Hybridization Dynamics and Extensive Introgression in theDaphnia longispinaSpecies Complex: New Insights from a High-QualityDaphnia galeataReference Genome

Abstract

Hybridization and introgression are recognized as an important source of variation that influence adaptive processes; both phenomena are frequent in the genus Daphnia, a keystone zooplankton taxon in freshwater ecosystems that comprises several species complexes. To investigate genome-wide consequences of introgression between species, we provide here the first high-quality genome assembly for a member of the Daphnia longispina species complex, Daphnia galeata. We further re-sequenced 49 whole genomes of three species of the complex and their interspecific hybrids both from genotypes sampled in the water column and from single resting eggs extracted from sediment cores. Populations from habitats with diverse ecological conditions offered an opportunity to study the dynamics of hybridization linked to ecological changes and revealed a high prevalence of hybrids. Using phylogenetic and population genomic approaches, we provide first insights into the intra- and interspecific genome-wide variability in this species complex and identify regions of high divergence. Finally, we assess the length of ancestry tracts in hybrids to characterize introgression patterns across the genome. Our analyses uncover a complex history of hybridization and introgression reflecting multiple generations of hybridization and backcrossing in the Daphnia longispina species complex. Overall, this study and the new resources presented here pave the way for a better understanding of ancient and contemporary gene flow in the species complex and facilitate future studies on resting egg banks accumulating in lake sediment.

Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

“…pulex TCO [ 41 ], D . galeata M5 [ 42 ], D . magna SK [ 43 ] and Eulimnadia texana JT4(4)5-L [ 44 ].…”

Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

“…Separate de novo assemblies for were performed on the Blue and Gardisky samples using Trinity v. r20140413p1 [41] with parameter min_kmer_cov set to 2. Transcriptome completeness was assessed using BUSCO v. 5.2.2 [42] with the arthopoda_odb10 lineage dataset, and also by comparison to the following published, annotated genomes: D. pulicaria LK16 [43], D. pulex TCO [44], D. galeata M5 [45], D. magna SK [46] and Eulimnadia texana JT4(4)5-L [47].…”

Cost‐saving population genomic investigation of Daphnia longispina complex resting eggs using whole‐genome amplification and pre‐sequencing screening

“…In addition, adapter trimming and quality filtering of the nine NovaSeq datasets from Nickel et al (2021) were performed using Trimmomatic v0.38 with the following parameters: ILLUMINACLIP: TruSeq3‐PE.fa:2:30:10 TRAILING: 15 SLIDINGWINDOW: 4:15 MINLEN:70. Following GATK4 best practices for pre‐processing and variant calling (Van der Auwera et al, 2013) the trimmed reads were mapped to the D. galeata genome using BWA v0.7.17 with the mem and –M options (Li & Durbin, 2009).…”

“…As an unamplified control for the WGA samples, high‐molecular‐weight genomic DNA was extracted from 20 pooled adult Daphnia individuals (M5 clone; Nickel et al, 2021 ) using a modified CTAB extraction method as described in Cristescu et al ( 2006 ).…”

“…Using only the eight WGA samples that were identified as largely Daphnia sequences in the previous low‐coverage MiSeq sequencing step as well as one unamplified CTAB sample (9 total), new libraries were prepared with the NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina®. Then, 150 bp paired‐end sequencing was generated on the Illumina NovaSeq 6000 platform as part of a previous study (Nickel et al, 2021 ). This whole‐genome data was used here to have sufficient coverage to assess genome coverage and is available from the European Nucleotide Archive (accession numbers: ERR4610186‐ERR4610192, ERR4610229, and ERR5235052).…”