Integrating Cytogenetics and Population Genomics: Allopatry and Neo-Sex Chromosomes May Have Shaped the Genetic Divergence in the Erythrinus erythrinus Species Complex (Teleostei, Characiformes)

Abstract

Diversity found in Neotropical freshwater fish is remarkable. It can even hinder a proper delimitation of many species, with the wolf fish Erythrinus erythrinus (Teleostei, Characiformes) being a notable example. This nominal species shows remarkable intra-specific variation, with extensive karyotype diversity found among populations in terms of different diploid chromosome numbers (2n), karyotype compositions and sex chromosome systems. Here, we analyzed three distinct populations (one of them cytogenetically investigated for the first time) that differed in terms of their chromosomal features (termed karyomorphs) and by the presence or absence of heteromorphic sex chromosomes. We combined cytogenetics with genomic approaches to investigate how the evolution of multiple sex chromosomes together with allopatry is linked to genetic diversity and speciation. The results indicated the presence of high genetic differentiation among populations both from cytogenetic and genomic aspects, with long-distance allopatry potentially being the main agent of genetic divergence. One population showed a neo-X₁X₂Y sexual chromosome system and we hypothesize that this system is associated with enhanced inter-population genetic differentiation which could have potentially accelerated speciation compared to the effect of allopatry alone.

Keywords: DArTseq; Neotropical fish; evolution; karyotype; population structure; speciation.

Figure 1

Map of South America indicating E. erythrinus sampling sites. The Brazilian hydrographic basins in which the samples were collected are shown; colored circles specify the sampling sites, with their corresponding karyomorphs: A, green; D, red. Sampling site codes follow those presented in Table 1. The idiograms on the right represent partial karyotypes of each karyomorph.

Figure 2

Karyotypes of E. erythrinus karyomorph A2 analyzed by conventional Giemsa staining (A) and double FISH with 18S (green) and 5S rDNAs (red) as probes (B). Bar = 5 µm.

Figure 3

Representative idiograms of Erythrinus erythrinus karyomorphs A1, A2, and D highlighting the chromosomal distribution of the 18S rDNA (green) and 5S rDNA sequences (red). The sex chromosomes are boxed.

Figure 4

Mitotic chromosome spreads of E. erythrinus males after CGH—interkaryomorph comparison. (a–d) Male-derived genomic probe from karyomorph A1 (b) and A2 (c) mapped against male chromosomes of karyomorph A1. (e–h) Male-derived genomic probe from karyomorph A1 (f) and D (g) mapped against male chromosomes of karyomorph A1. (i–l) Male-derived genomic probe from karyomorph D (j) and A2 (k) mapped against male chromosomes of karyomorph D. First column (a,e,i): DAPI images (blue); second and third columns (b,c,f,g,j,k): hybridization pattern using the male-derived probe (red) of each analyzed karyomorph; fourth column (d,h,l): merged images of both genomic probes and DAPI staining. The common genomic regions of both compared karyomorphs are depicted in yellow and discrepant regions are indicated by arrowheads in the merged images (d,h,l). Bar = 10 μm.

Figure 5

(A) Principal coordinate analysis. Individuals are represented in different colors as follows: A1 in dark green; A2 in light green; D in red. (B) FastStructure result for K = 2. Each vertical bar represents an individual; karyomorphs and sampling locations are indicated below; bar colors indicate the population to which each individual was classified. (C) ConStruct result for K = 2. Each vertical bar represents an individual; karyomorphs and sampling locations are indicated below.