Phylogeny and phylogeography of Altolamprologus: ancient introgression and recent divergence in a rock-dwelling Lake Tanganyika cichlid genus

Abstract

Stenotopic specialization to a fragmented habitat promotes the evolution of genetic structure. It is not yet clear whether small-scale population structure generally translates into large-scale intraspecific divergence. In the present survey of mitochondrial genetic structure in the Lake Tanganyika endemic Altolamprologus (Teleostei, Cichlidae), a rock-dwelling cichlid genus comprising A. compressiceps and A. calvus, habitat-induced population fragmentation contrasts with weak phylogeographic structure and recent divergence among genetic clades. Low rates of dispersal, perhaps along gastropod shell beds that connect patches of rocky habitat, and periodic secondary contact during lake level fluctuations are apparently sufficient to maintain genetic connectivity within each of the two Altolamprologus species. The picture of genetic cohesion was interrupted by a single highly divergent haplotype clade in A. compressiceps restricted to the northern part of the lake. Comparisons between mitochondrial and nuclear phylogenetic reconstructions suggested that the divergent mitochondrial clade originated from ancient interspecific introgression. Finally, 'isolation-with-migration' models indicated that divergence between the two Altolamprologus species was recent (67-142 KYA) and proceeded with little if any gene flow. As in other rock-dwelling cichlids, recent population expansions were inferred in both Altolamprologus species, which may be connected with drastic lake level fluctuations.

A separate lowstand lake at the northern edge of Lake Tanganyika? Evidence from phylogeographic patterns in the cichlid genus Tropheus

“…'black' (Van Steenberge, 2014), our new AFLP data, in concordance with Egger et al (2007), do not find evidence for large-scale genomic admixture in these introgressed populations. There is increasing evidence that in animals local or even range wide replacement of mitochondrial DNA, without signatures of nuclear genomic admixis, seems to be more common than previously thought (e.g., Nevado et al, 2009;Tang et al, 2012;Melo-Ferreira et al, 2014;Good et al, 2015;Koblmüller et al, 2016), such that taxonomic assignment based on mitochondrial data alone might be misleading.…”

Evolutionary transitions to cooperative societies in fishes revisited

“…The deviations between single-locus trees (such as the mitochondrial tree) and multilocus trees can be attributed to (ancient) incomplete lineage sorting and (ancient) hybridization/introgression on individual loci, both particularly evident in studies of lamprologine cichlids (Day et al, 2007;Koblmüller et al, 2007Koblmüller et al, , 2017Nevado et al, 2009;Salzburger, Baric, & Sturmbauer, 2002;Schelly, Salzburger, Koblmüller, Duftner, & Sturmbauer, 2006;Sturmbauer et al, 2010). Dey et al (2017)).…”

“…With so little nuclear data actually included in the dataset, the resulting phylogenetic tree necessarily reflects mainly the mitochondrial relationships. Second, given the low substitution rate of nuclear sequences, the five nuclear loci provide limited phylogenetic information and, for instance, fail to resolve the branching order of many lamprologine species (low node support in Figure 2a; also shown by Nevado et al (2009);Koblmüller et al (2017)).…”

“…Dey et al () incorporated five nuclear genes into a large dataset of three commonly used mitochondrial genes to account for this problem. Unfortunately, these five nuclear genes are available for only a small number of species, and, in contrast to the mitochondrial data, contain only little phylogenetic information (e.g., Koblmüller et al, ). Therefore, Dey et al’s () tree topology mainly reflects mitochondrial relationships, contradicting recent phylogenomic evidence (McGee et al, ; Takahashi & Sota, ; Irisarri et al, ) and concordant morphological classifications.…”

Preface: Advances in cichlid research II: behavior, ecology and evolutionary biology

“…Thus, the results are consistent with divergent evolution into ecomorphs taking place in response to the availability of new habitat, consistent with theory of ''ecological opportunity'' as a promoter of adaptive radiation. Koblmüller et al (2017) investigated the phylogeographic structure in two closely related species of the genus Altolamprologus. Using mitochondrial and nuclear DNA sequences, they found (a) that divergence between these two species was fairly recent (approximately 100 kya) and proceeded with little if any gene flow, (b) that a geographically restricted divergent haplogroup originated from ancient introgression, and (c) that habitatinduced population fragmentation contrasts with weak phylogeographic structure, a pattern consistent with low levels of periodic gene flow mediating genetic connectivity across large geographic distances.…”