DOI: 10.5061/dryad.gqnk98t02
title: Patterns of gene family evolution and selection across <em>Daphnia</em>

description: Gene family expansion underlies a host of biological innovations across
 the tree of life. Understanding why specific gene families expand or
 contract requires comparative genomic investigations, clarifying further
 how species adapt in the wild. This study investigates the gene family
 change dynamics within several species of Daphnia, a group of freshwater
 microcrustaceans that are useful model systems for evolutionary genetics.
 We employ comparative genomics approaches to understand the forces driving
 gene evolution and draw upon candidate gene families that change gene
 numbers across Daphnia. Our results suggest that genes related to stress
 responses and glycoproteins generally expand across taxa, and we
 investigate evolutionary hypotheses of adaptation that may underpin
 expansions. Through these analyses, we shed light on the interplay between
 gene expansions and selection within other ecologically relevant stress
 response gene families. While we show generalities in gene family turnover
 in genes related to stress response (i.e., DNA repair mechanisms), most
 gene family evolution is driven in a species-specific manner.
 Additionally, while we show general trends towards positive selection
 within some expanding gene families, many genes are not undergoing
 selection, highlighting the complex nature of diversification and
 evolution within Daphnia. Our research enhances the understanding of
 individual gene family evolution within Daphnia and provides a case study
 of ecologically relevant genes prone to change.
description: # Patterns of gene family evolution and selection across *Daphnia*
 *Dataset DOI:* [10.5061/dryad.gqnk98t02](10.5061/dryad.gqnk98t02) ##
 Description of the data and file structure **CAFE5 report of the
 significant gene family evolution:** * CAFE_k3p_Gamma_report.cafe
 **Aligned protein family codons for recreating figures:** *
 *OG0002427_hsc.trans.clip.fa* * This fasta contains the sequences for the
 "*hsc70-interacting*" protein family. *
 *OG0003195_oxoglutarate.trans.clip.fa* * This fasta contains the sequences
 for the "*H2-oxoglutarate and iron-dependent oxygenase
 JMJD4-like*" protein family. * *OG0005474_centrosomal.trans.clip.fa*
 * This fasta contains the sequences for the "*centrosomal protein*
 *of 164 kDa-like*" protein family. *
 *OG0007254_defense.trans.clip.fa* * This fasta contains the sequences for
 the "*putative defense protein 3*" protein family. *
 *OG0009038_glycoprotein.trans.clip.fa* * This fasta contains the sequences
 for the "*Glycoprotein-N-acetylgalactosamine 3-
 beta-galactosyltransferase*" protein family. ## Code/software See the
 methodology section of the associated article. ## Access information
 ***Daphnia whole-genome dataset.*** Chromosome and scaffold-level
 assemblies of seven species from the genus *Daphnia *were collected from
 the NCBI Genome search engine
 ([https://www.ncbi.nlm.nih.gov/datasets/genome/](https://www.ncbi.nlm.nih.gov/datasets/genome/)) accessed in January 2025(Kitts et al., 2016). We chose North American *D. pulex* (KAP4; RefSeq: GCF_021134715.1), European *D. pulex* (D84A; GenBank: GCA_023526725; Barnard-Kubow et al., 2022), North American *D. pulicaria* (RefSeq: GCF_021234035.1; Wersebe et al., 2023), *D. sinensis* (GenBank: GCA_013167095.2, Jia et al., 2022), *D. carinata* (RefSeq: GCF_022539665.2), *D. galeata* (GenBank: GCA_030770115.1; Nickel et al., 2021), and *D. magna* (RefSeq: GCF_020631705.1) for analyses because they are the most complete species representatives and were annotated for protein-coding genes. and these genomes were the highest quality and newest available for each unique species. We also included *Artemia franciscana* (i.e., brine shrimp; GenBank: GCF_032884065.1) and *Penaeus monodon* (i.e, black tiger shrimp; GenBank: GCF_015228065.2) as Crustacean outgroups for our tree-based analyses.