Illustrated below is a phylogenetic tree of extinct and existing bears (J. Kraus
ID: 66901 • Letter: I
Question
Illustrated below is a phylogenetic tree of extinct and existing bears (J. Krauss et al, BMC Evolutionary Biology 8:220, 2008, Mitochondria gen reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary). The numbers at each node indicate the number of million years ago (Ma) at which the node appeared. What is the outgroup used for this tree? How long ago was there a common ancestor between the spectacled bear and the sloth bear? Is the American black bear more closely related to the polar bear or the or the American giant short-faced bear? There seem to be a large number of nodes associated with the thick line running from top to bottom in the diagram. Can you provide a short explanation why?Explanation / Answer
a) The impact of outgroup composition on root position, bootstrap support and tree topology in our AFLP dataset likely originates from the combination of the large genetic distance between the available outgroup taxa and the ingroup on the one hand, and the short basal branches within the ingroup on the other hand. Moreover, considerable differences in branch lengths between ingroup and some outgroup taxa might promote random outgroup effects (Wheeler, 1990; Huelsenbeck et al., 2002). With an age of 5–6 MY (or more, contingent on the calibration; Genner et al., 2007; Schwarzer et al., 2009; but see Koblmüller et al., 2008a,b), the split between the Limnochromini and the outgroup taxa is approximately twice as old as the most recent common ancestor of the extant limnochromines, from which the major limnochromine lineages radiated almost simultaneously (Duftner et al., 2005; present data). This allowed different sets of outgroup taxa to attach to different branches of the ingroup and pull certain ingroup taxa towards the base of the tree, which naturally affected bootstrap support and topology of the ingroup clades.
Prompted by these observations, we examined whether previous AFLP-based phylogenetic reconstructions of various Lake Tanganyika cichlid lineages were robust to the removal of the outgroup. No substantial outgroup effect on inferences of ingroup relationships was detected in these dataset as changes in branching order concerned only those clades, which had low statistical support irrespective of whether or not the outgroup was included in the analyses (data not shown). Notably, in none of these datasets was the basal ingroup radiation as rapid and the relative divergence from the outgroup as large as it was in the Limnochromini dataset. However, outgroup effects may underlie the different AFLP tree topologies of the Perissodini radiation.
b)The sloth bear (Melursus ursinus), also known as the Stickney bear or labiated bear,[3] is a nocturnal insectivorous bear species found wild within the Indian Subcontinent. The sloth bear evolved from ancestral brown bears during the Pleistocene and shares features found in insect-eating mammals through convergent evolution. The population isolated in Sri Lanka is considered a subspecies. Unlike brown and black bears, sloth bears have lankier builds, long, shaggy coats that form a mane around the face, long, sickle-shaped claws, and a specially adapted lower lip and palate used for sucking insects. Sloth bears breed during spring and early summer and give birth near the beginning of winter. They feed on termites, honeybee colonies, and fruits. Sloth bears sometimes attack humans who encroach on their territories. Historically, humans have drastically reduced their habitat and diminished their population by hunting them for food and products such as their bacula and claws. These bears have been used as performing pets due to their tameable nature.