A genomic perspective of the pink-headed duck Rhodonessa caryophyllacea suggests a long history of low effective population size

Abstract

The first molecular phylogenetic hypothesis for the possibly extinct pink-headed duck Rhodonessa caryophyllacea unambiguously shows that it belongs to the pochard radiation that also includes the genera Aythya and Netta. It is the sister to all modern-day pochards and belongs to a lineage that branched off from the others more than 2.8 million years ago. Rhodonessa caryophyllacea is believed to never have been common in modern time and we show this has probably been the situation for as long as 100,000 years. Our results suggest that their effective population size varied between 15,000 and 25,000 individuals during the last 150,000 years of the Pleistocene. The reasons behind this are largely unknown as very little is known about the life-history and biology of this species. Presumably it is due to factors related to feeding or to breeding, but we may never know this for sure.

A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins

“…Since the publication of Mundy et al (1997), footpads have been the most commonly used source for hDNA from avian study skins and they have been shown to yield more DNA than other potential sources from study skins, such as skin punches and bone (Tsai et al, 2020). Our observations support this conclusion and we have now successfully sequenced the genomes of >700 birds from museum study skin footpads, including small birds such as passerines (Ericson et al, 2019) and larger birds (Cibois et al, 2019; Ericson et al, 2017, our unpublished data). However, we have observed a negative correlation between the size of the bird and the success rate in producing genome‐sequencing libraries from footpads.…”

“…In this paper, we provide an overview of our workflow and discuss the challenges associated with generating genome‐scale data sets from historical avian specimens. The paper draws on our extensive experience in obtaining genetic data from avian study skins for more than 15 years (e.g., Irestedt et al, 2006; Jonsson et al, 2007; Jonsson et al, 2012), and in particular our extensive recent work with the resequencing of entire genomes from avian study skins (see, e.g., Ericson et al, 2021; Ericson et al, 2017; Ericson et al, 2019; Ernst et al, 2022; Irestedt et al, 2019; Jonsson et al, 2019; Kennedy et al, 2022). It is not our aim to review the entire field of museomics, as there are numerous laboratory and analytical methods described in the literature both for DNA extraction (e.g., Tsai et al, 2020) and for genome library preparation from museum samples (Carøe et al, 2018; Kapp et al, 2021; Meyer & Kircher, 2010); each has its own benefits and potential drawbacks.…”

Different spatial distribution of inflammatory cells in the tumor microenvironment of ABC and GBC subgroups of diffuse large B cell lymphoma

“…From an experimental standpoint, fractal dimension has been used to quantitatively characterize the irregular morphology of tumors [ 22 ] and vasculature [ 23 ], and digital pathology has provided several opportunities [ 24 ] to estimate quantitative parameters of the involved cell populations by improving and automating tasks such as cell counting [ 25 ] and cell position mapping [ 26 ].…”

Genomic, genetic and phylogenetic evidence for a new falcon species using chromosome-level genome assembly of the gyrfalcon and population genomics

“…Autosomal SNPs were used to generate the PSMC files using the following command: Finally, the PSMC files were plotted using the saker’s generation time of 6.6 years/generation according to previous estimates ( 18 ). A genomic mutation rate of 4.6×10 −9 per base per generation that was obtained in a germline-based study for the collared flycatcher Ficedula albicollis ( 114 ) and has since been used as a reliable estimate for other birds as well ( 115, 116 ).…”

“…The raw sequencing reads were mapped to the reference, and heterozygous SNPs were called using SAMtools mpileup as in: samtools mpileup -C50 -uf .. /utils/fq2psmcfa -q20 $name.fq.gz > $name.psmcfa psmc -N25 -t15 -r5 -p "4+25*2+4+6" -o $name.psmc $name.psmcfa Finally, the PSMC files were plotted using the saker's generation time of 6.6 years/generation according to previous estimates (18). A genomic mutation rate of 4.6x10 -9 per base per generation that was obtained in a germline-based study for the collared flycatcher Ficedula albicollis (114) and has since been used as a reliable estimate for other birds as well (115,116).…”