Personality Traits in the Budgerigar, Melopsittacus undulatus

This study investigated bold-shy personality in the budgerigar, Melopsittacus undulatus . Adult budgerigars (14 females, 9 males) fed either a control diet, or one supplemented with docosahexaenoic acid (DHA), were subjected to seven behavioral tests and two immunocompetence assays. Behavioral responses were categorized by context: fear, feeding, or activity. Correlations were obtained within contexts and among immunocompetence variables and all behavioral variables. Kruskal-Wallis analysis was used to investigate effects of gender and DHA on all variables. Budgerigars behaved consistently within activity and feeding contexts. Males had higher feeding rates, and their feeding responses were negatively correlated with a measure of innate immunity. Cluster analysis characterized birds by activity levels; bold birds were highly active and shy birds were less active. The results of this study suggest that budgerigars exhibit consistent behaviors in two contexts, feeding and activity, which are unrelated to each other, and that activity is the predominant personality trait

Population Declines and Genetic Variation: Effects of Serial Bottlenecks

Islands foster unique biodiversity, yet also present biogeographic limitations that impose increased risk for population extinction through demographic and genetic constraints and decreased probability of surviving a catastrophe. Of particular interest, especially with regard to endangered species, is the genetic response of insular species to severe population declines or translocations. Both types of events, considered population bottlenecks, are expected to reduce genetic variation, and correspondingly, adaptive potential. For these reasons, it is important to understand how bottlenecks interact with insular population dynamics to affect genetic diversity. I used a combination of a laboratory model experiment and population genetics study of an in situ bottleneck in an endangered species to investigate how quantitative and molecular genetic variation are affected during bottlenecks. I used a laboratory animal model (red flour beetle, Tribolium castaneum) to compare how quantitative genetic variation is affected if a serial bottleneck occurs in a novel versus familiar environment. The experiment was designed to model a founder event or translocation to a new island with a novel environment. I found that phenotypic and additive variance for a quantitative trait were larger following a bottleneck occurring in the novel environment, suggesting that the novel environment could improve adaptive potential in bottlenecked populations. Next, I used molecular genetic markers to assess variation and signatures of selection in the Laysan finch (Telespiza cantans), a Hawaiian honeycreeper endemic to a small Northwestern Hawaiian island. Laysan finches experienced a major bottleneck on Laysan in the early 20th century, followed by a translocation and series of founder events as populations were established on the islets of Pearl and Hermes Reef (PHR) in the 1960s – 70s. I found that, contrary to expectation, bottlenecked Laysan finch populations did not show declines in genetic variation and were not differentiated as a result of genetic drift. These results are potentially caused by insular demographic dynamics. I identified loci with extreme differentiation between modern populations, potentially indicating genomic signals of selection. These regions could be important for adaptation to the novel environment on PHR and are candidates for future study

Taxonomic similarity does not predict necessary sample size for ex situ conservation: A comparison among five genera

Effectively conserving biodiversity with limited resources requires scientifically informed and efficient strategies. Guidance is particularly needed on how many living plants are necessary to conserve a threshold level of genetic diversity in ex situ collections. We investigated this question for 11 taxa across five genera. In this first study analysing and optimizing ex situ genetic diversity across multiple genera, we found that the percentage of extant genetic diversity currently conserved varies among taxa from 40% to 95%. Most taxa are well below genetic conservation targets. Resampling datasets showed that ideal collection sizes vary widely even within a genus: one taxon typically required at least 50% more individuals than another (though Quercus was an exception). Still, across taxa, the minimum collection size to achieve genetic conservation goals is within one order of magnitude. Current collections are also suboptimal: they could remain the same size yet capture twice the genetic diversity with an improved sampling design. We term this deficiency the ‘genetic conservation gap’. Lastly, we show that minimum collection sizes are influenced by collection priorities regarding the genetic diversity target. In summary, current collections are insufficient (not reaching targets) and suboptimal (not efficiently designed), and we show how improvements can be made

Genomic resources for the endangered Hawaiian honeycreepers.

