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Keywords:

  • allopatric speciation;
  • cytochrome b;
  • karyotype evolution;
  • Rodentia;
  • sympatric species

Abstract

  1. Top of page
  2. Abstract
  3. Introduction
  4. Methods
  5. Results
  6. Discussion
  7. References
  8. Supporting Information

A meta-analysis approach was used to test for chromosomal speciation in rodents. Forty-one pairs of sister species, identified in the two most species-rich rodent families (Cricetidae and Muridae), were used as phylogenetically independent data points, each resulting from a speciation event. About 30% of sister species have an identical karyotype. There was a significant difference in the number of chromosomal differences between sympatric and allopatric sister species, compatible with a direct role of chromosomal rearrangements in speciation.


Introduction

  1. Top of page
  2. Abstract
  3. Introduction
  4. Methods
  5. Results
  6. Discussion
  7. References
  8. Supporting Information

The extent to which chromosomal rearrangements play a role in speciation events is controversial. There are various opinions about their importance, ranging from the idea that they play a role in most speciation events (King 1993) to the view that they are largely irrelevant and limited to particular cases (Coyne & Orr 1998). The ‘classical’ models of chromosomal speciation, the ‘hybrid dysfunction’ models, are based on the observation that heterokaryotypes are often less fertile than homokaryotypes because of total or partial disruption at meiosis (King 1993). More recently, a different mechanism, the ‘suppressed recombination’ model, was proposed, supporting a mode of speciation in which regions of low recombination, linked to chromosomal rearrangements, can facilitate genetic divergence (GD) in the presence of gene flow (Faria & Navarro 2010).

Considerable effort has been devoted to searching for signs of chromosomal speciation in the wild. Empirical support mainly comes from detailed genetic studies of natural hybrid zones or closely related species (Faria & Navarro 2010). These analyses provide important clues to the mechanism underlying chromosomal speciation, but since they are restricted to single case studies, they do not provide information about the extent of the phenomenon. Another approach is to compare chromosomal characteristics in allopatric and sympatric species. In fact, if karyotypic differences contribute to the establishment and/or maintenance of reproductive isolation, sister species with secondary sympatric distributions should be more karyotypically differentiated than sister species with allopatric distributions (Noor et al. 2001, Brown et al. 2004, Kandul et al. 2007, Faria & Navarro 2010). This outcome is expected since nascent species, which have accumulated in allopatry multiple chromosomal rearrangements, can persist in secondary sympatry as biological species, whereas populations displaying similar or identical karyotypes are likely to merge and lose their distinctiveness (Kandul et al. 2007, Pinho & Hey 2010). This prediction was firstly made in the context of the suppressed-recombination model (Noor et al. 2001), but it also fits with a hybrid-dysfunction scenario (Kandul et al. 2007). However, this analysis has only been performed in invertebrates such as Drosophila and the butterfly genus Agrodietus (Noor et al. 2001, Kandul et al. 2007).

Rodents are considered emblematic of chromosomal speciation (King 1993). In fact, they are the most diversified group of mammals, with about three thousand species (Wilson & Reeder 2005), a diversity coupled with high chromosomal variability (Graphodatsky et al. 2011). Moreover, there are many instances of related species showing high levels of chromosomal divergence without detectable molecular variation (e.g. Searle 1993).

In this study, a meta-analysis approach was used to test for chromosomal speciation in rodents. Empirical data favour allopatric over parapatric and sympatric speciation in rodents (Fitzpatrick & Turelli 2006). Thus, it is assumed here that sympatric and parapatric species occur after a secondary contact of the range. Pairs of sister species, identified in the two most species-rich rodent families, were used as phylogenetically independent data points, each resulting from a speciation event. The karyotypic differences and the level of GD between sister species was compared in sympatric and allopatric sister species.

