals, it is still not clear what factors influence composition of social groups. As animals need to adapt to multiple habitat and environmental conditions throughout their range, variation in group composition should be influenced by adaptive adjustment to different ecological factors. Relevant to anthropogenic disturbance, increased habitat modification by humans can alter species' presence, density, and population structure.

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries.

Phylogenetic community structure of North American desert bats: influence of environment at multiple spatial and taxonomic scales.

Numerous processes influence community structure. The relative importance of these processes is thought to vary with spatial, temporal and taxonomic scales: density-dependent interactions are thought to be most important at small scales; at intermediate scales, environmental conditions may be the most influential factor; and biogeographic processes are thought to be of greater importance at larger scales. Additionally, the stress-dominance hypothesis suggests that communities experiencing harsher environmental conditions will be predominantly structured by habitat filtering, whereas communities experiencing more favourable conditions will be structured predominantly by density-dependent interactions such as competition.

Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis.

Identification of retrotransposon insertions in nonmodel taxa can be technically challenging and costly. This has inhibited progress in understanding retrotransposon insertion dynamics outside of a few well-studied species. To address this problem, we have extended a retrotransposon-based capture and sequence method (ME-Scan [mobile element scanning]) to identify insertions belonging to the Ves family of short interspersed elements (SINEs) across seven species of the bat genus Myotis.

Differential SINE evolution in vesper and non-vesper bats.

Background: Short interspersed elements (SINEs) have a powerful influence on genome evolution and can be useful markers for phylogenetic inference and population genetic analyses. In this study, we examined survey sequence and whole genome data to determine the evolutionary dynamics of Ves SINEs in the genomes of 11 bats, nine from Vespertilionidae.

Results: We identified 41 subfamilies of Ves and linked several to specific lineages.

Fragmentation of Atlantic forest has not affected gene flow of a widespread seed-dispersing bat.

Habitat loss and resultant fragmentation are major threats to biodiversity, particularly in tropical and subtropical ecosystems. It is increasingly urgent to understand fragmentation effects, which are often complex and vary across taxa, time and space. We determined whether recent fragmentation of Atlantic forest is causing population subdivision in a widespread and important Neotropical seed disperser: Artibeus lituratus (Chiroptera: Phyllostomidae).

Stronger tests of mechanisms underlying geographic gradients of biodiversity: insights from the dimensionality of biodiversity.

Inference involving diversity gradients typically is gathered by mechanistic tests involving single dimensions of biodiversity such as species richness. Nonetheless, because traits such as geographic range size, trophic status or phenotypic characteristics are tied to a particular species, mechanistic effects driving broad diversity patterns should manifest across numerous dimensions of biodiversity. We develop an approach of stronger inference based on numerous dimensions of biodiversity and apply it to evaluate one such putative mechanism: the mid-domain effect (MDE).

Survey sequencing reveals elevated DNA transposon activity, novel elements, and variation in repetitive landscapes among vesper bats.

The repetitive landscapes of mammalian genomes typically display high Class I (retrotransposon) transposable element (TE) content, which usually comprises around half of the genome. In contrast, the Class II (DNA transposon) contribution is typically small (<3% in model mammals). Most mammalian genomes exhibit a precipitous decline in Class II activity beginning roughly 40 Ma.

Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera.

Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven.

Phylogenetic structure illuminates the mechanistic role of environmental heterogeneity in community organization.

1. Diversity begets diversity. Numerous published positive correlations between environmental heterogeneity and species diversity indicate ubiquity of this phenomenon.

Rapid development and screening of microsatellite loci for Artibeus lituratus and their utility for six related species within Phyllostomidae.

Microsatellites are often the marker of choice for population genetic studies at intermediate spatial and temporal scales. Developing large numbers of markers has traditionally been technically difficult, and this has limited our ability to investigate evolutionary phenomena that emerge across short temporal scales. Moreover, few markers tend to successfully amplify across species boundaries.