Biology subjects

Kirk, H.

Publications and source records attributed to Kirk, H..

3 recordsLinked to original sources

bioRxiv2022

Urban ecological connectivity as a planning tool for different animal species.

The application of ecological theory to urban planning is becoming more important as land managers focus on increasing urban biodiversity as a way to improve human welfare. City authorities must decide not only what types of biodiversity-focused infrastructure should be prioritized, but also where new resources should be positioned and existing resources protected or enhanced. Careful spatial planning can contribute to the successful return and conservation of urban nature by maximizing the contribution of green infrastructure to landscape connectivity. By using ecological connectivity theory as a planning tool, governments can quantify the effect of different interventions on the ease with which wildlife can move across the landscape. Here we outline an approach to a) quantify ecological connectivity for different urban wildlife species and b) use this to test different urban planning scenarios using QGIS. We demonstrate four extensions to the work by Deslaurier et al. (2018) and Spanowicz & Jaeger (2019) which improve the application of this method as a planning tool for local government: O_LIA step-by-step method for calculating effective mesh size using the open-source software QGIS. C_LIO_LIConversion of the effective mesh size value (meff) to a "probability of connectedness" (Pc, for easier interpretation by local government and comparisons between planning scenarios). C_LIO_LIGuidance for measuring species-specific connectivity, including how to decide what spatial information should be included and which types of species might be most responsive to connectivity planning. C_LIO_LIAdvice for using the method to measure the outcome of different urban planning scenarios on ecological connectivity. C_LI

ecology↗

bioRxiv2019

Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the 5.5 Mbp mitochondrial genome of Sitka spruce (Picea sitchensis), the largest complete mitochondrial genome of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from these long reads. The assembly graph shows a multipartite genome structure, composed of one smaller 168 kbp circular segment of DNA, and a larger 5.4 Mbp component with a branching structure. The assembly graph gives insight into a putative complex physical genome structure, and its branching points may represent active sites of recombination.

genomics↗

bioRxiv2017

It’s okay to be green: Draft genome of the North American Bullfrog (Rana [Lithobates] catesbeiana)

Frogs play important ecological roles as sentinels, insect control and food sources. Several species are important model organisms for scientific research to study embryogenesis, development, immune function, and endocrine signaling. The globally-distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Consequently, the extensive Xenopus genomic resources are of limited utility for Ranids and related frog species. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines.\n\nHerein, we report on the first genome sequence of a Ranid species, an adult male North American bullfrog (Rana [Lithobates] catesbeiana). We assembled high-depth Illumina reads (66-fold coverage), into a 5.8 Gbp (NG50 = 57.7 kbp) draft genome using ABySS v1.9.0. The assembly was scaffolded with LINKS and RAILS using pseudo-long-reads from targeted denovo assembler Kollector and Illumina Synthetic Long-Reads, as well as reads from long fragment (MPET) libraries. We predicted over 22,000 protein-coding genes using the MAKER2 pipeline and identified the genomic loci of 6,227 candidate long noncoding RNAs (IncRNAs) from a composite reference bullfrog transcriptome. Mitochondrial sequence analysis supported Lithobates as a subgenus of Rana. RNA-Seq experiments identified ~6,000 thyroid hormone- responsive transcripts in the back skin of premetamorphic tadpoles; the majority of which regulate DNA/RNA processing. Moreover, 1/6th of differentially-expressed transcripts were putative lncRNAs. Our draft bullfrog genome will serve as a useful resource for the amphibian research community.

genomics↗