Methods

  1. Top of page
  2. Abstract
  3. Introduction
  4. Methods
  5. Results
  6. Discussion
  7. References
  8. Supporting Information

Identification of sister species

The direct comparison of sister species assures the phylogenetic independence of each data point (tip contrasts; Felsenstein 1985). Cricetidae and Muridae represent about 60% of all rodent species (Wilson & Reeder 2005). Published data on species relationships based on single or multigene molecular phylogenetic data were retrieved for each genus in the two families (280 genera). The total number of species in each genus was obtained from Wilson and Reeder (2005) as the primary starting point. However, new species described after 2005 were also considered. Only genera with at least 80% of their currently recognized species included in phylogenetic studies were used to identify sister species. Genera with species paraphyly or taxonomic uncertainty were not considered. Pairs of species, indicated in the literature, for which monophyly was supported by high Bayesian posterior probability (≥95%) or high bootstrap values for Maximum Likelihood and Maximum Parsimony (≥90%) were considered well-supported sister species (hereafter ‘sister species’). Sister species for which distributions were separated by a maritime gap (e.g. island–mainland vicariance) were removed from the analysis because such pairs of species are forced to stay in allopatry without a high chance of secondary overlap. In fact, the inclusion of these species may bias the comparison of karyotypic differences of sympatric vs. allopatric species, if sympatric species arose by secondary contact. Finally, only pairs of sister species with published karyotypes were retained in the final analysis.

Genetic divergence between sister species

For each pair of sister species, the net GD (Kimura 2-parameter model – K2P), was calculated from cytochrome b (cytb) gene sequences downloaded from GenBank. The K2P model was chosen because it is usually used for cytb in mammalian species (e.g. Baker & Bradley 2006). Cytb is the most commonly used molecular marker for species-level phylogenies, although for many species only one or two cytb sequences are available in GenBank. Therefore, one or two sequences per species were selected to estimate GD between sister species. The GD values were considered to be roughly related to the time since speciation and were compared across the different genera. This procedure was used because available data indicate that the molecular substitution rate for mitochondrial DNA is rather similar within and among the two rodent families considered here (Horn et al. 2011).

Chromosomal differences between sister species

Chromosomal data for each species were retrieved from the literature and karyotypes were inspected visually. These included G-banded and standard stained karyotypes. The magnitude of the autosomal karyotypic differences (AKD) between sister species was calculated as the sum of absolute differences in diploid number (2n) divided by two, and the absolute differences in the autosomal fundamental number (number of chromosomal arms, NFa) also divided by two. If more than one karyotype was reported for one species, the minimum AKD was considered based on the assumption that chromosomal evolution proceeds toward divergence of karyotypes. For the subset of sister species for which G-banding was also available (66%), the number of euchromatic rearrangements on autosomes and the X chromosome were also counted. A preliminary analysis using species with available data for both conventional and G-band staining showed that AKD and the number of euchromatic rearrangements on autosomes were comparable in the data set (n = 27; Spearman r = 0.93, p < 0.001; slope 1.06; intercept 0.026); therefore, AKD can be used as a proxy for fine-scale chromosomal rearrangements. The euchromatic rearrangements on autosomes and the X chromosome were taken into consideration only for the count of sister species with identical karyotype.

Species distribution

The distribution of each species was taken primarily from the International Union for Conservation of Nature's Red List of Threatened Species (version 2012.1; http://www.iucnredlist.org/). For each species, the range size was calculated with the application provided by http://eyeonearth.maps.arcgis.com/home/index.html. Pairs of sister species were classified as sympatric or allopatric based on the presence or absence of range overlap. All the sister species classified as allopatric have ranges that are considerably distant (minimum 105 km). Seven pairs of sister species were not easily classifiable as sympatric or allopatric since the overlap was limited to one or a few localities or because of the proximity of the two ranges (less than 2 km). In view of the possibility of sample bias and the small distance of dispersal of rodents (Bowman et al. 2002), these instances were classified as parapatrics. Pairs of parapatric sister species were either eliminated from the analysis or pooled with the sympatric sister species (para-sympatric). There was no direct evidence of current hybridization between any pairs of sister species in the sample.

Results

  1. Top of page
  2. Abstract
  3. Introduction
  4. Methods
  5. Results
  6. Discussion
  7. References
  8. Supporting Information

Forty-one pairs of sister species were identified. For each pair, information on GD, AKD and area of distribution is provided in Table S1, along with bibliographic sources. Among the 41 pairs of sister species, 20 occurred in sympatry, 14 were allopatric and 7 parapatric.

