FNZ 70 - Periegopidae (Arachnida: Araneae) - Phylogenetic analysis
Vink, CJ; Dupérré, N; Malumbres-Olarte, J 2013. Periegopidae (Arachnida: Araneae). Fauna of New Zealand 70, 41 pages.
(
ISSN 0111-5383 (print),
ISSN 1179-7193 (online)
;
no.
70.
ISBN 978-0-478-34740-1 (print),
ISBN 978-0-478-34741-8 (online)
).
Published 7 Mar 2013
ZooBank: http://zoobank.org/References/E8D9D21A-46FD-4E6B-9E79-DBE67BAE57D1
Phylogenetic analysis
Methods. Sequences were aligned using Sequencher 4.6. There was no evidence of insertions/deletions or stop codons in the COI sequences and alignment was straightforward.
Uncorrected COI pairwise distances were calculated using PAUP* version 4.0b10 (Swofford 2002). Distances using the Kimura-2-Parameter (K2P) model (Kimura 1980) were also calculated for comparison with previously reported intraspecific distances in spiders (Robinson et al. 2009). Although K2P has been commonly used in most DNA barcoding studies (e.g., Robinson et al. 2009), there is no evidence that this model is better for species identification than simpler metrics such as uncorrected pairwise distances (Astrin et al. 2006; Collins et al. 2012).
Partitioned Bayesian analysis implemented in MrBayes version 3.1.2 (Ronquist & Huelsenbeck 2003) was used to estimate the COI phylogenetic tree topology. MrModeltest version 2.3 (Nylander 2008) implemented in PAUP* version 4.0b10 (Swofford 2002) was used to select the optimal model and model parameters. Within MrModeltest the Akaike Information Criterion was used for model selection (Posada & Buckley 2004). Based on the results of Brandley et al. (2005), the COI data were partitioned by codon with models selected for each codon; GTR+I (Lanave et al. 1984; Tavaré 1986) for the 1st and 3rd codon positions and HKY+I (Hasegawa et al. 1985) for the 2nd codon positions. Bayesian analysis was conducted by running two simultaneous, completely independent analyses each with four heated chains, sampling every 1000th tree. The analysis was run for 20 million generations, by which time the average standard deviation of split frequencies had dropped below 0.002, which indicated that the two tree samples had converged. Tracer version 1.5 (Rambaut & Drummond 2009) was also used to determine if the analyses had sufficient effective sample sizes. MrBayes was used to construct majority rule consensus trees, discarding the first 25% of trees generated as burn-in. TreeView 1.6.6 (Page 1996) was used to view and save trees in graphic format.
Results. A 1031 base pair (bp) COI fragment was sequenced from eight specimens of P. suterii and three specimens of P. keani. Four COI haplotypes occurred among the eight specimens of P. suterii. Each of the three specimens of P. keani had a different COI haplotype. Inter- and intraspecific uncorrected pairwise distances between COI sequences of P. suterii and P. keani are shown in Table 2. The minimum divergence between the two species was 13.0% (uncorrected) and the mean divergence was 13.5% (uncorrected). The mean intraspecific divergences in P. suterii and P. keani, were 4.0% (uncorrected) and 0.6% (uncorrected), respectively. The maximum intraspecific divergence in P. suterii was 8.6% (uncorrected, 9.2% K2P-distance) and was 0.7% (uncorrected and K2P-distance) in P. keani.
The 1360 bp fragments of 28S from two specimens of P. suterii were identical. The amplification of 28S from two specimens of P. keani (Pk1 and Pk2) was only partially successful with an 821 bp fragment from Pk1 and an 833 bp fragment from Pk2; however, the 281 bp overlap was identical. There were 12 nucleotides that varied between the two species.
The phylogenetic analysis of the COI data (Text-fig. 1) showed that P. suterii and P. keani are monophyletic with P. suterii divided into two clades.
Discussion. Periegops COI sequences were very similar or identical (Table 2) for specimens collected at the same sites; however, specimens of P. suterii collected at Kennedys Bush Reserve, in the west of the Banks Peninsula (Map 1), were 8.2–8.6% (8.7–9.2% K2P-distance) divergent from P. suterii specimens collected from three localities in the eastern Bank Peninsula (Map 1). This high divergence was not found in the slower evolving nuclear marker; 28S sequences were identical from specimens from Kennedys Bush Reserve and Montgomery Park Reserve (Map 1). We also did not observe any morphological differences between Kennedys Bush Reserve specimens and specimens collected from other locations on the Banks Peninsula; therefore we are confident that all specimens are one species, P. suterii. A difference of 8.7–9.2% (K2P-distance) in COI sequence divergence is very high in spiders; much more than the average maximum intraspecific divergence of 3.16% (K2P-distance) observed in other spiders (Robinson et al. 2009). However, higher intraspecific divergences (>10%) have been observed in other haplogynes (Astrin et al. 2006; Binford et al. 2008), Hypochilidae (Hedin 2001), and Mygalomorphae (Bond et al. 2001), so perhaps COI divergence is higher in ancestral spiders than it is in the Entelegynae. Nevertheless, it is curious that high (8.2–8.6%) COI divergence was observed between specimens from localities only just over 23 km apart and at similar altitudes, while there was much less divergence (0.7–1.3%) between specimens from eastern Bank Peninsula localities, which were 5–15 km apart. Specimens from localities between Kennedys Bush Reserve and Montgomery Park Reserve, such as Kaituna Valley, could reveal if COI divergence is correlated with distance or whether there has been some sort of genetic isolation between the east and west of Banks Peninsula, similar to the geographic distribution of two closely related weta species in the genus Hemideina (Townsend et al. 1997).