Question

Lake Tanganyika harbors a high diversity of Cichlid fish. A study constructed phylogenies of Cichlids based on 38 retroposon insertion sites. 24 of these yielded the same phylogeny, but 14 supported a variety of different phylogenies. From this the researchers concluded that there must have been rapid speciation going on in the lake. Explain this reasoning. Why is it significant that the traits being used were retroposon insertion sites? In your answer, explain the difference between a gene tree and a species tree.

Answer 1

Lake Tanganyika harbors many endemic species of incredibly varied cichlid fish which have been classified in twelve main taxonomic groups referred to as tribes. Analysis of quick interspersed component (SINE) insertion information was recognized to become a strong tool for the elucidation of phylogenetic human relationships, and also we used the technique in an effort to make clear such associations with these cichlids. We learned insertion patterns of thirty eight SINEs in total, twenty four of which supported the monophyly of 3 clades. The additional fourteen loci disclosed considerable incongruence in terminology of the patterns of SINE insertions. These incongruencies likely stem from several adaptive radiation. A possible reason behind this particular trend is definitely the considerable unfinished lineage sorting of alleles because of the presence or maybe lack of a SINE throughout successive speciation events which had taken place aproximatelly 5 -10 MYA.
Even though the patterns of insertion of AFC SINEs found at the twenty four loci examined previously unambiguously indicated support for the 3 monophyletic groups of cichlids, the fresh tree of ours contained 3 sets of polytomies. One of these simple polytomies was because of incongruent patterns of insertion of AFC SINEs at fourteen loci. In the situation of locus two, insertion of an AFC sequence was noticed especially in the genomes of Limnochromis staneri as well as Lamprologus lemairii, representatives of the Lamprologini and Limnochromini tribes, respectively (fig. 1 IVA). Nevertheless, when outcomes for locus four have been taken into consideration, these species didn't appear to be sister species, since at this particular locus L. lemairii discussed insertion of an AFC SINE with Paracyprichromis brieni (tribe Cyprichromini), with the genome of L. staneri lacking this particular device. The style from evaluation of locus 259 additionally contradicted the outcomes obtained for locus two, since at locus 259 the lineage leading to L. staneri seemed to have diverged first in the MVhL clade. By comparison, evaluation of locus 1220 revealed a struggle with the close connection between L. lemairii as well as P. brieni, that had been recommended by the evaluation of locus four, as the latter species discussed an AFC SINE with species from the MVHT clade and also Eretmodus cyanostictus (tribe Eretmodini) and P. microlepis (tribe Perissodini), while the device wasn't shared by L. lemairii. An additional example of the a struggle was found in the situation of patterns gotten for locus 1225 and locus 1284, that revealed a discrepancy in terminology of the species - also E. cyanostictus or maybe Cyathopharynx furcifer (tribe Ectodini) - that's closest to the MVHT clade. Additional instances of "incongruent" patterns of insertion of SINEs in the AFC family are revealed in. Insertion of SINE devices at that "incongruent" loci seems to have occurred specifically at a particular period throughout the evolution of the different species