The GD between sister species was very variable, ranging from 1.2% to 21.7%. There was a positive relationship between AKD and GD (Spearman r = 0.32, n = 41, p = 0.04; Fig. 1). However, when a single outlier value was removed, the relationship was no longer significant (r = 0.14, n = 40, p = 0.39). This relationship was also not significant when calculated separately for allopatric, sympatric and para-sympatric species. Allopatric and sympatric species had similar mean GD: 7.5% and 9.2%, respectively (Mann–Whitney U-test, p = 0.27; Table 1).

figure

Figure 1. Scatterplot of the correlation between genetic divergence (%) and autosomal karyotypic difference for 41 sister species contrasts. When the outlier, indicated by an arrow, is removed, the relationship is no longer significant.

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Table 1. Mean ± standard deviation and range (min. – max.) of both genetic divergence (GD) and autosomal karyotypic difference (AKD) in allopatric, sympatric and parapatric sister species in rodents
 N° sister speciesGD (%)AKDN° sister species (%) with the same karyotype
Allopatric147.46 ± 4.39 (1.8–16.1)1.64 ± 2.62 (0–7)7 (50%)
Sympatric209.23 ± 4.61 (2.8–21.7)6.45 ± 6.32 (0–20)2 (10%)
Parapatric78.98 ± 5.87 (1.2–17.9)3.00 ± 3.51 (0–10)2 (29%)
Total418.85 ± 4.71 (1.2–21.7)4.22 ± 5.32 (0–20)11 (27%)

Autosomal karyotypic differences between sister species (AKD) ranged from 0 to 20 (Table 1, Fig. 2). There was a significant difference in AKD between sympatric and allopatric sister species (Mann–Whitney U-test, p = 0.013): sympatric sister species differed by 6.45 ± 6.3 (mean ± standard deviation) rearrangements (range 0–20), while allopatric sister species differed by 1.64 ± 2.62 rearrangements (range 0–7). The difference was also significant when parapatric and sympatric species were pooled (Mann–Whitney U-test, p = 0.019). The distribution of AKD between sympatric and allopatric sister species was also different (Fig. 2; Kolmogorov–Smirnov test, p = 0.026).

figure

Figure 2. Distribution of autosomal karyotypic differences between sister species in the total sample (white), in allopatric (grey) and in sympatric (black) sister species.

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Only two of the 20 sympatric sister species pairs had identical karyotypes, whereas seven of the 14 allopatric sister species had identical karyotypes (Fisher's exact test, p = 0.017; Table 1). Significance was maintained when para-sympatric sister species were compared with allopatric ones (p = 0.026).

Discussion

  1. Top of page
  2. Abstract
  3. Introduction
  4. Methods
  5. Results
  6. Discussion
  7. References
  8. Supporting Information

In this data set, the sympatric sister species were more chromosomally differentiated than the allopatric ones, as shown by comparison of both the mean AKD and the AKD distribution in allopatric vs. sympatric sister species. This result did not change when parapatric species were pooled with sympatric ones. These differences were not caused by a trivial accumulation of AKD over time. In fact, the GD between sister species (roughly dependent on time of divergence) was not correlated to their chromosomal differences. This is not surprising, since the rate of karyotypic evolution in rodents seems to be uncoupled from the time of divergence; rates vary by as much as 10 times in various branches of the rodent phylogenetic tree (Romanenko et al. 2012).

The observed pattern of AKD in allopatric vs. sympatric sister species can be explained by considering that when the ranges overlap, after allopatric divergence, the nascent species showing more karyotypic differences are more likely to remain distinct than the ones with similar karyotypes.