BACKGROUND: The Hawaiian honeycreepers are an avian adaptive radiation containing many endangered and extinct species. They display a dramatic range of phenotypic variation and are a model system for studies of evolution, conservation, disease dynamics and population genetics. Development of a genome-scale resources for this group would augment the quality of research focusing on Hawaiian honeycreepers and facilitate comparative avian genomic research. RESULTS: We assembled the genome sequence of a Hawaii amakihi (Hemignathus virens),and identified ~3.9 million single nucleotide polymorphisms (SNPs) in the genome. Using the amakihi genome as a reference, we also identified ~156,000 SNPs in RAD tag (restriction site associated DNA) sequencing of five honeycreeper species (palila [Loxioides bailleui], Nihoa finch [Telespiza ultima], iiwi [Vestiaria coccinea], apapane [Himatione sanguinea], and amakihi). SNPs are distributed throughout the amakihi genome, and the individual sequenced shows several large regions of low heterozygosity on chromosomes 1, 5, 6, 8 and 11. SNPs from RAD tag sequencing were also found throughout the genome but were found to be more densely located on microchromosomes, apparently a result of differential distribution of the particular site recognized by restriction enzyme BseXI. CONCLUSIONS: The amakihi genome sequence will be useful for comparative avian genomics research and provides a significant resource for studies in such areas as disease ecology, evolution, and conservation genetics. The genome sequences will enable mapping of transcriptome data for honeycreepers and comparison of gene sequences between avian taxa. Researchers will be able to use the large number of SNP markers to genotype honeycreepers in regions of interest or across the whole genome. There are enough markers to enable use of methods such as genome-wide association studies (GWAS) that will allow researchers to make connections between phenotypic diversity of honeycreepers and specific genetic variants. Genome-wide markers will also help resolve phylogenetic and population genetic questions in honeycreepers

Dryad_ModernSquirrelDemux

This file contains the 454 barcode information to demultiplex the samples from the two 454 sff files

Data from: In-solution hybridization for mammalian mitogenome enrichment: pros, cons and challenges associated with multiplexing degraded DNA

Here, we present a set of RNA-based probes for whole mitochondrial genome in-solution enrichment, targeting a diversity of mammalian mitogenomes. This probes set was designed from seven mammalian orders and tested to determine the utility for enriching degraded DNA. We generated 63 mitogenomes representing five orders and 22 genera of mammals that yielded varying coverage ranging from 0 to >5400X. Based on a threshold of 70% mitogenome recovery and at least 10× average coverage, 32 individuals or 51% of samples were considered successful. The estimated sequence divergence of samples from the probe sequences used to construct the array ranged up to nearly 20%. Sample type was more predictive of mitogenome recovery than sample age. The proportion of reads from each individual in multiplexed enrichments was highly skewed, with each pool having one sample that yielded a majority of the reads. Recovery across each mitochondrial gene varied with most samples exhibiting regions with gaps or ambiguous sites. We estimated the ability of the probes to capture mitogenomes from a diversity of mammalian taxa not included here by performing a clustering analysis of published sequences for 100 taxa representing most mammalian orders. Our study demonstrates that a general array can be cost and time effective when there is a need to screen a modest number of individuals from a variety of taxa. We also address the practical concerns for using such a tool, with regard to pooling samples, generating high quality mitogenomes and detail a pipeline to remove chimeric molecules

chimera_ID

This script sorts capture sequences that hit to non-closest-relative (NCR) MMA probes

H3FTPWM01

454 Sequencing reads for some of newly generated mitogenomes, a text file is provided with demultiplexing information and for this run

pero_in.454.fasta

This file contains 454 generated fastq reads for the Peromyscus samples used for the probe development. Both individuals included in the concatenated reference sequence are within this file, with USNM 569292 represented as 92. Sample USNM 569298 is represented as reads ID'd as 98