Insights into the karyotype and genome evolution of haplogyne spiders indicate a polyploid origin of lineage with holokinetic chromosomes

Abstract

Spiders are an ancient and extremely diverse animal order. They show a considerable diversity of genome sizes, karyotypes and sex chromosomes, which makes them promising models to analyse the evolution of these traits. Our study is focused on the evolution of the genome and chromosomes in haplogyne spiders with holokinetic chromosomes. Although holokinetic chromosomes in spiders were discovered a long time ago, information on their distribution and evolution in these arthropods is very limited. Here we show that holokinetic chromosomes are an autapomorphy of the superfamily Dysderoidea. According to our hypothesis, the karyotype of ancestral Dysderoidea comprised three autosome pairs and a single X chromosome. The subsequent evolution has frequently included inverted meiosis of the sex chromosome and an increase of 2n. We demonstrate that caponiids, a sister clade to Dysderoidea, have enormous genomes and high diploid and sex chromosome numbers. This pattern suggests a polyploid event in the ancestors of caponiids. Holokinetic chromosomes could have arisen by subsequent multiple chromosome fusions and a considerable reduction of the genome size. We propose that spider sex chromosomes probably do not pose a major barrier to polyploidy due to specific mechanisms that promote the integration of sex chromosome copies into the genome.

Figure 1

Spiders with holokinetic chromosomes, male mitosis and meiosis. Symbol: ↑ (sex chromosome X). (a) Afrilobus sp., Orsolobidae (2n = 5, X0), mitotic metaphase, the sex chromosome is the smallest element of the karyotype; (b) Gamasomorpha lutzi, Oonopidae, mitotic metaphase (2n = 7, X0), all chromosomes have similar length; (c) Dysderocrates storkani, Dysderidae, mitotic metaphase (2n = 21, X0), note the considerable length of the sex chromosome; (d) G. lutzi, mitotic anaphase; (e) Harpactocrates sp., Dysderidae, diakinesis plate formed by four bivalents and a sex chromosome (2n = 9, X0), each bivalent contains a single chiasma; (f) Harpactea cecconii, Dysderidae, late metaphase I consisisting of three bivalents and an X chromosome (2n = 7, X0): chiasmata are already disintegrated, the sex chromosome is less condensed than bivalents; (g) Harpactocrates sp., anaphase I, chromosomes show telokinetic activity; (h) D. storkani, anaphase I, the sex chromosome is more condensed than autosomes and exhibits a delayed segregation; (i) Ariadna sp., Segestriidae, metaphase II (n = 4). In contrast to autosomes, chromatids of the sex chromosome are tightly attached; (j) Dysderocrates sp., Dysderidae, late metaphase II (n = 5): note the arc-shaped morphology of the autosome chromatids, the sex chromosome is more condensed than autosomes; (k) H. cecconii, metaphase II, the sex chromosome is formed by a single chromatid only (result of inverted meiosis of the sex chromosome); (l) Ariadna sp., anaphase II: the two left half-plates (n = 4) contain each a sex chromosome, the two right half-plates (n = 3) are without this element. Chromosomes exhibit telokinetic activity.

Figure 2

Caponiidae (Nopinae), karyotypes, based on metaphase II (a) or mitotic metaphase (b). (a) Nops aff. variabilis, male (2n = 55). Chromosome pairs are metacentric except for two submetacentric (nos 18, 25) and subtelocentric pairs (nos 17, 19), sex chromosomes are metacentric except for submetacentric X₂ and X₃; (b) Tarsonops sp., female (2n = 60). Chromosome pairs are metacentric except for eight submetacentric (nos 6, 14–16, 18, 26, 28, 29) and five subtelocentric pairs (nos 7, 17, 23, 27, 30).