Moreover, it should be noted that 27% of the sister species had identical karyotypes, indicating that not all speciation events are accompanied by detectable chromosomal rearrangements. However, sister species with the same karyotype were not randomly distributed but were more common in allopatric sister species than in sympatric ones. This pattern is also compatible with a direct role of chromosomal rearrangements in the data set. Indeed, models of chromosomal speciation do not postulate that all speciation events are due to chromosomal rearrangements. Instead, populations are likely to diverge genetically in allopatry and, under certain conditions, also have the opportunity to accumulate chromosomal rearrangements (Searle 1993, Faria & Navarro 2010). The present study concurs with these models since they indicate that, after secondary contact, species that diverge karyotypically have a higher chance of remaining distinct than species that diverge only genetically. Under the hybrid dysfunction models, this could occur because hetero-karyotypes are expected to be less fit than homo-karyotypes (e.g. Searle 1993). According to the suppressed recombination scenario, genes associated with partial reproductive barriers could be protected from recombination thanks to the tight linkage with chromosomal rearrangements that reduce crossing over (Faria & Navarro 2010).

References

  1. Top of page
  2. Abstract
  3. Introduction
  4. Methods
  5. Results
  6. Discussion
  7. References
  8. Supporting Information
  • Baker RJ, Bradley RD (2006) Speciation in mammals and the genetic species concept. Journal of Mammalogy 87: 643662.
  • Bowman J, Jaeger A, Fahrig L (2002) Dispersal distance of mammals is proportional to home range size. Ecology 83: 20492055.
  • Brown KM, Burk LM, Henagan LM, Noor MAF (2004) A test of the chromosomal arrangement model of speciation in Drosophila pseudoobscura. Evolution 58: 18561860.
  • Coyne JA, Orr HA (1998) The evolutionary genetics of speciation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 353: 287305.
  • Faria R, Navarro A (2010) Chromosomal speciation revisited: rearranging theory with pieces of evidence. Trends in Ecology and Evolution 25: 660669.
  • Felsenstein J (1985) Phylogenies and the comparative method. The American Naturalist 125: 115.
  • Fitzpatrick BM, Turelli M (2006) The geography of mammalian speciation: mixed signals from phylogenies and range maps. Evolution 60: 601615.
  • Graphodatsky AS, Trifonov VA, Stanyon R (2011) The genome diversity and karyotype evolution of mammals. Molecular Cytogenetics 4: 22.
  • Horn S, Durka W, Wolf R, Ermala A, Stubbe A, Stubbe M, Hofreiter M (2011) Mitochondrial genomes reveal slow rates of molecular evolution and the timing of speciation in beavers (Castor), one of the largest rodent species. PLoS ONE 6: e14622.
  • Kandul NP, Lukhtanov VA, Pierce NE (2007) Karyotypic diversity and speciation in Agrodiaetus butterflies. Evolution 61: 546559.
  • King M (1993) Species Evolution. The Role of Chromosome Change. Cambridge University Press, Cambridge, UK.
  • Noor MAF, Grams KL, Bertucci LA, Reiland J (2001) Chromosomal inversions and the reproductive isolation of species. Proceedings of the National Academy of Sciences of the United States of America 98: 1208412088.
  • Pinho C, Hey J (2010) Divergence with gene flow: models and data. Annual Review of Ecology, Evolution, and Systematics 41: 215230.
  • Romanenko SA, Perelman PL, Trifonov VA, Graphodatsky AS (2012) Chromosomal evolution in Rodentia. Heredity 108: 416.
  • Searle JB (1993) Chromosomal hybrid zones in eutherian mammals. In: Harrison RG (ed.) Hybrid Zones and the Evolutionary Process, 309353. Oxford University Press, Oxford, UK.
  • Wilson DE, Reeder DAN (2005) Mammal Species of the World. A Taxonomic and Geographic Reference, 3rd ed. Johns Hopkins University Press, Baltimore, Maryland, USA.

Supporting Information

  1. Top of page
  2. Abstract
  3. Introduction
  4. Methods
  5. Results
  6. Discussion
  7. References
  8. Supporting Information
FilenameFormatSizeDescription
mam12009-sup-0001-si.docx40K

Table S1. Chromosomal characteristics, diploid (2n) and autosomal fundamental (NFa) numbers, autosomal karyotypic differences evaluated with standard staining (AKD), genetic divergence (Kimura 2-parameter, GD), karyotypic differences on G-banded karyotypes (including the X chromosome) (KDG), and area of distribution in 41 pairs of sister species identified in this study. Bibliographic source for sister species support and chromosomal characteristics are also indicated.

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