Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation

Table 1 Comparison of key divergence times, taxa and markers in the pellonuline phylogeny between studies

	Divergence time estimate (MYA)
	This study	Egan et al. 2018	Bloom and Lovejoy 2014	Wilson et al. 2008	Lavoué et al. 2013
Markers	PCGs	CYT-B, 16S, rag1, rag2, slc, zic1	16S, CYT-B, rag1, rag2	16S, 12S, CYT-B	PCGs, tRNAs, rRNAs
Number of taxa (excl. outgroup)	107	190	153	49	82
Number of sites (bp)	18,279	7135	5211	1049–1811	10,733
Node
Limnothrissa miodon—Stolothrissa tanganicae	3.64 [0.99–6.29]	3.91 [1.19–6.64]	6.61 [2.20–11.01]	7.6 [2.1–15.9]	-
LT sardines– Potamothrissa obtusirostris	10.92 [6.37–15.48]	10.04 [5.62–14.47]	23.35 [16.37–30.33]	–	–
LT sardines– other pellonulines	–	–	–	27 [25.0–53.3]	–
Incursion 1: pellonulines–other clupeids	43.71 [31.79–55.63]¹	34.30 [25.56–43.03]¹	47.58 [35.68–59.47]¹	37 [25.0–53.3]²	46.05 [33.38–58.71]¹
Incursion 2: Gilchristella–Sauvagella	–	25.00 [13.39–36.61]	33.92 [18.94–48.90]	20 [7.5–34.4]	–
Ehiravini–Pellonulini	64.57 [50.17–78.97]	70.13 [59.74–83.44]	98.24 [85.02–111.46]	48 [34.0–66.2]	89.02 [80.97–97.08]

Numbers between square brackets indicate 95% credibility intervals. Divergence times from our study were estimated in BEAST, those from other studies were directly reported or extracted from time-calibrated trees using WebPlotDigitizer. Markers indicated in bold were available for both Stolothrissa tanganicae and Limnothrissa miodon. PCGs = all mitochondrial protein coding genes, CYT-B = cytochrome B, 16S = 16S rRNA, 12S = 12S rRNA. ¹Split Pellonulini – Ethmalosa fimbriata. ²Split Pellonulini—other clupeids (E. fimbriata not included in the study)

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