Figure 3

Caponiidae, male meiosis and sex chromosomes. Symbols: ↑ (sex chromosome multivalent), ▲ (bivalent with two chiasmata). Schemes of sex chromosome pairing: dark blue elements – X chromosomes (both chromosome ends involved into pairing); light blue elements – X chromosomes (one chromosome end involved into pairing only); red elements – Y chromosomes. (a) Nops aff. variabilis, incomplete diplotene, X chromosomes are positively heteropycnotic, associated at both ends with a tiny Y chromosome; (b) Caponia natalensis, metaphase I (73 bivalents and a sex chromosome multivalent, separated from bivalents by dotted line). Each bivalent contains a single chiasma. The sex chromosome cluster is formed by six X chromosomes, which are associated at both ends except for one element (*); (c) C. hastifera, metaphase I (58 bivalents and a sex chromosome multivalent, separated from bivalents by dotted line). Each bivalent contains a single chiasma. The sex chromosome multivalent is intersected by a bivalent (+); (d) C. natalensis, sex chromosomes. From left to right: (1) metaphase I, a sex chromosome cluster composed of six X chromosomes associated at both ends; (2) scheme of sex chromosome pairing; (3) morphology of X chromosomes (metaphase II); (e) C. hastifera, sex chromosomes. First row, from left to right: (1) metaphase I, a sex chromosome cluster formed by 10 X chromosomes and two Y microchromosomes. Both ends of two biarmed X chromosomes (open arrowheads) take part in pairing. In contrast, only one end of the acrocentric X chromosomes is involved in pairing. Tiny Y chromosomes are in the middle of the cluster; (2) scheme of sex chromosome pairing; (3) another metaphase I, centre of multivalent: note the uneven size of the two Y chromosomes. Second row, from left to right: (1) morphology of sex chromosomes (metaphase II); (2) morphology of Y microchromosomes (metaphase II). Note the metacentric Y₁ chromosome. The Y₂ chromosome is probably acrocentric.

Figure 4

Genome evolution in haplogyne spiders. Karyotype and genome parameters (each species is represented by one value; see Table S3 for the values used) are mapped on the phylogeny of haplogyne spiders (holokinetic clades in red, monocentric in black). The female data are used except Nops aff. variabilis, in which only male data were available. (a) Diploid number of chromosomes (2n); (b) genome size (2C in Gbp); (c) genome GC content (in %); (d) average chromosome size (i.e., genome size/chromosome number = 2C/2n in Mbp/chromatid). Simplified tree topology is adopted from a phylogenomic study. Boxplots show median (squares), interquartile range (boxes), and non-outlier range (whiskers).

Figure 5

Hypotheses on haplogyne chromosome evolution. Suggested events (numbers in bold): 1 (2n♂~40, X₁X₂Y; ancestral karyotype of haplogynes), 2 (duplication of genome in common ancestor of Caponiidae and Dysderoidea; the latter includes Segestriidae, Oonopidae, Orsolobidae, and Dysderidae), 3 (X₁X₂X₃X₄Y₁Y₂, ancestral sex chromosome system of Nopinae), 4 (duplication of genome in Caponia ancestor), 5 (X₁X₂X₃X₄X₅X₆Y₁Y₂, ancestral sex chromosome system of Caponia), 6 (origin of holokinetic chromosomes), 7 (2n♂ = 7, X0, ancestral karyotype of Dysderoidea), 8 (concerted fission of all chromosomes in ancestor of Segestria), 9 (origin of inverted meiosis of sex chromosome in ancestor of Harpacteinae), 10 (2n♂ = 25, 2n of Harpactea lepida), 11 (2n♂ = 9, ancestral 2n of Dysderinae), 12 (prominent X chromosome, synapomorphy of Dysdera and Dysderocrates). Tree topology is based on Wheeler et al., except for filistatids (resolved according to Gray), nopines (based on Sánchez-Ruiz & Brescovit), and Harpactea (based on cytogenetic data of this study).

Figure 6

Caponiidae, hypothesis of sex chromosome evolution. Abbreviation: WGD (whole genome duplication). (a) diploid ancestor of caponiids (a₁: sex chromosome pairing, male meiosis); (b) ancestor of supposed tetraploid lineage; (c) Nops aff. variabilis (c₁: sex chromosome pairing, male meiosis); (d) ancestor of Caponia lineage; (e) ancestral karyotype of Caponia; (f) C. natalensis (f₁: sex chromosome pairing, male meiosis); (g) C. hastifera (g₁: sex chromosome pairing, male meiosis).